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...tadaptive__mcmc_1_1AdaptiveMCMCStruct.html | 275 -- 202 files changed, 10655 insertions(+), 9775 deletions(-) create mode 100644 AdaptiveMCMCHandler_8cpp.html create mode 100644 AdaptiveMCMCHandler_8cpp_source.html rename adaptiveMCMCStruct_8h.html => AdaptiveMCMCHandler_8h.html (67%) create mode 100644 AdaptiveMCMCHandler_8h_source.html create mode 100644 SECURITY_8md.html delete mode 100644 adaptiveMCMCStruct_8h_source.html create mode 100644 classadaptive__mcmc_1_1AdaptiveMCMCHandler-members.html create mode 100644 classadaptive__mcmc_1_1AdaptiveMCMCHandler.html create mode 100644 md__2github_2workspace_2SECURITY.html delete mode 100644 structadaptive__mcmc_1_1AdaptiveMCMCStruct-members.html delete mode 100644 structadaptive__mcmc_1_1AdaptiveMCMCStruct.html diff --git a/AdaptiveMCMCHandler_8cpp.html b/AdaptiveMCMCHandler_8cpp.html new file mode 100644 index 000000000..541b72647 --- /dev/null +++ b/AdaptiveMCMCHandler_8cpp.html @@ -0,0 +1,98 @@ + + + + + + + +MaCh3: /github/workspace/covariance/AdaptiveMCMCHandler.cpp File Reference + + + + + + + + + +
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#include "covariance/AdaptiveMCMCHandler.h"
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AdaptiveMCMCHandler.cpp
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1#include "covariance/AdaptiveMCMCHandler.h"
+
2
+
+
3namespace adaptive_mcmc{
+
4
+
5// ********************************************
+
+
6AdaptiveMCMCHandler::AdaptiveMCMCHandler() {
+
7// ********************************************
+
8 start_adaptive_throw = 0;
+
9 start_adaptive_update = 0;
+
10 end_adaptive_update = 1;
+
11 adaptive_update_step = 1000;
+
12
+
13 par_means = {};
+
14 adaptive_covariance = nullptr;
+
15}
+
+
16
+
17// ********************************************
+
+
18AdaptiveMCMCHandler::~AdaptiveMCMCHandler() {
+
19// ********************************************
+
20 if(adaptive_covariance != nullptr) {
+
21 delete adaptive_covariance;
+
22 }
+
23}
+
+
24
+
25
+
26// ********************************************
+
+
27void AdaptiveMCMCHandler::InitFromConfig(const YAML::Node& adapt_manager, const std::string& matrix_name_str, const int Npars) {
+
28// ********************************************
+
29 // setAdaptionDefaults();
+
30 if(GetFromManager<std::string>(adapt_manager["AdaptionOptions"]["Covariance"][matrix_name_str], "")==""){
+
31 MACH3LOG_WARN("Adaptive Settings not found for {}, this is fine if you don't want adaptive MCMC", matrix_name_str);
+
32 return;
+
33 }
+
34
+
35 // We"re going to grab this info from the YAML manager
+
36 if(GetFromManager<bool>(adapt_manager["AdaptionOptions"]["Covariance"][matrix_name_str]["DoAdaption"], false)) {
+
37 MACH3LOG_WARN("Not using adaption for {}", matrix_name_str);
+
38 return;
+
39 }
+
40
+
41 start_adaptive_throw = GetFromManager<int>(adapt_manager["AdaptionOptions"]["Settings"]["AdaptionStartThrow"], 10);
+
42 start_adaptive_update = GetFromManager<int>(adapt_manager["AdaptionOptions"]["Settings"]["AdaptionStartUpdate"], 0);
+
43 end_adaptive_update = GetFromManager<int>(adapt_manager["AdaptionOptions"]["Settings"]["AdaptionEndUpdate"], 10000);
+
44 adaptive_update_step = GetFromManager<int>(adapt_manager["AdaptionOptions"]["Settings"]["AdaptionUpdateStep"], 100);
+
45
+
46
+
47 // We also want to check for "blocks" by default all parameters "know" about each other
+
48 // but we can split the matrix into independent block matrices
+
49
+
50 // We"ll set a dummy variable here
+
51 auto matrix_blocks = GetFromManager<std::vector<std::vector<int>>>(adapt_manager["AdaptionOptions"]["Settings"][matrix_name_str]["AdaptionUpdateStep"], {{}});
+
52
+
53 SetAdaptiveBlocks(matrix_blocks, Npars);
+
54}
+
+
55
+
56// ********************************************
+
+
57void AdaptiveMCMCHandler::CreateNewAdaptiveCovariance(const int Npars) {
+
58// ********************************************
+
59 adaptive_covariance = new TMatrixDSym(Npars);
+
60 adaptive_covariance->Zero();
+
61 par_means = std::vector<double>(Npars, 0);
+
62}
+
+
63
+
64
+
65// ********************************************
+
+
66void AdaptiveMCMCHandler::SetAdaptiveBlocks(std::vector<std::vector<int>> block_indices, const int Npars) {
+
67// ********************************************
+
68 /*
+
69 * In order to adapt efficient we want to setup our throw matrix to be a serious of block-diagonal (ish) matrices
+
70 *
+
71 * To do this we set sub-block in the config by parameter index. For example having
+
72 * [[0,4],[4, 6]] in your config will set up two blocks one with all indices 0<=i<4 and the other with 4<=i<6
+
73 */
+
74 // Set up block regions
+
75 adapt_block_matrix_indices = std::vector<int>(Npars, 0);
+
76
+
77 // Should also make a matrix of block sizes
+
78 adapt_block_sizes = std::vector<int>((int)block_indices.size()+1, 0);
+
79 adapt_block_sizes[0] = Npars;
+
80
+
81 if(block_indices.size()==0 || block_indices[0].size()==0) return;
+
82
+
83 // Now we loop over our blocks
+
84 for(int iblock=0; iblock<(int)block_indices.size(); iblock++){
+
85 // Loop over blocks in the block
+
86 for(int isubblock=0; isubblock<(int)block_indices[iblock].size()-1; isubblock+=2){
+
87 int block_lb = block_indices[iblock][isubblock];
+
88 int block_ub = block_indices[iblock][isubblock+1];
+
89
+
90 //std::cout<<block_lb<<" "<<block_ub<<std::endl;
+
91 if(block_lb > Npars || block_ub > Npars){
+
92 MACH3LOG_ERROR("Cannot set matrix block with edges {}, {} for matrix of size {}",
+
93 block_lb, block_ub, Npars);
+
94 throw MaCh3Exception(__FILE__, __LINE__);;
+
95 }
+
96 for(int ipar = block_lb; ipar < block_ub; ipar++){
+
97 adapt_block_matrix_indices[ipar] = iblock+1;
+
98 adapt_block_sizes[iblock+1] += 1;
+
99 adapt_block_sizes[0] -= 1;
+
100 }
+
101 }
+
102 }
+
103}
+
+
104
+
105
+
106// ********************************************
+
107//HW: Truly adaptive MCMC!
+
+
108void AdaptiveMCMCHandler::SaveAdaptiveToFile(const TString& outFileName, const TString& systematicName){
+
109// ********************************************
+
110 TFile* outFile = new TFile(outFileName, "UPDATE");
+
111 if(outFile->IsZombie()){
+
112 MACH3LOG_ERROR("Couldn't find {}", outFileName);
+
113 throw;
+
114 }
+
115 TVectorD* outMeanVec = new TVectorD((int)par_means.size());
+
116 for(int i = 0; i < (int)par_means.size(); i++){
+
117 (*outMeanVec)(i) = par_means[i];
+
118 }
+
119 outFile->cd();
+
120 adaptive_covariance->Write(systematicName+"_postfit_matrix");
+
121 outMeanVec->Write(systematicName+"_mean_vec");
+
122 outFile->Close();
+
123 delete outMeanVec;
+
124 delete outFile;
+
125}
+
+
126
+
127// ********************************************
+
128// HW : I would like this to be less painful to use!
+
129// First things first we need setters
+
+
130void AdaptiveMCMCHandler::SetThrowMatrixFromFile(const std::string& matrix_file_name,
+
131 const std::string& matrix_name,
+
132 const std::string& means_name,
+
133 bool& use_adaptive,
+
134 const int Npars) {
+
135// ********************************************
+
136 // Lets you set the throw matrix externally
+
137 // Open file
+
138 std::unique_ptr<TFile>matrix_file(new TFile(matrix_file_name.c_str()));
+
139 use_adaptive = true;
+
140
+
141 if(matrix_file->IsZombie()){
+
142 MACH3LOG_ERROR("Couldn't find {}", matrix_file_name);
+
143 throw;
+
144 }
+
145
+
146 // Next we grab our matrix
+
147 adaptive_covariance = static_cast<TMatrixDSym*>(matrix_file->Get(matrix_name.c_str()));
+
148 if(!adaptive_covariance){
+
149 MACH3LOG_ERROR("Couldn't find {} in {}", matrix_name, matrix_file_name);
+
150 throw;
+
151 }
+
152
+
153 // Finally we grab the means vector
+
154 TVectorD* means_vector = static_cast<TVectorD*>(matrix_file->Get(means_name.c_str()));
+
155
+
156 // This is fine to not exist!
+
157 if(means_vector){
+
158 // Yay our vector exists! Let's loop and fill it
+
159 // Should check this is done
+
160 if(means_vector->GetNrows()){
+
161 MACH3LOG_ERROR("External means vec size ({}) != matrix size ({})", means_vector->GetNrows(), Npars);
+
162 throw MaCh3Exception(__FILE__, __LINE__);
+
163 }
+
164
+
165 par_means = std::vector<double>(Npars);
+
166 for(int i = 0; i < Npars; i++){
+
167 par_means[i] = (*means_vector)(i);
+
168 }
+
169 MACH3LOG_INFO("Found Means in External File, Will be able to adapt");
+
170 }
+
171 // Totally fine if it doesn't exist, we just can't do adaption
+
172 else{
+
173 // We don't need a means vector, set the adaption=false
+
174 MACH3LOG_WARN("Cannot find means vector in {}, therefore I will not be able to adapt!", matrix_file_name);
+
175 use_adaptive = false;
+
176 }
+
177
+
178 matrix_file->Close();
+
179 MACH3LOG_INFO("Set up matrix from external file");
+
180}
+
+
181
+
182
+
183// ********************************************
+
+
184void AdaptiveMCMCHandler::UpdateAdaptiveCovariance(const std::vector<double>& _fCurrVal, const int steps_post_burn, const int Npars) {
+
185// ********************************************
+
186 std::vector<double> par_means_prev = par_means;
+
187
+
188 #ifdef MULTITHREAD
+
189 #pragma omp parallel for
+
190 #endif
+
191 for(int iRow = 0; iRow < Npars; iRow++) {
+
192 par_means[iRow] = (_fCurrVal[iRow]+par_means[iRow]*steps_post_burn)/(steps_post_burn+1);
+
193 }
+
194
+
195 //Now we update the covariances using cov(x,y)=E(xy)-E(x)E(y)
+
196 #ifdef MULTITHREAD
+
197 #pragma omp parallel for
+
198 #endif
+
199 for(int irow = 0; irow < Npars; irow++){
+
200 int block = adapt_block_matrix_indices[irow];
+
201 // int scale_factor = 5.76/double(adapt_block_sizes[block]);
+
202 for(int icol = 0; icol <= irow; icol++){
+
203 double cov_val=0;
+
204 // Not in the same blocks
+
205 if(adapt_block_matrix_indices[icol] == block){
+
206 // Calculate Covariance for block
+
207 // https://projecteuclid.org/journals/bernoulli/volume-7/issue-2/An-adaptive-Metropolis-algorithm/bj/1080222083.full
+
208 cov_val = (*adaptive_covariance)(irow, icol)*Npars/5.6644;
+
209 cov_val += par_means_prev[irow]*par_means_prev[icol]; //First we remove the current means
+
210 cov_val = (cov_val*steps_post_burn+_fCurrVal[irow]*_fCurrVal[icol])/(steps_post_burn+1); //Now get mean(iRow*iCol)
+
211 cov_val -= par_means[icol]*par_means[irow];
+
212 cov_val*=5.6644/Npars;
+
213 }
+
214 (*adaptive_covariance)(icol, irow) = cov_val;
+
215 (*adaptive_covariance)(irow, icol) = cov_val;
+
216 }
+
217 }
+
218}
+
+
219
+
220// ********************************************
+
+
221void AdaptiveMCMCHandler::Print() {
+
222// ********************************************
+
223 MACH3LOG_INFO("Adaptive MCMC Info:");
+
224 MACH3LOG_INFO("Throwing from New Matrix from Step : {}", start_adaptive_throw);
+
225 MACH3LOG_INFO("Adaption Matrix Start Update : {}", start_adaptive_update);
+
226 MACH3LOG_INFO("Adaption Matrix Ending Updates : {}", end_adaptive_update);
+
227 MACH3LOG_INFO("Steps Between Updates : {}", adaptive_update_step);
+
228}
+
+
229
+
230
+
231} //end adaptive_mcmc
+
+ +
size
int size
Definition GetPenaltyTerm.cpp:42
+
MACH3LOG_ERROR
#define MACH3LOG_ERROR
Definition MaCh3Logger.h:18
+
MACH3LOG_INFO
#define MACH3LOG_INFO
Definition MaCh3Logger.h:16
+
MACH3LOG_WARN
#define MACH3LOG_WARN
Definition MaCh3Logger.h:17
+
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:21
+
MaCh3Exception
Custom exception class for MaCh3 errors.
Definition MaCh3Exception.h:12
+
adaptive_mcmc::AdaptiveMCMCHandler::par_means
std::vector< double > par_means
Mean values for all parameters.
Definition AdaptiveMCMCHandler.h:78
+
adaptive_mcmc::AdaptiveMCMCHandler::adapt_block_matrix_indices
std::vector< int > adapt_block_matrix_indices
Indices for block-matrix adaption.
Definition AdaptiveMCMCHandler.h:71
+
adaptive_mcmc::AdaptiveMCMCHandler::Print
void Print()
Print all class members.
Definition AdaptiveMCMCHandler.cpp:221
+
adaptive_mcmc::AdaptiveMCMCHandler::start_adaptive_update
int start_adaptive_update
When do we stop update the adaptive matrix.
Definition AdaptiveMCMCHandler.h:62
+
adaptive_mcmc::AdaptiveMCMCHandler::adapt_block_sizes
std::vector< int > adapt_block_sizes
Size of blocks for adaption.
Definition AdaptiveMCMCHandler.h:74
+
adaptive_mcmc::AdaptiveMCMCHandler::~AdaptiveMCMCHandler
~AdaptiveMCMCHandler()
Destructor.
Definition AdaptiveMCMCHandler.cpp:18
+
adaptive_mcmc::AdaptiveMCMCHandler::SaveAdaptiveToFile
void SaveAdaptiveToFile(const TString &outFileName, const TString &systematicName)
HW: Save adaptive throw matrix to file.
Definition AdaptiveMCMCHandler.cpp:108
+
adaptive_mcmc::AdaptiveMCMCHandler::AdaptiveMCMCHandler
AdaptiveMCMCHandler()
Constructor.
Definition AdaptiveMCMCHandler.cpp:6
+
adaptive_mcmc::AdaptiveMCMCHandler::start_adaptive_throw
int start_adaptive_throw
Definition AdaptiveMCMCHandler.h:59
+
adaptive_mcmc::AdaptiveMCMCHandler::end_adaptive_update
int end_adaptive_update
Steps between changing throw matrix.
Definition AdaptiveMCMCHandler.h:65
+
adaptive_mcmc::AdaptiveMCMCHandler::UpdateAdaptiveCovariance
void UpdateAdaptiveCovariance(const std::vector< double > &_fCurrVal, const int steps_post_burn, const int Npars)
Method to update adaptive MCMC.
Definition AdaptiveMCMCHandler.cpp:184
+
adaptive_mcmc::AdaptiveMCMCHandler::adaptive_update_step
int adaptive_update_step
Steps between changing throw matrix.
Definition AdaptiveMCMCHandler.h:68
+
adaptive_mcmc::AdaptiveMCMCHandler::SetAdaptiveBlocks
void SetAdaptiveBlocks(std::vector< std::vector< int > > block_indices, const int Npars)
HW: sets adaptive block matrix.
Definition AdaptiveMCMCHandler.cpp:66
+
adaptive_mcmc::AdaptiveMCMCHandler::CreateNewAdaptiveCovariance
void CreateNewAdaptiveCovariance(const int Npars)
If we don't have a covariance matrix to start from for adaptive tune we need to make one!
Definition AdaptiveMCMCHandler.cpp:57
+
adaptive_mcmc::AdaptiveMCMCHandler::InitFromConfig
void InitFromConfig(const YAML::Node &adapt_manager, const std::string &matrix_name_str, const int Npars)
Read initial values from config file.
Definition AdaptiveMCMCHandler.cpp:27
+
adaptive_mcmc::AdaptiveMCMCHandler::SetThrowMatrixFromFile
void SetThrowMatrixFromFile(const std::string &matrix_file_name, const std::string &matrix_name, const std::string &means_name, bool &use_adaptive, const int Npars)
sets throw matrix from a file
Definition AdaptiveMCMCHandler.cpp:130
+
adaptive_mcmc::AdaptiveMCMCHandler::adaptive_covariance
TMatrixDSym * adaptive_covariance
Full adaptive covariance matrix.
Definition AdaptiveMCMCHandler.h:81
+
adaptive_mcmc
Definition AdaptiveMCMCHandler.cpp:3
+
+ +
+Generated by doxygen 1.9.8 +
+ + diff --git a/adaptiveMCMCStruct_8h.html b/AdaptiveMCMCHandler_8h.html similarity index 67% rename from adaptiveMCMCStruct_8h.html rename to AdaptiveMCMCHandler_8h.html index d20065f0e..8fb98aaee 100644 --- a/adaptiveMCMCStruct_8h.html +++ b/AdaptiveMCMCHandler_8h.html @@ -5,7 +5,7 @@ -MaCh3: /github/workspace/covariance/adaptiveMCMCStruct.h File Reference +MaCh3: /github/workspace/covariance/AdaptiveMCMCHandler.h File Reference @@ -77,34 +77,26 @@
Classes | -Namespaces | -Functions
-
adaptiveMCMCStruct.h File Reference
+Namespaces
+
AdaptiveMCMCHandler.h File Reference
#include "manager/MaCh3Logger.h"
-#include "TMatrixDSym.h"
-#include <vector>
+#include "manager/manager.h"
+#include "covariance/CovarianceUtils.h"
-

Go to the source code of this file.

+

Go to the source code of this file.

- - + +

Classes

struct  adaptive_mcmc::AdaptiveMCMCStruct
 struct encapsulating all adaptive MCMC information More...
class  adaptive_mcmc::AdaptiveMCMCHandler
 Contains information about adaptive covariance matrix. More...
 
- -

Namespaces

namespace  adaptive_mcmc
 Contains information about adaptive covariance matrix.
 
- - - -

-Functions

void adaptive_mcmc::print_adaptive_struct (AdaptiveMCMCStruct adaptive_struct)
 Basic printer method for AMCMC struct.
 
diff --git a/AdaptiveMCMCHandler_8h_source.html b/AdaptiveMCMCHandler_8h_source.html new file mode 100644 index 000000000..d8bc737d1 --- /dev/null +++ b/AdaptiveMCMCHandler_8h_source.html @@ -0,0 +1,173 @@ + + + + + + + +MaCh3: /github/workspace/covariance/AdaptiveMCMCHandler.h Source File + + + + + + + + + +
+
+ + + + + + + +
+
MaCh3 1.1.0 +
+
Reference Guide
+
+
+ + + + + + + + + +
+
+ + +
+
+
+
+
+
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+
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+
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+
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+ + +
+
+
AdaptiveMCMCHandler.h
+
+
+Go to the documentation of this file.
1#pragma once
+
2
+
3// MaCh3 Includes
+
4#include "manager/MaCh3Logger.h"
+
5#include "manager/manager.h"
+
6#include "covariance/CovarianceUtils.h"
+
7
+
8namespace adaptive_mcmc{
+
9
+
+
13class AdaptiveMCMCHandler{
+
14 public:
+
15
+
17 AdaptiveMCMCHandler();
+
18
+
20 ~AdaptiveMCMCHandler();
+
21
+
23 void Print();
+
24
+
27 void InitFromConfig(const YAML::Node& adapt_manager, const std::string& matrix_name_str, const int Npars);
+
28
+
30 void CreateNewAdaptiveCovariance(const int Npars);
+
31
+
34 void SetAdaptiveBlocks(std::vector<std::vector<int>> block_indices, const int Npars);
+
35
+
37 void SaveAdaptiveToFile(const TString& outFileName, const TString& systematicName);
+
38
+
43 void SetThrowMatrixFromFile(const std::string& matrix_file_name,
+
44 const std::string& matrix_name,
+
45 const std::string& means_name,
+
46 bool& use_adaptive,
+
47 const int Npars);
+
48
+
49
+
50
+
51
+
55 void UpdateAdaptiveCovariance(const std::vector<double>& _fCurrVal, const int steps_post_burn, const int Npars);
+
56
+
59 int start_adaptive_throw;
+
60
+
62 int start_adaptive_update;
+
63
+
65 int end_adaptive_update;
+
66
+
68 int adaptive_update_step;
+
69
+
71 std::vector<int> adapt_block_matrix_indices;
+
72
+
74 std::vector<int> adapt_block_sizes;
+
75
+
76 // Variables directedly linked to adaption
+
78 std::vector<double> par_means;
+
79
+
81 TMatrixDSym* adaptive_covariance;
+
82};
+
+
83
+
84} // adaptive_mcmc namespace
+ + +
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:21
+
adaptive_mcmc::AdaptiveMCMCHandler
Contains information about adaptive covariance matrix.
Definition AdaptiveMCMCHandler.h:13
+
adaptive_mcmc::AdaptiveMCMCHandler::par_means
std::vector< double > par_means
Mean values for all parameters.
Definition AdaptiveMCMCHandler.h:78
+
adaptive_mcmc::AdaptiveMCMCHandler::adapt_block_matrix_indices
std::vector< int > adapt_block_matrix_indices
Indices for block-matrix adaption.
Definition AdaptiveMCMCHandler.h:71
+
adaptive_mcmc::AdaptiveMCMCHandler::Print
void Print()
Print all class members.
Definition AdaptiveMCMCHandler.cpp:221
+
adaptive_mcmc::AdaptiveMCMCHandler::start_adaptive_update
int start_adaptive_update
When do we stop update the adaptive matrix.
Definition AdaptiveMCMCHandler.h:62
+
adaptive_mcmc::AdaptiveMCMCHandler::adapt_block_sizes
std::vector< int > adapt_block_sizes
Size of blocks for adaption.
Definition AdaptiveMCMCHandler.h:74
+
adaptive_mcmc::AdaptiveMCMCHandler::~AdaptiveMCMCHandler
~AdaptiveMCMCHandler()
Destructor.
Definition AdaptiveMCMCHandler.cpp:18
+
adaptive_mcmc::AdaptiveMCMCHandler::SaveAdaptiveToFile
void SaveAdaptiveToFile(const TString &outFileName, const TString &systematicName)
HW: Save adaptive throw matrix to file.
Definition AdaptiveMCMCHandler.cpp:108
+
adaptive_mcmc::AdaptiveMCMCHandler::AdaptiveMCMCHandler
AdaptiveMCMCHandler()
Constructor.
Definition AdaptiveMCMCHandler.cpp:6
+
adaptive_mcmc::AdaptiveMCMCHandler::start_adaptive_throw
int start_adaptive_throw
Definition AdaptiveMCMCHandler.h:59
+
adaptive_mcmc::AdaptiveMCMCHandler::end_adaptive_update
int end_adaptive_update
Steps between changing throw matrix.
Definition AdaptiveMCMCHandler.h:65
+
adaptive_mcmc::AdaptiveMCMCHandler::UpdateAdaptiveCovariance
void UpdateAdaptiveCovariance(const std::vector< double > &_fCurrVal, const int steps_post_burn, const int Npars)
Method to update adaptive MCMC.
Definition AdaptiveMCMCHandler.cpp:184
+
adaptive_mcmc::AdaptiveMCMCHandler::adaptive_update_step
int adaptive_update_step
Steps between changing throw matrix.
Definition AdaptiveMCMCHandler.h:68
+
adaptive_mcmc::AdaptiveMCMCHandler::SetAdaptiveBlocks
void SetAdaptiveBlocks(std::vector< std::vector< int > > block_indices, const int Npars)
HW: sets adaptive block matrix.
Definition AdaptiveMCMCHandler.cpp:66
+
adaptive_mcmc::AdaptiveMCMCHandler::CreateNewAdaptiveCovariance
void CreateNewAdaptiveCovariance(const int Npars)
If we don't have a covariance matrix to start from for adaptive tune we need to make one!
Definition AdaptiveMCMCHandler.cpp:57
+
adaptive_mcmc::AdaptiveMCMCHandler::InitFromConfig
void InitFromConfig(const YAML::Node &adapt_manager, const std::string &matrix_name_str, const int Npars)
Read initial values from config file.
Definition AdaptiveMCMCHandler.cpp:27
+
adaptive_mcmc::AdaptiveMCMCHandler::SetThrowMatrixFromFile
void SetThrowMatrixFromFile(const std::string &matrix_file_name, const std::string &matrix_name, const std::string &means_name, bool &use_adaptive, const int Npars)
sets throw matrix from a file
Definition AdaptiveMCMCHandler.cpp:130
+
adaptive_mcmc::AdaptiveMCMCHandler::adaptive_covariance
TMatrixDSym * adaptive_covariance
Full adaptive covariance matrix.
Definition AdaptiveMCMCHandler.h:81
+ +
adaptive_mcmc
Definition AdaptiveMCMCHandler.cpp:3
+
+ +
+Generated by doxygen 1.9.8 +
+ + diff --git a/CombineMaCh3Chains_8cpp.html b/CombineMaCh3Chains_8cpp.html index 6ed649db5..45e893ff0 100644 --- a/CombineMaCh3Chains_8cpp.html +++ b/CombineMaCh3Chains_8cpp.html @@ -191,10 +191,10 @@

51 }
52 return weirdFile;
53}
-
MACH3LOG_DEBUG
#define MACH3LOG_DEBUG
Definition MaCh3Logger.h:12
-
MACH3LOG_ERROR
#define MACH3LOG_ERROR
Definition MaCh3Logger.h:15
-
MACH3LOG_WARN
#define MACH3LOG_WARN
Definition MaCh3Logger.h:14
-
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:18
+
MACH3LOG_DEBUG
#define MACH3LOG_DEBUG
Definition MaCh3Logger.h:15
+
MACH3LOG_ERROR
#define MACH3LOG_ERROR
Definition MaCh3Logger.h:18
+
MACH3LOG_WARN
#define MACH3LOG_WARN
Definition MaCh3Logger.h:17
+
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:21
@@ -324,8 +324,8 @@

forceOverwrite
bool forceOverwrite
Definition CombineMaCh3Chains.cpp:15
targetCompression
int targetCompression
Definition CombineMaCh3Chains.cpp:13
inpFileList
std::vector< std::string > inpFileList
Definition CombineMaCh3Chains.cpp:14
-
MACH3LOG_INFO
#define MACH3LOG_INFO
Definition MaCh3Logger.h:13
-
MaCh3Exception
Custom exception class for MaCh3 errors.
Definition MaCh3Exception.h:10
+
MACH3LOG_INFO
#define MACH3LOG_INFO
Definition MaCh3Logger.h:16
+
MaCh3Exception
Custom exception class for MaCh3 errors.
Definition MaCh3Exception.h:12
@@ -419,7 +419,7 @@

275}
ParseArg
void ParseArg(int argc, char *argv[])
Definition CombineMaCh3Chains.cpp:208
CombineChain
void CombineChain()
Definition CombineMaCh3Chains.cpp:91
-
SetMaCh3LoggerFormat
void SetMaCh3LoggerFormat()
Set messaging format of the logger.
Definition MaCh3Logger.h:20
+
SetMaCh3LoggerFormat
void SetMaCh3LoggerFormat()
Set messaging format of the logger.
Definition MaCh3Logger.h:23
diff --git a/CombineMaCh3Chains_8cpp_source.html b/CombineMaCh3Chains_8cpp_source.html index 893051c1e..4095eceb6 100644 --- a/CombineMaCh3Chains_8cpp_source.html +++ b/CombineMaCh3Chains_8cpp_source.html @@ -379,13 +379,13 @@
targetCompression
int targetCompression
Definition CombineMaCh3Chains.cpp:13
inpFileList
std::vector< std::string > inpFileList
Definition CombineMaCh3Chains.cpp:14
CombineChain
void CombineChain()
Definition CombineMaCh3Chains.cpp:91
-
MACH3LOG_DEBUG
#define MACH3LOG_DEBUG
Definition MaCh3Logger.h:12
-
MACH3LOG_ERROR
#define MACH3LOG_ERROR
Definition MaCh3Logger.h:15
-
MACH3LOG_INFO
#define MACH3LOG_INFO
Definition MaCh3Logger.h:13
-
SetMaCh3LoggerFormat
void SetMaCh3LoggerFormat()
Set messaging format of the logger.
Definition MaCh3Logger.h:20
-
MACH3LOG_WARN
#define MACH3LOG_WARN
Definition MaCh3Logger.h:14
-
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:18
-
MaCh3Exception
Custom exception class for MaCh3 errors.
Definition MaCh3Exception.h:10
+
MACH3LOG_DEBUG
#define MACH3LOG_DEBUG
Definition MaCh3Logger.h:15
+
MACH3LOG_ERROR
#define MACH3LOG_ERROR
Definition MaCh3Logger.h:18
+
MACH3LOG_INFO
#define MACH3LOG_INFO
Definition MaCh3Logger.h:16
+
SetMaCh3LoggerFormat
void SetMaCh3LoggerFormat()
Set messaging format of the logger.
Definition MaCh3Logger.h:23
+
MACH3LOG_WARN
#define MACH3LOG_WARN
Definition MaCh3Logger.h:17
+
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:21
+
MaCh3Exception
Custom exception class for MaCh3 errors.
Definition MaCh3Exception.h:12
diff --git a/CovarianceUtils_8h.html b/CovarianceUtils_8h.html index ef337c872..9e31a7758 100644 --- a/CovarianceUtils_8h.html +++ b/CovarianceUtils_8h.html @@ -85,15 +85,12 @@ #include "TMatrixDSym.h"
#include "TVectorT.h"
#include "TVectorD.h"
-#include "TCanvas.h"
#include "TH1D.h"
#include "TH2D.h"
#include "TTree.h"
#include "TFile.h"
-#include "TAxis.h"
#include "TRandom3.h"
#include "TMath.h"
-#include "math.h"
#include "TDecompChol.h"
#include "TStopwatch.h"
#include "TMatrix.h"
diff --git a/CovarianceUtils_8h_source.html b/CovarianceUtils_8h_source.html index ed8708d7e..d71e3dd42 100644 --- a/CovarianceUtils_8h_source.html +++ b/CovarianceUtils_8h_source.html @@ -90,127 +90,123 @@
5#include "TMatrixDSym.h"
6#include "TVectorT.h"
7#include "TVectorD.h"
-
8#include "TCanvas.h"
-
9#include "TH1D.h"
-
10#include "TH2D.h"
-
11#include "TTree.h"
-
12#include "TFile.h"
-
13#include "TAxis.h"
-
14#include "TRandom3.h"
-
15#include "TMath.h"
-
16#include "math.h"
-
17#include "TDecompChol.h"
-
18#include "TStopwatch.h"
-
19#include "TMatrix.h"
-
20#include "TMatrixDSymEigen.h"
-
21#include "TMatrixDEigen.h"
-
22#include "TDecompSVD.h"
-
23
+
8#include "TH1D.h"
+
9#include "TH2D.h"
+
10#include "TTree.h"
+
11#include "TFile.h"
+
12#include "TRandom3.h"
+
13#include "TMath.h"
+
14#include "TDecompChol.h"
+
15#include "TStopwatch.h"
+
16#include "TMatrix.h"
+
17#include "TMatrixDSymEigen.h"
+
18#include "TMatrixDEigen.h"
+
19#include "TDecompSVD.h"
+
20
+
21#ifdef MULTITHREAD
+
22#include "omp.h"
+
23#endif
24
-
25#ifdef MULTITHREAD
-
26#include "omp.h"
-
27#endif
-
28
-
29namespace MaCh3Utils
-
30{
-
-
32 inline int GetNThreads()
-
33 {
-
34 #ifdef MULTITHREAD
-
35 int nThreads = omp_get_max_threads();
-
36 #else
-
37 int nThreads = 1;
-
38 #endif
-
39
-
40 return nThreads;
-
41 }
+
25namespace MaCh3Utils
+
26{
+
+
28 inline int GetNThreads()
+
29 {
+
30 #ifdef MULTITHREAD
+
31 int nThreads = omp_get_max_threads();
+
32 #else
+
33 int nThreads = 1;
+
34 #endif
+
35
+
36 return nThreads;
+
37 }
-
42
-
-
44 inline double* MatrixMult(double *A, double *B, int n) {
-
45 //CW: First transpose to increse cache hits
-
46 double *BT = new double[n*n];
-
47 #ifdef MULTITHREAD
-
48 #pragma omp parallel for
-
49 #endif
-
50 for (int i = 0; i < n; i++) {
-
51 for (int j = 0; j < n; j++) {
-
52 BT[j*n+i] = B[i*n+j];
-
53 }
-
54 }
-
55
-
56 // Now multiply
-
57 double *C = new double[n*n];
-
58 #ifdef MULTITHREAD
-
59 #pragma omp parallel for
-
60 #endif
-
61 for (int i = 0; i < n; i++) {
-
62 for (int j = 0; j < n; j++) {
-
63 double sum = 0;
-
64 for (int k = 0; k < n; k++) {
-
65 sum += A[i*n+k]*BT[j*n+k];
-
66 }
-
67 C[i*n+j] = sum;
-
68 }
-
69 }
-
70 delete BT;
-
71
-
72 return C;
-
73 }
+
38
+
+
40 inline double* MatrixMult(double *A, double *B, int n) {
+
41 //CW: First transpose to increse cache hits
+
42 double *BT = new double[n*n];
+
43 #ifdef MULTITHREAD
+
44 #pragma omp parallel for
+
45 #endif
+
46 for (int i = 0; i < n; i++) {
+
47 for (int j = 0; j < n; j++) {
+
48 BT[j*n+i] = B[i*n+j];
+
49 }
+
50 }
+
51
+
52 // Now multiply
+
53 double *C = new double[n*n];
+
54 #ifdef MULTITHREAD
+
55 #pragma omp parallel for
+
56 #endif
+
57 for (int i = 0; i < n; i++) {
+
58 for (int j = 0; j < n; j++) {
+
59 double sum = 0;
+
60 for (int k = 0; k < n; k++) {
+
61 sum += A[i*n+k]*BT[j*n+k];
+
62 }
+
63 C[i*n+j] = sum;
+
64 }
+
65 }
+
66 delete BT;
+
67
+
68 return C;
+
69 }
-
74
-
-
76 inline double** MatrixMult(double **A, double **B, int n) {
-
77 // First make into monolithic array
-
78 double *A_mon = new double[n*n];
-
79 double *B_mon = new double[n*n];
-
80
-
81 #ifdef MULTITHREAD
-
82 #pragma omp parallel for
-
83 #endif
-
84 for (int i = 0; i < n; ++i) {
-
85 for (int j = 0; j < n; ++j) {
-
86 A_mon[i*n+j] = A[i][j];
-
87 B_mon[i*n+j] = B[i][j];
-
88 }
-
89 }
-
90 //CW: Now call the monolithic calculator
-
91 double *C_mon = MatrixMult(A_mon, B_mon, n);
-
92 delete A_mon;
-
93 delete B_mon;
-
94
-
95 // Return the double pointer
-
96 double **C = new double*[n];
-
97 #ifdef MULTITHREAD
-
98 #pragma omp parallel for
-
99 #endif
-
100 for (int i = 0; i < n; ++i) {
-
101 C[i] = new double[n];
-
102 for (int j = 0; j < n; ++j) {
-
103 C[i][j] = C_mon[i*n+j];
-
104 }
-
105 }
-
106 delete C_mon;
-
107
-
108 return C;
-
109 }
+
70
+
+
72 inline double** MatrixMult(double **A, double **B, int n) {
+
73 // First make into monolithic array
+
74 double *A_mon = new double[n*n];
+
75 double *B_mon = new double[n*n];
+
76
+
77 #ifdef MULTITHREAD
+
78 #pragma omp parallel for
+
79 #endif
+
80 for (int i = 0; i < n; ++i) {
+
81 for (int j = 0; j < n; ++j) {
+
82 A_mon[i*n+j] = A[i][j];
+
83 B_mon[i*n+j] = B[i][j];
+
84 }
+
85 }
+
86 //CW: Now call the monolithic calculator
+
87 double *C_mon = MatrixMult(A_mon, B_mon, n);
+
88 delete A_mon;
+
89 delete B_mon;
+
90
+
91 // Return the double pointer
+
92 double **C = new double*[n];
+
93 #ifdef MULTITHREAD
+
94 #pragma omp parallel for
+
95 #endif
+
96 for (int i = 0; i < n; ++i) {
+
97 C[i] = new double[n];
+
98 for (int j = 0; j < n; ++j) {
+
99 C[i][j] = C_mon[i*n+j];
+
100 }
+
101 }
+
102 delete C_mon;
+
103
+
104 return C;
+
105 }
-
110
-
-
112 inline TMatrixD MatrixMult(TMatrixD A, TMatrixD B)
-
113 {
-
114 double *C_mon = MatrixMult(A.GetMatrixArray(), B.GetMatrixArray(), A.GetNcols());
-
115 TMatrixD C;
-
116 C.Use(A.GetNcols(), A.GetNrows(), C_mon);
-
117 return C;
-
118 }
+
106
+
+
108 inline TMatrixD MatrixMult(TMatrixD A, TMatrixD B)
+
109 {
+
110 double *C_mon = MatrixMult(A.GetMatrixArray(), B.GetMatrixArray(), A.GetNcols());
+
111 TMatrixD C;
+
112 C.Use(A.GetNcols(), A.GetNrows(), C_mon);
+
113 return C;
+
114 }
-
119
-
120}
-
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:18
+
115
+
116}
+
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:21
-
MaCh3Utils::MatrixMult
double * MatrixMult(double *A, double *B, int n)
CW: Multi-threaded matrix multiplication.
Definition CovarianceUtils.h:44
-
MaCh3Utils::GetNThreads
int GetNThreads()
number of threads which we need for example for TRandom3
Definition CovarianceUtils.h:32
+
MaCh3Utils::MatrixMult
double * MatrixMult(double *A, double *B, int n)
CW: Multi-threaded matrix multiplication.
Definition CovarianceUtils.h:40
+
MaCh3Utils::GetNThreads
int GetNThreads()
number of threads which we need for example for TRandom3
Definition CovarianceUtils.h:28
diff --git a/DiagMCMC_8cpp.html b/DiagMCMC_8cpp.html index 463b80d4c..c6cc53bb1 100644 --- a/DiagMCMC_8cpp.html +++ b/DiagMCMC_8cpp.html @@ -145,8 +145,8 @@

47 delete Processor;

48}
config
YAML::Node config
Definition GetPostfitParamPlots.cpp:30
-
MACH3LOG_INFO
#define MACH3LOG_INFO
Definition MaCh3Logger.h:13
-
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:18
+
MACH3LOG_INFO
#define MACH3LOG_INFO
Definition MaCh3Logger.h:16
+
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:21
MCMCProcessor
Class responsible for processing MCMC chains, performing diagnostics, generating plots,...
Definition MCMCProcessor.h:61
@@ -193,9 +193,9 @@

20 return 0;
21}
DiagMCMC
void DiagMCMC(std::string inputFile, std::string config)
Definition DiagMCMC.cpp:24
-
MACH3LOG_ERROR
#define MACH3LOG_ERROR
Definition MaCh3Logger.h:15
-
SetMaCh3LoggerFormat
void SetMaCh3LoggerFormat()
Set messaging format of the logger.
Definition MaCh3Logger.h:20
-
MaCh3Exception
Custom exception class for MaCh3 errors.
Definition MaCh3Exception.h:10
+
MACH3LOG_ERROR
#define MACH3LOG_ERROR
Definition MaCh3Logger.h:18
+
SetMaCh3LoggerFormat
void SetMaCh3LoggerFormat()
Set messaging format of the logger.
Definition MaCh3Logger.h:23
+
MaCh3Exception
Custom exception class for MaCh3 errors.
Definition MaCh3Exception.h:12
diff --git a/DiagMCMC_8cpp_source.html b/DiagMCMC_8cpp_source.html index d195bdde5..4baee6e4a 100644 --- a/DiagMCMC_8cpp_source.html +++ b/DiagMCMC_8cpp_source.html @@ -141,12 +141,12 @@
DiagMCMC
void DiagMCMC(std::string inputFile, std::string config)
Definition DiagMCMC.cpp:24
config
YAML::Node config
Definition GetPostfitParamPlots.cpp:30
-
MACH3LOG_ERROR
#define MACH3LOG_ERROR
Definition MaCh3Logger.h:15
-
MACH3LOG_INFO
#define MACH3LOG_INFO
Definition MaCh3Logger.h:13
-
SetMaCh3LoggerFormat
void SetMaCh3LoggerFormat()
Set messaging format of the logger.
Definition MaCh3Logger.h:20
-
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:18
+
MACH3LOG_ERROR
#define MACH3LOG_ERROR
Definition MaCh3Logger.h:18
+
MACH3LOG_INFO
#define MACH3LOG_INFO
Definition MaCh3Logger.h:16
+
SetMaCh3LoggerFormat
void SetMaCh3LoggerFormat()
Set messaging format of the logger.
Definition MaCh3Logger.h:23
+
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:21
MCMCProcessor
Class responsible for processing MCMC chains, performing diagnostics, generating plots,...
Definition MCMCProcessor.h:61
-
MaCh3Exception
Custom exception class for MaCh3 errors.
Definition MaCh3Exception.h:10
+
MaCh3Exception
Custom exception class for MaCh3 errors.
Definition MaCh3Exception.h:12
diff --git a/FDMCStruct_8h_source.html b/FDMCStruct_8h_source.html index 4d6ee8871..eb7c29fbc 100644 --- a/FDMCStruct_8h_source.html +++ b/FDMCStruct_8h_source.html @@ -155,7 +155,7 @@
73#endif
74};
-
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:18
+
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:21
splineFDBase
Bin-by-bin class calculating response for spline parameters.
Definition splineFDBase.h:11
fdmc_base
constructors are same for all three so put in here
Definition FDMCStruct.h:5
fdmc_base::flavourName
std::string flavourName
Definition FDMCStruct.h:12
diff --git a/FitterBase_8cpp_source.html b/FitterBase_8cpp_source.html index 686178467..b9cc34af7 100644 --- a/FitterBase_8cpp_source.html +++ b/FitterBase_8cpp_source.html @@ -1195,7 +1195,7 @@
1081 //KS: this is only relevant if PlotByMode is turned on
1082 //Checking each mode is time consuming so we only consider one which are relevant for particular analysis
1083 const int nRelevantModes = 2;
-
1084 MaCh3Modes_t RelevantModes[nRelevantModes] = {Modes->GetMode("CCQE"), Modes->GetMode("2p2h")};
+
1084 MaCh3Modes_t RelevantModes[nRelevantModes] = {Modes->GetMode("CCQE"), Modes->GetMode("2p2h")};
1085 bool DoByMode = GetFromManager<int>(fitMan->raw()["General"]["DoByMode"], false);
1086
1087 //KS: If true it will make additional plots with LLH sample contribution in each bin, should make it via config file...
@@ -1564,66 +1564,66 @@
BranchNames
std::vector< TString > BranchNames
Definition GetPenaltyTerm.cpp:40
-
MACH3LOG_CRITICAL
#define MACH3LOG_CRITICAL
Definition MaCh3Logger.h:16
-
MACH3LOG_ERROR
#define MACH3LOG_ERROR
Definition MaCh3Logger.h:15
-
MACH3LOG_INFO
#define MACH3LOG_INFO
Definition MaCh3Logger.h:13
-
MACH3LOG_WARN
#define MACH3LOG_WARN
Definition MaCh3Logger.h:14
-
MaCh3Modes_t
int MaCh3Modes_t
Enumerator of MaCh3Mode.
Definition MaCh3Modes.h:13
+
MACH3LOG_CRITICAL
#define MACH3LOG_CRITICAL
Definition MaCh3Logger.h:19
+
MACH3LOG_ERROR
#define MACH3LOG_ERROR
Definition MaCh3Logger.h:18
+
MACH3LOG_INFO
#define MACH3LOG_INFO
Definition MaCh3Logger.h:16
+
MACH3LOG_WARN
#define MACH3LOG_WARN
Definition MaCh3Logger.h:17
+
MaCh3Modes_t
int MaCh3Modes_t
Enumerator of MaCh3Mode.
Definition MaCh3Modes.h:14
PolyProjectionX
TH1D * PolyProjectionX(TObject *poly, std::string TempName, std::vector< double > xbins, bool computeErrors)
WP: Poly Projectors.
Definition Structs.cpp:156
PolyProjectionY
TH1D * PolyProjectionY(TObject *poly, std::string TempName, std::vector< double > ybins, bool computeErrors)
WP: Poly Projectors.
Definition Structs.cpp:227
_int_
#define _int_
Definition Structs.h:12
-
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:18
-
FitterBase::Modes
MaCh3Modes * Modes
MaCh3 Modes.
Definition FitterBase.h:95
+
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:21
+
FitterBase::Modes
MaCh3Modes * Modes
MaCh3 Modes.
Definition FitterBase.h:96
FitterBase::RunLLHScan
void RunLLHScan()
Perform a 1D likelihood scan.
Definition FitterBase.cpp:479
-
FitterBase::osc
covarianceOsc * osc
handles oscillation parameters
Definition FitterBase.h:125
+
FitterBase::osc
covarianceOsc * osc
handles oscillation parameters
Definition FitterBase.h:126
FitterBase::addSystObj
void addSystObj(covarianceBase *cov)
This function adds a Covariance object to the analysis framework. The Covariance object will be utili...
Definition FitterBase.cpp:278
FitterBase::ProcessMCMC
void ProcessMCMC()
Process MCMC output.
Definition FitterBase.cpp:373
-
FitterBase::stepClock
TStopwatch * stepClock
tells how long single step/fit iteration took
Definition FitterBase.h:132
-
FitterBase::osc2
covarianceOsc * osc2
handles oscillation parameters
Definition FitterBase.h:127
-
FitterBase::accCount
int accCount
counts accepted steps
Definition FitterBase.h:106
-
FitterBase::random
TRandom3 * random
Random number.
Definition FitterBase.h:137
+
FitterBase::stepClock
TStopwatch * stepClock
tells how long single step/fit iteration took
Definition FitterBase.h:133
+
FitterBase::osc2
covarianceOsc * osc2
handles oscillation parameters
Definition FitterBase.h:128
+
FitterBase::accCount
int accCount
counts accepted steps
Definition FitterBase.h:107
+
FitterBase::random
TRandom3 * random
Random number.
Definition FitterBase.h:138
FitterBase::FitterBase
FitterBase(manager *const fitMan)
Constructor.
Definition FitterBase.cpp:11
-
FitterBase::GetName
virtual std::string GetName() const
Get name of class.
Definition FitterBase.h:70
-
FitterBase::systematics
std::vector< covarianceBase * > systematics
Systematic holder.
Definition FitterBase.h:122
-
FitterBase::OutputPrepared
bool OutputPrepared
Checks if output prepared not repeat some operations.
Definition FitterBase.h:160
+
FitterBase::GetName
virtual std::string GetName() const
Get name of class.
Definition FitterBase.h:71
+
FitterBase::systematics
std::vector< covarianceBase * > systematics
Systematic holder.
Definition FitterBase.h:123
+
FitterBase::OutputPrepared
bool OutputPrepared
Checks if output prepared not repeat some operations.
Definition FitterBase.h:161
FitterBase::SaveOutput
void SaveOutput()
Save output and close files.
Definition FitterBase.cpp:241
-
FitterBase::outputFile
TFile * outputFile
Output.
Definition FitterBase.h:140
+
FitterBase::outputFile
TFile * outputFile
Output.
Definition FitterBase.h:141
FitterBase::SaveSettings
void SaveSettings()
Save the settings that the MCMC was run with.
Definition FitterBase.cpp:103
-
FitterBase::SaveProposal
bool SaveProposal
Save proposal at each step.
Definition FitterBase.h:153
-
FitterBase::fitMan
manager * fitMan
The manager.
Definition FitterBase.h:92
-
FitterBase::step
unsigned int step
current state
Definition FitterBase.h:98
+
FitterBase::SaveProposal
bool SaveProposal
Save proposal at each step.
Definition FitterBase.h:154
+
FitterBase::fitMan
manager * fitMan
The manager.
Definition FitterBase.h:93
+
FitterBase::step
unsigned int step
current state
Definition FitterBase.h:99
FitterBase::PrepareOutput
void PrepareOutput()
Prepare the output file.
Definition FitterBase.cpp:169
-
FitterBase::SettingsSaved
bool SettingsSaved
Checks if setting saved not repeat some operations.
Definition FitterBase.h:158
-
FitterBase::accProb
double accProb
current acceptance prob
Definition FitterBase.h:104
+
FitterBase::SettingsSaved
bool SettingsSaved
Checks if setting saved not repeat some operations.
Definition FitterBase.h:159
+
FitterBase::accProb
double accProb
current acceptance prob
Definition FitterBase.h:105
FitterBase::GetStepScaleBasedOnLLHScan
void GetStepScaleBasedOnLLHScan()
LLH scan is good first estimate of step scale.
Definition FitterBase.cpp:825
-
FitterBase::FileSaved
bool FileSaved
Checks if file saved not repeat some operations.
Definition FitterBase.h:156
+
FitterBase::FileSaved
bool FileSaved
Checks if file saved not repeat some operations.
Definition FitterBase.h:157
FitterBase::RunSigmaVar
void RunSigmaVar()
Perform a 2D and 1D sigma var for all samples.
Definition FitterBase.cpp:1066
-
FitterBase::sample_llh
double * sample_llh
store the llh breakdowns
Definition FitterBase.h:112
-
FitterBase::stepTime
double stepTime
Time of single step.
Definition FitterBase.h:134
-
FitterBase::CovFolder
TDirectory * CovFolder
Output cov folder.
Definition FitterBase.h:142
-
FitterBase::clock
TStopwatch * clock
tells global time how long fit took
Definition FitterBase.h:130
+
FitterBase::sample_llh
double * sample_llh
store the llh breakdowns
Definition FitterBase.h:113
+
FitterBase::stepTime
double stepTime
Time of single step.
Definition FitterBase.h:135
+
FitterBase::CovFolder
TDirectory * CovFolder
Output cov folder.
Definition FitterBase.h:143
+
FitterBase::clock
TStopwatch * clock
tells global time how long fit took
Definition FitterBase.h:131
FitterBase::addOscHandler
void addOscHandler(covarianceOsc *oscf)
Adds an oscillation handler for covariance objects.
Definition FitterBase.cpp:307
FitterBase::MakeAsymGraph
TGraphAsymmErrors * MakeAsymGraph(TH1D *sigmaArrayLeft, TH1D *sigmaArrayCentr, TH1D *sigmaArrayRight, std::string title)
Used by sigma variation, check how 1 sigma changes spectra.
Definition FitterBase.cpp:1417
FitterBase::DragRace
void DragRace(const int NLaps=100)
Calculates the required time for each sample or covariance object in a drag race simulation....
Definition FitterBase.cpp:423
FitterBase::Run2DLLHScan
void Run2DLLHScan()
Perform a 2D likelihood scan.
Definition FitterBase.cpp:872
FitterBase::addSamplePDF
void addSamplePDF(samplePDFBase *sample)
This function adds a sample PDF object to the analysis framework. The sample PDF object will be utili...
Definition FitterBase.cpp:267
-
FitterBase::TotalNSamples
unsigned int TotalNSamples
Total number of samples used.
Definition FitterBase.h:119
-
FitterBase::logLCurr
double logLCurr
current likelihood
Definition FitterBase.h:100
-
FitterBase::osc_llh
double osc_llh
Definition FitterBase.h:110
-
FitterBase::syst_llh
double * syst_llh
systematic llh breakdowns
Definition FitterBase.h:114
-
FitterBase::auto_save
int auto_save
auto save every N steps
Definition FitterBase.h:146
-
FitterBase::fTestLikelihood
bool fTestLikelihood
Necessary for some fitting algorithms like PSO.
Definition FitterBase.h:149
+
FitterBase::TotalNSamples
unsigned int TotalNSamples
Total number of samples used.
Definition FitterBase.h:120
+
FitterBase::logLCurr
double logLCurr
current likelihood
Definition FitterBase.h:101
+
FitterBase::osc_llh
double osc_llh
Definition FitterBase.h:111
+
FitterBase::syst_llh
double * syst_llh
systematic llh breakdowns
Definition FitterBase.h:115
+
FitterBase::auto_save
int auto_save
auto save every N steps
Definition FitterBase.h:147
+
FitterBase::fTestLikelihood
bool fTestLikelihood
Necessary for some fitting algorithms like PSO.
Definition FitterBase.h:150
FitterBase::~FitterBase
virtual ~FitterBase()
Destructor for the FitterBase class.
Definition FitterBase.cpp:81
-
FitterBase::outTree
TTree * outTree
Output tree with posteriors.
Definition FitterBase.h:144
-
FitterBase::save_nominal
bool save_nominal
save nominal matrix info or not
Definition FitterBase.h:151
-
FitterBase::samples
std::vector< samplePDFBase * > samples
Sample holder.
Definition FitterBase.h:117
+
FitterBase::outTree
TTree * outTree
Output tree with posteriors.
Definition FitterBase.h:145
+
FitterBase::save_nominal
bool save_nominal
save nominal matrix info or not
Definition FitterBase.h:152
+
FitterBase::samples
std::vector< samplePDFBase * > samples
Sample holder.
Definition FitterBase.h:118
MCMCProcessor
Class responsible for processing MCMC chains, performing diagnostics, generating plots,...
Definition MCMCProcessor.h:61
-
MaCh3Exception
Custom exception class for MaCh3 errors.
Definition MaCh3Exception.h:10
+
MaCh3Exception
Custom exception class for MaCh3 errors.
Definition MaCh3Exception.h:12
+
MaCh3Modes::GetMode
MaCh3Modes_t GetMode(const std::string &name)
KS: Get mode number based on name, if mode not known you will get UNKNOWN_BAD.
Definition MaCh3Modes.cpp:154
MaCh3Modes::GetMaCh3ModeName
std::string GetMaCh3ModeName(const int Index)
KS: Get normal name of mode, if mode not known you will get UNKNOWN_BAD.
Definition MaCh3Modes.cpp:124
-
MaCh3Modes::GetMode
MaCh3Modes_t GetMode(std::string name)
KS: Get mode number based on name, if mode not known you will get UNKNOWN_BAD.
Definition MaCh3Modes.cpp:154
-
covarianceBase
Base class responsible for handling of systematic error parameters. Capable of using PCA or using ada...
Definition covarianceBase.h:33
-
covarianceBase::SetBranches
void SetBranches(TTree &tree, bool SaveProposal=false)
set branches for output file
Definition covarianceBase.cpp:1096
-
covarianceBase::getNominalArray
virtual std::vector< double > getNominalArray()
Definition covarianceBase.cpp:1707
+
covarianceBase
Base class responsible for handling of systematic error parameters. Capable of using PCA or using ada...
Definition covarianceBase.h:34
+
covarianceBase::SetBranches
void SetBranches(TTree &tree, bool SaveProposal=false)
set branches for output file
Definition covarianceBase.cpp:1098
+
covarianceBase::getNominalArray
virtual std::vector< double > getNominalArray()
Definition covarianceBase.cpp:1522
covarianceOsc
Class responsible for handling of neutrino oscillation parameters.
Definition covarianceOsc.h:8
manager
The manager class is responsible for managing configurations and settings.
Definition manager.h:28
manager::SaveSettings
void SaveSettings(TFile *const OutputFile)
Add manager useful information's to TFile, in most cases to Fitter.
Definition manager.cpp:58
diff --git a/FitterBase_8h_source.html b/FitterBase_8h_source.html index 03225331d..63472f105 100644 --- a/FitterBase_8h_source.html +++ b/FitterBase_8h_source.html @@ -85,160 +85,161 @@
Go to the documentation of this file.
1#pragma once
2
-
3#include <iostream>
-
4#include <fstream>
-
5#include <sstream>
-
6
-
7#include "samplePDF/samplePDFBase.h"
-
8#include "covariance/covarianceBase.h"
-
9#include "covariance/covarianceOsc.h"
-
10
-
11#include "manager/manager.h"
-
12#include "mcmc/MCMCProcessor.h"
-
13
-
14//KS: Joy of forward declaration https://gieseanw.wordpress.com/2018/02/25/the-joys-of-forward-declarations-results-from-the-real-world/
-
15class TRandom3;
-
16class TStopwatch;
-
17class TTree;
-
18class TGraphAsymmErrors;
-
19class TDirectory;
-
20
-
-
23class FitterBase {
-
24 public:
-
27 FitterBase(manager * const fitMan);
-
29 virtual ~FitterBase();
-
30
-
33 void addSamplePDF(samplePDFBase* sample);
-
34
-
37 void addSystObj(covarianceBase* cov);
-
38
-
41 void addOscHandler(covarianceOsc* oscf);
-
42
-
46 void addOscHandler(covarianceOsc* osca, covarianceOsc* oscb);
-
47
-
49 virtual void runMCMC() = 0;
-
50
-
53 void DragRace(const int NLaps = 100);
-
54
-
56 void RunLLHScan();
-
57
-
59 void GetStepScaleBasedOnLLHScan();
-
60
-
63 void Run2DLLHScan();
-
64
-
67 void RunSigmaVar();
-
68
-
70 virtual inline std::string GetName()const {return "FitterBase";};
-
71 protected:
-
73 void ProcessMCMC();
-
74
-
76 void PrepareOutput();
-
77
-
79 void SaveOutput();
-
80
-
82 void SaveSettings();
-
83
-
89 inline TGraphAsymmErrors* MakeAsymGraph(TH1D* sigmaArrayLeft, TH1D* sigmaArrayCentr, TH1D* sigmaArrayRight, std::string title);
-
90
-
92 manager *fitMan;
-
93
-
95 MaCh3Modes* Modes;
-
96
-
98 unsigned int step;
-
100 double logLCurr;
-
102 double logLProp;
-
104 double accProb;
-
106 int accCount;
-
107
-
110 double osc_llh;
-
112 double *sample_llh;
-
114 double *syst_llh;
-
115
-
117 std::vector<samplePDFBase*> samples;
-
119 unsigned int TotalNSamples;
-
120
-
122 std::vector<covarianceBase*> systematics;
-
123
-
125 covarianceOsc *osc;
-
127 covarianceOsc *osc2;
-
128
-
130 TStopwatch* clock;
-
132 TStopwatch* stepClock;
-
134 double stepTime;
-
135
-
137 TRandom3* random;
-
138
-
140 TFile *outputFile;
-
142 TDirectory *CovFolder;
-
144 TTree *outTree;
-
146 int auto_save;
-
147
-
149 bool fTestLikelihood;
-
151 bool save_nominal;
-
153 bool SaveProposal;
-
154
-
156 bool FileSaved;
-
158 bool SettingsSaved;
-
160 bool OutputPrepared;
-
161
-
162 #ifdef DEBUG
-
164 bool debug;
-
166 std::ofstream debugFile;
-
167 #endif
-
168};
+
3// C++ includes
+
4#include <iostream>
+
5#include <fstream>
+
6#include <sstream>
+
7
+
8// MaCh3 Includes
+
9#include "samplePDF/samplePDFBase.h"
+
10#include "covariance/covarianceBase.h"
+
11#include "covariance/covarianceOsc.h"
+
12#include "manager/manager.h"
+
13#include "mcmc/MCMCProcessor.h"
+
14
+
15//KS: Joy of forward declaration https://gieseanw.wordpress.com/2018/02/25/the-joys-of-forward-declarations-results-from-the-real-world/
+
16class TRandom3;
+
17class TStopwatch;
+
18class TTree;
+
19class TGraphAsymmErrors;
+
20class TDirectory;
+
21
+
+
24class FitterBase {
+
25 public:
+
28 FitterBase(manager * const fitMan);
+
30 virtual ~FitterBase();
+
31
+
34 void addSamplePDF(samplePDFBase* sample);
+
35
+
38 void addSystObj(covarianceBase* cov);
+
39
+
42 void addOscHandler(covarianceOsc* oscf);
+
43
+
47 void addOscHandler(covarianceOsc* osca, covarianceOsc* oscb);
+
48
+
50 virtual void runMCMC() = 0;
+
51
+
54 void DragRace(const int NLaps = 100);
+
55
+
57 void RunLLHScan();
+
58
+
60 void GetStepScaleBasedOnLLHScan();
+
61
+
64 void Run2DLLHScan();
+
65
+
68 void RunSigmaVar();
+
69
+
71 virtual inline std::string GetName()const {return "FitterBase";};
+
72 protected:
+
74 void ProcessMCMC();
+
75
+
77 void PrepareOutput();
+
78
+
80 void SaveOutput();
+
81
+
83 void SaveSettings();
+
84
+
90 inline TGraphAsymmErrors* MakeAsymGraph(TH1D* sigmaArrayLeft, TH1D* sigmaArrayCentr, TH1D* sigmaArrayRight, std::string title);
+
91
+
93 manager *fitMan;
+
94
+
96 MaCh3Modes* Modes;
+
97
+
99 unsigned int step;
+
101 double logLCurr;
+
103 double logLProp;
+
105 double accProb;
+
107 int accCount;
+
108
+
111 double osc_llh;
+
113 double *sample_llh;
+
115 double *syst_llh;
+
116
+
118 std::vector<samplePDFBase*> samples;
+
120 unsigned int TotalNSamples;
+
121
+
123 std::vector<covarianceBase*> systematics;
+
124
+
126 covarianceOsc *osc;
+
128 covarianceOsc *osc2;
+
129
+
131 TStopwatch* clock;
+
133 TStopwatch* stepClock;
+
135 double stepTime;
+
136
+
138 TRandom3* random;
+
139
+
141 TFile *outputFile;
+
143 TDirectory *CovFolder;
+
145 TTree *outTree;
+
147 int auto_save;
+
148
+
150 bool fTestLikelihood;
+
152 bool save_nominal;
+
154 bool SaveProposal;
+
155
+
157 bool FileSaved;
+
159 bool SettingsSaved;
+
161 bool OutputPrepared;
+
162
+
163 #ifdef DEBUG
+
165 bool debug;
+
167 std::ofstream debugFile;
+
168 #endif
+
169};
-
169
+
170
-
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:18
-
FitterBase
Base class for implementing fitting algorithms.
Definition FitterBase.h:23
-
FitterBase::Modes
MaCh3Modes * Modes
MaCh3 Modes.
Definition FitterBase.h:95
+
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:21
+
FitterBase
Base class for implementing fitting algorithms.
Definition FitterBase.h:24
+
FitterBase::Modes
MaCh3Modes * Modes
MaCh3 Modes.
Definition FitterBase.h:96
FitterBase::RunLLHScan
void RunLLHScan()
Perform a 1D likelihood scan.
Definition FitterBase.cpp:479
-
FitterBase::osc
covarianceOsc * osc
handles oscillation parameters
Definition FitterBase.h:125
-
FitterBase::logLProp
double logLProp
proposed likelihood
Definition FitterBase.h:102
+
FitterBase::osc
covarianceOsc * osc
handles oscillation parameters
Definition FitterBase.h:126
+
FitterBase::logLProp
double logLProp
proposed likelihood
Definition FitterBase.h:103
FitterBase::runMCMC
virtual void runMCMC()=0
The specific fitting algorithm implemented in this function depends on the derived class....
FitterBase::addSystObj
void addSystObj(covarianceBase *cov)
This function adds a Covariance object to the analysis framework. The Covariance object will be utili...
Definition FitterBase.cpp:278
FitterBase::ProcessMCMC
void ProcessMCMC()
Process MCMC output.
Definition FitterBase.cpp:373
-
FitterBase::stepClock
TStopwatch * stepClock
tells how long single step/fit iteration took
Definition FitterBase.h:132
-
FitterBase::osc2
covarianceOsc * osc2
handles oscillation parameters
Definition FitterBase.h:127
-
FitterBase::accCount
int accCount
counts accepted steps
Definition FitterBase.h:106
-
FitterBase::random
TRandom3 * random
Random number.
Definition FitterBase.h:137
-
FitterBase::GetName
virtual std::string GetName() const
Get name of class.
Definition FitterBase.h:70
-
FitterBase::systematics
std::vector< covarianceBase * > systematics
Systematic holder.
Definition FitterBase.h:122
-
FitterBase::OutputPrepared
bool OutputPrepared
Checks if output prepared not repeat some operations.
Definition FitterBase.h:160
+
FitterBase::stepClock
TStopwatch * stepClock
tells how long single step/fit iteration took
Definition FitterBase.h:133
+
FitterBase::osc2
covarianceOsc * osc2
handles oscillation parameters
Definition FitterBase.h:128
+
FitterBase::accCount
int accCount
counts accepted steps
Definition FitterBase.h:107
+
FitterBase::random
TRandom3 * random
Random number.
Definition FitterBase.h:138
+
FitterBase::GetName
virtual std::string GetName() const
Get name of class.
Definition FitterBase.h:71
+
FitterBase::systematics
std::vector< covarianceBase * > systematics
Systematic holder.
Definition FitterBase.h:123
+
FitterBase::OutputPrepared
bool OutputPrepared
Checks if output prepared not repeat some operations.
Definition FitterBase.h:161
FitterBase::SaveOutput
void SaveOutput()
Save output and close files.
Definition FitterBase.cpp:241
-
FitterBase::outputFile
TFile * outputFile
Output.
Definition FitterBase.h:140
+
FitterBase::outputFile
TFile * outputFile
Output.
Definition FitterBase.h:141
FitterBase::SaveSettings
void SaveSettings()
Save the settings that the MCMC was run with.
Definition FitterBase.cpp:103
-
FitterBase::SaveProposal
bool SaveProposal
Save proposal at each step.
Definition FitterBase.h:153
-
FitterBase::fitMan
manager * fitMan
The manager.
Definition FitterBase.h:92
-
FitterBase::step
unsigned int step
current state
Definition FitterBase.h:98
+
FitterBase::SaveProposal
bool SaveProposal
Save proposal at each step.
Definition FitterBase.h:154
+
FitterBase::fitMan
manager * fitMan
The manager.
Definition FitterBase.h:93
+
FitterBase::step
unsigned int step
current state
Definition FitterBase.h:99
FitterBase::PrepareOutput
void PrepareOutput()
Prepare the output file.
Definition FitterBase.cpp:169
-
FitterBase::SettingsSaved
bool SettingsSaved
Checks if setting saved not repeat some operations.
Definition FitterBase.h:158
-
FitterBase::accProb
double accProb
current acceptance prob
Definition FitterBase.h:104
+
FitterBase::SettingsSaved
bool SettingsSaved
Checks if setting saved not repeat some operations.
Definition FitterBase.h:159
+
FitterBase::accProb
double accProb
current acceptance prob
Definition FitterBase.h:105
FitterBase::GetStepScaleBasedOnLLHScan
void GetStepScaleBasedOnLLHScan()
LLH scan is good first estimate of step scale.
Definition FitterBase.cpp:825
-
FitterBase::FileSaved
bool FileSaved
Checks if file saved not repeat some operations.
Definition FitterBase.h:156
+
FitterBase::FileSaved
bool FileSaved
Checks if file saved not repeat some operations.
Definition FitterBase.h:157
FitterBase::RunSigmaVar
void RunSigmaVar()
Perform a 2D and 1D sigma var for all samples.
Definition FitterBase.cpp:1066
-
FitterBase::sample_llh
double * sample_llh
store the llh breakdowns
Definition FitterBase.h:112
-
FitterBase::stepTime
double stepTime
Time of single step.
Definition FitterBase.h:134
-
FitterBase::CovFolder
TDirectory * CovFolder
Output cov folder.
Definition FitterBase.h:142
-
FitterBase::clock
TStopwatch * clock
tells global time how long fit took
Definition FitterBase.h:130
+
FitterBase::sample_llh
double * sample_llh
store the llh breakdowns
Definition FitterBase.h:113
+
FitterBase::stepTime
double stepTime
Time of single step.
Definition FitterBase.h:135
+
FitterBase::CovFolder
TDirectory * CovFolder
Output cov folder.
Definition FitterBase.h:143
+
FitterBase::clock
TStopwatch * clock
tells global time how long fit took
Definition FitterBase.h:131
FitterBase::addOscHandler
void addOscHandler(covarianceOsc *oscf)
Adds an oscillation handler for covariance objects.
Definition FitterBase.cpp:307
FitterBase::MakeAsymGraph
TGraphAsymmErrors * MakeAsymGraph(TH1D *sigmaArrayLeft, TH1D *sigmaArrayCentr, TH1D *sigmaArrayRight, std::string title)
Used by sigma variation, check how 1 sigma changes spectra.
Definition FitterBase.cpp:1417
FitterBase::DragRace
void DragRace(const int NLaps=100)
Calculates the required time for each sample or covariance object in a drag race simulation....
Definition FitterBase.cpp:423
FitterBase::Run2DLLHScan
void Run2DLLHScan()
Perform a 2D likelihood scan.
Definition FitterBase.cpp:872
FitterBase::addSamplePDF
void addSamplePDF(samplePDFBase *sample)
This function adds a sample PDF object to the analysis framework. The sample PDF object will be utili...
Definition FitterBase.cpp:267
-
FitterBase::TotalNSamples
unsigned int TotalNSamples
Total number of samples used.
Definition FitterBase.h:119
-
FitterBase::logLCurr
double logLCurr
current likelihood
Definition FitterBase.h:100
-
FitterBase::osc_llh
double osc_llh
Definition FitterBase.h:110
-
FitterBase::syst_llh
double * syst_llh
systematic llh breakdowns
Definition FitterBase.h:114
-
FitterBase::auto_save
int auto_save
auto save every N steps
Definition FitterBase.h:146
-
FitterBase::fTestLikelihood
bool fTestLikelihood
Necessary for some fitting algorithms like PSO.
Definition FitterBase.h:149
+
FitterBase::TotalNSamples
unsigned int TotalNSamples
Total number of samples used.
Definition FitterBase.h:120
+
FitterBase::logLCurr
double logLCurr
current likelihood
Definition FitterBase.h:101
+
FitterBase::osc_llh
double osc_llh
Definition FitterBase.h:111
+
FitterBase::syst_llh
double * syst_llh
systematic llh breakdowns
Definition FitterBase.h:115
+
FitterBase::auto_save
int auto_save
auto save every N steps
Definition FitterBase.h:147
+
FitterBase::fTestLikelihood
bool fTestLikelihood
Necessary for some fitting algorithms like PSO.
Definition FitterBase.h:150
FitterBase::~FitterBase
virtual ~FitterBase()
Destructor for the FitterBase class.
Definition FitterBase.cpp:81
-
FitterBase::outTree
TTree * outTree
Output tree with posteriors.
Definition FitterBase.h:144
-
FitterBase::save_nominal
bool save_nominal
save nominal matrix info or not
Definition FitterBase.h:151
-
FitterBase::samples
std::vector< samplePDFBase * > samples
Sample holder.
Definition FitterBase.h:117
-
MaCh3Modes
KS: Class describing MaCh3 modes used in the analysis, it is being initialised from config.
Definition MaCh3Modes.h:32
-
covarianceBase
Base class responsible for handling of systematic error parameters. Capable of using PCA or using ada...
Definition covarianceBase.h:33
+
FitterBase::outTree
TTree * outTree
Output tree with posteriors.
Definition FitterBase.h:145
+
FitterBase::save_nominal
bool save_nominal
save nominal matrix info or not
Definition FitterBase.h:152
+
FitterBase::samples
std::vector< samplePDFBase * > samples
Sample holder.
Definition FitterBase.h:118
+
MaCh3Modes
KS: Class describing MaCh3 modes used in the analysis, it is being initialised from config.
Definition MaCh3Modes.h:33
+
covarianceBase
Base class responsible for handling of systematic error parameters. Capable of using PCA or using ada...
Definition covarianceBase.h:34
covarianceOsc
Class responsible for handling of neutrino oscillation parameters.
Definition covarianceOsc.h:8
manager
The manager class is responsible for managing configurations and settings.
Definition manager.h:28
samplePDFBase
Class responsible for handling implementation of samples used in analysis, reweighting and returning ...
Definition samplePDFBase.h:28
diff --git a/GetPenaltyTerm_8cpp.html b/GetPenaltyTerm_8cpp.html index 0a473b198..9fd1f816a 100644 --- a/GetPenaltyTerm_8cpp.html +++ b/GetPenaltyTerm_8cpp.html @@ -413,8 +413,8 @@

BranchNames
std::vector< TString > BranchNames
Definition GetPenaltyTerm.cpp:40

ReadXSecFile
void ReadXSecFile(std::string inputFile)
Definition GetPenaltyTerm.cpp:313
isFlat
std::vector< bool > isFlat
Definition GetPenaltyTerm.cpp:39
-
MACH3LOG_INFO
#define MACH3LOG_INFO
Definition MaCh3Logger.h:13
-
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:18
+
MACH3LOG_INFO
#define MACH3LOG_INFO
Definition MaCh3Logger.h:16
+
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:21
MaCh3Utils::PrintProgressBar
void PrintProgressBar(const int Done, const int All)
KS: Simply print progress bar.
Definition Monitor.cpp:193
@@ -462,9 +462,9 @@

60}
GetPenaltyTerm
void GetPenaltyTerm(std::string inputFile, std::string configFile)
Definition GetPenaltyTerm.cpp:63
config
YAML::Node config
Definition GetPostfitParamPlots.cpp:30
-
SetMaCh3LoggerFormat
void SetMaCh3LoggerFormat()
Set messaging format of the logger.
Definition MaCh3Logger.h:20
-
MACH3LOG_WARN
#define MACH3LOG_WARN
Definition MaCh3Logger.h:14
-
MaCh3Exception
Custom exception class for MaCh3 errors.
Definition MaCh3Exception.h:10
+
SetMaCh3LoggerFormat
void SetMaCh3LoggerFormat()
Set messaging format of the logger.
Definition MaCh3Logger.h:23
+
MACH3LOG_WARN
#define MACH3LOG_WARN
Definition MaCh3Logger.h:17
+
MaCh3Exception
Custom exception class for MaCh3 errors.
Definition MaCh3Exception.h:12
@@ -568,8 +568,8 @@

394 TempFile->Close();
395 delete TempFile;
396}
-
MACH3LOG_ERROR
#define MACH3LOG_ERROR
Definition MaCh3Logger.h:15
-
TMacroToYAML
YAML::Node TMacroToYAML(const TMacro &macro)
KS: Convert a ROOT TMacro object to a YAML node.
Definition YamlHelper.h:144
+
MACH3LOG_ERROR
#define MACH3LOG_ERROR
Definition MaCh3Logger.h:18
+
TMacroToYAML
YAML::Node TMacroToYAML(const TMacro &macro)
KS: Convert a ROOT TMacro object to a YAML node.
Definition YamlHelper.h:147
MaCh3Utils::PrintConfig
void PrintConfig(const YAML::Node &node)
KS: Print Yaml config using logger.
Definition Monitor.cpp:279
diff --git a/GetPenaltyTerm_8cpp_source.html b/GetPenaltyTerm_8cpp_source.html index 972a32bc2..a360d70c1 100644 --- a/GetPenaltyTerm_8cpp_source.html +++ b/GetPenaltyTerm_8cpp_source.html @@ -495,13 +495,13 @@
ReadXSecFile
void ReadXSecFile(std::string inputFile)
Definition GetPenaltyTerm.cpp:313
isFlat
std::vector< bool > isFlat
Definition GetPenaltyTerm.cpp:39
config
YAML::Node config
Definition GetPostfitParamPlots.cpp:30
-
MACH3LOG_ERROR
#define MACH3LOG_ERROR
Definition MaCh3Logger.h:15
-
MACH3LOG_INFO
#define MACH3LOG_INFO
Definition MaCh3Logger.h:13
-
SetMaCh3LoggerFormat
void SetMaCh3LoggerFormat()
Set messaging format of the logger.
Definition MaCh3Logger.h:20
-
MACH3LOG_WARN
#define MACH3LOG_WARN
Definition MaCh3Logger.h:14
-
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:18
-
TMacroToYAML
YAML::Node TMacroToYAML(const TMacro &macro)
KS: Convert a ROOT TMacro object to a YAML node.
Definition YamlHelper.h:144
-
MaCh3Exception
Custom exception class for MaCh3 errors.
Definition MaCh3Exception.h:10
+
MACH3LOG_ERROR
#define MACH3LOG_ERROR
Definition MaCh3Logger.h:18
+
MACH3LOG_INFO
#define MACH3LOG_INFO
Definition MaCh3Logger.h:16
+
SetMaCh3LoggerFormat
void SetMaCh3LoggerFormat()
Set messaging format of the logger.
Definition MaCh3Logger.h:23
+
MACH3LOG_WARN
#define MACH3LOG_WARN
Definition MaCh3Logger.h:17
+
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:21
+
TMacroToYAML
YAML::Node TMacroToYAML(const TMacro &macro)
KS: Convert a ROOT TMacro object to a YAML node.
Definition YamlHelper.h:147
+
MaCh3Exception
Custom exception class for MaCh3 errors.
Definition MaCh3Exception.h:12
MaCh3Utils::PrintProgressBar
void PrintProgressBar(const int Done, const int All)
KS: Simply print progress bar.
Definition Monitor.cpp:193
MaCh3Utils::PrintConfig
void PrintConfig(const YAML::Node &node)
KS: Print Yaml config using logger.
Definition Monitor.cpp:279
diff --git a/GetPostfitParamPlots_8cpp.html b/GetPostfitParamPlots_8cpp.html index 2b87de188..28fa8a0f5 100644 --- a/GetPostfitParamPlots_8cpp.html +++ b/GetPostfitParamPlots_8cpp.html @@ -273,7 +273,7 @@

105 blockHist->GetXaxis()->LabelsOption("v");
106 }
107}
-
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:18
+
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:21
@@ -981,7 +981,7 @@

985}
GetViolinPlots
void GetViolinPlots(std::string FileName1="", std::string FileName2="")
Definition GetPostfitParamPlots.cpp:718
GetPostfitParamPlots
void GetPostfitParamPlots()
Definition GetPostfitParamPlots.cpp:555
-
SetMaCh3LoggerFormat
void SetMaCh3LoggerFormat()
Set messaging format of the logger.
Definition MaCh3Logger.h:20
+
SetMaCh3LoggerFormat
void SetMaCh3LoggerFormat()
Set messaging format of the logger.
Definition MaCh3Logger.h:23
diff --git a/GetPostfitParamPlots_8cpp_source.html b/GetPostfitParamPlots_8cpp_source.html index 98aac6c4e..fd2f523dd 100644 --- a/GetPostfitParamPlots_8cpp_source.html +++ b/GetPostfitParamPlots_8cpp_source.html @@ -1150,8 +1150,8 @@
setTH1Style
void setTH1Style(TH1 *hist, std::string styleName)
Definition GetPostfitParamPlots.cpp:109
p2
TPad * p2
Definition GetPostfitParamPlots.cpp:62
MakeFDDetPlots
void MakeFDDetPlots()
Definition GetPostfitParamPlots.cpp:507
-
SetMaCh3LoggerFormat
void SetMaCh3LoggerFormat()
Set messaging format of the logger.
Definition MaCh3Logger.h:20
-
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:18
+
SetMaCh3LoggerFormat
void SetMaCh3LoggerFormat()
Set messaging format of the logger.
Definition MaCh3Logger.h:23
+
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:21
diff --git a/LikelihoodFit_8cpp_source.html b/LikelihoodFit_8cpp_source.html index cdafb7513..20dbdf9d1 100644 --- a/LikelihoodFit_8cpp_source.html +++ b/LikelihoodFit_8cpp_source.html @@ -246,25 +246,25 @@
154
-
MACH3LOG_INFO
#define MACH3LOG_INFO
Definition MaCh3Logger.h:13
-
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:18
-
FitterBase
Base class for implementing fitting algorithms.
Definition FitterBase.h:23
-
FitterBase::osc
covarianceOsc * osc
handles oscillation parameters
Definition FitterBase.h:125
-
FitterBase::logLProp
double logLProp
proposed likelihood
Definition FitterBase.h:102
-
FitterBase::stepClock
TStopwatch * stepClock
tells how long single step/fit iteration took
Definition FitterBase.h:132
-
FitterBase::accCount
int accCount
counts accepted steps
Definition FitterBase.h:106
-
FitterBase::systematics
std::vector< covarianceBase * > systematics
Systematic holder.
Definition FitterBase.h:122
+
MACH3LOG_INFO
#define MACH3LOG_INFO
Definition MaCh3Logger.h:16
+
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:21
+
FitterBase
Base class for implementing fitting algorithms.
Definition FitterBase.h:24
+
FitterBase::osc
covarianceOsc * osc
handles oscillation parameters
Definition FitterBase.h:126
+
FitterBase::logLProp
double logLProp
proposed likelihood
Definition FitterBase.h:103
+
FitterBase::stepClock
TStopwatch * stepClock
tells how long single step/fit iteration took
Definition FitterBase.h:133
+
FitterBase::accCount
int accCount
counts accepted steps
Definition FitterBase.h:107
+
FitterBase::systematics
std::vector< covarianceBase * > systematics
Systematic holder.
Definition FitterBase.h:123
FitterBase::SaveSettings
void SaveSettings()
Save the settings that the MCMC was run with.
Definition FitterBase.cpp:103
-
FitterBase::step
unsigned int step
current state
Definition FitterBase.h:98
+
FitterBase::step
unsigned int step
current state
Definition FitterBase.h:99
FitterBase::PrepareOutput
void PrepareOutput()
Prepare the output file.
Definition FitterBase.cpp:169
-
FitterBase::accProb
double accProb
current acceptance prob
Definition FitterBase.h:104
-
FitterBase::sample_llh
double * sample_llh
store the llh breakdowns
Definition FitterBase.h:112
-
FitterBase::stepTime
double stepTime
Time of single step.
Definition FitterBase.h:134
-
FitterBase::logLCurr
double logLCurr
current likelihood
Definition FitterBase.h:100
-
FitterBase::syst_llh
double * syst_llh
systematic llh breakdowns
Definition FitterBase.h:114
-
FitterBase::auto_save
int auto_save
auto save every N steps
Definition FitterBase.h:146
-
FitterBase::outTree
TTree * outTree
Output tree with posteriors.
Definition FitterBase.h:144
-
FitterBase::samples
std::vector< samplePDFBase * > samples
Sample holder.
Definition FitterBase.h:117
+
FitterBase::accProb
double accProb
current acceptance prob
Definition FitterBase.h:105
+
FitterBase::sample_llh
double * sample_llh
store the llh breakdowns
Definition FitterBase.h:113
+
FitterBase::stepTime
double stepTime
Time of single step.
Definition FitterBase.h:135
+
FitterBase::logLCurr
double logLCurr
current likelihood
Definition FitterBase.h:101
+
FitterBase::syst_llh
double * syst_llh
systematic llh breakdowns
Definition FitterBase.h:115
+
FitterBase::auto_save
int auto_save
auto save every N steps
Definition FitterBase.h:147
+
FitterBase::outTree
TTree * outTree
Output tree with posteriors.
Definition FitterBase.h:145
+
FitterBase::samples
std::vector< samplePDFBase * > samples
Sample holder.
Definition FitterBase.h:118
LikelihoodFit::NParsPCA
int NParsPCA
Number of all parameters from all covariances in PCA base.
Definition LikelihoodFit.h:29
LikelihoodFit::LikelihoodFit
LikelihoodFit(manager *const fitMan)
Constructor.
Definition LikelihoodFit.cpp:5
LikelihoodFit::~LikelihoodFit
virtual ~LikelihoodFit()
Destructor.
Definition LikelihoodFit.cpp:15
diff --git a/LikelihoodFit_8h_source.html b/LikelihoodFit_8h_source.html index b783c8b49..b7fe56343 100644 --- a/LikelihoodFit_8h_source.html +++ b/LikelihoodFit_8h_source.html @@ -108,8 +108,8 @@
33
-
FitterBase
Base class for implementing fitting algorithms.
Definition FitterBase.h:23
-
FitterBase::fitMan
manager * fitMan
The manager.
Definition FitterBase.h:92
+
FitterBase
Base class for implementing fitting algorithms.
Definition FitterBase.h:24
+
FitterBase::fitMan
manager * fitMan
The manager.
Definition FitterBase.h:93
LikelihoodFit
Implementation of base Likelihood Fit class, it is mostly responsible for likelihood calculation whil...
Definition LikelihoodFit.h:6
LikelihoodFit::NParsPCA
int NParsPCA
Number of all parameters from all covariances in PCA base.
Definition LikelihoodFit.h:29
LikelihoodFit::GetNPars
int GetNPars()
Get total number of params, this sums over all covariance objects.
Definition LikelihoodFit.h:16
diff --git a/MCMCProcessor_8cpp_source.html b/MCMCProcessor_8cpp_source.html index acee56ced..6e3a3b234 100644 --- a/MCMCProcessor_8cpp_source.html +++ b/MCMCProcessor_8cpp_source.html @@ -3151,7 +3151,7 @@
2998// ***************
2999// Find Param Index based on name
-
3000int MCMCProcessor::GetParamIndexFromName(const std::string Name){
+
3000int MCMCProcessor::GetParamIndexFromName(const std::string& Name){
3001// **************************
3002 int ParamNo = _UNDEF_;
3003 for (int i = 0; i < nDraw; ++i)
@@ -3217,7 +3217,7 @@
3059 for(unsigned int k = 0; k < ParNames.size(); ++k)
3060 {
3061 //KS: First we need to find parameter number based on name
-
3062 int ParamNo = GetParamIndexFromName(ParNames[k]);
+
3062 int ParamNo = GetParamIndexFromName(ParNames[k]);
3063 bool skip = false;
3064 if(ParamNo == _UNDEF_)
3065 {
@@ -3294,7 +3294,7 @@
3134 for(unsigned int k = 0; k < ParNames.size(); ++k)
3135 {
3136 //KS: First we need to find parameter number based on name
-
3137 int ParamNo = GetParamIndexFromName(ParNames[k]);
+
3137 int ParamNo = GetParamIndexFromName(ParNames[k]);
3138 bool skip = false;
3139 if(ParamNo == _UNDEF_)
3140 {
@@ -3361,7 +3361,7 @@
3199 for(unsigned int k = 0; k < ParNames.size(); ++k)
3200 {
3201 //KS: First we need to find parameter number based on name
-
3202 int ParamNo = GetParamIndexFromName(ParNames[k]);
+
3202 int ParamNo = GetParamIndexFromName(ParNames[k]);
3203 bool skip = false;
3204 if(ParamNo == _UNDEF_)
3205 {
@@ -3513,7 +3513,7 @@
3349 for(unsigned int k = 0; k < Names.size(); ++k)
3350 {
3351 //KS: First we need to find parameter number based on name
-
3352 int ParamNo = GetParamIndexFromName(Names[k]);
+
3352 int ParamNo = GetParamIndexFromName(Names[k]);
3353 if(ParamNo == _UNDEF_)
3354 {
3355 MACH3LOG_WARN("Couldn't find param {}. Can't reweight Prior", Names[k]);
@@ -4801,18 +4801,18 @@
kXSecPar
@ kXSecPar
Definition MCMCProcessor.h:50
kNParameterEnum
@ kNParameterEnum
Definition MCMCProcessor.h:55
kFDDetPar
@ kFDDetPar
Definition MCMCProcessor.h:52
-
MACH3LOG_ERROR
#define MACH3LOG_ERROR
Definition MaCh3Logger.h:15
-
MACH3LOG_INFO
#define MACH3LOG_INFO
Definition MaCh3Logger.h:13
-
SetMaCh3LoggerFormat
void SetMaCh3LoggerFormat()
Set messaging format of the logger.
Definition MaCh3Logger.h:20
-
MACH3LOG_WARN
#define MACH3LOG_WARN
Definition MaCh3Logger.h:14
+
MACH3LOG_ERROR
#define MACH3LOG_ERROR
Definition MaCh3Logger.h:18
+
MACH3LOG_INFO
#define MACH3LOG_INFO
Definition MaCh3Logger.h:16
+
SetMaCh3LoggerFormat
void SetMaCh3LoggerFormat()
Set messaging format of the logger.
Definition MaCh3Logger.h:23
+
MACH3LOG_WARN
#define MACH3LOG_WARN
Definition MaCh3Logger.h:17
EffectiveSampleSize
double * EffectiveSampleSize
Definition RHat.cpp:57
GetSigmaValue
double GetSigmaValue(const int sigma)
KS: Convert sigma from normal distribution into percentage.
Definition StatisticalUtils.h:51
GetSubOptimality
double GetSubOptimality(std::vector< double > EigenValues, const int TotalTarameters)
Based on http://probability.ca/jeff/ftpdir/adaptex.pdf.
Definition StatisticalUtils.h:220
GetJeffreysScale
std::string GetJeffreysScale(const double BayesFactor)
KS: Following H. Jeffreys. The theory of probability. UOP Oxford, 1998. DOI: 10.2307/3619118.
Definition StatisticalUtils.h:17
GetDunneKaboth
std::string GetDunneKaboth(const double BayesFactor)
KS: Based on Table 1 in https://www.t2k.org/docs/technotes/435.
Definition StatisticalUtils.h:34
RemoveFitter
void RemoveFitter(TH1D *hist, std::string name)
KS: Remove fitted TF1 from hist to make comparison easier.
Definition Structs.cpp:437
-
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:18
-
TMacroToYAML
YAML::Node TMacroToYAML(const TMacro &macro)
KS: Convert a ROOT TMacro object to a YAML node.
Definition YamlHelper.h:144
+
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:21
+
TMacroToYAML
YAML::Node TMacroToYAML(const TMacro &macro)
KS: Convert a ROOT TMacro object to a YAML node.
Definition YamlHelper.h:147
MCMCProcessor::ScanParameterOrder
void ScanParameterOrder()
Scan order of params from a different groups.
Definition MCMCProcessor.cpp:2353
MCMCProcessor::nBatches
int nBatches
Number of batches for Batched Mean.
Definition MCMCProcessor.h:471
MCMCProcessor::MakePrefit
TH1D * MakePrefit()
Prepare prefit histogram for parameter overlay plot.
Definition MCMCProcessor.cpp:2371
@@ -4859,6 +4859,7 @@
MCMCProcessor::hviolin
TH2D * hviolin
Holds violin plot for all dials.
Definition MCMCProcessor.h:450
MCMCProcessor::StepCut
std::string StepCut
BurnIn Cuts.
Definition MCMCProcessor.h:324
MCMCProcessor::GetPostfit_Ind
void GetPostfit_Ind(TVectorD *&Central, TVectorD *&Errors, TVectorD *&Peaks, ParameterEnum kParam)
Or the individual post-fits.
Definition MCMCProcessor.cpp:179
+
MCMCProcessor::GetParamIndexFromName
int GetParamIndexFromName(const std::string &Name)
Get parameter number based on name.
Definition MCMCProcessor.cpp:3000
MCMCProcessor::DrawCorrelations1D
void DrawCorrelations1D()
Draw 1D correlations which might be more helpful than looking at huge 2D Corr matrix.
Definition MCMCProcessor.cpp:1497
MCMCProcessor::GetPostfit
void GetPostfit(TVectorD *&Central, TVectorD *&Errors, TVectorD *&Central_Gauss, TVectorD *&Errors_Gauss, TVectorD *&Peaks)
Get the post-fit results (arithmetic and Gaussian)
Definition MCMCProcessor.cpp:164
MCMCProcessor::Means_Gauss
TVectorD * Means_Gauss
Vector with mean values using Gaussian fit.
Definition MCMCProcessor.h:428
@@ -4871,7 +4872,6 @@
MCMCProcessor::Chain
TChain * Chain
Main chain storing all steps etc.
Definition MCMCProcessor.h:322
MCMCProcessor::MCMCFile
std::string MCMCFile
Name of MCMC file.
Definition MCMCProcessor.h:315
MCMCProcessor::ExcludedNames
std::vector< std::string > ExcludedNames
Definition MCMCProcessor.h:345
-
MCMCProcessor::GetParamIndexFromName
int GetParamIndexFromName(const std::string Name)
Get parameter number based on name.
Definition MCMCProcessor.cpp:3000
MCMCProcessor::Errors_HPD_Negative
TVectorD * Errors_HPD_Negative
Vector with negative error (left hand side) values using Highest Posterior Density.
Definition MCMCProcessor.h:438
MCMCProcessor::CovPos
std::vector< std::vector< std::string > > CovPos
Covariance matrix name position.
Definition MCMCProcessor.h:319
MCMCProcessor::ParamSums
double * ParamSums
Total parameter sum for each param.
Definition MCMCProcessor.h:476
diff --git a/MCMCProcessor_8h_source.html b/MCMCProcessor_8h_source.html index 2378ac1da..6bcef028b 100644 --- a/MCMCProcessor_8h_source.html +++ b/MCMCProcessor_8h_source.html @@ -219,7 +219,7 @@
193
195 const std::vector<TString>& GetBranchNames() const { return BranchNames;};
197 void GetNthParameter(const int param, double &Prior, double &PriorError, TString &Title);
-
199 int GetParamIndexFromName(const std::string Name);
+
199 int GetParamIndexFromName(const std::string& Name);
201 inline int GetnEntries(){return nEntries;};
203 inline int GetnSteps(){return nSteps;};
204
@@ -408,7 +408,7 @@
kNParameterEnum
@ kNParameterEnum
Definition MCMCProcessor.h:55
kFDDetPar
@ kFDDetPar
Definition MCMCProcessor.h:52
-
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:18
+
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:21
MCMCProcessor
Class responsible for processing MCMC chains, performing diagnostics, generating plots,...
Definition MCMCProcessor.h:61
MCMCProcessor::ScanParameterOrder
void ScanParameterOrder()
Scan order of params from a different groups.
Definition MCMCProcessor.cpp:2353
MCMCProcessor::nBatches
int nBatches
Number of batches for Batched Mean.
Definition MCMCProcessor.h:471
@@ -465,6 +465,7 @@
MCMCProcessor::hviolin
TH2D * hviolin
Holds violin plot for all dials.
Definition MCMCProcessor.h:450
MCMCProcessor::StepCut
std::string StepCut
BurnIn Cuts.
Definition MCMCProcessor.h:324
MCMCProcessor::GetPostfit_Ind
void GetPostfit_Ind(TVectorD *&Central, TVectorD *&Errors, TVectorD *&Peaks, ParameterEnum kParam)
Or the individual post-fits.
Definition MCMCProcessor.cpp:179
+
MCMCProcessor::GetParamIndexFromName
int GetParamIndexFromName(const std::string &Name)
Get parameter number based on name.
Definition MCMCProcessor.cpp:3000
MCMCProcessor::DrawCorrelations1D
void DrawCorrelations1D()
Draw 1D correlations which might be more helpful than looking at huge 2D Corr matrix.
Definition MCMCProcessor.cpp:1497
MCMCProcessor::SetnBatches
void SetnBatches(const int Batches)
Set value of Nbatches used for batched mean, this need to be done earlier as batches are made when re...
Definition MCMCProcessor.h:233
MCMCProcessor::GetPostfit
void GetPostfit(TVectorD *&Central, TVectorD *&Errors, TVectorD *&Central_Gauss, TVectorD *&Errors_Gauss, TVectorD *&Peaks)
Get the post-fit results (arithmetic and Gaussian)
Definition MCMCProcessor.cpp:164
@@ -484,7 +485,6 @@
MCMCProcessor::GetHpost
TH1D * GetHpost(const int i)
Get 1D posterior for a given parameter.
Definition MCMCProcessor.h:169
MCMCProcessor::ExcludedNames
std::vector< std::string > ExcludedNames
Definition MCMCProcessor.h:345
MCMCProcessor::GetHpost2D
TH2D * GetHpost2D(const int i, const int j)
Get 2D posterior for a given parameter combination.
Definition MCMCProcessor.h:173
-
MCMCProcessor::GetParamIndexFromName
int GetParamIndexFromName(const std::string Name)
Get parameter number based on name.
Definition MCMCProcessor.cpp:3000
MCMCProcessor::Errors_HPD_Negative
TVectorD * Errors_HPD_Negative
Vector with negative error (left hand side) values using Highest Posterior Density.
Definition MCMCProcessor.h:438
MCMCProcessor::CovPos
std::vector< std::vector< std::string > > CovPos
Covariance matrix name position.
Definition MCMCProcessor.h:319
MCMCProcessor::ParamSums
double * ParamSums
Total parameter sum for each param.
Definition MCMCProcessor.h:476
diff --git a/MaCh3Exception_8h_source.html b/MaCh3Exception_8h_source.html index 5a8dea0ac..c86b89803 100644 --- a/MaCh3Exception_8h_source.html +++ b/MaCh3Exception_8h_source.html @@ -85,44 +85,46 @@
Go to the documentation of this file.
1#pragma once
2
-
3#include <iostream>
-
4#include <string>
-
5#include <stdexcept>
-
6
-
7#include "manager/MaCh3Logger.h"
-
8
-
-
10class MaCh3Exception : public std::exception {
-
11public:
-
-
16 explicit MaCh3Exception(std::string File, int Line, std::string Message = "")
-
17 {
-
18 size_t lastSlashPos = File.find_last_of('/');
-
19 std::string fileName = (lastSlashPos != std::string::npos) ? File.substr(lastSlashPos + 1) : File;
-
20
-
21 errorMessage = ((Message.empty()) ? "Terminating MaCh3" : Message);
+
3// C++ Includes
+
4#include <iostream>
+
5#include <string>
+
6#include <stdexcept>
+
7
+
8// MaCh3 Includes
+
9#include "manager/MaCh3Logger.h"
+
10
+
+
12class MaCh3Exception : public std::exception {
+
13public:
+
+
18 explicit MaCh3Exception(std::string File, int Line, std::string Message = "")
+
19 {
+
20 size_t lastSlashPos = File.find_last_of('/');
+
21 std::string fileName = (lastSlashPos != std::string::npos) ? File.substr(lastSlashPos + 1) : File;
22
-
23 MACH3LOG_ERROR("Find me here: {}::{}", fileName, Line);
-
24 }
+
23 errorMessage = ((Message.empty()) ? "Terminating MaCh3" : Message);
+
24
+
25 MACH3LOG_ERROR("Find me here: {}::{}", fileName, Line);
+
26 }
-
25
-
-
28 const char* what() const noexcept override {
-
29 return errorMessage.c_str();
-
30 }
+
27
+
+
30 const char* what() const noexcept override {
+
31 return errorMessage.c_str();
+
32 }
-
31
-
32private:
-
34 std::string errorMessage;
-
35};
+
33
+
34private:
+
36 std::string errorMessage;
+
37};
-
MACH3LOG_ERROR
#define MACH3LOG_ERROR
Definition MaCh3Logger.h:15
-
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:18
-
MaCh3Exception
Custom exception class for MaCh3 errors.
Definition MaCh3Exception.h:10
-
MaCh3Exception::what
const char * what() const noexcept override
Returns the error message associated with this exception.
Definition MaCh3Exception.h:28
-
MaCh3Exception::MaCh3Exception
MaCh3Exception(std::string File, int Line, std::string Message="")
Constructs a MaCh3Exception object with the specified error message.
Definition MaCh3Exception.h:16
-
MaCh3Exception::errorMessage
std::string errorMessage
The error message associated with this exception.
Definition MaCh3Exception.h:34
+
MACH3LOG_ERROR
#define MACH3LOG_ERROR
Definition MaCh3Logger.h:18
+
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:21
+
MaCh3Exception
Custom exception class for MaCh3 errors.
Definition MaCh3Exception.h:12
+
MaCh3Exception::what
const char * what() const noexcept override
Returns the error message associated with this exception.
Definition MaCh3Exception.h:30
+
MaCh3Exception::MaCh3Exception
MaCh3Exception(std::string File, int Line, std::string Message="")
Constructs a MaCh3Exception object with the specified error message.
Definition MaCh3Exception.h:18
+
MaCh3Exception::errorMessage
std::string errorMessage
The error message associated with this exception.
Definition MaCh3Exception.h:36
diff --git a/MaCh3Factory_8cpp.html b/MaCh3Factory_8cpp.html index 808e49eae..06516ca41 100644 --- a/MaCh3Factory_8cpp.html +++ b/MaCh3Factory_8cpp.html @@ -152,9 +152,9 @@

31

32 return MaCh3Fitter;
33}
-
MACH3LOG_ERROR
#define MACH3LOG_ERROR
Definition MaCh3Logger.h:15
-
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:18
-
MaCh3Exception
Custom exception class for MaCh3 errors.
Definition MaCh3Exception.h:10
+
MACH3LOG_ERROR
#define MACH3LOG_ERROR
Definition MaCh3Logger.h:18
+
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:21
+
MaCh3Exception
Custom exception class for MaCh3 errors.
Definition MaCh3Exception.h:12
manager::raw
YAML::Node const & raw()
Return config.
Definition manager.h:48
diff --git a/MaCh3Factory_8cpp_source.html b/MaCh3Factory_8cpp_source.html index 0aa392c59..79c94b7e7 100644 --- a/MaCh3Factory_8cpp_source.html +++ b/MaCh3Factory_8cpp_source.html @@ -120,9 +120,9 @@
MaCh3FitterFactory
std::unique_ptr< FitterBase > MaCh3FitterFactory(manager *fitMan, std::vector< samplePDFBase * > &Samples, std::vector< covarianceBase * > &Covariances)
Definition MaCh3Factory.cpp:4
-
MACH3LOG_ERROR
#define MACH3LOG_ERROR
Definition MaCh3Logger.h:15
-
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:18
-
MaCh3Exception
Custom exception class for MaCh3 errors.
Definition MaCh3Exception.h:10
+
MACH3LOG_ERROR
#define MACH3LOG_ERROR
Definition MaCh3Logger.h:18
+
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:21
+
MaCh3Exception
Custom exception class for MaCh3 errors.
Definition MaCh3Exception.h:12
manager
The manager class is responsible for managing configurations and settings.
Definition manager.h:28
manager::raw
YAML::Node const & raw()
Return config.
Definition manager.h:48
diff --git a/MaCh3Factory_8h_source.html b/MaCh3Factory_8h_source.html index bfcd5b94d..ca1b0629c 100644 --- a/MaCh3Factory_8h_source.html +++ b/MaCh3Factory_8h_source.html @@ -100,7 +100,7 @@
MaCh3FitterFactory
std::unique_ptr< FitterBase > MaCh3FitterFactory(manager *fitMan, std::vector< samplePDFBase > &Samples, std::vector< covarianceBase > &Covariances)
MaCh3 Factory initiates one of implemented fitting algorithms.
-
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:18
+
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:21
manager
The manager class is responsible for managing configurations and settings.
Definition manager.h:28
diff --git a/MaCh3Logger_8h.html b/MaCh3Logger_8h.html index 128c43d1d..99ef3a12d 100644 --- a/MaCh3Logger_8h.html +++ b/MaCh3Logger_8h.html @@ -129,7 +129,7 @@

-

Definition at line 16 of file MaCh3Logger.h.

+

Definition at line 19 of file MaCh3Logger.h.

@@ -145,7 +145,7 @@

-

Definition at line 12 of file MaCh3Logger.h.

+

Definition at line 15 of file MaCh3Logger.h.

@@ -161,7 +161,7 @@

-

Definition at line 15 of file MaCh3Logger.h.

+

Definition at line 18 of file MaCh3Logger.h.

@@ -177,7 +177,7 @@

-

Definition at line 13 of file MaCh3Logger.h.

+

Definition at line 16 of file MaCh3Logger.h.

@@ -193,7 +193,7 @@

-

Definition at line 17 of file MaCh3Logger.h.

+

Definition at line 20 of file MaCh3Logger.h.

@@ -209,7 +209,7 @@

-

Definition at line 11 of file MaCh3Logger.h.

+

Definition at line 14 of file MaCh3Logger.h.

@@ -225,7 +225,7 @@

-

Definition at line 14 of file MaCh3Logger.h.

+

Definition at line 17 of file MaCh3Logger.h.

@@ -295,41 +295,41 @@

return 0;
}
main
int main(int argc, char *argv[])
Definition CombineMaCh3Chains.cpp:269
-
MACH3LOG_INFO
#define MACH3LOG_INFO
Definition MaCh3Logger.h:13
-
LoggerPrint
void LoggerPrint(const std::string &LibName, LogFunc logFunction, Func &&func, Args &&... args)
KS: This is bit convoluted but this is to allow redirecting cout and errors from external library int...
Definition MaCh3Logger.h:57
-
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:18
+
MACH3LOG_INFO
#define MACH3LOG_INFO
Definition MaCh3Logger.h:16
+
LoggerPrint
void LoggerPrint(const std::string &LibName, LogFunc logFunction, Func &&func, Args &&... args)
KS: This is bit convoluted but this is to allow redirecting cout and errors from external library int...
Definition MaCh3Logger.h:60
+
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:21
Note
second argument is lambda fucniton whih convers mach3 so template works, it is bit faff... This approach allows seamless integration of func into an existing logging mechanism without modifying func itself
-

Definition at line 57 of file MaCh3Logger.h.

-
58{
-
59 // Create a stringstream to capture the output
-
60 std::stringstream sss;
-
61 // Save the original stream buffers
-
62 std::streambuf* coutBuf = std::cout.rdbuf();
-
63 std::streambuf* cerrBuf = std::cerr.rdbuf();
-
64
-
65 // Redirect std::cout and std::cerr to the stringstream buffer
-
66 std::cout.rdbuf(sss.rdbuf());
-
67 std::cerr.rdbuf(sss.rdbuf());
-
68
-
69 // Call the provided function
-
70 func(std::forward<Args>(args)...);
+

Definition at line 60 of file MaCh3Logger.h.

+
61{
+
62 // Create a stringstream to capture the output
+
63 std::stringstream sss;
+
64 // Save the original stream buffers
+
65 std::streambuf* coutBuf = std::cout.rdbuf();
+
66 std::streambuf* cerrBuf = std::cerr.rdbuf();
+
67
+
68 // Redirect std::cout and std::cerr to the stringstream buffer
+
69 std::cout.rdbuf(sss.rdbuf());
+
70 std::cerr.rdbuf(sss.rdbuf());
71
-
72 // Restore the original stream buffers
-
73 std::cout.rdbuf(coutBuf);
-
74 std::cerr.rdbuf(cerrBuf);
-
75
-
76 std::string line;
-
77 while (std::getline(sss, line))
-
78 {
-
79 auto formatted_message = fmt::format("[{}] {}", LibName, line);
-
80 logFunction(formatted_message);
-
81 }
-
82}
+
72 // Call the provided function
+
73 func(std::forward<Args>(args)...);
+
74
+
75 // Restore the original stream buffers
+
76 std::cout.rdbuf(coutBuf);
+
77 std::cerr.rdbuf(cerrBuf);
+
78
+
79 std::string line;
+
80 while (std::getline(sss, line))
+
81 {
+
82 auto formatted_message = fmt::format("[{}] {}", LibName, line);
+
83 logFunction(formatted_message);
+
84 }
+
85}
@@ -358,18 +358,18 @@

Definition at line 20 of file MaCh3Logger.h.

-
21{
-
22 //KS: %H for hour, %M for minute, %S for second, [%s:%#] for class and line
-
23 //For documentation see https://github.com/gabime/spdlog/wiki/3.-Custom-formatting
-
24 #ifdef DEBUG
-
25 //spdlog::set_pattern("[%H:%M:%S][%s:%#][%^%l%$] %v");
-
26 spdlog::set_pattern("[%s:%#][%^%l%$] %v");
-
27 #else
-
28 //spdlog::set_pattern("[%H:%M:%S][%s][%^%l%$] %v");
-
29 spdlog::set_pattern("[%s][%^%l%$] %v");
-
30 #endif
-
31}
+

Definition at line 23 of file MaCh3Logger.h.

+
24{
+
25 //KS: %H for hour, %M for minute, %S for second, [%s:%#] for class and line
+
26 //For documentation see https://github.com/gabime/spdlog/wiki/3.-Custom-formatting
+
27 #ifdef DEBUG
+
28 //spdlog::set_pattern("[%H:%M:%S][%s:%#][%^%l%$] %v");
+
29 spdlog::set_pattern("[%s:%#][%^%l%$] %v");
+
30 #else
+
31 //spdlog::set_pattern("[%H:%M:%S][%s][%^%l%$] %v");
+
32 spdlog::set_pattern("[%s][%^%l%$] %v");
+
33 #endif
+
34}
diff --git a/MaCh3Logger_8h_source.html b/MaCh3Logger_8h_source.html index 891ea51ac..41ea1feae 100644 --- a/MaCh3Logger_8h_source.html +++ b/MaCh3Logger_8h_source.html @@ -85,69 +85,72 @@
Go to the documentation of this file.
1#pragma once
2
-
3#include "spdlog/spdlog.h"
-
4#include <iostream>
-
5#include <sstream>
-
6#include <functional>
-
7#include <string>
-
8
-
9//KS: Based on this https://github.com/gabime/spdlog/blob/a2b4262090fd3f005c2315dcb5be2f0f1774a005/include/spdlog/spdlog.h#L284
-
10
-
11#define MACH3LOG_TRACE SPDLOG_TRACE
-
12#define MACH3LOG_DEBUG SPDLOG_DEBUG
-
13#define MACH3LOG_INFO SPDLOG_INFO
-
14#define MACH3LOG_WARN SPDLOG_WARN
-
15#define MACH3LOG_ERROR SPDLOG_ERROR
-
16#define MACH3LOG_CRITICAL SPDLOG_CRITICAL
-
17#define MACH3LOG_OFF SPDLOG_OFF
-
18
-
-
20inline void SetMaCh3LoggerFormat()
-
21{
-
22 //KS: %H for hour, %M for minute, %S for second, [%s:%#] for class and line
-
23 //For documentation see https://github.com/gabime/spdlog/wiki/3.-Custom-formatting
-
24 #ifdef DEBUG
-
25 //spdlog::set_pattern("[%H:%M:%S][%s:%#][%^%l%$] %v");
-
26 spdlog::set_pattern("[%s:%#][%^%l%$] %v");
-
27 #else
-
28 //spdlog::set_pattern("[%H:%M:%S][%s][%^%l%$] %v");
-
29 spdlog::set_pattern("[%s][%^%l%$] %v");
-
30 #endif
-
31}
+
3// spdlog Includes
+
4#include "spdlog/spdlog.h"
+
5
+
6// C++ Includes
+
7#include <iostream>
+
8#include <sstream>
+
9#include <functional>
+
10#include <string>
+
11
+
12//KS: Based on this https://github.com/gabime/spdlog/blob/a2b4262090fd3f005c2315dcb5be2f0f1774a005/include/spdlog/spdlog.h#L284
+
13
+
14#define MACH3LOG_TRACE SPDLOG_TRACE
+
15#define MACH3LOG_DEBUG SPDLOG_DEBUG
+
16#define MACH3LOG_INFO SPDLOG_INFO
+
17#define MACH3LOG_WARN SPDLOG_WARN
+
18#define MACH3LOG_ERROR SPDLOG_ERROR
+
19#define MACH3LOG_CRITICAL SPDLOG_CRITICAL
+
20#define MACH3LOG_OFF SPDLOG_OFF
+
21
+
+
23inline void SetMaCh3LoggerFormat()
+
24{
+
25 //KS: %H for hour, %M for minute, %S for second, [%s:%#] for class and line
+
26 //For documentation see https://github.com/gabime/spdlog/wiki/3.-Custom-formatting
+
27 #ifdef DEBUG
+
28 //spdlog::set_pattern("[%H:%M:%S][%s:%#][%^%l%$] %v");
+
29 spdlog::set_pattern("[%s:%#][%^%l%$] %v");
+
30 #else
+
31 //spdlog::set_pattern("[%H:%M:%S][%s][%^%l%$] %v");
+
32 spdlog::set_pattern("[%s][%^%l%$] %v");
+
33 #endif
+
34}
-
32
-
56template <typename Func, typename LogFunc, typename... Args>
-
-
57void LoggerPrint(const std::string& LibName, LogFunc logFunction, Func&& func, Args&&... args)
-
58{
-
59 // Create a stringstream to capture the output
-
60 std::stringstream sss;
-
61 // Save the original stream buffers
-
62 std::streambuf* coutBuf = std::cout.rdbuf();
-
63 std::streambuf* cerrBuf = std::cerr.rdbuf();
-
64
-
65 // Redirect std::cout and std::cerr to the stringstream buffer
-
66 std::cout.rdbuf(sss.rdbuf());
-
67 std::cerr.rdbuf(sss.rdbuf());
-
68
-
69 // Call the provided function
-
70 func(std::forward<Args>(args)...);
+
35
+
59template <typename Func, typename LogFunc, typename... Args>
+
+
60void LoggerPrint(const std::string& LibName, LogFunc logFunction, Func&& func, Args&&... args)
+
61{
+
62 // Create a stringstream to capture the output
+
63 std::stringstream sss;
+
64 // Save the original stream buffers
+
65 std::streambuf* coutBuf = std::cout.rdbuf();
+
66 std::streambuf* cerrBuf = std::cerr.rdbuf();
+
67
+
68 // Redirect std::cout and std::cerr to the stringstream buffer
+
69 std::cout.rdbuf(sss.rdbuf());
+
70 std::cerr.rdbuf(sss.rdbuf());
71
-
72 // Restore the original stream buffers
-
73 std::cout.rdbuf(coutBuf);
-
74 std::cerr.rdbuf(cerrBuf);
-
75
-
76 std::string line;
-
77 while (std::getline(sss, line))
-
78 {
-
79 auto formatted_message = fmt::format("[{}] {}", LibName, line);
-
80 logFunction(formatted_message);
-
81 }
-
82}
+
72 // Call the provided function
+
73 func(std::forward<Args>(args)...);
+
74
+
75 // Restore the original stream buffers
+
76 std::cout.rdbuf(coutBuf);
+
77 std::cerr.rdbuf(cerrBuf);
+
78
+
79 std::string line;
+
80 while (std::getline(sss, line))
+
81 {
+
82 auto formatted_message = fmt::format("[{}] {}", LibName, line);
+
83 logFunction(formatted_message);
+
84 }
+
85}
-
SetMaCh3LoggerFormat
void SetMaCh3LoggerFormat()
Set messaging format of the logger.
Definition MaCh3Logger.h:20
-
LoggerPrint
void LoggerPrint(const std::string &LibName, LogFunc logFunction, Func &&func, Args &&... args)
KS: This is bit convoluted but this is to allow redirecting cout and errors from external library int...
Definition MaCh3Logger.h:57
-
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:18
+
SetMaCh3LoggerFormat
void SetMaCh3LoggerFormat()
Set messaging format of the logger.
Definition MaCh3Logger.h:23
+
LoggerPrint
void LoggerPrint(const std::string &LibName, LogFunc logFunction, Func &&func, Args &&... args)
KS: This is bit convoluted but this is to allow redirecting cout and errors from external library int...
Definition MaCh3Logger.h:60
+
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:21
diff --git a/MaCh3Modes_8cpp_source.html b/MaCh3Modes_8cpp_source.html index 5920ff538..cdfcf5e61 100644 --- a/MaCh3Modes_8cpp_source.html +++ b/MaCh3Modes_8cpp_source.html @@ -251,7 +251,7 @@
152
153// *******************
-
154MaCh3Modes_t MaCh3Modes::GetMode(std::string name) {
+
154MaCh3Modes_t MaCh3Modes::GetMode(const std::string& name) {
155// *******************
156 if (Mode.count(name)) {
157 return Mode[name];
@@ -279,30 +279,30 @@
177}
config
YAML::Node config
Definition GetPostfitParamPlots.cpp:30
-
MACH3LOG_CRITICAL
#define MACH3LOG_CRITICAL
Definition MaCh3Logger.h:16
-
MACH3LOG_DEBUG
#define MACH3LOG_DEBUG
Definition MaCh3Logger.h:12
-
MACH3LOG_ERROR
#define MACH3LOG_ERROR
Definition MaCh3Logger.h:15
-
MACH3LOG_INFO
#define MACH3LOG_INFO
Definition MaCh3Logger.h:13
+
MACH3LOG_CRITICAL
#define MACH3LOG_CRITICAL
Definition MaCh3Logger.h:19
+
MACH3LOG_DEBUG
#define MACH3LOG_DEBUG
Definition MaCh3Logger.h:15
+
MACH3LOG_ERROR
#define MACH3LOG_ERROR
Definition MaCh3Logger.h:18
+
MACH3LOG_INFO
#define MACH3LOG_INFO
Definition MaCh3Logger.h:16
-
MaCh3Modes_t
int MaCh3Modes_t
Enumerator of MaCh3Mode.
Definition MaCh3Modes.h:13
-
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:18
-
MaCh3Modes::Mode
std::map< std::string, MaCh3Modes_t > Mode
KS: Handy map which helps find mode number based on string.
Definition MaCh3Modes.h:68
+
MaCh3Modes_t
int MaCh3Modes_t
Enumerator of MaCh3Mode.
Definition MaCh3Modes.h:14
+
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:21
+
MaCh3Modes::Mode
std::map< std::string, MaCh3Modes_t > Mode
KS: Handy map which helps find mode number based on string.
Definition MaCh3Modes.h:69
MaCh3Modes::GetMaCh3ModeFancyName
std::string GetMaCh3ModeFancyName(const int Index)
KS: Get fancy name of mode, if mode not known you will get UNKNOWN_BAD.
Definition MaCh3Modes.cpp:139
MaCh3Modes::MaCh3Modes
MaCh3Modes(std::string const &filename)
KS: Initialise MaCh3 modes.
Definition MaCh3Modes.cpp:5
-
MaCh3Modes::NModes
int NModes
KS: Number of modes, keep in mind actual number is +1 greater due to unknown category.
Definition MaCh3Modes.h:79
-
MaCh3Modes::ModeMap
std::vector< int > ModeMap
KS: Handy map helping us find MaCh3 mode based on Generator mode value.
Definition MaCh3Modes.h:72
+
MaCh3Modes::GetMode
MaCh3Modes_t GetMode(const std::string &name)
KS: Get mode number based on name, if mode not known you will get UNKNOWN_BAD.
Definition MaCh3Modes.cpp:154
+
MaCh3Modes::NModes
int NModes
KS: Number of modes, keep in mind actual number is +1 greater due to unknown category.
Definition MaCh3Modes.h:80
+
MaCh3Modes::ModeMap
std::vector< int > ModeMap
KS: Handy map helping us find MaCh3 mode based on Generator mode value.
Definition MaCh3Modes.h:73
MaCh3Modes::Print
void Print()
KS: Print info about initialised modes.
Definition MaCh3Modes.cpp:38
-
MaCh3Modes::Generator
std::string Generator
KS: Name of generator like NEUT, NuWro etc. this is to make stuff fancy.
Definition MaCh3Modes.h:77
-
MaCh3Modes::Title
std::string Title
KS: Name of loaded modes.
Definition MaCh3Modes.h:75
+
MaCh3Modes::Generator
std::string Generator
KS: Name of generator like NEUT, NuWro etc. this is to make stuff fancy.
Definition MaCh3Modes.h:78
+
MaCh3Modes::Title
std::string Title
KS: Name of loaded modes.
Definition MaCh3Modes.h:76
MaCh3Modes::EnsureModeNameRegistered
MaCh3Modes_t EnsureModeNameRegistered(std::string const &name)
KS: Make sure we don't have two modes with the same name.
Definition MaCh3Modes.cpp:69
MaCh3Modes::GetMaCh3ModeName
std::string GetMaCh3ModeName(const int Index)
KS: Get normal name of mode, if mode not known you will get UNKNOWN_BAD.
Definition MaCh3Modes.cpp:124
MaCh3Modes::DeclareNewMode
void DeclareNewMode(std::string const &name, std::string const &fancyname, std::vector< int > const &GenMap)
KS: Add new mode.
Definition MaCh3Modes.cpp:80
MaCh3Modes::PrepareMap
void PrepareMap()
KS: Fill ModeMap.
Definition MaCh3Modes.cpp:96
MaCh3Modes::GetModeFromGenerator
MaCh3Modes_t GetModeFromGenerator(const int Index)
KS: Get MaCh3 mode from generator mode.
Definition MaCh3Modes.cpp:166
-
MaCh3Modes::GetMode
MaCh3Modes_t GetMode(std::string name)
KS: Get mode number based on name, if mode not known you will get UNKNOWN_BAD.
Definition MaCh3Modes.cpp:154
-
MaCh3Modes::fMode
std::map< MaCh3Modes_t, MaCh3ModeInfo > fMode
KS: Main map storing info about used modes.
Definition MaCh3Modes.h:70
-
MaCh3ModeInfo
KS: Class containing information for a single MaCh3Mode.
Definition MaCh3Modes.h:16
-
MaCh3ModeInfo::GeneratorMaping
std::vector< int > GeneratorMaping
Mapping between mode and generator integers.
Definition MaCh3Modes.h:22
+
MaCh3Modes::fMode
std::map< MaCh3Modes_t, MaCh3ModeInfo > fMode
KS: Main map storing info about used modes.
Definition MaCh3Modes.h:71
+
MaCh3ModeInfo
KS: Class containing information for a single MaCh3Mode.
Definition MaCh3Modes.h:17
+
MaCh3ModeInfo::GeneratorMaping
std::vector< int > GeneratorMaping
Mapping between mode and generator integers.
Definition MaCh3Modes.h:23
diff --git a/MaCh3Modes_8h.html b/MaCh3Modes_8h.html index cdd352a6c..b495f07e5 100644 --- a/MaCh3Modes_8h.html +++ b/MaCh3Modes_8h.html @@ -120,7 +120,7 @@

Definition at line 13 of file MaCh3Modes.h.

+

Definition at line 14 of file MaCh3Modes.h.

diff --git a/MaCh3Modes_8h_source.html b/MaCh3Modes_8h_source.html index 0b23095d4..7413b628f 100644 --- a/MaCh3Modes_8h_source.html +++ b/MaCh3Modes_8h_source.html @@ -85,92 +85,93 @@
Go to the documentation of this file.
1#pragma once
2
-
3#include <cmath>
-
4#include <map>
-
5#include <string>
-
6
-
7//MaCh3 includes
-
8#include "manager/YamlHelper.h"
-
9#include "manager/Monitor.h"
-
10#include "manager/MaCh3Exception.h"
-
11
-
13using MaCh3Modes_t = int;
-
14
-
-
16struct MaCh3ModeInfo {
-
18 std::string Name;
-
20 std::string FancyName;
-
22 std::vector<int> GeneratorMaping;
-
-
24 inline bool IsMode(const int GenMode) {
-
25 bool exists = std::find(GeneratorMaping.begin(), GeneratorMaping.end(), GenMode) != GeneratorMaping.end();
-
26 return exists;
-
27 }
+
3// C++ Includes
+
4#include <cmath>
+
5#include <map>
+
6#include <string>
+
7
+
8//MaCh3 includes
+
9#include "manager/YamlHelper.h"
+
10#include "manager/Monitor.h"
+
11#include "manager/MaCh3Exception.h"
+
12
+
14using MaCh3Modes_t = int;
+
15
+
+
17struct MaCh3ModeInfo {
+
19 std::string Name;
+
21 std::string FancyName;
+
23 std::vector<int> GeneratorMaping;
+
+
25 inline bool IsMode(const int GenMode) {
+
26 bool exists = std::find(GeneratorMaping.begin(), GeneratorMaping.end(), GenMode) != GeneratorMaping.end();
+
27 return exists;
+
28 }
-
28};
+
29};
-
29
-
-
32class MaCh3Modes {
-
33 public:
-
35 MaCh3Modes(std::string const &filename);
-
37 virtual ~MaCh3Modes(){};
-
38
-
40 void Print();
-
41
-
43 inline int GetNModes(){return NModes;}
-
45 MaCh3Modes_t GetMode(std::string name);
-
47 std::string GetMaCh3ModeName(const int Index);
-
49 std::string GetMaCh3ModeFancyName(const int Index);
-
51 MaCh3Modes_t GetModeFromGenerator(const int Index);
-
53 inline std::string GetName()const {return "MaCh3Modes";};
-
54
-
55 private:
-
57 inline MaCh3Modes_t EnsureModeNameRegistered(std::string const &name);
-
58
-
60 inline void DeclareNewMode(std::string const &name,
-
61 std::string const &fancyname,
-
62 std::vector<int> const &GenMap);
-
63
-
65 inline void PrepareMap();
-
66
-
68 std::map<std::string, MaCh3Modes_t> Mode;
-
70 std::map<MaCh3Modes_t, MaCh3ModeInfo> fMode;
-
72 std::vector<int> ModeMap;
-
73
-
75 std::string Title;
-
77 std::string Generator;
-
79 int NModes;
-
80};
+
30
+
+
33class MaCh3Modes {
+
34 public:
+
36 MaCh3Modes(std::string const &filename);
+
38 virtual ~MaCh3Modes(){};
+
39
+
41 void Print();
+
42
+
44 inline int GetNModes(){return NModes;}
+
46 MaCh3Modes_t GetMode(const std::string& name);
+
48 std::string GetMaCh3ModeName(const int Index);
+
50 std::string GetMaCh3ModeFancyName(const int Index);
+
52 MaCh3Modes_t GetModeFromGenerator(const int Index);
+
54 inline std::string GetName()const {return "MaCh3Modes";};
+
55
+
56 private:
+
58 inline MaCh3Modes_t EnsureModeNameRegistered(std::string const &name);
+
59
+
61 inline void DeclareNewMode(std::string const &name,
+
62 std::string const &fancyname,
+
63 std::vector<int> const &GenMap);
+
64
+
66 inline void PrepareMap();
+
67
+
69 std::map<std::string, MaCh3Modes_t> Mode;
+
71 std::map<MaCh3Modes_t, MaCh3ModeInfo> fMode;
+
73 std::vector<int> ModeMap;
+
74
+
76 std::string Title;
+
78 std::string Generator;
+
80 int NModes;
+
81};
-
MaCh3Modes_t
int MaCh3Modes_t
Enumerator of MaCh3Mode.
Definition MaCh3Modes.h:13
+
MaCh3Modes_t
int MaCh3Modes_t
Enumerator of MaCh3Mode.
Definition MaCh3Modes.h:14
-
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:18
-
MaCh3Modes
KS: Class describing MaCh3 modes used in the analysis, it is being initialised from config.
Definition MaCh3Modes.h:32
-
MaCh3Modes::Mode
std::map< std::string, MaCh3Modes_t > Mode
KS: Handy map which helps find mode number based on string.
Definition MaCh3Modes.h:68
+
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:21
+
MaCh3Modes
KS: Class describing MaCh3 modes used in the analysis, it is being initialised from config.
Definition MaCh3Modes.h:33
+
MaCh3Modes::Mode
std::map< std::string, MaCh3Modes_t > Mode
KS: Handy map which helps find mode number based on string.
Definition MaCh3Modes.h:69
MaCh3Modes::GetMaCh3ModeFancyName
std::string GetMaCh3ModeFancyName(const int Index)
KS: Get fancy name of mode, if mode not known you will get UNKNOWN_BAD.
Definition MaCh3Modes.cpp:139
-
MaCh3Modes::NModes
int NModes
KS: Number of modes, keep in mind actual number is +1 greater due to unknown category.
Definition MaCh3Modes.h:79
-
MaCh3Modes::ModeMap
std::vector< int > ModeMap
KS: Handy map helping us find MaCh3 mode based on Generator mode value.
Definition MaCh3Modes.h:72
+
MaCh3Modes::GetMode
MaCh3Modes_t GetMode(const std::string &name)
KS: Get mode number based on name, if mode not known you will get UNKNOWN_BAD.
Definition MaCh3Modes.cpp:154
+
MaCh3Modes::NModes
int NModes
KS: Number of modes, keep in mind actual number is +1 greater due to unknown category.
Definition MaCh3Modes.h:80
+
MaCh3Modes::ModeMap
std::vector< int > ModeMap
KS: Handy map helping us find MaCh3 mode based on Generator mode value.
Definition MaCh3Modes.h:73
MaCh3Modes::Print
void Print()
KS: Print info about initialised modes.
Definition MaCh3Modes.cpp:38
-
MaCh3Modes::Generator
std::string Generator
KS: Name of generator like NEUT, NuWro etc. this is to make stuff fancy.
Definition MaCh3Modes.h:77
-
MaCh3Modes::Title
std::string Title
KS: Name of loaded modes.
Definition MaCh3Modes.h:75
+
MaCh3Modes::Generator
std::string Generator
KS: Name of generator like NEUT, NuWro etc. this is to make stuff fancy.
Definition MaCh3Modes.h:78
+
MaCh3Modes::Title
std::string Title
KS: Name of loaded modes.
Definition MaCh3Modes.h:76
MaCh3Modes::EnsureModeNameRegistered
MaCh3Modes_t EnsureModeNameRegistered(std::string const &name)
KS: Make sure we don't have two modes with the same name.
Definition MaCh3Modes.cpp:69
-
MaCh3Modes::GetNModes
int GetNModes()
KS: Get number of modes, keep in mind actual number is +1 greater due to unknown category.
Definition MaCh3Modes.h:43
+
MaCh3Modes::GetNModes
int GetNModes()
KS: Get number of modes, keep in mind actual number is +1 greater due to unknown category.
Definition MaCh3Modes.h:44
MaCh3Modes::GetMaCh3ModeName
std::string GetMaCh3ModeName(const int Index)
KS: Get normal name of mode, if mode not known you will get UNKNOWN_BAD.
Definition MaCh3Modes.cpp:124
MaCh3Modes::DeclareNewMode
void DeclareNewMode(std::string const &name, std::string const &fancyname, std::vector< int > const &GenMap)
KS: Add new mode.
Definition MaCh3Modes.cpp:80
-
MaCh3Modes::GetName
std::string GetName() const
Get class name.
Definition MaCh3Modes.h:53
+
MaCh3Modes::GetName
std::string GetName() const
Get class name.
Definition MaCh3Modes.h:54
MaCh3Modes::PrepareMap
void PrepareMap()
KS: Fill ModeMap.
Definition MaCh3Modes.cpp:96
-
MaCh3Modes::~MaCh3Modes
virtual ~MaCh3Modes()
KS: Empty destructor.
Definition MaCh3Modes.h:37
+
MaCh3Modes::~MaCh3Modes
virtual ~MaCh3Modes()
KS: Empty destructor.
Definition MaCh3Modes.h:38
MaCh3Modes::GetModeFromGenerator
MaCh3Modes_t GetModeFromGenerator(const int Index)
KS: Get MaCh3 mode from generator mode.
Definition MaCh3Modes.cpp:166
-
MaCh3Modes::GetMode
MaCh3Modes_t GetMode(std::string name)
KS: Get mode number based on name, if mode not known you will get UNKNOWN_BAD.
Definition MaCh3Modes.cpp:154
-
MaCh3Modes::fMode
std::map< MaCh3Modes_t, MaCh3ModeInfo > fMode
KS: Main map storing info about used modes.
Definition MaCh3Modes.h:70
-
MaCh3ModeInfo
KS: Class containing information for a single MaCh3Mode.
Definition MaCh3Modes.h:16
-
MaCh3ModeInfo::GeneratorMaping
std::vector< int > GeneratorMaping
Mapping between mode and generator integers.
Definition MaCh3Modes.h:22
-
MaCh3ModeInfo::FancyName
std::string FancyName
Mode fancy name.
Definition MaCh3Modes.h:20
-
MaCh3ModeInfo::Name
std::string Name
Mode name.
Definition MaCh3Modes.h:18
-
MaCh3ModeInfo::IsMode
bool IsMode(const int GenMode)
KS: Checks MaCh3 modes is associated with a given generator mode.
Definition MaCh3Modes.h:24
+
MaCh3Modes::fMode
std::map< MaCh3Modes_t, MaCh3ModeInfo > fMode
KS: Main map storing info about used modes.
Definition MaCh3Modes.h:71
+
MaCh3ModeInfo
KS: Class containing information for a single MaCh3Mode.
Definition MaCh3Modes.h:17
+
MaCh3ModeInfo::GeneratorMaping
std::vector< int > GeneratorMaping
Mapping between mode and generator integers.
Definition MaCh3Modes.h:23
+
MaCh3ModeInfo::FancyName
std::string FancyName
Mode fancy name.
Definition MaCh3Modes.h:21
+
MaCh3ModeInfo::Name
std::string Name
Mode name.
Definition MaCh3Modes.h:19
+
MaCh3ModeInfo::IsMode
bool IsMode(const int GenMode)
KS: Checks MaCh3 modes is associated with a given generator mode.
Definition MaCh3Modes.h:25
diff --git a/MinuitFit_8cpp_source.html b/MinuitFit_8cpp_source.html index d069dea3a..ef7eaa7b2 100644 --- a/MinuitFit_8cpp_source.html +++ b/MinuitFit_8cpp_source.html @@ -280,13 +280,13 @@
190}
191
-
MACH3LOG_INFO
#define MACH3LOG_INFO
Definition MaCh3Logger.h:13
+
MACH3LOG_INFO
#define MACH3LOG_INFO
Definition MaCh3Logger.h:16
-
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:18
-
FitterBase::systematics
std::vector< covarianceBase * > systematics
Systematic holder.
Definition FitterBase.h:122
+
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:21
+
FitterBase::systematics
std::vector< covarianceBase * > systematics
Systematic holder.
Definition FitterBase.h:123
FitterBase::SaveOutput
void SaveOutput()
Save output and close files.
Definition FitterBase.cpp:241
-
FitterBase::outputFile
TFile * outputFile
Output.
Definition FitterBase.h:140
-
FitterBase::fitMan
manager * fitMan
The manager.
Definition FitterBase.h:92
+
FitterBase::outputFile
TFile * outputFile
Output.
Definition FitterBase.h:141
+
FitterBase::fitMan
manager * fitMan
The manager.
Definition FitterBase.h:93
LikelihoodFit
Implementation of base Likelihood Fit class, it is mostly responsible for likelihood calculation whil...
Definition LikelihoodFit.h:6
LikelihoodFit::NParsPCA
int NParsPCA
Number of all parameters from all covariances in PCA base.
Definition LikelihoodFit.h:29
LikelihoodFit::NPars
int NPars
Number of all parameters from all covariances.
Definition LikelihoodFit.h:27
diff --git a/MinuitFit_8h_source.html b/MinuitFit_8h_source.html index 6a46f5325..63fde3247 100644 --- a/MinuitFit_8h_source.html +++ b/MinuitFit_8h_source.html @@ -109,7 +109,7 @@
29
-
FitterBase::fitMan
manager * fitMan
The manager.
Definition FitterBase.h:92
+
FitterBase::fitMan
manager * fitMan
The manager.
Definition FitterBase.h:93
LikelihoodFit
Implementation of base Likelihood Fit class, it is mostly responsible for likelihood calculation whil...
Definition LikelihoodFit.h:6
MinuitFit
Implementation of Minuit fitting algorithm.
Definition MinuitFit.h:12
MinuitFit::GetName
std::string GetName() const
Get name of class.
Definition MinuitFit.h:23
diff --git a/Monitor_8cpp_source.html b/Monitor_8cpp_source.html index 371fc7117..5823f9e09 100644 --- a/Monitor_8cpp_source.html +++ b/Monitor_8cpp_source.html @@ -403,10 +403,10 @@
293
294}
-
MACH3LOG_ERROR
#define MACH3LOG_ERROR
Definition MaCh3Logger.h:15
-
MACH3LOG_INFO
#define MACH3LOG_INFO
Definition MaCh3Logger.h:13
+
MACH3LOG_ERROR
#define MACH3LOG_ERROR
Definition MaCh3Logger.h:18
+
MACH3LOG_INFO
#define MACH3LOG_INFO
Definition MaCh3Logger.h:16
-
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:18
+
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:21
GetNumGPUThreads
int GetNumGPUThreads(const int Device)
KS: Get number of GPU threads for currently used GPU.
Definition gpuUtils.cu:110
diff --git a/Monitor_8h_source.html b/Monitor_8h_source.html index 3d0450626..237ebe7d5 100644 --- a/Monitor_8h_source.html +++ b/Monitor_8h_source.html @@ -99,8 +99,8 @@
14#include "TChain.h"
15#include "TStopwatch.h"
16
-
17#include "manager/MaCh3Logger.h"
-
18
+
17// MaCh3 includes
+
18#include "manager/MaCh3Logger.h"
19#include "samplePDF/Structs.h"
20#include "manager/YamlHelper.h"
21
@@ -121,7 +121,7 @@ -
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:18
+
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:21
MaCh3Utils::GetOSInfo
void GetOSInfo()
KS: Find out more about operational system.
Definition Monitor.cpp:86
MaCh3Utils::getValue
int getValue(std::string Type)
CW: Get info like RAM.
Definition Monitor.cpp:217
diff --git a/OscClass__CUDAProb3_8cpp_source.html b/OscClass__CUDAProb3_8cpp_source.html index 52e113816..6f8357cf5 100644 --- a/OscClass__CUDAProb3_8cpp_source.html +++ b/OscClass__CUDAProb3_8cpp_source.html @@ -1901,7 +1901,7 @@
OscClass_CUDAProb3.h
FLOAT_T
double FLOAT_T
Definition OscClass_CUDAProb3.h:24
-
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:18
+
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:21
Oscillator::fineCoarseRatioEnergy
double fineCoarseRatioEnergy
Definition OscClass_CUDAProb3.h:239
diff --git a/OscClass__CUDAProb3_8h_source.html b/OscClass__CUDAProb3_8h_source.html index f4b0bef24..c7286e197 100644 --- a/OscClass__CUDAProb3_8h_source.html +++ b/OscClass__CUDAProb3_8h_source.html @@ -346,7 +346,7 @@
248};
FLOAT_T
double FLOAT_T
Definition OscClass_CUDAProb3.h:24
-
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:18
+
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:21
diff --git a/PSO_8cpp_source.html b/PSO_8cpp_source.html index 1d738a157..4ad873d0b 100644 --- a/PSO_8cpp_source.html +++ b/PSO_8cpp_source.html @@ -656,65 +656,65 @@
550}
-
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:18
-
FitterBase::stepClock
TStopwatch * stepClock
tells how long single step/fit iteration took
Definition FitterBase.h:132
-
FitterBase::accCount
int accCount
counts accepted steps
Definition FitterBase.h:106
-
FitterBase::random
TRandom3 * random
Random number.
Definition FitterBase.h:137
-
FitterBase::systematics
std::vector< covarianceBase * > systematics
Systematic holder.
Definition FitterBase.h:122
+
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:21
+
FitterBase::stepClock
TStopwatch * stepClock
tells how long single step/fit iteration took
Definition FitterBase.h:133
+
FitterBase::accCount
int accCount
counts accepted steps
Definition FitterBase.h:107
+
FitterBase::random
TRandom3 * random
Random number.
Definition FitterBase.h:138
+
FitterBase::systematics
std::vector< covarianceBase * > systematics
Systematic holder.
Definition FitterBase.h:123
FitterBase::SaveOutput
void SaveOutput()
Save output and close files.
Definition FitterBase.cpp:241
-
FitterBase::outputFile
TFile * outputFile
Output.
Definition FitterBase.h:140
-
FitterBase::fitMan
manager * fitMan
The manager.
Definition FitterBase.h:92
-
FitterBase::step
unsigned int step
current state
Definition FitterBase.h:98
-
FitterBase::accProb
double accProb
current acceptance prob
Definition FitterBase.h:104
-
FitterBase::stepTime
double stepTime
Time of single step.
Definition FitterBase.h:134
-
FitterBase::logLCurr
double logLCurr
current likelihood
Definition FitterBase.h:100
-
FitterBase::auto_save
int auto_save
auto save every N steps
Definition FitterBase.h:146
-
FitterBase::fTestLikelihood
bool fTestLikelihood
Necessary for some fitting algorithms like PSO.
Definition FitterBase.h:149
-
FitterBase::outTree
TTree * outTree
Output tree with posteriors.
Definition FitterBase.h:144
+
FitterBase::outputFile
TFile * outputFile
Output.
Definition FitterBase.h:141
+
FitterBase::fitMan
manager * fitMan
The manager.
Definition FitterBase.h:93
+
FitterBase::step
unsigned int step
current state
Definition FitterBase.h:99
+
FitterBase::accProb
double accProb
current acceptance prob
Definition FitterBase.h:105
+
FitterBase::stepTime
double stepTime
Time of single step.
Definition FitterBase.h:135
+
FitterBase::logLCurr
double logLCurr
current likelihood
Definition FitterBase.h:101
+
FitterBase::auto_save
int auto_save
auto save every N steps
Definition FitterBase.h:147
+
FitterBase::fTestLikelihood
bool fTestLikelihood
Necessary for some fitting algorithms like PSO.
Definition FitterBase.h:150
+
FitterBase::outTree
TTree * outTree
Output tree with posteriors.
Definition FitterBase.h:145
LikelihoodFit
Implementation of base Likelihood Fit class, it is mostly responsible for likelihood calculation whil...
Definition LikelihoodFit.h:6
LikelihoodFit::PrepareFit
void PrepareFit()
prepare output and perform sanity checks
Definition LikelihoodFit.cpp:21
LikelihoodFit::CalcChi2
virtual double CalcChi2(const double *x)
Chi2 calculation over all included samples and syst objects.
Definition LikelihoodFit.cpp:44
-
PSO::vector_add
std::vector< double > vector_add(std::vector< double > v1, std::vector< double > v2)
Definition PSO.h:104
+
PSO::vector_add
std::vector< double > vector_add(std::vector< double > v1, std::vector< double > v2)
Definition PSO.h:105
PSO::PSO
PSO(manager *const fitMan)
constructor
Definition PSO.cpp:3
-
PSO::vector_subtract
std::vector< double > vector_subtract(std::vector< double > v1, std::vector< double > v2)
Definition PSO.h:109
-
PSO::ranges_max
std::vector< double > ranges_max
Definition PSO.h:139
-
PSO::fConstriction
double fConstriction
Definition PSO.h:147
+
PSO::vector_subtract
std::vector< double > vector_subtract(std::vector< double > v1, std::vector< double > v2)
Definition PSO.h:110
+
PSO::ranges_max
std::vector< double > ranges_max
Definition PSO.h:140
+
PSO::fConstriction
double fConstriction
Definition PSO.h:148
PSO::init
void init()
Definition PSO.cpp:43
-
PSO::vector_multiply
std::vector< double > vector_multiply(std::vector< double > velocity, double mul)
Definition PSO.h:99
+
PSO::vector_multiply
std::vector< double > vector_multiply(std::vector< double > velocity, double mul)
Definition PSO.h:100
PSO::CalcChi2
double CalcChi2(const double *x)
Chi2 calculation over all included samples and syst objects.
Definition PSO.cpp:516
-
PSO::three_vector_addition
std::vector< double > three_vector_addition(std::vector< double > vec1, std::vector< double > vec2, std::vector< double > vec3)
Definition PSO.h:114
-
PSO::fTwo
double fTwo
Definition PSO.h:144
-
PSO::fixed
std::vector< bool > fixed
Definition PSO.h:138
-
PSO::fInertia
double fInertia
Definition PSO.h:142
-
PSO::get_best_particle
particle * get_best_particle()
Definition PSO.h:81
-
PSO::fParticles
int fParticles
Definition PSO.h:150
-
PSO::fOne
double fOne
Definition PSO.h:143
-
PSO::fIterations
int fIterations
Definition PSO.h:146
+
PSO::three_vector_addition
std::vector< double > three_vector_addition(std::vector< double > vec1, std::vector< double > vec2, std::vector< double > vec3)
Definition PSO.h:115
+
PSO::fTwo
double fTwo
Definition PSO.h:145
+
PSO::fixed
std::vector< bool > fixed
Definition PSO.h:139
+
PSO::fInertia
double fInertia
Definition PSO.h:143
+
PSO::get_best_particle
particle * get_best_particle()
Definition PSO.h:82
+
PSO::fParticles
int fParticles
Definition PSO.h:151
+
PSO::fOne
double fOne
Definition PSO.h:144
+
PSO::fIterations
int fIterations
Definition PSO.h:147
PSO::uncertainty_check
void uncertainty_check(std::vector< double > previous_pos)
Definition PSO.cpp:285
-
PSO::set_best_particle
void set_best_particle(particle *n)
Definition PSO.h:84
-
PSO::paramlist
std::vector< double * > paramlist
Definition PSO.h:152
-
PSO::system
std::vector< particle * > system
Definition PSO.h:141
-
PSO::vel
double vel[kMaxParticles]
Definition PSO.h:153
-
PSO::fConvergence
double fConvergence
Definition PSO.h:145
-
PSO::CalcChi
double CalcChi(std::vector< double > x)
Definition PSO.h:127
-
PSO::fBestValue
double fBestValue
Definition PSO.h:136
-
PSO::uncertainties
std::vector< std::vector< double > > uncertainties
Definition PSO.h:148
-
PSO::ranges_min
std::vector< double > ranges_min
Definition PSO.h:140
-
PSO::par
double * par
Definition PSO.h:154
-
PSO::fDim
int fDim
Definition PSO.h:156
+
PSO::set_best_particle
void set_best_particle(particle *n)
Definition PSO.h:85
+
PSO::paramlist
std::vector< double * > paramlist
Definition PSO.h:153
+
PSO::system
std::vector< particle * > system
Definition PSO.h:142
+
PSO::vel
double vel[kMaxParticles]
Definition PSO.h:154
+
PSO::fConvergence
double fConvergence
Definition PSO.h:146
+
PSO::CalcChi
double CalcChi(std::vector< double > x)
Definition PSO.h:128
+
PSO::fBestValue
double fBestValue
Definition PSO.h:137
+
PSO::uncertainties
std::vector< std::vector< double > > uncertainties
Definition PSO.h:149
+
PSO::ranges_min
std::vector< double > ranges_min
Definition PSO.h:141
+
PSO::par
double * par
Definition PSO.h:155
+
PSO::fDim
int fDim
Definition PSO.h:157
PSO::calc_uncertainty
std::vector< std::vector< double > > calc_uncertainty(std::vector< double >position, double minimum)
Definition PSO.cpp:222
PSO::run
void run()
Definition PSO.cpp:381
PSO::WriteOutput
void WriteOutput()
Definition PSO.cpp:427
PSO::bisection
std::vector< std::vector< double > > bisection(std::vector< double >position, double minimum, double range, double precision)
Definition PSO.cpp:144
PSO::swarmIterate
double swarmIterate()
Definition PSO.cpp:321
PSO::rastriginFunc
double rastriginFunc(const double *x)
Definition PSO.cpp:531
-
PSO::prior
std::vector< double > prior
Definition PSO.h:137
+
PSO::prior
std::vector< double > prior
Definition PSO.h:138
PSO::runMCMC
void runMCMC() override
Implementation of fitting algorithm.
Definition PSO.cpp:21
manager
The manager class is responsible for managing configurations and settings.
Definition manager.h:28
manager::raw
YAML::Node const & raw()
Return config.
Definition manager.h:48
-
particle
Class particle - stores the position, velocity and personal best With functions which move particle a...
Definition PSO.h:17
-
particle::get_personal_best_position
std::vector< double > get_personal_best_position()
Definition PSO.h:36
-
particle::get_personal_best_value
double get_personal_best_value()
Definition PSO.h:44
+
particle
Class particle - stores the position, velocity and personal best With functions which move particle a...
Definition PSO.h:18
+
particle::get_personal_best_position
std::vector< double > get_personal_best_position()
Definition PSO.h:37
+
particle::get_personal_best_value
double get_personal_best_value()
Definition PSO.h:45
diff --git a/PSO_8h_source.html b/PSO_8h_source.html index 38948eadd..3fff32b7b 100644 --- a/PSO_8h_source.html +++ b/PSO_8h_source.html @@ -89,255 +89,256 @@
4//
5// Created by Emily Ip on 26/1/2023.
6//
-
7#include <algorithm>
-
8#include <functional>
-
9#include <numeric>
-
10
-
11// MaCh3 includes
-
12#include "mcmc/LikelihoodFit.h"
-
13
+
7// C++ includes
+
8#include <algorithm>
+
9#include <functional>
+
10#include <numeric>
+
11
+
12// MaCh3 includes
+
13#include "mcmc/LikelihoodFit.h"
14
-
-
17class particle{
-
18 public:
-
19 particle(){};
-
20 particle(std::vector<double> pos, std::vector<double> vel) : position(pos), velocity(vel){};
-
22 virtual ~particle() {};
-
23
-
-
24 void set_position(std::vector<double> new_position) {
-
25 position = new_position;
-
26 };
+
15
+
+
18class particle{
+
19 public:
+
20 particle(){};
+
21 particle(std::vector<double> pos, std::vector<double> vel) : position(pos), velocity(vel){};
+
23 virtual ~particle() {};
+
24
+
+
25 void set_position(std::vector<double> new_position) {
+
26 position = new_position;
+
27 };
-
27
-
-
28 std::vector<double> get_position() {
-
29 return position;
-
30 };
+
28
+
+
29 std::vector<double> get_position() {
+
30 return position;
+
31 };
-
31
-
-
32 void set_personal_best_position(std::vector<double> new_pos){
-
33 personal_best_position = new_pos;
-
34 };
+
32
+
+
33 void set_personal_best_position(std::vector<double> new_pos){
+
34 personal_best_position = new_pos;
+
35 };
-
35
-
-
36 std::vector<double> get_personal_best_position(){
-
37 return personal_best_position;
-
38 };
+
36
+
+
37 std::vector<double> get_personal_best_position(){
+
38 return personal_best_position;
+
39 };
-
39
-
-
40 void set_personal_best_value(double new_val){
-
41 personal_best_value = new_val;
-
42 };
+
40
+ -
43
-
-
44 double get_personal_best_value(){
-
45 return personal_best_value;
-
46 };
+
44
+
+
45 double get_personal_best_value(){
+
46 return personal_best_value;
+
47 };
-
47
-
-
48 std::vector<double> get_velocity(){
-
49 return velocity;
-
50 };
+
48
+
+
49 std::vector<double> get_velocity(){
+
50 return velocity;
+
51 };
-
51
-
-
52 void set_velocity(std::vector<double> new_velocity){
-
53 velocity = new_velocity;
-
54 };
+
52
+
+
53 void set_velocity(std::vector<double> new_velocity){
+
54 velocity = new_velocity;
+
55 };
-
55
-
-
56 double get_value(){
-
57 return curr_value;
-
58 };
+
56
+
+
57 double get_value(){
+
58 return curr_value;
+
59 };
-
-
59 void set_value(double val){
-
60 curr_value = val;
-
61 };
+
+
60 void set_value(double val){
+
61 curr_value = val;
+
62 };
-
62
-
63 private:
-
64 std::vector<double> position;
-
65 std::vector<double> velocity;
-
66 double personal_best_value;
-
67 double curr_value;
-
68 std::vector<double> personal_best_position;
-
69};
+
63
+
64 private:
+
65 std::vector<double> position;
+
66 std::vector<double> velocity;
+
67 double personal_best_value;
+
68 double curr_value;
+
69 std::vector<double> personal_best_position;
+
70};
-
70
-
-
74class PSO : public LikelihoodFit {
-
75 public:
-
77 PSO(manager * const fitMan);
-
79 virtual ~PSO() {};
-
80
-
-
81 particle* get_best_particle(){
-
82 return best_particle;
-
83 }
+
71
+
+
75class PSO : public LikelihoodFit {
+
76 public:
+
78 PSO(manager * const fitMan);
+
80 virtual ~PSO() {};
+
81
+
+
82 particle* get_best_particle(){
+
83 return best_particle;
+
84 }
-
-
84 void set_best_particle(particle* n){
-
85 best_particle = n;
-
86 }
+
+
85 void set_best_particle(particle* n){
+
86 best_particle = n;
+
87 }
-
87
-
88 std::vector<std::vector<double>> bisection(std::vector<double>position,double minimum, double range, double precision);
-
89 std::vector<std::vector<double>> calc_uncertainty(std::vector<double>position,double minimum);
-
90 void init();
-
91 void uncertainty_check(std::vector<double> previous_pos);
-
92 void run();
-
93 void WriteOutput();
-
94 void runMCMC() override;
-
95 double CalcChi2(const double* x);
-
96 double rastriginFunc(const double* x);
-
97 double swarmIterate();
-
98
-
-
99 std::vector<double> vector_multiply(std::vector<double> velocity, double mul){
-
100 transform(velocity.begin(),velocity.end(),velocity.begin(),std::bind1st(std::multiplies<double>(),mul));
-
101 return velocity;
-
102 };
+
88
+
89 std::vector<std::vector<double>> bisection(std::vector<double>position,double minimum, double range, double precision);
+
90 std::vector<std::vector<double>> calc_uncertainty(std::vector<double>position,double minimum);
+
91 void init();
+
92 void uncertainty_check(std::vector<double> previous_pos);
+
93 void run();
+
94 void WriteOutput();
+
95 void runMCMC() override;
+
96 double CalcChi2(const double* x);
+
97 double rastriginFunc(const double* x);
+
98 double swarmIterate();
+
99
+
+
100 std::vector<double> vector_multiply(std::vector<double> velocity, double mul){
+
101 transform(velocity.begin(),velocity.end(),velocity.begin(),std::bind1st(std::multiplies<double>(),mul));
+
102 return velocity;
+
103 };
-
103
-
-
104 std::vector<double> vector_add(std::vector<double> v1, std::vector<double> v2){
-
105 std::vector<double> v3;
-
106 transform(v1.begin(), v1.end(), v2.begin(), back_inserter(v3), std::plus<double>());
-
107 return v3;
-
108 };
+
104
+
+
105 std::vector<double> vector_add(std::vector<double> v1, std::vector<double> v2){
+
106 std::vector<double> v3;
+
107 transform(v1.begin(), v1.end(), v2.begin(), back_inserter(v3), std::plus<double>());
+
108 return v3;
+
109 };
-
-
109 std::vector<double> vector_subtract(std::vector<double> v1, std::vector<double> v2){
-
110 std::vector<double> v3 ;
-
111 transform(v1.begin(), v1.end(), v2.begin(), back_inserter(v3), std::minus<double>());
-
112 return v3;
-
113 };
+
+
110 std::vector<double> vector_subtract(std::vector<double> v1, std::vector<double> v2){
+
111 std::vector<double> v3 ;
+
112 transform(v1.begin(), v1.end(), v2.begin(), back_inserter(v3), std::minus<double>());
+
113 return v3;
+
114 };
-
-
114 std::vector<double> three_vector_addition(std::vector<double> vec1, std::vector<double> vec2,std::vector<double> vec3){
-
115 for (size_t i = 0; i < vec1.size(); ++i) {
-
116 vec1[i] += vec2[i] + vec3[i];
-
117 }
-
118 return vec1;
-
119 };
+
+
115 std::vector<double> three_vector_addition(std::vector<double> vec1, std::vector<double> vec2,std::vector<double> vec3){
+
116 for (size_t i = 0; i < vec1.size(); ++i) {
+
117 vec1[i] += vec2[i] + vec3[i];
+
118 }
+
119 return vec1;
+
120 };
-
-
120 std::vector<double> four_vector_addition(std::vector<double> vec1, std::vector<double> vec2,std::vector<double> vec3,std::vector<double> vec4){
-
121 for (size_t i = 0; i < vec1.size(); ++i) {
-
122 vec1[i] += vec2[i] + vec3[i] + vec4[i];
-
123 }
-
124 return vec1;
-
125 };
+
+
121 std::vector<double> four_vector_addition(std::vector<double> vec1, std::vector<double> vec2,std::vector<double> vec3,std::vector<double> vec4){
+
122 for (size_t i = 0; i < vec1.size(); ++i) {
+
123 vec1[i] += vec2[i] + vec3[i] + vec4[i];
+
124 }
+
125 return vec1;
+
126 };
-
126
-
-
127 double CalcChi(std::vector<double> x){
-
128 double* a = &x[0];
-
129 return CalcChi2(a);
-
130 };
+
127
+
+
128 double CalcChi(std::vector<double> x){
+
129 double* a = &x[0];
+
130 return CalcChi2(a);
+
131 };
-
131
-
132 inline std::string GetName()const {return "PSO";};
-
133
-
134 private:
-
135 particle* best_particle;
-
136 double fBestValue;
-
137 std::vector<double> prior;
-
138 std::vector<bool> fixed;
-
139 std::vector<double> ranges_max;
-
140 std::vector<double> ranges_min;
-
141 std::vector<particle*> system;
-
142 double fInertia;
-
143 double fOne;
-
144 double fTwo;
-
145 double fConvergence;
-
146 int fIterations;
-
147 double fConstriction;
-
148 std::vector<std::vector<double> > uncertainties;
-
149
-
150 int fParticles;
-
151 static const int kMaxParticles = 10000;
-
152 std::vector<double*> paramlist;
-
153 double vel[kMaxParticles];
-
154 double* par;
-
155
-
156 int fDim;
-
157};
+
132
+
133 inline std::string GetName()const {return "PSO";};
+
134
+
135 private:
+
136 particle* best_particle;
+
137 double fBestValue;
+
138 std::vector<double> prior;
+
139 std::vector<bool> fixed;
+
140 std::vector<double> ranges_max;
+
141 std::vector<double> ranges_min;
+
142 std::vector<particle*> system;
+
143 double fInertia;
+
144 double fOne;
+
145 double fTwo;
+
146 double fConvergence;
+
147 int fIterations;
+
148 double fConstriction;
+
149 std::vector<std::vector<double> > uncertainties;
+
150
+
151 int fParticles;
+
152 static const int kMaxParticles = 10000;
+
153 std::vector<double*> paramlist;
+
154 double vel[kMaxParticles];
+
155 double* par;
+
156
+
157 int fDim;
+
158};
-
158
+
159
-
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:18
-
FitterBase::fitMan
manager * fitMan
The manager.
Definition FitterBase.h:92
+
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:21
+
FitterBase::fitMan
manager * fitMan
The manager.
Definition FitterBase.h:93
LikelihoodFit
Implementation of base Likelihood Fit class, it is mostly responsible for likelihood calculation whil...
Definition LikelihoodFit.h:6
-
PSO
Class PSO, consist of a vector of object Class Particle and global best Takes in the size (number of ...
Definition PSO.h:74
-
PSO::vector_add
std::vector< double > vector_add(std::vector< double > v1, std::vector< double > v2)
Definition PSO.h:104
-
PSO::kMaxParticles
static const int kMaxParticles
Definition PSO.h:151
-
PSO::~PSO
virtual ~PSO()
Destructor.
Definition PSO.h:79
-
PSO::vector_subtract
std::vector< double > vector_subtract(std::vector< double > v1, std::vector< double > v2)
Definition PSO.h:109
-
PSO::ranges_max
std::vector< double > ranges_max
Definition PSO.h:139
-
PSO::fConstriction
double fConstriction
Definition PSO.h:147
+
PSO
Class PSO, consist of a vector of object Class Particle and global best Takes in the size (number of ...
Definition PSO.h:75
+
PSO::vector_add
std::vector< double > vector_add(std::vector< double > v1, std::vector< double > v2)
Definition PSO.h:105
+
PSO::kMaxParticles
static const int kMaxParticles
Definition PSO.h:152
+
PSO::~PSO
virtual ~PSO()
Destructor.
Definition PSO.h:80
+
PSO::vector_subtract
std::vector< double > vector_subtract(std::vector< double > v1, std::vector< double > v2)
Definition PSO.h:110
+
PSO::ranges_max
std::vector< double > ranges_max
Definition PSO.h:140
+
PSO::fConstriction
double fConstriction
Definition PSO.h:148
PSO::init
void init()
Definition PSO.cpp:43
-
PSO::vector_multiply
std::vector< double > vector_multiply(std::vector< double > velocity, double mul)
Definition PSO.h:99
+
PSO::vector_multiply
std::vector< double > vector_multiply(std::vector< double > velocity, double mul)
Definition PSO.h:100
PSO::CalcChi2
double CalcChi2(const double *x)
Chi2 calculation over all included samples and syst objects.
Definition PSO.cpp:516
-
PSO::three_vector_addition
std::vector< double > three_vector_addition(std::vector< double > vec1, std::vector< double > vec2, std::vector< double > vec3)
Definition PSO.h:114
-
PSO::fTwo
double fTwo
Definition PSO.h:144
-
PSO::fixed
std::vector< bool > fixed
Definition PSO.h:138
-
PSO::GetName
std::string GetName() const
Get name of class.
Definition PSO.h:132
-
PSO::fInertia
double fInertia
Definition PSO.h:142
-
PSO::get_best_particle
particle * get_best_particle()
Definition PSO.h:81
-
PSO::fParticles
int fParticles
Definition PSO.h:150
-
PSO::fOne
double fOne
Definition PSO.h:143
-
PSO::fIterations
int fIterations
Definition PSO.h:146
+
PSO::three_vector_addition
std::vector< double > three_vector_addition(std::vector< double > vec1, std::vector< double > vec2, std::vector< double > vec3)
Definition PSO.h:115
+
PSO::fTwo
double fTwo
Definition PSO.h:145
+
PSO::fixed
std::vector< bool > fixed
Definition PSO.h:139
+
PSO::GetName
std::string GetName() const
Get name of class.
Definition PSO.h:133
+
PSO::fInertia
double fInertia
Definition PSO.h:143
+
PSO::get_best_particle
particle * get_best_particle()
Definition PSO.h:82
+
PSO::fParticles
int fParticles
Definition PSO.h:151
+
PSO::fOne
double fOne
Definition PSO.h:144
+
PSO::fIterations
int fIterations
Definition PSO.h:147
PSO::uncertainty_check
void uncertainty_check(std::vector< double > previous_pos)
Definition PSO.cpp:285
-
PSO::best_particle
particle * best_particle
Definition PSO.h:135
-
PSO::set_best_particle
void set_best_particle(particle *n)
Definition PSO.h:84
-
PSO::paramlist
std::vector< double * > paramlist
Definition PSO.h:152
-
PSO::system
std::vector< particle * > system
Definition PSO.h:141
-
PSO::vel
double vel[kMaxParticles]
Definition PSO.h:153
-
PSO::four_vector_addition
std::vector< double > four_vector_addition(std::vector< double > vec1, std::vector< double > vec2, std::vector< double > vec3, std::vector< double > vec4)
Definition PSO.h:120
-
PSO::fConvergence
double fConvergence
Definition PSO.h:145
-
PSO::CalcChi
double CalcChi(std::vector< double > x)
Definition PSO.h:127
-
PSO::fBestValue
double fBestValue
Definition PSO.h:136
-
PSO::uncertainties
std::vector< std::vector< double > > uncertainties
Definition PSO.h:148
-
PSO::ranges_min
std::vector< double > ranges_min
Definition PSO.h:140
-
PSO::par
double * par
Definition PSO.h:154
-
PSO::fDim
int fDim
Definition PSO.h:156
+
PSO::best_particle
particle * best_particle
Definition PSO.h:136
+
PSO::set_best_particle
void set_best_particle(particle *n)
Definition PSO.h:85
+
PSO::paramlist
std::vector< double * > paramlist
Definition PSO.h:153
+
PSO::system
std::vector< particle * > system
Definition PSO.h:142
+
PSO::vel
double vel[kMaxParticles]
Definition PSO.h:154
+
PSO::four_vector_addition
std::vector< double > four_vector_addition(std::vector< double > vec1, std::vector< double > vec2, std::vector< double > vec3, std::vector< double > vec4)
Definition PSO.h:121
+
PSO::fConvergence
double fConvergence
Definition PSO.h:146
+
PSO::CalcChi
double CalcChi(std::vector< double > x)
Definition PSO.h:128
+
PSO::fBestValue
double fBestValue
Definition PSO.h:137
+
PSO::uncertainties
std::vector< std::vector< double > > uncertainties
Definition PSO.h:149
+
PSO::ranges_min
std::vector< double > ranges_min
Definition PSO.h:141
+
PSO::par
double * par
Definition PSO.h:155
+
PSO::fDim
int fDim
Definition PSO.h:157
PSO::calc_uncertainty
std::vector< std::vector< double > > calc_uncertainty(std::vector< double >position, double minimum)
Definition PSO.cpp:222
PSO::run
void run()
Definition PSO.cpp:381
PSO::WriteOutput
void WriteOutput()
Definition PSO.cpp:427
PSO::bisection
std::vector< std::vector< double > > bisection(std::vector< double >position, double minimum, double range, double precision)
Definition PSO.cpp:144
PSO::swarmIterate
double swarmIterate()
Definition PSO.cpp:321
PSO::rastriginFunc
double rastriginFunc(const double *x)
Definition PSO.cpp:531
-
PSO::prior
std::vector< double > prior
Definition PSO.h:137
+
PSO::prior
std::vector< double > prior
Definition PSO.h:138
PSO::runMCMC
void runMCMC() override
Implementation of fitting algorithm.
Definition PSO.cpp:21
manager
The manager class is responsible for managing configurations and settings.
Definition manager.h:28
-
particle
Class particle - stores the position, velocity and personal best With functions which move particle a...
Definition PSO.h:17
-
particle::position
std::vector< double > position
Definition PSO.h:64
-
particle::particle
particle()
Definition PSO.h:19
-
particle::curr_value
double curr_value
Definition PSO.h:67
-
particle::particle
particle(std::vector< double > pos, std::vector< double > vel)
Definition PSO.h:20
-
particle::~particle
virtual ~particle()
Destructor.
Definition PSO.h:22
-
particle::get_personal_best_position
std::vector< double > get_personal_best_position()
Definition PSO.h:36
-
particle::get_personal_best_value
double get_personal_best_value()
Definition PSO.h:44
-
particle::set_personal_best_position
void set_personal_best_position(std::vector< double > new_pos)
Definition PSO.h:32
-
particle::velocity
std::vector< double > velocity
Definition PSO.h:65
-
particle::get_position
std::vector< double > get_position()
Definition PSO.h:28
-
particle::personal_best_position
std::vector< double > personal_best_position
Definition PSO.h:68
-
particle::set_personal_best_value
void set_personal_best_value(double new_val)
Definition PSO.h:40
-
particle::get_value
double get_value()
Definition PSO.h:56
-
particle::set_value
void set_value(double val)
Definition PSO.h:59
-
particle::get_velocity
std::vector< double > get_velocity()
Definition PSO.h:48
-
particle::set_velocity
void set_velocity(std::vector< double > new_velocity)
Definition PSO.h:52
-
particle::personal_best_value
double personal_best_value
Definition PSO.h:66
-
particle::set_position
void set_position(std::vector< double > new_position)
Definition PSO.h:24
+
particle
Class particle - stores the position, velocity and personal best With functions which move particle a...
Definition PSO.h:18
+
particle::position
std::vector< double > position
Definition PSO.h:65
+
particle::particle
particle()
Definition PSO.h:20
+
particle::curr_value
double curr_value
Definition PSO.h:68
+
particle::particle
particle(std::vector< double > pos, std::vector< double > vel)
Definition PSO.h:21
+
particle::~particle
virtual ~particle()
Destructor.
Definition PSO.h:23
+
particle::get_personal_best_position
std::vector< double > get_personal_best_position()
Definition PSO.h:37
+
particle::get_personal_best_value
double get_personal_best_value()
Definition PSO.h:45
+
particle::set_personal_best_position
void set_personal_best_position(std::vector< double > new_pos)
Definition PSO.h:33
+
particle::velocity
std::vector< double > velocity
Definition PSO.h:66
+
particle::get_position
std::vector< double > get_position()
Definition PSO.h:29
+
particle::personal_best_position
std::vector< double > personal_best_position
Definition PSO.h:69
+
particle::set_personal_best_value
void set_personal_best_value(double new_val)
Definition PSO.h:41
+
particle::get_value
double get_value()
Definition PSO.h:57
+
particle::set_value
void set_value(double val)
Definition PSO.h:60
+
particle::get_velocity
std::vector< double > get_velocity()
Definition PSO.h:49
+
particle::set_velocity
void set_velocity(std::vector< double > new_velocity)
Definition PSO.h:53
+
particle::personal_best_value
double personal_best_value
Definition PSO.h:67
+
particle::set_position
void set_position(std::vector< double > new_position)
Definition PSO.h:25
diff --git a/PlotAutoCorrelations_8C.html b/PlotAutoCorrelations_8C.html index 6a9ec44cd..ba7cc3cd6 100644 --- a/PlotAutoCorrelations_8C.html +++ b/PlotAutoCorrelations_8C.html @@ -138,7 +138,7 @@

31 }

32 */
33}
-
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:18
+
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:21
diff --git a/PlotAutoCorrelations_8C_source.html b/PlotAutoCorrelations_8C_source.html index e576bea36..9931e1a7d 100644 --- a/PlotAutoCorrelations_8C_source.html +++ b/PlotAutoCorrelations_8C_source.html @@ -119,7 +119,7 @@
33}
PlotAutoCorrelations
void PlotAutoCorrelations(TString FileName)
Definition PlotAutoCorrelations.C:6
-
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:18
+
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:21
diff --git a/PlotLLH_8cpp.html b/PlotLLH_8cpp.html index d0a15876b..8ec5ce4d6 100644 --- a/PlotLLH_8cpp.html +++ b/PlotLLH_8cpp.html @@ -244,7 +244,7 @@

119 return !(gundamName == NOT_FOUND_STR); // true if found, false if not

120}
NOT_FOUND_STR
std::string NOT_FOUND_STR
Definition PlotLLH.cpp:42
-
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:18
+
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:21
@@ -591,7 +591,7 @@

717

718 return PlotLLH();
719}
-
SetMaCh3LoggerFormat
void SetMaCh3LoggerFormat()
Set messaging format of the logger.
Definition MaCh3Logger.h:20
+
SetMaCh3LoggerFormat
void SetMaCh3LoggerFormat()
Set messaging format of the logger.
Definition MaCh3Logger.h:23
plotRatios
bool plotRatios
Definition PlotLLH.cpp:31
parseFileLabels
void parseFileLabels(std::string labelString, std::vector< std::string > &labelVec)
Definition PlotLLH.cpp:63
drawGrid
bool drawGrid
Definition PlotLLH.cpp:32
diff --git a/PlotLLH_8cpp_source.html b/PlotLLH_8cpp_source.html index 5f23de165..a548c50a3 100644 --- a/PlotLLH_8cpp_source.html +++ b/PlotLLH_8cpp_source.html @@ -822,7 +822,7 @@
720
-
SetMaCh3LoggerFormat
void SetMaCh3LoggerFormat()
Set messaging format of the logger.
Definition MaCh3Logger.h:20
+
SetMaCh3LoggerFormat
void SetMaCh3LoggerFormat()
Set messaging format of the logger.
Definition MaCh3Logger.h:23
plotRatios
bool plotRatios
Definition PlotLLH.cpp:31
sameAxis
bool sameAxis
Definition PlotLLH.cpp:40
ratioLabelScaling
double ratioLabelScaling
Definition PlotLLH.cpp:61
@@ -851,7 +851,7 @@
splitBySample
bool splitBySample
Definition PlotLLH.cpp:30
prettify_name
std::string prettify_name(std::string fullName)
Definition PlotLLH.cpp:213
FileLabels_default
std::vector< std::string > FileLabels_default
Definition PlotLLH.cpp:25
-
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:18
+
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:21
diff --git a/PlotMCMC__Diagnosis_8cpp.html b/PlotMCMC__Diagnosis_8cpp.html index fe913bfa6..71d315e60 100644 --- a/PlotMCMC__Diagnosis_8cpp.html +++ b/PlotMCMC__Diagnosis_8cpp.html @@ -159,7 +159,7 @@

244 }

245 return MinVale;
246}
-
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:18
+
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:21
diff --git a/PlotMCMC__Diagnosis_8cpp_source.html b/PlotMCMC__Diagnosis_8cpp_source.html index 0f7c2e0aa..ee191b672 100644 --- a/PlotMCMC__Diagnosis_8cpp_source.html +++ b/PlotMCMC__Diagnosis_8cpp_source.html @@ -353,7 +353,7 @@
RemoveFitter
void RemoveFitter(TH1D *hist)
Definition PlotMCMC_Diagnosis.cpp:24
PlotMCMC_Diagnosis
void PlotMCMC_Diagnosis(TString fname1)
Definition PlotMCMC_Diagnosis.cpp:33
DUMMYFILE
TString DUMMYFILE
Definition PlotMCMC_Diagnosis.cpp:21
-
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:18
+
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:21
diff --git a/ProcessMCMC_8cpp.html b/ProcessMCMC_8cpp.html index 6abe2ee00..68dca5115 100644 --- a/ProcessMCMC_8cpp.html +++ b/ProcessMCMC_8cpp.html @@ -168,7 +168,7 @@

338 return;
339}
config
std::string config
Definition ProcessMCMC.cpp:19
-
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:18
+
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:21
@@ -774,13 +774,13 @@

58
59 return 0;
60}
-
MACH3LOG_ERROR
#define MACH3LOG_ERROR
Definition MaCh3Logger.h:15
-
MACH3LOG_INFO
#define MACH3LOG_INFO
Definition MaCh3Logger.h:13
-
SetMaCh3LoggerFormat
void SetMaCh3LoggerFormat()
Set messaging format of the logger.
Definition MaCh3Logger.h:20
+
MACH3LOG_ERROR
#define MACH3LOG_ERROR
Definition MaCh3Logger.h:18
+
MACH3LOG_INFO
#define MACH3LOG_INFO
Definition MaCh3Logger.h:16
+
SetMaCh3LoggerFormat
void SetMaCh3LoggerFormat()
Set messaging format of the logger.
Definition MaCh3Logger.h:23
MultipleProcessMCMC
void MultipleProcessMCMC()
Definition ProcessMCMC.cpp:141
FileNames
std::vector< std::string > FileNames
Definition ProcessMCMC.cpp:17
ProcessMCMC
void ProcessMCMC(std::string inputFile)
Definition ProcessMCMC.cpp:62
-
MaCh3Exception
Custom exception class for MaCh3 errors.
Definition MaCh3Exception.h:10
+
MaCh3Exception
Custom exception class for MaCh3 errors.
Definition MaCh3Exception.h:12
diff --git a/ProcessMCMC_8cpp_source.html b/ProcessMCMC_8cpp_source.html index 7778e1904..77290a252 100644 --- a/ProcessMCMC_8cpp_source.html +++ b/ProcessMCMC_8cpp_source.html @@ -857,9 +857,9 @@
_UNDEF_
#define _UNDEF_
Definition MCMCProcessor.h:4
-
MACH3LOG_ERROR
#define MACH3LOG_ERROR
Definition MaCh3Logger.h:15
-
MACH3LOG_INFO
#define MACH3LOG_INFO
Definition MaCh3Logger.h:13
-
SetMaCh3LoggerFormat
void SetMaCh3LoggerFormat()
Set messaging format of the logger.
Definition MaCh3Logger.h:20
+
MACH3LOG_ERROR
#define MACH3LOG_ERROR
Definition MaCh3Logger.h:18
+
MACH3LOG_INFO
#define MACH3LOG_INFO
Definition MaCh3Logger.h:16
+
SetMaCh3LoggerFormat
void SetMaCh3LoggerFormat()
Set messaging format of the logger.
Definition MaCh3Logger.h:23
GetTrianglePlot
void GetTrianglePlot(MCMCProcessor *Processor)
Definition ProcessMCMC.cpp:378
DiagnoseCovarianceMatrix
void DiagnoseCovarianceMatrix(MCMCProcessor *Processor, std::string inputFile)
Definition ProcessMCMC.cpp:400
main
int main(int argc, char *argv[])
Definition ProcessMCMC.cpp:21
@@ -876,9 +876,9 @@
KolmogorovSmirnovTest
void KolmogorovSmirnovTest(MCMCProcessor **Processor, TCanvas *Posterior, TString canvasname)
Definition ProcessMCMC.cpp:609
CalcSavageDickey
void CalcSavageDickey(MCMCProcessor *Processor)
Definition ProcessMCMC.cpp:341
RemoveFitter
void RemoveFitter(TH1D *hist, std::string name)
KS: Remove fitted TF1 from hist to make comparison easier.
Definition Structs.cpp:437
-
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:18
+
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:21
MCMCProcessor
Class responsible for processing MCMC chains, performing diagnostics, generating plots,...
Definition MCMCProcessor.h:61
-
MaCh3Exception
Custom exception class for MaCh3 errors.
Definition MaCh3Exception.h:10
+
MaCh3Exception
Custom exception class for MaCh3 errors.
Definition MaCh3Exception.h:12
diff --git a/RHat_8cpp.html b/RHat_8cpp.html index dbd4ee604..f0a648b66 100644 --- a/RHat_8cpp.html +++ b/RHat_8cpp.html @@ -216,7 +216,7 @@

846 return (double)(arr[(size-1)/2] + arr[size/2])/2.0;
847}
size
int size
Definition GetPenaltyTerm.cpp:42
-
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:18
+
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:21
@@ -383,7 +383,7 @@

583 clock.Stop();
584 MACH3LOG_INFO("Finished calculating RHat, it took {:.2f}s to finish", clock.RealTime());
585}
-
MACH3LOG_INFO
#define MACH3LOG_INFO
Definition MaCh3Logger.h:13
+
MACH3LOG_INFO
#define MACH3LOG_INFO
Definition MaCh3Logger.h:16
Nchains
int Nchains
Definition RHat.cpp:38
StandardDeviationGlobalFolded
double * StandardDeviationGlobalFolded
Definition RHat.cpp:66
CapVariable
void CapVariable(double var, double cap)
Definition RHat.cpp:852
@@ -687,16 +687,16 @@

159
160 return 0;
161}
-
MACH3LOG_ERROR
#define MACH3LOG_ERROR
Definition MaCh3Logger.h:15
-
SetMaCh3LoggerFormat
void SetMaCh3LoggerFormat()
Set messaging format of the logger.
Definition MaCh3Logger.h:20
-
MACH3LOG_WARN
#define MACH3LOG_WARN
Definition MaCh3Logger.h:14
+
MACH3LOG_ERROR
#define MACH3LOG_ERROR
Definition MaCh3Logger.h:18
+
SetMaCh3LoggerFormat
void SetMaCh3LoggerFormat()
Set messaging format of the logger.
Definition MaCh3Logger.h:23
+
MACH3LOG_WARN
#define MACH3LOG_WARN
Definition MaCh3Logger.h:17
SaveResults
void SaveResults()
Definition RHat.cpp:589
InitialiseArrays
void InitialiseArrays()
Definition RHat.cpp:369
RunDiagnostic
void RunDiagnostic()
Definition RHat.cpp:430
MCMCFile
std::vector< std::string > MCMCFile
Definition RHat.cpp:43
DestroyArrays
void DestroyArrays()
Definition RHat.cpp:795
PrepareChains
void PrepareChains()
Definition RHat.cpp:165
-
MaCh3Exception
Custom exception class for MaCh3 errors.
Definition MaCh3Exception.h:10
+
MaCh3Exception
Custom exception class for MaCh3 errors.
Definition MaCh3Exception.h:12
MaCh3Utils::MaCh3Welcome
void MaCh3Welcome()
KS: Prints welcome message with MaCh3 logo.
Definition Monitor.cpp:11
@@ -918,7 +918,7 @@

363 clock.Stop();
364 MACH3LOG_INFO("Finished calculating Toys, it took {:.2f}s to finish", clock.RealTime());
365}
-
MACH3LOG_DEBUG
#define MACH3LOG_DEBUG
Definition MaCh3Logger.h:12
+
MACH3LOG_DEBUG
#define MACH3LOG_DEBUG
Definition MaCh3Logger.h:15
ValidPar
std::vector< bool > ValidPar
Definition RHat.cpp:44
BranchNames
std::vector< TString > BranchNames
Definition RHat.cpp:42
CalcMedian
double CalcMedian(double arr[], int size)
Definition RHat.cpp:841
@@ -1171,7 +1171,7 @@

789
790 MACH3LOG_INFO("Finished and wrote results to {}", NameTemp);
791}
-
MACH3LOG_CRITICAL
#define MACH3LOG_CRITICAL
Definition MaCh3Logger.h:16
+
MACH3LOG_CRITICAL
#define MACH3LOG_CRITICAL
Definition MaCh3Logger.h:19
diff --git a/RHat_8cpp_source.html b/RHat_8cpp_source.html index a056955a8..8a71892a2 100644 --- a/RHat_8cpp_source.html +++ b/RHat_8cpp_source.html @@ -958,12 +958,12 @@
856}
size
int size
Definition GetPenaltyTerm.cpp:42
-
MACH3LOG_CRITICAL
#define MACH3LOG_CRITICAL
Definition MaCh3Logger.h:16
-
MACH3LOG_DEBUG
#define MACH3LOG_DEBUG
Definition MaCh3Logger.h:12
-
MACH3LOG_ERROR
#define MACH3LOG_ERROR
Definition MaCh3Logger.h:15
-
MACH3LOG_INFO
#define MACH3LOG_INFO
Definition MaCh3Logger.h:13
-
SetMaCh3LoggerFormat
void SetMaCh3LoggerFormat()
Set messaging format of the logger.
Definition MaCh3Logger.h:20
-
MACH3LOG_WARN
#define MACH3LOG_WARN
Definition MaCh3Logger.h:14
+
MACH3LOG_CRITICAL
#define MACH3LOG_CRITICAL
Definition MaCh3Logger.h:19
+
MACH3LOG_DEBUG
#define MACH3LOG_DEBUG
Definition MaCh3Logger.h:15
+
MACH3LOG_ERROR
#define MACH3LOG_ERROR
Definition MaCh3Logger.h:18
+
MACH3LOG_INFO
#define MACH3LOG_INFO
Definition MaCh3Logger.h:16
+
SetMaCh3LoggerFormat
void SetMaCh3LoggerFormat()
Set messaging format of the logger.
Definition MaCh3Logger.h:23
+
MACH3LOG_WARN
#define MACH3LOG_WARN
Definition MaCh3Logger.h:17
main
int main(int argc, char *argv[])
Definition RHat.cpp:86
SaveResults
void SaveResults()
Definition RHat.cpp:589
Nchains
int Nchains
Definition RHat.cpp:38
@@ -998,8 +998,8 @@
PrepareChains
void PrepareChains()
Definition RHat.cpp:165
MarginalPosteriorVarianceFolded
double * MarginalPosteriorVarianceFolded
Definition RHat.cpp:69
Ntoys
int Ntoys
Definition RHat.cpp:37
-
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:18
-
MaCh3Exception
Custom exception class for MaCh3 errors.
Definition MaCh3Exception.h:10
+
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:21
+
MaCh3Exception
Custom exception class for MaCh3 errors.
Definition MaCh3Exception.h:12
MaCh3Utils::PrintProgressBar
void PrintProgressBar(const int Done, const int All)
KS: Simply print progress bar.
Definition Monitor.cpp:193
MaCh3Utils::MaCh3Welcome
void MaCh3Welcome()
KS: Prints welcome message with MaCh3 logo.
Definition Monitor.cpp:11
diff --git a/SECURITY_8md.html b/SECURITY_8md.html new file mode 100644 index 000000000..947e405a5 --- /dev/null +++ b/SECURITY_8md.html @@ -0,0 +1,83 @@ + + + + + + + +MaCh3: /github/workspace/SECURITY.md File Reference + + + + + + + + + +
+
+ + + + + + + +
+
MaCh3 1.1.0 +
+
Reference Guide
+
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+
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+
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+
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+ + diff --git a/SampleSummary_8cpp_source.html b/SampleSummary_8cpp_source.html index d4d43f20b..9416fb22a 100644 --- a/SampleSummary_8cpp_source.html +++ b/SampleSummary_8cpp_source.html @@ -2851,8 +2851,8 @@
NormalisePoly
TH2Poly * NormalisePoly(TH2Poly *Histogram)
WP: Helper to Normalise histograms.
Definition Structs.cpp:298
PolyProjectionY
TH1D * PolyProjectionY(TObject *poly, std::string TempName, std::vector< double > ybins, bool computeErrors)
WP: Poly Projectors.
Definition Structs.cpp:227
_int_
#define _int_
Definition Structs.h:12
-
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:18
-
MaCh3Modes::GetNModes
int GetNModes()
KS: Get number of modes, keep in mind actual number is +1 greater due to unknown category.
Definition MaCh3Modes.h:43
+
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:21
+
MaCh3Modes::GetNModes
int GetNModes()
KS: Get number of modes, keep in mind actual number is +1 greater due to unknown category.
Definition MaCh3Modes.h:44
MaCh3Modes::GetMaCh3ModeName
std::string GetMaCh3ModeName(const int Index)
KS: Get normal name of mode, if mode not known you will get UNKNOWN_BAD.
Definition MaCh3Modes.cpp:124
SampleSummary::AddThrowByMode
void AddThrowByMode(std::vector< std::vector< TH2Poly * > > &SampleVector_ByMode)
KS: Add histograms for each mode.
Definition SampleSummary.cpp:571
SampleSummary::LLHPenaltyVector
std::vector< double > LLHPenaltyVector
Vector to hold the penalty term.
Definition SampleSummary.h:145
diff --git a/SampleSummary_8h_source.html b/SampleSummary_8h_source.html index 7ad7190c9..0f99ae1e1 100644 --- a/SampleSummary_8h_source.html +++ b/SampleSummary_8h_source.html @@ -308,8 +308,8 @@
_int_
#define _int_
Definition Structs.h:12
TestStatistic
TestStatistic
Make an enum of the test statistic that we're using.
Definition Structs.h:353
-
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:18
-
MaCh3Modes
KS: Class describing MaCh3 modes used in the analysis, it is being initialised from config.
Definition MaCh3Modes.h:32
+
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:21
+
MaCh3Modes
KS: Class describing MaCh3 modes used in the analysis, it is being initialised from config.
Definition MaCh3Modes.h:33
SampleSummary
Class to calculate pvalue produce posterior predictive and many fancy Bayesian stuff.
Definition SampleSummary.h:25
SampleSummary::AddThrowByMode
void AddThrowByMode(std::vector< std::vector< TH2Poly * > > &SampleVector_ByMode)
KS: Add histograms for each mode.
Definition SampleSummary.cpp:571
SampleSummary::LLHPenaltyVector
std::vector< double > LLHPenaltyVector
Vector to hold the penalty term.
Definition SampleSummary.h:145
diff --git a/ShiftFunctors_8h_source.html b/ShiftFunctors_8h_source.html index c6165db6e..f83df83f9 100644 --- a/ShiftFunctors_8h_source.html +++ b/ShiftFunctors_8h_source.html @@ -127,7 +127,7 @@
37
38};
-
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:18
+
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:21
BaseFuncPar::SetUncertainty
void SetUncertainty(double sigma)
Definition ShiftFunctors.h:10
diff --git a/SplineMonolith_8cpp_source.html b/SplineMonolith_8cpp_source.html index bf47b0b0d..b965dcd29 100644 --- a/SplineMonolith_8cpp_source.html +++ b/SplineMonolith_8cpp_source.html @@ -1919,15 +1919,15 @@
1781}
isFlat
std::vector< bool > isFlat
Definition GetPenaltyTerm.cpp:39
-
MACH3LOG_ERROR
#define MACH3LOG_ERROR
Definition MaCh3Logger.h:15
-
MACH3LOG_INFO
#define MACH3LOG_INFO
Definition MaCh3Logger.h:13
-
MACH3LOG_WARN
#define MACH3LOG_WARN
Definition MaCh3Logger.h:14
+
MACH3LOG_ERROR
#define MACH3LOG_ERROR
Definition MaCh3Logger.h:18
+
MACH3LOG_INFO
#define MACH3LOG_INFO
Definition MaCh3Logger.h:16
+
MACH3LOG_WARN
#define MACH3LOG_WARN
Definition MaCh3Logger.h:17
_nCoeff_
#define _nCoeff_
KS: We store coefficients {y,b,c,d} in one array one by one, this is only to define it once rather th...
Definition SplineCommon.h:8
_nTF1Coeff_
#define _nTF1Coeff_
KS: For TF1 we store at most 5 coefficients, we could make it more flexible but for now define it her...
Definition SplineCommon.h:10
_int_
#define _int_
Definition Structs.h:12
_float_
#define _float_
Definition Structs.h:11
-
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:18
+
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:21
SMonolith::cpu_nParamPerEvent
std::vector< unsigned int > cpu_nParamPerEvent
KS: CPU map keeping track how many parameters applies to each event, we keep two numbers here {number...
Definition SplineMonolith.h:171
SMonolith::gpu_nKnots_arr
unsigned int * gpu_nKnots_arr
KS: GPU Number of knots per spline.
Definition SplineMonolith.h:187
SMonolith::gpu_weights
float * gpu_weights
GPU arrays to hold weight for each spline.
Definition SplineMonolith.h:164
@@ -1982,17 +1982,17 @@
SplineBase
Base class for calculating weight from spline.
Definition SplineBase.h:28
TF1_red
CW: A reduced TF1 class only. Only saves parameters for each TF1 and how many parameters each paramet...
Definition SplineStructs.h:144
TSpline3_red
CW: Reduced TSpline3 class.
Definition SplineStructs.h:260
-
CopyToGPU_SepMany
__host__ void CopyToGPU_SepMany(short int *gpu_paramNo_arr, unsigned int *gpu_nKnots_arr, float *gpu_x_array, float *gpu_many_array, std::vector< short int > paramNo_arr, std::vector< unsigned int > nKnots_arr, std::vector< float > cpu_x_array, std::vector< float > cpu_many_array, int n_events, std::vector< unsigned int > cpu_nParamPerEvent, unsigned int *gpu_nParamPerEvent, int n_params, unsigned int n_splines, short int spline_size, unsigned int sizeof_array)
Copy to GPU for x array and separate ybcd array.
Definition gpuSplineUtils.cu:251
-
InitGPU_SepMany
__host__ void InitGPU_SepMany(float **gpu_x_array, float **gpu_many_array, float **gpu_weights, short int **gpu_paramNo_arr, unsigned int **gpu_nKnots_arr, float **cpu_total_weights, float **gpu_total_weights, int n_events, unsigned int **gpu_nParamPerEvent, unsigned int sizeof_array, unsigned int n_splines, int Eve_size)
Initialiser when using the x array and combined y,b,c,d array.
Definition gpuSplineUtils.cu:106
-
CopyToGPU_TF1
__host__ void CopyToGPU_TF1(float *gpu_coeffs, short int *gpu_paramNo_arr, short int *gpu_nPoints_arr, std::vector< float > cpu_coeffs, std::vector< short int > paramNo_arr, std::vector< short int > nPoints_arr, int n_events, std::vector< unsigned int > cpu_nParamPerEvent, unsigned int *gpu_nParamPerEvent, int n_params, unsigned int n_splines, short int _max_knots)
Copy to GPU for x array and separate ybcd array.
Definition gpuSplineUtils.cu:357
-
InitGPU_TF1
__host__ void InitGPU_TF1(float **gpu_coeffs, short int **gpu_paramNo_arr, short int **gpu_nPoints_arr, float **gpu_weights, float **cpu_total_weights, float **gpu_total_weights, int n_events, unsigned int **gpu_nParamPerEvent, unsigned int n_splines)
Initialiser when using the x array and combined y,b,c,d array.
Definition gpuSplineUtils.cu:168
-
InitGPU_Segments
__host__ void InitGPU_Segments(short int **segment)
Definition gpuSplineUtils.cu:226
-
RunGPU_TF1
__host__ void RunGPU_TF1(const float *gpu_coeffs, const short int *gpu_paramNo_arr, const short int *gpu_nPoints_arr, float *gpu_weights, float *gpu_total_weights, float *cpu_total_weights, float *vals, const unsigned int h_n_splines)
Run the GPU code for the TF1.
Definition gpuSplineUtils.cu:696
-
CleanupGPU_SepMany
__host__ void CleanupGPU_SepMany(short int *gpu_paramNo_arr, unsigned int *gpu_nKnots_arr, float *gpu_x_array, float *gpu_many_array, float *gpu_total_weights, unsigned int *gpu_nParamPerEvent, float *cpu_total_weights, float *gpu_weights)
Clean up the {x},{ybcd} arrays.
Definition gpuSplineUtils.cu:805
-
InitGPU_Vals
__host__ void InitGPU_Vals(float **vals)
Definition gpuSplineUtils.cu:236
-
CleanupGPU_Segments
__host__ void CleanupGPU_Segments(short int *segment, float *vals)
Clean up pinned variables at CPU.
Definition gpuSplineUtils.cu:841
-
RunGPU_SepMany
__host__ void RunGPU_SepMany(const short int *gpu_paramNo_arr, const unsigned int *gpu_nKnots_arr, const float *gpu_coeff_many, float *gpu_weights, float *gpu_total_weights, float *cpu_total_weights, float *vals, short int *segment, const unsigned int h_n_splines)
Definition gpuSplineUtils.cu:589
-
CleanupGPU_TF1
__host__ void CleanupGPU_TF1(float *gpu_coeffs, short int *gpu_paramNo_arr, short int *gpu_nPoints_arr, float *gpu_total_weights, float *cpu_total_weights, float *gpu_weights)
Clean up the TF1 arrays.
Definition gpuSplineUtils.cu:854
+
CopyToGPU_SepMany
__host__ void CopyToGPU_SepMany(short int *gpu_paramNo_arr, unsigned int *gpu_nKnots_arr, float *gpu_x_array, float *gpu_many_array, std::vector< short int > paramNo_arr, std::vector< unsigned int > nKnots_arr, std::vector< float > cpu_x_array, std::vector< float > cpu_many_array, int n_events, std::vector< unsigned int > cpu_nParamPerEvent, unsigned int *gpu_nParamPerEvent, int n_params, unsigned int n_splines, short int spline_size, unsigned int sizeof_array)
Copy to GPU for x array and separate ybcd array.
Definition gpuSplineUtils.cu:256
+
InitGPU_SepMany
__host__ void InitGPU_SepMany(float **gpu_x_array, float **gpu_many_array, float **gpu_weights, short int **gpu_paramNo_arr, unsigned int **gpu_nKnots_arr, float **cpu_total_weights, float **gpu_total_weights, int n_events, unsigned int **gpu_nParamPerEvent, unsigned int sizeof_array, unsigned int n_splines, int Eve_size)
Initialiser when using the x array and combined y,b,c,d array.
Definition gpuSplineUtils.cu:112
+
CopyToGPU_TF1
__host__ void CopyToGPU_TF1(float *gpu_coeffs, short int *gpu_paramNo_arr, short int *gpu_nPoints_arr, std::vector< float > cpu_coeffs, std::vector< short int > paramNo_arr, std::vector< short int > nPoints_arr, int n_events, std::vector< unsigned int > cpu_nParamPerEvent, unsigned int *gpu_nParamPerEvent, int n_params, unsigned int n_splines, short int _max_knots)
Copy to GPU for x array and separate ybcd array.
Definition gpuSplineUtils.cu:362
+
InitGPU_TF1
__host__ void InitGPU_TF1(float **gpu_coeffs, short int **gpu_paramNo_arr, short int **gpu_nPoints_arr, float **gpu_weights, float **cpu_total_weights, float **gpu_total_weights, int n_events, unsigned int **gpu_nParamPerEvent, unsigned int n_splines)
Initialiser when using the x array and combined y,b,c,d array.
Definition gpuSplineUtils.cu:174
+
InitGPU_Segments
__host__ void InitGPU_Segments(short int **segment)
Allocate memory for spline segments.
Definition gpuSplineUtils.cu:232
+
RunGPU_TF1
__host__ void RunGPU_TF1(const float *gpu_coeffs, const short int *gpu_paramNo_arr, const short int *gpu_nPoints_arr, float *gpu_weights, float *gpu_total_weights, float *cpu_total_weights, float *vals, const unsigned int h_n_splines)
Run the GPU code for the TF1.
Definition gpuSplineUtils.cu:698
+
CleanupGPU_SepMany
__host__ void CleanupGPU_SepMany(short int *gpu_paramNo_arr, unsigned int *gpu_nKnots_arr, float *gpu_x_array, float *gpu_many_array, float *gpu_total_weights, unsigned int *gpu_nParamPerEvent, float *cpu_total_weights, float *gpu_weights)
Clean up the {x},{ybcd} arrays.
Definition gpuSplineUtils.cu:807
+
InitGPU_Vals
__host__ void InitGPU_Vals(float **vals)
Definition gpuSplineUtils.cu:241
+
CleanupGPU_Segments
__host__ void CleanupGPU_Segments(short int *segment, float *vals)
Clean up pinned variables at CPU.
Definition gpuSplineUtils.cu:843
+
RunGPU_SepMany
__host__ void RunGPU_SepMany(const short int *gpu_paramNo_arr, const unsigned int *gpu_nKnots_arr, const float *gpu_coeff_many, float *gpu_weights, float *gpu_total_weights, float *cpu_total_weights, float *vals, short int *segment, const unsigned int h_n_splines)
Run the GPU code for the separate many arrays. As in separate {x}, {y,b,c,d} arrays Pass the segment ...
Definition gpuSplineUtils.cu:591
+
CleanupGPU_TF1
__host__ void CleanupGPU_TF1(float *gpu_coeffs, short int *gpu_paramNo_arr, short int *gpu_nPoints_arr, float *gpu_total_weights, float *cpu_total_weights, float *gpu_weights)
Clean up the TF1 arrays.
Definition gpuSplineUtils.cu:856
FastSplineInfo
CW: Add a struct to hold info about the splinified xsec parameters and help with FindSplineSegment.
Definition SplineStructs.h:9
FastSplineInfo::nPts
_int_ nPts
Number of points in spline.
Definition SplineStructs.h:12
FastSplineInfo::splineParsPointer
const double * splineParsPointer
Array of the knots positions.
Definition SplineStructs.h:21
diff --git a/SplineMonolith_8h_source.html b/SplineMonolith_8h_source.html index a20305d94..9fae97e58 100644 --- a/SplineMonolith_8h_source.html +++ b/SplineMonolith_8h_source.html @@ -196,7 +196,7 @@
isFlat
std::vector< bool > isFlat
Definition GetPenaltyTerm.cpp:39
_int_
#define _int_
Definition Structs.h:12
-
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:18
+
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:21
SMonolith
Even-by-event class calculating response for spline parameters. It is possible to use GPU acceleratio...
Definition SplineMonolith.h:11
SMonolith::cpu_nParamPerEvent
std::vector< unsigned int > cpu_nParamPerEvent
KS: CPU map keeping track how many parameters applies to each event, we keep two numbers here {number...
Definition SplineMonolith.h:171
SMonolith::gpu_nKnots_arr
unsigned int * gpu_nKnots_arr
KS: GPU Number of knots per spline.
Definition SplineMonolith.h:187
@@ -254,7 +254,7 @@
SplineBase
Base class for calculating weight from spline.
Definition SplineBase.h:28
TF1_red
CW: A reduced TF1 class only. Only saves parameters for each TF1 and how many parameters each paramet...
Definition SplineStructs.h:144
TSpline3_red
CW: Reduced TSpline3 class.
Definition SplineStructs.h:260
-
SynchroniseSplines
__host__ void SynchroniseSplines()
Make sure all Cuda threads finished execution.
Definition gpuSplineUtils.cu:795
+
SynchroniseSplines
__host__ void SynchroniseSplines()
Make sure all Cuda threads finished execution.
Definition gpuSplineUtils.cu:797
FastSplineInfo
CW: Add a struct to hold info about the splinified xsec parameters and help with FindSplineSegment.
Definition SplineStructs.h:9
diff --git a/SplineStructs_8h.html b/SplineStructs_8h.html index 70a6e6f1d..5d08a39e7 100644 --- a/SplineStructs_8h.html +++ b/SplineStructs_8h.html @@ -203,12 +203,12 @@

139 }
140}
isFlat
std::vector< bool > isFlat
Definition GetPenaltyTerm.cpp:39
-
MACH3LOG_ERROR
#define MACH3LOG_ERROR
Definition MaCh3Logger.h:15
-
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:18
-
MaCh3Exception
Custom exception class for MaCh3 errors.
Definition MaCh3Exception.h:10
-
covarianceBase::GetParFancyName
std::string GetParFancyName(const int i)
Get fancy name of the Parameter.
Definition covarianceBase.h:153
-
covarianceXsec::GetParSplineKnotLowerBound
double GetParSplineKnotLowerBound(const int i)
EM: value at which we cap spline knot weight.
Definition covarianceXsec.h:53
-
covarianceXsec::GetParSplineKnotUpperBound
double GetParSplineKnotUpperBound(const int i)
EM: value at which we cap spline knot weight.
Definition covarianceXsec.h:50
+
MACH3LOG_ERROR
#define MACH3LOG_ERROR
Definition MaCh3Logger.h:18
+
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:21
+
MaCh3Exception
Custom exception class for MaCh3 errors.
Definition MaCh3Exception.h:12
+
covarianceBase::GetParFancyName
std::string GetParFancyName(const int i)
Get fancy name of the Parameter.
Definition covarianceBase.h:154
+
covarianceXsec::GetParSplineKnotLowerBound
double GetParSplineKnotLowerBound(const int i)
EM: value at which we cap spline knot weight.
Definition covarianceXsec.h:52
+
covarianceXsec::GetParSplineKnotUpperBound
double GetParSplineKnotUpperBound(const int i)
EM: value at which we cap spline knot weight.
Definition covarianceXsec.h:49
diff --git a/SplineStructs_8h_source.html b/SplineStructs_8h_source.html index baff91c92..26fe883a8 100644 --- a/SplineStructs_8h_source.html +++ b/SplineStructs_8h_source.html @@ -853,7 +853,7 @@
752};
isFlat
std::vector< bool > isFlat
Definition GetPenaltyTerm.cpp:39
-
MACH3LOG_ERROR
#define MACH3LOG_ERROR
Definition MaCh3Logger.h:15
+
MACH3LOG_ERROR
#define MACH3LOG_ERROR
Definition MaCh3Logger.h:18
ApplyKnotWeightCap
void ApplyKnotWeightCap(TGraph *xsecgraph, int splineParsIndex, covarianceXsec *XsecCov)
EM: Apply capping to knot weight for specified spline parameter. param graph needs to have been set i...
Definition SplineStructs.h:93
_int_
#define _int_
Definition Structs.h:12
@@ -863,8 +863,8 @@
kMonotonic
@ kMonotonic
Definition Structs.h:115
kLinear
@ kLinear
Definition Structs.h:114
kAkima
@ kAkima
Definition Structs.h:116
-
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:18
-
MaCh3Exception
Custom exception class for MaCh3 errors.
Definition MaCh3Exception.h:10
+
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:21
+
MaCh3Exception
Custom exception class for MaCh3 errors.
Definition MaCh3Exception.h:12
TF1_red
CW: A reduced TF1 class only. Only saves parameters for each TF1 and how many parameters each paramet...
Definition SplineStructs.h:144
TF1_red::~TF1_red
~TF1_red()
Empty destructor.
Definition SplineStructs.h:154
TF1_red::Par
_float_ * Par
The parameters.
Definition SplineStructs.h:251
@@ -916,10 +916,10 @@
XSecStruct::Func
T * Func
The function.
Definition SplineStructs.h:87
XSecStruct::Eval
double Eval(const _int_ nSpline, const _float_ variation)
CW: Eval the current variation.
Definition SplineStructs.h:75
XSecStruct::~XSecStruct
~XSecStruct()
CW: The light destructor.
Definition SplineStructs.h:46
-
covarianceBase::GetParFancyName
std::string GetParFancyName(const int i)
Get fancy name of the Parameter.
Definition covarianceBase.h:153
-
covarianceXsec
Class responsible for handling of systematic error parameters with different types defined in the con...
Definition covarianceXsec.h:15
-
covarianceXsec::GetParSplineKnotLowerBound
double GetParSplineKnotLowerBound(const int i)
EM: value at which we cap spline knot weight.
Definition covarianceXsec.h:53
-
covarianceXsec::GetParSplineKnotUpperBound
double GetParSplineKnotUpperBound(const int i)
EM: value at which we cap spline knot weight.
Definition covarianceXsec.h:50
+
covarianceBase::GetParFancyName
std::string GetParFancyName(const int i)
Get fancy name of the Parameter.
Definition covarianceBase.h:154
+
covarianceXsec
Class responsible for handling of systematic error parameters with different types defined in the con...
Definition covarianceXsec.h:14
+
covarianceXsec::GetParSplineKnotLowerBound
double GetParSplineKnotLowerBound(const int i)
EM: value at which we cap spline knot weight.
Definition covarianceXsec.h:52
+
covarianceXsec::GetParSplineKnotUpperBound
double GetParSplineKnotUpperBound(const int i)
EM: value at which we cap spline knot weight.
Definition covarianceXsec.h:49
tau
#define tau
Definition probGpu.cu:68
FastSplineInfo
CW: Add a struct to hold info about the splinified xsec parameters and help with FindSplineSegment.
Definition SplineStructs.h:9
diff --git a/StatisticalUtils_8h.html b/StatisticalUtils_8h.html index 39226e76d..2acba522c 100644 --- a/StatisticalUtils_8h.html +++ b/StatisticalUtils_8h.html @@ -211,8 +211,8 @@

152 }
153 std::cout<<""<<std::endl;
154}
-
MACH3LOG_ERROR
#define MACH3LOG_ERROR
Definition MaCh3Logger.h:15
-
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:18
+
MACH3LOG_ERROR
#define MACH3LOG_ERROR
Definition MaCh3Logger.h:18
+
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:21
diff --git a/StatisticalUtils_8h_source.html b/StatisticalUtils_8h_source.html index a66d08318..ef4eea5dd 100644 --- a/StatisticalUtils_8h_source.html +++ b/StatisticalUtils_8h_source.html @@ -345,7 +345,7 @@
247 return quartiles[2] - quartiles[0];
248}
-
MACH3LOG_ERROR
#define MACH3LOG_ERROR
Definition MaCh3Logger.h:15
+
MACH3LOG_ERROR
#define MACH3LOG_ERROR
Definition MaCh3Logger.h:18
GetSigmaValue
double GetSigmaValue(const int sigma)
KS: Convert sigma from normal distribution into percentage.
Definition StatisticalUtils.h:51
GetSubOptimality
double GetSubOptimality(std::vector< double > EigenValues, const int TotalTarameters)
Based on http://probability.ca/jeff/ftpdir/adaptex.pdf.
Definition StatisticalUtils.h:220
GetBIC
double GetBIC(const double llh, const int data, const int nPars)
Get the Bayesian Information Criterion (BIC) or Schwarz information criterion (also SIC,...
Definition StatisticalUtils.h:85
@@ -360,7 +360,7 @@
TestStatistic
TestStatistic
Make an enum of the test statistic that we're using.
Definition Structs.h:353
kDembinskiAbdelmottele
@ kDembinskiAbdelmottele
Definition Structs.h:358
-
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:18
+
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:21
diff --git a/Structs_8cpp.html b/Structs_8cpp.html index 4f3309797..1d42972c2 100644 --- a/Structs_8cpp.html +++ b/Structs_8cpp.html @@ -204,7 +204,7 @@

496 return Enu;
497
498}
-
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:18
+
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:21
diff --git a/Structs_8cpp_source.html b/Structs_8cpp_source.html index a21075a51..0321940be 100644 --- a/Structs_8cpp_source.html +++ b/Structs_8cpp_source.html @@ -626,7 +626,7 @@
PolyProjectionY
TH1D * PolyProjectionY(TObject *poly, std::string TempName, std::vector< double > ybins, bool computeErrors)
WP: Poly Projectors.
Definition Structs.cpp:227
RemoveFitter
void RemoveFitter(TH1D *hist, std::string name)
KS: Remove fitted TF1 from hist to make comparison easier.
Definition Structs.cpp:437
-
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:18
+
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:21
MaCh3Utils::nKnownDetIDs
int nKnownDetIDs
Definition Structs.cpp:90
MaCh3Utils::GetMassFromPDG
double GetMassFromPDG(int PDG)
Return mass for given PDG.
Definition Structs.cpp:11
diff --git a/Structs_8h.html b/Structs_8h.html index 19b2ec259..ff1628265 100644 --- a/Structs_8h.html +++ b/Structs_8h.html @@ -90,14 +90,14 @@ #include <iostream>
#include <vector>
#include <iomanip>
-#include "set"
+#include <set>
+#include <list>
+#include <unordered_map>
#include "TSpline.h"
#include "TF1.h"
#include "TLorentzVector.h"
#include "TObjString.h"
-#include "unordered_map"
#include "TH2Poly.h"
-#include "list"
#include "TFile.h"

Go to the source code of this file.

@@ -814,7 +814,7 @@

496 return Enu;
497
498}
-
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:18
+
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:21
diff --git a/Structs_8h_source.html b/Structs_8h_source.html index d3452fb31..0c9926b17 100644 --- a/Structs_8h_source.html +++ b/Structs_8h_source.html @@ -121,16 +121,16 @@
43#include <iostream>
44#include <vector>
45#include <iomanip>
-
46
-
47// ROOT include
-
48#include "set"
-
49#include "TSpline.h"
-
50#include "TF1.h"
-
51#include "TLorentzVector.h"
-
52#include "TObjString.h"
-
53#include "unordered_map"
-
54#include "TH2Poly.h"
-
55#include "list"
+
46#include <set>
+
47#include <list>
+
48#include <unordered_map>
+
49
+
50// ROOT include
+
51#include "TSpline.h"
+
52#include "TF1.h"
+
53#include "TLorentzVector.h"
+
54#include "TObjString.h"
+
55#include "TH2Poly.h"
56#include "TFile.h"
57
58#ifdef MULTITHREAD
@@ -656,7 +656,7 @@
kSpline
@ kSpline
Definition Structs.h:152
kSystTypes
@ kSystTypes
Definition Structs.h:154
kFunc
@ kFunc
Definition Structs.h:153
-
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:18
+
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:21
MaCh3Utils::nKnownDetIDs
int nKnownDetIDs
Definition Structs.cpp:90
MaCh3Utils::GetMassFromPDG
double GetMassFromPDG(int PDG)
Return mass for given PDG.
Definition Structs.cpp:11
diff --git a/ThrowParms_8cpp_source.html b/ThrowParms_8cpp_source.html index d784fd0fa..9f6b2e19a 100644 --- a/ThrowParms_8cpp_source.html +++ b/ThrowParms_8cpp_source.html @@ -198,7 +198,7 @@
104
-
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:18
+
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:21
ThrowParms::ThrowSet
void ThrowSet(std::vector< double > &parms)
Definition ThrowParms.cpp:38
ThrowParms::pvals
TVectorD * pvals
Definition ThrowParms.h:21
diff --git a/ThrowParms_8h_source.html b/ThrowParms_8h_source.html index 208367c29..e20d7dbcd 100644 --- a/ThrowParms_8h_source.html +++ b/ThrowParms_8h_source.html @@ -121,7 +121,7 @@
37
38};
-
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:18
+
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:21
ThrowParms
No idea really...
Definition ThrowParms.h:19
ThrowParms::GetSize
int GetSize()
Definition ThrowParms.h:35
diff --git a/YamlHelper_8h.html b/YamlHelper_8h.html index 185134d8b..e619da0ef 100644 --- a/YamlHelper_8h.html +++ b/YamlHelper_8h.html @@ -163,13 +163,13 @@

Definition at line 53 of file YamlHelper.h.

-
53 {
-
54// **********************
-
55 return CheckNodeExistsHelper(node, args...);
-
56}
-
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:18
-
CheckNodeExistsHelper
bool CheckNodeExistsHelper(const T &node)
Use this like this CheckNodeExists(config, "LikelihoodOptions", "TestStatistic"); KS: Base case for r...
Definition YamlHelper.h:32
+

Definition at line 56 of file YamlHelper.h.

+
56 {
+
57// **********************
+
58 return CheckNodeExistsHelper(node, args...);
+
59}
+
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:21
+
CheckNodeExistsHelper
bool CheckNodeExistsHelper(const T &node)
Use this like this CheckNodeExists(config, "LikelihoodOptions", "TestStatistic"); KS: Base case for r...
Definition YamlHelper.h:35
@@ -193,12 +193,12 @@

-

Definition at line 32 of file YamlHelper.h.

-
32 {
-
33// **********************
-
34 (void)node;
-
35 return true; // Node exists, return true
-
36}
+

Definition at line 35 of file YamlHelper.h.

+
35 {
+
36// **********************
+
37 (void)node;
+
38 return true; // Node exists, return true
+
39}
@@ -238,15 +238,15 @@

Definition at line 41 of file YamlHelper.h.

-
41 {\
-
42// **********************
-
43 if (!node[key]) {
-
44 //std::cerr << "Node " << key << " doesn't exist." << std::endl;
-
45 return false;
-
46 }
-
47 return CheckNodeExistsHelper(node[key], args...);
-
48}
+

Definition at line 44 of file YamlHelper.h.

+
44 {\
+
45// **********************
+
46 if (!node[key]) {
+
47 //std::cerr << "Node " << key << " doesn't exist." << std::endl;
+
48 return false;
+
49 }
+
50 return CheckNodeExistsHelper(node[key], args...);
+
51}
@@ -280,11 +280,11 @@

Definition at line 82 of file YamlHelper.h.

-
82 {
-
83// **********************
-
84 return FindFromManagerHelper<T>(node, args...);
-
85}
+

Definition at line 85 of file YamlHelper.h.

+
85 {
+
86// **********************
+
87 return FindFromManagerHelper<T>(node, args...);
+
88}
@@ -307,11 +307,11 @@

Use this like this FindFromManager<std::string>(config, "LikelihoodOptions", "TestStatistic"); Base case for recursion

-

Definition at line 62 of file YamlHelper.h.

-
62 {
-
63// **********************
-
64 return node.as<T>(); // Convert YAML node to the specified type
-
65}
+

Definition at line 65 of file YamlHelper.h.

+
65 {
+
66// **********************
+
67 return node.as<T>(); // Convert YAML node to the specified type
+
68}
@@ -351,16 +351,16 @@

Definition at line 70 of file YamlHelper.h.

-
70 {
-
71 // **********************
-
72 if (!node[key]) {
-
73 std::cerr << "Node " << key << " doesn't exist." << std::endl;
-
74 throw;
-
75 return T();
-
76 }
-
77 return FindFromManagerHelper<T>(node[key], args...); // Recursive call
-
78}
+

Definition at line 73 of file YamlHelper.h.

+
73 {
+
74 // **********************
+
75 if (!node[key]) {
+
76 std::cerr << "Node " << key << " doesn't exist." << std::endl;
+
77 throw;
+
78 return T();
+
79 }
+
80 return FindFromManagerHelper<T>(node[key], args...); // Recursive call
+
81}
@@ -401,16 +401,16 @@

Definition at line 18 of file YamlHelper.h.

-
18 {
-
19// **********************
-
20 YAML::Node tmpNode = node;
-
21
-
22 if(!tmpNode){
-
23 return defval;
-
24 }
-
25 return tmpNode.as<Type>();
-
26}
+

Definition at line 21 of file YamlHelper.h.

+
21 {
+
22// **********************
+
23 YAML::Node tmpNode = node;
+
24
+
25 if(!tmpNode){
+
26 return defval;
+
27 }
+
28 return tmpNode.as<Type>();
+
29}
@@ -446,16 +446,16 @@

Definition at line 90 of file YamlHelper.h.

-
90 {
-
91// **********************
-
92 try {
-
93 return YAML::Load(yaml_string);
-
94 } catch (const YAML::ParserException& e) {
-
95 std::cerr << "Error parsing YAML string: " << e.what() << std::endl;
-
96 return YAML::Node();
-
97 }
-
98}
+

Definition at line 93 of file YamlHelper.h.

+
93 {
+
94// **********************
+
95 try {
+
96 return YAML::Load(yaml_string);
+
97 } catch (const YAML::ParserException& e) {
+
98 std::cerr << "Error parsing YAML string: " << e.what() << std::endl;
+
99 return YAML::Node();
+
100 }
+
101}
@@ -492,31 +492,31 @@

Returns
std::string The string representation of the TMacro object.
-

Definition at line 115 of file YamlHelper.h.

-
115 {
-
116// **********************
-
117 std::stringstream ss;
-
118
-
119 // Retrieve lines from TMacro
-
120 TList* linesList = macro.GetListOfLines();
-
121 if (!linesList) {
-
122 std::cerr << "Error: Failed to retrieve lines from TMacro." << std::endl;
-
123 return "";
-
124 }
-
125
-
126 TIter nextLine(linesList);
-
127 TObject *obj = nullptr;
-
128 while ((obj = nextLine())) {
-
129 TObjString* line = dynamic_cast<TObjString*>(obj);
-
130 if (!line) {
-
131 std::cerr << "Error: Failed to cast object to TObjString." << std::endl;
-
132 continue;
-
133 }
-
134 ss << line->GetString() << std::endl;
-
135 }
-
136
-
137 return ss.str();
-
138}
+

Definition at line 118 of file YamlHelper.h.

+
118 {
+
119// **********************
+
120 std::stringstream ss;
+
121
+
122 // Retrieve lines from TMacro
+
123 TList* linesList = macro.GetListOfLines();
+
124 if (!linesList) {
+
125 std::cerr << "Error: Failed to retrieve lines from TMacro." << std::endl;
+
126 return "";
+
127 }
+
128
+
129 TIter nextLine(linesList);
+
130 TObject *obj = nullptr;
+
131 while ((obj = nextLine())) {
+
132 TObjString* line = dynamic_cast<TObjString*>(obj);
+
133 if (!line) {
+
134 std::cerr << "Error: Failed to cast object to TObjString." << std::endl;
+
135 continue;
+
136 }
+
137 ss << line->GetString() << std::endl;
+
138 }
+
139
+
140 return ss.str();
+
141}
@@ -553,19 +553,18 @@

Returns
YAML::Node The YAML node representing the TMacro object.
-

Definition at line 144 of file YamlHelper.h.

-
144 {
-
145// **********************
-
146
-
147 std::string yaml_string = TMacroToString(macro);
-
148
-
149 // Convert the YAML string to a YAML node
-
150 YAML::Node yaml_node = STRINGtoYAML(yaml_string);
-
151
-
152 return yaml_node;
-
153}
-
STRINGtoYAML
YAML::Node STRINGtoYAML(const std::string &yaml_string)
Function to convert a YAML string to a YAML node.
Definition YamlHelper.h:90
-
TMacroToString
std::string TMacroToString(const TMacro &macro)
KS: Convert a ROOT TMacro object to a string representation.
Definition YamlHelper.h:115
+

Definition at line 147 of file YamlHelper.h.

+
147 {
+
148// **********************
+
149 std::string yaml_string = TMacroToString(macro);
+
150
+
151 // Convert the YAML string to a YAML node
+
152 YAML::Node yaml_node = STRINGtoYAML(yaml_string);
+
153
+
154 return yaml_node;
+
155}
+
STRINGtoYAML
YAML::Node STRINGtoYAML(const std::string &yaml_string)
Function to convert a YAML string to a YAML node.
Definition YamlHelper.h:93
+
TMacroToString
std::string TMacroToString(const TMacro &macro)
KS: Convert a ROOT TMacro object to a string representation.
Definition YamlHelper.h:118
@@ -602,13 +601,13 @@

Returns
std::string The string representation of the YAML node.
-

Definition at line 104 of file YamlHelper.h.

-
104 {
-
105// **********************
-
106 YAML::Emitter emitter;
-
107 emitter << node;
-
108 return emitter.c_str();
-
109}
+

Definition at line 107 of file YamlHelper.h.

+
107 {
+
108// **********************
+
109 YAML::Emitter emitter;
+
110 emitter << node;
+
111 return emitter.c_str();
+
112}
diff --git a/YamlHelper_8h_source.html b/YamlHelper_8h_source.html index 2de0da9a8..8f21006e8 100644 --- a/YamlHelper_8h_source.html +++ b/YamlHelper_8h_source.html @@ -85,167 +85,169 @@
Go to the documentation of this file.
1#pragma once
2
-
3#include <iostream>
-
4#include <fstream>
-
5#include <string>
-
6
-
7#include "TMacro.h"
-
8#include "TList.h"
-
9#include "TObjString.h"
-
10
-
11#include "yaml-cpp/yaml.h"
+
3// C++ Includes
+
4#include <iostream>
+
5#include <fstream>
+
6#include <string>
+
7
+
8// ROOT Includes
+
9#include "TMacro.h"
+
10#include "TList.h"
+
11#include "TObjString.h"
12
-
13// **********************
-
17template<typename Type>
-
-
18Type GetFromManager(const YAML::Node& node, Type defval) {
-
19// **********************
-
20 YAML::Node tmpNode = node;
-
21
-
22 if(!tmpNode){
-
23 return defval;
-
24 }
-
25 return tmpNode.as<Type>();
-
26}
-
-
27
-
28// **********************
-
31template<typename T>
-
-
32bool CheckNodeExistsHelper(const T& node) {
-
33// **********************
-
34 (void)node;
-
35 return true; // Node exists, return true
-
36}
-
-
37
-
38// **********************
-
40template<typename T, typename... Args>
-
-
41bool CheckNodeExistsHelper(const T& node, const std::string& key, Args... args) {\
-
42// **********************
-
43 if (!node[key]) {
-
44 //std::cerr << "Node " << key << " doesn't exist." << std::endl;
-
45 return false;
-
46 }
-
47 return CheckNodeExistsHelper(node[key], args...);
-
48}
-
-
49
-
50// **********************
-
52template<typename... Args>
-
-
53bool CheckNodeExists(const YAML::Node& node, Args... args) {
-
54// **********************
-
55 return CheckNodeExistsHelper(node, args...);
-
56}
-
-
57
-
58// **********************
-
61template<typename T>
-
-
62T FindFromManagerHelper(const YAML::Node& node) {
-
63// **********************
-
64 return node.as<T>(); // Convert YAML node to the specified type
-
65}
-
-
66
-
67// **********************
-
69template<typename T, typename... Args>
-
-
70T FindFromManagerHelper(const YAML::Node& node, const std::string& key, Args... args) {
-
71 // **********************
-
72 if (!node[key]) {
-
73 std::cerr << "Node " << key << " doesn't exist." << std::endl;
-
74 throw;
-
75 return T();
-
76 }
-
77 return FindFromManagerHelper<T>(node[key], args...); // Recursive call
-
78}
-
-
79// **********************
-
81template<typename T, typename... Args>
-
-
82T FindFromManager(const YAML::Node& node, Args... args) {
-
83// **********************
-
84 return FindFromManagerHelper<T>(node, args...);
-
85}
-
-
86
-
87// **********************
-
-
90inline YAML::Node STRINGtoYAML(const std::string& yaml_string){
-
91// **********************
-
92 try {
-
93 return YAML::Load(yaml_string);
-
94 } catch (const YAML::ParserException& e) {
-
95 std::cerr << "Error parsing YAML string: " << e.what() << std::endl;
-
96 return YAML::Node();
-
97 }
-
98}
-
-
99
-
100// **********************
-
-
104inline std::string YAMLtoSTRING(const YAML::Node& node) {
-
105// **********************
-
106 YAML::Emitter emitter;
-
107 emitter << node;
-
108 return emitter.c_str();
-
109}
-
-
110
-
111// **********************
-
-
115inline std::string TMacroToString(const TMacro& macro) {
-
116// **********************
-
117 std::stringstream ss;
-
118
-
119 // Retrieve lines from TMacro
-
120 TList* linesList = macro.GetListOfLines();
-
121 if (!linesList) {
-
122 std::cerr << "Error: Failed to retrieve lines from TMacro." << std::endl;
-
123 return "";
-
124 }
-
125
-
126 TIter nextLine(linesList);
-
127 TObject *obj = nullptr;
-
128 while ((obj = nextLine())) {
-
129 TObjString* line = dynamic_cast<TObjString*>(obj);
-
130 if (!line) {
-
131 std::cerr << "Error: Failed to cast object to TObjString." << std::endl;
-
132 continue;
-
133 }
-
134 ss << line->GetString() << std::endl;
-
135 }
-
136
-
137 return ss.str();
-
138}
+
13// yaml Includes
+
14#include "yaml-cpp/yaml.h"
+
15
+
16// **********************
+
20template<typename Type>
+
+
21Type GetFromManager(const YAML::Node& node, Type defval) {
+
22// **********************
+
23 YAML::Node tmpNode = node;
+
24
+
25 if(!tmpNode){
+
26 return defval;
+
27 }
+
28 return tmpNode.as<Type>();
+
29}
+
30
+
31// **********************
+
34template<typename T>
+
+
35bool CheckNodeExistsHelper(const T& node) {
+
36// **********************
+
37 (void)node;
+
38 return true; // Node exists, return true
+
39}
+
+
40
+
41// **********************
+
43template<typename T, typename... Args>
+
+
44bool CheckNodeExistsHelper(const T& node, const std::string& key, Args... args) {\
+
45// **********************
+
46 if (!node[key]) {
+
47 //std::cerr << "Node " << key << " doesn't exist." << std::endl;
+
48 return false;
+
49 }
+
50 return CheckNodeExistsHelper(node[key], args...);
+
51}
+
+
52
+
53// **********************
+
55template<typename... Args>
+
+
56bool CheckNodeExists(const YAML::Node& node, Args... args) {
+
57// **********************
+
58 return CheckNodeExistsHelper(node, args...);
+
59}
+
+
60
+
61// **********************
+
64template<typename T>
+
+
65T FindFromManagerHelper(const YAML::Node& node) {
+
66// **********************
+
67 return node.as<T>(); // Convert YAML node to the specified type
+
68}
+
+
69
+
70// **********************
+
72template<typename T, typename... Args>
+
+
73T FindFromManagerHelper(const YAML::Node& node, const std::string& key, Args... args) {
+
74 // **********************
+
75 if (!node[key]) {
+
76 std::cerr << "Node " << key << " doesn't exist." << std::endl;
+
77 throw;
+
78 return T();
+
79 }
+
80 return FindFromManagerHelper<T>(node[key], args...); // Recursive call
+
81}
+
+
82// **********************
+
84template<typename T, typename... Args>
+
+
85T FindFromManager(const YAML::Node& node, Args... args) {
+
86// **********************
+
87 return FindFromManagerHelper<T>(node, args...);
+
88}
+
+
89
+
90// **********************
+
+
93inline YAML::Node STRINGtoYAML(const std::string& yaml_string){
+
94// **********************
+
95 try {
+
96 return YAML::Load(yaml_string);
+
97 } catch (const YAML::ParserException& e) {
+
98 std::cerr << "Error parsing YAML string: " << e.what() << std::endl;
+
99 return YAML::Node();
+
100 }
+
101}
+
+
102
+
103// **********************
+
+
107inline std::string YAMLtoSTRING(const YAML::Node& node) {
+
108// **********************
+
109 YAML::Emitter emitter;
+
110 emitter << node;
+
111 return emitter.c_str();
+
112}
+
+
113
+
114// **********************
+
+
118inline std::string TMacroToString(const TMacro& macro) {
+
119// **********************
+
120 std::stringstream ss;
+
121
+
122 // Retrieve lines from TMacro
+
123 TList* linesList = macro.GetListOfLines();
+
124 if (!linesList) {
+
125 std::cerr << "Error: Failed to retrieve lines from TMacro." << std::endl;
+
126 return "";
+
127 }
+
128
+
129 TIter nextLine(linesList);
+
130 TObject *obj = nullptr;
+
131 while ((obj = nextLine())) {
+
132 TObjString* line = dynamic_cast<TObjString*>(obj);
+
133 if (!line) {
+
134 std::cerr << "Error: Failed to cast object to TObjString." << std::endl;
+
135 continue;
+
136 }
+
137 ss << line->GetString() << std::endl;
+
138 }
139
-
140// **********************
-
-
144inline YAML::Node TMacroToYAML(const TMacro& macro) {
-
145// **********************
-
146
-
147 std::string yaml_string = TMacroToString(macro);
-
148
-
149 // Convert the YAML string to a YAML node
-
150 YAML::Node yaml_node = STRINGtoYAML(yaml_string);
-
151
-
152 return yaml_node;
-
153}
-
-
154
-
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:18
-
FindFromManagerHelper
T FindFromManagerHelper(const YAML::Node &node)
Definition YamlHelper.h:62
-
FindFromManager
T FindFromManager(const YAML::Node &node, Args... args)
Wrapper function to call the recursive helper.
Definition YamlHelper.h:82
-
CheckNodeExistsHelper
bool CheckNodeExistsHelper(const T &node)
Use this like this CheckNodeExists(config, "LikelihoodOptions", "TestStatistic"); KS: Base case for r...
Definition YamlHelper.h:32
-
STRINGtoYAML
YAML::Node STRINGtoYAML(const std::string &yaml_string)
Function to convert a YAML string to a YAML node.
Definition YamlHelper.h:90
-
TMacroToYAML
YAML::Node TMacroToYAML(const TMacro &macro)
KS: Convert a ROOT TMacro object to a YAML node.
Definition YamlHelper.h:144
-
TMacroToString
std::string TMacroToString(const TMacro &macro)
KS: Convert a ROOT TMacro object to a string representation.
Definition YamlHelper.h:115
-
YAMLtoSTRING
std::string YAMLtoSTRING(const YAML::Node &node)
KS: Convert a YAML node to a string representation.
Definition YamlHelper.h:104
-
CheckNodeExists
bool CheckNodeExists(const YAML::Node &node, Args... args)
KS: Wrapper function to call the recursive helper.
Definition YamlHelper.h:53
+
140 return ss.str();
+
141}
+
+
142
+
143// **********************
+
+
147inline YAML::Node TMacroToYAML(const TMacro& macro) {
+
148// **********************
+
149 std::string yaml_string = TMacroToString(macro);
+
150
+
151 // Convert the YAML string to a YAML node
+
152 YAML::Node yaml_node = STRINGtoYAML(yaml_string);
+
153
+
154 return yaml_node;
+
155}
+
+
156
+
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:21
+
FindFromManagerHelper
T FindFromManagerHelper(const YAML::Node &node)
Definition YamlHelper.h:65
+
FindFromManager
T FindFromManager(const YAML::Node &node, Args... args)
Wrapper function to call the recursive helper.
Definition YamlHelper.h:85
+
CheckNodeExistsHelper
bool CheckNodeExistsHelper(const T &node)
Use this like this CheckNodeExists(config, "LikelihoodOptions", "TestStatistic"); KS: Base case for r...
Definition YamlHelper.h:35
+
STRINGtoYAML
YAML::Node STRINGtoYAML(const std::string &yaml_string)
Function to convert a YAML string to a YAML node.
Definition YamlHelper.h:93
+
TMacroToYAML
YAML::Node TMacroToYAML(const TMacro &macro)
KS: Convert a ROOT TMacro object to a YAML node.
Definition YamlHelper.h:147
+
TMacroToString
std::string TMacroToString(const TMacro &macro)
KS: Convert a ROOT TMacro object to a string representation.
Definition YamlHelper.h:118
+
YAMLtoSTRING
std::string YAMLtoSTRING(const YAML::Node &node)
KS: Convert a YAML node to a string representation.
Definition YamlHelper.h:107
+
CheckNodeExists
bool CheckNodeExists(const YAML::Node &node, Args... args)
KS: Wrapper function to call the recursive helper.
Definition YamlHelper.h:56
diff --git a/adaptiveMCMCStruct_8h_source.html b/adaptiveMCMCStruct_8h_source.html deleted file mode 100644 index 04850c7db..000000000 --- a/adaptiveMCMCStruct_8h_source.html +++ /dev/null @@ -1,153 +0,0 @@ - - - - - - - -MaCh3: /github/workspace/covariance/adaptiveMCMCStruct.h Source File - - - - - - - - - -
-
- - - - - - - -
-
MaCh3 1.1.0 -
-
Reference Guide
-
-
- - - - - - - - - -
-
- - -
-
-
-
-
-
Loading...
-
Searching...
-
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-
-
-
-
- - -
-
-
adaptiveMCMCStruct.h
-
-
-Go to the documentation of this file.
1#pragma once
-
2
-
3// MaCh3 Includes
-
4#include "manager/MaCh3Logger.h"
-
5
-
6// ROOT Includes
-
7#include "TMatrixDSym.h"
-
8
-
9// C++ Includes
-
10#include <vector>
-
11
-
14
-
15
-
-
16namespace adaptive_mcmc{
-
17
-
-
19struct AdaptiveMCMCStruct{
-
20 // Meta variables related to adaption run time
-
22 int start_adaptive_throw;
-
24 int start_adaptive_update;
-
26 int end_adaptive_update;
-
28 int adaptive_update_step;
-
30 std::vector<int> adapt_block_matrix_indices;
-
32 std::vector<int> adapt_block_sizes;
-
33
-
34 // Variables directely linked to adaption
-
36 std::vector<double> par_means;
-
38 TMatrixDSym* adaptive_covariance;
-
39};
-
-
40
-
41
-
-
43inline void print_adaptive_struct(AdaptiveMCMCStruct adaptive_struct){
-
44 MACH3LOG_INFO("Adaptive MCMC Info:");
-
45 MACH3LOG_INFO("Throwing from New Matrix from Step : {}", adaptive_struct.start_adaptive_throw);
-
46 MACH3LOG_INFO("Adaption Matrix Start Update : {}", adaptive_struct.start_adaptive_update);
-
47 MACH3LOG_INFO("Adaption Matrix Ending Updates : {}", adaptive_struct.end_adaptive_update);
-
48 MACH3LOG_INFO("Steps Between Updates : {}", adaptive_struct.adaptive_update_step);
-
49}
-
-
50
-
51
-
52
-
53
-
54} // adaptive_mcmc namespace
-
- -
MACH3LOG_INFO
#define MACH3LOG_INFO
Definition MaCh3Logger.h:13
-
adaptive_mcmc
Contains information about adaptive covariance matrix.
Definition adaptiveMCMCStruct.h:16
-
adaptive_mcmc::print_adaptive_struct
void print_adaptive_struct(AdaptiveMCMCStruct adaptive_struct)
Basic printer method for AMCMC struct.
Definition adaptiveMCMCStruct.h:43
-
adaptive_mcmc::AdaptiveMCMCStruct
struct encapsulating all adaptive MCMC information
Definition adaptiveMCMCStruct.h:19
-
adaptive_mcmc::AdaptiveMCMCStruct::adaptive_covariance
TMatrixDSym * adaptive_covariance
Full adaptive covariance matrix.
Definition adaptiveMCMCStruct.h:38
-
adaptive_mcmc::AdaptiveMCMCStruct::par_means
std::vector< double > par_means
Mean values for all parameters.
Definition adaptiveMCMCStruct.h:36
-
adaptive_mcmc::AdaptiveMCMCStruct::adapt_block_sizes
std::vector< int > adapt_block_sizes
Size of blocks for adaption.
Definition adaptiveMCMCStruct.h:32
-
adaptive_mcmc::AdaptiveMCMCStruct::end_adaptive_update
int end_adaptive_update
Steps between changing throw matrix.
Definition adaptiveMCMCStruct.h:26
-
adaptive_mcmc::AdaptiveMCMCStruct::adaptive_update_step
int adaptive_update_step
Steps between changing throw matrix.
Definition adaptiveMCMCStruct.h:28
-
adaptive_mcmc::AdaptiveMCMCStruct::start_adaptive_throw
int start_adaptive_throw
When do we start throwing.
Definition adaptiveMCMCStruct.h:22
-
adaptive_mcmc::AdaptiveMCMCStruct::start_adaptive_update
int start_adaptive_update
When do we stop update the adaptive matrix.
Definition adaptiveMCMCStruct.h:24
-
adaptive_mcmc::AdaptiveMCMCStruct::adapt_block_matrix_indices
std::vector< int > adapt_block_matrix_indices
Indices for block-matrix adaption.
Definition adaptiveMCMCStruct.h:30
-
- -
-Generated by doxygen 1.9.8 -
- - diff --git a/annotated.html b/annotated.html index 28e0db888..c1a7e2f29 100644 --- a/annotated.html +++ b/annotated.html @@ -76,8 +76,8 @@
Here are the classes, structs, unions and interfaces with brief descriptions:
[detail level 12]
- - + + diff --git a/classBaseFuncPar.html b/classBaseFuncPar.html index b5b1f39b5..c419b590c 100644 --- a/classBaseFuncPar.html +++ b/classBaseFuncPar.html @@ -218,7 +218,7 @@

Definition at line 10 of file ShiftFunctors.h.

10{ScaleUncertainty = sigma;}
-
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:18
+
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:21
BaseFuncPar::ScaleUncertainty
double ScaleUncertainty
Definition ShiftFunctors.h:9
diff --git a/classFitterBase.html b/classFitterBase.html index 5401a8a3d..209d04fe6 100644 --- a/classFitterBase.html +++ b/classFitterBase.html @@ -250,7 +250,7 @@

Base class for implementing fitting algorithms.

See also
For more details, visit the Wiki.
-

Definition at line 23 of file FitterBase.h.

+

Definition at line 24 of file FitterBase.h.

Constructor & Destructor Documentation

◆ FitterBase()

@@ -344,30 +344,30 @@

75 TotalNSamples = 0;
76 fTestLikelihood = GetFromManager<bool>(fitMan->raw()["General"]["Fitter"]["FitTestLikelihood"], false);;
77}
-
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:18
-
FitterBase::Modes
MaCh3Modes * Modes
MaCh3 Modes.
Definition FitterBase.h:95
-
FitterBase::osc
covarianceOsc * osc
handles oscillation parameters
Definition FitterBase.h:125
-
FitterBase::stepClock
TStopwatch * stepClock
tells how long single step/fit iteration took
Definition FitterBase.h:132
-
FitterBase::accCount
int accCount
counts accepted steps
Definition FitterBase.h:106
-
FitterBase::random
TRandom3 * random
Random number.
Definition FitterBase.h:137
-
FitterBase::systematics
std::vector< covarianceBase * > systematics
Systematic holder.
Definition FitterBase.h:122
-
FitterBase::OutputPrepared
bool OutputPrepared
Checks if output prepared not repeat some operations.
Definition FitterBase.h:160
-
FitterBase::outputFile
TFile * outputFile
Output.
Definition FitterBase.h:140
-
FitterBase::SaveProposal
bool SaveProposal
Save proposal at each step.
Definition FitterBase.h:153
-
FitterBase::fitMan
manager * fitMan
The manager.
Definition FitterBase.h:92
-
FitterBase::step
unsigned int step
current state
Definition FitterBase.h:98
-
FitterBase::SettingsSaved
bool SettingsSaved
Checks if setting saved not repeat some operations.
Definition FitterBase.h:158
-
FitterBase::FileSaved
bool FileSaved
Checks if file saved not repeat some operations.
Definition FitterBase.h:156
-
FitterBase::sample_llh
double * sample_llh
store the llh breakdowns
Definition FitterBase.h:112
-
FitterBase::CovFolder
TDirectory * CovFolder
Output cov folder.
Definition FitterBase.h:142
-
FitterBase::clock
TStopwatch * clock
tells global time how long fit took
Definition FitterBase.h:130
-
FitterBase::TotalNSamples
unsigned int TotalNSamples
Total number of samples used.
Definition FitterBase.h:119
-
FitterBase::syst_llh
double * syst_llh
systematic llh breakdowns
Definition FitterBase.h:114
-
FitterBase::auto_save
int auto_save
auto save every N steps
Definition FitterBase.h:146
-
FitterBase::fTestLikelihood
bool fTestLikelihood
Necessary for some fitting algorithms like PSO.
Definition FitterBase.h:149
-
FitterBase::outTree
TTree * outTree
Output tree with posteriors.
Definition FitterBase.h:144
-
FitterBase::save_nominal
bool save_nominal
save nominal matrix info or not
Definition FitterBase.h:151
-
FitterBase::samples
std::vector< samplePDFBase * > samples
Sample holder.
Definition FitterBase.h:117
+
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:21
+
FitterBase::Modes
MaCh3Modes * Modes
MaCh3 Modes.
Definition FitterBase.h:96
+
FitterBase::osc
covarianceOsc * osc
handles oscillation parameters
Definition FitterBase.h:126
+
FitterBase::stepClock
TStopwatch * stepClock
tells how long single step/fit iteration took
Definition FitterBase.h:133
+
FitterBase::accCount
int accCount
counts accepted steps
Definition FitterBase.h:107
+
FitterBase::random
TRandom3 * random
Random number.
Definition FitterBase.h:138
+
FitterBase::systematics
std::vector< covarianceBase * > systematics
Systematic holder.
Definition FitterBase.h:123
+
FitterBase::OutputPrepared
bool OutputPrepared
Checks if output prepared not repeat some operations.
Definition FitterBase.h:161
+
FitterBase::outputFile
TFile * outputFile
Output.
Definition FitterBase.h:141
+
FitterBase::SaveProposal
bool SaveProposal
Save proposal at each step.
Definition FitterBase.h:154
+
FitterBase::fitMan
manager * fitMan
The manager.
Definition FitterBase.h:93
+
FitterBase::step
unsigned int step
current state
Definition FitterBase.h:99
+
FitterBase::SettingsSaved
bool SettingsSaved
Checks if setting saved not repeat some operations.
Definition FitterBase.h:159
+
FitterBase::FileSaved
bool FileSaved
Checks if file saved not repeat some operations.
Definition FitterBase.h:157
+
FitterBase::sample_llh
double * sample_llh
store the llh breakdowns
Definition FitterBase.h:113
+
FitterBase::CovFolder
TDirectory * CovFolder
Output cov folder.
Definition FitterBase.h:143
+
FitterBase::clock
TStopwatch * clock
tells global time how long fit took
Definition FitterBase.h:131
+
FitterBase::TotalNSamples
unsigned int TotalNSamples
Total number of samples used.
Definition FitterBase.h:120
+
FitterBase::syst_llh
double * syst_llh
systematic llh breakdowns
Definition FitterBase.h:115
+
FitterBase::auto_save
int auto_save
auto save every N steps
Definition FitterBase.h:147
+
FitterBase::fTestLikelihood
bool fTestLikelihood
Necessary for some fitting algorithms like PSO.
Definition FitterBase.h:150
+
FitterBase::outTree
TTree * outTree
Output tree with posteriors.
Definition FitterBase.h:145
+
FitterBase::save_nominal
bool save_nominal
save nominal matrix info or not
Definition FitterBase.h:152
+
FitterBase::samples
std::vector< samplePDFBase * > samples
Sample holder.
Definition FitterBase.h:118
manager::GetMaCh3Modes
MaCh3Modes * GetMaCh3Modes() const
Return pointer to MaCh3 modes.
Definition manager.h:50
manager::raw
YAML::Node const & raw()
Return config.
Definition manager.h:48
@@ -417,7 +417,7 @@

96 stepClock = nullptr;
97 MACH3LOG_INFO("Closing MaCh3 Fitter Engine");
98}
-
MACH3LOG_INFO
#define MACH3LOG_INFO
Definition MaCh3Logger.h:13
+
MACH3LOG_INFO
#define MACH3LOG_INFO
Definition MaCh3Logger.h:16
FitterBase::SaveOutput
void SaveOutput()
Save output and close files.
Definition FitterBase.cpp:241
@@ -496,8 +496,8 @@

367
368 return;
369}
-
FitterBase::osc2
covarianceOsc * osc2
handles oscillation parameters
Definition FitterBase.h:127
-
covarianceBase::getNominalArray
virtual std::vector< double > getNominalArray()
Definition covarianceBase.cpp:1707
+
FitterBase::osc2
covarianceOsc * osc2
handles oscillation parameters
Definition FitterBase.h:128
+
covarianceBase::getNominalArray
virtual std::vector< double > getNominalArray()
Definition covarianceBase.cpp:1522
@@ -749,8 +749,8 @@

LikelihoodFit, mcmc, MinuitFit, and PSO.

-

Definition at line 70 of file FitterBase.h.

-
70{return "FitterBase";};
+

Definition at line 71 of file FitterBase.h.

+
71{return "FitterBase";};
@@ -816,7 +816,7 @@

866 (*it)->SaveUpdatedMatrixConfig();
867 }
868}
-
MACH3LOG_WARN
#define MACH3LOG_WARN
Definition MaCh3Logger.h:14
+
MACH3LOG_WARN
#define MACH3LOG_WARN
Definition MaCh3Logger.h:17
FitterBase::RunLLHScan
void RunLLHScan()
Perform a 1D likelihood scan.
Definition FitterBase.cpp:479
@@ -1009,12 +1009,12 @@

236
237 OutputPrepared = true;
238}
-
MACH3LOG_CRITICAL
#define MACH3LOG_CRITICAL
Definition MaCh3Logger.h:16
-
FitterBase::accProb
double accProb
current acceptance prob
Definition FitterBase.h:104
-
FitterBase::stepTime
double stepTime
Time of single step.
Definition FitterBase.h:134
-
FitterBase::logLCurr
double logLCurr
current likelihood
Definition FitterBase.h:100
-
FitterBase::osc_llh
double osc_llh
Definition FitterBase.h:110
-
covarianceBase::SetBranches
void SetBranches(TTree &tree, bool SaveProposal=false)
set branches for output file
Definition covarianceBase.cpp:1096
+
MACH3LOG_CRITICAL
#define MACH3LOG_CRITICAL
Definition MaCh3Logger.h:19
+
FitterBase::accProb
double accProb
current acceptance prob
Definition FitterBase.h:105
+
FitterBase::stepTime
double stepTime
Time of single step.
Definition FitterBase.h:135
+
FitterBase::logLCurr
double logLCurr
current likelihood
Definition FitterBase.h:101
+
FitterBase::osc_llh
double osc_llh
Definition FitterBase.h:111
+
covarianceBase::SetBranches
void SetBranches(TTree &tree, bool SaveProposal=false)
set branches for output file
Definition covarianceBase.cpp:1098
@@ -1741,7 +1741,7 @@

1081 //KS: this is only relevant if PlotByMode is turned on
1082 //Checking each mode is time consuming so we only consider one which are relevant for particular analysis
1083 const int nRelevantModes = 2;
-
1084 MaCh3Modes_t RelevantModes[nRelevantModes] = {Modes->GetMode("CCQE"), Modes->GetMode("2p2h")};
+
1084 MaCh3Modes_t RelevantModes[nRelevantModes] = {Modes->GetMode("CCQE"), Modes->GetMode("2p2h")};
1085 bool DoByMode = GetFromManager<int>(fitMan->raw()["General"]["DoByMode"], false);
1086
1087 //KS: If true it will make additional plots with LLH sample contribution in each bin, should make it via config file...
@@ -2072,15 +2072,15 @@

1412 } // end looping over xsec parameters (i)
1413 } // end looping over covarianceBase objects
1414}
-
MACH3LOG_ERROR
#define MACH3LOG_ERROR
Definition MaCh3Logger.h:15
-
MaCh3Modes_t
int MaCh3Modes_t
Enumerator of MaCh3Mode.
Definition MaCh3Modes.h:13
+
MACH3LOG_ERROR
#define MACH3LOG_ERROR
Definition MaCh3Logger.h:18
+
MaCh3Modes_t
int MaCh3Modes_t
Enumerator of MaCh3Mode.
Definition MaCh3Modes.h:14
PolyProjectionX
TH1D * PolyProjectionX(TObject *poly, std::string TempName, std::vector< double > xbins, bool computeErrors)
WP: Poly Projectors.
Definition Structs.cpp:156
PolyProjectionY
TH1D * PolyProjectionY(TObject *poly, std::string TempName, std::vector< double > ybins, bool computeErrors)
WP: Poly Projectors.
Definition Structs.cpp:227
-
FitterBase::GetName
virtual std::string GetName() const
Get name of class.
Definition FitterBase.h:70
+
FitterBase::GetName
virtual std::string GetName() const
Get name of class.
Definition FitterBase.h:71
FitterBase::MakeAsymGraph
TGraphAsymmErrors * MakeAsymGraph(TH1D *sigmaArrayLeft, TH1D *sigmaArrayCentr, TH1D *sigmaArrayRight, std::string title)
Used by sigma variation, check how 1 sigma changes spectra.
Definition FitterBase.cpp:1417
-
MaCh3Exception
Custom exception class for MaCh3 errors.
Definition MaCh3Exception.h:10
+
MaCh3Exception
Custom exception class for MaCh3 errors.
Definition MaCh3Exception.h:12
+
MaCh3Modes::GetMode
MaCh3Modes_t GetMode(const std::string &name)
KS: Get mode number based on name, if mode not known you will get UNKNOWN_BAD.
Definition MaCh3Modes.cpp:154
MaCh3Modes::GetMaCh3ModeName
std::string GetMaCh3ModeName(const int Index)
KS: Get normal name of mode, if mode not known you will get UNKNOWN_BAD.
Definition MaCh3Modes.cpp:124
-
MaCh3Modes::GetMode
MaCh3Modes_t GetMode(std::string name)
KS: Get mode number based on name, if mode not known you will get UNKNOWN_BAD.
Definition MaCh3Modes.cpp:154
@@ -2253,7 +2253,7 @@

Definition at line 106 of file FitterBase.h.

+

Definition at line 107 of file FitterBase.h.

@@ -2279,7 +2279,7 @@

Definition at line 104 of file FitterBase.h.

+

Definition at line 105 of file FitterBase.h.

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Definition at line 146 of file FitterBase.h.

+

Definition at line 147 of file FitterBase.h.

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Definition at line 130 of file FitterBase.h.

+

Definition at line 131 of file FitterBase.h.

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Definition at line 142 of file FitterBase.h.

+

Definition at line 143 of file FitterBase.h.

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Definition at line 156 of file FitterBase.h.

+

Definition at line 157 of file FitterBase.h.

@@ -2409,7 +2409,7 @@

Definition at line 92 of file FitterBase.h.

+

Definition at line 93 of file FitterBase.h.

@@ -2435,7 +2435,7 @@

PSO.

-

Definition at line 149 of file FitterBase.h.

+

Definition at line 150 of file FitterBase.h.

@@ -2461,7 +2461,7 @@

Definition at line 100 of file FitterBase.h.

+

Definition at line 101 of file FitterBase.h.

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Definition at line 102 of file FitterBase.h.

+

Definition at line 103 of file FitterBase.h.

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Definition at line 95 of file FitterBase.h.

+

Definition at line 96 of file FitterBase.h.

@@ -2539,7 +2539,7 @@

Definition at line 125 of file FitterBase.h.

+

Definition at line 126 of file FitterBase.h.

@@ -2565,7 +2565,7 @@

Definition at line 127 of file FitterBase.h.

+

Definition at line 128 of file FitterBase.h.

@@ -2590,7 +2590,7 @@

LLH for samples/syst objects oscillation covariance llh

-

Definition at line 110 of file FitterBase.h.

+

Definition at line 111 of file FitterBase.h.

@@ -2616,7 +2616,7 @@

Definition at line 140 of file FitterBase.h.

+

Definition at line 141 of file FitterBase.h.

@@ -2642,7 +2642,7 @@

Definition at line 160 of file FitterBase.h.

+

Definition at line 161 of file FitterBase.h.

@@ -2668,7 +2668,7 @@

Definition at line 144 of file FitterBase.h.

+

Definition at line 145 of file FitterBase.h.

@@ -2694,7 +2694,7 @@

Definition at line 137 of file FitterBase.h.

+

Definition at line 138 of file FitterBase.h.

@@ -2720,7 +2720,7 @@

Definition at line 112 of file FitterBase.h.

+

Definition at line 113 of file FitterBase.h.

@@ -2746,7 +2746,7 @@

Definition at line 117 of file FitterBase.h.

+

Definition at line 118 of file FitterBase.h.

@@ -2772,7 +2772,7 @@

Definition at line 151 of file FitterBase.h.

+

Definition at line 152 of file FitterBase.h.

@@ -2798,7 +2798,7 @@

Definition at line 153 of file FitterBase.h.

+

Definition at line 154 of file FitterBase.h.

@@ -2824,7 +2824,7 @@

Definition at line 158 of file FitterBase.h.

+

Definition at line 159 of file FitterBase.h.

@@ -2850,7 +2850,7 @@

Definition at line 98 of file FitterBase.h.

+

Definition at line 99 of file FitterBase.h.

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Definition at line 132 of file FitterBase.h.

+

Definition at line 133 of file FitterBase.h.

@@ -2902,7 +2902,7 @@

Definition at line 134 of file FitterBase.h.

+

Definition at line 135 of file FitterBase.h.

@@ -2928,7 +2928,7 @@

Definition at line 114 of file FitterBase.h.

+

Definition at line 115 of file FitterBase.h.

@@ -2954,7 +2954,7 @@

Definition at line 122 of file FitterBase.h.

+

Definition at line 123 of file FitterBase.h.

@@ -2980,7 +2980,7 @@

Definition at line 119 of file FitterBase.h.

+

Definition at line 120 of file FitterBase.h.

diff --git a/classLikelihoodFit.html b/classLikelihoodFit.html index 1f3ebfc8b..da5fece0f 100644 --- a/classLikelihoodFit.html +++ b/classLikelihoodFit.html @@ -302,8 +302,8 @@

8 NParsPCA = 0;
9 fMirroring = true;
10}
-
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:18
-
FitterBase
Base class for implementing fitting algorithms.
Definition FitterBase.h:23
+
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:21
+
FitterBase
Base class for implementing fitting algorithms.
Definition FitterBase.h:24
LikelihoodFit::NParsPCA
int NParsPCA
Number of all parameters from all covariances in PCA base.
Definition LikelihoodFit.h:29
LikelihoodFit::NPars
int NPars
Number of all parameters from all covariances.
Definition LikelihoodFit.h:27
LikelihoodFit::fMirroring
bool fMirroring
Flag telling if mirroring is used or not.
Definition LikelihoodFit.h:31
@@ -483,21 +483,21 @@

151 llh = 2.0*llh;
152 return llh;
153}
-
MACH3LOG_INFO
#define MACH3LOG_INFO
Definition MaCh3Logger.h:13
-
FitterBase::osc
covarianceOsc * osc
handles oscillation parameters
Definition FitterBase.h:125
-
FitterBase::logLProp
double logLProp
proposed likelihood
Definition FitterBase.h:102
-
FitterBase::stepClock
TStopwatch * stepClock
tells how long single step/fit iteration took
Definition FitterBase.h:132
-
FitterBase::accCount
int accCount
counts accepted steps
Definition FitterBase.h:106
-
FitterBase::systematics
std::vector< covarianceBase * > systematics
Systematic holder.
Definition FitterBase.h:122
-
FitterBase::step
unsigned int step
current state
Definition FitterBase.h:98
-
FitterBase::accProb
double accProb
current acceptance prob
Definition FitterBase.h:104
-
FitterBase::sample_llh
double * sample_llh
store the llh breakdowns
Definition FitterBase.h:112
-
FitterBase::stepTime
double stepTime
Time of single step.
Definition FitterBase.h:134
-
FitterBase::logLCurr
double logLCurr
current likelihood
Definition FitterBase.h:100
-
FitterBase::syst_llh
double * syst_llh
systematic llh breakdowns
Definition FitterBase.h:114
-
FitterBase::auto_save
int auto_save
auto save every N steps
Definition FitterBase.h:146
-
FitterBase::outTree
TTree * outTree
Output tree with posteriors.
Definition FitterBase.h:144
-
FitterBase::samples
std::vector< samplePDFBase * > samples
Sample holder.
Definition FitterBase.h:117
+
MACH3LOG_INFO
#define MACH3LOG_INFO
Definition MaCh3Logger.h:16
+
FitterBase::osc
covarianceOsc * osc
handles oscillation parameters
Definition FitterBase.h:126
+
FitterBase::logLProp
double logLProp
proposed likelihood
Definition FitterBase.h:103
+
FitterBase::stepClock
TStopwatch * stepClock
tells how long single step/fit iteration took
Definition FitterBase.h:133
+
FitterBase::accCount
int accCount
counts accepted steps
Definition FitterBase.h:107
+
FitterBase::systematics
std::vector< covarianceBase * > systematics
Systematic holder.
Definition FitterBase.h:123
+
FitterBase::step
unsigned int step
current state
Definition FitterBase.h:99
+
FitterBase::accProb
double accProb
current acceptance prob
Definition FitterBase.h:105
+
FitterBase::sample_llh
double * sample_llh
store the llh breakdowns
Definition FitterBase.h:113
+
FitterBase::stepTime
double stepTime
Time of single step.
Definition FitterBase.h:135
+
FitterBase::logLCurr
double logLCurr
current likelihood
Definition FitterBase.h:101
+
FitterBase::syst_llh
double * syst_llh
systematic llh breakdowns
Definition FitterBase.h:115
+
FitterBase::auto_save
int auto_save
auto save every N steps
Definition FitterBase.h:147
+
FitterBase::outTree
TTree * outTree
Output tree with posteriors.
Definition FitterBase.h:145
+
FitterBase::samples
std::vector< samplePDFBase * > samples
Sample holder.
Definition FitterBase.h:118
covarianceOsc::getPropPars
double * getPropPars()
Retrieves the proposed parameters.
Definition covarianceOsc.cpp:147
diff --git a/classMCMCProcessor-members.html b/classMCMCProcessor-members.html index a7e0e64d8..5dc599bb7 100644 --- a/classMCMCProcessor-members.html +++ b/classMCMCProcessor-members.html @@ -135,7 +135,7 @@

- + diff --git a/classMCMCProcessor.html b/classMCMCProcessor.html index 49733b8ab..d627c7d91 100644 --- a/classMCMCProcessor.html +++ b/classMCMCProcessor.html @@ -195,9 +195,9 @@ - - - + + + @@ -686,9 +686,9 @@

96}
_UNDEF_
#define _UNDEF_
Definition MCMCProcessor.h:4
kNParameterEnum
@ kNParameterEnum
Definition MCMCProcessor.h:55
-
MACH3LOG_INFO
#define MACH3LOG_INFO
Definition MaCh3Logger.h:13
-
SetMaCh3LoggerFormat
void SetMaCh3LoggerFormat()
Set messaging format of the logger.
Definition MaCh3Logger.h:20
-
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:18
+
MACH3LOG_INFO
#define MACH3LOG_INFO
Definition MaCh3Logger.h:16
+
SetMaCh3LoggerFormat
void SetMaCh3LoggerFormat()
Set messaging format of the logger.
Definition MaCh3Logger.h:23
+
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:21
MCMCProcessor::nBatches
int nBatches
Number of batches for Batched Mean.
Definition MCMCProcessor.h:471
MCMCProcessor::StepNumber
int * StepNumber
Step number for step, important if chains were merged.
Definition MCMCProcessor.h:457
MCMCProcessor::ParStep
double ** ParStep
Array holding values for all parameters.
Definition MCMCProcessor.h:455
@@ -1240,7 +1240,7 @@

4257 delete[] C_Nominator;
4258 delete[] C_Denominator;
4259}
-
MACH3LOG_ERROR
#define MACH3LOG_ERROR
Definition MaCh3Logger.h:15
+
MACH3LOG_ERROR
#define MACH3LOG_ERROR
Definition MaCh3Logger.h:18
@@ -2357,8 +2357,8 @@

2526}
kOSCPar
@ kOSCPar
Definition MCMCProcessor.h:53
kFDDetPar
@ kFDDetPar
Definition MCMCProcessor.h:52
-
MACH3LOG_WARN
#define MACH3LOG_WARN
Definition MaCh3Logger.h:14
-
TMacroToYAML
YAML::Node TMacroToYAML(const TMacro &macro)
KS: Convert a ROOT TMacro object to a YAML node.
Definition YamlHelper.h:144
+
MACH3LOG_WARN
#define MACH3LOG_WARN
Definition MaCh3Logger.h:17
+
TMacroToYAML
YAML::Node TMacroToYAML(const TMacro &macro)
KS: Convert a ROOT TMacro object to a YAML node.
Definition YamlHelper.h:147
MaCh3Utils::PrintConfig
void PrintConfig(const YAML::Node &node)
KS: Print Yaml config using logger.
Definition Monitor.cpp:279
@@ -2477,7 +2477,7 @@

3134 for(unsigned int k = 0; k < ParNames.size(); ++k)
3135 {
3136 //KS: First we need to find parameter number based on name
-
3137 int ParamNo = GetParamIndexFromName(ParNames[k]);
+
3137 int ParamNo = GetParamIndexFromName(ParNames[k]);
3138 bool skip = false;
3139 if(ParamNo == _UNDEF_)
3140 {
@@ -2520,7 +2520,7 @@

3177}
GetJeffreysScale
std::string GetJeffreysScale(const double BayesFactor)
KS: Following H. Jeffreys. The theory of probability. UOP Oxford, 1998. DOI: 10.2307/3619118.
Definition StatisticalUtils.h:17
GetDunneKaboth
std::string GetDunneKaboth(const double BayesFactor)
KS: Based on Table 1 in https://www.t2k.org/docs/technotes/435.
Definition StatisticalUtils.h:34
-
MCMCProcessor::GetParamIndexFromName
int GetParamIndexFromName(const std::string Name)
Get parameter number based on name.
Definition MCMCProcessor.cpp:3000
+
MCMCProcessor::GetParamIndexFromName
int GetParamIndexFromName(const std::string &Name)
Get parameter number based on name.
Definition MCMCProcessor.cpp:3000
MCMCProcessor::MakePostfit
void MakePostfit()
Make 1D projection for each parameter and prepare structure.
Definition MCMCProcessor.cpp:240
@@ -3474,8 +3474,8 @@

-

◆ GetParamIndexFromName()

+ +

◆ GetParamIndexFromName()

@@ -3483,7 +3483,7 @@

int MCMCProcessor::GetParamIndexFromName

- + @@ -3493,7 +3493,7 @@

Definition at line 3000 of file MCMCProcessor.cpp.

-
3000 {
+
3000 {
3001// **************************
3002 int ParamNo = _UNDEF_;
3003 for (int i = 0; i < nDraw; ++i)
@@ -3562,7 +3562,7 @@

3059 for(unsigned int k = 0; k < ParNames.size(); ++k)

3060 {
3061 //KS: First we need to find parameter number based on name
-
3062 int ParamNo = GetParamIndexFromName(ParNames[k]);
+
3062 int ParamNo = GetParamIndexFromName(ParNames[k]);
3063 bool skip = false;
3064 if(ParamNo == _UNDEF_)
3065 {
@@ -3796,7 +3796,7 @@

3199 for(unsigned int k = 0; k < ParNames.size(); ++k)

3200 {
3201 //KS: First we need to find parameter number based on name
-
3202 int ParamNo = GetParamIndexFromName(ParNames[k]);
+
3202 int ParamNo = GetParamIndexFromName(ParNames[k]);
3203 bool skip = false;
3204 if(ParamNo == _UNDEF_)
3205 {
@@ -6909,7 +6909,7 @@

3349 for(unsigned int k = 0; k < Names.size(); ++k)
3350 {
3351 //KS: First we need to find parameter number based on name
-
3352 int ParamNo = GetParamIndexFromName(Names[k]);
+
3352 int ParamNo = GetParamIndexFromName(Names[k]);
3353 if(ParamNo == _UNDEF_)
3354 {
3355 MACH3LOG_WARN("Couldn't find param {}. Can't reweight Prior", Names[k]);
diff --git a/classMaCh3Exception.html b/classMaCh3Exception.html index fa6ae65c5..cb80540d9 100644 --- a/classMaCh3Exception.html +++ b/classMaCh3Exception.html @@ -108,7 +108,7 @@

Detailed Description

Custom exception class for MaCh3 errors.

-

Definition at line 10 of file MaCh3Exception.h.

+

Definition at line 12 of file MaCh3Exception.h.

Constructor & Destructor Documentation

◆ MaCh3Exception()

@@ -160,18 +160,18 @@

Definition at line 16 of file MaCh3Exception.h.

-
17 {
-
18 size_t lastSlashPos = File.find_last_of('/');
-
19 std::string fileName = (lastSlashPos != std::string::npos) ? File.substr(lastSlashPos + 1) : File;
-
20
-
21 errorMessage = ((Message.empty()) ? "Terminating MaCh3" : Message);
+

Definition at line 18 of file MaCh3Exception.h.

+
19 {
+
20 size_t lastSlashPos = File.find_last_of('/');
+
21 std::string fileName = (lastSlashPos != std::string::npos) ? File.substr(lastSlashPos + 1) : File;
22
-
23 MACH3LOG_ERROR("Find me here: {}::{}", fileName, Line);
-
24 }
-
MACH3LOG_ERROR
#define MACH3LOG_ERROR
Definition MaCh3Logger.h:15
-
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:18
-
MaCh3Exception::errorMessage
std::string errorMessage
The error message associated with this exception.
Definition MaCh3Exception.h:34
+
23 errorMessage = ((Message.empty()) ? "Terminating MaCh3" : Message);
+
24
+
25 MACH3LOG_ERROR("Find me here: {}::{}", fileName, Line);
+
26 }
+
MACH3LOG_ERROR
#define MACH3LOG_ERROR
Definition MaCh3Logger.h:18
+
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:21
+
MaCh3Exception::errorMessage
std::string errorMessage
The error message associated with this exception.
Definition MaCh3Exception.h:36
@@ -202,10 +202,10 @@

Returns
A pointer to the error message string.
-

Definition at line 28 of file MaCh3Exception.h.

-
28 {
-
29 return errorMessage.c_str();
-
30 }
+

Definition at line 30 of file MaCh3Exception.h.

+
30 {
+
31 return errorMessage.c_str();
+
32 }
@@ -232,7 +232,7 @@

Definition at line 34 of file MaCh3Exception.h.

+

Definition at line 36 of file MaCh3Exception.h.

diff --git a/classMaCh3Modes-members.html b/classMaCh3Modes-members.html index 31d361a23..39de0d002 100644 --- a/classMaCh3Modes-members.html +++ b/classMaCh3Modes-members.html @@ -83,7 +83,7 @@

- + diff --git a/classMaCh3Modes.html b/classMaCh3Modes.html index d002f9ffa..bdbd7a8e8 100644 --- a/classMaCh3Modes.html +++ b/classMaCh3Modes.html @@ -99,9 +99,9 @@ - - - + + + @@ -152,7 +152,7 @@

KS: Class describing MaCh3 modes used in the analysis, it is being initialised from config.

See also
For more details, visit the Wiki.
-

Definition at line 32 of file MaCh3Modes.h.

+

Definition at line 33 of file MaCh3Modes.h.

Constructor & Destructor Documentation

◆ MaCh3Modes()

@@ -205,11 +205,11 @@

34 Print();
35}
config
YAML::Node config
Definition GetPostfitParamPlots.cpp:30
-
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:18
-
MaCh3Modes::NModes
int NModes
KS: Number of modes, keep in mind actual number is +1 greater due to unknown category.
Definition MaCh3Modes.h:79
+
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:21
+
MaCh3Modes::NModes
int NModes
KS: Number of modes, keep in mind actual number is +1 greater due to unknown category.
Definition MaCh3Modes.h:80
MaCh3Modes::Print
void Print()
KS: Print info about initialised modes.
Definition MaCh3Modes.cpp:38
-
MaCh3Modes::Generator
std::string Generator
KS: Name of generator like NEUT, NuWro etc. this is to make stuff fancy.
Definition MaCh3Modes.h:77
-
MaCh3Modes::Title
std::string Title
KS: Name of loaded modes.
Definition MaCh3Modes.h:75
+
MaCh3Modes::Generator
std::string Generator
KS: Name of generator like NEUT, NuWro etc. this is to make stuff fancy.
Definition MaCh3Modes.h:78
+
MaCh3Modes::Title
std::string Title
KS: Name of loaded modes.
Definition MaCh3Modes.h:76
MaCh3Modes::GetMaCh3ModeName
std::string GetMaCh3ModeName(const int Index)
KS: Get normal name of mode, if mode not known you will get UNKNOWN_BAD.
Definition MaCh3Modes.cpp:124
MaCh3Modes::DeclareNewMode
void DeclareNewMode(std::string const &name, std::string const &fancyname, std::vector< int > const &GenMap)
KS: Add new mode.
Definition MaCh3Modes.cpp:80
MaCh3Modes::PrepareMap
void PrepareMap()
KS: Fill ModeMap.
Definition MaCh3Modes.cpp:96
@@ -241,8 +241,8 @@

Definition at line 37 of file MaCh3Modes.h.

-
37{};
+

Definition at line 38 of file MaCh3Modes.h.

+
38{};
@@ -302,11 +302,11 @@

91 fMode.emplace(index, newinfo);
92 NModes++;
93}
-
MaCh3Modes_t
int MaCh3Modes_t
Enumerator of MaCh3Mode.
Definition MaCh3Modes.h:13
+
MaCh3Modes_t
int MaCh3Modes_t
Enumerator of MaCh3Mode.
Definition MaCh3Modes.h:14
MaCh3Modes::EnsureModeNameRegistered
MaCh3Modes_t EnsureModeNameRegistered(std::string const &name)
KS: Make sure we don't have two modes with the same name.
Definition MaCh3Modes.cpp:69
-
MaCh3Modes::fMode
std::map< MaCh3Modes_t, MaCh3ModeInfo > fMode
KS: Main map storing info about used modes.
Definition MaCh3Modes.h:70
-
MaCh3ModeInfo
KS: Class containing information for a single MaCh3Mode.
Definition MaCh3Modes.h:16
-
MaCh3ModeInfo::GeneratorMaping
std::vector< int > GeneratorMaping
Mapping between mode and generator integers.
Definition MaCh3Modes.h:22
+
MaCh3Modes::fMode
std::map< MaCh3Modes_t, MaCh3ModeInfo > fMode
KS: Main map storing info about used modes.
Definition MaCh3Modes.h:71
+
MaCh3ModeInfo
KS: Class containing information for a single MaCh3Mode.
Definition MaCh3Modes.h:17
+
MaCh3ModeInfo::GeneratorMaping
std::vector< int > GeneratorMaping
Mapping between mode and generator integers.
Definition MaCh3Modes.h:23
@@ -346,7 +346,7 @@

75 Mode[name] = index;
76 return index;
77}
-
MaCh3Modes::Mode
std::map< std::string, MaCh3Modes_t > Mode
KS: Handy map which helps find mode number based on string.
Definition MaCh3Modes.h:68
+
MaCh3Modes::Mode
std::map< std::string, MaCh3Modes_t > Mode
KS: Handy map which helps find mode number based on string.
Definition MaCh3Modes.h:69
@@ -382,8 +382,8 @@

149 }
150 return fMode[Index].FancyName;
151}
-
MACH3LOG_CRITICAL
#define MACH3LOG_CRITICAL
Definition MaCh3Logger.h:16
-
MACH3LOG_DEBUG
#define MACH3LOG_DEBUG
Definition MaCh3Logger.h:12
+
MACH3LOG_CRITICAL
#define MACH3LOG_CRITICAL
Definition MaCh3Logger.h:19
+
MACH3LOG_DEBUG
#define MACH3LOG_DEBUG
Definition MaCh3Logger.h:15
@@ -422,8 +422,8 @@

-

◆ GetMode()

+ +

◆ GetMode()

@@ -431,7 +431,7 @@

MaCh3Modes_t MaCh3Modes::GetMode

- + @@ -441,7 +441,7 @@

Definition at line 154 of file MaCh3Modes.cpp.

-
154 {
+
154 {
155// *******************
156 if (Mode.count(name)) {
157 return Mode[name];
@@ -485,7 +485,7 @@

175 }

176 return ModeMap[Index];
177}
-
MaCh3Modes::ModeMap
std::vector< int > ModeMap
KS: Handy map helping us find MaCh3 mode based on Generator mode value.
Definition MaCh3Modes.h:72
+
MaCh3Modes::ModeMap
std::vector< int > ModeMap
KS: Handy map helping us find MaCh3 mode based on Generator mode value.
Definition MaCh3Modes.h:73
@@ -514,8 +514,8 @@

Definition at line 53 of file MaCh3Modes.h.

-
53{return "MaCh3Modes";};
+

Definition at line 54 of file MaCh3Modes.h.

+
54{return "MaCh3Modes";};
@@ -544,8 +544,8 @@

Definition at line 43 of file MaCh3Modes.h.

-
43{return NModes;}
+

Definition at line 44 of file MaCh3Modes.h.

+
44{return NModes;}
@@ -601,7 +601,7 @@

119 }
120 }
121}
-
MACH3LOG_ERROR
#define MACH3LOG_ERROR
Definition MaCh3Logger.h:15
+
MACH3LOG_ERROR
#define MACH3LOG_ERROR
Definition MaCh3Logger.h:18
@@ -652,7 +652,7 @@

64 }
65 MACH3LOG_INFO("==========================");
66}
-
MACH3LOG_INFO
#define MACH3LOG_INFO
Definition MaCh3Logger.h:13
+
MACH3LOG_INFO
#define MACH3LOG_INFO
Definition MaCh3Logger.h:16
@@ -679,7 +679,7 @@

Definition at line 70 of file MaCh3Modes.h.

+

Definition at line 71 of file MaCh3Modes.h.

@@ -705,7 +705,7 @@

Definition at line 77 of file MaCh3Modes.h.

+

Definition at line 78 of file MaCh3Modes.h.

@@ -731,7 +731,7 @@

Definition at line 68 of file MaCh3Modes.h.

+

Definition at line 69 of file MaCh3Modes.h.

@@ -757,7 +757,7 @@

Definition at line 72 of file MaCh3Modes.h.

+

Definition at line 73 of file MaCh3Modes.h.

@@ -783,7 +783,7 @@

Definition at line 79 of file MaCh3Modes.h.

+

Definition at line 80 of file MaCh3Modes.h.

@@ -809,7 +809,7 @@

Definition at line 75 of file MaCh3Modes.h.

+

Definition at line 76 of file MaCh3Modes.h.

diff --git a/classMinuitFit.html b/classMinuitFit.html index f6ec2787b..6e399a1a6 100644 --- a/classMinuitFit.html +++ b/classMinuitFit.html @@ -314,8 +314,8 @@

10 //Other then Migrad available are Simplex,Combined,Scan
11 minuit = ROOT::Math::Factory::CreateMinimizer("Minuit2", "Migrad");
12}
-
MACH3LOG_INFO
#define MACH3LOG_INFO
Definition MaCh3Logger.h:13
-
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:18
+
MACH3LOG_INFO
#define MACH3LOG_INFO
Definition MaCh3Logger.h:16
+
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:21
LikelihoodFit
Implementation of base Likelihood Fit class, it is mostly responsible for likelihood calculation whil...
Definition LikelihoodFit.h:6
MinuitFit::minuit
ROOT::Math::Minimizer * minuit
Pointer to minimizer, which most often is Minuit.
Definition MinuitFit.h:27
@@ -582,10 +582,10 @@

188 // Save all the output
189 SaveOutput();
190}
-
FitterBase::systematics
std::vector< covarianceBase * > systematics
Systematic holder.
Definition FitterBase.h:122
+
FitterBase::systematics
std::vector< covarianceBase * > systematics
Systematic holder.
Definition FitterBase.h:123
FitterBase::SaveOutput
void SaveOutput()
Save output and close files.
Definition FitterBase.cpp:241
-
FitterBase::outputFile
TFile * outputFile
Output.
Definition FitterBase.h:140
-
FitterBase::fitMan
manager * fitMan
The manager.
Definition FitterBase.h:92
+
FitterBase::outputFile
TFile * outputFile
Output.
Definition FitterBase.h:141
+
FitterBase::fitMan
manager * fitMan
The manager.
Definition FitterBase.h:93
LikelihoodFit::NParsPCA
int NParsPCA
Number of all parameters from all covariances in PCA base.
Definition LikelihoodFit.h:29
LikelihoodFit::NPars
int NPars
Number of all parameters from all covariances.
Definition LikelihoodFit.h:27
LikelihoodFit::PrepareFit
void PrepareFit()
prepare output and perform sanity checks
Definition LikelihoodFit.cpp:21
diff --git a/classOscillator.html b/classOscillator.html index 2a3266634..3ef2e64b1 100644 --- a/classOscillator.html +++ b/classOscillator.html @@ -631,7 +631,7 @@

263 InitPropagator();
264}
FLOAT_T
double FLOAT_T
Definition OscClass_CUDAProb3.h:24
-
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:18
+
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:21
Oscillator::fineCoarseRatioEnergy
double fineCoarseRatioEnergy
Definition OscClass_CUDAProb3.h:239
diff --git a/classPSO.html b/classPSO.html index 538e1269b..636fffc1a 100644 --- a/classPSO.html +++ b/classPSO.html @@ -358,7 +358,7 @@

Detailed Description

Class PSO, consist of a vector of object Class Particle and global best Takes in the size (number of particle) and number of iteration functions includes: finding global best, updating velocity, actual minimisation function.

-

Definition at line 74 of file PSO.h.

+

Definition at line 75 of file PSO.h.

Constructor & Destructor Documentation

◆ PSO()

@@ -396,18 +396,18 @@

17 fDim = fitMan->raw()["General"]["PSO"]["TestLikelihoodDim"].as<int>();
18 }
19}
-
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:18
-
FitterBase::fitMan
manager * fitMan
The manager.
Definition FitterBase.h:92
-
FitterBase::fTestLikelihood
bool fTestLikelihood
Necessary for some fitting algorithms like PSO.
Definition FitterBase.h:149
+
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:21
+
FitterBase::fitMan
manager * fitMan
The manager.
Definition FitterBase.h:93
+
FitterBase::fTestLikelihood
bool fTestLikelihood
Necessary for some fitting algorithms like PSO.
Definition FitterBase.h:150
LikelihoodFit
Implementation of base Likelihood Fit class, it is mostly responsible for likelihood calculation whil...
Definition LikelihoodFit.h:6
-
PSO::fConstriction
double fConstriction
Definition PSO.h:147
-
PSO::fTwo
double fTwo
Definition PSO.h:144
-
PSO::fInertia
double fInertia
Definition PSO.h:142
-
PSO::fParticles
int fParticles
Definition PSO.h:150
-
PSO::fOne
double fOne
Definition PSO.h:143
-
PSO::fIterations
int fIterations
Definition PSO.h:146
-
PSO::fConvergence
double fConvergence
Definition PSO.h:145
-
PSO::fDim
int fDim
Definition PSO.h:156
+
PSO::fConstriction
double fConstriction
Definition PSO.h:148
+
PSO::fTwo
double fTwo
Definition PSO.h:145
+
PSO::fInertia
double fInertia
Definition PSO.h:143
+
PSO::fParticles
int fParticles
Definition PSO.h:151
+
PSO::fOne
double fOne
Definition PSO.h:144
+
PSO::fIterations
int fIterations
Definition PSO.h:147
+
PSO::fConvergence
double fConvergence
Definition PSO.h:146
+
PSO::fDim
int fDim
Definition PSO.h:157
manager::raw
YAML::Node const & raw()
Return config.
Definition manager.h:48
@@ -437,8 +437,8 @@

Definition at line 79 of file PSO.h.

-
79{};
+

Definition at line 80 of file PSO.h.

+
80{};
@@ -559,7 +559,7 @@

218 }
219 return uncertainties_list;
220}
-
PSO::CalcChi
double CalcChi(std::vector< double > x)
Definition PSO.h:127
+
PSO::CalcChi
double CalcChi(std::vector< double > x)
Definition PSO.h:128
@@ -679,11 +679,11 @@

-

Definition at line 127 of file PSO.h.

-
127 {
-
128 double* a = &x[0];
-
129 return CalcChi2(a);
-
130 };
+

Definition at line 128 of file PSO.h.

+
128 {
+
129 double* a = &x[0];
+
130 return CalcChi2(a);
+
131 };
PSO::CalcChi2
double CalcChi2(const double *x)
Chi2 calculation over all included samples and syst objects.
Definition PSO.cpp:516
@@ -780,13 +780,13 @@

-

Definition at line 120 of file PSO.h.

-
120 {
-
121 for (size_t i = 0; i < vec1.size(); ++i) {
-
122 vec1[i] += vec2[i] + vec3[i] + vec4[i];
-
123 }
-
124 return vec1;
-
125 };
+

Definition at line 121 of file PSO.h.

+
121 {
+
122 for (size_t i = 0; i < vec1.size(); ++i) {
+
123 vec1[i] += vec2[i] + vec3[i] + vec4[i];
+
124 }
+
125 return vec1;
+
126 };
@@ -813,11 +813,11 @@

-

Definition at line 81 of file PSO.h.

-
81 {
-
82 return best_particle;
-
83 }
-
PSO::best_particle
particle * best_particle
Definition PSO.h:135
+

Definition at line 82 of file PSO.h.

+
82 {
+
83 return best_particle;
+
84 }
+
PSO::best_particle
particle * best_particle
Definition PSO.h:136
@@ -848,8 +848,8 @@

LikelihoodFit.

-

Definition at line 132 of file PSO.h.

-
132{return "PSO";};
+

Definition at line 133 of file PSO.h.

+
133{return "PSO";};
@@ -969,16 +969,16 @@

140 }
141 }
142}
-
FitterBase::random
TRandom3 * random
Random number.
Definition FitterBase.h:137
-
FitterBase::systematics
std::vector< covarianceBase * > systematics
Systematic holder.
Definition FitterBase.h:122
-
PSO::ranges_max
std::vector< double > ranges_max
Definition PSO.h:139
-
PSO::fixed
std::vector< bool > fixed
Definition PSO.h:138
-
PSO::set_best_particle
void set_best_particle(particle *n)
Definition PSO.h:84
-
PSO::system
std::vector< particle * > system
Definition PSO.h:141
-
PSO::fBestValue
double fBestValue
Definition PSO.h:136
-
PSO::ranges_min
std::vector< double > ranges_min
Definition PSO.h:140
-
PSO::prior
std::vector< double > prior
Definition PSO.h:137
-
particle
Class particle - stores the position, velocity and personal best With functions which move particle a...
Definition PSO.h:17
+
FitterBase::random
TRandom3 * random
Random number.
Definition FitterBase.h:138
+
FitterBase::systematics
std::vector< covarianceBase * > systematics
Systematic holder.
Definition FitterBase.h:123
+
PSO::ranges_max
std::vector< double > ranges_max
Definition PSO.h:140
+
PSO::fixed
std::vector< bool > fixed
Definition PSO.h:139
+
PSO::set_best_particle
void set_best_particle(particle *n)
Definition PSO.h:85
+
PSO::system
std::vector< particle * > system
Definition PSO.h:142
+
PSO::fBestValue
double fBestValue
Definition PSO.h:137
+
PSO::ranges_min
std::vector< double > ranges_min
Definition PSO.h:141
+
PSO::prior
std::vector< double > prior
Definition PSO.h:138
+
particle
Class particle - stores the position, velocity and personal best With functions which move particle a...
Definition PSO.h:18
@@ -1019,9 +1019,9 @@

548
549 return llh;
550}
-
FitterBase::stepClock
TStopwatch * stepClock
tells how long single step/fit iteration took
Definition FitterBase.h:132
-
FitterBase::accProb
double accProb
current acceptance prob
Definition FitterBase.h:104
-
FitterBase::stepTime
double stepTime
Time of single step.
Definition FitterBase.h:134
+
FitterBase::stepClock
TStopwatch * stepClock
tells how long single step/fit iteration took
Definition FitterBase.h:133
+
FitterBase::accProb
double accProb
current acceptance prob
Definition FitterBase.h:105
+
FitterBase::stepTime
double stepTime
Time of single step.
Definition FitterBase.h:135
@@ -1086,17 +1086,17 @@

423 std::cout << " Dim " << i << " = " << std::setprecision(10) << get_best_particle()->get_personal_best_position()[i] << " +" << uncertainties[i][1] << ", -" << uncertainties[i][0] << std::endl;
424 }
425}
-
FitterBase::accCount
int accCount
counts accepted steps
Definition FitterBase.h:106
-
FitterBase::step
unsigned int step
current state
Definition FitterBase.h:98
-
FitterBase::logLCurr
double logLCurr
current likelihood
Definition FitterBase.h:100
-
FitterBase::auto_save
int auto_save
auto save every N steps
Definition FitterBase.h:146
-
FitterBase::outTree
TTree * outTree
Output tree with posteriors.
Definition FitterBase.h:144
-
PSO::get_best_particle
particle * get_best_particle()
Definition PSO.h:81
-
PSO::uncertainties
std::vector< std::vector< double > > uncertainties
Definition PSO.h:148
+
FitterBase::accCount
int accCount
counts accepted steps
Definition FitterBase.h:107
+
FitterBase::step
unsigned int step
current state
Definition FitterBase.h:99
+
FitterBase::logLCurr
double logLCurr
current likelihood
Definition FitterBase.h:101
+
FitterBase::auto_save
int auto_save
auto save every N steps
Definition FitterBase.h:147
+
FitterBase::outTree
TTree * outTree
Output tree with posteriors.
Definition FitterBase.h:145
+
PSO::get_best_particle
particle * get_best_particle()
Definition PSO.h:82
+
PSO::uncertainties
std::vector< std::vector< double > > uncertainties
Definition PSO.h:149
PSO::bisection
std::vector< std::vector< double > > bisection(std::vector< double >position, double minimum, double range, double precision)
Definition PSO.cpp:144
PSO::swarmIterate
double swarmIterate()
Definition PSO.cpp:321
-
particle::get_personal_best_position
std::vector< double > get_personal_best_position()
Definition PSO.h:36
-
particle::get_personal_best_value
double get_personal_best_value()
Definition PSO.h:44
+
particle::get_personal_best_position
std::vector< double > get_personal_best_position()
Definition PSO.h:37
+
particle::get_personal_best_value
double get_personal_best_value()
Definition PSO.h:45
@@ -1150,9 +1150,9 @@

40}
LikelihoodFit::PrepareFit
void PrepareFit()
prepare output and perform sanity checks
Definition LikelihoodFit.cpp:21
PSO::init
void init()
Definition PSO.cpp:43
-
PSO::paramlist
std::vector< double * > paramlist
Definition PSO.h:152
-
PSO::vel
double vel[kMaxParticles]
Definition PSO.h:153
-
PSO::par
double * par
Definition PSO.h:154
+
PSO::paramlist
std::vector< double * > paramlist
Definition PSO.h:153
+
PSO::vel
double vel[kMaxParticles]
Definition PSO.h:154
+
PSO::par
double * par
Definition PSO.h:155
PSO::run
void run()
Definition PSO.cpp:381
PSO::WriteOutput
void WriteOutput()
Definition PSO.cpp:427
@@ -1182,10 +1182,10 @@

-

Definition at line 84 of file PSO.h.

-
84 {
-
85 best_particle = n;
-
86 }
+

Definition at line 85 of file PSO.h.

+
85 {
+
86 best_particle = n;
+
87 }
@@ -1264,10 +1264,10 @@

377
378 return mean_dist_sq;
379}
-
PSO::vector_add
std::vector< double > vector_add(std::vector< double > v1, std::vector< double > v2)
Definition PSO.h:104
-
PSO::vector_subtract
std::vector< double > vector_subtract(std::vector< double > v1, std::vector< double > v2)
Definition PSO.h:109
-
PSO::vector_multiply
std::vector< double > vector_multiply(std::vector< double > velocity, double mul)
Definition PSO.h:99
-
PSO::three_vector_addition
std::vector< double > three_vector_addition(std::vector< double > vec1, std::vector< double > vec2, std::vector< double > vec3)
Definition PSO.h:114
+
PSO::vector_add
std::vector< double > vector_add(std::vector< double > v1, std::vector< double > v2)
Definition PSO.h:105
+
PSO::vector_subtract
std::vector< double > vector_subtract(std::vector< double > v1, std::vector< double > v2)
Definition PSO.h:110
+
PSO::vector_multiply
std::vector< double > vector_multiply(std::vector< double > velocity, double mul)
Definition PSO.h:100
+
PSO::three_vector_addition
std::vector< double > three_vector_addition(std::vector< double > vec1, std::vector< double > vec2, std::vector< double > vec3)
Definition PSO.h:115
@@ -1311,13 +1311,13 @@

-

Definition at line 114 of file PSO.h.

-
114 {
-
115 for (size_t i = 0; i < vec1.size(); ++i) {
-
116 vec1[i] += vec2[i] + vec3[i];
-
117 }
-
118 return vec1;
-
119 };
+

Definition at line 115 of file PSO.h.

+
115 {
+
116 for (size_t i = 0; i < vec1.size(); ++i) {
+
117 vec1[i] += vec2[i] + vec3[i];
+
118 }
+
119 return vec1;
+
120 };
@@ -1410,12 +1410,12 @@

-

Definition at line 104 of file PSO.h.

-
104 {
-
105 std::vector<double> v3;
-
106 transform(v1.begin(), v1.end(), v2.begin(), back_inserter(v3), std::plus<double>());
-
107 return v3;
-
108 };
+

Definition at line 105 of file PSO.h.

+
105 {
+
106 std::vector<double> v3;
+
107 transform(v1.begin(), v1.end(), v2.begin(), back_inserter(v3), std::plus<double>());
+
108 return v3;
+
109 };
@@ -1453,11 +1453,11 @@

-

Definition at line 99 of file PSO.h.

-
99 {
-
100 transform(velocity.begin(),velocity.end(),velocity.begin(),std::bind1st(std::multiplies<double>(),mul));
-
101 return velocity;
-
102 };
+

Definition at line 100 of file PSO.h.

+
100 {
+
101 transform(velocity.begin(),velocity.end(),velocity.begin(),std::bind1st(std::multiplies<double>(),mul));
+
102 return velocity;
+
103 };
@@ -1495,12 +1495,12 @@

-

Definition at line 109 of file PSO.h.

-
109 {
-
110 std::vector<double> v3 ;
-
111 transform(v1.begin(), v1.end(), v2.begin(), back_inserter(v3), std::minus<double>());
-
112 return v3;
-
113 };
+

Definition at line 110 of file PSO.h.

+
110 {
+
111 std::vector<double> v3 ;
+
112 transform(v1.begin(), v1.end(), v2.begin(), back_inserter(v3), std::minus<double>());
+
113 return v3;
+
114 };
@@ -1606,7 +1606,7 @@

510 SaveOutput();
511}
FitterBase::SaveOutput
void SaveOutput()
Save output and close files.
Definition FitterBase.cpp:241
-
FitterBase::outputFile
TFile * outputFile
Output.
Definition FitterBase.h:140
+
FitterBase::outputFile
TFile * outputFile
Output.
Definition FitterBase.h:141
@@ -1631,7 +1631,7 @@

-

Definition at line 135 of file PSO.h.

+

Definition at line 136 of file PSO.h.

@@ -1655,7 +1655,7 @@

-

Definition at line 136 of file PSO.h.

+

Definition at line 137 of file PSO.h.

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-

Definition at line 147 of file PSO.h.

+

Definition at line 148 of file PSO.h.

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-

Definition at line 145 of file PSO.h.

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Definition at line 146 of file PSO.h.

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-

Definition at line 156 of file PSO.h.

+

Definition at line 157 of file PSO.h.

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Definition at line 142 of file PSO.h.

+

Definition at line 143 of file PSO.h.

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-

Definition at line 146 of file PSO.h.

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Definition at line 147 of file PSO.h.

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-

Definition at line 138 of file PSO.h.

+

Definition at line 139 of file PSO.h.

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-

Definition at line 143 of file PSO.h.

+

Definition at line 144 of file PSO.h.

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-

Definition at line 150 of file PSO.h.

+

Definition at line 151 of file PSO.h.

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-

Definition at line 144 of file PSO.h.

+

Definition at line 145 of file PSO.h.

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Definition at line 151 of file PSO.h.

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Definition at line 152 of file PSO.h.

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-

Definition at line 154 of file PSO.h.

+

Definition at line 155 of file PSO.h.

@@ -1943,7 +1943,7 @@

-

Definition at line 152 of file PSO.h.

+

Definition at line 153 of file PSO.h.

@@ -1967,7 +1967,7 @@

-

Definition at line 137 of file PSO.h.

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Definition at line 138 of file PSO.h.

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-

Definition at line 139 of file PSO.h.

+

Definition at line 140 of file PSO.h.

@@ -2015,7 +2015,7 @@

-

Definition at line 140 of file PSO.h.

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Definition at line 141 of file PSO.h.

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Definition at line 141 of file PSO.h.

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Definition at line 142 of file PSO.h.

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Definition at line 148 of file PSO.h.

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Definition at line 149 of file PSO.h.

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Definition at line 153 of file PSO.h.

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Definition at line 154 of file PSO.h.

diff --git a/classSMonolith.html b/classSMonolith.html index d5a4ee454..cdf507ddb 100644 --- a/classSMonolith.html +++ b/classSMonolith.html @@ -339,8 +339,8 @@

196 std::vector<std::vector<TSpline3_red*> > ReducedSpline = ReduceTSpline3(MasterSpline);
197 PrepareForGPU(ReducedSpline);
198}
-
MACH3LOG_INFO
#define MACH3LOG_INFO
Definition MaCh3Logger.h:13
-
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:18
+
MACH3LOG_INFO
#define MACH3LOG_INFO
Definition MaCh3Logger.h:16
+
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:21
SMonolith::ReduceTSpline3
std::vector< std::vector< TSpline3_red * > > ReduceTSpline3(std::vector< std::vector< TSpline3 * > > &MasterSpline)
CW: Reduced the TSpline3 to TSpline3_red.
Definition SplineMonolith.cpp:1292
SMonolith::Initialise
void Initialise()
KS: Set everything to null etc.
Definition SplineMonolith.cpp:147
SMonolith::PrepareForGPU
void PrepareForGPU(std::vector< std::vector< TSpline3_red * > > &MasterSpline)
CW: Prepare the TSpline3_red objects for the GPU.
Definition SplineMonolith.cpp:250
@@ -587,8 +587,8 @@

SMonolith::gpu_coeff_many
float * gpu_coeff_many
GPU arrays to hold other coefficients.
Definition SplineMonolith.h:195
SMonolith::index_cpu
int * index_cpu
holds the index for good splines; don't do unsigned since starts with negative value!
Definition SplineMonolith.h:150
SMonolith::cpu_coeff_x
std::vector< float > cpu_coeff_x
KS: CPU arrays to hold X coefficient.
Definition SplineMonolith.h:189
-
CleanupGPU_SepMany
__host__ void CleanupGPU_SepMany(short int *gpu_paramNo_arr, unsigned int *gpu_nKnots_arr, float *gpu_x_array, float *gpu_many_array, float *gpu_total_weights, unsigned int *gpu_nParamPerEvent, float *cpu_total_weights, float *gpu_weights)
Clean up the {x},{ybcd} arrays.
Definition gpuSplineUtils.cu:805
-
CleanupGPU_Segments
__host__ void CleanupGPU_Segments(short int *segment, float *vals)
Clean up pinned variables at CPU.
Definition gpuSplineUtils.cu:841
+
CleanupGPU_SepMany
__host__ void CleanupGPU_SepMany(short int *gpu_paramNo_arr, unsigned int *gpu_nKnots_arr, float *gpu_x_array, float *gpu_many_array, float *gpu_total_weights, unsigned int *gpu_nParamPerEvent, float *cpu_total_weights, float *gpu_weights)
Clean up the {x},{ybcd} arrays.
Definition gpuSplineUtils.cu:807
+
CleanupGPU_Segments
__host__ void CleanupGPU_Segments(short int *segment, float *vals)
Clean up pinned variables at CPU.
Definition gpuSplineUtils.cu:843
@@ -1074,7 +1074,7 @@

1421 #endif
1422}
isFlat
std::vector< bool > isFlat
Definition GetPenaltyTerm.cpp:39
-
MACH3LOG_ERROR
#define MACH3LOG_ERROR
Definition MaCh3Logger.h:15
+
MACH3LOG_ERROR
#define MACH3LOG_ERROR
Definition MaCh3Logger.h:18
@@ -1444,8 +1444,8 @@

618 PrepareForGPU_TSpline3();
619}
SMonolith::PrepareForGPU_TSpline3
void PrepareForGPU_TSpline3()
CW: The shared initialiser from constructors of TSpline3 and TSpline3_red.
Definition SplineMonolith.cpp:734
-
InitGPU_Segments
__host__ void InitGPU_Segments(short int **segment)
Definition gpuSplineUtils.cu:226
-
InitGPU_Vals
__host__ void InitGPU_Vals(float **vals)
Definition gpuSplineUtils.cu:236
+
InitGPU_Segments
__host__ void InitGPU_Segments(short int **segment)
Allocate memory for spline segments.
Definition gpuSplineUtils.cu:232
+
InitGPU_Vals
__host__ void InitGPU_Vals(float **vals)
Definition gpuSplineUtils.cu:241
FastSplineInfo
CW: Add a struct to hold info about the splinified xsec parameters and help with FindSplineSegment.
Definition SplineStructs.h:9
@@ -2059,7 +2059,7 @@

477
478 PrepareForGPU_TSpline3();
479}
-
MACH3LOG_WARN
#define MACH3LOG_WARN
Definition MaCh3Logger.h:14
+
MACH3LOG_WARN
#define MACH3LOG_WARN
Definition MaCh3Logger.h:17
SMonolith::PrepareSplineFile
void PrepareSplineFile()
KS: Prepare spline file that can be used for fast loading.
Definition SplineMonolith.cpp:623
SMonolith::getSplineCoeff_SepMany
void getSplineCoeff_SepMany(TSpline3_red *&spl, int &nPoints, float *&xArray, float *&manyArray)
CW: This loads up coefficients into two arrays: one x array and one yabcd array.
Definition SplineMonolith.cpp:1368
TSpline3_red
CW: Reduced TSpline3 class.
Definition SplineStructs.h:260
@@ -2158,8 +2158,8 @@

1083
1084 return;
1085}
-
CopyToGPU_TF1
__host__ void CopyToGPU_TF1(float *gpu_coeffs, short int *gpu_paramNo_arr, short int *gpu_nPoints_arr, std::vector< float > cpu_coeffs, std::vector< short int > paramNo_arr, std::vector< short int > nPoints_arr, int n_events, std::vector< unsigned int > cpu_nParamPerEvent, unsigned int *gpu_nParamPerEvent, int n_params, unsigned int n_splines, short int _max_knots)
Copy to GPU for x array and separate ybcd array.
Definition gpuSplineUtils.cu:357
-
InitGPU_TF1
__host__ void InitGPU_TF1(float **gpu_coeffs, short int **gpu_paramNo_arr, short int **gpu_nPoints_arr, float **gpu_weights, float **cpu_total_weights, float **gpu_total_weights, int n_events, unsigned int **gpu_nParamPerEvent, unsigned int n_splines)
Initialiser when using the x array and combined y,b,c,d array.
Definition gpuSplineUtils.cu:168
+
CopyToGPU_TF1
__host__ void CopyToGPU_TF1(float *gpu_coeffs, short int *gpu_paramNo_arr, short int *gpu_nPoints_arr, std::vector< float > cpu_coeffs, std::vector< short int > paramNo_arr, std::vector< short int > nPoints_arr, int n_events, std::vector< unsigned int > cpu_nParamPerEvent, unsigned int *gpu_nParamPerEvent, int n_params, unsigned int n_splines, short int _max_knots)
Copy to GPU for x array and separate ybcd array.
Definition gpuSplineUtils.cu:362
+
InitGPU_TF1
__host__ void InitGPU_TF1(float **gpu_coeffs, short int **gpu_paramNo_arr, short int **gpu_nPoints_arr, float **gpu_weights, float **cpu_total_weights, float **gpu_total_weights, int n_events, unsigned int **gpu_nParamPerEvent, unsigned int n_splines)
Initialiser when using the x array and combined y,b,c,d array.
Definition gpuSplineUtils.cu:174
@@ -2271,8 +2271,8 @@

813#endif
814 return;
815}
-
CopyToGPU_SepMany
__host__ void CopyToGPU_SepMany(short int *gpu_paramNo_arr, unsigned int *gpu_nKnots_arr, float *gpu_x_array, float *gpu_many_array, std::vector< short int > paramNo_arr, std::vector< unsigned int > nKnots_arr, std::vector< float > cpu_x_array, std::vector< float > cpu_many_array, int n_events, std::vector< unsigned int > cpu_nParamPerEvent, unsigned int *gpu_nParamPerEvent, int n_params, unsigned int n_splines, short int spline_size, unsigned int sizeof_array)
Copy to GPU for x array and separate ybcd array.
Definition gpuSplineUtils.cu:251
-
InitGPU_SepMany
__host__ void InitGPU_SepMany(float **gpu_x_array, float **gpu_many_array, float **gpu_weights, short int **gpu_paramNo_arr, unsigned int **gpu_nKnots_arr, float **cpu_total_weights, float **gpu_total_weights, int n_events, unsigned int **gpu_nParamPerEvent, unsigned int sizeof_array, unsigned int n_splines, int Eve_size)
Initialiser when using the x array and combined y,b,c,d array.
Definition gpuSplineUtils.cu:106
+
CopyToGPU_SepMany
__host__ void CopyToGPU_SepMany(short int *gpu_paramNo_arr, unsigned int *gpu_nKnots_arr, float *gpu_x_array, float *gpu_many_array, std::vector< short int > paramNo_arr, std::vector< unsigned int > nKnots_arr, std::vector< float > cpu_x_array, std::vector< float > cpu_many_array, int n_events, std::vector< unsigned int > cpu_nParamPerEvent, unsigned int *gpu_nParamPerEvent, int n_params, unsigned int n_splines, short int spline_size, unsigned int sizeof_array)
Copy to GPU for x array and separate ybcd array.
Definition gpuSplineUtils.cu:256
+
InitGPU_SepMany
__host__ void InitGPU_SepMany(float **gpu_x_array, float **gpu_many_array, float **gpu_weights, short int **gpu_paramNo_arr, unsigned int **gpu_nKnots_arr, float **cpu_total_weights, float **gpu_total_weights, int n_events, unsigned int **gpu_nParamPerEvent, unsigned int sizeof_array, unsigned int n_splines, int Eve_size)
Initialiser when using the x array and combined y,b,c,d array.
Definition gpuSplineUtils.cu:112
@@ -2939,7 +2939,7 @@

45 #endif
46 return;
47 };
-
SynchroniseSplines
__host__ void SynchroniseSplines()
Make sure all Cuda threads finished execution.
Definition gpuSplineUtils.cu:795
+
SynchroniseSplines
__host__ void SynchroniseSplines()
Make sure all Cuda threads finished execution.
Definition gpuSplineUtils.cu:797
diff --git a/classSampleSummary.html b/classSampleSummary.html index 23af9fbad..31b085d48 100644 --- a/classSampleSummary.html +++ b/classSampleSummary.html @@ -699,7 +699,7 @@

173 Debug = 0;
174}
_int_
#define _int_
Definition Structs.h:12
-
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:18
+
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:21
SampleSummary::llh_data_predfluc
double * llh_data_predfluc
Data vs Fluctuated Predictive.
Definition SampleSummary.h:273
SampleSummary::RandomHist
TH1D * RandomHist
Holds the history of which entries have been drawn in the MCMC file.
Definition SampleSummary.h:224
SampleSummary::lnLHist
TH1D * lnLHist
The histogram containing the lnL for each throw.
Definition SampleSummary.h:179
@@ -903,7 +903,7 @@

290 delete[] llh_data_draw_ProjectX;
291 delete[] llh_drawfluc_draw_ProjectX;
292}
-
MaCh3Modes::GetNModes
int GetNModes()
KS: Get number of modes, keep in mind actual number is +1 greater due to unknown category.
Definition MaCh3Modes.h:43
+
MaCh3Modes::GetNModes
int GetNModes()
KS: Get number of modes, keep in mind actual number is +1 greater due to unknown category.
Definition MaCh3Modes.h:44
SampleSummary::llh_drawfluc_draw_ProjectX
double * llh_drawfluc_draw_ProjectX
Definition SampleSummary.h:288
SampleSummary::llh_data_draw_ProjectX
double * llh_data_draw_ProjectX
Projection X (most likely muon momentum) of LLH.
Definition SampleSummary.h:287
diff --git a/classTF1__red.html b/classTF1__red.html index bfc260e53..6c8ed6e4a 100644 --- a/classTF1__red.html +++ b/classTF1__red.html @@ -169,7 +169,7 @@

149 length = 0;
150 Par = NULL;
151 }
-
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:18
+
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:21
TF1_red::Par
_float_ * Par
The parameters.
Definition SplineStructs.h:251
TF1_red::length
_int_ length
Definition SplineStructs.h:252
diff --git a/classTSpline3__red.html b/classTSpline3__red.html index 997e0c5b8..3ea4b2a1a 100644 --- a/classTSpline3__red.html +++ b/classTSpline3__red.html @@ -183,7 +183,7 @@

267 XPos = NULL;
268 YResp = NULL;
269 }
-
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:18
+
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:21
TSpline3_red::nPoints
_int_ nPoints
Number of points/knot in TSpline3.
Definition SplineStructs.h:654
TSpline3_red::YResp
_float_ * YResp
y-value for each knot
Definition SplineStructs.h:660
TSpline3_red::Par
_float_ ** Par
Always uses a third order polynomial, so hard-code the number of coefficients in implementation.
Definition SplineStructs.h:656
diff --git a/classThrowParms.html b/classThrowParms.html index c0faba185..74a1ff42c 100644 --- a/classThrowParms.html +++ b/classThrowParms.html @@ -174,7 +174,7 @@

27 chel_dec = new TMatrixD(chdcmp.GetU());
28 CheloskyDecomp((*chel_dec));
29}
-
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:18
+
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:21
ThrowParms::pvals
TVectorD * pvals
Definition ThrowParms.h:21
ThrowParms::chel_dec
TMatrixD * chel_dec
Definition ThrowParms.h:23
diff --git a/classTruncated__Spline.html b/classTruncated__Spline.html index cc346a676..6404a247a 100644 --- a/classTruncated__Spline.html +++ b/classTruncated__Spline.html @@ -240,7 +240,7 @@

679 :TSpline3_red(spline, Param)
680 {
681 }
-
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:18
+
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:21
diff --git a/classXSecStruct.html b/classXSecStruct.html index 39435b4de..e5d47c554 100644 --- a/classXSecStruct.html +++ b/classXSecStruct.html @@ -165,7 +165,7 @@

35 Func[i] = NULL;
36 }
37 }
-
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:18
+
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:21
XSecStruct::nParams
_int_ nParams
Number of parameters.
Definition SplineStructs.h:85
XSecStruct::Func
T * Func
The function.
Definition SplineStructs.h:87
diff --git a/classadaptive__mcmc_1_1AdaptiveMCMCHandler-members.html b/classadaptive__mcmc_1_1AdaptiveMCMCHandler-members.html new file mode 100644 index 000000000..4cbb9993d --- /dev/null +++ b/classadaptive__mcmc_1_1AdaptiveMCMCHandler-members.html @@ -0,0 +1,107 @@ + + + + + + + +MaCh3: Member List + + + + + + + + + +
+
+

 ▼Nadaptive_mcmcContains information about adaptive covariance matrix
 CAdaptiveMCMCStructStruct encapsulating all adaptive MCMC information
 ▼Nadaptive_mcmc
 CAdaptiveMCMCHandlerContains information about adaptive covariance matrix
 CBaseFuncPar
 CBox
 CCorner
GetNXSec()MCMCProcessorinline
GetOSC()MCMCProcessorinline
GetOscCov() constMCMCProcessorinline
GetParamIndexFromName(const std::string Name)MCMCProcessor
GetParamIndexFromName(const std::string &Name)MCMCProcessor
GetPolarPlot(const std::vector< std::string > &ParNames)MCMCProcessor
GetPostfit(TVectorD *&Central, TVectorD *&Errors, TVectorD *&Central_Gauss, TVectorD *&Errors_Gauss, TVectorD *&Peaks)MCMCProcessor
GetPostfit_Ind(TVectorD *&Central, TVectorD *&Errors, TVectorD *&Peaks, ParameterEnum kParam)MCMCProcessor
void GetNthParameter (const int param, double &Prior, double &PriorError, TString &Title)
 Get properties of parameter by passing it number.
 
int GetParamIndexFromName (const std::string Name)
 Get parameter number based on name.
 
int GetParamIndexFromName (const std::string &Name)
 Get parameter number based on name.
 
int GetnEntries ()
 Get Number of entries that Chain has, for merged chains will not be the same Nsteps.
 
(const std::string const std::string &  Name)
GeneratorMaCh3Modesprivate
GetMaCh3ModeFancyName(const int Index)MaCh3Modes
GetMaCh3ModeName(const int Index)MaCh3Modes
GetMode(std::string name)MaCh3Modes
GetMode(const std::string &name)MaCh3Modes
GetModeFromGenerator(const int Index)MaCh3Modes
GetName() constMaCh3Modesinline
GetNModes()MaCh3Modesinline
int GetNModes ()
 KS: Get number of modes, keep in mind actual number is +1 greater due to unknown category.
 
MaCh3Modes_t GetMode (std::string name)
 KS: Get mode number based on name, if mode not known you will get UNKNOWN_BAD.
 
MaCh3Modes_t GetMode (const std::string &name)
 KS: Get mode number based on name, if mode not known you will get UNKNOWN_BAD.
 
std::string GetMaCh3ModeName (const int Index)
 KS: Get normal name of mode, if mode not known you will get UNKNOWN_BAD.
 
(std::string const std::string &  name)
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adaptive_mcmc::AdaptiveMCMCHandler Member List
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This is the complete list of members for adaptive_mcmc::AdaptiveMCMCHandler, including all inherited members.

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adapt_block_matrix_indicesadaptive_mcmc::AdaptiveMCMCHandler
adapt_block_sizesadaptive_mcmc::AdaptiveMCMCHandler
adaptive_covarianceadaptive_mcmc::AdaptiveMCMCHandler
adaptive_update_stepadaptive_mcmc::AdaptiveMCMCHandler
AdaptiveMCMCHandler()adaptive_mcmc::AdaptiveMCMCHandler
CreateNewAdaptiveCovariance(const int Npars)adaptive_mcmc::AdaptiveMCMCHandler
end_adaptive_updateadaptive_mcmc::AdaptiveMCMCHandler
InitFromConfig(const YAML::Node &adapt_manager, const std::string &matrix_name_str, const int Npars)adaptive_mcmc::AdaptiveMCMCHandler
par_meansadaptive_mcmc::AdaptiveMCMCHandler
Print()adaptive_mcmc::AdaptiveMCMCHandler
SaveAdaptiveToFile(const TString &outFileName, const TString &systematicName)adaptive_mcmc::AdaptiveMCMCHandler
SetAdaptiveBlocks(std::vector< std::vector< int > > block_indices, const int Npars)adaptive_mcmc::AdaptiveMCMCHandler
SetThrowMatrixFromFile(const std::string &matrix_file_name, const std::string &matrix_name, const std::string &means_name, bool &use_adaptive, const int Npars)adaptive_mcmc::AdaptiveMCMCHandler
start_adaptive_throwadaptive_mcmc::AdaptiveMCMCHandler
start_adaptive_updateadaptive_mcmc::AdaptiveMCMCHandler
UpdateAdaptiveCovariance(const std::vector< double > &_fCurrVal, const int steps_post_burn, const int Npars)adaptive_mcmc::AdaptiveMCMCHandler
~AdaptiveMCMCHandler()adaptive_mcmc::AdaptiveMCMCHandler
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+ + diff --git a/classadaptive__mcmc_1_1AdaptiveMCMCHandler.html b/classadaptive__mcmc_1_1AdaptiveMCMCHandler.html new file mode 100644 index 000000000..f6da74602 --- /dev/null +++ b/classadaptive__mcmc_1_1AdaptiveMCMCHandler.html @@ -0,0 +1,822 @@ + + + + + + + +MaCh3: adaptive_mcmc::AdaptiveMCMCHandler Class Reference + + + + + + + + + +
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+Public Member Functions | +Public Attributes | +List of all members
+
adaptive_mcmc::AdaptiveMCMCHandler Class Reference
+
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+ +

Contains information about adaptive covariance matrix. + More...

+ +

#include <AdaptiveMCMCHandler.h>

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

+Public Member Functions

 AdaptiveMCMCHandler ()
 Constructor.
 
 ~AdaptiveMCMCHandler ()
 Destructor.
 
void Print ()
 Print all class members.
 
void InitFromConfig (const YAML::Node &adapt_manager, const std::string &matrix_name_str, const int Npars)
 Read initial values from config file.
 
void CreateNewAdaptiveCovariance (const int Npars)
 If we don't have a covariance matrix to start from for adaptive tune we need to make one!
 
void SetAdaptiveBlocks (std::vector< std::vector< int > > block_indices, const int Npars)
 HW: sets adaptive block matrix.
 
void SaveAdaptiveToFile (const TString &outFileName, const TString &systematicName)
 HW: Save adaptive throw matrix to file.
 
void SetThrowMatrixFromFile (const std::string &matrix_file_name, const std::string &matrix_name, const std::string &means_name, bool &use_adaptive, const int Npars)
 sets throw matrix from a file
 
void UpdateAdaptiveCovariance (const std::vector< double > &_fCurrVal, const int steps_post_burn, const int Npars)
 Method to update adaptive MCMC.
 
+ + + + + + + + + + + + + + + + + + + + + + + + +

+Public Attributes

int start_adaptive_throw
 
int start_adaptive_update
 When do we stop update the adaptive matrix.
 
int end_adaptive_update
 Steps between changing throw matrix.
 
int adaptive_update_step
 Steps between changing throw matrix.
 
std::vector< int > adapt_block_matrix_indices
 Indices for block-matrix adaption.
 
std::vector< int > adapt_block_sizes
 Size of blocks for adaption.
 
std::vector< double > par_means
 Mean values for all parameters.
 
TMatrixDSym * adaptive_covariance
 Full adaptive covariance matrix.
 
+

Detailed Description

+

Contains information about adaptive covariance matrix.

+
See also
An adaptive Metropolis algorithm, H.Haario et al., 2001 for more info!
+

struct encapsulating all adaptive MCMC information

+ +

Definition at line 13 of file AdaptiveMCMCHandler.h.

+

Constructor & Destructor Documentation

+ +

◆ AdaptiveMCMCHandler()

+ +
+
+ + + + + + + +
adaptive_mcmc::AdaptiveMCMCHandler::AdaptiveMCMCHandler ()
+
+ +

Constructor.

+ +

Definition at line 6 of file AdaptiveMCMCHandler.cpp.

+
6 {
+
7// ********************************************
+
8 start_adaptive_throw = 0;
+
9 start_adaptive_update = 0;
+
10 end_adaptive_update = 1;
+
11 adaptive_update_step = 1000;
+
12
+
13 par_means = {};
+
14 adaptive_covariance = nullptr;
+
15}
+
adaptive_mcmc::AdaptiveMCMCHandler::par_means
std::vector< double > par_means
Mean values for all parameters.
Definition AdaptiveMCMCHandler.h:78
+
adaptive_mcmc::AdaptiveMCMCHandler::start_adaptive_update
int start_adaptive_update
When do we stop update the adaptive matrix.
Definition AdaptiveMCMCHandler.h:62
+
adaptive_mcmc::AdaptiveMCMCHandler::start_adaptive_throw
int start_adaptive_throw
Definition AdaptiveMCMCHandler.h:59
+
adaptive_mcmc::AdaptiveMCMCHandler::end_adaptive_update
int end_adaptive_update
Steps between changing throw matrix.
Definition AdaptiveMCMCHandler.h:65
+
adaptive_mcmc::AdaptiveMCMCHandler::adaptive_update_step
int adaptive_update_step
Steps between changing throw matrix.
Definition AdaptiveMCMCHandler.h:68
+
adaptive_mcmc::AdaptiveMCMCHandler::adaptive_covariance
TMatrixDSym * adaptive_covariance
Full adaptive covariance matrix.
Definition AdaptiveMCMCHandler.h:81
+
+
+
+ +

◆ ~AdaptiveMCMCHandler()

+ +
+
+ + + + + + + +
adaptive_mcmc::AdaptiveMCMCHandler::~AdaptiveMCMCHandler ()
+
+ +

Destructor.

+ +

Definition at line 18 of file AdaptiveMCMCHandler.cpp.

+
18 {
+
19// ********************************************
+
20 if(adaptive_covariance != nullptr) {
+
21 delete adaptive_covariance;
+
22 }
+
23}
+
+
+
+

Member Function Documentation

+ +

◆ CreateNewAdaptiveCovariance()

+ +
+
+ + + + + + + + +
void adaptive_mcmc::AdaptiveMCMCHandler::CreateNewAdaptiveCovariance (const int Npars)
+
+ +

If we don't have a covariance matrix to start from for adaptive tune we need to make one!

+ +

Definition at line 57 of file AdaptiveMCMCHandler.cpp.

+
57 {
+
58// ********************************************
+
59 adaptive_covariance = new TMatrixDSym(Npars);
+
60 adaptive_covariance->Zero();
+
61 par_means = std::vector<double>(Npars, 0);
+
62}
+
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:21
+
+
+
+ +

◆ InitFromConfig()

+ +
+
+ + + + + + + + + + + + + + + + + + + + + + + + +
void adaptive_mcmc::AdaptiveMCMCHandler::InitFromConfig (const YAML::Node & adapt_manager,
const std::string & matrix_name_str,
const int Npars 
)
+
+ +

Read initial values from config file.

+
Parameters
+ + +
adapt_managerConfig file from which we update matrix
+
+
+ +

Definition at line 27 of file AdaptiveMCMCHandler.cpp.

+
27 {
+
28// ********************************************
+
29 // setAdaptionDefaults();
+
30 if(GetFromManager<std::string>(adapt_manager["AdaptionOptions"]["Covariance"][matrix_name_str], "")==""){
+
31 MACH3LOG_WARN("Adaptive Settings not found for {}, this is fine if you don't want adaptive MCMC", matrix_name_str);
+
32 return;
+
33 }
+
34
+
35 // We"re going to grab this info from the YAML manager
+
36 if(GetFromManager<bool>(adapt_manager["AdaptionOptions"]["Covariance"][matrix_name_str]["DoAdaption"], false)) {
+
37 MACH3LOG_WARN("Not using adaption for {}", matrix_name_str);
+
38 return;
+
39 }
+
40
+
41 start_adaptive_throw = GetFromManager<int>(adapt_manager["AdaptionOptions"]["Settings"]["AdaptionStartThrow"], 10);
+
42 start_adaptive_update = GetFromManager<int>(adapt_manager["AdaptionOptions"]["Settings"]["AdaptionStartUpdate"], 0);
+
43 end_adaptive_update = GetFromManager<int>(adapt_manager["AdaptionOptions"]["Settings"]["AdaptionEndUpdate"], 10000);
+
44 adaptive_update_step = GetFromManager<int>(adapt_manager["AdaptionOptions"]["Settings"]["AdaptionUpdateStep"], 100);
+
45
+
46
+
47 // We also want to check for "blocks" by default all parameters "know" about each other
+
48 // but we can split the matrix into independent block matrices
+
49
+
50 // We"ll set a dummy variable here
+
51 auto matrix_blocks = GetFromManager<std::vector<std::vector<int>>>(adapt_manager["AdaptionOptions"]["Settings"][matrix_name_str]["AdaptionUpdateStep"], {{}});
+
52
+
53 SetAdaptiveBlocks(matrix_blocks, Npars);
+
54}
+
MACH3LOG_WARN
#define MACH3LOG_WARN
Definition MaCh3Logger.h:17
+
adaptive_mcmc::AdaptiveMCMCHandler::SetAdaptiveBlocks
void SetAdaptiveBlocks(std::vector< std::vector< int > > block_indices, const int Npars)
HW: sets adaptive block matrix.
Definition AdaptiveMCMCHandler.cpp:66
+
+
+
+ +

◆ Print()

+ +
+
+ + + + + + + +
void adaptive_mcmc::AdaptiveMCMCHandler::Print ()
+
+ +

Print all class members.

+ +

Definition at line 221 of file AdaptiveMCMCHandler.cpp.

+
221 {
+
222// ********************************************
+
223 MACH3LOG_INFO("Adaptive MCMC Info:");
+
224 MACH3LOG_INFO("Throwing from New Matrix from Step : {}", start_adaptive_throw);
+
225 MACH3LOG_INFO("Adaption Matrix Start Update : {}", start_adaptive_update);
+
226 MACH3LOG_INFO("Adaption Matrix Ending Updates : {}", end_adaptive_update);
+
227 MACH3LOG_INFO("Steps Between Updates : {}", adaptive_update_step);
+
228}
+
MACH3LOG_INFO
#define MACH3LOG_INFO
Definition MaCh3Logger.h:16
+
+
+
+ +

◆ SaveAdaptiveToFile()

+ +
+
+ + + + + + + + + + + + + + + + + + +
void adaptive_mcmc::AdaptiveMCMCHandler::SaveAdaptiveToFile (const TString & outFileName,
const TString & systematicName 
)
+
+ +

HW: Save adaptive throw matrix to file.

+ +

Definition at line 108 of file AdaptiveMCMCHandler.cpp.

+
108 {
+
109// ********************************************
+
110 TFile* outFile = new TFile(outFileName, "UPDATE");
+
111 if(outFile->IsZombie()){
+
112 MACH3LOG_ERROR("Couldn't find {}", outFileName);
+
113 throw;
+
114 }
+
115 TVectorD* outMeanVec = new TVectorD((int)par_means.size());
+
116 for(int i = 0; i < (int)par_means.size(); i++){
+
117 (*outMeanVec)(i) = par_means[i];
+
118 }
+
119 outFile->cd();
+
120 adaptive_covariance->Write(systematicName+"_postfit_matrix");
+
121 outMeanVec->Write(systematicName+"_mean_vec");
+
122 outFile->Close();
+
123 delete outMeanVec;
+
124 delete outFile;
+
125}
+
MACH3LOG_ERROR
#define MACH3LOG_ERROR
Definition MaCh3Logger.h:18
+
+
+
+ +

◆ SetAdaptiveBlocks()

+ +
+
+ + + + + + + + + + + + + + + + + + +
void adaptive_mcmc::AdaptiveMCMCHandler::SetAdaptiveBlocks (std::vector< std::vector< int > > block_indices,
const int Npars 
)
+
+ +

HW: sets adaptive block matrix.

+
Parameters
+ + +
block_indicesValues for sub-matrix blocks
+
+
+ +

Definition at line 66 of file AdaptiveMCMCHandler.cpp.

+
66 {
+
67// ********************************************
+
68 /*
+
69 * In order to adapt efficient we want to setup our throw matrix to be a serious of block-diagonal (ish) matrices
+
70 *
+
71 * To do this we set sub-block in the config by parameter index. For example having
+
72 * [[0,4],[4, 6]] in your config will set up two blocks one with all indices 0<=i<4 and the other with 4<=i<6
+
73 */
+
74 // Set up block regions
+
75 adapt_block_matrix_indices = std::vector<int>(Npars, 0);
+
76
+
77 // Should also make a matrix of block sizes
+
78 adapt_block_sizes = std::vector<int>((int)block_indices.size()+1, 0);
+
79 adapt_block_sizes[0] = Npars;
+
80
+
81 if(block_indices.size()==0 || block_indices[0].size()==0) return;
+
82
+
83 // Now we loop over our blocks
+
84 for(int iblock=0; iblock<(int)block_indices.size(); iblock++){
+
85 // Loop over blocks in the block
+
86 for(int isubblock=0; isubblock<(int)block_indices[iblock].size()-1; isubblock+=2){
+
87 int block_lb = block_indices[iblock][isubblock];
+
88 int block_ub = block_indices[iblock][isubblock+1];
+
89
+
90 //std::cout<<block_lb<<" "<<block_ub<<std::endl;
+
91 if(block_lb > Npars || block_ub > Npars){
+
92 MACH3LOG_ERROR("Cannot set matrix block with edges {}, {} for matrix of size {}",
+
93 block_lb, block_ub, Npars);
+
94 throw MaCh3Exception(__FILE__, __LINE__);;
+
95 }
+
96 for(int ipar = block_lb; ipar < block_ub; ipar++){
+
97 adapt_block_matrix_indices[ipar] = iblock+1;
+
98 adapt_block_sizes[iblock+1] += 1;
+
99 adapt_block_sizes[0] -= 1;
+
100 }
+
101 }
+
102 }
+
103}
+
size
int size
Definition GetPenaltyTerm.cpp:42
+
MaCh3Exception
Custom exception class for MaCh3 errors.
Definition MaCh3Exception.h:12
+
adaptive_mcmc::AdaptiveMCMCHandler::adapt_block_matrix_indices
std::vector< int > adapt_block_matrix_indices
Indices for block-matrix adaption.
Definition AdaptiveMCMCHandler.h:71
+
adaptive_mcmc::AdaptiveMCMCHandler::adapt_block_sizes
std::vector< int > adapt_block_sizes
Size of blocks for adaption.
Definition AdaptiveMCMCHandler.h:74
+
+
+
+ +

◆ SetThrowMatrixFromFile()

+ +
+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
void adaptive_mcmc::AdaptiveMCMCHandler::SetThrowMatrixFromFile (const std::string & matrix_file_name,
const std::string & matrix_name,
const std::string & means_name,
bool & use_adaptive,
const int Npars 
)
+
+ +

sets throw matrix from a file

+
Parameters
+ + + + +
matrix_file_namename of file matrix lives in
matrix_namename of matrix in file
means_namename of means vec in file
+
+
+ +

Definition at line 130 of file AdaptiveMCMCHandler.cpp.

+
134 {
+
135// ********************************************
+
136 // Lets you set the throw matrix externally
+
137 // Open file
+
138 std::unique_ptr<TFile>matrix_file(new TFile(matrix_file_name.c_str()));
+
139 use_adaptive = true;
+
140
+
141 if(matrix_file->IsZombie()){
+
142 MACH3LOG_ERROR("Couldn't find {}", matrix_file_name);
+
143 throw;
+
144 }
+
145
+
146 // Next we grab our matrix
+
147 adaptive_covariance = static_cast<TMatrixDSym*>(matrix_file->Get(matrix_name.c_str()));
+
148 if(!adaptive_covariance){
+
149 MACH3LOG_ERROR("Couldn't find {} in {}", matrix_name, matrix_file_name);
+
150 throw;
+
151 }
+
152
+
153 // Finally we grab the means vector
+
154 TVectorD* means_vector = static_cast<TVectorD*>(matrix_file->Get(means_name.c_str()));
+
155
+
156 // This is fine to not exist!
+
157 if(means_vector){
+
158 // Yay our vector exists! Let's loop and fill it
+
159 // Should check this is done
+
160 if(means_vector->GetNrows()){
+
161 MACH3LOG_ERROR("External means vec size ({}) != matrix size ({})", means_vector->GetNrows(), Npars);
+
162 throw MaCh3Exception(__FILE__, __LINE__);
+
163 }
+
164
+
165 par_means = std::vector<double>(Npars);
+
166 for(int i = 0; i < Npars; i++){
+
167 par_means[i] = (*means_vector)(i);
+
168 }
+
169 MACH3LOG_INFO("Found Means in External File, Will be able to adapt");
+
170 }
+
171 // Totally fine if it doesn't exist, we just can't do adaption
+
172 else{
+
173 // We don't need a means vector, set the adaption=false
+
174 MACH3LOG_WARN("Cannot find means vector in {}, therefore I will not be able to adapt!", matrix_file_name);
+
175 use_adaptive = false;
+
176 }
+
177
+
178 matrix_file->Close();
+
179 MACH3LOG_INFO("Set up matrix from external file");
+
180}
+
+
+
+ +

◆ UpdateAdaptiveCovariance()

+ +
+
+ + + + + + + + + + + + + + + + + + + + + + + + +
void adaptive_mcmc::AdaptiveMCMCHandler::UpdateAdaptiveCovariance (const std::vector< double > & _fCurrVal,
const int steps_post_burn,
const int Npars 
)
+
+ +

Method to update adaptive MCMC.

+
See also
https://projecteuclid.org/journals/bernoulli/volume-7/issue-2/An-adaptive-Metropolis-algorithm/bj/1080222083.full
+
Parameters
+ + +
_fCurrValValue of each parameter necessary for updating throw matrix
+
+
+ +

Definition at line 184 of file AdaptiveMCMCHandler.cpp.

+
184 {
+
185// ********************************************
+
186 std::vector<double> par_means_prev = par_means;
+
187
+
188 #ifdef MULTITHREAD
+
189 #pragma omp parallel for
+
190 #endif
+
191 for(int iRow = 0; iRow < Npars; iRow++) {
+
192 par_means[iRow] = (_fCurrVal[iRow]+par_means[iRow]*steps_post_burn)/(steps_post_burn+1);
+
193 }
+
194
+
195 //Now we update the covariances using cov(x,y)=E(xy)-E(x)E(y)
+
196 #ifdef MULTITHREAD
+
197 #pragma omp parallel for
+
198 #endif
+
199 for(int irow = 0; irow < Npars; irow++){
+
200 int block = adapt_block_matrix_indices[irow];
+
201 // int scale_factor = 5.76/double(adapt_block_sizes[block]);
+
202 for(int icol = 0; icol <= irow; icol++){
+
203 double cov_val=0;
+
204 // Not in the same blocks
+
205 if(adapt_block_matrix_indices[icol] == block){
+
206 // Calculate Covariance for block
+
207 // https://projecteuclid.org/journals/bernoulli/volume-7/issue-2/An-adaptive-Metropolis-algorithm/bj/1080222083.full
+
208 cov_val = (*adaptive_covariance)(irow, icol)*Npars/5.6644;
+
209 cov_val += par_means_prev[irow]*par_means_prev[icol]; //First we remove the current means
+
210 cov_val = (cov_val*steps_post_burn+_fCurrVal[irow]*_fCurrVal[icol])/(steps_post_burn+1); //Now get mean(iRow*iCol)
+
211 cov_val -= par_means[icol]*par_means[irow];
+
212 cov_val*=5.6644/Npars;
+
213 }
+
214 (*adaptive_covariance)(icol, irow) = cov_val;
+
215 (*adaptive_covariance)(irow, icol) = cov_val;
+
216 }
+
217 }
+
218}
+
+
+
+

Member Data Documentation

+ +

◆ adapt_block_matrix_indices

+ +
+
+ + + + +
std::vector<int> adaptive_mcmc::AdaptiveMCMCHandler::adapt_block_matrix_indices
+
+ +

Indices for block-matrix adaption.

+ +

Definition at line 71 of file AdaptiveMCMCHandler.h.

+ +
+
+ +

◆ adapt_block_sizes

+ +
+
+ + + + +
std::vector<int> adaptive_mcmc::AdaptiveMCMCHandler::adapt_block_sizes
+
+ +

Size of blocks for adaption.

+ +

Definition at line 74 of file AdaptiveMCMCHandler.h.

+ +
+
+ +

◆ adaptive_covariance

+ +
+
+ + + + +
TMatrixDSym* adaptive_mcmc::AdaptiveMCMCHandler::adaptive_covariance
+
+ +

Full adaptive covariance matrix.

+ +

Definition at line 81 of file AdaptiveMCMCHandler.h.

+ +
+
+ +

◆ adaptive_update_step

+ +
+
+ + + + +
int adaptive_mcmc::AdaptiveMCMCHandler::adaptive_update_step
+
+ +

Steps between changing throw matrix.

+ +

Definition at line 68 of file AdaptiveMCMCHandler.h.

+ +
+
+ +

◆ end_adaptive_update

+ +
+
+ + + + +
int adaptive_mcmc::AdaptiveMCMCHandler::end_adaptive_update
+
+ +

Steps between changing throw matrix.

+ +

Definition at line 65 of file AdaptiveMCMCHandler.h.

+ +
+
+ +

◆ par_means

+ +
+
+ + + + +
std::vector<double> adaptive_mcmc::AdaptiveMCMCHandler::par_means
+
+ +

Mean values for all parameters.

+ +

Definition at line 78 of file AdaptiveMCMCHandler.h.

+ +
+
+ +

◆ start_adaptive_throw

+ +
+
+ + + + +
int adaptive_mcmc::AdaptiveMCMCHandler::start_adaptive_throw
+
+

Meta variables related to adaption run time When do we start throwing

+ +

Definition at line 59 of file AdaptiveMCMCHandler.h.

+ +
+
+ +

◆ start_adaptive_update

+ +
+
+ + + + +
int adaptive_mcmc::AdaptiveMCMCHandler::start_adaptive_update
+
+ +

When do we stop update the adaptive matrix.

+ +

Definition at line 62 of file AdaptiveMCMCHandler.h.

+ +
+
+
The documentation for this class was generated from the following files: +
+ +
+Generated by doxygen 1.9.8 +
+ + diff --git a/classcovarianceBase-members.html b/classcovarianceBase-members.html index b70fae246..ff2c45eb1 100644 --- a/classcovarianceBase-members.html +++ b/classcovarianceBase-members.html @@ -94,7 +94,7 @@ _fUpBoundcovarianceBaseprotected _fYAMLDoccovarianceBaseprotected acceptStep()covarianceBase - adaption_structcovarianceBaseprotected + AdaptiveHandlercovarianceBaseprotected CalcLikelihood()covarianceBase calcReWeight(const int bin)covarianceBaseinline CheckBounds()covarianceBasevirtual @@ -106,131 +106,128 @@ covarianceBase(const char *name, const char *file, int seed)covarianceBase covarianceBase(const char *name, const char *file, int seed, double threshold, int FirstPCAdpar, int LastPCAdpar)covarianceBase covMatrixcovarianceBaseprotected - createNewAdaptiveCovariance()covarianceBaseprotected - eigen_thresholdcovarianceBaseprotected - eigen_valuescovarianceBaseprotected - eigen_values_mastercovarianceBaseprotected - eigen_vectorscovarianceBaseprotected - FirstPCAdparcovarianceBaseprotected - fParCurr_PCAcovarianceBaseprotected - fParProp_PCAcovarianceBaseprotected - fParSigma_PCAcovarianceBaseprotected - GetCorrelationMatrix()covarianceBase - getCovMatrix()covarianceBaseinline - getDiagonalError(const int i)covarianceBaseinline - getDoAdaption()covarianceBaseinline - getEigenValues()covarianceBaseinline - getEigenValuesMaster()covarianceBaseinline - getEigenVectors()covarianceBaseinline - getFlatPrior(const int i)covarianceBaseinline - GetGenerated(const int i)covarianceBaseinline - getGeneratedValues()covarianceBaseinline - GetIndivStepScale(const int ParameterIndex)covarianceBaseinline - getInputFile() constcovarianceBaseinline - getInvCovMatrix()covarianceBaseinline - GetLikelihood()covarianceBasevirtual - GetLowerBound(const int i)covarianceBaseinline - getName()covarianceBaseinline - getNominal(const int i)covarianceBaseinlinevirtual - getNominalArray()covarianceBasevirtual - getNpars()covarianceBaseinline - GetNumParams()covarianceBaseinline - getParameterMeans()covarianceBaseinline - getParCurr(const int i)covarianceBaseinline - getParCurr_PCA(const int i)covarianceBaseinline - GetParFancyName(const int i)covarianceBaseinline - GetParFancyName(const int i) constcovarianceBaseinline - getParInit(const int i)covarianceBaseinline - GetParName(const int i)covarianceBaseinline - GetParName(const int i) constcovarianceBaseinline - getParProp(const int i)covarianceBaseinline - getParProp_PCA(const int i)covarianceBaseinline - getPreFitValues()covarianceBaseinline - getProposed() constcovarianceBase - getSize()covarianceBaseinline - getThrowMatrix()covarianceBaseinline - getThrowMatrix_CholDecomp()covarianceBaseinline - getTransferMatrix()covarianceBaseinline - GetUpperBound(const int i)covarianceBaseinline - init(const char *name, const char *file)covarianceBaseprotected - init(const std::vector< std::string > &YAMLFile)covarianceBaseprotected - init(TMatrixDSym *covMat)covarianceBaseprotected - initialiseAdaption(const YAML::Node &adapt_manager)covarianceBase - inputFilecovarianceBaseprotected - invCovMatrixcovarianceBaseprotected - InvertCovMatrixcovarianceBaseprotected - isDecomposed_PCAcovarianceBaseprotected - isParameterFixed(const int i)covarianceBaseinline - isParameterFixed(const std::string &name)covarianceBase - isParameterFixedPCA(const int i)covarianceBaseinline - IsPCA()covarianceBaseinline - LastPCAdparcovarianceBaseprotected - makeClosestPosDef(TMatrixDSym *cov)covarianceBaseprotected - MakePosDef(TMatrixDSym *cov=nullptr)covarianceBaseprotected - matrixNamecovarianceBaseprotected - MatrixVectorMulti(double *_restrict_ VecMulti, double **_restrict_ matrix, const double *_restrict_ vector, const int n)covarianceBaseinline - MatrixVectorMultiSingle(double **_restrict_ matrix, const double *_restrict_ vector, const int Length, const int i)covarianceBaseinline - nKeptPCAparscovarianceBaseprotected - pcacovarianceBaseprotected - printIndivStepScale()covarianceBase - PrintLengthcovarianceBaseprotected - printNominal()covarianceBase - printNominalCurrProp()covarianceBase - printPars()covarianceBase - proposeStep()covarianceBasevirtual - random_numbercovarianceBaseprotected - RandomConfiguration()covarianceBase - randomize()covarianceBaseprotected - randParamscovarianceBaseprotected - ReserveMemory(const int size)covarianceBaseprotected - resetIndivStepScale()covarianceBase - retPointer(const int iParam)covarianceBaseinline - ReturnUnity()covarianceBaseinlineprotected - saveAdaptiveToFile(const TString &outFileName, const TString &systematicName)covarianceBase + eigen_thresholdcovarianceBaseprotected + eigen_valuescovarianceBaseprotected + eigen_values_mastercovarianceBaseprotected + eigen_vectorscovarianceBaseprotected + FirstPCAdparcovarianceBaseprotected + fParCurr_PCAcovarianceBaseprotected + fParProp_PCAcovarianceBaseprotected + fParSigma_PCAcovarianceBaseprotected + GetCorrelationMatrix()covarianceBase + getCovMatrix()covarianceBaseinline + getDiagonalError(const int i)covarianceBaseinline + getDoAdaption()covarianceBaseinline + getEigenValues()covarianceBaseinline + getEigenValuesMaster()covarianceBaseinline + getEigenVectors()covarianceBaseinline + getFlatPrior(const int i)covarianceBaseinline + GetGenerated(const int i)covarianceBaseinline + getGeneratedValues()covarianceBaseinline + GetIndivStepScale(const int ParameterIndex)covarianceBaseinline + getInputFile() constcovarianceBaseinline + getInvCovMatrix()covarianceBaseinline + GetLikelihood()covarianceBasevirtual + GetLowerBound(const int i)covarianceBaseinline + getName()covarianceBaseinline + getNominal(const int i)covarianceBaseinlinevirtual + getNominalArray()covarianceBasevirtual + getNpars()covarianceBaseinline + GetNumParams()covarianceBaseinline + getParameterMeans()covarianceBaseinline + getParCurr(const int i)covarianceBaseinline + getParCurr_PCA(const int i)covarianceBaseinline + GetParFancyName(const int i)covarianceBaseinline + GetParFancyName(const int i) constcovarianceBaseinline + getParInit(const int i)covarianceBaseinline + GetParName(const int i)covarianceBaseinline + GetParName(const int i) constcovarianceBaseinline + getParProp(const int i)covarianceBaseinline + getParProp_PCA(const int i)covarianceBaseinline + getPreFitValues()covarianceBaseinline + getProposed() constcovarianceBase + getSize()covarianceBaseinline + getThrowMatrix()covarianceBaseinline + getThrowMatrix_CholDecomp()covarianceBaseinline + getTransferMatrix()covarianceBaseinline + GetUpperBound(const int i)covarianceBaseinline + init(const char *name, const char *file)covarianceBaseprotected + init(const std::vector< std::string > &YAMLFile)covarianceBaseprotected + init(TMatrixDSym *covMat)covarianceBaseprotected + initialiseAdaption(const YAML::Node &adapt_manager)covarianceBase + inputFilecovarianceBaseprotected + invCovMatrixcovarianceBaseprotected + InvertCovMatrixcovarianceBaseprotected + isDecomposed_PCAcovarianceBaseprotected + isParameterFixed(const int i)covarianceBaseinline + isParameterFixed(const std::string &name)covarianceBase + isParameterFixedPCA(const int i)covarianceBaseinline + IsPCA()covarianceBaseinline + LastPCAdparcovarianceBaseprotected + makeClosestPosDef(TMatrixDSym *cov)covarianceBaseprotected + MakePosDef(TMatrixDSym *cov=nullptr)covarianceBaseprotected + matrixNamecovarianceBaseprotected + MatrixVectorMulti(double *_restrict_ VecMulti, double **_restrict_ matrix, const double *_restrict_ vector, const int n)covarianceBaseinline + MatrixVectorMultiSingle(double **_restrict_ matrix, const double *_restrict_ vector, const int Length, const int i)covarianceBaseinline + nKeptPCAparscovarianceBaseprotected + pcacovarianceBaseprotected + printIndivStepScale()covarianceBase + PrintLengthcovarianceBaseprotected + printNominal()covarianceBase + printNominalCurrProp()covarianceBase + printPars()covarianceBase + proposeStep()covarianceBasevirtual + random_numbercovarianceBaseprotected + RandomConfiguration()covarianceBase + randomize()covarianceBaseprotected + randParamscovarianceBaseprotected + ReserveMemory(const int size)covarianceBaseprotected + resetIndivStepScale()covarianceBase + retPointer(const int iParam)covarianceBaseinline + ReturnUnity()covarianceBaseinlineprotected SaveUpdatedMatrixConfig()covarianceBase setAdaptionDefaults()covarianceBaseprotected - setAdaptiveBlocks(std::vector< std::vector< int > > block_indices)covarianceBaseprotected - SetBranches(TTree &tree, bool SaveProposal=false)covarianceBase - setCovMatrix(TMatrixDSym *cov)covarianceBase - setFlatPrior(const int i, const bool eL)covarianceBase - setIndivStepScale(const int ParameterIndex, const double StepScale)covarianceBaseinline - setIndivStepScale(const std::vector< double > &stepscale)covarianceBase - setName(const char *name)covarianceBaseinline - setNumberOfSteps(const int nsteps)covarianceBaseinline - setPar(const int i, const double val)covarianceBase - setParameters(const std::vector< double > &pars={})covarianceBase - setParameters_PCA(const std::vector< double > &pars)covarianceBaseinline - setParCurr_PCA(const int i, const double value)covarianceBaseinline - setParCurrProp(const int i, const double val)covarianceBase - setParName(int i, char *name)covarianceBaseinline - setParProp(const int i, const double val)covarianceBaseinline - setParProp_PCA(const int i, const double value)covarianceBaseinline - setPrintLength(const unsigned int PriLen)covarianceBaseinline - setSingleParameter(const int parNo, const double parVal)covarianceBase - setStepScale(const double scale)covarianceBase - setThrowMatrix(TMatrixDSym *cov)covarianceBase - setThrowMatrixFromFile(const std::string &matrix_file_name, const std::string &matrix_name, const std::string &means_name)covarianceBaseprotected - sizecovarianceBaseprotected - throwMatrixcovarianceBaseprotected - throwMatrix_CholDecompcovarianceBaseprotected - throwMatrixCholDecompcovarianceBaseprotected - throwNominal(const bool nomValues=false, const int seed=0)covarianceBase - throwParameters()covarianceBase - throwParCurr(const double mag=1.)covarianceBase - throwParProp(const double mag=1.)covarianceBase - toggleFixAllParameters()covarianceBase - toggleFixParameter(const int i)covarianceBase - toggleFixParameter(const std::string &name)covarianceBase - total_stepscovarianceBaseprotected - TransferMatcovarianceBaseprotected - TransferMatTcovarianceBaseprotected - TransferToParam()covarianceBaseprotected - TransferToPCA()covarianceBaseprotected - UnitycovarianceBaseprotected - updateAdaptiveCovariance()covarianceBaseprotected - updateThrowMatrix(TMatrixDSym *cov)covarianceBase - use_adaptivecovarianceBaseprotected - ~covarianceBase()covarianceBasevirtual + SetBranches(TTree &tree, bool SaveProposal=false)covarianceBase + setCovMatrix(TMatrixDSym *cov)covarianceBase + setFlatPrior(const int i, const bool eL)covarianceBase + setIndivStepScale(const int ParameterIndex, const double StepScale)covarianceBaseinline + setIndivStepScale(const std::vector< double > &stepscale)covarianceBase + setName(const char *name)covarianceBaseinline + setNumberOfSteps(const int nsteps)covarianceBaseinline + setPar(const int i, const double val)covarianceBase + setParameters(const std::vector< double > &pars={})covarianceBase + setParameters_PCA(const std::vector< double > &pars)covarianceBaseinline + setParCurr_PCA(const int i, const double value)covarianceBaseinline + setParCurrProp(const int i, const double val)covarianceBase + setParName(int i, char *name)covarianceBaseinline + setParProp(const int i, const double val)covarianceBaseinline + setParProp_PCA(const int i, const double value)covarianceBaseinline + setPrintLength(const unsigned int PriLen)covarianceBaseinline + setSingleParameter(const int parNo, const double parVal)covarianceBase + setStepScale(const double scale)covarianceBase + setThrowMatrix(TMatrixDSym *cov)covarianceBase + setThrowMatrixFromFile(const std::string &matrix_file_name, const std::string &matrix_name, const std::string &means_name)covarianceBaseprotected + sizecovarianceBaseprotected + throwMatrixcovarianceBaseprotected + throwMatrix_CholDecompcovarianceBaseprotected + throwMatrixCholDecompcovarianceBaseprotected + throwNominal(const bool nomValues=false, const int seed=0)covarianceBase + throwParameters()covarianceBase + throwParCurr(const double mag=1.)covarianceBase + throwParProp(const double mag=1.)covarianceBase + toggleFixAllParameters()covarianceBase + toggleFixParameter(const int i)covarianceBase + toggleFixParameter(const std::string &name)covarianceBase + total_stepscovarianceBaseprotected + TransferMatcovarianceBaseprotected + TransferMatTcovarianceBaseprotected + TransferToParam()covarianceBaseprotected + TransferToPCA()covarianceBaseprotected + UnitycovarianceBaseprotected + updateAdaptiveCovariance()covarianceBaseprotected + updateThrowMatrix(TMatrixDSym *cov)covarianceBase + use_adaptivecovarianceBaseprotected + ~covarianceBase()covarianceBasevirtual
diff --git a/classcovarianceBase.html b/classcovarianceBase.html index f1552a118..bef48eb31 100644 --- a/classcovarianceBase.html +++ b/classcovarianceBase.html @@ -216,17 +216,16 @@ void initialiseAdaption (const YAML::Node &adapt_manager)  Initialise adaptive MCMC.
  -void saveAdaptiveToFile (const TString &outFileName, const TString &systematicName) - Save adaptive throw matrix to file.
-  bool getDoAdaption ()  Do we adapt or not.
  void setThrowMatrix (TMatrixDSym *cov) + Use new throw matrix, used in adaptive MCMC.
  void updateThrowMatrix (TMatrixDSym *cov)   void setNumberOfSteps (const int nsteps) + Set number of MCMC step, when running adaptive MCMC it is updated with given frequency. We need number of steps to determine frequency.
  TMatrixDSym * getThrowMatrix ()   @@ -363,6 +362,7 @@

Protected Member Functions

void init (const char *name, const char *file) + Initialisation of the class using matrix from root file.
  void init (const std::vector< std::string > &YAMLFile)  Initialisation of the class using config.
@@ -397,18 +397,12 @@ void setAdaptionDefaults ()  sets default values for adaptive MCMC parameters
  -void setAdaptiveBlocks (std::vector< std::vector< int > > block_indices) - sets adaptive block matrix
-  void setThrowMatrixFromFile (const std::string &matrix_file_name, const std::string &matrix_name, const std::string &means_name)  sets throw matrix from a file
  void updateAdaptiveCovariance ()  Method to update adaptive MCMC.
  -void createNewAdaptiveCovariance () - method to create new throw matrix
-  @@ -416,7 +410,7 @@ - + @@ -536,8 +530,10 @@ + + @@ -546,16 +542,17 @@ + - - - + + +

Protected Attributes

 The input root file we read in.
 
int size
 Total number of parmas, deprecated, please don't use it.
 Total number of params, deprecated, please don't use it.
 
const char * matrixName
 Name of cov matrix.
 If param is decomposed this will return -1, if not this will return enumerator to param in normal base. This way we can map stuff like step scale etc between normal base and undecomposed param in eigen base.
 
TMatrixDSym * throwMatrix
 Matrix which we use for step proposal before Cholesky decomposition (not actually used for step proposal)
 
TMatrixD * throwMatrix_CholDecomp
 Matrix which we use for step proposal after Cholesky decomposition.
 
double ** throwMatrixCholDecomp
 Throw matrix that is being used in the fit, much faster as TMatrixDSym cache miss.
 Are we using AMCMC?
 
int total_steps
 Total number of MCMC steps.
 
adaptive_mcmc::AdaptiveMCMCStruct adaption_struct
 Struct containing information about adaption.
 
adaptive_mcmc::AdaptiveMCMCHandler AdaptiveHandler
 Struct containing information about adaption.
 

Detailed Description

Base class responsible for handling of systematic error parameters. Capable of using PCA or using adaptive throw matrix.

See also
For more details, visit the Wiki.
-

Definition at line 33 of file covarianceBase.h.

+

Definition at line 34 of file covarianceBase.h.

Constructor & Destructor Documentation

◆ covarianceBase() [1/4]

@@ -636,16 +633,16 @@

31 // Call the innocent helper function
32 if (pca) ConstructPCA();
33}
-
MACH3LOG_INFO
#define MACH3LOG_INFO
Definition MaCh3Logger.h:13
-
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:18
-
covarianceBase::matrixName
const char * matrixName
Name of cov matrix.
Definition covarianceBase.h:413
-
covarianceBase::inputFile
const std::string inputFile
The input root file we read in.
Definition covarianceBase.h:408
-
covarianceBase::LastPCAdpar
int LastPCAdpar
Index of the last param that is being decomposed.
Definition covarianceBase.h:473
-
covarianceBase::ConstructPCA
void ConstructPCA()
CW: Calculate eigen values, prepare transition matrices and remove param based on defined threshold.
Definition covarianceBase.cpp:122
-
covarianceBase::pca
bool pca
perform PCA or not
Definition covarianceBase.h:465
-
covarianceBase::FirstPCAdpar
int FirstPCAdpar
Index of the first param that is being decomposed.
Definition covarianceBase.h:471
-
covarianceBase::init
void init(const char *name, const char *file)
Definition covarianceBase.cpp:256
-
covarianceBase::eigen_threshold
double eigen_threshold
CW: Threshold based on which we remove parameters in eigen base.
Definition covarianceBase.h:467
+
MACH3LOG_INFO
#define MACH3LOG_INFO
Definition MaCh3Logger.h:16
+
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:21
+
covarianceBase::matrixName
const char * matrixName
Name of cov matrix.
Definition covarianceBase.h:427
+
covarianceBase::inputFile
const std::string inputFile
The input root file we read in.
Definition covarianceBase.h:422
+
covarianceBase::LastPCAdpar
int LastPCAdpar
Index of the last param that is being decomposed.
Definition covarianceBase.h:487
+
covarianceBase::ConstructPCA
void ConstructPCA()
CW: Calculate eigen values, prepare transition matrices and remove param based on defined threshold.
Definition covarianceBase.cpp:117
+
covarianceBase::pca
bool pca
perform PCA or not
Definition covarianceBase.h:479
+
covarianceBase::FirstPCAdpar
int FirstPCAdpar
Index of the first param that is being decomposed.
Definition covarianceBase.h:485
+
covarianceBase::init
void init(const char *name, const char *file)
Initialisation of the class using matrix from root file.
Definition covarianceBase.cpp:251
+
covarianceBase::eigen_threshold
double eigen_threshold
CW: Threshold based on which we remove parameters in eigen base.
Definition covarianceBase.h:481
@@ -684,10 +681,9 @@

Definition at line 3 of file covarianceBase.cpp.

-
3 : inputFile(std::string(file)), pca(false) {
-
4// ********************************************
-
5
+

Definition at line 4 of file covarianceBase.cpp.

+
4 : inputFile(std::string(file)), pca(false) {
+
5// ********************************************
6 MACH3LOG_INFO("Constructing instance of covarianceBase");
7 init(name, file);
8 FirstPCAdpar = -999;
@@ -756,7 +752,7 @@

50 FirstPCAdpar = -999;

51 LastPCAdpar = -999;
52}
-
MACH3LOG_WARN
#define MACH3LOG_WARN
Definition MaCh3Logger.h:14
+
MACH3LOG_WARN
#define MACH3LOG_WARN
Definition MaCh3Logger.h:17
@@ -909,33 +905,26 @@

111 for (int iThread = 0;iThread < nThreads; iThread++) delete random_number[iThread];
112 delete[] random_number;
113 if (throwMatrix != NULL) delete throwMatrix;
-
114
-
115 if(adaption_struct.adaptive_covariance != nullptr){
-
116 delete adaption_struct.adaptive_covariance;
-
117 }
-
118
-
119}
-
covarianceBase::_fPropVal
std::vector< double > _fPropVal
Proposed value of the parameter.
Definition covarianceBase.h:447
-
covarianceBase::_fUpBound
std::vector< double > _fUpBound
Upper physical bound, parameter will not be able to go beyond it.
Definition covarianceBase.h:455
-
covarianceBase::_fError
std::vector< double > _fError
Prior error on the parameter.
Definition covarianceBase.h:451
-
covarianceBase::invCovMatrix
TMatrixDSym * invCovMatrix
The inverse covariance matrix.
Definition covarianceBase.h:417
-
covarianceBase::_fIndivStepScale
std::vector< double > _fIndivStepScale
Individual step scale used by MCMC algorithm.
Definition covarianceBase.h:457
-
covarianceBase::InvertCovMatrix
double ** InvertCovMatrix
KS: Same as above but much faster as TMatrixDSym cache miss.
Definition covarianceBase.h:419
-
covarianceBase::random_number
TRandom3 ** random_number
KS: Set Random numbers for each thread so each thread has different seed.
Definition covarianceBase.h:422
-
covarianceBase::adaption_struct
adaptive_mcmc::AdaptiveMCMCStruct adaption_struct
Struct containing information about adaption.
Definition covarianceBase.h:526
-
covarianceBase::covMatrix
TMatrixDSym * covMatrix
The covariance matrix.
Definition covarianceBase.h:415
-
covarianceBase::throwMatrix
TMatrixDSym * throwMatrix
Definition covarianceBase.h:498
-
covarianceBase::randParams
double * randParams
Random number taken from gaussian around prior error used for corr_throw.
Definition covarianceBase.h:425
-
covarianceBase::_fPreFitValue
std::vector< double > _fPreFitValue
Parameter value dictated by the prior model. Based on it penalty term is calculated.
Definition covarianceBase.h:443
-
covarianceBase::corr_throw
double * corr_throw
Result of multiplication of Cholesky matrix and randParams.
Definition covarianceBase.h:427
-
covarianceBase::_fLowBound
std::vector< double > _fLowBound
Lowest physical bound, parameter will not be able to go beyond it.
Definition covarianceBase.h:453
-
covarianceBase::throwMatrix_CholDecomp
TMatrixD * throwMatrix_CholDecomp
Definition covarianceBase.h:499
-
covarianceBase::_fNumPar
int _fNumPar
Number of systematic parameters.
Definition covarianceBase.h:441
-
covarianceBase::throwMatrixCholDecomp
double ** throwMatrixCholDecomp
Throw matrix that is being used in the fit, much faster as TMatrixDSym cache miss.
Definition covarianceBase.h:501
-
covarianceBase::_fFlatPrior
std::vector< bool > _fFlatPrior
Whether to apply flat prior or not.
Definition covarianceBase.h:459
-
covarianceBase::_fCurrVal
std::vector< double > _fCurrVal
Current value of the parameter.
Definition covarianceBase.h:445
-
MaCh3Utils::GetNThreads
int GetNThreads()
number of threads which we need for example for TRandom3
Definition CovarianceUtils.h:32
-
adaptive_mcmc::AdaptiveMCMCStruct::adaptive_covariance
TMatrixDSym * adaptive_covariance
Full adaptive covariance matrix.
Definition adaptiveMCMCStruct.h:38
+
114}
+
covarianceBase::_fPropVal
std::vector< double > _fPropVal
Proposed value of the parameter.
Definition covarianceBase.h:461
+
covarianceBase::_fUpBound
std::vector< double > _fUpBound
Upper physical bound, parameter will not be able to go beyond it.
Definition covarianceBase.h:469
+
covarianceBase::_fError
std::vector< double > _fError
Prior error on the parameter.
Definition covarianceBase.h:465
+
covarianceBase::invCovMatrix
TMatrixDSym * invCovMatrix
The inverse covariance matrix.
Definition covarianceBase.h:431
+
covarianceBase::_fIndivStepScale
std::vector< double > _fIndivStepScale
Individual step scale used by MCMC algorithm.
Definition covarianceBase.h:471
+
covarianceBase::InvertCovMatrix
double ** InvertCovMatrix
KS: Same as above but much faster as TMatrixDSym cache miss.
Definition covarianceBase.h:433
+
covarianceBase::random_number
TRandom3 ** random_number
KS: Set Random numbers for each thread so each thread has different seed.
Definition covarianceBase.h:436
+
covarianceBase::covMatrix
TMatrixDSym * covMatrix
The covariance matrix.
Definition covarianceBase.h:429
+
covarianceBase::throwMatrix
TMatrixDSym * throwMatrix
Matrix which we use for step proposal before Cholesky decomposition (not actually used for step propo...
Definition covarianceBase.h:512
+
covarianceBase::randParams
double * randParams
Random number taken from gaussian around prior error used for corr_throw.
Definition covarianceBase.h:439
+
covarianceBase::_fPreFitValue
std::vector< double > _fPreFitValue
Parameter value dictated by the prior model. Based on it penalty term is calculated.
Definition covarianceBase.h:457
+
covarianceBase::corr_throw
double * corr_throw
Result of multiplication of Cholesky matrix and randParams.
Definition covarianceBase.h:441
+
covarianceBase::_fLowBound
std::vector< double > _fLowBound
Lowest physical bound, parameter will not be able to go beyond it.
Definition covarianceBase.h:467
+
covarianceBase::throwMatrix_CholDecomp
TMatrixD * throwMatrix_CholDecomp
Matrix which we use for step proposal after Cholesky decomposition.
Definition covarianceBase.h:514
+
covarianceBase::_fNumPar
int _fNumPar
Number of systematic parameters.
Definition covarianceBase.h:455
+
covarianceBase::throwMatrixCholDecomp
double ** throwMatrixCholDecomp
Throw matrix that is being used in the fit, much faster as TMatrixDSym cache miss.
Definition covarianceBase.h:516
+
covarianceBase::_fFlatPrior
std::vector< bool > _fFlatPrior
Whether to apply flat prior or not.
Definition covarianceBase.h:473
+
covarianceBase::_fCurrVal
std::vector< double > _fCurrVal
Current value of the parameter.
Definition covarianceBase.h:459
+
MaCh3Utils::GetNThreads
int GetNThreads()
number of threads which we need for example for TRandom3
Definition CovarianceUtils.h:28
@@ -957,32 +946,33 @@

Definition at line 886 of file covarianceBase.cpp.

-
886 {
-
887 if (!pca) {
-
888#ifdef MULTITHREAD
-
889#pragma omp parallel for
-
890#endif
-
891 for (int i = 0; i < _fNumPar; ++i) {
-
892 // Update state so that current state is proposed state
-
893 _fCurrVal[i] = _fPropVal[i];
-
894 }
-
895 } else {
-
896 // Update the book-keeping for the output
-
897#ifdef MULTITHREAD
-
898#pragma omp parallel for
-
899#endif
-
900 for (int i = 0; i < _fNumParPCA; ++i) {
-
901 fParCurr_PCA(i) = fParProp_PCA(i);
-
902 }
-
903 // Then update the parameter basis
-
904 TransferToParam();
-
905 }
-
906}
-
covarianceBase::fParProp_PCA
TVectorD fParProp_PCA
CW: Current parameter value in PCA base.
Definition covarianceBase.h:489
-
covarianceBase::TransferToParam
void TransferToParam()
Transfer param values from PCA base to normal base.
Definition covarianceBase.cpp:589
-
covarianceBase::fParCurr_PCA
TVectorD fParCurr_PCA
CW: Proposed parameter value in PCA base.
Definition covarianceBase.h:491
-
covarianceBase::_fNumParPCA
int _fNumParPCA
Number of parameters in PCA base.
Definition covarianceBase.h:469
+

Definition at line 887 of file covarianceBase.cpp.

+
887 {
+
888// ********************************************
+
889 if (!pca) {
+
890 #ifdef MULTITHREAD
+
891 #pragma omp parallel for
+
892 #endif
+
893 for (int i = 0; i < _fNumPar; ++i) {
+
894 // Update state so that current state is proposed state
+
895 _fCurrVal[i] = _fPropVal[i];
+
896 }
+
897 } else {
+
898 // Update the book-keeping for the output
+
899 #ifdef MULTITHREAD
+
900 #pragma omp parallel for
+
901 #endif
+
902 for (int i = 0; i < _fNumParPCA; ++i) {
+
903 fParCurr_PCA(i) = fParProp_PCA(i);
+
904 }
+
905 // Then update the parameter basis
+
906 TransferToParam();
+
907 }
+
908}
+
covarianceBase::fParProp_PCA
TVectorD fParProp_PCA
CW: Current parameter value in PCA base.
Definition covarianceBase.h:503
+
covarianceBase::TransferToParam
void TransferToParam()
Transfer param values from PCA base to normal base.
Definition covarianceBase.cpp:587
+
covarianceBase::fParCurr_PCA
TVectorD fParCurr_PCA
CW: Proposed parameter value in PCA base.
Definition covarianceBase.h:505
+
covarianceBase::_fNumParPCA
int _fNumParPCA
Number of parameters in PCA base.
Definition covarianceBase.h:483
@@ -1003,25 +993,25 @@

Definition at line 999 of file covarianceBase.cpp.

-
999 {
-
1000// ********************************************
-
1001
-
1002 double logL = 0.0;
-
1003 #ifdef MULTITHREAD
-
1004 #pragma omp parallel for reduction(+:logL)
-
1005 #endif
-
1006 for(int i = 0; i < _fNumPar; ++i){
-
1007 for (int j = 0; j <= i; ++j) {
-
1008 if (!_fFlatPrior[i] && !_fFlatPrior[j]) {
-
1009 //KS: Since matrix is symmetric we can calculate non diagonal elements only once and multiply by 2, can bring up to factor speed decrease.
-
1010 short int scale = (i != j) ? 2 : 1;
-
1011 logL += scale * 0.5*(_fPropVal[i] - _fPreFitValue[i])*(_fPropVal[j] - _fPreFitValue[j])*InvertCovMatrix[i][j];
-
1012 }
-
1013 }
-
1014 }
-
1015 return logL;
-
1016}
+

Definition at line 1002 of file covarianceBase.cpp.

+
1002 {
+
1003// ********************************************
+
1004
+
1005 double logL = 0.0;
+
1006 #ifdef MULTITHREAD
+
1007 #pragma omp parallel for reduction(+:logL)
+
1008 #endif
+
1009 for(int i = 0; i < _fNumPar; ++i){
+
1010 for (int j = 0; j <= i; ++j) {
+
1011 if (!_fFlatPrior[i] && !_fFlatPrior[j]) {
+
1012 //KS: Since matrix is symmetric we can calculate non diagonal elements only once and multiply by 2, can bring up to factor speed decrease.
+
1013 short int scale = (i != j) ? 2 : 1;
+
1014 logL += scale * 0.5*(_fPropVal[i] - _fPreFitValue[i])*(_fPropVal[j] - _fPreFitValue[j])*InvertCovMatrix[i][j];
+
1015 }
+
1016 }
+
1017 }
+
1018 return logL;
+
1019}
@@ -1057,18 +1047,18 @@

Definition at line 190 of file covarianceBase.h.

-
190 {
-
191 if (bin >= 0 && bin < _fNumPar) {
-
192 return _fPropVal[bin];
-
193 } else {
-
194 MACH3LOG_WARN("Specified bin is <= 0 OR bin > npar!");
-
195 MACH3LOG_WARN("bin = {}, npar = {}", bin, _fNumPar);
-
196 MACH3LOG_WARN("This won't ruin much that this step in the MCMC, but does indicate something wrong in memory!");
-
197 return 1.0;
-
198 }
-
199 return 1.0;
-
200 }
+

Definition at line 191 of file covarianceBase.h.

+
191 {
+
192 if (bin >= 0 && bin < _fNumPar) {
+
193 return _fPropVal[bin];
+
194 } else {
+
195 MACH3LOG_WARN("Specified bin is <= 0 OR bin > npar!");
+
196 MACH3LOG_WARN("bin = {}, npar = {}", bin, _fNumPar);
+
197 MACH3LOG_WARN("This won't ruin much that this step in the MCMC, but does indicate something wrong in memory!");
+
198 return 1.0;
+
199 }
+
200 return 1.0;
+
201 }
@@ -1099,21 +1089,21 @@

covarianceOsc.

-

Definition at line 1019 of file covarianceBase.cpp.

-
1019 {
-
1020// ********************************************
-
1021
-
1022 int NOutside = 0;
-
1023 #ifdef MULTITHREAD
-
1024 #pragma omp parallel for reduction(+:NOutside)
-
1025 #endif
-
1026 for (int i = 0; i < _fNumPar; ++i){
-
1027 if(_fPropVal[i] > _fUpBound[i] || _fPropVal[i] < _fLowBound[i]){
-
1028 NOutside++;
-
1029 }
-
1030 }
-
1031 return NOutside;
-
1032}
+

Definition at line 1022 of file covarianceBase.cpp.

+
1022 {
+
1023// ********************************************
+
1024
+
1025 int NOutside = 0;
+
1026 #ifdef MULTITHREAD
+
1027 #pragma omp parallel for reduction(+:NOutside)
+
1028 #endif
+
1029 for (int i = 0; i < _fNumPar; ++i){
+
1030 if(_fPropVal[i] > _fUpBound[i] || _fPropVal[i] < _fLowBound[i]){
+
1031 NOutside++;
+
1032 }
+
1033 }
+
1034 return NOutside;
+
1035}
@@ -1135,150 +1125,150 @@

See also
For more details, visit the Wiki.
-

Definition at line 122 of file covarianceBase.cpp.

-
122 {
-
123// ********************************************
-
124
-
125 // Check that covariance matrix exists
-
126 if (covMatrix == NULL) {
-
127 MACH3LOG_ERROR("Covariance matrix for {} has not yet been set", matrixName);
-
128 MACH3LOG_ERROR("Can not construct PCA until it is set");
-
129 throw;
-
130 }
-
131
-
132 //Check whether first and last pcadpar are set and if not just PCA everything
-
133 if(FirstPCAdpar == -999 || LastPCAdpar == -999){
-
134 if(FirstPCAdpar == -999 && LastPCAdpar == -999){
-
135 FirstPCAdpar = 0;
-
136 LastPCAdpar = covMatrix->GetNrows()-1;
-
137 }
-
138 else{
-
139 MACH3LOG_ERROR("You must either leave FirstPCAdpar and LastPCAdpar at -999 or set them both to something");
-
140 throw;
-
141 }
+

Definition at line 117 of file covarianceBase.cpp.

+
117 {
+
118// ********************************************
+
119
+
120 // Check that covariance matrix exists
+
121 if (covMatrix == NULL) {
+
122 MACH3LOG_ERROR("Covariance matrix for {} has not yet been set", matrixName);
+
123 MACH3LOG_ERROR("Can not construct PCA until it is set");
+
124 throw;
+
125 }
+
126
+
127 //Check whether first and last pcadpar are set and if not just PCA everything
+
128 if(FirstPCAdpar == -999 || LastPCAdpar == -999){
+
129 if(FirstPCAdpar == -999 && LastPCAdpar == -999){
+
130 FirstPCAdpar = 0;
+
131 LastPCAdpar = covMatrix->GetNrows()-1;
+
132 }
+
133 else{
+
134 MACH3LOG_ERROR("You must either leave FirstPCAdpar and LastPCAdpar at -999 or set them both to something");
+
135 throw;
+
136 }
+
137 }
+
138 if(FirstPCAdpar > covMatrix->GetNrows()-1 || LastPCAdpar>covMatrix->GetNrows()-1){
+
139 MACH3LOG_ERROR("FirstPCAdpar and LastPCAdpar are higher than the number of parameters");
+
140 MACH3LOG_ERROR("first: {} last: {}, params: {}", FirstPCAdpar, LastPCAdpar, covMatrix->GetNrows()-1);
+
141 throw;
142 }
-
143 if(FirstPCAdpar > covMatrix->GetNrows()-1 || LastPCAdpar>covMatrix->GetNrows()-1){
-
144 MACH3LOG_ERROR("FirstPCAdpar and LastPCAdpar are higher than the number of parameters");
-
145 MACH3LOG_ERROR("first: {} last: {}, params: {}", FirstPCAdpar, LastPCAdpar, covMatrix->GetNrows()-1);
+
143 if(FirstPCAdpar < 0 || LastPCAdpar < 0){
+
144 MACH3LOG_ERROR("FirstPCAdpar and LastPCAdpar are less than 0 but not default -999");
+
145 MACH3LOG_ERROR("first: {} last: {}", FirstPCAdpar, LastPCAdpar);
146 throw;
147 }
-
148 if(FirstPCAdpar < 0 || LastPCAdpar < 0){
-
149 MACH3LOG_ERROR("FirstPCAdpar and LastPCAdpar are less than 0 but not default -999");
-
150 MACH3LOG_ERROR("first: {} last: {}", FirstPCAdpar, LastPCAdpar);
-
151 throw;
-
152 }
+
148
+
149 MACH3LOG_INFO("PCAing parameters {} through {} inclusive", FirstPCAdpar, LastPCAdpar);
+
150 int numunpcadpars = covMatrix->GetNrows()-(LastPCAdpar-FirstPCAdpar+1);
+
151
+
152 TMatrixDSym submat(covMatrix->GetSub(FirstPCAdpar,LastPCAdpar,FirstPCAdpar,LastPCAdpar));
153
-
154 MACH3LOG_INFO("PCAing parameters {} through {} inclusive", FirstPCAdpar, LastPCAdpar);
-
155 int numunpcadpars = covMatrix->GetNrows()-(LastPCAdpar-FirstPCAdpar+1);
-
156
-
157 TMatrixDSym submat(covMatrix->GetSub(FirstPCAdpar,LastPCAdpar,FirstPCAdpar,LastPCAdpar));
-
158
-
159 //CW: Calculate how many eigen values this threshold corresponds to
-
160 TMatrixDSymEigen eigen(submat);
-
161 eigen_values.ResizeTo(eigen.GetEigenValues());
-
162 eigen_vectors.ResizeTo(eigen.GetEigenVectors());
-
163 eigen_values = eigen.GetEigenValues();
-
164 eigen_vectors = eigen.GetEigenVectors();
-
165 double sum = 0;
-
166 // Loop over eigen values and sum them up
+
154 //CW: Calculate how many eigen values this threshold corresponds to
+
155 TMatrixDSymEigen eigen(submat);
+
156 eigen_values.ResizeTo(eigen.GetEigenValues());
+
157 eigen_vectors.ResizeTo(eigen.GetEigenVectors());
+
158 eigen_values = eigen.GetEigenValues();
+
159 eigen_vectors = eigen.GetEigenVectors();
+
160 double sum = 0;
+
161 // Loop over eigen values and sum them up
+
162 for (int i = 0; i < eigen_values.GetNrows(); ++i) {
+
163 sum += eigen_values(i);
+
164 }
+
165 nKeptPCApars = eigen_values.GetNrows();
+
166 //CW: Now go through again and see how many eigen values correspond to threshold
167 for (int i = 0; i < eigen_values.GetNrows(); ++i) {
-
168 sum += eigen_values(i);
-
169 }
-
170 nKeptPCApars = eigen_values.GetNrows();
-
171 //CW: Now go through again and see how many eigen values correspond to threshold
-
172 for (int i = 0; i < eigen_values.GetNrows(); ++i) {
-
173 // Get the relative size of the eigen value
-
174 double sig = eigen_values(i)/sum;
-
175 // Check against the threshold
-
176 if (sig < eigen_threshold) {
-
177 nKeptPCApars = i;
-
178 break;
-
179 }
-
180 }
-
181 _fNumParPCA = numunpcadpars+nKeptPCApars;
-
182 MACH3LOG_INFO("Threshold of {} on eigen values relative sum of eigen value ({}) generates {} eigen vectors, plus we have {} unpcad pars, for a total of {}", eigen_threshold, sum, nKeptPCApars, numunpcadpars, _fNumParPCA);
-
183
-
184 //DB Create array of correct size so eigen_values can be used in CorrelateSteps
-
185 eigen_values_master = std::vector<double>(_fNumParPCA, 1.0);
-
186 for (int i = FirstPCAdpar; i < FirstPCAdpar+nKeptPCApars; ++i) {eigen_values_master[i] = eigen_values(i-FirstPCAdpar);}
+
168 // Get the relative size of the eigen value
+
169 double sig = eigen_values(i)/sum;
+
170 // Check against the threshold
+
171 if (sig < eigen_threshold) {
+
172 nKeptPCApars = i;
+
173 break;
+
174 }
+
175 }
+
176 _fNumParPCA = numunpcadpars+nKeptPCApars;
+
177 MACH3LOG_INFO("Threshold of {} on eigen values relative sum of eigen value ({}) generates {} eigen vectors, plus we have {} unpcad pars, for a total of {}", eigen_threshold, sum, nKeptPCApars, numunpcadpars, _fNumParPCA);
+
178
+
179 //DB Create array of correct size so eigen_values can be used in CorrelateSteps
+
180 eigen_values_master = std::vector<double>(_fNumParPCA, 1.0);
+
181 for (int i = FirstPCAdpar; i < FirstPCAdpar+nKeptPCApars; ++i) {eigen_values_master[i] = eigen_values(i-FirstPCAdpar);}
+
182
+
183 // Now construct the transfer matrices
+
184 //These matrices will be as big as number of unPCAd pars plus number of eigenvalues kept
+
185 TransferMat.ResizeTo(covMatrix->GetNrows(), _fNumParPCA);
+
186 TransferMatT.ResizeTo(covMatrix->GetNrows(), _fNumParPCA);
187
-
188 // Now construct the transfer matrices
-
189 //These matrices will be as big as number of unPCAd pars plus number of eigenvalues kept
-
190 TransferMat.ResizeTo(covMatrix->GetNrows(), _fNumParPCA);
-
191 TransferMatT.ResizeTo(covMatrix->GetNrows(), _fNumParPCA);
-
192
-
193 // Get a subset of the eigen vector matrix
-
194 TMatrixD temp(eigen_vectors.GetSub(0, eigen_vectors.GetNrows()-1, 0, nKeptPCApars-1));
-
195
-
196 //Make transfer matrix which is two blocks of identity with a block of the PCA transfer matrix in between
-
197 TMatrixD temp2;
-
198 temp2.ResizeTo(covMatrix->GetNrows(), _fNumParPCA);
-
199
-
200 //First set the whole thing to 0
-
201 for(int iRow = 0; iRow < covMatrix->GetNrows(); iRow++){
-
202 for(int iCol = 0; iCol < _fNumParPCA; iCol++){
-
203 temp2[iRow][iCol] = 0;
-
204 }
-
205 }
-
206 //Set the first identity block
-
207 if(FirstPCAdpar != 0){
-
208 for(int iRow = 0; iRow < FirstPCAdpar; iRow++){
-
209 temp2[iRow][iRow] = 1;
-
210 }
-
211 }
-
212
-
213 //Set the transfer matrix block for the PCAd pars
-
214 temp2.SetSub(FirstPCAdpar,FirstPCAdpar,temp);
-
215
-
216 //Set the second identity block
-
217 if(LastPCAdpar != covMatrix->GetNrows()-1){
-
218 for(int iRow = 0;iRow < (covMatrix->GetNrows()-1)-LastPCAdpar; iRow++){
-
219 temp2[LastPCAdpar+1+iRow][FirstPCAdpar+nKeptPCApars+iRow] = 1;
-
220 }
-
221 }
-
222
-
223 TransferMat = temp2;
-
224 // Copy the contents
-
225 TransferMatT = TransferMat;
-
226 // And then transpose
-
227 TransferMatT.T();
-
228
-
229 // Make a note that we have now done PCA
-
230 pca = true;
+
188 // Get a subset of the eigen vector matrix
+
189 TMatrixD temp(eigen_vectors.GetSub(0, eigen_vectors.GetNrows()-1, 0, nKeptPCApars-1));
+
190
+
191 //Make transfer matrix which is two blocks of identity with a block of the PCA transfer matrix in between
+
192 TMatrixD temp2;
+
193 temp2.ResizeTo(covMatrix->GetNrows(), _fNumParPCA);
+
194
+
195 //First set the whole thing to 0
+
196 for(int iRow = 0; iRow < covMatrix->GetNrows(); iRow++){
+
197 for(int iCol = 0; iCol < _fNumParPCA; iCol++){
+
198 temp2[iRow][iCol] = 0;
+
199 }
+
200 }
+
201 //Set the first identity block
+
202 if(FirstPCAdpar != 0){
+
203 for(int iRow = 0; iRow < FirstPCAdpar; iRow++){
+
204 temp2[iRow][iRow] = 1;
+
205 }
+
206 }
+
207
+
208 //Set the transfer matrix block for the PCAd pars
+
209 temp2.SetSub(FirstPCAdpar,FirstPCAdpar,temp);
+
210
+
211 //Set the second identity block
+
212 if(LastPCAdpar != covMatrix->GetNrows()-1){
+
213 for(int iRow = 0;iRow < (covMatrix->GetNrows()-1)-LastPCAdpar; iRow++){
+
214 temp2[LastPCAdpar+1+iRow][FirstPCAdpar+nKeptPCApars+iRow] = 1;
+
215 }
+
216 }
+
217
+
218 TransferMat = temp2;
+
219 // Copy the contents
+
220 TransferMatT = TransferMat;
+
221 // And then transpose
+
222 TransferMatT.T();
+
223
+
224 // Make a note that we have now done PCA
+
225 pca = true;
+
226
+
227 // Make the PCA parameter arrays
+
228 fParCurr_PCA.ResizeTo(_fNumParPCA);
+
229 fParProp_PCA.ResizeTo(_fNumParPCA);
+
230 _fPreFitValue_PCA.resize(_fNumParPCA);
231
-
232 // Make the PCA parameter arrays
-
233 fParCurr_PCA.ResizeTo(_fNumParPCA);
-
234 fParProp_PCA.ResizeTo(_fNumParPCA);
-
235 _fPreFitValue_PCA.resize(_fNumParPCA);
-
236
-
237 //KS: make easy map so we could easily find un-decomposed parameters
-
238 isDecomposed_PCA.resize(_fNumParPCA);
-
239 fParSigma_PCA.resize(_fNumParPCA);
-
240 for (int i = 0; i < _fNumParPCA; ++i)
-
241 {
-
242 fParSigma_PCA[i] = 1;
-
243 isDecomposed_PCA[i] = -1;
-
244 }
-
245 for (int i = 0; i < FirstPCAdpar; ++i) isDecomposed_PCA[i] = i;
-
246
-
247 for (int i = FirstPCAdpar+nKeptPCApars+1; i < _fNumParPCA; ++i) isDecomposed_PCA[i] = i+(size-_fNumParPCA);
-
248
-
249 #ifdef DEBUG_PCA
-
250 //KS: Let's dump all useful matrices to properly validate PCA
-
251 DebugPCA(sum, temp, submat);
-
252 #endif
-
253}
-
MACH3LOG_ERROR
#define MACH3LOG_ERROR
Definition MaCh3Logger.h:15
-
covarianceBase::nKeptPCApars
int nKeptPCApars
Total number that remained after applying PCA Threshold.
Definition covarianceBase.h:475
-
covarianceBase::TransferMatT
TMatrixD TransferMatT
Matrix used to converting from normal base to PCA base.
Definition covarianceBase.h:487
-
covarianceBase::TransferMat
TMatrixD TransferMat
Matrix used to converting from PCA base to normal base.
Definition covarianceBase.h:485
-
covarianceBase::fParSigma_PCA
std::vector< double > fParSigma_PCA
Tells if parameter is fixed in PCA base or not.
Definition covarianceBase.h:493
-
covarianceBase::size
int size
Total number of parmas, deprecated, please don't use it.
Definition covarianceBase.h:411
-
covarianceBase::eigen_vectors
TMatrixD eigen_vectors
Eigen vectors only of params which are being decomposed.
Definition covarianceBase.h:479
-
covarianceBase::eigen_values
TVectorD eigen_values
Eigen value only of particles which are being decomposed.
Definition covarianceBase.h:477
-
covarianceBase::_fPreFitValue_PCA
std::vector< double > _fPreFitValue_PCA
Prefit value for PCA params.
Definition covarianceBase.h:483
-
covarianceBase::isDecomposed_PCA
std::vector< int > isDecomposed_PCA
If param is decomposed this will return -1, if not this will return enumerator to param in normal bas...
Definition covarianceBase.h:495
-
covarianceBase::eigen_values_master
std::vector< double > eigen_values_master
Eigen values which have dimension equal to _fNumParPCA, and can be used in CorrelateSteps.
Definition covarianceBase.h:481
+
232 //KS: make easy map so we could easily find un-decomposed parameters
+
233 isDecomposed_PCA.resize(_fNumParPCA);
+
234 fParSigma_PCA.resize(_fNumParPCA);
+
235 for (int i = 0; i < _fNumParPCA; ++i)
+
236 {
+
237 fParSigma_PCA[i] = 1;
+
238 isDecomposed_PCA[i] = -1;
+
239 }
+
240 for (int i = 0; i < FirstPCAdpar; ++i) isDecomposed_PCA[i] = i;
+
241
+
242 for (int i = FirstPCAdpar+nKeptPCApars+1; i < _fNumParPCA; ++i) isDecomposed_PCA[i] = i+(size-_fNumParPCA);
+
243
+
244 #ifdef DEBUG_PCA
+
245 //KS: Let's dump all useful matrices to properly validate PCA
+
246 DebugPCA(sum, temp, submat);
+
247 #endif
+
248}
+
MACH3LOG_ERROR
#define MACH3LOG_ERROR
Definition MaCh3Logger.h:18
+
covarianceBase::nKeptPCApars
int nKeptPCApars
Total number that remained after applying PCA Threshold.
Definition covarianceBase.h:489
+
covarianceBase::TransferMatT
TMatrixD TransferMatT
Matrix used to converting from normal base to PCA base.
Definition covarianceBase.h:501
+
covarianceBase::TransferMat
TMatrixD TransferMat
Matrix used to converting from PCA base to normal base.
Definition covarianceBase.h:499
+
covarianceBase::fParSigma_PCA
std::vector< double > fParSigma_PCA
Tells if parameter is fixed in PCA base or not.
Definition covarianceBase.h:507
+
covarianceBase::size
int size
Total number of params, deprecated, please don't use it.
Definition covarianceBase.h:425
+
covarianceBase::eigen_vectors
TMatrixD eigen_vectors
Eigen vectors only of params which are being decomposed.
Definition covarianceBase.h:493
+
covarianceBase::eigen_values
TVectorD eigen_values
Eigen value only of particles which are being decomposed.
Definition covarianceBase.h:491
+
covarianceBase::_fPreFitValue_PCA
std::vector< double > _fPreFitValue_PCA
Prefit value for PCA params.
Definition covarianceBase.h:497
+
covarianceBase::isDecomposed_PCA
std::vector< int > isDecomposed_PCA
If param is decomposed this will return -1, if not this will return enumerator to param in normal bas...
Definition covarianceBase.h:509
+
covarianceBase::eigen_values_master
std::vector< double > eigen_values_master
Eigen values which have dimension equal to _fNumParPCA, and can be used in CorrelateSteps.
Definition covarianceBase.h:495
@@ -1307,94 +1297,55 @@

Definition at line 838 of file covarianceBase.cpp.

-
838 {
-
839// ************************************************
-
840 //KS: Using custom function compared to ROOT one with 8 threads we have almost factor 2 performance increase, by replacing TMatrix with just double we increase it even more
-
841 MatrixVectorMulti(corr_throw, throwMatrixCholDecomp, randParams, _fNumPar);
-
842
-
843 // If not doing PCA
-
844 if (!pca) {
-
845#ifdef MULTITHREAD
-
846#pragma omp parallel for
-
847#endif
-
848 for (int i = 0; i < _fNumPar; ++i) {
-
849 if (_fError[i] > 0.) {
-
850 _fPropVal[i] = _fCurrVal[i] + corr_throw[i]*_fGlobalStepScale*_fIndivStepScale[i];
-
851 }
-
852 }
-
853 // If doing PCA throw uncorrelated in PCA basis (orthogonal basis by definition)
-
854 } else {
-
855 // Throw around the current step
-
856#ifdef MULTITHREAD
-
857#pragma omp parallel for
-
858#endif
-
859 for (int i = 0; i < _fNumParPCA; ++i)
-
860 {
-
861 if (fParSigma_PCA[i] > 0.)
-
862 {
-
863 double IndStepScale = 1.;
-
864 //KS: If undecomposed parameter apply individual step scale and Cholesky for better acceptance rate
-
865 if(isDecomposed_PCA[i] >= 0)
-
866 {
-
867 IndStepScale *= _fIndivStepScale[isDecomposed_PCA[i]];
-
868 IndStepScale *= corr_throw[isDecomposed_PCA[i]];
-
869 }
-
870 //If decomposed apply only random number
-
871 else
-
872 {
-
873 IndStepScale *= randParams[i];
-
874 //KS: All PCA-ed parameters have the same step scale
-
875 IndStepScale *= _fIndivStepScale[FirstPCAdpar];
-
876 }
-
877 fParProp_PCA(i) = fParCurr_PCA(i)+_fGlobalStepScale*IndStepScale*eigen_values_master[i];
-
878 }
-
879 }
-
880 // Then update the parameter basis
-
881 TransferToParam();
-
882 }
-
883}
-
covarianceBase::_fGlobalStepScale
double _fGlobalStepScale
Global step scale applied ot all params in this class.
Definition covarianceBase.h:429
-
covarianceBase::MatrixVectorMulti
void MatrixVectorMulti(double *_restrict_ VecMulti, double **_restrict_ matrix, const double *_restrict_ vector, const int n)
KS: Custom function to perform multiplication of matrix and vector with multithreading.
Definition covarianceBase.cpp:1222
-
- - - -

◆ createNewAdaptiveCovariance()

- -
-
- - - - - -
- - - - - - - -
void covarianceBase::createNewAdaptiveCovariance ()
- 		-protected
-
- -

method to create new throw matrix

- -

Definition at line 1590 of file covarianceBase.cpp.

-
1590 {
-
1591// ********************************************
-
1592 // If we don't have a covariance matrix to start from for adaptive tune we need to make one!
-
1593 use_adaptive=true;
-
1594 adaption_struct.adaptive_covariance = new TMatrixDSym(size);
-
1595 adaption_struct.adaptive_covariance->Zero();
-
1596 adaption_struct.par_means = std::vector<double>(size, 0);
-
1597}
-
covarianceBase::use_adaptive
bool use_adaptive
Are we using AMCMC?
Definition covarianceBase.h:522
-
adaptive_mcmc::AdaptiveMCMCStruct::par_means
std::vector< double > par_means
Mean values for all parameters.
Definition adaptiveMCMCStruct.h:36
+

Definition at line 839 of file covarianceBase.cpp.

+
839 {
+
840// ************************************************
+
841 //KS: Using custom function compared to ROOT one with 8 threads we have almost factor 2 performance increase, by replacing TMatrix with just double we increase it even more
+
842 MatrixVectorMulti(corr_throw, throwMatrixCholDecomp, randParams, _fNumPar);
+
843
+
844 // If not doing PCA
+
845 if (!pca) {
+
846 #ifdef MULTITHREAD
+
847 #pragma omp parallel for
+
848 #endif
+
849 for (int i = 0; i < _fNumPar; ++i) {
+
850 if (_fError[i] > 0.) {
+
851 _fPropVal[i] = _fCurrVal[i] + corr_throw[i]*_fGlobalStepScale*_fIndivStepScale[i];
+
852 }
+
853 }
+
854 // If doing PCA throw uncorrelated in PCA basis (orthogonal basis by definition)
+
855 } else {
+
856 // Throw around the current step
+
857 #ifdef MULTITHREAD
+
858 #pragma omp parallel for
+
859 #endif
+
860 for (int i = 0; i < _fNumParPCA; ++i)
+
861 {
+
862 if (fParSigma_PCA[i] > 0.)
+
863 {
+
864 double IndStepScale = 1.;
+
865 //KS: If undecomposed parameter apply individual step scale and Cholesky for better acceptance rate
+
866 if(isDecomposed_PCA[i] >= 0)
+
867 {
+
868 IndStepScale *= _fIndivStepScale[isDecomposed_PCA[i]];
+
869 IndStepScale *= corr_throw[isDecomposed_PCA[i]];
+
870 }
+
871 //If decomposed apply only random number
+
872 else
+
873 {
+
874 IndStepScale *= randParams[i];
+
875 //KS: All PCA-ed parameters have the same step scale
+
876 IndStepScale *= _fIndivStepScale[FirstPCAdpar];
+
877 }
+
878 fParProp_PCA(i) = fParCurr_PCA(i)+_fGlobalStepScale*IndStepScale*eigen_values_master[i];
+
879 }
+
880 }
+
881 // Then update the parameter basis
+
882 TransferToParam();
+
883 }
+
884}
+
covarianceBase::_fGlobalStepScale
double _fGlobalStepScale
Global step scale applied ot all params in this class.
Definition covarianceBase.h:443
+
covarianceBase::MatrixVectorMulti
void MatrixVectorMulti(double *_restrict_ VecMulti, double **_restrict_ matrix, const double *_restrict_ vector, const int n)
KS: Custom function to perform multiplication of matrix and vector with multithreading.
Definition covarianceBase.cpp:1223
@@ -1415,36 +1366,35 @@

Definition at line 1720 of file covarianceBase.cpp.

-
1720 {
-
1721// ********************************************
-
1722
-
1723 TH2D* hMatrix = new TH2D(getName(), getName(), _fNumPar, 0.0, _fNumPar, _fNumPar, 0.0, _fNumPar);
-
1724
-
1725 for(int i = 0; i < _fNumPar; i++)
-
1726 {
-
1727 hMatrix->SetBinContent(i+1, i+1, 1.);
-
1728 hMatrix->GetXaxis()->SetBinLabel(i+1, GetParFancyName(i).c_str());
-
1729 hMatrix->GetYaxis()->SetBinLabel(i+1, GetParFancyName(i).c_str());
-
1730 }
-
1731
-
1732 #ifdef MULTITHREAD
-
1733 #pragma omp parallel for
-
1734 #endif
-
1735 for(int i = 0; i < _fNumPar; i++)
-
1736 {
-
1737 for(int j = 0; j <= i; j++)
-
1738 {
-
1739 const double Corr = (*covMatrix)(i,j) / ( getDiagonalError(i) * getDiagonalError(j));
-
1740 hMatrix->SetBinContent(i+1, j+1, Corr);
-
1741 hMatrix->SetBinContent(j+1, i+1, Corr);
-
1742 }
-
1743 }
-
1744 return hMatrix;
-
1745}
-
covarianceBase::getDiagonalError
double getDiagonalError(const int i)
Get diagonal error for ith parameter.
Definition covarianceBase.h:162
-
covarianceBase::GetParFancyName
std::string GetParFancyName(const int i)
Get fancy name of the Parameter.
Definition covarianceBase.h:153
-
covarianceBase::getName
const char * getName()
Get name of covariance.
Definition covarianceBase.h:144
+

Definition at line 1535 of file covarianceBase.cpp.

+
1535 {
+
1536// ********************************************
+
1537 TH2D* hMatrix = new TH2D(getName(), getName(), _fNumPar, 0.0, _fNumPar, _fNumPar, 0.0, _fNumPar);
+
1538
+
1539 for(int i = 0; i < _fNumPar; i++)
+
1540 {
+
1541 hMatrix->SetBinContent(i+1, i+1, 1.);
+
1542 hMatrix->GetXaxis()->SetBinLabel(i+1, GetParFancyName(i).c_str());
+
1543 hMatrix->GetYaxis()->SetBinLabel(i+1, GetParFancyName(i).c_str());
+
1544 }
+
1545
+
1546 #ifdef MULTITHREAD
+
1547 #pragma omp parallel for
+
1548 #endif
+
1549 for(int i = 0; i < _fNumPar; i++)
+
1550 {
+
1551 for(int j = 0; j <= i; j++)
+
1552 {
+
1553 const double Corr = (*covMatrix)(i,j) / ( getDiagonalError(i) * getDiagonalError(j));
+
1554 hMatrix->SetBinContent(i+1, j+1, Corr);
+
1555 hMatrix->SetBinContent(j+1, i+1, Corr);
+
1556 }
+
1557 }
+
1558 return hMatrix;
+
1559}
+
covarianceBase::getDiagonalError
double getDiagonalError(const int i)
Get diagonal error for ith parameter.
Definition covarianceBase.h:163
+
covarianceBase::GetParFancyName
std::string GetParFancyName(const int i)
Get fancy name of the Parameter.
Definition covarianceBase.h:154
+
covarianceBase::getName
const char * getName()
Get name of covariance.
Definition covarianceBase.h:145

@@ -1473,8 +1423,8 @@

Definition at line 136 of file covarianceBase.h.

-
136{ return covMatrix; }
+

Definition at line 137 of file covarianceBase.h.

+
137{ return covMatrix; }
@@ -1510,8 +1460,8 @@

Definition at line 162 of file covarianceBase.h.

-
162{ return std::sqrt((*covMatrix)(i,i)); }
+

Definition at line 163 of file covarianceBase.h.

+
163{ return std::sqrt((*covMatrix)(i,i)); }
@@ -1542,6 +1492,7 @@

Definition at line 173 of file covarianceBase.h.

173{return use_adaptive;}
+
covarianceBase::use_adaptive
bool use_adaptive
Are we using AMCMC?
Definition covarianceBase.h:519
@@ -1570,11 +1521,11 @@

Definition at line 273 of file covarianceBase.h.

-
273 {
-
274 if (!pca) { MACH3LOG_ERROR("Am not running in PCA mode"); throw; }
-
275 return eigen_values;
-
276 }
+

Definition at line 274 of file covarianceBase.h.

+
274 {
+
275 if (!pca) { MACH3LOG_ERROR("Am not running in PCA mode"); throw; }
+
276 return eigen_values;
+
277 }
@@ -1603,11 +1554,11 @@

Definition at line 278 of file covarianceBase.h.

-
278 {
-
279 if (!pca) { MACH3LOG_ERROR("Am not running in PCA mode"); throw; }
-
280 return eigen_values_master;
-
281 }
+

Definition at line 279 of file covarianceBase.h.

+
279 {
+
280 if (!pca) { MACH3LOG_ERROR("Am not running in PCA mode"); throw; }
+
281 return eigen_values_master;
+
282 }
@@ -1636,11 +1587,11 @@

Definition at line 268 of file covarianceBase.h.

-
268 {
-
269 if (!pca) { MACH3LOG_ERROR("Am not running in PCA mode"); throw; }
-
270 return eigen_vectors;
-
271 }
+

Definition at line 269 of file covarianceBase.h.

+
269 {
+
270 if (!pca) { MACH3LOG_ERROR("Am not running in PCA mode"); throw; }
+
271 return eigen_vectors;
+
272 }
@@ -1676,8 +1627,8 @@

Definition at line 141 of file covarianceBase.h.

-
141{ return _fFlatPrior[i]; }
+

Definition at line 142 of file covarianceBase.h.

+
142{ return _fFlatPrior[i]; }
@@ -1713,9 +1664,9 @@

Definition at line 232 of file covarianceBase.h.

-
232{ return _fGenerated[i];}
-
covarianceBase::_fGenerated
std::vector< double > _fGenerated
Generated value of the parameter.
Definition covarianceBase.h:449
+

Definition at line 233 of file covarianceBase.h.

+
233{ return _fGenerated[i];}
+
covarianceBase::_fGenerated
std::vector< double > _fGenerated
Generated value of the parameter.
Definition covarianceBase.h:463
@@ -1742,8 +1693,8 @@

-

Definition at line 215 of file covarianceBase.h.

-
215{return _fGenerated;}
+

Definition at line 216 of file covarianceBase.h.

+
216{return _fGenerated;}
@@ -1779,8 +1730,8 @@

Definition at line 241 of file covarianceBase.h.

-
241{return _fIndivStepScale.at(ParameterIndex); }
+

Definition at line 242 of file covarianceBase.h.

+
242{return _fIndivStepScale.at(ParameterIndex); }
@@ -1809,8 +1760,8 @@

Definition at line 158 of file covarianceBase.h.

-
158{ return inputFile; }
+

Definition at line 159 of file covarianceBase.h.

+
159{ return inputFile; }
@@ -1839,8 +1790,8 @@

Definition at line 138 of file covarianceBase.h.

-
138{ return invCovMatrix; }
+

Definition at line 139 of file covarianceBase.h.

+
139{ return invCovMatrix; }
@@ -1871,21 +1822,20 @@

covarianceOsc.

-

Definition at line 1034 of file covarianceBase.cpp.

-
1034 {
-
1035// ********************************************
-
1036
-
1037 // Checkbounds and calclikelihood are virtual
-
1038 // Default behaviour is to reject negative values + do std llh calculation
-
1039 const int NOutside = CheckBounds();
-
1040
-
1041 if(NOutside > 0)
-
1042 return NOutside*_LARGE_LOGL_;
-
1043
-
1044 return CalcLikelihood();
-
1045}
-
covarianceBase::CalcLikelihood
double CalcLikelihood()
Calc penalty term based on inverted covariance matrix.
Definition covarianceBase.cpp:999
-
covarianceBase::CheckBounds
virtual int CheckBounds()
Check if parameters were proposed outside physical boundary.
Definition covarianceBase.cpp:1019
+

Definition at line 1037 of file covarianceBase.cpp.

+
1037 {
+
1038// ********************************************
+
1039 // Checkbounds and calclikelihood are virtual
+
1040 // Default behaviour is to reject negative values + do std llh calculation
+
1041 const int NOutside = CheckBounds();
+
1042
+
1043 if(NOutside > 0)
+
1044 return NOutside*_LARGE_LOGL_;
+
1045
+
1046 return CalcLikelihood();
+
1047}
+
covarianceBase::CalcLikelihood
double CalcLikelihood()
Calc penalty term based on inverted covariance matrix.
Definition covarianceBase.cpp:1002
+
covarianceBase::CheckBounds
virtual int CheckBounds()
Check if parameters were proposed outside physical boundary.
Definition covarianceBase.cpp:1022
_LARGE_LOGL_
#define _LARGE_LOGL_
Large Likelihood is used it parameter go out of physical boundary, this indicates in MCMC that such s...
Definition covarianceBase.h:12
@@ -1922,8 +1872,8 @@

Definition at line 238 of file covarianceBase.h.

-
238{ return _fLowBound[i]; }
+

Definition at line 239 of file covarianceBase.h.

+
239{ return _fLowBound[i]; }
@@ -1952,8 +1902,8 @@

Definition at line 144 of file covarianceBase.h.

-
144{ return matrixName; }
+

Definition at line 145 of file covarianceBase.h.

+
145{ return matrixName; }
@@ -1991,9 +1941,9 @@

covarianceXsec.

-

Definition at line 229 of file covarianceBase.h.

-
229{ return getParInit(i); }
-
covarianceBase::getParInit
double getParInit(const int i)
Get prior parameter value.
Definition covarianceBase.h:226
+

Definition at line 230 of file covarianceBase.h.

+
230{ return getParInit(i); }
+
covarianceBase::getParInit
double getParInit(const int i)
Get prior parameter value.
Definition covarianceBase.h:227
@@ -2022,17 +1972,17 @@

covarianceXsec.

-

Definition at line 1707 of file covarianceBase.cpp.

-
1707 {
-
1708// ********************************************
-
1709
-
1710 std::vector<double> nominal(_fNumPar);
-
1711 for (int i = 0; i < _fNumPar; ++i)
-
1712 {
-
1713 nominal[i] = _fPreFitValue[i];
-
1714 }
-
1715 return nominal;
-
1716}
+

Definition at line 1522 of file covarianceBase.cpp.

+
1522 {
+
1523// ********************************************
+
1524
+
1525 std::vector<double> nominal(_fNumPar);
+
1526 for (int i = 0; i < _fNumPar; ++i)
+
1527 {
+
1528 nominal[i] = _fPreFitValue[i];
+
1529 }
+
1530 return nominal;
+
1531}
nominal
std::vector< int > nominal
Definition GetPenaltyTerm.cpp:38
@@ -2062,11 +2012,11 @@

Definition at line 319 of file covarianceBase.h.

-
319 {
-
320 if (pca) return _fNumParPCA;
-
321 else return _fNumPar;
-
322 }
+

Definition at line 320 of file covarianceBase.h.

+
320 {
+
321 if (pca) return _fNumParPCA;
+
322 else return _fNumPar;
+
323 }
@@ -2095,8 +2045,8 @@

Definition at line 212 of file covarianceBase.h.

-
212{return _fNumPar;}
+

Definition at line 213 of file covarianceBase.h.

+
213{return _fNumPar;}
@@ -2123,8 +2073,10 @@

-

Definition at line 184 of file covarianceBase.h.

-
184{return adaption_struct.par_means;}
+

Definition at line 185 of file covarianceBase.h.

+
185{return AdaptiveHandler.par_means;}
+
adaptive_mcmc::AdaptiveMCMCHandler::par_means
std::vector< double > par_means
Mean values for all parameters.
Definition AdaptiveMCMCHandler.h:78
+
covarianceBase::AdaptiveHandler
adaptive_mcmc::AdaptiveMCMCHandler AdaptiveHandler
Struct containing information about adaption.
Definition covarianceBase.h:524
@@ -2160,8 +2112,8 @@

Definition at line 223 of file covarianceBase.h.

-
223{ return _fCurrVal[i]; }
+

Definition at line 224 of file covarianceBase.h.

+
224{ return _fCurrVal[i]; }
@@ -2197,11 +2149,11 @@

Definition at line 251 of file covarianceBase.h.

-
251 {
-
252 if (!pca) { MACH3LOG_ERROR("Am not running in PCA mode"); throw; }
-
253 return fParCurr_PCA(i);
-
254 }
+

Definition at line 252 of file covarianceBase.h.

+
252 {
+
253 if (!pca) { MACH3LOG_ERROR("Am not running in PCA mode"); throw; }
+
254 return fParCurr_PCA(i);
+
255 }
@@ -2237,9 +2189,9 @@

Definition at line 153 of file covarianceBase.h.

-
153{return _fFancyNames[i];}
-
covarianceBase::_fFancyNames
std::vector< std::string > _fFancyNames
Fancy name for example rather than xsec_0 it is MAQE, useful for human reading.
Definition covarianceBase.h:437
+

Definition at line 154 of file covarianceBase.h.

+
154{return _fFancyNames[i];}
+
covarianceBase::_fFancyNames
std::vector< std::string > _fFancyNames
Fancy name for example rather than xsec_0 it is MAQE, useful for human reading.
Definition covarianceBase.h:451
@@ -2275,8 +2227,8 @@

Definition at line 156 of file covarianceBase.h.

-
156{ return _fFancyNames[i].c_str(); }
+

Definition at line 157 of file covarianceBase.h.

+
157{ return _fFancyNames[i].c_str(); }
@@ -2312,8 +2264,8 @@

Definition at line 226 of file covarianceBase.h.

-
226{ return _fPreFitValue[i]; }
+

Definition at line 227 of file covarianceBase.h.

+
227{ return _fPreFitValue[i]; }
@@ -2349,9 +2301,9 @@

Definition at line 147 of file covarianceBase.h.

-
147{return _fNames[i];}
-
covarianceBase::_fNames
std::vector< std::string > _fNames
ETA _fNames is set automatically in the covariance class to be something like xsec_i,...
Definition covarianceBase.h:435
+

Definition at line 148 of file covarianceBase.h.

+
148{return _fNames[i];}
+
covarianceBase::_fNames
std::vector< std::string > _fNames
ETA _fNames is set automatically in the covariance class to be something like xsec_i,...
Definition covarianceBase.h:449
@@ -2387,8 +2339,8 @@

Definition at line 150 of file covarianceBase.h.

-
150{ return _fNames[i].c_str(); }
+

Definition at line 151 of file covarianceBase.h.

+
151{ return _fNames[i].c_str(); }
@@ -2424,8 +2376,8 @@

Definition at line 220 of file covarianceBase.h.

-
220{ return _fPropVal[i]; }
+

Definition at line 221 of file covarianceBase.h.

+
221{ return _fPropVal[i]; }
@@ -2461,11 +2413,11 @@

Definition at line 244 of file covarianceBase.h.

-
244 {
-
245 if (!pca) { MACH3LOG_ERROR("Am not running in PCA mode"); throw; }
-
246 return fParProp_PCA(i);
-
247 }
+

Definition at line 245 of file covarianceBase.h.

+
245 {
+
246 if (!pca) { MACH3LOG_ERROR("Am not running in PCA mode"); throw; }
+
247 return fParProp_PCA(i);
+
248 }
@@ -2492,8 +2444,8 @@

-

Definition at line 214 of file covarianceBase.h.

-
214{return _fPreFitValue;}
+

Definition at line 215 of file covarianceBase.h.

+
215{return _fPreFitValue;}
@@ -2514,13 +2466,13 @@

Definition at line 607 of file covarianceBase.cpp.

-
607 {
-
608// ********************************************
-
609 std::vector<double> props(_fNumPar);
-
610 for (int i = 0; i < _fNumPar; ++i) props[i] = _fPropVal[i];
-
611 return props;
-
612}
+

Definition at line 606 of file covarianceBase.cpp.

+
606 {
+
607// ********************************************
+
608 std::vector<double> props(_fNumPar);
+
609 for (int i = 0; i < _fNumPar; ++i) props[i] = _fPropVal[i];
+
610 return props;
+
611}
@@ -2549,8 +2501,8 @@

getNpars()

-

Definition at line 317 of file covarianceBase.h.

-
317{ return _fNumPar; }
+

Definition at line 318 of file covarianceBase.h.

+
318{ return _fNumPar; }
@@ -2577,8 +2529,8 @@

-

Definition at line 182 of file covarianceBase.h.

-
182{return throwMatrix;}
+

Definition at line 183 of file covarianceBase.h.

+
183{return throwMatrix;}
@@ -2605,8 +2557,8 @@

-

Definition at line 183 of file covarianceBase.h.

-
183{return throwMatrix_CholDecomp;}
+

Definition at line 184 of file covarianceBase.h.

+
184{return throwMatrix_CholDecomp;}
@@ -2635,11 +2587,11 @@

Definition at line 263 of file covarianceBase.h.

-
263 {
-
264 if (!pca) { MACH3LOG_ERROR("Am not running in PCA mode"); throw; }
-
265 return TransferMat;
-
266 }
+

Definition at line 264 of file covarianceBase.h.

+
264 {
+
265 if (!pca) { MACH3LOG_ERROR("Am not running in PCA mode"); throw; }
+
266 return TransferMat;
+
267 }
@@ -2675,8 +2627,8 @@

Definition at line 235 of file covarianceBase.h.

-
235{ return _fUpBound[i];}
+

Definition at line 236 of file covarianceBase.h.

+
236{ return _fUpBound[i];}
@@ -2714,83 +2666,85 @@

-

Definition at line 256 of file covarianceBase.cpp.

-
256 {
-
257// ********************************************
-
258
-
259 // Set the covariance matrix from input ROOT file (e.g. flux, ND280, NIWG)
-
260 TFile *infile = new TFile(file, "READ");
-
261 if (infile->IsZombie()) {
-
262 MACH3LOG_ERROR("Could not open input covariance ROOT file {} !!!", file);
-
263 MACH3LOG_ERROR("Was about to retrieve matrix with name {}", name);
-
264 throw;
-
265 }
-
266
-
267 // Should put in a
-
268 TMatrixDSym *CovMat = (TMatrixDSym*)(infile->Get(name));
-
269 if (CovMat == NULL) {
-
270 MACH3LOG_ERROR("Could not find covariance matrix name {} in file {}", name, file);
-
271 MACH3LOG_ERROR("Are you really sure {} exists in the file?", name);
-
272 throw MaCh3Exception(__FILE__ , __LINE__ );
-
273 }
-
274
-
275 PrintLength = 35;
-
276
-
277 const int nThreads = MaCh3Utils::GetNThreads();
-
278 //KS: set Random numbers for each thread so each thread has different seed
-
279 //or for one thread if without MULTITHREAD
-
280 random_number = new TRandom3*[nThreads]();
-
281 for (int iThread = 0; iThread < nThreads; iThread++) {
-
282 random_number[iThread] = new TRandom3(0);
-
283 }
-
284
-
285 // Not using adaptive by default
-
286 setAdaptionDefaults();
-
287 // Set the covariance matrix
-
288 size = CovMat->GetNrows();
-
289 _fNumPar = size;
-
290
-
291 InvertCovMatrix = new double*[_fNumPar]();
-
292 throwMatrixCholDecomp = new double*[_fNumPar]();
-
293 // Set the defaults to true
-
294 for(int i = 0; i < _fNumPar; i++)
-
295 {
-
296 InvertCovMatrix[i] = new double[_fNumPar]();
-
297 throwMatrixCholDecomp[i] = new double[_fNumPar]();
-
298 for (int j = 0; j < _fNumPar; j++)
-
299 {
-
300 InvertCovMatrix[i][j] = 0.;
-
301 throwMatrixCholDecomp[i][j] = 0.;
-
302 }
-
303 }
-
304
-
305 setName(name);
-
306 MakePosDef(CovMat);
-
307 setCovMatrix(CovMat);
-
308
-
309 if (_fNumPar <= 0) {
-
310 MACH3LOG_CRITICAL("Covariance matrix {} has {} entries!", getName(), _fNumPar);
-
311 throw;
-
312 }
-
313 _fNumParPCA = _fNumPar;
-
314
-
315 ReserveMemory(_fNumPar);
+

Initialisation of the class using matrix from root file.

+ +

Definition at line 251 of file covarianceBase.cpp.

+
251 {
+
252// ********************************************
+
253
+
254 // Set the covariance matrix from input ROOT file (e.g. flux, ND280, NIWG)
+
255 TFile *infile = new TFile(file, "READ");
+
256 if (infile->IsZombie()) {
+
257 MACH3LOG_ERROR("Could not open input covariance ROOT file {} !!!", file);
+
258 MACH3LOG_ERROR("Was about to retrieve matrix with name {}", name);
+
259 throw;
+
260 }
+
261
+
262 // Should put in a
+
263 TMatrixDSym *CovMat = (TMatrixDSym*)(infile->Get(name));
+
264 if (CovMat == NULL) {
+
265 MACH3LOG_ERROR("Could not find covariance matrix name {} in file {}", name, file);
+
266 MACH3LOG_ERROR("Are you really sure {} exists in the file?", name);
+
267 throw MaCh3Exception(__FILE__ , __LINE__ );
+
268 }
+
269
+
270 PrintLength = 35;
+
271
+
272 const int nThreads = MaCh3Utils::GetNThreads();
+
273 //KS: set Random numbers for each thread so each thread has different seed
+
274 //or for one thread if without MULTITHREAD
+
275 random_number = new TRandom3*[nThreads]();
+
276 for (int iThread = 0; iThread < nThreads; iThread++) {
+
277 random_number[iThread] = new TRandom3(0);
+
278 }
+
279
+
280 // Not using adaptive by default
+
281 setAdaptionDefaults();
+
282 // Set the covariance matrix
+
283 size = CovMat->GetNrows();
+
284 _fNumPar = size;
+
285
+
286 InvertCovMatrix = new double*[_fNumPar]();
+
287 throwMatrixCholDecomp = new double*[_fNumPar]();
+
288 // Set the defaults to true
+
289 for(int i = 0; i < _fNumPar; i++)
+
290 {
+
291 InvertCovMatrix[i] = new double[_fNumPar]();
+
292 throwMatrixCholDecomp[i] = new double[_fNumPar]();
+
293 for (int j = 0; j < _fNumPar; j++)
+
294 {
+
295 InvertCovMatrix[i][j] = 0.;
+
296 throwMatrixCholDecomp[i][j] = 0.;
+
297 }
+
298 }
+
299
+
300 setName(name);
+
301 MakePosDef(CovMat);
+
302 setCovMatrix(CovMat);
+
303
+
304 if (_fNumPar <= 0) {
+
305 MACH3LOG_CRITICAL("Covariance matrix {} has {} entries!", getName(), _fNumPar);
+
306 throw;
+
307 }
+
308 _fNumParPCA = _fNumPar;
+
309
+
310 ReserveMemory(_fNumPar);
+
311
+
312 infile->Close();
+
313
+
314 MACH3LOG_INFO("Created covariance matrix named: {}", getName());
+
315 MACH3LOG_INFO("from file: {}", file);
316
-
317 infile->Close();
-
318
-
319 MACH3LOG_INFO("Created covariance matrix named: {}", getName());
-
320 MACH3LOG_INFO("from file: {}", file);
-
321
-
322 delete infile;
-
323}
-
MACH3LOG_CRITICAL
#define MACH3LOG_CRITICAL
Definition MaCh3Logger.h:16
-
MaCh3Exception
Custom exception class for MaCh3 errors.
Definition MaCh3Exception.h:10
-
covarianceBase::setCovMatrix
void setCovMatrix(TMatrixDSym *cov)
Set covariance matrix.
Definition covarianceBase.cpp:500
-
covarianceBase::setName
void setName(const char *name)
Set matrix name.
Definition covarianceBase.h:68
-
covarianceBase::ReserveMemory
void ReserveMemory(const int size)
Initialise vectors with parameters information.
Definition covarianceBase.cpp:521
-
covarianceBase::PrintLength
unsigned int PrintLength
KS: This is used when printing parameters, sometimes we have super long parameters name,...
Definition covarianceBase.h:432
+
317 delete infile;
+
318}
+
MACH3LOG_CRITICAL
#define MACH3LOG_CRITICAL
Definition MaCh3Logger.h:19
+
MaCh3Exception
Custom exception class for MaCh3 errors.
Definition MaCh3Exception.h:12
+
covarianceBase::setCovMatrix
void setCovMatrix(TMatrixDSym *cov)
Set covariance matrix.
Definition covarianceBase.cpp:495
+
covarianceBase::setName
void setName(const char *name)
Set matrix name.
Definition covarianceBase.h:69
+
covarianceBase::ReserveMemory
void ReserveMemory(const int size)
Initialise vectors with parameters information.
Definition covarianceBase.cpp:516
+
covarianceBase::PrintLength
unsigned int PrintLength
KS: This is used when printing parameters, sometimes we have super long parameters name,...
Definition covarianceBase.h:446
covarianceBase::MakePosDef
void MakePosDef(TMatrixDSym *cov=nullptr)
Make matrix positive definite by adding small values to diagonal, necessary for inverting matrix.
Definition covarianceBase.cpp:1283
-
covarianceBase::setAdaptionDefaults
void setAdaptionDefaults()
sets default values for adaptive MCMC parameters
Definition covarianceBase.cpp:1409
+
covarianceBase::setAdaptionDefaults
void setAdaptionDefaults()
sets default values for adaptive MCMC parameters
Definition covarianceBase.cpp:1391
@@ -2826,148 +2780,148 @@

Definition at line 330 of file covarianceBase.cpp.

-
330 {
-
331// ********************************************
-
332 _fYAMLDoc["Systematics"] = YAML::Node(YAML::NodeType::Sequence);
-
333 for(unsigned int i = 0; i < YAMLFile.size(); i++)
-
334 {
-
335 YAML::Node YAMLDocTemp = YAML::LoadFile(YAMLFile[i]);
-
336 for (const auto& item : YAMLDocTemp["Systematics"]) {
-
337 _fYAMLDoc["Systematics"].push_back(item);
-
338 }
-
339 }
-
340
-
341 const int nThreads = MaCh3Utils::GetNThreads();
-
342 //KS: set Random numbers for each thread so each thread has different seed
-
343 //or for one thread if without MULTITHREAD
-
344 random_number = new TRandom3*[nThreads]();
-
345 for (int iThread = 0; iThread < nThreads; iThread++) {
-
346 random_number[iThread] = new TRandom3(0);
-
347 }
-
348
-
349 PrintLength = 35;
+

Definition at line 325 of file covarianceBase.cpp.

+
325 {
+
326// ********************************************
+
327 _fYAMLDoc["Systematics"] = YAML::Node(YAML::NodeType::Sequence);
+
328 for(unsigned int i = 0; i < YAMLFile.size(); i++)
+
329 {
+
330 YAML::Node YAMLDocTemp = YAML::LoadFile(YAMLFile[i]);
+
331 for (const auto& item : YAMLDocTemp["Systematics"]) {
+
332 _fYAMLDoc["Systematics"].push_back(item);
+
333 }
+
334 }
+
335
+
336 const int nThreads = MaCh3Utils::GetNThreads();
+
337 //KS: set Random numbers for each thread so each thread has different seed
+
338 //or for one thread if without MULTITHREAD
+
339 random_number = new TRandom3*[nThreads]();
+
340 for (int iThread = 0; iThread < nThreads; iThread++) {
+
341 random_number[iThread] = new TRandom3(0);
+
342 }
+
343
+
344 PrintLength = 35;
+
345
+
346
+
347 // Set the covariance matrix
+
348 _fNumPar = _fYAMLDoc["Systematics"].size();
+
349 size = _fNumPar;
350
-
351
-
352 // Set the covariance matrix
-
353 _fNumPar = _fYAMLDoc["Systematics"].size();
-
354 size = _fNumPar;
-
355
-
356 setAdaptionDefaults();
-
357
-
358 InvertCovMatrix = new double*[_fNumPar]();
-
359 throwMatrixCholDecomp = new double*[_fNumPar]();
-
360 // Set the defaults to true
-
361 for(int i = 0; i < _fNumPar; i++)
-
362 {
-
363 InvertCovMatrix[i] = new double[_fNumPar]();
-
364 throwMatrixCholDecomp[i] = new double[_fNumPar]();
-
365 for (int j = 0; j < _fNumPar; j++)
-
366 {
-
367 InvertCovMatrix[i][j] = 0.;
-
368 throwMatrixCholDecomp[i][j] = 0.;
-
369 }
-
370 }
+
351 setAdaptionDefaults();
+
352
+
353 InvertCovMatrix = new double*[_fNumPar]();
+
354 throwMatrixCholDecomp = new double*[_fNumPar]();
+
355 // Set the defaults to true
+
356 for(int i = 0; i < _fNumPar; i++)
+
357 {
+
358 InvertCovMatrix[i] = new double[_fNumPar]();
+
359 throwMatrixCholDecomp[i] = new double[_fNumPar]();
+
360 for (int j = 0; j < _fNumPar; j++)
+
361 {
+
362 InvertCovMatrix[i][j] = 0.;
+
363 throwMatrixCholDecomp[i][j] = 0.;
+
364 }
+
365 }
+
366
+
367 ReserveMemory(_fNumPar);
+
368
+
369 TMatrixDSym* _fCovMatrix = new TMatrixDSym(_fNumPar);
+
370 //_fDetString = std::vector<std::string>(_fNumPar);
371
-
372 ReserveMemory(_fNumPar);
-
373
-
374 TMatrixDSym* _fCovMatrix = new TMatrixDSym(_fNumPar);
-
375 //_fDetString = std::vector<std::string>(_fNumPar);
-
376
-
377 int i = 0;
-
378 std::vector<std::map<std::string,double>> Correlations(_fNumPar);
-
379 std::map<std::string, int> CorrNamesMap;
-
380
-
381 //ETA - read in the systematics. Would be good to add in some checks to make sure
-
382 //that there are the correct number of entries i.e. are the _fNumPar for Names,
-
383 //PreFitValues etc etc.
-
384 for (auto const &param : _fYAMLDoc["Systematics"])
-
385 {
-
386 _fFancyNames[i] = (param["Systematic"]["Names"]["FancyName"].as<std::string>());
-
387 _fPreFitValue[i] = (param["Systematic"]["ParameterValues"]["PreFitValue"].as<double>());
-
388 _fGenerated[i] = (param["Systematic"]["ParameterValues"]["Generated"].as<double>());
-
389 _fIndivStepScale[i] = (param["Systematic"]["StepScale"]["MCMC"].as<double>());
-
390 _fError[i] = (param["Systematic"]["Error"].as<double>());
+
372 int i = 0;
+
373 std::vector<std::map<std::string,double>> Correlations(_fNumPar);
+
374 std::map<std::string, int> CorrNamesMap;
+
375
+
376 //ETA - read in the systematics. Would be good to add in some checks to make sure
+
377 //that there are the correct number of entries i.e. are the _fNumPar for Names,
+
378 //PreFitValues etc etc.
+
379 for (auto const &param : _fYAMLDoc["Systematics"])
+
380 {
+
381 _fFancyNames[i] = (param["Systematic"]["Names"]["FancyName"].as<std::string>());
+
382 _fPreFitValue[i] = (param["Systematic"]["ParameterValues"]["PreFitValue"].as<double>());
+
383 _fGenerated[i] = (param["Systematic"]["ParameterValues"]["Generated"].as<double>());
+
384 _fIndivStepScale[i] = (param["Systematic"]["StepScale"]["MCMC"].as<double>());
+
385 _fError[i] = (param["Systematic"]["Error"].as<double>());
+
386
+
387 //ETA - a bit of a fudge but works
+
388 std::vector<double> TempBoundsVec = param["Systematic"]["ParameterBounds"].as<std::vector<double>>();
+
389 _fLowBound[i] = TempBoundsVec[0];
+
390 _fUpBound[i] = TempBoundsVec[1];
391
-
392 //ETA - a bit of a fudge but works
-
393 std::vector<double> TempBoundsVec = param["Systematic"]["ParameterBounds"].as<std::vector<double>>();
-
394 _fLowBound[i] = TempBoundsVec[0];
-
395 _fUpBound[i] = TempBoundsVec[1];
-
396
-
397 //ETA - now for parameters which are optional and have default values
-
398 _fFlatPrior[i] = GetFromManager<bool>(param["Systematic"]["FlatPrior"], false);
-
399
-
400 //Fill the map to get the correlations later as well
-
401 CorrNamesMap[param["Systematic"]["Names"]["FancyName"].as<std::string>()]=i;
-
402
-
403 //Also loop through the correlations
-
404 if(param["Systematic"]["Correlations"]) {
-
405 for(unsigned int Corr_i = 0; Corr_i < param["Systematic"]["Correlations"].size(); ++Corr_i){
-
406 for (YAML::const_iterator it=param["Systematic"]["Correlations"][Corr_i].begin();it!=param["Systematic"]["Correlations"][Corr_i].end();++it) {
-
407 Correlations[i][it->first.as<std::string>()] = it->second.as<double>();
-
408 }
-
409 }
-
410 }
-
411 i++;
-
412 }
-
413
-
414 //ETA
-
415 //Now that we've been through all systematic let's fill the covmatrix
-
416 //This makes the root TCov from YAML
-
417 for(int j = 0; j < _fNumPar;j++) {
-
418 (*_fCovMatrix)(j, j)=_fError[j]*_fError[j];
-
419 //Get the map of parameter name to correlation from the Correlations object
-
420 for (auto const& pair : Correlations[j]) {
-
421 auto const& key = pair.first;
-
422 auto const& val = pair.second;
-
423 int index = -1;
-
424 //If you found the parameter name then get the index
-
425 if (CorrNamesMap.find(key) != CorrNamesMap.end()) {
-
426 index = CorrNamesMap[key];
-
427 }
-
428 else {
-
429 MACH3LOG_ERROR("Parameter {} not in list! Check your spelling?", key);
-
430 throw MaCh3Exception(__FILE__ , __LINE__ );
-
431 }
-
432 double Corr1 = val;
-
433 double Corr2 = 0;
-
434 if(Correlations[index].find(_fFancyNames[j]) != Correlations[index].end()) {
-
435 Corr2 = Correlations[index][_fFancyNames[j]];
-
436 //Do they agree to better than float precision?
-
437 if(std::abs(Corr2 - Corr1) > FLT_EPSILON) {
-
438 MACH3LOG_ERROR("Correlations are not equal between {} and {}", _fFancyNames[j], key);
-
439 MACH3LOG_ERROR("Got : {} and {}", Corr2, Corr1);
-
440 throw MaCh3Exception(__FILE__ , __LINE__ );
-
441 }
-
442 } else {
-
443 MACH3LOG_ERROR("Correlation does not appear reciprocally between {} and {}", _fFancyNames[j], key);
-
444 throw MaCh3Exception(__FILE__ , __LINE__ );
-
445 }
-
446 (*_fCovMatrix)(j, index)= (*_fCovMatrix)(index, j) = Corr1*_fError[j]*_fError[index];
-
447 }
-
448 }
-
449
-
450 //Now make positive definite
-
451 MakePosDef(_fCovMatrix);
-
452 setCovMatrix(_fCovMatrix);
-
453
-
454 if (_fNumPar <= 0) {
-
455 MACH3LOG_ERROR("Covariance object has {} systematics!", _fNumPar);
-
456 throw;
-
457 }
-
458 _fNumParPCA = _fNumPar;
-
459
-
460 MACH3LOG_INFO("Created covariance matrix from files: ");
-
461 for(const auto &file : YAMLFile){
-
462 MACH3LOG_INFO("{} ", file);
-
463 }
-
464 MACH3LOG_INFO("----------------");
-
465 MACH3LOG_INFO("Found {} systematics parameters in total", _fNumPar);
-
466 MACH3LOG_INFO("----------------");
-
467
-
468 return;
-
469}
-
covarianceBase::_fYAMLDoc
YAML::Node _fYAMLDoc
Stores config describing systematics.
Definition covarianceBase.h:439
+
392 //ETA - now for parameters which are optional and have default values
+
393 _fFlatPrior[i] = GetFromManager<bool>(param["Systematic"]["FlatPrior"], false);
+
394
+
395 //Fill the map to get the correlations later as well
+
396 CorrNamesMap[param["Systematic"]["Names"]["FancyName"].as<std::string>()]=i;
+
397
+
398 //Also loop through the correlations
+
399 if(param["Systematic"]["Correlations"]) {
+
400 for(unsigned int Corr_i = 0; Corr_i < param["Systematic"]["Correlations"].size(); ++Corr_i){
+
401 for (YAML::const_iterator it=param["Systematic"]["Correlations"][Corr_i].begin();it!=param["Systematic"]["Correlations"][Corr_i].end();++it) {
+
402 Correlations[i][it->first.as<std::string>()] = it->second.as<double>();
+
403 }
+
404 }
+
405 }
+
406 i++;
+
407 }
+
408
+
409 //ETA
+
410 //Now that we've been through all systematic let's fill the covmatrix
+
411 //This makes the root TCov from YAML
+
412 for(int j = 0; j < _fNumPar;j++) {
+
413 (*_fCovMatrix)(j, j)=_fError[j]*_fError[j];
+
414 //Get the map of parameter name to correlation from the Correlations object
+
415 for (auto const& pair : Correlations[j]) {
+
416 auto const& key = pair.first;
+
417 auto const& val = pair.second;
+
418 int index = -1;
+
419 //If you found the parameter name then get the index
+
420 if (CorrNamesMap.find(key) != CorrNamesMap.end()) {
+
421 index = CorrNamesMap[key];
+
422 }
+
423 else {
+
424 MACH3LOG_ERROR("Parameter {} not in list! Check your spelling?", key);
+
425 throw MaCh3Exception(__FILE__ , __LINE__ );
+
426 }
+
427 double Corr1 = val;
+
428 double Corr2 = 0;
+
429 if(Correlations[index].find(_fFancyNames[j]) != Correlations[index].end()) {
+
430 Corr2 = Correlations[index][_fFancyNames[j]];
+
431 //Do they agree to better than float precision?
+
432 if(std::abs(Corr2 - Corr1) > FLT_EPSILON) {
+
433 MACH3LOG_ERROR("Correlations are not equal between {} and {}", _fFancyNames[j], key);
+
434 MACH3LOG_ERROR("Got : {} and {}", Corr2, Corr1);
+
435 throw MaCh3Exception(__FILE__ , __LINE__ );
+
436 }
+
437 } else {
+
438 MACH3LOG_ERROR("Correlation does not appear reciprocally between {} and {}", _fFancyNames[j], key);
+
439 throw MaCh3Exception(__FILE__ , __LINE__ );
+
440 }
+
441 (*_fCovMatrix)(j, index)= (*_fCovMatrix)(index, j) = Corr1*_fError[j]*_fError[index];
+
442 }
+
443 }
+
444
+
445 //Now make positive definite
+
446 MakePosDef(_fCovMatrix);
+
447 setCovMatrix(_fCovMatrix);
+
448
+
449 if (_fNumPar <= 0) {
+
450 MACH3LOG_ERROR("Covariance object has {} systematics!", _fNumPar);
+
451 throw;
+
452 }
+
453 _fNumParPCA = _fNumPar;
+
454
+
455 MACH3LOG_INFO("Created covariance matrix from files: ");
+
456 for(const auto &file : YAMLFile){
+
457 MACH3LOG_INFO("{} ", file);
+
458 }
+
459 MACH3LOG_INFO("----------------");
+
460 MACH3LOG_INFO("Found {} systematics parameters in total", _fNumPar);
+
461 MACH3LOG_INFO("----------------");
+
462
+
463 return;
+
464}
+
covarianceBase::_fYAMLDoc
YAML::Node _fYAMLDoc
Stores config describing systematics.
Definition covarianceBase.h:453
@@ -2997,32 +2951,32 @@

Definition at line 472 of file covarianceBase.cpp.

-
472 {
-
473// ********************************************
-
474 size = covMat->GetNrows();
-
475 _fNumPar = size;
-
476 InvertCovMatrix = new double*[_fNumPar]();
-
477 throwMatrixCholDecomp = new double*[_fNumPar]();
-
478 // Set the defaults to true
-
479 for(int i = 0; i < _fNumPar; i++)
-
480 {
-
481 InvertCovMatrix[i] = new double[_fNumPar]();
-
482 throwMatrixCholDecomp[i] = new double[_fNumPar]();
-
483 for (int j = 0; j < _fNumPar; j++)
-
484 {
-
485 InvertCovMatrix[i][j] = 0.;
-
486 throwMatrixCholDecomp[i][j] = 0.;
-
487 }
-
488 }
+

Definition at line 467 of file covarianceBase.cpp.

+
467 {
+
468// ********************************************
+
469 size = covMat->GetNrows();
+
470 _fNumPar = size;
+
471 InvertCovMatrix = new double*[_fNumPar]();
+
472 throwMatrixCholDecomp = new double*[_fNumPar]();
+
473 // Set the defaults to true
+
474 for(int i = 0; i < _fNumPar; i++)
+
475 {
+
476 InvertCovMatrix[i] = new double[_fNumPar]();
+
477 throwMatrixCholDecomp[i] = new double[_fNumPar]();
+
478 for (int j = 0; j < _fNumPar; j++)
+
479 {
+
480 InvertCovMatrix[i][j] = 0.;
+
481 throwMatrixCholDecomp[i][j] = 0.;
+
482 }
+
483 }
+
484
+
485 setAdaptionDefaults();
+
486 setCovMatrix(covMat);
+
487
+
488 ReserveMemory(_fNumPar);
489
-
490 setAdaptionDefaults();
-
491 setCovMatrix(covMat);
-
492
-
493 ReserveMemory(_fNumPar);
-
494
-
495 MACH3LOG_INFO("Created covariance matrix named: {}", getName());
-
496}
+
490 MACH3LOG_INFO("Created covariance matrix named: {}", getName());
+
491}
@@ -3050,82 +3004,60 @@

Definition at line 1423 of file covarianceBase.cpp.

-
1423 {
-
1424// ********************************************
-
1425 /*
-
1426 HW: Idea is that adaption can simply read the YAML config
-
1427 Options :
-
1428 External Info:
-
1429 * UseExternalMatrix [bool] : Use an external matrix
-
1430 * ExternalMatrixFileName [str] : Name of file containing external info
-
1431 * ExternalMatrixName [str] : Name of external Matrix
-
1432 * ExternalMeansName [str] : Name of external means vector [for updates]
-
1433
-
1434 General Info:
-
1435 * DoAdaption [bool] : Do we want to do adaption?
-
1436 * AdaptionStartThrow [int] : Step we start throwing adaptive matrix from
-
1437 * AdaptionEndUpdate [int] : Step we stop updating adaptive matrix
-
1438 * AdaptionStartUpdate [int] : Do we skip the first N steps?
-
1439 * AdaptionUpdateStep [int] : Number of steps between matrix updates
-
1440 * Adaption blocks [vector<vector<int>>] : Splits the throw matrix into several block matrices
-
1441 */
-
1442
-
1443 // need to cast matrixName to string
-
1444 std::string matrix_name_str(matrixName);
-
1445
-
1446 // setAdaptionDefaults();
-
1447 if(GetFromManager<std::string>(adapt_manager["AdaptionOptions"]["Covariance"][matrix_name_str], "")==""){
-
1448 MACH3LOG_WARN("Adaptive Settings not found for {}, this is fine if you don't want adaptive MCMC", matrix_name_str);
-
1449 return;
-
1450 }
-
1451
-
1452 // We"re going to grab this info from the YAML manager
-
1453 if(GetFromManager<bool>(adapt_manager["AdaptionOptions"]["Covariance"][matrix_name_str]["DoAdaption"], false)) {
-
1454 MACH3LOG_INFO("Not using adaption for {}", matrix_name_str);
-
1455 return;
-
1456 }
-
1457
-
1458 // Now we read the general settings [these SHOULD be common across all matrices!]
-
1459 adaption_struct.start_adaptive_throw = GetFromManager<int>(adapt_manager["AdaptionOptions"]["Settings"]["AdaptionStartThrow"], 10);
-
1460 adaption_struct.start_adaptive_update = GetFromManager<int>(adapt_manager["AdaptionOptions"]["Settings"]["AdaptionStartUpdate"], 0);
-
1461 adaption_struct.end_adaptive_update = GetFromManager<int>(adapt_manager["AdaptionOptions"]["Settings"]["AdaptionEndUpdate"], 10000);
-
1462 adaption_struct.adaptive_update_step = GetFromManager<int>(adapt_manager["AdaptionOptions"]["Settings"]["AdaptionUpdateStep"], 100);
-
1463
-
1464 adaptive_mcmc::print_adaptive_struct(adaption_struct);
-
1465
-
1466 // We also want to check for "blocks" by default all parameters "know" about each other
-
1467 // but we can split the matrix into independent block matrices
-
1468
-
1469 // We"ll set a dummy variable here
-
1470 auto matrix_blocks = GetFromManager<std::vector<std::vector<int>>>(adapt_manager["AdaptionOptions"]["Settings"][matrix_name_str]["AdaptionUpdateStep"], {{}});
-
1471
-
1472 setAdaptiveBlocks(matrix_blocks);
-
1473
-
1474 // Next let"s check for external matrices
-
1475 // We"re going to grab this info from the YAML manager
-
1476 if(!GetFromManager<bool>(adapt_manager["AdaptionOptions"]["Covariance"][matrix_name_str]["UseExternalMatrix"], false)) {
-
1477 MACH3LOG_INFO("Not using external matrix for {}, initialising adaption from scratch", matrix_name_str);
-
1478 createNewAdaptiveCovariance();
-
1479 return;
-
1480 }
-
1481
-
1482 // Finally, we accept that we want to read the matrix from a file!
-
1483 //
-
1484 std::string external_file_name = GetFromManager<std::string>(adapt_manager["AdaptionOptions"]["Covariance"][matrix_name_str]["ExternalMatrixFileName"], "");
-
1485 std::string external_matrix_name = GetFromManager<std::string>(adapt_manager["AdaptionOptions"]["Covariance"][matrix_name_str]["ExternalMatrixName"], "");
-
1486 std::string external_mean_name = GetFromManager<std::string>(adapt_manager["AdaptionOptions"]["Covariance"][matrix_name_str]["ExternalMeansName"], "");
-
1487
-
1488 setThrowMatrixFromFile(external_file_name, external_matrix_name, external_mean_name);
-
1489}
-
covarianceBase::setThrowMatrixFromFile
void setThrowMatrixFromFile(const std::string &matrix_file_name, const std::string &matrix_name, const std::string &means_name)
sets throw matrix from a file
Definition covarianceBase.cpp:1493
-
covarianceBase::createNewAdaptiveCovariance
void createNewAdaptiveCovariance()
method to create new throw matrix
Definition covarianceBase.cpp:1590
-
covarianceBase::setAdaptiveBlocks
void setAdaptiveBlocks(std::vector< std::vector< int > > block_indices)
sets adaptive block matrix
Definition covarianceBase.cpp:1547
-
adaptive_mcmc::print_adaptive_struct
void print_adaptive_struct(AdaptiveMCMCStruct adaptive_struct)
Basic printer method for AMCMC struct.
Definition adaptiveMCMCStruct.h:43
-
adaptive_mcmc::AdaptiveMCMCStruct::end_adaptive_update
int end_adaptive_update
Steps between changing throw matrix.
Definition adaptiveMCMCStruct.h:26
-
adaptive_mcmc::AdaptiveMCMCStruct::adaptive_update_step
int adaptive_update_step
Steps between changing throw matrix.
Definition adaptiveMCMCStruct.h:28
-
adaptive_mcmc::AdaptiveMCMCStruct::start_adaptive_throw
int start_adaptive_throw
When do we start throwing.
Definition adaptiveMCMCStruct.h:22
-
adaptive_mcmc::AdaptiveMCMCStruct::start_adaptive_update
int start_adaptive_update
When do we stop update the adaptive matrix.
Definition adaptiveMCMCStruct.h:24
+

Definition at line 1400 of file covarianceBase.cpp.

+
1400 {
+
1401// ********************************************
+
1402 /*
+
1403 HW: Idea is that adaption can simply read the YAML config
+
1404 Options :
+
1405 External Info:
+
1406 * UseExternalMatrix [bool] : Use an external matrix
+
1407 * ExternalMatrixFileName [str] : Name of file containing external info
+
1408 * ExternalMatrixName [str] : Name of external Matrix
+
1409 * ExternalMeansName [str] : Name of external means vector [for updates]
+
1410
+
1411 General Info:
+
1412 * DoAdaption [bool] : Do we want to do adaption?
+
1413 * AdaptionStartThrow [int] : Step we start throwing adaptive matrix from
+
1414 * AdaptionEndUpdate [int] : Step we stop updating adaptive matrix
+
1415 * AdaptionStartUpdate [int] : Do we skip the first N steps?
+
1416 * AdaptionUpdateStep [int] : Number of steps between matrix updates
+
1417 * Adaption blocks [vector<vector<int>>] : Splits the throw matrix into several block matrices
+
1418 */
+
1419
+
1420 // need to cast matrixName to string
+
1421 std::string matrix_name_str(matrixName);
+
1422
+
1423 // Now we read the general settings [these SHOULD be common across all matrices!]
+
1424 AdaptiveHandler.InitFromConfig(adapt_manager, matrix_name_str, getNpars());
+
1425 AdaptiveHandler.Print();
+
1426
+
1427 // Next let"s check for external matrices
+
1428 // We"re going to grab this info from the YAML manager
+
1429 if(!GetFromManager<bool>(adapt_manager["AdaptionOptions"]["Covariance"][matrix_name_str]["UseExternalMatrix"], false)) {
+
1430 MACH3LOG_WARN("Not using external matrix for {}, initialising adaption from scratch", matrix_name_str);
+
1431 // If we don't have a covariance matrix to start from for adaptive tune we need to make one!
+
1432 use_adaptive = true;
+
1433 AdaptiveHandler.CreateNewAdaptiveCovariance(_fNumPar);
+
1434 return;
+
1435 }
+
1436
+
1437 // Finally, we accept that we want to read the matrix from a file!
+
1438 std::string external_file_name = GetFromManager<std::string>(adapt_manager["AdaptionOptions"]["Covariance"][matrix_name_str]["ExternalMatrixFileName"], "");
+
1439 std::string external_matrix_name = GetFromManager<std::string>(adapt_manager["AdaptionOptions"]["Covariance"][matrix_name_str]["ExternalMatrixName"], "");
+
1440 std::string external_mean_name = GetFromManager<std::string>(adapt_manager["AdaptionOptions"]["Covariance"][matrix_name_str]["ExternalMeansName"], "");
+
1441
+
1442 AdaptiveHandler.SetThrowMatrixFromFile(external_file_name, external_matrix_name, external_mean_name, use_adaptive, _fNumPar);
+
1443 setThrowMatrix(AdaptiveHandler.adaptive_covariance);
+
1444 MACH3LOG_INFO("Successfully Set External Throw Matrix Stored in {}", external_file_name);
+
1445}
+
adaptive_mcmc::AdaptiveMCMCHandler::Print
void Print()
Print all class members.
Definition AdaptiveMCMCHandler.cpp:221
+
adaptive_mcmc::AdaptiveMCMCHandler::CreateNewAdaptiveCovariance
void CreateNewAdaptiveCovariance(const int Npars)
If we don't have a covariance matrix to start from for adaptive tune we need to make one!
Definition AdaptiveMCMCHandler.cpp:57
+
adaptive_mcmc::AdaptiveMCMCHandler::InitFromConfig
void InitFromConfig(const YAML::Node &adapt_manager, const std::string &matrix_name_str, const int Npars)
Read initial values from config file.
Definition AdaptiveMCMCHandler.cpp:27
+
adaptive_mcmc::AdaptiveMCMCHandler::SetThrowMatrixFromFile
void SetThrowMatrixFromFile(const std::string &matrix_file_name, const std::string &matrix_name, const std::string &means_name, bool &use_adaptive, const int Npars)
sets throw matrix from a file
Definition AdaptiveMCMCHandler.cpp:130
+
adaptive_mcmc::AdaptiveMCMCHandler::adaptive_covariance
TMatrixDSym * adaptive_covariance
Full adaptive covariance matrix.
Definition AdaptiveMCMCHandler.h:81
+
covarianceBase::getNpars
int getNpars()
Get number of params which will be different depending if using Eigen decomposition or not.
Definition covarianceBase.h:320
+
covarianceBase::setThrowMatrix
void setThrowMatrix(TMatrixDSym *cov)
Use new throw matrix, used in adaptive MCMC.
Definition covarianceBase.cpp:1340
@@ -3161,11 +3093,11 @@

Definition at line 348 of file covarianceBase.h.

-
348 {
-
349 if (_fError[i] < 0) { return true; }
-
350 else { return false; }
-
351 }
+

Definition at line 349 of file covarianceBase.h.

+
349 {
+
350 if (_fError[i] < 0) { return true; }
+
351 else { return false; }
+
352 }
@@ -3193,18 +3125,18 @@

Definition at line 1190 of file covarianceBase.cpp.

-
1190 {
-
1191// ********************************************
-
1192 for (int i = 0; i <_fNumPar; ++i) {
-
1193 if(name == _fFancyNames[i]) {
-
1194 return isParameterFixed(i);
-
1195 }
-
1196 }
-
1197 MACH3LOG_WARN("I couldn't find parameter with name {}, therefore will not fix it", name);
-
1198 return false;
-
1199}
-
covarianceBase::isParameterFixed
bool isParameterFixed(const int i)
Is parameter fixed or not.
Definition covarianceBase.h:348
+

Definition at line 1191 of file covarianceBase.cpp.

+
1191 {
+
1192// ********************************************
+
1193 for (int i = 0; i <_fNumPar; ++i) {
+
1194 if(name == _fFancyNames[i]) {
+
1195 return isParameterFixed(i);
+
1196 }
+
1197 }
+
1198 MACH3LOG_WARN("I couldn't find parameter with name {}, therefore will not fix it", name);
+
1199 return false;
+
1200}
+
covarianceBase::isParameterFixed
bool isParameterFixed(const int i)
Is parameter fixed or not.
Definition covarianceBase.h:349
@@ -3240,11 +3172,11 @@

Definition at line 258 of file covarianceBase.h.

-
258 {
-
259 if (fParSigma_PCA[i] < 0) { return true; }
-
260 else { return false; }
-
261 }
+

Definition at line 259 of file covarianceBase.h.

+
259 {
+
260 if (fParSigma_PCA[i] < 0) { return true; }
+
261 else { return false; }
+
262 }
@@ -3273,8 +3205,8 @@

Definition at line 365 of file covarianceBase.h.

-
365{ return pca; }
+

Definition at line 366 of file covarianceBase.h.

+
366{ return pca; }
@@ -3304,53 +3236,51 @@

Definition at line 1660 of file covarianceBase.cpp.

-
1660 {
-
1661// ********************************************
-
1662
-
1663 // Want to get cov' = (cov_sym+cov_polar)/2
-
1664 // cov_sym=(cov+cov^T)/2
-
1665 // cov_polar-> SVD cov to cov=USV^T then cov_polar=VSV^T
-
1666
-
1667 //Get frob norm of cov
-
1668// Double_t cov_norm=cov->E2Norm();
-
1669
-
1670 TMatrixDSym* cov_trans = cov;
-
1671 cov_trans->T();
-
1672 TMatrixDSym cov_sym = 0.5*(*cov+*cov_trans); //If cov is symmetric does nothing, otherwise just ensures symmetry
-
1673
-
1674 //Do SVD to get polar form
-
1675 TDecompSVD cov_sym_svd=TDecompSVD(cov_sym);
-
1676 if(!cov_sym_svd.Decompose()){
-
1677 MACH3LOG_ERROR("Cannot do SVD on input matrix!");
-
1678 throw;
-
1679 }
-
1680
-
1681 TMatrixD cov_sym_v = (TMatrixD)cov_sym_svd.GetV();
-
1682 TMatrixD cov_sym_vt = cov_sym_v;
-
1683 cov_sym_vt.T();
-
1684 //SVD returns as vector (grrr) so need to get into matrix form for multiplying!
-
1685 TVectorD cov_sym_sigvect = (TVectorD)cov_sym_svd.GetSig();
-
1686 const Int_t nCols = cov_sym_v.GetNcols(); //square so only need rows hence lack of cols
-
1687 TMatrixDSym cov_sym_sig(nCols);
-
1688 TMatrixDDiag cov_sym_sig_diag(cov_sym_sig);
-
1689 cov_sym_sig_diag=cov_sym_sigvect;
-
1690
-
1691
-
1692 //Can finally get H=VSV
-
1693 TMatrixDSym cov_sym_polar = cov_sym_sig.SimilarityT(cov_sym_vt);//V*S*V^T (this took forver to find!)
-
1694
-
1695 //Now we can construct closest approximater Ahat=0.5*(B+H)
-
1696 TMatrixDSym cov_closest_approx = 0.5*(cov_sym+cov_sym_polar);//Not fully sure why this is even needed since symmetric B -> U=V
-
1697 //Get norm of transformed
-
1698// Double_t approx_norm=cov_closest_approx.E2Norm();
-
1699
-
1700 //std::cout<<"Initial Norm : "<<cov_norm<<" | Norm after transformation : "<<approx_norm<<" | Ratio : "<<cov_norm/approx_norm<<std::endl;
-
1701
-
1702 *cov = cov_closest_approx;
-
1703 //Now can just add a makeposdef!
-
1704 MakePosDef(cov);
-
1705}
+

Definition at line 1476 of file covarianceBase.cpp.

+
1476 {
+
1477// ********************************************
+
1478
+
1479 // Want to get cov' = (cov_sym+cov_polar)/2
+
1480 // cov_sym=(cov+cov^T)/2
+
1481 // cov_polar-> SVD cov to cov=USV^T then cov_polar=VSV^T
+
1482
+
1483 //Get frob norm of cov
+
1484 // Double_t cov_norm=cov->E2Norm();
+
1485
+
1486 TMatrixDSym* cov_trans = cov;
+
1487 cov_trans->T();
+
1488 TMatrixDSym cov_sym = 0.5*(*cov+*cov_trans); //If cov is symmetric does nothing, otherwise just ensures symmetry
+
1489
+
1490 //Do SVD to get polar form
+
1491 TDecompSVD cov_sym_svd=TDecompSVD(cov_sym);
+
1492 if(!cov_sym_svd.Decompose()){
+
1493 MACH3LOG_ERROR("Cannot do SVD on input matrix!");
+
1494 throw;
+
1495 }
+
1496
+
1497 TMatrixD cov_sym_v = (TMatrixD)cov_sym_svd.GetV();
+
1498 TMatrixD cov_sym_vt = cov_sym_v;
+
1499 cov_sym_vt.T();
+
1500 //SVD returns as vector (grrr) so need to get into matrix form for multiplying!
+
1501 TVectorD cov_sym_sigvect = (TVectorD)cov_sym_svd.GetSig();
+
1502 const Int_t nCols = cov_sym_v.GetNcols(); //square so only need rows hence lack of cols
+
1503 TMatrixDSym cov_sym_sig(nCols);
+
1504 TMatrixDDiag cov_sym_sig_diag(cov_sym_sig);
+
1505 cov_sym_sig_diag=cov_sym_sigvect;
+
1506
+
1507 //Can finally get H=VSV
+
1508 TMatrixDSym cov_sym_polar = cov_sym_sig.SimilarityT(cov_sym_vt);//V*S*V^T (this took forver to find!)
+
1509
+
1510 //Now we can construct closest approximater Ahat=0.5*(B+H)
+
1511 TMatrixDSym cov_closest_approx = 0.5*(cov_sym+cov_sym_polar);//Not fully sure why this is even needed since symmetric B -> U=V
+
1512 //Get norm of transformed
+
1513 // Double_t approx_norm=cov_closest_approx.E2Norm();
+
1514 //std::cout<<"Initial Norm : "<<cov_norm<<" | Norm after transformation : "<<approx_norm<<" | Ratio : "<<cov_norm/approx_norm<<std::endl;
+
1515
+
1516 *cov = cov_closest_approx;
+
1517 //Now can just add a makeposdef!
+
1518 MakePosDef(cov);
+
1519}
@@ -3388,50 +3318,51 @@

Definition at line 1283 of file covarianceBase.cpp.

1283 {
-
1284 //DB Save original warning state and then increase it in this function to suppress 'matrix not positive definite' messages
-
1285 //Means we no longer need to overload
-
1286 if(cov == nullptr){
-
1287 cov = &*covMatrix;
-
1288 }
-
1289
-
1290 int originalErrorWarning = gErrorIgnoreLevel;
-
1291 gErrorIgnoreLevel = kFatal;
-
1292
-
1293 //DB Loop 1000 times adding 1e-9 which tops out at 1e-6 shift on the diagonal before throwing error
-
1294 int MaxAttempts = 1e5;
-
1295 int iAttempt = 0;
-
1296 bool CanDecomp = false;
-
1297 TDecompChol chdcmp;
-
1298
-
1299 for (iAttempt = 0; iAttempt < MaxAttempts; iAttempt++) {
-
1300 chdcmp = TDecompChol(*cov);
-
1301 if (chdcmp.Decompose()) {
-
1302 CanDecomp = true;
-
1303 break;
-
1304 } else {
-
1305#ifdef MULTITHREAD
-
1306#pragma omp parallel for
-
1307#endif
-
1308 for (int iVar = 0 ; iVar < _fNumPar; iVar++) {
-
1309 (*cov)(iVar,iVar) += pow(10,-9);
-
1310 }
-
1311 }
-
1312 }
-
1313
-
1314 if (!CanDecomp) {
-
1315 MACH3LOG_ERROR("Tried {} times to shift diagonal but still can not decompose the matrix", MaxAttempts);
-
1316 MACH3LOG_ERROR("This indicates that something is wrong with the input matrix");
-
1317 throw;
-
1318 }
-
1319 if(total_steps < 2) {
-
1320 MACH3LOG_INFO("Had to shift diagonal {} time(s) to allow the covariance matrix to be decomposed", iAttempt);
-
1321 }
-
1322 //DB Resetting warning level
-
1323 gErrorIgnoreLevel = originalErrorWarning;
-
1324
-
1325 return;
-
1326}
- +
1284// ********************************************
+
1285 //DB Save original warning state and then increase it in this function to suppress 'matrix not positive definite' messages
+
1286 //Means we no longer need to overload
+
1287 if(cov == nullptr){
+
1288 cov = &*covMatrix;
+
1289 }
+
1290
+
1291 int originalErrorWarning = gErrorIgnoreLevel;
+
1292 gErrorIgnoreLevel = kFatal;
+
1293
+
1294 //DB Loop 1000 times adding 1e-9 which tops out at 1e-6 shift on the diagonal before throwing error
+
1295 int MaxAttempts = 1e5;
+
1296 int iAttempt = 0;
+
1297 bool CanDecomp = false;
+
1298 TDecompChol chdcmp;
+
1299
+
1300 for (iAttempt = 0; iAttempt < MaxAttempts; iAttempt++) {
+
1301 chdcmp = TDecompChol(*cov);
+
1302 if (chdcmp.Decompose()) {
+
1303 CanDecomp = true;
+
1304 break;
+
1305 } else {
+
1306 #ifdef MULTITHREAD
+
1307 #pragma omp parallel for
+
1308 #endif
+
1309 for (int iVar = 0 ; iVar < _fNumPar; iVar++) {
+
1310 (*cov)(iVar,iVar) += pow(10,-9);
+
1311 }
+
1312 }
+
1313 }
+
1314
+
1315 if (!CanDecomp) {
+
1316 MACH3LOG_ERROR("Tried {} times to shift diagonal but still can not decompose the matrix", MaxAttempts);
+
1317 MACH3LOG_ERROR("This indicates that something is wrong with the input matrix");
+
1318 throw;
+
1319 }
+
1320 if(total_steps < 2) {
+
1321 MACH3LOG_INFO("Had to shift diagonal {} time(s) to allow the covariance matrix to be decomposed", iAttempt);
+
1322 }
+
1323 //DB Resetting warning level
+
1324 gErrorIgnoreLevel = originalErrorWarning;
+
1325
+
1326 return;
+
1327}
+
covarianceBase::total_steps
int total_steps
Total number of MCMC steps.
Definition covarianceBase.h:521
@@ -3492,22 +3423,22 @@

Definition at line 1222 of file covarianceBase.cpp.

-
1222 {
-
1223// ********************************************
-
1224 #ifdef MULTITHREAD
-
1225 #pragma omp parallel for
-
1226 #endif
-
1227 for (int i = 0; i < n; ++i)
-
1228 {
-
1229 double result = 0.0;
-
1230 for (int j = 0; j < n; ++j)
-
1231 {
-
1232 result += matrix[i][j]*vector[j];
-
1233 }
-
1234 VecMulti[i] = result;
-
1235 }
-
1236}
+

Definition at line 1223 of file covarianceBase.cpp.

+
1223 {
+
1224// ********************************************
+
1225 #ifdef MULTITHREAD
+
1226 #pragma omp parallel for
+
1227 #endif
+
1228 for (int i = 0; i < n; ++i)
+
1229 {
+
1230 double result = 0.0;
+
1231 for (int j = 0; j < n; ++j)
+
1232 {
+
1233 result += matrix[i][j]*vector[j];
+
1234 }
+
1235 VecMulti[i] = result;
+
1236 }
+
1237}
@@ -3559,16 +3490,16 @@

Definition at line 1239 of file covarianceBase.cpp.

-
1239 {
-
1240// ********************************************
-
1241
-
1242 double Element = 0.0;
-
1243 for (int j = 0; j < Length; ++j) {
-
1244 Element += matrix[i][j]*vector[j];
-
1245 }
-
1246 return Element;
-
1247}
+

Definition at line 1240 of file covarianceBase.cpp.

+
1240 {
+
1241// ********************************************
+
1242
+
1243 double Element = 0.0;
+
1244 for (int j = 0; j < Length; ++j) {
+
1245 Element += matrix[i][j]*vector[j];
+
1246 }
+
1247 return Element;
+
1248}
@@ -3619,13 +3550,13 @@

Definition at line 966 of file covarianceBase.cpp.

-
966 {
-
967 MACH3LOG_INFO("Prior values for {} covarianceBase:", getName());
-
968 for (int i = 0; i < _fNumPar; i++) {
-
969 MACH3LOG_INFO(" {} {} ", GetParFancyName(i), getParInit(i));
-
970 }
-
971}
+

Definition at line 969 of file covarianceBase.cpp.

+
969 {
+
970 MACH3LOG_INFO("Prior values for {} covarianceBase:", getName());
+
971 for (int i = 0; i < _fNumPar; i++) {
+
972 MACH3LOG_INFO(" {} {} ", GetParFancyName(i), getParInit(i));
+
973 }
+
974}
@@ -3646,24 +3577,24 @@

Definition at line 976 of file covarianceBase.cpp.

-
976 {
-
977// ********************************************
-
978 MACH3LOG_INFO("Printing parameters for {}", getName());
-
979 // Dump out the PCA parameters too
-
980 if (pca) {
-
981 MACH3LOG_INFO("PCA:");
-
982 for (int i = 0; i < _fNumParPCA; ++i) {
-
983 MACH3LOG_INFO("PCA {:<2} Current: {:<10.2f} Proposed: {:<10.2f}", i, fParCurr_PCA(i), fParProp_PCA(i));
-
984 }
-
985 }
-
986 MACH3LOG_INFO("{:<30} {:<10} {:<10} {:<10}", "Name", "Prior", "Current", "Proposed");
-
987 for (int i = 0; i < _fNumPar; ++i) {
-
988 MACH3LOG_INFO("{:<30} {:<10.2f} {:<10.2f} {:<10.2f}", GetParFancyName(i), _fPreFitValue[i], _fCurrVal[i], _fPropVal[i]);
-
989 }
-
990 //KS: "\n" is faster performance wise, keep std::endl at the end to flush just in case, also looks pretty
-
991 //std::cout << std::endl;
-
992}
+

Definition at line 979 of file covarianceBase.cpp.

+
979 {
+
980// ********************************************
+
981 MACH3LOG_INFO("Printing parameters for {}", getName());
+
982 // Dump out the PCA parameters too
+
983 if (pca) {
+
984 MACH3LOG_INFO("PCA:");
+
985 for (int i = 0; i < _fNumParPCA; ++i) {
+
986 MACH3LOG_INFO("PCA {:<2} Current: {:<10.2f} Proposed: {:<10.2f}", i, fParCurr_PCA(i), fParProp_PCA(i));
+
987 }
+
988 }
+
989 MACH3LOG_INFO("{:<30} {:<10} {:<10} {:<10}", "Name", "Prior", "Current", "Proposed");
+
990 for (int i = 0; i < _fNumPar; ++i) {
+
991 MACH3LOG_INFO("{:<30} {:<10.2f} {:<10.2f} {:<10.2f}", GetParFancyName(i), _fPreFitValue[i], _fCurrVal[i], _fPropVal[i]);
+
992 }
+
993 //KS: "\n" is faster performance wise, keep std::endl at the end to flush just in case, also looks pretty
+
994 //std::cout << std::endl;
+
995}
@@ -3682,16 +3613,16 @@

-

Definition at line 1048 of file covarianceBase.cpp.

-
1048 {
-
1049// ********************************************
-
1050 MACH3LOG_INFO("Number of pars: {}", _fNumPar);
-
1051 MACH3LOG_INFO("Current {} parameters:", matrixName);
-
1052 for(int i = 0; i < _fNumPar; i++) {
-
1053 std::cout << std::fixed << std::setprecision(5) << _fNames[i].c_str() << " current: \t" << _fCurrVal[i] << " \tproposed: \t" << _fPropVal[i] << std::endl;
-
1054 }
-
1055 return;
-
1056}
+

Definition at line 1050 of file covarianceBase.cpp.

+
1050 {
+
1051// ********************************************
+
1052 MACH3LOG_INFO("Number of pars: {}", _fNumPar);
+
1053 MACH3LOG_INFO("Current {} parameters:", matrixName);
+
1054 for(int i = 0; i < _fNumPar; i++) {
+
1055 std::cout << std::fixed << std::setprecision(5) << _fNames[i].c_str() << " current: \t" << _fCurrVal[i] << " \tproposed: \t" << _fPropVal[i] << std::endl;
+
1056 }
+
1057 return;
+
1058}
@@ -3724,17 +3655,18 @@

Definition at line 779 of file covarianceBase.cpp.

779 {
-
780 // Make the random numbers for the step proposal
-
781 randomize();
-
782 CorrelateSteps();
-
783 if(use_adaptive){
-
784 updateAdaptiveCovariance();
-
785 total_steps++;
-
786 }
-
787}
-
covarianceBase::randomize
void randomize()
"Randomize" the parameters in the covariance class for the proposed step. Used the proposal kernel an...
Definition covarianceBase.cpp:793
-
covarianceBase::updateAdaptiveCovariance
void updateAdaptiveCovariance()
Method to update adaptive MCMC.
Definition covarianceBase.cpp:1600
-
covarianceBase::CorrelateSteps
void CorrelateSteps()
Use Cholesky throw matrix for better step proposal.
Definition covarianceBase.cpp:838
+
780// ************************************************
+
781 // Make the random numbers for the step proposal
+
782 randomize();
+
783 CorrelateSteps();
+
784 if(use_adaptive){
+
785 updateAdaptiveCovariance();
+
786 total_steps++;
+
787 }
+
788}
+
covarianceBase::randomize
void randomize()
"Randomize" the parameters in the covariance class for the proposed step. Used the proposal kernel an...
Definition covarianceBase.cpp:794
+
covarianceBase::updateAdaptiveCovariance
void updateAdaptiveCovariance()
Method to update adaptive MCMC.
Definition covarianceBase.cpp:1449
+
covarianceBase::CorrelateSteps
void CorrelateSteps()
Use Cholesky throw matrix for better step proposal.
Definition covarianceBase.cpp:839
@@ -3755,43 +3687,43 @@

Definition at line 723 of file covarianceBase.cpp.

-
723 {
-
724 // *************************************
-
725 // Have the 1 sigma for each parameter in each covariance class, sweet!
-
726 // Don't want to change the nominal array because that's what determines our likelihood
-
727 // Want to change the fParProp, fParCurr, fParInit
-
728 // fParInit and the others will already be set
-
729 for (int i = 0; i < _fNumPar; ++i) {
-
730 // Check if parameter is fixed first: if so don't randomly throw
-
731 if (isParameterFixed(i)) continue;
-
732 // Check that the sigma range is larger than the parameter range
-
733 // If not, throw in the valid parameter range instead
-
734 const double paramrange = _fUpBound[i] - _fLowBound[i];
-
735 const double sigma = sqrt((*covMatrix)(i,i));
-
736 double throwrange = sigma;
-
737 if (paramrange < sigma) throwrange = paramrange;
-
738
-
739 _fPropVal[i] = _fPreFitValue[i] + random_number[0]->Gaus(0, 1)*throwrange;
-
740 // Try again if we the initial parameter proposal falls outside of the range of the parameter
-
741 // Really only relevant for the xsec parameters; the flux and ND280 have -999 and 999 set to the limits!
-
742 int throws = 0;
-
743 while (_fPropVal[i] > _fUpBound[i] || _fPropVal[i] < _fLowBound[i]) {
-
744 if (throws > 1000) {
-
745 MACH3LOG_WARN("Tried {} times to throw parameter {} but failed", throws, i);
-
746 MACH3LOG_WARN("Matrix: {}", matrixName);
-
747 MACH3LOG_WARN("Param: {}", _fNames[i]);
-
748 throw MaCh3Exception(__FILE__ , __LINE__ );
-
749 }
-
750 _fPropVal[i] = _fPreFitValue[i] + random_number[0]->Gaus(0, 1)*throwrange;
-
751 throws++;
-
752 }
-
753 MACH3LOG_INFO("Setting current step in {} param {} = {} from {}", matrixName, i, _fPropVal[i], _fCurrVal[i]);
-
754 _fCurrVal[i] = _fPropVal[i];
-
755 }
-
756 if (pca) TransferToPCA();
-
757}
-
covarianceBase::TransferToPCA
void TransferToPCA()
Transfer param values from normal base to PCA base.
Definition covarianceBase.cpp:571
+

Definition at line 721 of file covarianceBase.cpp.

+
721 {
+
722// *************************************
+
723 // Have the 1 sigma for each parameter in each covariance class, sweet!
+
724 // Don't want to change the nominal array because that's what determines our likelihood
+
725 // Want to change the fParProp, fParCurr, fParInit
+
726 // fParInit and the others will already be set
+
727 for (int i = 0; i < _fNumPar; ++i) {
+
728 // Check if parameter is fixed first: if so don't randomly throw
+
729 if (isParameterFixed(i)) continue;
+
730 // Check that the sigma range is larger than the parameter range
+
731 // If not, throw in the valid parameter range instead
+
732 const double paramrange = _fUpBound[i] - _fLowBound[i];
+
733 const double sigma = sqrt((*covMatrix)(i,i));
+
734 double throwrange = sigma;
+
735 if (paramrange < sigma) throwrange = paramrange;
+
736
+
737 _fPropVal[i] = _fPreFitValue[i] + random_number[0]->Gaus(0, 1)*throwrange;
+
738 // Try again if we the initial parameter proposal falls outside of the range of the parameter
+
739 // Really only relevant for the xsec parameters; the flux and ND280 have -999 and 999 set to the limits!
+
740 int throws = 0;
+
741 while (_fPropVal[i] > _fUpBound[i] || _fPropVal[i] < _fLowBound[i]) {
+
742 if (throws > 1000) {
+
743 MACH3LOG_WARN("Tried {} times to throw parameter {} but failed", throws, i);
+
744 MACH3LOG_WARN("Matrix: {}", matrixName);
+
745 MACH3LOG_WARN("Param: {}", _fNames[i]);
+
746 throw MaCh3Exception(__FILE__ , __LINE__ );
+
747 }
+
748 _fPropVal[i] = _fPreFitValue[i] + random_number[0]->Gaus(0, 1)*throwrange;
+
749 throws++;
+
750 }
+
751 MACH3LOG_INFO("Setting current step in {} param {} = {} from {}", matrixName, i, _fPropVal[i], _fCurrVal[i]);
+
752 _fCurrVal[i] = _fPropVal[i];
+
753 }
+
754 if (pca) TransferToPCA();
+
755}
+
covarianceBase::TransferToPCA
void TransferToPCA()
Transfer param values from normal base to PCA base.
Definition covarianceBase.cpp:568
@@ -3820,48 +3752,48 @@

-

Definition at line 793 of file covarianceBase.cpp.

-
793 {
-
794// ************************************************
-
795 if (!pca) {
-
796//KS: By multithreading here we gain at least factor 2 with 8 threads with ND only fit
-
797#ifdef MULTITHREAD
-
798#pragma omp parallel for
-
799#endif
-
800 for (int i = 0; i < _fNumPar; ++i) {
-
801 // If parameter isn't fixed
-
802 if (_fError[i] > 0.0) {
-
803#ifdef MULTITHREAD
-
804 randParams[i] = random_number[omp_get_thread_num()]->Gaus(0, 1);
-
805#else
-
806 randParams[i] = random_number[0]->Gaus(0, 1);
-
807#endif
-
808 // If parameter IS fixed
-
809 } else {
-
810 randParams[i] = 0.0;
-
811 }
-
812 } // end for
-
813 // If we're in the PCA basis we instead throw parameters there (only _fNumParPCA parameter)
-
814 } else {
-
815 // Scale the random parameters by the sqrt of eigen values for the throw
-
816#ifdef MULTITHREAD
-
817#pragma omp parallel for
-
818#endif
-
819 for (int i = 0; i < _fNumPar; ++i)
-
820 {
-
821 if (fParSigma_PCA[i] > 0. && i < _fNumParPCA)
-
822 {
-
823#ifdef MULTITHREAD
-
824 randParams[i] = random_number[omp_get_thread_num()]->Gaus(0,1);
-
825#else
-
826 randParams[i] = random_number[0]->Gaus(0,1);
-
827#endif
-
828 } else { // If parameter IS fixed or out od bounds
-
829 randParams[i] = 0.0;
-
830 }
-
831 }
-
832 }
-
833}
+

Definition at line 794 of file covarianceBase.cpp.

+
794 {
+
795// ************************************************
+
796 if (!pca) {
+
797//KS: By multithreading here we gain at least factor 2 with 8 threads with ND only fit
+
798 #ifdef MULTITHREAD
+
799 #pragma omp parallel for
+
800 #endif
+
801 for (int i = 0; i < _fNumPar; ++i) {
+
802 // If parameter isn't fixed
+
803 if (_fError[i] > 0.0) {
+
804#ifdef MULTITHREAD
+
805 randParams[i] = random_number[omp_get_thread_num()]->Gaus(0, 1);
+
806#else
+
807 randParams[i] = random_number[0]->Gaus(0, 1);
+
808#endif
+
809 // If parameter IS fixed
+
810 } else {
+
811 randParams[i] = 0.0;
+
812 }
+
813 } // end for
+
814 // If we're in the PCA basis we instead throw parameters there (only _fNumParPCA parameter)
+
815 } else {
+
816 // Scale the random parameters by the sqrt of eigen values for the throw
+
817 #ifdef MULTITHREAD
+
818 #pragma omp parallel for
+
819 #endif
+
820 for (int i = 0; i < _fNumPar; ++i)
+
821 {
+
822 if (fParSigma_PCA[i] > 0. && i < _fNumParPCA)
+
823 {
+
824#ifdef MULTITHREAD
+
825 randParams[i] = random_number[omp_get_thread_num()]->Gaus(0,1);
+
826#else
+
827 randParams[i] = random_number[0]->Gaus(0,1);
+
828#endif
+
829 } else { // If parameter IS fixed or out od bounds
+
830 randParams[i] = 0.0;
+
831 }
+
832 }
+
833 }
+
834}
@@ -3897,41 +3829,41 @@

Definition at line 521 of file covarianceBase.cpp.

-
521 {
-
522
-
523 _fNames = std::vector<std::string>(SizeVec);
-
524 _fFancyNames = std::vector<std::string>(SizeVec);
-
525 _fGenerated = std::vector<double>(SizeVec);
-
526 _fPreFitValue = std::vector<double>(SizeVec);
-
527 _fError = std::vector<double>(SizeVec);
-
528 _fCurrVal = std::vector<double>(SizeVec);
-
529 _fPropVal = std::vector<double>(SizeVec);
-
530 _fLowBound = std::vector<double>(SizeVec);
-
531 _fUpBound = std::vector<double>(SizeVec);
-
532 _fFlatPrior = std::vector<bool>(SizeVec);
-
533 _fIndivStepScale = std::vector<double>(SizeVec);
-
534
-
535 corr_throw = new double[SizeVec]();
-
536 // set random parameter vector (for correlated steps)
-
537 randParams = new double[SizeVec];
-
538
-
539 // Set the defaults to true
-
540 for(int i = 0; i < SizeVec; i++) {
-
541 _fGenerated.at(i) = 1.;
-
542 _fPreFitValue.at(i) = 1.;
-
543 _fError.at(i) = 0.;
-
544 _fCurrVal.at(i) = 0.;
-
545 _fPropVal.at(i) = 0.;
-
546 _fLowBound.at(i) = -999.99;
-
547 _fUpBound.at(i) = 999.99;
-
548 _fFlatPrior.at(i) = false;
-
549 _fIndivStepScale.at(i) = 1.;
-
550 corr_throw[i] = 0.0;
-
551 }
-
552
-
553 _fGlobalStepScale = 1.0;
-
554}
+

Definition at line 516 of file covarianceBase.cpp.

+
516 {
+
517// ********************************************
+
518 _fNames = std::vector<std::string>(SizeVec);
+
519 _fFancyNames = std::vector<std::string>(SizeVec);
+
520 _fGenerated = std::vector<double>(SizeVec);
+
521 _fPreFitValue = std::vector<double>(SizeVec);
+
522 _fError = std::vector<double>(SizeVec);
+
523 _fCurrVal = std::vector<double>(SizeVec);
+
524 _fPropVal = std::vector<double>(SizeVec);
+
525 _fLowBound = std::vector<double>(SizeVec);
+
526 _fUpBound = std::vector<double>(SizeVec);
+
527 _fFlatPrior = std::vector<bool>(SizeVec);
+
528 _fIndivStepScale = std::vector<double>(SizeVec);
+
529
+
530 corr_throw = new double[SizeVec]();
+
531 // set random parameter vector (for correlated steps)
+
532 randParams = new double[SizeVec];
+
533
+
534 // Set the defaults to true
+
535 for(int i = 0; i < SizeVec; i++) {
+
536 _fGenerated.at(i) = 1.;
+
537 _fPreFitValue.at(i) = 1.;
+
538 _fError.at(i) = 0.;
+
539 _fCurrVal.at(i) = 0.;
+
540 _fPropVal.at(i) = 0.;
+
541 _fLowBound.at(i) = -999.99;
+
542 _fUpBound.at(i) = 999.99;
+
543 _fFlatPrior.at(i) = false;
+
544 _fIndivStepScale.at(i) = 1.;
+
545 corr_throw[i] = 0.0;
+
546 }
+
547
+
548 _fGlobalStepScale = 1.0;
+
549}
@@ -3952,16 +3884,17 @@

Definition at line 1328 of file covarianceBase.cpp.

-
1328 {
-
1329 std::vector<double> stepScales(_fNumPar);
-
1330 for (int i = 0; i <_fNumPar; i++) {
-
1331 stepScales[i] = 1.;
-
1332 }
-
1333 _fGlobalStepScale = 1.0;
-
1334 setIndivStepScale(stepScales);
-
1335}
-
covarianceBase::setIndivStepScale
void setIndivStepScale(const int ParameterIndex, const double StepScale)
DB Function to set fIndivStepScale from a vector (Can be used from execs and inside covariance constr...
Definition covarianceBase.h:106
+

Definition at line 1329 of file covarianceBase.cpp.

+
1329 {
+
1330// ********************************************
+
1331 std::vector<double> stepScales(_fNumPar);
+
1332 for (int i = 0; i <_fNumPar; i++) {
+
1333 stepScales[i] = 1.;
+
1334 }
+
1335 _fGlobalStepScale = 1.0;
+
1336 setIndivStepScale(stepScales);
+
1337}
+
covarianceBase::setIndivStepScale
void setIndivStepScale(const int ParameterIndex, const double StepScale)
DB Function to set fIndivStepScale from a vector (Can be used from execs and inside covariance constr...
Definition covarianceBase.h:107
@@ -3991,8 +3924,8 @@

Definition at line 208 of file covarianceBase.h.

-
208{return &(_fPropVal.data()[iParam]);}
+

Definition at line 209 of file covarianceBase.h.

+
209{return &(_fPropVal.data()[iParam]);}
@@ -4021,59 +3954,9 @@

Definition at line 405 of file covarianceBase.h.

-
405{return &Unity;}
-
covarianceBase::Unity
const double Unity
Unity for null systs to point back to.
Definition covarianceBase.h:462
-
- - - -

◆ saveAdaptiveToFile()

- -
-
- - - - - - - - - - - - - - - - - - -
void covarianceBase::saveAdaptiveToFile (const TString & outFileName,
const TString & systematicName 
)
-
- -

Save adaptive throw matrix to file.

- -

Definition at line 1389 of file covarianceBase.cpp.

-
1389 {
-
1390// ********************************************
-
1391 TFile* outFile = new TFile(outFileName, "UPDATE");
-
1392 if(outFile->IsZombie()){
-
1393 MACH3LOG_ERROR("Couldn't find {}", outFileName);
-
1394 throw;
-
1395 }
-
1396 TVectorD* outMeanVec = new TVectorD((int)adaption_struct.par_means.size());
-
1397 for(int i = 0; i < (int)adaption_struct.par_means.size(); i++){
-
1398 (*outMeanVec)(i)=adaption_struct.par_means[i];
-
1399 }
-
1400 outFile->cd();
-
1401 adaption_struct.adaptive_covariance->Write(systematicName+"_postfit_matrix");
-
1402 outMeanVec->Write(systematicName+"_mean_vec");
-
1403 outFile->Close();
-
1404 delete outMeanVec;
-
1405 delete outFile;
-
1406}
+

Definition at line 406 of file covarianceBase.h.

+
406{return &Unity;}
+
covarianceBase::Unity
const double Unity
Unity for null systs to point back to.
Definition covarianceBase.h:476
@@ -4094,32 +3977,32 @@

Definition at line 1749 of file covarianceBase.cpp.

-
1749 {
-
1750// ********************************************
-
1751
-
1752 if (!_fYAMLDoc)
-
1753 {
-
1754 MACH3LOG_CRITICAL("Yaml node hasn't been initialised for matrix {}, something is not right", matrixName);
-
1755 MACH3LOG_CRITICAL("I am not throwing error but should be investigated");
-
1756 return;
-
1757 }
-
1758
-
1759 YAML::Node copyNode = _fYAMLDoc;
-
1760 int i = 0;
-
1761
-
1762 for (YAML::Node param : copyNode["Systematics"])
-
1763 {
-
1764 //KS: Feel free to update it, if you need updated prefit value etc
-
1765 param["Systematic"]["StepScale"]["MCMC"] = std::round(_fIndivStepScale[i] * 100.0) / 100.0; // Round to 2 decimal places
-
1766
-
1767 i++;
-
1768 }
-
1769 // Save the modified node to a file
-
1770 std::ofstream fout("Modified_Matrix.yaml");
-
1771 fout << copyNode;
-
1772 fout.close();
-
1773}
+

Definition at line 1563 of file covarianceBase.cpp.

+
1563 {
+
1564// ********************************************
+
1565
+
1566 if (!_fYAMLDoc)
+
1567 {
+
1568 MACH3LOG_CRITICAL("Yaml node hasn't been initialised for matrix {}, something is not right", matrixName);
+
1569 MACH3LOG_CRITICAL("I am not throwing error but should be investigated");
+
1570 return;
+
1571 }
+
1572
+
1573 YAML::Node copyNode = _fYAMLDoc;
+
1574 int i = 0;
+
1575
+
1576 for (YAML::Node param : copyNode["Systematics"])
+
1577 {
+
1578 //KS: Feel free to update it, if you need updated prefit value etc
+
1579 param["Systematic"]["StepScale"]["MCMC"] = std::round(_fIndivStepScale[i] * 100.0) / 100.0; // Round to 2 decimal places
+
1580
+
1581 i++;
+
1582 }
+
1583 // Save the modified node to a file
+
1584 std::ofstream fout("Modified_Matrix.yaml");
+
1585 fout << copyNode;
+
1586 fout.close();
+
1587}

@@ -4148,99 +4031,13 @@

Definition at line 1409 of file covarianceBase.cpp.

-
1409 {
-
1410 // Puts adaptive MCMC default attributes somewhere obvious
-
1411 use_adaptive = false;
-
1412 total_steps = 0;
-
1413 adaption_struct.start_adaptive_throw = 0;
-
1414 adaption_struct.start_adaptive_update = 0;
-
1415 adaption_struct.end_adaptive_update = 1;
-
1416 adaption_struct.adaptive_update_step = 1000;
-
1417
-
1418 adaption_struct.par_means = {};
-
1419 adaption_struct.adaptive_covariance = nullptr;
-
1420}
-
- - - -

◆ setAdaptiveBlocks()

- -
-
- - - - - -
- - - - - - - - -
void covarianceBase::setAdaptiveBlocks (std::vector< std::vector< int > > block_indices)
- 		-protected
-
- -

sets adaptive block matrix

-
Parameters
- - -
block_indicesValues for sub-matrix blocks
-
-
- -

Definition at line 1547 of file covarianceBase.cpp.

-
1547 {
-
1548 /*
-
1549 In order to adapt efficient we want to setup our throw matrix to be a serious of block-diagonal (ish) matrices
-
1550
-
1551 To do this we set sub-block in the config by parameter index. For example having
-
1552 [[0,4],[4, 6]] in your config will set up two blocks one with all indices 0<=i<4 and the other with 4<=i<6
-
1553 */
-
1554 // Set up block regions
-
1555 adaption_struct.adapt_block_matrix_indices = std::vector<int>(getNpars(), 0);
-
1556
-
1557 // Should also make a matrix of block sizes
-
1558 adaption_struct.adapt_block_sizes = std::vector<int>((int)block_indices.size()+1, 0);
-
1559 adaption_struct.adapt_block_sizes[0]=getNpars();
-
1560
-
1561 if(block_indices.size()==0 || block_indices[0].size()==0) return;
-
1562
-
1563
-
1564 // Now we loop over our blocks
-
1565 for(int iblock=0; iblock<(int)block_indices.size(); iblock++){
-
1566 // Loop over blocks in the block
-
1567 for(int isubblock=0; isubblock<(int)block_indices[iblock].size()-1; isubblock+=2){
-
1568 int block_lb = block_indices[iblock][isubblock];
-
1569 int block_ub = block_indices[iblock][isubblock+1];
-
1570
-
1571 // std::cout<<block_lb<<" "<<block_ub<<std::endl;
-
1572
-
1573 if(block_lb>getNpars() || block_ub>getNpars()){
-
1574 MACH3LOG_ERROR("Cannot set matrix block with edges {}, {} for matrix of size {}",
-
1575 block_lb, block_ub, getNpars());
-
1576 throw MaCh3Exception(__FILE__, __LINE__);;
-
1577 }
-
1578
-
1579 for(int ipar=block_lb; ipar<block_ub; ipar++){
-
1580 adaption_struct.adapt_block_matrix_indices[ipar]=iblock+1;
-
1581 adaption_struct.adapt_block_sizes[iblock+1]+=1;
-
1582 adaption_struct.adapt_block_sizes[0]-=1;
-
1583 }
-
1584
-
1585 }
-
1586 }
-
1587}
-
covarianceBase::getNpars
int getNpars()
Get number of params which will be different depending if using Eigen decomposition or not.
Definition covarianceBase.h:319
-
adaptive_mcmc::AdaptiveMCMCStruct::adapt_block_sizes
std::vector< int > adapt_block_sizes
Size of blocks for adaption.
Definition adaptiveMCMCStruct.h:32
-
adaptive_mcmc::AdaptiveMCMCStruct::adapt_block_matrix_indices
std::vector< int > adapt_block_matrix_indices
Indices for block-matrix adaption.
Definition adaptiveMCMCStruct.h:30
+

Definition at line 1391 of file covarianceBase.cpp.

+
1391 {
+
1392// ********************************************
+
1393 // Puts adaptive MCMC default attributes somewhere obvious
+
1394 use_adaptive = false;
+
1395 total_steps = 0;
+
1396}
@@ -4279,34 +4076,34 @@

Definition at line 1096 of file covarianceBase.cpp.

-
1096 {
-
1097// ********************************************
-
1098
-
1099 // loop over parameters and set a branch
-
1100 for (int i = 0; i < _fNumPar; ++i) {
-
1101 tree.Branch(_fNames[i].c_str(), &_fCurrVal[i], Form("%s/D", _fNames[i].c_str()));
-
1102 }
-
1103 // When running PCA, also save PCA parameters
-
1104 if (pca) {
-
1105 for (int i = 0; i < _fNumParPCA; ++i) {
-
1106 tree.Branch(Form("%s_PCA", _fNames[i].c_str()), (double*)&(fParCurr_PCA.GetMatrixArray()[i]), Form("%s_PCA/D", _fNames[i].c_str()));
-
1107 }
-
1108 }
-
1109 if(SaveProposal)
-
1110 {
-
1111 // loop over parameters and set a branch
-
1112 for (int i = 0; i < _fNumPar; ++i) {
-
1113 tree.Branch(Form("%s_Prop", _fNames[i].c_str()), &_fPropVal[i], Form("%s_Prop/D", _fNames[i].c_str()));
-
1114 }
-
1115 // When running PCA, also save PCA parameters
-
1116 if (pca) {
-
1117 for (int i = 0; i < _fNumParPCA; ++i) {
-
1118 tree.Branch(Form("%s_PCA_Prop", _fNames[i].c_str()), (double*)&(fParProp_PCA.GetMatrixArray()[i]), Form("%s_PCA_Prop/D", _fNames[i].c_str()));
-
1119 }
-
1120 }
-
1121 }
-
1122}
+

Definition at line 1098 of file covarianceBase.cpp.

+
1098 {
+
1099// ********************************************
+
1100
+
1101 // loop over parameters and set a branch
+
1102 for (int i = 0; i < _fNumPar; ++i) {
+
1103 tree.Branch(_fNames[i].c_str(), &_fCurrVal[i], Form("%s/D", _fNames[i].c_str()));
+
1104 }
+
1105 // When running PCA, also save PCA parameters
+
1106 if (pca) {
+
1107 for (int i = 0; i < _fNumParPCA; ++i) {
+
1108 tree.Branch(Form("%s_PCA", _fNames[i].c_str()), (double*)&(fParCurr_PCA.GetMatrixArray()[i]), Form("%s_PCA/D", _fNames[i].c_str()));
+
1109 }
+
1110 }
+
1111 if(SaveProposal)
+
1112 {
+
1113 // loop over parameters and set a branch
+
1114 for (int i = 0; i < _fNumPar; ++i) {
+
1115 tree.Branch(Form("%s_Prop", _fNames[i].c_str()), &_fPropVal[i], Form("%s_Prop/D", _fNames[i].c_str()));
+
1116 }
+
1117 // When running PCA, also save PCA parameters
+
1118 if (pca) {
+
1119 for (int i = 0; i < _fNumParPCA; ++i) {
+
1120 tree.Branch(Form("%s_PCA_Prop", _fNames[i].c_str()), (double*)&(fParProp_PCA.GetMatrixArray()[i]), Form("%s_PCA_Prop/D", _fNames[i].c_str()));
+
1121 }
+
1122 }
+
1123 }
+
1124}

@@ -4334,28 +4131,27 @@

Definition at line 500 of file covarianceBase.cpp.

-
500 {
-
501// ********************************************
-
502 if (cov == NULL) {
-
503 MACH3LOG_ERROR("Could not find covariance matrix you provided to setCovMatrix");
-
504 throw MaCh3Exception(__FILE__ , __LINE__ );
-
505 }
-
506 covMatrix = cov;
-
507 invCovMatrix = (TMatrixDSym*)cov->Clone();
-
508 invCovMatrix->Invert();
-
509 //KS: ROOT has bad memory management, using standard double means we can decrease most operation by factor 2 simply due to cache hits
-
510 for (int i = 0; i < _fNumPar; i++)
-
511 {
-
512 for (int j = 0; j < _fNumPar; ++j)
-
513 {
-
514 InvertCovMatrix[i][j] = (*invCovMatrix)(i,j);
-
515 }
-
516 }
-
517
-
518 setThrowMatrix(cov);
-
519}
-
covarianceBase::setThrowMatrix
void setThrowMatrix(TMatrixDSym *cov)
Definition covarianceBase.cpp:1338
+

Definition at line 495 of file covarianceBase.cpp.

+
495 {
+
496// ********************************************
+
497 if (cov == NULL) {
+
498 MACH3LOG_ERROR("Could not find covariance matrix you provided to setCovMatrix");
+
499 throw MaCh3Exception(__FILE__ , __LINE__ );
+
500 }
+
501 covMatrix = cov;
+
502 invCovMatrix = (TMatrixDSym*)cov->Clone();
+
503 invCovMatrix->Invert();
+
504 //KS: ROOT has bad memory management, using standard double means we can decrease most operation by factor 2 simply due to cache hits
+
505 for (int i = 0; i < _fNumPar; i++)
+
506 {
+
507 for (int j = 0; j < _fNumPar; ++j)
+
508 {
+
509 InvertCovMatrix[i][j] = (*invCovMatrix)(i,j);
+
510 }
+
511 }
+
512
+
513 setThrowMatrix(cov);
+
514}
@@ -4394,25 +4190,25 @@

Definition at line 1202 of file covarianceBase.cpp.

-
1202 {
-
1203// ********************************************
-
1204 if (i > _fNumPar) {
-
1205 MACH3LOG_INFO("Can't setEvalLikelihood for Cov={}/Param={} because size of Covariance = {}", getName(), i, _fNumPar);
-
1206 MACH3LOG_ERROR("Fix this in your config file please!");
-
1207 throw;
-
1208 } else {
-
1209 if(eL){
-
1210 MACH3LOG_INFO("Setting {} (parameter {}) to flat prior", GetParName(i), i);
-
1211 }
-
1212 else{
-
1213 // HW :: This is useful
-
1214 MACH3LOG_INFO("Setting {} (parameter {}) to non-flat prior", GetParName(i), i);
-
1215 }
-
1216 _fFlatPrior[i] = eL;
-
1217 }
-
1218}
-
covarianceBase::GetParName
std::string GetParName(const int i)
Get name of covariance.
Definition covarianceBase.h:147
+

Definition at line 1203 of file covarianceBase.cpp.

+
1203 {
+
1204// ********************************************
+
1205 if (i > _fNumPar) {
+
1206 MACH3LOG_INFO("Can't setEvalLikelihood for Cov={}/Param={} because size of Covariance = {}", getName(), i, _fNumPar);
+
1207 MACH3LOG_ERROR("Fix this in your config file please!");
+
1208 throw;
+
1209 } else {
+
1210 if(eL){
+
1211 MACH3LOG_INFO("Setting {} (parameter {}) to flat prior", GetParName(i), i);
+
1212 }
+
1213 else{
+
1214 // HW :: This is useful
+
1215 MACH3LOG_INFO("Setting {} (parameter {}) to non-flat prior", GetParName(i), i);
+
1216 }
+
1217 _fFlatPrior[i] = eL;
+
1218 }
+
1219}
+
covarianceBase::GetParName
std::string GetParName(const int i)
Get name of covariance.
Definition covarianceBase.h:148
@@ -4459,8 +4255,8 @@

Definition at line 106 of file covarianceBase.h.

-
106{ _fIndivStepScale.at(ParameterIndex) = StepScale; }
+

Definition at line 107 of file covarianceBase.h.

+
107{ _fIndivStepScale.at(ParameterIndex) = StepScale; }
@@ -4488,10 +4284,9 @@

Definition at line 1250 of file covarianceBase.cpp.

-
1250 {
-
1251// ********************************************
-
1252
+

Definition at line 1251 of file covarianceBase.cpp.

+
1251 {
+
1252// ********************************************
1253 if ((int)stepscale.size() != _fNumPar)
1254 {
1255 MACH3LOG_WARN("Stepscale vector not equal to number of parameters. Quitting..");
@@ -4538,8 +4333,8 @@

Definition at line 68 of file covarianceBase.h.

-
68{ matrixName = name; }
+

Definition at line 69 of file covarianceBase.h.

+
69{ matrixName = name; }

@@ -4567,12 +4362,15 @@

-

Definition at line 177 of file covarianceBase.h.

-
177 {
-
178 total_steps = nsteps;
-
179 if(total_steps >= adaption_struct.start_adaptive_throw) resetIndivStepScale();
-
180 }
-
covarianceBase::resetIndivStepScale
void resetIndivStepScale()
Adaptive Step Tuning Stuff.
Definition covarianceBase.cpp:1328
+

Set number of MCMC step, when running adaptive MCMC it is updated with given frequency. We need number of steps to determine frequency.

+ +

Definition at line 178 of file covarianceBase.h.

+
178 {
+
179 total_steps = nsteps;
+
180 if(total_steps >= AdaptiveHandler.start_adaptive_throw) resetIndivStepScale();
+
181 }
+
adaptive_mcmc::AdaptiveMCMCHandler::start_adaptive_throw
int start_adaptive_throw
Definition AdaptiveMCMCHandler.h:59
+
covarianceBase::resetIndivStepScale
void resetIndivStepScale()
Adaptive Step Tuning Stuff.
Definition covarianceBase.cpp:1329

@@ -4611,18 +4409,19 @@

Definition at line 558 of file covarianceBase.cpp.

-
558 {
-
559 MACH3LOG_INFO("Over-riding {}: ", GetParName(i));
-
560 MACH3LOG_INFO("_fPropVal ({}), _fCurrVal ({}), _fPreFitValue ({}) to ({})", _fPropVal[i], _fCurrVal[i], _fPreFitValue[i], val);
-
561
-
562 _fPropVal[i] = val;
-
563 _fCurrVal[i] = val;
-
564 _fPreFitValue[i] = val;
-
565
-
566 // Transfer the parameter values to the PCA basis
-
567 if (pca) TransferToPCA();
-
568}
+

Definition at line 554 of file covarianceBase.cpp.

+
554 {
+
555// ********************************************
+
556 MACH3LOG_INFO("Over-riding {}: ", GetParName(i));
+
557 MACH3LOG_INFO("_fPropVal ({}), _fCurrVal ({}), _fPreFitValue ({}) to ({})", _fPropVal[i], _fCurrVal[i], _fPreFitValue[i], val);
+
558
+
559 _fPropVal[i] = val;
+
560 _fCurrVal[i] = val;
+
561 _fPreFitValue[i] = val;
+
562
+
563 // Transfer the parameter values to the PCA basis
+
564 if (pca) TransferToPCA();
+
565}
@@ -4650,41 +4449,41 @@

Definition at line 1060 of file covarianceBase.cpp.

-
1060 {
-
1061// ********************************************
-
1062 // If empty, set the proposed to nominal
-
1063 if (pars.empty()) {
-
1064 // For xsec this means setting to the prior (because nominal is the prior)
-
1065 for (int i = 0; i < _fNumPar; i++) {
-
1066 _fPropVal[i] = _fPreFitValue[i];
-
1067 }
-
1068 // If not empty, set the parameters to the specified
-
1069 } else {
-
1070 if (pars.size() != size_t(_fNumPar)) {
-
1071 MACH3LOG_ERROR("Warning: parameter arrays of incompatible size! Not changing parameters! {} has size {} but was expecting {}", matrixName, pars.size(), _fNumPar);
-
1072 throw;
-
1073 }
-
1074
-
1075 unsigned int parsSize = pars.size();
-
1076 for (unsigned int i = 0; i < parsSize; i++) {
-
1077 //Make sure that you are actually passing a number to set the parameter to
-
1078 if(std::isnan(pars[i])) {
-
1079 std::cerr << "Error: trying to set parameter value to a nan for parameter " << GetParName(i) << " in matrix " << matrixName << ". This will not go well!" << std::endl;
-
1080 throw;
-
1081 } else {
-
1082 _fPropVal[i] = pars[i];
-
1083 }
-
1084 }
-
1085 }
-
1086
-
1087 // And if pca make the transfer
-
1088 if (pca) {
-
1089 TransferToPCA();
-
1090 TransferToParam();
-
1091 }
-
1092 return;
-
1093}
+

Definition at line 1062 of file covarianceBase.cpp.

+
1062 {
+
1063// ********************************************
+
1064 // If empty, set the proposed to nominal
+
1065 if (pars.empty()) {
+
1066 // For xsec this means setting to the prior (because nominal is the prior)
+
1067 for (int i = 0; i < _fNumPar; i++) {
+
1068 _fPropVal[i] = _fPreFitValue[i];
+
1069 }
+
1070 // If not empty, set the parameters to the specified
+
1071 } else {
+
1072 if (pars.size() != size_t(_fNumPar)) {
+
1073 MACH3LOG_ERROR("Warning: parameter arrays of incompatible size! Not changing parameters! {} has size {} but was expecting {}", matrixName, pars.size(), _fNumPar);
+
1074 throw;
+
1075 }
+
1076
+
1077 unsigned int parsSize = pars.size();
+
1078 for (unsigned int i = 0; i < parsSize; i++) {
+
1079 //Make sure that you are actually passing a number to set the parameter to
+
1080 if(std::isnan(pars[i])) {
+
1081 std::cerr << "Error: trying to set parameter value to a nan for parameter " << GetParName(i) << " in matrix " << matrixName << ". This will not go well!" << std::endl;
+
1082 throw;
+
1083 } else {
+
1084 _fPropVal[i] = pars[i];
+
1085 }
+
1086 }
+
1087 }
+
1088
+
1089 // And if pca make the transfer
+
1090 if (pca) {
+
1091 TransferToPCA();
+
1092 TransferToParam();
+
1093 }
+
1094 return;
+
1095}
@@ -4720,20 +4519,20 @@

Definition at line 303 of file covarianceBase.h.

-
303 {
-
304 if (!pca) { MACH3LOG_ERROR("Am not running in PCA mode"); throw; }
-
305 if (pars.size() != size_t(_fNumParPCA)) {
-
306 MACH3LOG_ERROR("Warning: parameter arrays of incompatible size! Not changing parameters! {} has size {} but was expecting {}", matrixName, pars.size(), _fNumPar);
-
307 throw;
-
308 }
-
309 unsigned int parsSize = pars.size();
-
310 for (unsigned int i = 0; i < parsSize; i++) {
-
311 fParProp_PCA(i) = pars[i];
-
312 }
-
313 //KS: Transfer to normal base
-
314 TransferToParam();
-
315 }
+

Definition at line 304 of file covarianceBase.h.

+
304 {
+
305 if (!pca) { MACH3LOG_ERROR("Am not running in PCA mode"); throw; }
+
306 if (pars.size() != size_t(_fNumParPCA)) {
+
307 MACH3LOG_ERROR("Warning: parameter arrays of incompatible size! Not changing parameters! {} has size {} but was expecting {}", matrixName, pars.size(), _fNumPar);
+
308 throw;
+
309 }
+
310 unsigned int parsSize = pars.size();
+
311 for (unsigned int i = 0; i < parsSize; i++) {
+
312 fParProp_PCA(i) = pars[i];
+
313 }
+
314 //KS: Transfer to normal base
+
315 TransferToParam();
+
316 }
@@ -4780,13 +4579,13 @@

Definition at line 294 of file covarianceBase.h.

-
294 {
-
295 if (!pca) { MACH3LOG_ERROR("Am not running in PCA mode"); throw; }
-
296 fParCurr_PCA(i) = value;
-
297 // And then transfer back to the parameter basis
-
298 TransferToParam();
-
299 }
+

Definition at line 295 of file covarianceBase.h.

+
295 {
+
296 if (!pca) { MACH3LOG_ERROR("Am not running in PCA mode"); throw; }
+
297 fParCurr_PCA(i) = value;
+
298 // And then transfer back to the parameter basis
+
299 TransferToParam();
+
300 }
@@ -4825,15 +4624,16 @@

Definition at line 770 of file covarianceBase.cpp.

-
770 {
-
771 _fPropVal[parNo] = parVal;
-
772 _fCurrVal[parNo] = parVal;
-
773 MACH3LOG_DEBUG("Setting {}(parameter {}) to {}", GetParName(parNo), parNo, parVal);
-
774
-
775 if (pca) TransferToPCA();
-
776}
-
MACH3LOG_DEBUG
#define MACH3LOG_DEBUG
Definition MaCh3Logger.h:12
+

Definition at line 768 of file covarianceBase.cpp.

+
768 {
+
769// ********************************************
+
770 _fPropVal[parNo] = parVal;
+
771 _fCurrVal[parNo] = parVal;
+
772 MACH3LOG_DEBUG("Setting {}(parameter {}) to {}", GetParName(parNo), parNo, parVal);
+
773
+
774 if (pca) TransferToPCA();
+
775}
+
MACH3LOG_DEBUG
#define MACH3LOG_DEBUG
Definition MaCh3Logger.h:15
@@ -4880,8 +4680,8 @@

Definition at line 72 of file covarianceBase.h.

-
72{ _fNames.at(i) = std::string(name); }
+

Definition at line 73 of file covarianceBase.h.

+
73{ _fNames.at(i) = std::string(name); }
@@ -4927,11 +4727,11 @@

Definition at line 84 of file covarianceBase.h.

-
84 {
-
85 _fPropVal[i] = val;
-
86 if (pca) TransferToPCA();
-
87 }
+

Definition at line 85 of file covarianceBase.h.

+
85 {
+
86 _fPropVal[i] = val;
+
87 if (pca) TransferToPCA();
+
88 }
@@ -4978,13 +4778,13 @@

Definition at line 285 of file covarianceBase.h.

-
285 {
-
286 if (!pca) { MACH3LOG_ERROR("Am not running in PCA mode"); throw; }
-
287 fParProp_PCA(i) = value;
-
288 // And then transfer back to the parameter basis
-
289 TransferToParam();
-
290 }
+

Definition at line 286 of file covarianceBase.h.

+
286 {
+
287 if (!pca) { MACH3LOG_ERROR("Am not running in PCA mode"); throw; }
+
288 fParProp_PCA(i) = value;
+
289 // And then transfer back to the parameter basis
+
290 TransferToParam();
+
291 }
@@ -5014,8 +4814,8 @@

Definition at line 111 of file covarianceBase.h.

-
111{ PrintLength = PriLen; }
+

Definition at line 112 of file covarianceBase.h.

+
112{ PrintLength = PriLen; }
@@ -5045,15 +4845,15 @@

-

Definition at line 761 of file covarianceBase.cpp.

-
761 {
-
762 // *************************************
-
763 _fPropVal[parNo] = parVal;
-
764 _fCurrVal[parNo] = parVal;
-
765 MACH3LOG_DEBUG("Setting {}(parameter {}) to {}", GetParName(parNo), parNo, parVal);
-
766
-
767 if (pca) TransferToPCA();
-
768}
+

Definition at line 759 of file covarianceBase.cpp.

+
759 {
+
760// *************************************
+
761 _fPropVal[parNo] = parVal;
+
762 _fCurrVal[parNo] = parVal;
+
763 MACH3LOG_DEBUG("Setting {}(parameter {}) to {}", GetParName(parNo), parNo, parVal);
+
764
+
765 if (pca) TransferToPCA();
+
766}
@@ -5081,17 +4881,17 @@

Definition at line 1124 of file covarianceBase.cpp.

-
1124 {
-
1125// ********************************************
-
1126 if(scale == 0)
-
1127 {
-
1128 MACH3LOG_ERROR("You are trying so set StepScale to 0 this will not work");
-
1129 throw;
-
1130 }
-
1131 MACH3LOG_INFO("{} setStepScale() = {}", getName(), scale);
-
1132 _fGlobalStepScale = scale;
-
1133}
+

Definition at line 1126 of file covarianceBase.cpp.

+
1126 {
+
1127// ********************************************
+
1128 if(scale == 0)
+
1129 {
+
1130 MACH3LOG_ERROR("You are trying so set StepScale to 0 this will not work");
+
1131 throw;
+
1132 }
+
1133 MACH3LOG_INFO("{} setStepScale() = {}", getName(), scale);
+
1134 _fGlobalStepScale = scale;
+
1135}
@@ -5111,47 +4911,49 @@

-

Definition at line 1338 of file covarianceBase.cpp.

-
1338 {
-
1339 if (cov == NULL) {
-
1340 MACH3LOG_ERROR("Could not find covariance matrix you provided to setThrowMatrix");
-
1341 throw MaCh3Exception(__FILE__ , __LINE__ );
-
1342 }
-
1343
-
1344 if (covMatrix->GetNrows() != cov->GetNrows()) {
-
1345 MACH3LOG_ERROR("Matrix given for throw Matrix is not the same size as the covariance matrix stored in object!");
-
1346 std::cerr << "Stored covariance matrix size:" << covMatrix->GetNrows() << std::endl;
-
1347 std::cerr << "Given matrix size:" << cov->GetNrows() << std::endl;
-
1348 throw MaCh3Exception(__FILE__ , __LINE__ );
-
1349 }
-
1350
-
1351 throwMatrix = (TMatrixDSym*)cov->Clone();
-
1352 if(use_adaptive && total_steps <= adaption_struct.start_adaptive_throw) makeClosestPosDef(throwMatrix);
-
1353 else MakePosDef(throwMatrix);
-
1354
-
1355 TDecompChol TDecompChol_throwMatrix(*throwMatrix);
+

Use new throw matrix, used in adaptive MCMC.

+ +

Definition at line 1340 of file covarianceBase.cpp.

+
1340 {
+
1341 if (cov == NULL) {
+
1342 MACH3LOG_ERROR("Could not find covariance matrix you provided to setThrowMatrix");
+
1343 throw MaCh3Exception(__FILE__ , __LINE__ );
+
1344 }
+
1345
+
1346 if (covMatrix->GetNrows() != cov->GetNrows()) {
+
1347 MACH3LOG_ERROR("Matrix given for throw Matrix is not the same size as the covariance matrix stored in object!");
+
1348 std::cerr << "Stored covariance matrix size:" << covMatrix->GetNrows() << std::endl;
+
1349 std::cerr << "Given matrix size:" << cov->GetNrows() << std::endl;
+
1350 throw MaCh3Exception(__FILE__ , __LINE__ );
+
1351 }
+
1352
+
1353 throwMatrix = (TMatrixDSym*)cov->Clone();
+
1354 if(use_adaptive && total_steps <= AdaptiveHandler.start_adaptive_throw) makeClosestPosDef(throwMatrix);
+
1355 else MakePosDef(throwMatrix);
1356
-
1357 if(!TDecompChol_throwMatrix.Decompose()) {
-
1358 MACH3LOG_ERROR("Cholesky decomposition failed for {} trying to make positive definite", matrixName);
-
1359 throw MaCh3Exception(__FILE__ , __LINE__ );
-
1360 }
-
1361
-
1362 throwMatrix_CholDecomp = new TMatrixD(TDecompChol_throwMatrix.GetU());
-
1363 throwMatrix_CholDecomp->T();
-
1364
-
1365 //KS: ROOT has bad memory management, using standard double means we can decrease most operation by factor 2 simply due to cache hits
-
1366#ifdef MULTITHREAD
-
1367#pragma omp parallel for
-
1368#endif
-
1369 for (int i = 0; i < _fNumPar; ++i)
-
1370 {
-
1371 for (int j = 0; j < _fNumPar; ++j)
-
1372 {
-
1373 throwMatrixCholDecomp[i][j] = (*throwMatrix_CholDecomp)(i,j);
-
1374 }
-
1375 }
-
1376}
-
covarianceBase::makeClosestPosDef
void makeClosestPosDef(TMatrixDSym *cov)
HW: Finds closest possible positive definite matrix in Frobenius Norm ||.||_frob Where ||X||_frob=sqr...
Definition covarianceBase.cpp:1660
+
1357 TDecompChol TDecompChol_throwMatrix(*throwMatrix);
+
1358
+
1359 if(!TDecompChol_throwMatrix.Decompose()) {
+
1360 MACH3LOG_ERROR("Cholesky decomposition failed for {} trying to make positive definite", matrixName);
+
1361 throw MaCh3Exception(__FILE__ , __LINE__ );
+
1362 }
+
1363
+
1364 throwMatrix_CholDecomp = new TMatrixD(TDecompChol_throwMatrix.GetU());
+
1365 throwMatrix_CholDecomp->T();
+
1366
+
1367 //KS: ROOT has bad memory management, using standard double means we can decrease most operation by factor 2 simply due to cache hits
+
1368 #ifdef MULTITHREAD
+
1369 #pragma omp parallel for
+
1370 #endif
+
1371 for (int i = 0; i < _fNumPar; ++i)
+
1372 {
+
1373 for (int j = 0; j < _fNumPar; ++j)
+
1374 {
+
1375 throwMatrixCholDecomp[i][j] = (*throwMatrix_CholDecomp)(i,j);
+
1376 }
+
1377 }
+
1378}
+
covarianceBase::makeClosestPosDef
void makeClosestPosDef(TMatrixDSym *cov)
HW: Finds closest possible positive definite matrix in Frobenius Norm ||.||_frob Where ||X||_frob=sqr...
Definition covarianceBase.cpp:1476
@@ -5205,61 +5007,6 @@

Definition at line 1493 of file covarianceBase.cpp.

-
1493 {
-
1494 // Lets you set the throw matrix externally
-
1495 // Open file
-
1496 std::unique_ptr<TFile>matrix_file(new TFile(matrix_file_name.c_str()));
-
1497 use_adaptive = true;
-
1498
-
1499 if(matrix_file->IsZombie()){
-
1500 MACH3LOG_ERROR("Couldn't find {}", matrix_file_name);
-
1501 throw;
-
1502 }
-
1503
-
1504 // Next we grab our matrix
-
1505 adaption_struct.adaptive_covariance = static_cast<TMatrixDSym*>(matrix_file->Get(matrix_name.c_str()));
-
1506 if(!adaption_struct.adaptive_covariance){
-
1507 MACH3LOG_ERROR("Couldn't find {} in {}", matrix_name, matrix_file_name);
-
1508 throw;
-
1509 }
-
1510
-
1511 MACH3LOG_INFO("Succesfully Set External Throw Matrix Stored in {}", matrix_file_name);
-
1512
-
1513 setThrowMatrix(adaption_struct.adaptive_covariance);
-
1514
-
1515 // Finally we grab the means vector
-
1516 TVectorD* means_vector = static_cast<TVectorD*>(matrix_file->Get(means_name.c_str()));
-
1517
-
1518 // This is fine to not exist!
-
1519 if(means_vector){
-
1520 // Yay our vector exists! Let's loop and fill it
-
1521
-
1522 // Should check this is done
-
1523 if(means_vector->GetNrows()){
-
1524 MACH3LOG_ERROR("External means vec size ({}) != matrix size ({})", means_vector->GetNrows(), size);
-
1525 throw MaCh3Exception(__FILE__, __LINE__);
-
1526 }
-
1527
-
1528 adaption_struct.par_means = std::vector<double>(size);
-
1529 for(int i=0; i<size; i++){
-
1530 adaption_struct.par_means[i] = (*means_vector)(i);
-
1531 }
-
1532 MACH3LOG_INFO("Found Means in External File, Will be able to adapt");
-
1533
-
1534 }
-
1535 // Totally fine if it doesn't exist, we just can't do adaption
-
1536 else{
-
1537 // We don't need a means vector, set the adaption=false
-
1538 MACH3LOG_WARN("Cannot find means vector in {}, therefore I will not be able to adapt!", matrix_file_name);
-
1539 use_adaptive=false;
-
1540 }
-
1541
-
1542 matrix_file->Close();
-
1543
-
1544 std::cout<<"Set up matrix from external file"<<std::endl;
-
1545}
-
@@ -5290,58 +5037,58 @@

Definition at line 615 of file covarianceBase.cpp.

-
615 {
-
616 TVectorD* vec = new TVectorD(_fNumPar);
-
617 for (int i = 0; i < _fNumPar; i++) {
-
618 (*vec)(i) = 1.0;
-
619 }
-
620
-
621 ThrowParms* nom_throws = new ThrowParms(*vec, (*covMatrix));
-
622 nom_throws->SetSeed(seed);
-
623 std::vector<double> nominal = getNominalArray();
-
624 nominal.clear();
-
625 nominal.resize(_fNumPar);
-
626
-
627 // If we want to put the nominals somewhere else than user specified
-
628 // Don't fully understand this though: won't we have to reweight the MC somehow?
-
629 // nominal[i] is used in GetLikelihood() as the penalty term, so we're essentially setting a random parameter penalty term?
-
630 if (!nomValues)
-
631 {
-
632 bool throw_again = true;
-
633
-
634 while(throw_again == true)
-
635 {
-
636 throw_again = false;
-
637 MACH3LOG_INFO("Setting {} nominal values to random throws.", getName());
-
638 nom_throws->ThrowSet(nominal);
-
639
-
640 for (int i = 0; i < _fNumPar; i++)
-
641 {
-
642 // if parameter is fixed, dont throw
-
643 if (_fError[i] < 0) {
-
644 nominal[i] = 1.0;
-
645 continue;
-
646 }
-
647
-
648 if (nominal[i] < 0) {
-
649 nominal[i] = 0.0;
-
650 throw_again = true;
-
651 }
-
652 }
-
653 }
-
654 } else {
-
655 // If we want nominal values, set all entries to 1 (defined as nominal in MaCh3)
-
656 for (int i = 0; i < int(nominal.size()); i++) {
-
657 nominal[i] = 1.0;
-
658 }
-
659 }
-
660
-
661 delete nom_throws;
-
662 delete vec;
-
663}
+

Definition at line 614 of file covarianceBase.cpp.

+
614 {
+
615 TVectorD* vec = new TVectorD(_fNumPar);
+
616 for (int i = 0; i < _fNumPar; i++) {
+
617 (*vec)(i) = 1.0;
+
618 }
+
619
+
620 ThrowParms* nom_throws = new ThrowParms(*vec, (*covMatrix));
+
621 nom_throws->SetSeed(seed);
+
622 std::vector<double> nominal = getNominalArray();
+
623 nominal.clear();
+
624 nominal.resize(_fNumPar);
+
625
+
626 // If we want to put the nominals somewhere else than user specified
+
627 // Don't fully understand this though: won't we have to reweight the MC somehow?
+
628 // nominal[i] is used in GetLikelihood() as the penalty term, so we're essentially setting a random parameter penalty term?
+
629 if (!nomValues)
+
630 {
+
631 bool throw_again = true;
+
632
+
633 while(throw_again == true)
+
634 {
+
635 throw_again = false;
+
636 MACH3LOG_INFO("Setting {} nominal values to random throws.", getName());
+
637 nom_throws->ThrowSet(nominal);
+
638
+
639 for (int i = 0; i < _fNumPar; i++)
+
640 {
+
641 // if parameter is fixed, dont throw
+
642 if (_fError[i] < 0) {
+
643 nominal[i] = 1.0;
+
644 continue;
+
645 }
+
646
+
647 if (nominal[i] < 0) {
+
648 nominal[i] = 0.0;
+
649 throw_again = true;
+
650 }
+
651 }
+
652 }
+
653 } else {
+
654 // If we want nominal values, set all entries to 1 (defined as nominal in MaCh3)
+
655 for (int i = 0; i < int(nominal.size()); i++) {
+
656 nominal[i] = 1.0;
+
657 }
+
658 }
+
659
+
660 delete nom_throws;
+
661 delete vec;
+
662}
ThrowParms
No idea really...
Definition ThrowParms.h:19
-
covarianceBase::getNominalArray
virtual std::vector< double > getNominalArray()
Definition covarianceBase.cpp:1707
+
covarianceBase::getNominalArray
virtual std::vector< double > getNominalArray()
Definition covarianceBase.cpp:1522
@@ -5362,59 +5109,58 @@

Definition at line 668 of file covarianceBase.cpp.

-
668 {
-
669// *************************************
-
670
-
671 // First draw new randParams
-
672 randomize();
-
673
-
674 if (!pca) {
-
675 MatrixVectorMulti(corr_throw, throwMatrixCholDecomp, randParams, _fNumPar);
-
676
-
677#ifdef MULTITHREAD
-
678#pragma omp parallel for
-
679#endif
-
680 for (int i = 0; i < _fNumPar; ++i) {
-
681 // Check if parameter is fixed first: if so don't randomly throw
-
682 if (isParameterFixed(i)) continue;
-
683
-
684 _fPropVal[i] = _fPreFitValue[i] + corr_throw[i];
-
685 int throws = 0;
-
686 // Try again if we the initial parameter proposal falls outside of the range of the parameter
-
687 while (_fPropVal[i] > _fUpBound[i] || _fPropVal[i] < _fLowBound[i]) {
-
688#ifdef MULTITHREAD
-
689 randParams[i] = random_number[omp_get_thread_num()]->Gaus(0, 1);
-
690#else
-
691 randParams[i] = random_number[0]->Gaus(0,1);
-
692#endif
-
693 const double corr_throw_single = MatrixVectorMultiSingle(throwMatrixCholDecomp, randParams, _fNumPar, i);
-
694 _fPropVal[i] = _fPreFitValue[i] + corr_throw_single;
-
695 if (throws > 10000)
-
696 {
-
697 //KS: Since we are multithreading there is danger that those messages
-
698 //will be all over the place, small price to pay for faster code
-
699 MACH3LOG_WARN("Tried {} times to throw parameter {} but failed", throws, i);
-
700 MACH3LOG_WARN("Matrix: {}", matrixName);
-
701 MACH3LOG_WARN("Param: {}", _fNames[i]);
-
702 MACH3LOG_WARN("Setting _fPropVal: {} to {}", _fPropVal[i], _fPreFitValue[i]);
-
703 MACH3LOG_WARN("I live at {}:{}", __FILE__, __LINE__);
-
704 _fPropVal[i] = _fPreFitValue[i];
-
705 //throw;
-
706 }
-
707 throws++;
-
708 }
-
709 _fCurrVal[i] = _fPropVal[i];
-
710 }
-
711 }
-
712 else
-
713 {
-
714 MACH3LOG_CRITICAL("Hold on, you are trying to run Prior Predicitve Code with PCA, which is wrong");
-
715 MACH3LOG_CRITICAL("Sorry I have to kill you, I mean your job");
-
716 throw;
-
717 }
-
718}
-
covarianceBase::MatrixVectorMultiSingle
double MatrixVectorMultiSingle(double **_restrict_ matrix, const double *_restrict_ vector, const int Length, const int i)
KS: Custom function to perform multiplication of matrix and single element which is thread safe.
Definition covarianceBase.cpp:1239
+

Definition at line 667 of file covarianceBase.cpp.

+
667 {
+
668// *************************************
+
669 // First draw new randParams
+
670 randomize();
+
671
+
672 if (!pca) {
+
673 MatrixVectorMulti(corr_throw, throwMatrixCholDecomp, randParams, _fNumPar);
+
674
+
675 #ifdef MULTITHREAD
+
676 #pragma omp parallel for
+
677 #endif
+
678 for (int i = 0; i < _fNumPar; ++i) {
+
679 // Check if parameter is fixed first: if so don't randomly throw
+
680 if (isParameterFixed(i)) continue;
+
681
+
682 _fPropVal[i] = _fPreFitValue[i] + corr_throw[i];
+
683 int throws = 0;
+
684 // Try again if we the initial parameter proposal falls outside of the range of the parameter
+
685 while (_fPropVal[i] > _fUpBound[i] || _fPropVal[i] < _fLowBound[i]) {
+
686#ifdef MULTITHREAD
+
687 randParams[i] = random_number[omp_get_thread_num()]->Gaus(0, 1);
+
688#else
+
689 randParams[i] = random_number[0]->Gaus(0,1);
+
690#endif
+
691 const double corr_throw_single = MatrixVectorMultiSingle(throwMatrixCholDecomp, randParams, _fNumPar, i);
+
692 _fPropVal[i] = _fPreFitValue[i] + corr_throw_single;
+
693 if (throws > 10000)
+
694 {
+
695 //KS: Since we are multithreading there is danger that those messages
+
696 //will be all over the place, small price to pay for faster code
+
697 MACH3LOG_WARN("Tried {} times to throw parameter {} but failed", throws, i);
+
698 MACH3LOG_WARN("Matrix: {}", matrixName);
+
699 MACH3LOG_WARN("Param: {}", _fNames[i]);
+
700 MACH3LOG_WARN("Setting _fPropVal: {} to {}", _fPropVal[i], _fPreFitValue[i]);
+
701 MACH3LOG_WARN("I live at {}:{}", __FILE__, __LINE__);
+
702 _fPropVal[i] = _fPreFitValue[i];
+
703 //throw;
+
704 }
+
705 throws++;
+
706 }
+
707 _fCurrVal[i] = _fPropVal[i];
+
708 }
+
709 }
+
710 else
+
711 {
+
712 MACH3LOG_CRITICAL("Hold on, you are trying to run Prior Predicitve Code with PCA, which is wrong");
+
713 MACH3LOG_CRITICAL("Sorry I have to kill you, I mean your job");
+
714 throw;
+
715 }
+
716}
+
covarianceBase::MatrixVectorMultiSingle
double MatrixVectorMultiSingle(double **_restrict_ matrix, const double *_restrict_ vector, const int Length, const int i)
KS: Custom function to perform multiplication of matrix and single element which is thread safe.
Definition covarianceBase.cpp:1240
@@ -5436,33 +5182,33 @@

Definition at line 937 of file covarianceBase.cpp.

-
938{
-
939 randomize();
-
940 if (!pca) {
-
941 // Get the correlated throw vector
-
942 MatrixVectorMulti(corr_throw, throwMatrixCholDecomp, randParams, _fNumPar);
-
943 // The number of sigmas to throw
-
944 // Should probably have this as a default parameter input to the function instead
-
945 for (int i = 0; i < _fNumPar; i++) {
-
946 if (_fError[i] > 0.){
-
947 _fCurrVal[i] = corr_throw[i]*mag;
-
948 }
-
949 }
-
950 } else {
-
951 for (int i = 0; i < _fNumPar; i++) {
-
952 fParProp_PCA(i) = mag*randParams[i];
-
953 }
-
954 // And update the fParCurr in the basis
-
955 // Then update the fParProp in the parameter basis using the transfer matrix, so likelihood is evaluated correctly
-
956 TVectorD current = TransferMat*fParCurr_PCA;
-
957 for (int i = 0; i < _fNumPar; ++i) {
-
958 if (fParSigma_PCA[i] > 0.) {
-
959 _fCurrVal[i] = current(i);
-
960 }
-
961 }
-
962 }
-
963}
+

Definition at line 940 of file covarianceBase.cpp.

+
941{
+
942 randomize();
+
943 if (!pca) {
+
944 // Get the correlated throw vector
+
945 MatrixVectorMulti(corr_throw, throwMatrixCholDecomp, randParams, _fNumPar);
+
946 // The number of sigmas to throw
+
947 // Should probably have this as a default parameter input to the function instead
+
948 for (int i = 0; i < _fNumPar; i++) {
+
949 if (_fError[i] > 0.){
+
950 _fCurrVal[i] = corr_throw[i]*mag;
+
951 }
+
952 }
+
953 } else {
+
954 for (int i = 0; i < _fNumPar; i++) {
+
955 fParProp_PCA(i) = mag*randParams[i];
+
956 }
+
957 // And update the fParCurr in the basis
+
958 // Then update the fParProp in the parameter basis using the transfer matrix, so likelihood is evaluated correctly
+
959 TVectorD current = TransferMat*fParCurr_PCA;
+
960 for (int i = 0; i < _fNumPar; ++i) {
+
961 if (fParSigma_PCA[i] > 0.) {
+
962 _fCurrVal[i] = current(i);
+
963 }
+
964 }
+
965 }
+
966}
@@ -5484,31 +5230,32 @@

Definition at line 910 of file covarianceBase.cpp.

-
910 {
-
911 randomize();
-
912 if (!pca) {
-
913 // Make the correlated throw
-
914 MatrixVectorMulti(corr_throw, throwMatrixCholDecomp, randParams, _fNumPar);
-
915 // Number of sigmas we throw
-
916 for (int i = 0; i < _fNumPar; i++) {
-
917 if (_fError[i] > 0.)
-
918 _fPropVal[i] = _fCurrVal[i] + corr_throw[i]*mag;
-
919 }
-
920 } else {
-
921 for (int i = 0; i < _fNumPar; i++) {
-
922 fParProp_PCA(i) = fParCurr_PCA(i)+mag*randParams[i];
-
923 }
-
924 // And update the fParCurr in the basis
-
925 // Then update the fParProp in the parameter basis using the transfer matrix, so likelihood is evaluated correctly
-
926 TVectorD proposed = TransferMat*fParProp_PCA;
-
927 for (int i = 0; i < _fNumPar; ++i) {
-
928 if (fParSigma_PCA[i] > 0.) {
-
929 _fPropVal[i] = proposed(i);
-
930 }
-
931 }
-
932 }
-
933}
+

Definition at line 912 of file covarianceBase.cpp.

+
912 {
+
913// ********************************************
+
914 randomize();
+
915 if (!pca) {
+
916 // Make the correlated throw
+
917 MatrixVectorMulti(corr_throw, throwMatrixCholDecomp, randParams, _fNumPar);
+
918 // Number of sigmas we throw
+
919 for (int i = 0; i < _fNumPar; i++) {
+
920 if (_fError[i] > 0.)
+
921 _fPropVal[i] = _fCurrVal[i] + corr_throw[i]*mag;
+
922 }
+
923 } else {
+
924 for (int i = 0; i < _fNumPar; i++) {
+
925 fParProp_PCA(i) = fParCurr_PCA(i)+mag*randParams[i];
+
926 }
+
927 // And update the fParCurr in the basis
+
928 // Then update the fParProp in the parameter basis using the transfer matrix, so likelihood is evaluated correctly
+
929 TVectorD proposed = TransferMat*fParProp_PCA;
+
930 for (int i = 0; i < _fNumPar; ++i) {
+
931 if (fParSigma_PCA[i] > 0.) {
+
932 _fPropVal[i] = proposed(i);
+
933 }
+
934 }
+
935 }
+
936}
@@ -5529,18 +5276,18 @@

Definition at line 1136 of file covarianceBase.cpp.

-
1136 {
-
1137// ********************************************
-
1138 // fix or unfix all parameters by multiplying by -1
-
1139 if(!pca)
-
1140 {
-
1141 for (int i = 0; i < _fNumPar; i++) _fError[i] *= -1.0;
-
1142 } else{
-
1143 for (int i = 0; i < _fNumParPCA; i++) fParSigma_PCA[i] *= -1.0;
-
1144 }
-
1145 return;
-
1146}
+

Definition at line 1138 of file covarianceBase.cpp.

+
1138 {
+
1139// ********************************************
+
1140 // fix or unfix all parameters by multiplying by -1
+
1141 if(!pca)
+
1142 {
+
1143 for (int i = 0; i < _fNumPar; i++) _fError[i] *= -1.0;
+
1144 } else{
+
1145 for (int i = 0; i < _fNumParPCA; i++) fParSigma_PCA[i] *= -1.0;
+
1146 }
+
1147 return;
+
1148}
@@ -5568,34 +5315,33 @@

Definition at line 1149 of file covarianceBase.cpp.

-
1149 {
-
1150// ********************************************
-
1151 if(!pca) {
-
1152 if (i > _fNumPar) {
-
1153 MACH3LOG_ERROR("Can't toggleFixParameter for parameter {} because size of covariance ={}", i, _fNumPar);
-
1154 MACH3LOG_ERROR("Fix this in your config file please!");
-
1155 throw;
-
1156 } else {
-
1157 _fError[i] *= -1.0;
-
1158 MACH3LOG_INFO("Setting {}(parameter {}) to fixed at {}", GetParFancyName(i), i, _fCurrVal[i]);
-
1159 }
-
1160 } else {
-
1161 int isDecom = -1;
-
1162 for (int im = 0; im < _fNumParPCA; ++im) {
-
1163 if(isDecomposed_PCA[im] == i) {isDecom = im;}
-
1164 }
-
1165 if(isDecom < 0) {
-
1166 MACH3LOG_ERROR("Parameter {} is PCA decomposed can't fix this", GetParName(i));
-
1167 //throw;
-
1168 } else {
-
1169 fParSigma_PCA[isDecom] *= -1.0;
-
1170 MACH3LOG_INFO("Setting un-decomposed {}(parameter {}/{} in PCA base) to fixed at {}", GetParName(i), i, isDecom, _fCurrVal[i]);
-
1171 }
-
1172 }
-
1173
-
1174 return;
-
1175}
+

Definition at line 1151 of file covarianceBase.cpp.

+
1151 {
+
1152// ********************************************
+
1153 if(!pca) {
+
1154 if (i > _fNumPar) {
+
1155 MACH3LOG_ERROR("Can't toggleFixParameter for parameter {} because size of covariance ={}", i, _fNumPar);
+
1156 MACH3LOG_ERROR("Fix this in your config file please!");
+
1157 throw;
+
1158 } else {
+
1159 _fError[i] *= -1.0;
+
1160 MACH3LOG_INFO("Setting {}(parameter {}) to fixed at {}", GetParFancyName(i), i, _fCurrVal[i]);
+
1161 }
+
1162 } else {
+
1163 int isDecom = -1;
+
1164 for (int im = 0; im < _fNumParPCA; ++im) {
+
1165 if(isDecomposed_PCA[im] == i) {isDecom = im;}
+
1166 }
+
1167 if(isDecom < 0) {
+
1168 MACH3LOG_ERROR("Parameter {} is PCA decomposed can't fix this", GetParName(i));
+
1169 //throw;
+
1170 } else {
+
1171 fParSigma_PCA[isDecom] *= -1.0;
+
1172 MACH3LOG_INFO("Setting un-decomposed {}(parameter {}/{} in PCA base) to fixed at {}", GetParName(i), i, isDecom, _fCurrVal[i]);
+
1173 }
+
1174 }
+
1175 return;
+
1176}
im
#define im
Definition probGpu.cu:70
@@ -5624,18 +5370,18 @@

Definition at line 1178 of file covarianceBase.cpp.

-
1178 {
-
1179// ********************************************
-
1180 for (int i = 0; i <_fNumPar; ++i) {
-
1181 if(name == _fFancyNames[i]) {
-
1182 toggleFixParameter(i);
-
1183 return;
-
1184 }
-
1185 }
-
1186 MACH3LOG_WARN("I couldn't find parameter with name {}, therefore will not fix it", name);
-
1187}
-
covarianceBase::toggleFixParameter
void toggleFixParameter(const int i)
fix parameter at prior values
Definition covarianceBase.cpp:1149
+

Definition at line 1179 of file covarianceBase.cpp.

+
1179 {
+
1180// ********************************************
+
1181 for (int i = 0; i <_fNumPar; ++i) {
+
1182 if(name == _fFancyNames[i]) {
+
1183 toggleFixParameter(i);
+
1184 return;
+
1185 }
+
1186 }
+
1187 MACH3LOG_WARN("I couldn't find parameter with name {}, therefore will not fix it", name);
+
1188}
+
covarianceBase::toggleFixParameter
void toggleFixParameter(const int i)
fix parameter at prior values
Definition covarianceBase.cpp:1151
@@ -5664,24 +5410,25 @@

Definition at line 589 of file covarianceBase.cpp.

-
589 {
-
590 if (!pca) {
-
591 MACH3LOG_ERROR("Can not transfer to PCA if PCA isn't enabled");
-
592 throw MaCh3Exception(__FILE__ , __LINE__ );
-
593 }
-
594
-
595 // Make the temporary vectors
-
596 TVectorD fParProp_vec = TransferMat*fParProp_PCA;
-
597 TVectorD fParCurr_vec = TransferMat*fParCurr_PCA;
-
598#ifdef MULTITHREAD
-
599#pragma omp parallel for
-
600#endif
-
601 for (int i = 0; i < _fNumPar; ++i) {
-
602 _fPropVal[i] = fParProp_vec(i);
-
603 _fCurrVal[i] = fParCurr_vec(i);
-
604 }
-
605}
+

Definition at line 587 of file covarianceBase.cpp.

+
587 {
+
588// ********************************************
+
589 if (!pca) {
+
590 MACH3LOG_ERROR("Can not transfer to PCA if PCA isn't enabled");
+
591 throw MaCh3Exception(__FILE__ , __LINE__ );
+
592 }
+
593
+
594 // Make the temporary vectors
+
595 TVectorD fParProp_vec = TransferMat*fParProp_PCA;
+
596 TVectorD fParCurr_vec = TransferMat*fParCurr_PCA;
+
597 #ifdef MULTITHREAD
+
598 #pragma omp parallel for
+
599 #endif
+
600 for (int i = 0; i < _fNumPar; ++i) {
+
601 _fPropVal[i] = fParProp_vec(i);
+
602 _fCurrVal[i] = fParCurr_vec(i);
+
603 }
+
604}
@@ -5710,23 +5457,23 @@

Definition at line 571 of file covarianceBase.cpp.

-
571 {
-
572 if (!pca) {
-
573 MACH3LOG_ERROR("Can not transfer to PCA if PCA isn't enabled");
-
574 throw MaCh3Exception(__FILE__ , __LINE__ );
-
575 }
-
576 // Make the temporary vectors
-
577 TVectorD fParCurr_vec(_fNumPar);
-
578 TVectorD fParProp_vec(_fNumPar);
-
579 for (int i = 0; i < _fNumPar; ++i) {
-
580 fParCurr_vec(i) = _fCurrVal[i];
-
581 fParProp_vec(i) = _fPropVal[i];
-
582 }
-
583
-
584 fParCurr_PCA = TransferMatT*fParCurr_vec;
-
585 fParProp_PCA = TransferMatT*fParProp_vec;
-
586}
+

Definition at line 568 of file covarianceBase.cpp.

+
568 {
+
569 if (!pca) {
+
570 MACH3LOG_ERROR("Can not transfer to PCA if PCA isn't enabled");
+
571 throw MaCh3Exception(__FILE__ , __LINE__ );
+
572 }
+
573 // Make the temporary vectors
+
574 TVectorD fParCurr_vec(_fNumPar);
+
575 TVectorD fParProp_vec(_fNumPar);
+
576 for (int i = 0; i < _fNumPar; ++i) {
+
577 fParCurr_vec(i) = _fCurrVal[i];
+
578 fParProp_vec(i) = _fPropVal[i];
+
579 }
+
580
+
581 fParCurr_PCA = TransferMatT*fParCurr_vec;
+
582 fParProp_PCA = TransferMatT*fParProp_vec;
+
583}
@@ -5754,64 +5501,36 @@

Method to update adaptive MCMC.

- -

Definition at line 1600 of file covarianceBase.cpp.

-
1600 {
-
1601 // https://projecteuclid.org/journals/bernoulli/volume-7/issue-2/An-adaptive-Metropolis-algorithm/bj/1080222083.full
-
1602 // Updates adaptive matrix
-
1603 // First we update the total means
-
1604
-
1605 // Skip this if we're at a large number of steps
-
1606 if(total_steps>adaption_struct.end_adaptive_update || total_steps<adaption_struct.start_adaptive_update) return;
-
1607
-
1608 int steps_post_burn = total_steps - adaption_struct.start_adaptive_update;
-
1609
-
1610 std::vector<double> par_means_prev = adaption_struct.par_means;
-
1611
-
1612 #ifdef MULTITHREAD
-
1613 #pragma omp parallel for
-
1614 #endif
-
1615 for(int iRow=0; iRow<size; iRow++){
-
1616 adaption_struct.par_means[iRow]=(_fCurrVal[iRow]+adaption_struct.par_means[iRow]*steps_post_burn)/(steps_post_burn+1);
-
1617 }
-
1618
-
1619 //Now we update the covariances using cov(x,y)=E(xy)-E(x)E(y)
-
1620 #ifdef MULTITHREAD
-
1621 #pragma omp parallel for
-
1622 #endif
-
1623 for(int irow=0; irow<size; irow++){
-
1624 int block = adaption_struct.adapt_block_matrix_indices[irow];
-
1625 // int scale_factor = 5.76/double(adapt_block_sizes[block]);
-
1626 for(int icol=0; icol<=irow; icol++){
-
1627 double cov_val=0;
-
1628 // Not in the same blocks
-
1629 if(adaption_struct.adapt_block_matrix_indices[icol]==block){
-
1630 // Calculate Covariance for block
-
1631 // https://projecteuclid.org/journals/bernoulli/volume-7/issue-2/An-adaptive-Metropolis-algorithm/bj/1080222083.full
-
1632 cov_val = (*adaption_struct.adaptive_covariance)(irow, icol)*size/5.6644;
-
1633 cov_val += par_means_prev[irow]*par_means_prev[icol]; //First we remove the current means
-
1634 cov_val = (cov_val*steps_post_burn+_fCurrVal[irow]*_fCurrVal[icol])/(steps_post_burn+1); //Now get mean(iRow*iCol)
-
1635 cov_val -= adaption_struct.par_means[icol]*adaption_struct.par_means[irow];
-
1636 cov_val*=5.6644/size;
-
1637 }
-
1638
-
1639 (*adaption_struct.adaptive_covariance)(icol, irow) = cov_val;
-
1640 (*adaption_struct.adaptive_covariance)(irow, icol) = cov_val;
-
1641 }
-
1642 }
-
1643
-
1644 //This is likely going to be the slow bit!
-
1645 if(total_steps==adaption_struct.start_adaptive_throw)
-
1646 {
-
1647 resetIndivStepScale();
-
1648 }
-
1649
-
1650 if(total_steps>=adaption_struct.start_adaptive_throw && (total_steps-adaption_struct.start_adaptive_throw)%adaption_struct.adaptive_update_step==0) {
-
1651 TMatrixDSym* update_matrix = static_cast<TMatrixDSym*>(adaption_struct.adaptive_covariance->Clone());
-
1652 updateThrowMatrix(update_matrix); //Now we update and continue!
-
1653 }
-
1654}
-
covarianceBase::updateThrowMatrix
void updateThrowMatrix(TMatrixDSym *cov)
Definition covarianceBase.cpp:1378
+
See also
https://projecteuclid.org/journals/bernoulli/volume-7/issue-2/An-adaptive-Metropolis-algorithm/bj/1080222083.full
+ +

Definition at line 1449 of file covarianceBase.cpp.

+
1449 {
+
1450// ********************************************
+
1451 // Updates adaptive matrix
+
1452 // First we update the total means
+
1453
+
1454 // Skip this if we're at a large number of steps
+
1455 if(total_steps>AdaptiveHandler.end_adaptive_update || total_steps<AdaptiveHandler.start_adaptive_update) return;
+
1456
+
1457 int steps_post_burn = total_steps - AdaptiveHandler.start_adaptive_update;
+
1458 // Call main adaption function
+
1459 AdaptiveHandler.UpdateAdaptiveCovariance(_fCurrVal, steps_post_burn, _fNumPar);
+
1460
+
1461 //This is likely going to be the slow bit!
+
1462 if(total_steps == AdaptiveHandler.start_adaptive_throw) {
+
1463 resetIndivStepScale();
+
1464 }
+
1465
+
1466 if(total_steps>=AdaptiveHandler.start_adaptive_throw && (total_steps-AdaptiveHandler.start_adaptive_throw)%AdaptiveHandler.adaptive_update_step==0) {
+
1467 TMatrixDSym* update_matrix = static_cast<TMatrixDSym*>(AdaptiveHandler.adaptive_covariance->Clone());
+
1468 updateThrowMatrix(update_matrix); //Now we update and continue!
+
1469 }
+
1470}
+
adaptive_mcmc::AdaptiveMCMCHandler::start_adaptive_update
int start_adaptive_update
When do we stop update the adaptive matrix.
Definition AdaptiveMCMCHandler.h:62
+
adaptive_mcmc::AdaptiveMCMCHandler::end_adaptive_update
int end_adaptive_update
Steps between changing throw matrix.
Definition AdaptiveMCMCHandler.h:65
+
adaptive_mcmc::AdaptiveMCMCHandler::UpdateAdaptiveCovariance
void UpdateAdaptiveCovariance(const std::vector< double > &_fCurrVal, const int steps_post_burn, const int Npars)
Method to update adaptive MCMC.
Definition AdaptiveMCMCHandler.cpp:184
+
adaptive_mcmc::AdaptiveMCMCHandler::adaptive_update_step
int adaptive_update_step
Steps between changing throw matrix.
Definition AdaptiveMCMCHandler.h:68
+
covarianceBase::updateThrowMatrix
void updateThrowMatrix(TMatrixDSym *cov)
Definition covarianceBase.cpp:1380
@@ -5831,15 +5550,15 @@

-

Definition at line 1378 of file covarianceBase.cpp.

-
1378 {
-
1379// ********************************************
-
1380 delete throwMatrix;
-
1381 throwMatrix = NULL;
-
1382 delete throwMatrix_CholDecomp;
-
1383 throwMatrix_CholDecomp = NULL;
-
1384 setThrowMatrix(cov);
-
1385}
+

Definition at line 1380 of file covarianceBase.cpp.

+
1380 {
+
1381// ********************************************
+
1382 delete throwMatrix;
+
1383 throwMatrix = NULL;
+
1384 delete throwMatrix_CholDecomp;
+
1385 throwMatrix_CholDecomp = NULL;
+
1386 setThrowMatrix(cov);
+
1387}
@@ -5866,7 +5585,7 @@

Definition at line 445 of file covarianceBase.h.

+

Definition at line 459 of file covarianceBase.h.

@@ -5892,7 +5611,7 @@

Definition at line 451 of file covarianceBase.h.

+

Definition at line 465 of file covarianceBase.h.

@@ -5918,7 +5637,7 @@

Definition at line 437 of file covarianceBase.h.

+

Definition at line 451 of file covarianceBase.h.

@@ -5944,7 +5663,7 @@

Definition at line 459 of file covarianceBase.h.

+

Definition at line 473 of file covarianceBase.h.

@@ -5970,7 +5689,7 @@

Definition at line 449 of file covarianceBase.h.

+

Definition at line 463 of file covarianceBase.h.

@@ -5996,7 +5715,7 @@

Definition at line 429 of file covarianceBase.h.

+

Definition at line 443 of file covarianceBase.h.

@@ -6022,7 +5741,7 @@

Definition at line 457 of file covarianceBase.h.

+

Definition at line 471 of file covarianceBase.h.

@@ -6048,7 +5767,7 @@

Definition at line 453 of file covarianceBase.h.

+

Definition at line 467 of file covarianceBase.h.

@@ -6074,7 +5793,7 @@

Definition at line 435 of file covarianceBase.h.

+

Definition at line 449 of file covarianceBase.h.

@@ -6100,7 +5819,7 @@

Definition at line 441 of file covarianceBase.h.

+

Definition at line 455 of file covarianceBase.h.

@@ -6126,7 +5845,7 @@

Definition at line 469 of file covarianceBase.h.

+

Definition at line 483 of file covarianceBase.h.

@@ -6152,7 +5871,7 @@

Definition at line 443 of file covarianceBase.h.

+

Definition at line 457 of file covarianceBase.h.

@@ -6178,7 +5897,7 @@

Definition at line 483 of file covarianceBase.h.

+

Definition at line 497 of file covarianceBase.h.

@@ -6204,7 +5923,7 @@

Definition at line 447 of file covarianceBase.h.

+

Definition at line 461 of file covarianceBase.h.

@@ -6230,7 +5949,7 @@

Definition at line 455 of file covarianceBase.h.

+

Definition at line 469 of file covarianceBase.h.

@@ -6256,12 +5975,12 @@

Definition at line 439 of file covarianceBase.h.

+

Definition at line 453 of file covarianceBase.h.

- -

◆ adaption_struct

+ +

◆ AdaptiveHandler

@@ -6270,7 +5989,7 @@

- +
adaptive_mcmc::AdaptiveMCMCStruct covarianceBase::adaption_structadaptive_mcmc::AdaptiveMCMCHandler covarianceBase::AdaptiveHandler
@@ -6282,7 +6001,7 @@

Definition at line 526 of file covarianceBase.h.

+

Definition at line 524 of file covarianceBase.h.

@@ -6308,7 +6027,7 @@

Definition at line 427 of file covarianceBase.h.

+

Definition at line 441 of file covarianceBase.h.

@@ -6334,7 +6053,7 @@

Definition at line 415 of file covarianceBase.h.

+

Definition at line 429 of file covarianceBase.h.

@@ -6360,7 +6079,7 @@

Definition at line 467 of file covarianceBase.h.

+

Definition at line 481 of file covarianceBase.h.

@@ -6386,7 +6105,7 @@

Definition at line 477 of file covarianceBase.h.

+

Definition at line 491 of file covarianceBase.h.

@@ -6412,7 +6131,7 @@

Definition at line 481 of file covarianceBase.h.

+

Definition at line 495 of file covarianceBase.h.

@@ -6438,7 +6157,7 @@

Definition at line 479 of file covarianceBase.h.

+

Definition at line 493 of file covarianceBase.h.

@@ -6464,7 +6183,7 @@

Definition at line 471 of file covarianceBase.h.

+

Definition at line 485 of file covarianceBase.h.

@@ -6490,7 +6209,7 @@

Definition at line 491 of file covarianceBase.h.

+

Definition at line 505 of file covarianceBase.h.

@@ -6516,7 +6235,7 @@

Definition at line 489 of file covarianceBase.h.

+

Definition at line 503 of file covarianceBase.h.

@@ -6542,7 +6261,7 @@

Definition at line 493 of file covarianceBase.h.

+

Definition at line 507 of file covarianceBase.h.

@@ -6568,7 +6287,7 @@

Definition at line 408 of file covarianceBase.h.

+

Definition at line 422 of file covarianceBase.h.

@@ -6594,7 +6313,7 @@

Definition at line 417 of file covarianceBase.h.

+

Definition at line 431 of file covarianceBase.h.

@@ -6620,7 +6339,7 @@

Definition at line 419 of file covarianceBase.h.

+

Definition at line 433 of file covarianceBase.h.

@@ -6646,7 +6365,7 @@

Definition at line 495 of file covarianceBase.h.

+

Definition at line 509 of file covarianceBase.h.

@@ -6672,7 +6391,7 @@

Definition at line 473 of file covarianceBase.h.

+

Definition at line 487 of file covarianceBase.h.

@@ -6698,7 +6417,7 @@

Definition at line 413 of file covarianceBase.h.

+

Definition at line 427 of file covarianceBase.h.

@@ -6724,7 +6443,7 @@

Definition at line 475 of file covarianceBase.h.

+

Definition at line 489 of file covarianceBase.h.

@@ -6750,7 +6469,7 @@

Definition at line 465 of file covarianceBase.h.

+

Definition at line 479 of file covarianceBase.h.

@@ -6776,7 +6495,7 @@

Definition at line 432 of file covarianceBase.h.

+

Definition at line 446 of file covarianceBase.h.

@@ -6802,7 +6521,7 @@

Definition at line 422 of file covarianceBase.h.

+

Definition at line 436 of file covarianceBase.h.

@@ -6828,7 +6547,7 @@

Definition at line 425 of file covarianceBase.h.

+

Definition at line 439 of file covarianceBase.h.

@@ -6852,9 +6571,9 @@

-

Total number of parmas, deprecated, please don't use it.

+

Total number of params, deprecated, please don't use it.

-

Definition at line 411 of file covarianceBase.h.

+

Definition at line 425 of file covarianceBase.h.

@@ -6878,7 +6597,9 @@

-

Definition at line 498 of file covarianceBase.h.

+

Matrix which we use for step proposal before Cholesky decomposition (not actually used for step proposal)

+ +

Definition at line 512 of file covarianceBase.h.

@@ -6902,7 +6623,9 @@

-

Definition at line 499 of file covarianceBase.h.

+

Matrix which we use for step proposal after Cholesky decomposition.

+ +

Definition at line 514 of file covarianceBase.h.

@@ -6928,7 +6651,7 @@

Definition at line 501 of file covarianceBase.h.

+

Definition at line 516 of file covarianceBase.h.

@@ -6952,7 +6675,9 @@

-

Definition at line 523 of file covarianceBase.h.

+

Total number of MCMC steps.

+ +

Definition at line 521 of file covarianceBase.h.

@@ -6978,7 +6703,7 @@

Definition at line 485 of file covarianceBase.h.

+

Definition at line 499 of file covarianceBase.h.

@@ -7004,7 +6729,7 @@

Definition at line 487 of file covarianceBase.h.

+

Definition at line 501 of file covarianceBase.h.

@@ -7030,7 +6755,7 @@

Definition at line 462 of file covarianceBase.h.

+

Definition at line 476 of file covarianceBase.h.

@@ -7056,7 +6781,7 @@

Definition at line 522 of file covarianceBase.h.

+

Definition at line 519 of file covarianceBase.h.

diff --git a/classcovarianceOsc-members.html b/classcovarianceOsc-members.html index 0be84672d..eaf75d8d6 100644 --- a/classcovarianceOsc-members.html +++ b/classcovarianceOsc-members.html @@ -94,7 +94,7 @@ _fUpBoundcovarianceBaseprotected _fYAMLDoccovarianceBaseprotected acceptStep()covarianceBase - adaption_structcovarianceBaseprotected + AdaptiveHandlercovarianceBaseprotected CalcLikelihood()covarianceBase calcReWeight(const int bin)covarianceBaseinline CheckBounds() overridecovarianceOscinlinevirtual @@ -108,152 +108,149 @@ covarianceBase(const char *name, const char *file, int seed, double threshold, int FirstPCAdpar, int LastPCAdpar)covarianceBase covarianceOsc(const char *name, const char *file)covarianceOsc covMatrixcovarianceBaseprotected - createNewAdaptiveCovariance()covarianceBaseprotected - densitycovarianceOscprotected - eigen_thresholdcovarianceBaseprotected - eigen_valuescovarianceBaseprotected - eigen_values_mastercovarianceBaseprotected - eigen_vectorscovarianceBaseprotected - FirstPCAdparcovarianceBaseprotected - flipBetacovarianceOscprotected - flipdelMcovarianceOscprotected - fParCurr_PCAcovarianceBaseprotected - fParProp_PCAcovarianceBaseprotected - fParSigma_PCAcovarianceBaseprotected - GetCorrelationMatrix()covarianceBase - getCovMatrix()covarianceBaseinline - GetDensity()covarianceOscinline - getDiagonalError(const int i)covarianceBaseinline - getDoAdaption()covarianceBaseinline - getEigenValues()covarianceBaseinline - getEigenValuesMaster()covarianceBaseinline - getEigenVectors()covarianceBaseinline - getFlatPrior(const int i)covarianceBaseinline - GetGenerated(const int i)covarianceBaseinline - getGeneratedValues()covarianceBaseinline - GetIndivStepScale(const int ParameterIndex)covarianceBaseinline - getInputFile() constcovarianceBaseinline - getInvCovMatrix()covarianceBaseinline - GetLikelihood() overridecovarianceOscvirtual - GetLowerBound(const int i)covarianceBaseinline - getName()covarianceBaseinline - getNominal(const int i)covarianceBaseinlinevirtual - getNominalArray()covarianceBasevirtual - getNpars()covarianceBaseinline - GetNumParams()covarianceBaseinline - getParameterMeans()covarianceBaseinline - getParCurr(const int i)covarianceBaseinline - getParCurr_PCA(const int i)covarianceBaseinline - GetParFancyName(const int i)covarianceBaseinline - GetParFancyName(const int i) constcovarianceBaseinline - getParInit(const int i)covarianceBaseinline - GetParName(const int i)covarianceBaseinline - GetParName(const int i) constcovarianceBaseinline - getParProp(const int i)covarianceBaseinline - getParProp_PCA(const int i)covarianceBaseinline - GetPathLength()covarianceOscinline - GetPerformBetaStudy()covarianceOscinline - getPreFitValues()covarianceBaseinline - getProposed() constcovarianceBase - getPropPars()covarianceOsc - getSize()covarianceBaseinline - getThrowMatrix()covarianceBaseinline - getThrowMatrix_CholDecomp()covarianceBaseinline - getTransferMatrix()covarianceBaseinline - GetUpperBound(const int i)covarianceBaseinline - init(const char *name, const char *file)covarianceBaseprotected - init(const std::vector< std::string > &YAMLFile)covarianceBaseprotected - init(TMatrixDSym *covMat)covarianceBaseprotected - initialiseAdaption(const YAML::Node &adapt_manager)covarianceBase - inputFilecovarianceBaseprotected - invCovMatrixcovarianceBaseprotected - InvertCovMatrixcovarianceBaseprotected - isDecomposed_PCAcovarianceBaseprotected - isParameterFixed(const int i)covarianceBaseinline - isParameterFixed(const std::string &name)covarianceBase - isParameterFixedPCA(const int i)covarianceBaseinline - IsPCA()covarianceBaseinline - kBetacovarianceOscprotected - kDeltaCPcovarianceOscprotected - kDeltaM23covarianceOscprotected - kSinTheta23covarianceOscprotected - LcovarianceOscprotected - LastPCAdparcovarianceBaseprotected - makeClosestPosDef(TMatrixDSym *cov)covarianceBaseprotected - MakePosDef(TMatrixDSym *cov=nullptr)covarianceBaseprotected - matrixNamecovarianceBaseprotected - MatrixVectorMulti(double *_restrict_ VecMulti, double **_restrict_ matrix, const double *_restrict_ vector, const int n)covarianceBaseinline - MatrixVectorMultiSingle(double **_restrict_ matrix, const double *_restrict_ vector, const int Length, const int i)covarianceBaseinline - nKeptPCAparscovarianceBaseprotected - oscpars1covarianceOscprotected - pcacovarianceBaseprotected - PerformBetaStudycovarianceOscprotected - Print()covarianceOsc - printIndivStepScale()covarianceBase - PrintLengthcovarianceBaseprotected - printNominal()covarianceBase - printNominalCurrProp()covarianceBase - printPars()covarianceBase - proposeStep() overridecovarianceOscvirtual - random_numbercovarianceBaseprotected - RandomConfiguration()covarianceBase - randomize()covarianceBaseprotected - randParamscovarianceBaseprotected - reactorPriorcovarianceOscprotected - ReserveMemory(const int size)covarianceBaseprotected - resetIndivStepScale()covarianceBase - retPointer(const int iParam)covarianceBaseinline - ReturnUnity()covarianceBaseinlineprotected - saveAdaptiveToFile(const TString &outFileName, const TString &systematicName)covarianceBase + densitycovarianceOscprotected + eigen_thresholdcovarianceBaseprotected + eigen_valuescovarianceBaseprotected + eigen_values_mastercovarianceBaseprotected + eigen_vectorscovarianceBaseprotected + FirstPCAdparcovarianceBaseprotected + flipBetacovarianceOscprotected + flipdelMcovarianceOscprotected + fParCurr_PCAcovarianceBaseprotected + fParProp_PCAcovarianceBaseprotected + fParSigma_PCAcovarianceBaseprotected + GetCorrelationMatrix()covarianceBase + getCovMatrix()covarianceBaseinline + GetDensity()covarianceOscinline + getDiagonalError(const int i)covarianceBaseinline + getDoAdaption()covarianceBaseinline + getEigenValues()covarianceBaseinline + getEigenValuesMaster()covarianceBaseinline + getEigenVectors()covarianceBaseinline + getFlatPrior(const int i)covarianceBaseinline + GetGenerated(const int i)covarianceBaseinline + getGeneratedValues()covarianceBaseinline + GetIndivStepScale(const int ParameterIndex)covarianceBaseinline + getInputFile() constcovarianceBaseinline + getInvCovMatrix()covarianceBaseinline + GetLikelihood() overridecovarianceOscvirtual + GetLowerBound(const int i)covarianceBaseinline + getName()covarianceBaseinline + getNominal(const int i)covarianceBaseinlinevirtual + getNominalArray()covarianceBasevirtual + getNpars()covarianceBaseinline + GetNumParams()covarianceBaseinline + getParameterMeans()covarianceBaseinline + getParCurr(const int i)covarianceBaseinline + getParCurr_PCA(const int i)covarianceBaseinline + GetParFancyName(const int i)covarianceBaseinline + GetParFancyName(const int i) constcovarianceBaseinline + getParInit(const int i)covarianceBaseinline + GetParName(const int i)covarianceBaseinline + GetParName(const int i) constcovarianceBaseinline + getParProp(const int i)covarianceBaseinline + getParProp_PCA(const int i)covarianceBaseinline + GetPathLength()covarianceOscinline + GetPerformBetaStudy()covarianceOscinline + getPreFitValues()covarianceBaseinline + getProposed() constcovarianceBase + getPropPars()covarianceOsc + getSize()covarianceBaseinline + getThrowMatrix()covarianceBaseinline + getThrowMatrix_CholDecomp()covarianceBaseinline + getTransferMatrix()covarianceBaseinline + GetUpperBound(const int i)covarianceBaseinline + init(const char *name, const char *file)covarianceBaseprotected + init(const std::vector< std::string > &YAMLFile)covarianceBaseprotected + init(TMatrixDSym *covMat)covarianceBaseprotected + initialiseAdaption(const YAML::Node &adapt_manager)covarianceBase + inputFilecovarianceBaseprotected + invCovMatrixcovarianceBaseprotected + InvertCovMatrixcovarianceBaseprotected + isDecomposed_PCAcovarianceBaseprotected + isParameterFixed(const int i)covarianceBaseinline + isParameterFixed(const std::string &name)covarianceBase + isParameterFixedPCA(const int i)covarianceBaseinline + IsPCA()covarianceBaseinline + kBetacovarianceOscprotected + kDeltaCPcovarianceOscprotected + kDeltaM23covarianceOscprotected + kSinTheta23covarianceOscprotected + LcovarianceOscprotected + LastPCAdparcovarianceBaseprotected + makeClosestPosDef(TMatrixDSym *cov)covarianceBaseprotected + MakePosDef(TMatrixDSym *cov=nullptr)covarianceBaseprotected + matrixNamecovarianceBaseprotected + MatrixVectorMulti(double *_restrict_ VecMulti, double **_restrict_ matrix, const double *_restrict_ vector, const int n)covarianceBaseinline + MatrixVectorMultiSingle(double **_restrict_ matrix, const double *_restrict_ vector, const int Length, const int i)covarianceBaseinline + nKeptPCAparscovarianceBaseprotected + oscpars1covarianceOscprotected + pcacovarianceBaseprotected + PerformBetaStudycovarianceOscprotected + Print()covarianceOsc + printIndivStepScale()covarianceBase + PrintLengthcovarianceBaseprotected + printNominal()covarianceBase + printNominalCurrProp()covarianceBase + printPars()covarianceBase + proposeStep() overridecovarianceOscvirtual + random_numbercovarianceBaseprotected + RandomConfiguration()covarianceBase + randomize()covarianceBaseprotected + randParamscovarianceBaseprotected + reactorPriorcovarianceOscprotected + ReserveMemory(const int size)covarianceBaseprotected + resetIndivStepScale()covarianceBase + retPointer(const int iParam)covarianceBaseinline + ReturnUnity()covarianceBaseinlineprotected SaveUpdatedMatrixConfig()covarianceBase setAdaptionDefaults()covarianceBaseprotected - setAdaptiveBlocks(std::vector< std::vector< int > > block_indices)covarianceBaseprotected - SetBranches(TTree &tree, bool SaveProposal=false)covarianceBase - setCovMatrix(TMatrixDSym *cov)covarianceBase - setExtraBranches(TTree &tree)covarianceOsc - setFlatPrior(const int i, const bool eL)covarianceBase - setFlipBeta(bool flip)covarianceOscinline - setFlipDeltaM23(bool flip)covarianceOscinline - setIndivStepScale(const int ParameterIndex, const double StepScale)covarianceBaseinline - setIndivStepScale(const std::vector< double > &stepscale)covarianceBase - setName(const char *name)covarianceBaseinline - setNumberOfSteps(const int nsteps)covarianceBaseinline - setPar(const int i, const double val)covarianceBase - setParameters(const std::vector< double > &pars={})covarianceBase - setParameters_PCA(const std::vector< double > &pars)covarianceBaseinline - setParCurr_PCA(const int i, const double value)covarianceBaseinline - setParCurrProp(const int i, const double val)covarianceBase - setParName(int i, char *name)covarianceBaseinline - setParProp(const int i, const double val)covarianceBaseinline - setParProp_PCA(const int i, const double value)covarianceBaseinline - setPrintLength(const unsigned int PriLen)covarianceBaseinline - setSingleParameter(const int parNo, const double parVal)covarianceBase - setStepScale(const double scale)covarianceBase - setThrowMatrix(TMatrixDSym *cov)covarianceBase - setThrowMatrixFromFile(const std::string &matrix_file_name, const std::string &matrix_name, const std::string &means_name)covarianceBaseprotected - sizecovarianceBaseprotected - throwMatrixcovarianceBaseprotected - throwMatrix_CholDecompcovarianceBaseprotected - throwMatrixCholDecompcovarianceBaseprotected - throwNominal(const bool nomValues=false, const int seed=0)covarianceBase - throwParameters()covarianceBase - throwParCurr(const double mag=1.)covarianceBase - throwParProp(const double mag=1.)covarianceBase - toggleFixAllParameters()covarianceBase - toggleFixParameter(const int i)covarianceBase - toggleFixParameter(const std::string &name)covarianceBase - total_stepscovarianceBaseprotected - TransferMatcovarianceBaseprotected - TransferMatTcovarianceBaseprotected - TransferToParam()covarianceBaseprotected - TransferToPCA()covarianceBaseprotected - UnitycovarianceBaseprotected - updateAdaptiveCovariance()covarianceBaseprotected - updateThrowMatrix(TMatrixDSym *cov)covarianceBase - use_adaptivecovarianceBaseprotected - useReactorPrior(bool reactor)covarianceOscinline - ~covarianceBase()covarianceBasevirtual - ~covarianceOsc()covarianceOscvirtual + SetBranches(TTree &tree, bool SaveProposal=false)covarianceBase + setCovMatrix(TMatrixDSym *cov)covarianceBase + setExtraBranches(TTree &tree)covarianceOsc + setFlatPrior(const int i, const bool eL)covarianceBase + setFlipBeta(bool flip)covarianceOscinline + setFlipDeltaM23(bool flip)covarianceOscinline + setIndivStepScale(const int ParameterIndex, const double StepScale)covarianceBaseinline + setIndivStepScale(const std::vector< double > &stepscale)covarianceBase + setName(const char *name)covarianceBaseinline + setNumberOfSteps(const int nsteps)covarianceBaseinline + setPar(const int i, const double val)covarianceBase + setParameters(const std::vector< double > &pars={})covarianceBase + setParameters_PCA(const std::vector< double > &pars)covarianceBaseinline + setParCurr_PCA(const int i, const double value)covarianceBaseinline + setParCurrProp(const int i, const double val)covarianceBase + setParName(int i, char *name)covarianceBaseinline + setParProp(const int i, const double val)covarianceBaseinline + setParProp_PCA(const int i, const double value)covarianceBaseinline + setPrintLength(const unsigned int PriLen)covarianceBaseinline + setSingleParameter(const int parNo, const double parVal)covarianceBase + setStepScale(const double scale)covarianceBase + setThrowMatrix(TMatrixDSym *cov)covarianceBase + setThrowMatrixFromFile(const std::string &matrix_file_name, const std::string &matrix_name, const std::string &means_name)covarianceBaseprotected + sizecovarianceBaseprotected + throwMatrixcovarianceBaseprotected + throwMatrix_CholDecompcovarianceBaseprotected + throwMatrixCholDecompcovarianceBaseprotected + throwNominal(const bool nomValues=false, const int seed=0)covarianceBase + throwParameters()covarianceBase + throwParCurr(const double mag=1.)covarianceBase + throwParProp(const double mag=1.)covarianceBase + toggleFixAllParameters()covarianceBase + toggleFixParameter(const int i)covarianceBase + toggleFixParameter(const std::string &name)covarianceBase + total_stepscovarianceBaseprotected + TransferMatcovarianceBaseprotected + TransferMatTcovarianceBaseprotected + TransferToParam()covarianceBaseprotected + TransferToPCA()covarianceBaseprotected + UnitycovarianceBaseprotected + updateAdaptiveCovariance()covarianceBaseprotected + updateThrowMatrix(TMatrixDSym *cov)covarianceBase + use_adaptivecovarianceBaseprotected + useReactorPrior(bool reactor)covarianceOscinline + ~covarianceBase()covarianceBasevirtual + ~covarianceOsc()covarianceOscvirtual
diff --git a/classcovarianceOsc.html b/classcovarianceOsc.html index 64b02c0f3..5edef6263 100644 --- a/classcovarianceOsc.html +++ b/classcovarianceOsc.html @@ -254,17 +254,16 @@ void initialiseAdaption (const YAML::Node &adapt_manager)  Initialise adaptive MCMC.
  -void saveAdaptiveToFile (const TString &outFileName, const TString &systematicName) - Save adaptive throw matrix to file.
-  bool getDoAdaption ()  Do we adapt or not.
  void setThrowMatrix (TMatrixDSym *cov) + Use new throw matrix, used in adaptive MCMC.
  void updateThrowMatrix (TMatrixDSym *cov)   void setNumberOfSteps (const int nsteps) + Set number of MCMC step, when running adaptive MCMC it is updated with given frequency. We need number of steps to determine frequency.
  TMatrixDSym * getThrowMatrix ()   @@ -435,7 +434,7 @@  The input root file we read in.
  int size - Total number of parmas, deprecated, please don't use it.
+ Total number of params, deprecated, please don't use it.
  const char * matrixName  Name of cov matrix.
@@ -555,8 +554,10 @@  If param is decomposed this will return -1, if not this will return enumerator to param in normal base. This way we can map stuff like step scale etc between normal base and undecomposed param in eigen base.
  TMatrixDSym * throwMatrix + Matrix which we use for step proposal before Cholesky decomposition (not actually used for step proposal)
  TMatrixD * throwMatrix_CholDecomp + Matrix which we use for step proposal after Cholesky decomposition.
  double ** throwMatrixCholDecomp  Throw matrix that is being used in the fit, much faster as TMatrixDSym cache miss.
@@ -565,15 +566,17 @@  Are we using AMCMC?
  int total_steps + Total number of MCMC steps.
  -adaptive_mcmc::AdaptiveMCMCStruct adaption_struct - Struct containing information about adaption.
-  +adaptive_mcmc::AdaptiveMCMCHandler AdaptiveHandler + Struct containing information about adaption.
+  + @@ -608,18 +611,12 @@ - - - - - -

Additional Inherited Members

- Protected Member Functions inherited from covarianceBase
void init (const char *name, const char *file)
 Initialisation of the class using matrix from root file.
 
void init (const std::vector< std::string > &YAMLFile)
 Initialisation of the class using config.
void setAdaptionDefaults ()
 sets default values for adaptive MCMC parameters
 
void setAdaptiveBlocks (std::vector< std::vector< int > > block_indices)
 sets adaptive block matrix
 
void setThrowMatrixFromFile (const std::string &matrix_file_name, const std::string &matrix_name, const std::string &means_name)
 sets throw matrix from a file
 
void updateAdaptiveCovariance ()
 Method to update adaptive MCMC.
 
void createNewAdaptiveCovariance ()
 method to create new throw matrix
 

Detailed Description

Class responsible for handling of neutrino oscillation parameters.

@@ -728,18 +725,18 @@

75

76 MACH3LOG_INFO("created oscillation parameter handler");
77}
-
MACH3LOG_INFO
#define MACH3LOG_INFO
Definition MaCh3Logger.h:13
-
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:18
-
covarianceBase
Base class responsible for handling of systematic error parameters. Capable of using PCA or using ada...
Definition covarianceBase.h:33
-
covarianceBase::_fPropVal
std::vector< double > _fPropVal
Proposed value of the parameter.
Definition covarianceBase.h:447
-
covarianceBase::setFlatPrior
void setFlatPrior(const int i, const bool eL)
Set if parameter should have flat prior or not.
Definition covarianceBase.cpp:1202
-
covarianceBase::randomize
void randomize()
"Randomize" the parameters in the covariance class for the proposed step. Used the proposal kernel an...
Definition covarianceBase.cpp:793
-
covarianceBase::_fError
std::vector< double > _fError
Prior error on the parameter.
Definition covarianceBase.h:451
-
covarianceBase::_fIndivStepScale
std::vector< double > _fIndivStepScale
Individual step scale used by MCMC algorithm.
Definition covarianceBase.h:457
-
covarianceBase::_fNames
std::vector< std::string > _fNames
ETA _fNames is set automatically in the covariance class to be something like xsec_i,...
Definition covarianceBase.h:435
-
covarianceBase::_fPreFitValue
std::vector< double > _fPreFitValue
Parameter value dictated by the prior model. Based on it penalty term is calculated.
Definition covarianceBase.h:443
-
covarianceBase::_fNumPar
int _fNumPar
Number of systematic parameters.
Definition covarianceBase.h:441
-
covarianceBase::_fCurrVal
std::vector< double > _fCurrVal
Current value of the parameter.
Definition covarianceBase.h:445
+
MACH3LOG_INFO
#define MACH3LOG_INFO
Definition MaCh3Logger.h:16
+
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:21
+
covarianceBase
Base class responsible for handling of systematic error parameters. Capable of using PCA or using ada...
Definition covarianceBase.h:34
+
covarianceBase::_fPropVal
std::vector< double > _fPropVal
Proposed value of the parameter.
Definition covarianceBase.h:461
+
covarianceBase::setFlatPrior
void setFlatPrior(const int i, const bool eL)
Set if parameter should have flat prior or not.
Definition covarianceBase.cpp:1203
+
covarianceBase::randomize
void randomize()
"Randomize" the parameters in the covariance class for the proposed step. Used the proposal kernel an...
Definition covarianceBase.cpp:794
+
covarianceBase::_fError
std::vector< double > _fError
Prior error on the parameter.
Definition covarianceBase.h:465
+
covarianceBase::_fIndivStepScale
std::vector< double > _fIndivStepScale
Individual step scale used by MCMC algorithm.
Definition covarianceBase.h:471
+
covarianceBase::_fNames
std::vector< std::string > _fNames
ETA _fNames is set automatically in the covariance class to be something like xsec_i,...
Definition covarianceBase.h:449
+
covarianceBase::_fPreFitValue
std::vector< double > _fPreFitValue
Parameter value dictated by the prior model. Based on it penalty term is calculated.
Definition covarianceBase.h:457
+
covarianceBase::_fNumPar
int _fNumPar
Number of systematic parameters.
Definition covarianceBase.h:455
+
covarianceBase::_fCurrVal
std::vector< double > _fCurrVal
Current value of the parameter.
Definition covarianceBase.h:459
covarianceOsc::flipBeta
bool flipBeta
Do we flip Beta or not.
Definition covarianceOsc.h:55
covarianceOsc::kDeltaM23
int kDeltaM23
There is special treatment for DeltaM23, therefore store enum keeping track when to apply special tre...
Definition covarianceOsc.h:64
covarianceOsc::L
double L
Value of baseline.
Definition covarianceOsc.h:47
@@ -885,8 +882,8 @@

262 throw MaCh3Exception(__FILE__ , __LINE__ );
263 }
264}
-
MACH3LOG_ERROR
#define MACH3LOG_ERROR
Definition MaCh3Logger.h:15
-
MaCh3Exception
Custom exception class for MaCh3 errors.
Definition MaCh3Exception.h:10
+
MACH3LOG_ERROR
#define MACH3LOG_ERROR
Definition MaCh3Logger.h:18
+
MaCh3Exception
Custom exception class for MaCh3 errors.
Definition MaCh3Exception.h:12
@@ -985,7 +982,7 @@

142 }
143 return logL;
144}
-
covarianceBase::GetLikelihood
virtual double GetLikelihood()
Return CalcLikelihood if some params were thrown out of boundary return LARGE_LOGL
Definition covarianceBase.cpp:1034
+
covarianceBase::GetLikelihood
virtual double GetLikelihood()
Return CalcLikelihood if some params were thrown out of boundary return LARGE_LOGL
Definition covarianceBase.cpp:1037
@@ -1118,7 +1115,7 @@

235 MACH3LOG_INFO("Baseline: {}", L);
236 MACH3LOG_INFO("Earth Density: {}", density);
237}
-
covarianceBase::matrixName
const char * matrixName
Name of cov matrix.
Definition covarianceBase.h:413
+
covarianceBase::matrixName
const char * matrixName
Name of cov matrix.
Definition covarianceBase.h:427
@@ -1181,7 +1178,7 @@

193 if(random_number[0]->Uniform() < 0.5) _fPropVal[kBeta] = 1-_fCurrVal[kBeta];
194 }
195}
-
covarianceBase::random_number
TRandom3 ** random_number
KS: Set Random numbers for each thread so each thread has different seed.
Definition covarianceBase.h:422
+
covarianceBase::random_number
TRandom3 ** random_number
KS: Set Random numbers for each thread so each thread has different seed.
Definition covarianceBase.h:436
covarianceBase::proposeStep
virtual void proposeStep()
Generate a new proposed state.
Definition covarianceBase.cpp:779
diff --git a/classcovarianceXsec-members.html b/classcovarianceXsec-members.html index d509d8b02..c4b5027c0 100644 --- a/classcovarianceXsec-members.html +++ b/classcovarianceXsec-members.html @@ -99,7 +99,7 @@ _fUpBoundcovarianceBaseprotected _fYAMLDoccovarianceBaseprotected acceptStep()covarianceBase - adaption_structcovarianceBaseprotected + AdaptiveHandlercovarianceBaseprotected CalcLikelihood()covarianceBase calcReWeight(const int bin)covarianceBaseinline CheckBounds()covarianceBasevirtual @@ -113,163 +113,160 @@ covarianceBase(const char *name, const char *file, int seed, double threshold, int FirstPCAdpar, int LastPCAdpar)covarianceBase covarianceXsec(const std::vector< std::string > &FileNames, const char *name="xsec_cov", double threshold=-1, int FirstPCAdpar=-999, int LastPCAdpar=-999)covarianceXsec covMatrixcovarianceBaseprotected - createNewAdaptiveCovariance()covarianceBaseprotected - eigen_thresholdcovarianceBaseprotected - eigen_valuescovarianceBaseprotected - eigen_values_mastercovarianceBaseprotected - eigen_vectorscovarianceBaseprotected - FirstPCAdparcovarianceBaseprotected - fParCurr_PCAcovarianceBaseprotected - fParProp_PCAcovarianceBaseprotected - fParSigma_PCAcovarianceBaseprotected - GetCorrelationMatrix()covarianceBase - getCovMatrix()covarianceBaseinline - getDiagonalError(const int i)covarianceBaseinline - getDoAdaption()covarianceBaseinline - getEigenValues()covarianceBaseinline - getEigenValuesMaster()covarianceBaseinline - getEigenVectors()covarianceBaseinline - GetFDSplineFileParsNamesFromDetID(const int DetID)covarianceXsec - getFlatPrior(const int i)covarianceBaseinline - GetFuncParsIndexFromDetID(const int DetID)covarianceXsecinline - GetFuncParsNamesFromDetID(const int DetID)covarianceXsecinline - GetGenerated(const int i)covarianceBaseinline - getGeneratedValues()covarianceBaseinline - GetIndivStepScale(const int ParameterIndex)covarianceBaseinline - getInputFile() constcovarianceBaseinline - getInvCovMatrix()covarianceBaseinline - GetLikelihood()covarianceBasevirtual - GetLowerBound(const int i)covarianceBaseinline - getName()covarianceBaseinline - GetNDSplineFileParsNamesFromDetID(const int DetID)covarianceXsec - getNominal(const int i) overridecovarianceXsecinlinevirtual - getNominalArray() overridecovarianceXsecinlinevirtual - GetNormParsFromDetID(const int DetID)covarianceXsec - getNpars()covarianceBaseinline - GetNumFuncParamsFromDetID(const int DetID)covarianceXsecinline - GetNumParams()covarianceBaseinline - GetNumParamsFromDetID(const int DetID, const SystType Type)covarianceXsec - GetNumSplineParamsFromDetID(const int DetID)covarianceXsecinline - getParameterMeans()covarianceBaseinline - GetParamType(const int i) constcovarianceXsecinline - GetParamTypeString(const int i) constcovarianceXsecinline - getParCurr(const int i)covarianceBaseinline - getParCurr_PCA(const int i)covarianceBaseinline - GetParDetID(const int i) constcovarianceXsecinline - GetParFancyName(const int i)covarianceBaseinline - GetParFancyName(const int i) constcovarianceBaseinline - getParInit(const int i)covarianceBaseinline - GetParName(const int i)covarianceBaseinline - GetParName(const int i) constcovarianceBaseinline - getParProp(const int i)covarianceBaseinline - getParProp_PCA(const int i)covarianceBaseinline - GetParsIndexFromDetID(const int DetID, const SystType Type)covarianceXsec - GetParsNamesFromDetID(const int DetID, const SystType Type)covarianceXsec - GetParSplineInterpolation(const int i)covarianceXsecinline - GetParSplineKnotLowerBound(const int i)covarianceXsecinline - GetParSplineKnotUpperBound(const int i)covarianceXsecinline - getPreFitValues()covarianceBaseinline - getProposed() constcovarianceBase - getSize()covarianceBaseinline - GetSplineFileParsNamesFromDetID(const int DetID)covarianceXsec - GetSplineModeVecFromDetID(const int DetID)covarianceXsec - GetSplineParsIndexFromDetID(const int DetID)covarianceXsecinline - GetSplineParsNamesFromDetID(const int DetID)covarianceXsec - getThrowMatrix()covarianceBaseinline - getThrowMatrix_CholDecomp()covarianceBaseinline - getTransferMatrix()covarianceBaseinline - GetUpperBound(const int i)covarianceBaseinline - GetXsecNorm(const YAML::Node &param, const int Index)covarianceXsecinlineprotected - GetXsecSpline(const YAML::Node &param)covarianceXsecinlineprotected - init(const char *name, const char *file)covarianceBaseprotected - init(const std::vector< std::string > &YAMLFile)covarianceBaseprotected - init(TMatrixDSym *covMat)covarianceBaseprotected - initialiseAdaption(const YAML::Node &adapt_manager)covarianceBase - initParams()covarianceXsecprotected - InitXsecFromConfig()covarianceXsecinlineprotected - inputFilecovarianceBaseprotected - invCovMatrixcovarianceBaseprotected - InvertCovMatrixcovarianceBaseprotected - isDecomposed_PCAcovarianceBaseprotected - isFluxcovarianceXsecprotected - isParameterFixed(const int i)covarianceBaseinline - isParameterFixed(const std::string &name)covarianceBase - isParameterFixedPCA(const int i)covarianceBaseinline - IsParFlux(const int i)covarianceXsecinline - IsPCA()covarianceBaseinline - LastPCAdparcovarianceBaseprotected - makeClosestPosDef(TMatrixDSym *cov)covarianceBaseprotected - MakePosDef(TMatrixDSym *cov=nullptr)covarianceBaseprotected - matrixNamecovarianceBaseprotected - MatrixVectorMulti(double *_restrict_ VecMulti, double **_restrict_ matrix, const double *_restrict_ vector, const int n)covarianceBaseinline - MatrixVectorMultiSingle(double **_restrict_ matrix, const double *_restrict_ vector, const int Length, const int i)covarianceBaseinline - nKeptPCAparscovarianceBaseprotected - NormParamscovarianceXsecprotected - pcacovarianceBaseprotected - Print()covarianceXsecinline - printIndivStepScale()covarianceBase - PrintLengthcovarianceBaseprotected - printNominal()covarianceBase - printNominalCurrProp()covarianceBase - printPars()covarianceBase - proposeStep()covarianceBasevirtual - random_numbercovarianceBaseprotected - RandomConfiguration()covarianceBase - randomize()covarianceBaseprotected - randParamscovarianceBaseprotected - ReserveMemory(const int size)covarianceBaseprotected - resetIndivStepScale()covarianceBase - retPointer(const int iParam)covarianceBaseinline - ReturnUnity()covarianceBaseinlineprotected - saveAdaptiveToFile(const TString &outFileName, const TString &systematicName)covarianceBase + eigen_thresholdcovarianceBaseprotected + eigen_valuescovarianceBaseprotected + eigen_values_mastercovarianceBaseprotected + eigen_vectorscovarianceBaseprotected + FirstPCAdparcovarianceBaseprotected + fParCurr_PCAcovarianceBaseprotected + fParProp_PCAcovarianceBaseprotected + fParSigma_PCAcovarianceBaseprotected + GetCorrelationMatrix()covarianceBase + getCovMatrix()covarianceBaseinline + getDiagonalError(const int i)covarianceBaseinline + getDoAdaption()covarianceBaseinline + getEigenValues()covarianceBaseinline + getEigenValuesMaster()covarianceBaseinline + getEigenVectors()covarianceBaseinline + GetFDSplineFileParsNamesFromDetID(const int DetID)covarianceXsec + getFlatPrior(const int i)covarianceBaseinline + GetFuncParsIndexFromDetID(const int DetID)covarianceXsecinline + GetFuncParsNamesFromDetID(const int DetID)covarianceXsecinline + GetGenerated(const int i)covarianceBaseinline + getGeneratedValues()covarianceBaseinline + GetIndivStepScale(const int ParameterIndex)covarianceBaseinline + getInputFile() constcovarianceBaseinline + getInvCovMatrix()covarianceBaseinline + GetLikelihood()covarianceBasevirtual + GetLowerBound(const int i)covarianceBaseinline + getName()covarianceBaseinline + GetNDSplineFileParsNamesFromDetID(const int DetID)covarianceXsec + getNominal(const int i) overridecovarianceXsecinlinevirtual + getNominalArray() overridecovarianceXsecinlinevirtual + GetNormParsFromDetID(const int DetID)covarianceXsec + getNpars()covarianceBaseinline + GetNumFuncParamsFromDetID(const int DetID)covarianceXsecinline + GetNumParams()covarianceBaseinline + GetNumParamsFromDetID(const int DetID, const SystType Type)covarianceXsec + GetNumSplineParamsFromDetID(const int DetID)covarianceXsecinline + getParameterMeans()covarianceBaseinline + GetParamType(const int i) constcovarianceXsecinline + GetParamTypeString(const int i) constcovarianceXsecinline + getParCurr(const int i)covarianceBaseinline + getParCurr_PCA(const int i)covarianceBaseinline + GetParDetID(const int i) constcovarianceXsecinline + GetParFancyName(const int i)covarianceBaseinline + GetParFancyName(const int i) constcovarianceBaseinline + getParInit(const int i)covarianceBaseinline + GetParName(const int i)covarianceBaseinline + GetParName(const int i) constcovarianceBaseinline + getParProp(const int i)covarianceBaseinline + getParProp_PCA(const int i)covarianceBaseinline + GetParsIndexFromDetID(const int DetID, const SystType Type)covarianceXsec + GetParsNamesFromDetID(const int DetID, const SystType Type)covarianceXsec + GetParSplineInterpolation(const int i)covarianceXsecinline + GetParSplineKnotLowerBound(const int i)covarianceXsecinline + GetParSplineKnotUpperBound(const int i)covarianceXsecinline + getPreFitValues()covarianceBaseinline + getProposed() constcovarianceBase + getSize()covarianceBaseinline + GetSplineFileParsNamesFromDetID(const int DetID)covarianceXsec + GetSplineModeVecFromDetID(const int DetID)covarianceXsec + GetSplineParsIndexFromDetID(const int DetID)covarianceXsecinline + GetSplineParsNamesFromDetID(const int DetID)covarianceXsec + getThrowMatrix()covarianceBaseinline + getThrowMatrix_CholDecomp()covarianceBaseinline + getTransferMatrix()covarianceBaseinline + GetUpperBound(const int i)covarianceBaseinline + GetXsecNorm(const YAML::Node &param, const int Index)covarianceXsecinlineprotected + GetXsecSpline(const YAML::Node &param)covarianceXsecinlineprotected + init(const char *name, const char *file)covarianceBaseprotected + init(const std::vector< std::string > &YAMLFile)covarianceBaseprotected + init(TMatrixDSym *covMat)covarianceBaseprotected + initialiseAdaption(const YAML::Node &adapt_manager)covarianceBase + initParams()covarianceXsecprotected + InitXsecFromConfig()covarianceXsecinlineprotected + inputFilecovarianceBaseprotected + invCovMatrixcovarianceBaseprotected + InvertCovMatrixcovarianceBaseprotected + isDecomposed_PCAcovarianceBaseprotected + isFluxcovarianceXsecprotected + isParameterFixed(const int i)covarianceBaseinline + isParameterFixed(const std::string &name)covarianceBase + isParameterFixedPCA(const int i)covarianceBaseinline + IsParFlux(const int i)covarianceXsecinline + IsPCA()covarianceBaseinline + LastPCAdparcovarianceBaseprotected + makeClosestPosDef(TMatrixDSym *cov)covarianceBaseprotected + MakePosDef(TMatrixDSym *cov=nullptr)covarianceBaseprotected + matrixNamecovarianceBaseprotected + MatrixVectorMulti(double *_restrict_ VecMulti, double **_restrict_ matrix, const double *_restrict_ vector, const int n)covarianceBaseinline + MatrixVectorMultiSingle(double **_restrict_ matrix, const double *_restrict_ vector, const int Length, const int i)covarianceBaseinline + nKeptPCAparscovarianceBaseprotected + NormParamscovarianceXsecprotected + pcacovarianceBaseprotected + Print()covarianceXsecinline + printIndivStepScale()covarianceBase + PrintLengthcovarianceBaseprotected + printNominal()covarianceBase + printNominalCurrProp()covarianceBase + printPars()covarianceBase + proposeStep()covarianceBasevirtual + random_numbercovarianceBaseprotected + RandomConfiguration()covarianceBase + randomize()covarianceBaseprotected + randParamscovarianceBaseprotected + ReserveMemory(const int size)covarianceBaseprotected + resetIndivStepScale()covarianceBase + retPointer(const int iParam)covarianceBaseinline + ReturnUnity()covarianceBaseinlineprotected SaveUpdatedMatrixConfig()covarianceBase setAdaptionDefaults()covarianceBaseprotected - setAdaptiveBlocks(std::vector< std::vector< int > > block_indices)covarianceBaseprotected - SetBranches(TTree &tree, bool SaveProposal=false)covarianceBase - setCovMatrix(TMatrixDSym *cov)covarianceBase - setFlatPrior(const int i, const bool eL)covarianceBase - setFluxOnlyParameters()covarianceXsec - setIndivStepScale(const int ParameterIndex, const double StepScale)covarianceBaseinline - setIndivStepScale(const std::vector< double > &stepscale)covarianceBase - setName(const char *name)covarianceBaseinline - setNumberOfSteps(const int nsteps)covarianceBaseinline - setPar(const int i, const double val)covarianceBase - setParameters(const std::vector< double > &pars={})covarianceBase - setParameters_PCA(const std::vector< double > &pars)covarianceBaseinline - setParCurr_PCA(const int i, const double value)covarianceBaseinline - setParCurrProp(const int i, const double val)covarianceBase - setParName(int i, char *name)covarianceBaseinline - setParProp(const int i, const double val)covarianceBaseinline - setParProp_PCA(const int i, const double value)covarianceBaseinline - setPrintLength(const unsigned int PriLen)covarianceBaseinline - setSingleParameter(const int parNo, const double parVal)covarianceBase - setStepScale(const double scale)covarianceBase - setThrowMatrix(TMatrixDSym *cov)covarianceBase - setThrowMatrixFromFile(const std::string &matrix_file_name, const std::string &matrix_name, const std::string &means_name)covarianceBaseprotected - setXsecOnlyParameters()covarianceXsec - sizecovarianceBaseprotected - SplineParamscovarianceXsecprotected - throwMatrixcovarianceBaseprotected - throwMatrix_CholDecompcovarianceBaseprotected - throwMatrixCholDecompcovarianceBaseprotected - throwNominal(const bool nomValues=false, const int seed=0)covarianceBase - throwParameters()covarianceBase - throwParCurr(const double mag=1.)covarianceBase - throwParProp(const double mag=1.)covarianceBase - toggleFixAllParameters()covarianceBase - toggleFixParameter(const int i)covarianceBase - toggleFixParameter(const std::string &name)covarianceBase - total_stepscovarianceBaseprotected - TransferMatcovarianceBaseprotected - TransferMatTcovarianceBaseprotected - TransferToParam()covarianceBaseprotected - TransferToPCA()covarianceBaseprotected - UnitycovarianceBaseprotected - updateAdaptiveCovariance()covarianceBaseprotected - updateThrowMatrix(TMatrixDSym *cov)covarianceBase - use_adaptivecovarianceBaseprotected - ~covarianceBase()covarianceBasevirtual - ~covarianceXsec()covarianceXsec + SetBranches(TTree &tree, bool SaveProposal=false)covarianceBase + setCovMatrix(TMatrixDSym *cov)covarianceBase + setFlatPrior(const int i, const bool eL)covarianceBase + setFluxOnlyParameters()covarianceXsec + setIndivStepScale(const int ParameterIndex, const double StepScale)covarianceBaseinline + setIndivStepScale(const std::vector< double > &stepscale)covarianceBase + setName(const char *name)covarianceBaseinline + setNumberOfSteps(const int nsteps)covarianceBaseinline + setPar(const int i, const double val)covarianceBase + setParameters(const std::vector< double > &pars={})covarianceBase + setParameters_PCA(const std::vector< double > &pars)covarianceBaseinline + setParCurr_PCA(const int i, const double value)covarianceBaseinline + setParCurrProp(const int i, const double val)covarianceBase + setParName(int i, char *name)covarianceBaseinline + setParProp(const int i, const double val)covarianceBaseinline + setParProp_PCA(const int i, const double value)covarianceBaseinline + setPrintLength(const unsigned int PriLen)covarianceBaseinline + setSingleParameter(const int parNo, const double parVal)covarianceBase + setStepScale(const double scale)covarianceBase + setThrowMatrix(TMatrixDSym *cov)covarianceBase + setThrowMatrixFromFile(const std::string &matrix_file_name, const std::string &matrix_name, const std::string &means_name)covarianceBaseprotected + setXsecOnlyParameters()covarianceXsec + sizecovarianceBaseprotected + SplineParamscovarianceXsecprotected + throwMatrixcovarianceBaseprotected + throwMatrix_CholDecompcovarianceBaseprotected + throwMatrixCholDecompcovarianceBaseprotected + throwNominal(const bool nomValues=false, const int seed=0)covarianceBase + throwParameters()covarianceBase + throwParCurr(const double mag=1.)covarianceBase + throwParProp(const double mag=1.)covarianceBase + toggleFixAllParameters()covarianceBase + toggleFixParameter(const int i)covarianceBase + toggleFixParameter(const std::string &name)covarianceBase + total_stepscovarianceBaseprotected + TransferMatcovarianceBaseprotected + TransferMatTcovarianceBaseprotected + TransferToParam()covarianceBaseprotected + TransferToPCA()covarianceBaseprotected + UnitycovarianceBaseprotected + updateAdaptiveCovariance()covarianceBaseprotected + updateThrowMatrix(TMatrixDSym *cov)covarianceBase + use_adaptivecovarianceBaseprotected + ~covarianceBase()covarianceBasevirtual + ~covarianceXsec()covarianceXsec
diff --git a/classcovarianceXsec.html b/classcovarianceXsec.html index 2a6ddcee7..4eb14aae6 100644 --- a/classcovarianceXsec.html +++ b/classcovarianceXsec.html @@ -111,9 +111,9 @@ int GetParDetID (const int i) const  ETA - just return the int of the DetID, this can be removed to do a string comp at some point.
  -const char * GetParamTypeString (const int i) const - ETA - just return a string of "spline", "norm" or "functional".
-  +std::string GetParamTypeString (const int i) const + ETA - just return a string of "spline", "norm" or "functional".
+  SystType GetParamType (const int i) const  Returns enum describing our param type.
  @@ -302,17 +302,16 @@ void initialiseAdaption (const YAML::Node &adapt_manager)  Initialise adaptive MCMC.
  -void saveAdaptiveToFile (const TString &outFileName, const TString &systematicName) - Save adaptive throw matrix to file.
-  bool getDoAdaption ()  Do we adapt or not.
  void setThrowMatrix (TMatrixDSym *cov) + Use new throw matrix, used in adaptive MCMC.
  void updateThrowMatrix (TMatrixDSym *cov)   void setNumberOfSteps (const int nsteps) + Set number of MCMC step, when running adaptive MCMC it is updated with given frequency. We need number of steps to determine frequency.
  TMatrixDSym * getThrowMatrix ()   @@ -457,6 +456,7 @@   - Protected Member Functions inherited from covarianceBase void init (const char *name, const char *file) + Initialisation of the class using matrix from root file.
  void init (const std::vector< std::string > &YAMLFile)  Initialisation of the class using config.
@@ -491,18 +491,12 @@ void setAdaptionDefaults ()  sets default values for adaptive MCMC parameters
  -void setAdaptiveBlocks (std::vector< std::vector< int > > block_indices) - sets adaptive block matrix
-  void setThrowMatrixFromFile (const std::string &matrix_file_name, const std::string &matrix_name, const std::string &means_name)  sets throw matrix from a file
  void updateAdaptiveCovariance ()  Method to update adaptive MCMC.
  -void createNewAdaptiveCovariance () - method to create new throw matrix
-  @@ -531,7 +525,7 @@ - + @@ -651,8 +645,10 @@ + + @@ -661,16 +657,17 @@ + - - - + + +

Protected Attributes

 The input root file we read in.
 
int size
 Total number of parmas, deprecated, please don't use it.
 Total number of params, deprecated, please don't use it.
 
const char * matrixName
 Name of cov matrix.
 If param is decomposed this will return -1, if not this will return enumerator to param in normal base. This way we can map stuff like step scale etc between normal base and undecomposed param in eigen base.
 
TMatrixDSym * throwMatrix
 Matrix which we use for step proposal before Cholesky decomposition (not actually used for step proposal)
 
TMatrixD * throwMatrix_CholDecomp
 Matrix which we use for step proposal after Cholesky decomposition.
 
double ** throwMatrixCholDecomp
 Throw matrix that is being used in the fit, much faster as TMatrixDSym cache miss.
 Are we using AMCMC?
 
int total_steps
 Total number of MCMC steps.
 
adaptive_mcmc::AdaptiveMCMCStruct adaption_struct
 Struct containing information about adaption.
 
adaptive_mcmc::AdaptiveMCMCHandler AdaptiveHandler
 Struct containing information about adaption.
 

Detailed Description

Class responsible for handling of systematic error parameters with different types defined in the config. Like spline, normalisation parameters etc.

See also
For more details, visit the Wiki.
-

Definition at line 15 of file covarianceXsec.h.

+

Definition at line 14 of file covarianceXsec.h.

Constructor & Destructor Documentation

◆ covarianceXsec()

@@ -746,12 +743,12 @@

22 // Print
23 Print();
24}
-
MACH3LOG_DEBUG
#define MACH3LOG_DEBUG
Definition MaCh3Logger.h:12
-
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:18
-
covarianceBase
Base class responsible for handling of systematic error parameters. Capable of using PCA or using ada...
Definition covarianceBase.h:33
-
covarianceBase::_fNames
std::vector< std::string > _fNames
ETA _fNames is set automatically in the covariance class to be something like xsec_i,...
Definition covarianceBase.h:435
-
covarianceBase::PrintLength
unsigned int PrintLength
KS: This is used when printing parameters, sometimes we have super long parameters name,...
Definition covarianceBase.h:432
-
covarianceBase::_fNumPar
int _fNumPar
Number of systematic parameters.
Definition covarianceBase.h:441
+
MACH3LOG_DEBUG
#define MACH3LOG_DEBUG
Definition MaCh3Logger.h:15
+
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:21
+
covarianceBase
Base class responsible for handling of systematic error parameters. Capable of using PCA or using ada...
Definition covarianceBase.h:34
+
covarianceBase::_fNames
std::vector< std::string > _fNames
ETA _fNames is set automatically in the covariance class to be something like xsec_i,...
Definition covarianceBase.h:449
+
covarianceBase::PrintLength
unsigned int PrintLength
KS: This is used when printing parameters, sometimes we have super long parameters name,...
Definition covarianceBase.h:446
+
covarianceBase::_fNumPar
int _fNumPar
Number of systematic parameters.
Definition covarianceBase.h:455
covarianceXsec::InitXsecFromConfig
void InitXsecFromConfig()
ETA - trying out the yaml parsing.
Definition covarianceXsec.cpp:27
covarianceXsec::Print
void Print()
Print information about the whole object once it is set.
Definition covarianceXsec.cpp:402
covarianceXsec::initParams
void initParams()
Initialise CovarianceXsec.
Definition covarianceXsec.cpp:371
@@ -823,11 +820,11 @@

507 CheckForDuplicates(_fNDSplineNames, "_fNDSplineNames");
508 CheckForDuplicates(_fFDSplineNames, "_fFDSplineNames");
509}
-
MACH3LOG_CRITICAL
#define MACH3LOG_CRITICAL
Definition MaCh3Logger.h:16
-
MaCh3Exception
Custom exception class for MaCh3 errors.
Definition MaCh3Exception.h:10
-
covarianceBase::_fFancyNames
std::vector< std::string > _fFancyNames
Fancy name for example rather than xsec_0 it is MAQE, useful for human reading.
Definition covarianceBase.h:437
-
covarianceXsec::_fFDSplineNames
std::vector< std::string > _fFDSplineNames
Definition covarianceXsec.h:139
-
covarianceXsec::_fNDSplineNames
std::vector< std::string > _fNDSplineNames
Definition covarianceXsec.h:138
+
MACH3LOG_CRITICAL
#define MACH3LOG_CRITICAL
Definition MaCh3Logger.h:19
+
MaCh3Exception
Custom exception class for MaCh3 errors.
Definition MaCh3Exception.h:12
+
covarianceBase::_fFancyNames
std::vector< std::string > _fFancyNames
Fancy name for example rather than xsec_0 it is MAQE, useful for human reading.
Definition covarianceBase.h:451
+
covarianceXsec::_fFDSplineNames
std::vector< std::string > _fFDSplineNames
Definition covarianceXsec.h:138
+
covarianceXsec::_fNDSplineNames
std::vector< std::string > _fNDSplineNames
Definition covarianceXsec.h:137
@@ -868,8 +865,8 @@

148 return returnVec;
149}
kSpline
@ kSpline
Definition Structs.h:152
-
covarianceXsec::GetParamType
SystType GetParamType(const int i) const
Returns enum describing our param type.
Definition covarianceXsec.h:42
-
covarianceXsec::GetParDetID
int GetParDetID(const int i) const
ETA - just return the int of the DetID, this can be removed to do a string comp at some point.
Definition covarianceXsec.h:36
+
covarianceXsec::GetParamType
SystType GetParamType(const int i) const
Returns enum describing our param type.
Definition covarianceXsec.h:41
+
covarianceXsec::GetParDetID
int GetParDetID(const int i) const
ETA - just return the int of the DetID, this can be removed to do a string comp at some point.
Definition covarianceXsec.h:35
@@ -899,8 +896,8 @@

Definition at line 89 of file covarianceXsec.h.

-
89{return GetParsIndexFromDetID(DetID, kFunc);}
+

Definition at line 88 of file covarianceXsec.h.

+
88{return GetParsIndexFromDetID(DetID, kFunc);}
kFunc
@ kFunc
Definition Structs.h:153
covarianceXsec::GetParsIndexFromDetID
const std::vector< int > GetParsIndexFromDetID(const int DetID, const SystType Type)
DB Grab the parameter indices for the relevant DetID.
Definition covarianceXsec.cpp:356
@@ -932,8 +929,8 @@

Definition at line 87 of file covarianceXsec.h.

-
87{return GetParsNamesFromDetID(DetID, kFunc);}
+

Definition at line 86 of file covarianceXsec.h.

+
86{return GetParsNamesFromDetID(DetID, kFunc);}
covarianceXsec::GetParsNamesFromDetID
const std::vector< std::string > GetParsNamesFromDetID(const int DetID, const SystType Type)
DB Grab the parameter names for the relevant DetID.
Definition covarianceXsec.cpp:340
@@ -1009,9 +1006,9 @@

covarianceBase.

-

Definition at line 103 of file covarianceXsec.h.

-
103{ return _fPreFitValue.at(i); };
-
covarianceBase::_fPreFitValue
std::vector< double > _fPreFitValue
Parameter value dictated by the prior model. Based on it penalty term is calculated.
Definition covarianceBase.h:443
+

Definition at line 102 of file covarianceXsec.h.

+
102{ return _fPreFitValue.at(i); };
+
covarianceBase::_fPreFitValue
std::vector< double > _fPreFitValue
Parameter value dictated by the prior model. Based on it penalty term is calculated.
Definition covarianceBase.h:457

@@ -1042,14 +1039,14 @@

covarianceBase.

-

Definition at line 93 of file covarianceXsec.h.

-
94 {
-
95 std::vector<double> nominal(_fNumPar);
-
96 for (int i = 0; i < _fNumPar; i++) {
-
97 nominal[i] = _fPreFitValue.at(i);
-
98 }
-
99 return nominal;
-
100 }
+

Definition at line 92 of file covarianceXsec.h.

+
93 {
+
94 std::vector<double> nominal(_fNumPar);
+
95 for (int i = 0; i < _fNumPar; i++) {
+
96 nominal[i] = _fPreFitValue.at(i);
+
97 }
+
98 return nominal;
+
99 }
nominal
std::vector< int > nominal
Definition GetPenaltyTerm.cpp:38
@@ -1092,7 +1089,7 @@

318 return returnVec;
319}
kNorm
@ kNorm
Definition Structs.h:151
-
covarianceXsec::NormParams
std::vector< XsecNorms4 > NormParams
Vector containing info for normalisation systematics.
Definition covarianceXsec.h:146
+
covarianceXsec::NormParams
std::vector< XsecNorms4 > NormParams
Vector containing info for normalisation systematics.
Definition covarianceXsec.h:145
XsecNorms4
ETA - Normalisations for cross-section parameters Carrier for whether you want to apply a systematic ...
Definition Structs.h:80
@@ -1123,8 +1120,8 @@

Definition at line 85 of file covarianceXsec.h.

-
85{return GetNumParamsFromDetID(DetID, kFunc);}
+

Definition at line 84 of file covarianceXsec.h.

+
84{return GetNumParamsFromDetID(DetID, kFunc);}
covarianceXsec::GetNumParamsFromDetID
int GetNumParamsFromDetID(const int DetID, const SystType Type)
DB Grab the number of parameters for the relevant DetID.
Definition covarianceXsec.cpp:324
@@ -1206,8 +1203,8 @@

Definition at line 79 of file covarianceXsec.h.

-
79{return GetNumParamsFromDetID(DetID, kSpline);}
+

Definition at line 78 of file covarianceXsec.h.

+
78{return GetNumParamsFromDetID(DetID, kSpline);}
@@ -1243,14 +1240,14 @@

Definition at line 42 of file covarianceXsec.h.

-
42{return _fParamType[i];}
-
covarianceXsec::_fParamType
std::vector< SystType > _fParamType
Type of parameter like norm, spline etc.
Definition covarianceXsec.h:135
+

Definition at line 41 of file covarianceXsec.h.

+
41{return _fParamType[i];}
+
covarianceXsec::_fParamType
std::vector< SystType > _fParamType
Type of parameter like norm, spline etc.
Definition covarianceXsec.h:134
- -

◆ GetParamTypeString()

+ +

◆ GetParamTypeString()

@@ -1259,7 +1256,7 @@

- + @@ -1281,8 +1278,8 @@

Definition at line 39 of file covarianceXsec.h.

-
39{return SystType_ToString(_fParamType[i]).c_str();}
+

Definition at line 38 of file covarianceXsec.h.

+
38{ return SystType_ToString(_fParamType[i]); }
SystType_ToString
std::string SystType_ToString(const SystType i)
Convert a Syst type type to a string.
Definition Structs.h:173
@@ -1319,9 +1316,9 @@

Definition at line 36 of file covarianceXsec.h.

-
36{ return _fDetID[i];};
-
covarianceXsec::_fDetID
std::vector< int > _fDetID
Tells to which samples object param should be applied.
Definition covarianceXsec.h:133
+

Definition at line 35 of file covarianceXsec.h.

+
35{ return _fDetID[i];};
+
covarianceXsec::_fDetID
std::vector< int > _fDetID
Tells to which samples object param should be applied.
Definition covarianceXsec.h:132
@@ -1424,7 +1421,7 @@

350 }
351 return returnVec;
352}
-
covarianceBase::GetParFancyName
std::string GetParFancyName(const int i)
Get fancy name of the Parameter.
Definition covarianceBase.h:153
+
covarianceBase::GetParFancyName
std::string GetParFancyName(const int i)
Get fancy name of the Parameter.
Definition covarianceBase.h:154
@@ -1460,9 +1457,9 @@

Definition at line 46 of file covarianceXsec.h.

-
46{return SplineParams.at(i).SplineInterpolationType;}
-
covarianceXsec::SplineParams
std::vector< XsecSplines1 > SplineParams
Vector containing info for normalisation systematics.
Definition covarianceXsec.h:143
+

Definition at line 45 of file covarianceXsec.h.

+
45{return SplineParams.at(i).SplineInterpolationType;}
+
covarianceXsec::SplineParams
std::vector< XsecSplines1 > SplineParams
Vector containing info for normalisation systematics.
Definition covarianceXsec.h:142
@@ -1498,8 +1495,8 @@

Definition at line 53 of file covarianceXsec.h.

-
53{return SplineParams.at(i).SplineKnotLowBound;}
+

Definition at line 52 of file covarianceXsec.h.

+
52{return SplineParams.at(i).SplineKnotLowBound;}
@@ -1535,8 +1532,8 @@

Definition at line 50 of file covarianceXsec.h.

-
50{return SplineParams.at(i).SplineKnotUpBound;}
+

Definition at line 49 of file covarianceXsec.h.

+
49{return SplineParams.at(i).SplineKnotUpBound;}
@@ -1622,7 +1619,7 @@

216 }
217 return returnVec;
218}
-
covarianceXsec::_fFDSplineModes
std::vector< std::vector< int > > _fFDSplineModes
Definition covarianceXsec.h:140
+
covarianceXsec::_fFDSplineModes
std::vector< std::vector< int > > _fFDSplineModes
Definition covarianceXsec.h:139
@@ -1652,8 +1649,8 @@

Definition at line 76 of file covarianceXsec.h.

-
76{return GetParsIndexFromDetID(DetID, kSpline);}
+

Definition at line 75 of file covarianceXsec.h.

+
75{return GetParsIndexFromDetID(DetID, kSpline);}
@@ -1702,7 +1699,7 @@

125
126 return returnVec;
127}
-
covarianceBase::GetParName
std::string GetParName(const int i)
Get name of covariance.
Definition covarianceBase.h:147
+
covarianceBase::GetParName
std::string GetParName(const int i)
Get name of covariance.
Definition covarianceBase.h:148
@@ -1923,18 +1920,18 @@

396 }
397 CorrelateSteps();
398}
-
covarianceBase::_fPropVal
std::vector< double > _fPropVal
Proposed value of the parameter.
Definition covarianceBase.h:447
-
covarianceBase::randomize
void randomize()
"Randomize" the parameters in the covariance class for the proposed step. Used the proposal kernel an...
Definition covarianceBase.cpp:793
-
covarianceBase::_fIndivStepScale
std::vector< double > _fIndivStepScale
Individual step scale used by MCMC algorithm.
Definition covarianceBase.h:457
-
covarianceBase::LastPCAdpar
int LastPCAdpar
Index of the last param that is being decomposed.
Definition covarianceBase.h:473
-
covarianceBase::TransferToPCA
void TransferToPCA()
Transfer param values from normal base to PCA base.
Definition covarianceBase.cpp:571
-
covarianceBase::fParCurr_PCA
TVectorD fParCurr_PCA
CW: Proposed parameter value in PCA base.
Definition covarianceBase.h:491
-
covarianceBase::pca
bool pca
perform PCA or not
Definition covarianceBase.h:465
-
covarianceBase::CorrelateSteps
void CorrelateSteps()
Use Cholesky throw matrix for better step proposal.
Definition covarianceBase.cpp:838
-
covarianceBase::FirstPCAdpar
int FirstPCAdpar
Index of the first param that is being decomposed.
Definition covarianceBase.h:471
-
covarianceBase::_fNumParPCA
int _fNumParPCA
Number of parameters in PCA base.
Definition covarianceBase.h:469
-
covarianceBase::_fPreFitValue_PCA
std::vector< double > _fPreFitValue_PCA
Prefit value for PCA params.
Definition covarianceBase.h:483
-
covarianceBase::_fCurrVal
std::vector< double > _fCurrVal
Current value of the parameter.
Definition covarianceBase.h:445
+
covarianceBase::_fPropVal
std::vector< double > _fPropVal
Proposed value of the parameter.
Definition covarianceBase.h:461
+
covarianceBase::randomize
void randomize()
"Randomize" the parameters in the covariance class for the proposed step. Used the proposal kernel an...
Definition covarianceBase.cpp:794
+
covarianceBase::_fIndivStepScale
std::vector< double > _fIndivStepScale
Individual step scale used by MCMC algorithm.
Definition covarianceBase.h:471
+
covarianceBase::LastPCAdpar
int LastPCAdpar
Index of the last param that is being decomposed.
Definition covarianceBase.h:487
+
covarianceBase::TransferToPCA
void TransferToPCA()
Transfer param values from normal base to PCA base.
Definition covarianceBase.cpp:568
+
covarianceBase::fParCurr_PCA
TVectorD fParCurr_PCA
CW: Proposed parameter value in PCA base.
Definition covarianceBase.h:505
+
covarianceBase::pca
bool pca
perform PCA or not
Definition covarianceBase.h:479
+
covarianceBase::CorrelateSteps
void CorrelateSteps()
Use Cholesky throw matrix for better step proposal.
Definition covarianceBase.cpp:839
+
covarianceBase::FirstPCAdpar
int FirstPCAdpar
Index of the first param that is being decomposed.
Definition covarianceBase.h:485
+
covarianceBase::_fNumParPCA
int _fNumParPCA
Number of parameters in PCA base.
Definition covarianceBase.h:483
+
covarianceBase::_fPreFitValue_PCA
std::vector< double > _fPreFitValue_PCA
Prefit value for PCA params.
Definition covarianceBase.h:497
+
covarianceBase::_fCurrVal
std::vector< double > _fCurrVal
Current value of the parameter.
Definition covarianceBase.h:459
@@ -2030,12 +2027,12 @@

90
91 return;
92}
-
MACH3LOG_ERROR
#define MACH3LOG_ERROR
Definition MaCh3Logger.h:15
+
MACH3LOG_ERROR
#define MACH3LOG_ERROR
Definition MaCh3Logger.h:18
SystType
SystType
Make an enum of systematic type recognised by covariance class.
Definition Structs.h:150
kSystTypes
@ kSystTypes
Definition Structs.h:154
-
covarianceBase::_fYAMLDoc
YAML::Node _fYAMLDoc
Stores config describing systematics.
Definition covarianceBase.h:439
+
covarianceBase::_fYAMLDoc
YAML::Node _fYAMLDoc
Stores config describing systematics.
Definition covarianceBase.h:453
covarianceXsec::GetXsecNorm
XsecNorms4 GetXsecNorm(const YAML::Node &param, const int Index)
Get Norm params.
Definition covarianceXsec.cpp:222
-
covarianceXsec::isFlux
std::vector< bool > isFlux
Definition covarianceXsec.h:130
+
covarianceXsec::isFlux
std::vector< bool > isFlux
Definition covarianceXsec.h:129
covarianceXsec::GetXsecSpline
XsecSplines1 GetXsecSpline(const YAML::Node &param)
Get Spline params.
Definition covarianceXsec.cpp:278
@@ -2073,8 +2070,8 @@

Warning
Will become deprecated
-

Definition at line 107 of file covarianceXsec.h.

-
107{ return isFlux[i]; }
+

Definition at line 106 of file covarianceXsec.h.

+
106{ return isFlux[i]; }
@@ -2188,16 +2185,16 @@

483
484 CheckCorrectInitialisation();
485} // End
-
MACH3LOG_INFO
#define MACH3LOG_INFO
Definition MaCh3Logger.h:13
-
covarianceBase::_fUpBound
std::vector< double > _fUpBound
Upper physical bound, parameter will not be able to go beyond it.
Definition covarianceBase.h:455
-
covarianceBase::_fError
std::vector< double > _fError
Prior error on the parameter.
Definition covarianceBase.h:451
-
covarianceBase::GetNumParams
int GetNumParams()
Get total number of parameters.
Definition covarianceBase.h:212
-
covarianceBase::_fLowBound
std::vector< double > _fLowBound
Lowest physical bound, parameter will not be able to go beyond it.
Definition covarianceBase.h:453
-
covarianceBase::_fGenerated
std::vector< double > _fGenerated
Generated value of the parameter.
Definition covarianceBase.h:449
+
MACH3LOG_INFO
#define MACH3LOG_INFO
Definition MaCh3Logger.h:16
+
covarianceBase::_fUpBound
std::vector< double > _fUpBound
Upper physical bound, parameter will not be able to go beyond it.
Definition covarianceBase.h:469
+
covarianceBase::_fError
std::vector< double > _fError
Prior error on the parameter.
Definition covarianceBase.h:465
+
covarianceBase::GetNumParams
int GetNumParams()
Get total number of parameters.
Definition covarianceBase.h:213
+
covarianceBase::_fLowBound
std::vector< double > _fLowBound
Lowest physical bound, parameter will not be able to go beyond it.
Definition covarianceBase.h:467
+
covarianceBase::_fGenerated
std::vector< double > _fGenerated
Generated value of the parameter.
Definition covarianceBase.h:463
covarianceXsec::CheckCorrectInitialisation
void CheckCorrectInitialisation()
KS: Check if matrix is correctly initialised.
Definition covarianceXsec.cpp:489
-
covarianceXsec::GetParSplineInterpolation
SplineInterpolation GetParSplineInterpolation(const int i)
Get interpolation type for a given parameter.
Definition covarianceXsec.h:46
-
covarianceXsec::GetParSplineKnotLowerBound
double GetParSplineKnotLowerBound(const int i)
EM: value at which we cap spline knot weight.
Definition covarianceXsec.h:53
-
covarianceXsec::GetParSplineKnotUpperBound
double GetParSplineKnotUpperBound(const int i)
EM: value at which we cap spline knot weight.
Definition covarianceXsec.h:50
+
covarianceXsec::GetParSplineInterpolation
SplineInterpolation GetParSplineInterpolation(const int i)
Get interpolation type for a given parameter.
Definition covarianceXsec.h:45
+
covarianceXsec::GetParSplineKnotLowerBound
double GetParSplineKnotLowerBound(const int i)
EM: value at which we cap spline knot weight.
Definition covarianceXsec.h:52
+
covarianceXsec::GetParSplineKnotUpperBound
double GetParSplineKnotUpperBound(const int i)
EM: value at which we cap spline knot weight.
Definition covarianceXsec.h:49
@@ -2290,7 +2287,7 @@

Definition at line 133 of file covarianceXsec.h.

+

Definition at line 132 of file covarianceXsec.h.

@@ -2314,7 +2311,7 @@

-

Definition at line 140 of file covarianceXsec.h.

+

Definition at line 139 of file covarianceXsec.h.

@@ -2338,7 +2335,7 @@

-

Definition at line 139 of file covarianceXsec.h.

+

Definition at line 138 of file covarianceXsec.h.

@@ -2362,7 +2359,7 @@

-

Definition at line 138 of file covarianceXsec.h.

+

Definition at line 137 of file covarianceXsec.h.

@@ -2388,7 +2385,7 @@

Definition at line 135 of file covarianceXsec.h.

+

Definition at line 134 of file covarianceXsec.h.

@@ -2413,7 +2410,7 @@

Is parameter flux or not, This might become deprecated in future

Warning
Will become deprecated
-

Definition at line 130 of file covarianceXsec.h.

+

Definition at line 129 of file covarianceXsec.h.

@@ -2439,7 +2436,7 @@

Definition at line 146 of file covarianceXsec.h.

+

Definition at line 145 of file covarianceXsec.h.

@@ -2465,7 +2462,7 @@

Definition at line 143 of file covarianceXsec.h.

+

Definition at line 142 of file covarianceXsec.h.

diff --git a/classes.html b/classes.html index 5aeabf1cc..f069a5c83 100644 --- a/classes.html +++ b/classes.html @@ -78,7 +78,7 @@
A
-
AdaptiveMCMCStruct (adaptive_mcmc)
+
AdaptiveMCMCHandler (adaptive_mcmc)
B
BaseFuncPar
Box
diff --git a/classmanager.html b/classmanager.html index 5475ffbb5..795fb0c36 100644 --- a/classmanager.html +++ b/classmanager.html @@ -205,9 +205,9 @@

41 std::string ModeInput = GetFromManager<std::string>(config["General"]["MaCh3Modes"], "null");

42 if(ModeInput != "null") Modes = new MaCh3Modes(ModeInput);
43}
-
MACH3LOG_ERROR
#define MACH3LOG_ERROR
Definition MaCh3Logger.h:15
-
MACH3LOG_INFO
#define MACH3LOG_INFO
Definition MaCh3Logger.h:13
-
SetMaCh3LoggerFormat
void SetMaCh3LoggerFormat()
Set messaging format of the logger.
Definition MaCh3Logger.h:20
+
MACH3LOG_ERROR
#define MACH3LOG_ERROR
Definition MaCh3Logger.h:18
+
MACH3LOG_INFO
#define MACH3LOG_INFO
Definition MaCh3Logger.h:16
+
SetMaCh3LoggerFormat
void SetMaCh3LoggerFormat()
Set messaging format of the logger.
Definition MaCh3Logger.h:23
TestStatistic
TestStatistic
Make an enum of the test statistic that we're using.
Definition Structs.h:353
kNTestStatistics
@ kNTestStatistics
Definition Structs.h:359
kPearson
@ kPearson
Definition Structs.h:357
@@ -216,9 +216,9 @@

kDembinskiAbdelmottele
@ kDembinskiAbdelmottele
Definition Structs.h:358
kPoisson
@ kPoisson
Definition Structs.h:354
TestStatistic_ToString
std::string TestStatistic_ToString(TestStatistic i)
Convert a LLH type to a string.
Definition Structs.h:364
-
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:18
-
MaCh3Exception
Custom exception class for MaCh3 errors.
Definition MaCh3Exception.h:10
-
MaCh3Modes
KS: Class describing MaCh3 modes used in the analysis, it is being initialised from config.
Definition MaCh3Modes.h:32
+
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:21
+
MaCh3Exception
Custom exception class for MaCh3 errors.
Definition MaCh3Exception.h:12
+
MaCh3Modes
KS: Class describing MaCh3 modes used in the analysis, it is being initialised from config.
Definition MaCh3Modes.h:33
manager::FileName
std::string FileName
The name of the configuration file.
Definition manager.h:57
manager::config
YAML::Node config
The YAML node containing the configuration data.
Definition manager.h:55
manager::mc_stat_llh
int mc_stat_llh
The likelihood type defined in the configuration.
Definition manager.h:59
diff --git a/classmcmc.html b/classmcmc.html index a28f34458..150ab5ec1 100644 --- a/classmcmc.html +++ b/classmcmc.html @@ -336,10 +336,10 @@

21 anneal = true;
22 }
23}
-
MACH3LOG_INFO
#define MACH3LOG_INFO
Definition MaCh3Logger.h:13
-
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:18
-
FitterBase
Base class for implementing fitting algorithms.
Definition FitterBase.h:23
-
FitterBase::fitMan
manager * fitMan
The manager.
Definition FitterBase.h:92
+
MACH3LOG_INFO
#define MACH3LOG_INFO
Definition MaCh3Logger.h:16
+
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:21
+
FitterBase
Base class for implementing fitting algorithms.
Definition FitterBase.h:24
+
FitterBase::fitMan
manager * fitMan
The manager.
Definition FitterBase.h:93
manager::raw
YAML::Node const & raw()
Return config.
Definition manager.h:48
mcmc::chainLength
unsigned int chainLength
number of steps in chain
Definition mcmc.h:41
mcmc::AnnealTemp
double AnnealTemp
simulated annealing temperature
Definition mcmc.h:46
@@ -456,18 +456,18 @@

107 // Write step to output tree
108 outTree->Fill();
109}
-
FitterBase::osc
covarianceOsc * osc
handles oscillation parameters
Definition FitterBase.h:125
-
FitterBase::logLProp
double logLProp
proposed likelihood
Definition FitterBase.h:102
-
FitterBase::stepClock
TStopwatch * stepClock
tells how long single step/fit iteration took
Definition FitterBase.h:132
-
FitterBase::accCount
int accCount
counts accepted steps
Definition FitterBase.h:106
-
FitterBase::random
TRandom3 * random
Random number.
Definition FitterBase.h:137
-
FitterBase::systematics
std::vector< covarianceBase * > systematics
Systematic holder.
Definition FitterBase.h:122
-
FitterBase::step
unsigned int step
current state
Definition FitterBase.h:98
-
FitterBase::accProb
double accProb
current acceptance prob
Definition FitterBase.h:104
-
FitterBase::stepTime
double stepTime
Time of single step.
Definition FitterBase.h:134
-
FitterBase::logLCurr
double logLCurr
current likelihood
Definition FitterBase.h:100
-
FitterBase::outTree
TTree * outTree
Output tree with posteriors.
Definition FitterBase.h:144
-
covarianceBase::acceptStep
void acceptStep()
Accepted this step.
Definition covarianceBase.cpp:886
+
FitterBase::osc
covarianceOsc * osc
handles oscillation parameters
Definition FitterBase.h:126
+
FitterBase::logLProp
double logLProp
proposed likelihood
Definition FitterBase.h:103
+
FitterBase::stepClock
TStopwatch * stepClock
tells how long single step/fit iteration took
Definition FitterBase.h:133
+
FitterBase::accCount
int accCount
counts accepted steps
Definition FitterBase.h:107
+
FitterBase::random
TRandom3 * random
Random number.
Definition FitterBase.h:138
+
FitterBase::systematics
std::vector< covarianceBase * > systematics
Systematic holder.
Definition FitterBase.h:123
+
FitterBase::step
unsigned int step
current state
Definition FitterBase.h:99
+
FitterBase::accProb
double accProb
current acceptance prob
Definition FitterBase.h:105
+
FitterBase::stepTime
double stepTime
Time of single step.
Definition FitterBase.h:135
+
FitterBase::logLCurr
double logLCurr
current likelihood
Definition FitterBase.h:101
+
FitterBase::outTree
TTree * outTree
Output tree with posteriors.
Definition FitterBase.h:145
+
covarianceBase::acceptStep
void acceptStep()
Accepted this step.
Definition covarianceBase.cpp:887
@@ -667,10 +667,10 @@

248 // Save the proposed likelihood (class member)
249 logLProp = llh;
250}
-
FitterBase::sample_llh
double * sample_llh
store the llh breakdowns
Definition FitterBase.h:112
-
FitterBase::osc_llh
double osc_llh
Definition FitterBase.h:110
-
FitterBase::syst_llh
double * syst_llh
systematic llh breakdowns
Definition FitterBase.h:114
-
FitterBase::samples
std::vector< samplePDFBase * > samples
Sample holder.
Definition FitterBase.h:117
+
FitterBase::sample_llh
double * sample_llh
store the llh breakdowns
Definition FitterBase.h:113
+
FitterBase::osc_llh
double osc_llh
Definition FitterBase.h:111
+
FitterBase::syst_llh
double * syst_llh
systematic llh breakdowns
Definition FitterBase.h:115
+
FitterBase::samples
std::vector< samplePDFBase * > samples
Sample holder.
Definition FitterBase.h:118
covarianceOsc::getPropPars
double * getPropPars()
Retrieves the proposed parameters.
Definition covarianceOsc.cpp:147
covarianceOsc::GetLikelihood
double GetLikelihood() override
Same implementation as in base class but accounts for applying reactor prior.
Definition covarianceOsc.cpp:109
covarianceOsc::proposeStep
void proposeStep() override
Propose MCMC step, including mass flipping.
Definition covarianceOsc.cpp:165
@@ -811,7 +811,7 @@

FitterBase::SaveOutput
void SaveOutput()
Save output and close files.
Definition FitterBase.cpp:241
FitterBase::SaveSettings
void SaveSettings()
Save the settings that the MCMC was run with.
Definition FitterBase.cpp:103
FitterBase::PrepareOutput
void PrepareOutput()
Prepare the output file.
Definition FitterBase.cpp:169
-
FitterBase::auto_save
int auto_save
auto save every N steps
Definition FitterBase.h:146
+
FitterBase::auto_save
int auto_save
auto save every N steps
Definition FitterBase.h:147
mcmc::CheckStep
void CheckStep()
Do we accept the step.
Definition mcmc.cpp:63
mcmc::ProposeStep
void ProposeStep()
Propose a step.
Definition mcmc.cpp:161
mcmc::PrintProgress
void PrintProgress()
Print the progress.
Definition mcmc.cpp:254
diff --git a/classparticle.html b/classparticle.html index 3f55bbc84..0f4bc4aa4 100644 --- a/classparticle.html +++ b/classparticle.html @@ -130,7 +130,7 @@

Detailed Description

Class particle - stores the position, velocity and personal best With functions which move particle and update velocity.

-

Definition at line 17 of file PSO.h.

+

Definition at line 18 of file PSO.h.

Constructor & Destructor Documentation

◆ particle() [1/2]

@@ -155,8 +155,8 @@

-

Definition at line 19 of file PSO.h.

-
19{};
+

Definition at line 20 of file PSO.h.

+
20{};
@@ -194,11 +194,11 @@

-

Definition at line 20 of file PSO.h.

-
20: position(pos), velocity(vel){};
-
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:18
-
particle::position
std::vector< double > position
Definition PSO.h:64
-
particle::velocity
std::vector< double > velocity
Definition PSO.h:65
+

Definition at line 21 of file PSO.h.

+
21: position(pos), velocity(vel){};
+
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:21
+
particle::position
std::vector< double > position
Definition PSO.h:65
+
particle::velocity
std::vector< double > velocity
Definition PSO.h:66
@@ -227,8 +227,8 @@

Definition at line 22 of file PSO.h.

-
22{};
+

Definition at line 23 of file PSO.h.

+
23{};
@@ -256,11 +256,11 @@

-

Definition at line 36 of file PSO.h.

-
36 {
-
37 return personal_best_position;
-
38 };
-
particle::personal_best_position
std::vector< double > personal_best_position
Definition PSO.h:68
+

Definition at line 37 of file PSO.h.

+
37 {
+
38 return personal_best_position;
+
39 };
+
particle::personal_best_position
std::vector< double > personal_best_position
Definition PSO.h:69
@@ -287,11 +287,11 @@

-

Definition at line 44 of file PSO.h.

-
44 {
-
45 return personal_best_value;
-
46 };
-
particle::personal_best_value
double personal_best_value
Definition PSO.h:66
+

Definition at line 45 of file PSO.h.

+
45 {
+
46 return personal_best_value;
+
47 };
+
particle::personal_best_value
double personal_best_value
Definition PSO.h:67
@@ -318,10 +318,10 @@

-

Definition at line 28 of file PSO.h.

-
28 {
-
29 return position;
-
30 };
+

Definition at line 29 of file PSO.h.

+
29 {
+
30 return position;
+
31 };
@@ -348,11 +348,11 @@

-

Definition at line 56 of file PSO.h.

-
56 {
-
57 return curr_value;
-
58 };
-
particle::curr_value
double curr_value
Definition PSO.h:67
+

Definition at line 57 of file PSO.h.

+
57 {
+
58 return curr_value;
+
59 };
+
particle::curr_value
double curr_value
Definition PSO.h:68
@@ -379,10 +379,10 @@

-

Definition at line 48 of file PSO.h.

-
48 {
-
49 return velocity;
-
50 };
+

Definition at line 49 of file PSO.h.

+
49 {
+
50 return velocity;
+
51 };
@@ -410,10 +410,10 @@

-

Definition at line 32 of file PSO.h.

-
32 {
-
33 personal_best_position = new_pos;
-
34 };
+

Definition at line 33 of file PSO.h.

+
33 {
+
34 personal_best_position = new_pos;
+
35 };
@@ -441,10 +441,10 @@

-

Definition at line 40 of file PSO.h.

-
40 {
-
41 personal_best_value = new_val;
-
42 };
+

Definition at line 41 of file PSO.h.

+
41 {
+
42 personal_best_value = new_val;
+
43 };
@@ -472,10 +472,10 @@

-

Definition at line 24 of file PSO.h.

-
24 {
-
25 position = new_position;
-
26 };
+

Definition at line 25 of file PSO.h.

+
25 {
+
26 position = new_position;
+
27 };
@@ -503,10 +503,10 @@

-

Definition at line 59 of file PSO.h.

-
59 {
-
60 curr_value = val;
-
61 };
+

Definition at line 60 of file PSO.h.

+
60 {
+
61 curr_value = val;
+
62 };
@@ -534,10 +534,10 @@

-

Definition at line 52 of file PSO.h.

-
52 {
-
53 velocity = new_velocity;
-
54 };
+

Definition at line 53 of file PSO.h.

+
53 {
+
54 velocity = new_velocity;
+
55 };
@@ -562,7 +562,7 @@

-

Definition at line 67 of file PSO.h.

+

Definition at line 68 of file PSO.h.

@@ -586,7 +586,7 @@

-

Definition at line 68 of file PSO.h.

+

Definition at line 69 of file PSO.h.

@@ -610,7 +610,7 @@

-

Definition at line 66 of file PSO.h.

+

Definition at line 67 of file PSO.h.

@@ -634,7 +634,7 @@

-

Definition at line 64 of file PSO.h.

+

Definition at line 65 of file PSO.h.

@@ -658,7 +658,7 @@

-

Definition at line 65 of file PSO.h.

+

Definition at line 66 of file PSO.h.

diff --git a/classsamplePDFBase.html b/classsamplePDFBase.html index 8546c2f34..16d24dfc6 100644 --- a/classsamplePDFBase.html +++ b/classsamplePDFBase.html @@ -295,7 +295,7 @@

10 dataSample = NULL;
11 dataSample2D = NULL;
12}
-
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:18
+
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:21
samplePDFBase::rnd
TRandom3 * rnd
Definition samplePDFBase.h:136
@@ -789,7 +789,7 @@

Definition at line 77 of file samplePDFBase.h.

77{ (void) Selection; throw MaCh3Exception(__FILE__ , __LINE__ , "Not implemented"); }
-
MaCh3Exception
Custom exception class for MaCh3 errors.
Definition MaCh3Exception.h:10
+
MaCh3Exception
Custom exception class for MaCh3 errors.
Definition MaCh3Exception.h:12
@@ -980,7 +980,7 @@

440 }
441
442}
-
MaCh3Modes::GetNModes
int GetNModes()
KS: Get number of modes, keep in mind actual number is +1 greater due to unknown category.
Definition MaCh3Modes.h:43
+
MaCh3Modes::GetNModes
int GetNModes()
KS: Get number of modes, keep in mind actual number is +1 greater due to unknown category.
Definition MaCh3Modes.h:44
MaCh3Modes::GetMaCh3ModeName
std::string GetMaCh3ModeName(const int Index)
KS: Get normal name of mode, if mode not known you will get UNKNOWN_BAD.
Definition MaCh3Modes.cpp:124
diff --git a/classsamplePDFFDBase.html b/classsamplePDFFDBase.html index b5ef96e6e..45074405e 100644 --- a/classsamplePDFFDBase.html +++ b/classsamplePDFFDBase.html @@ -474,7 +474,7 @@

23 fTestStatistic = kPoisson;
24}
kPoisson
@ kPoisson
Definition Structs.h:354
-
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:18
+
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:21
samplePDFBase::SampleName
std::vector< std::string > SampleName
Name of Sample.
Definition samplePDFBase.h:124
samplePDFBase::nSamples
_int_ nSamples
Contains how many samples we've got.
Definition samplePDFBase.h:120
@@ -933,7 +933,7 @@

827 }//end loop over events
828 return;
829}
-
covarianceXsec::GetParDetID
int GetParDetID(const int i) const
ETA - just return the int of the DetID, this can be removed to do a string comp at some point.
Definition covarianceXsec.h:36
+
covarianceXsec::GetParDetID
int GetParDetID(const int i) const
ETA - just return the int of the DetID, this can be removed to do a string comp at some point.
Definition covarianceXsec.h:35
samplePDFFDBase::ReturnKinematicParameter
virtual double ReturnKinematicParameter(std::string KinematicParamter, int iSample, int iEvent)=0
samplePDFFDBase::XsecCov
covarianceXsec * XsecCov
Definition samplePDFFDBase.h:233
@@ -2886,7 +2886,7 @@

712
713 return;
714}
-
covarianceBase::retPointer
const double * retPointer(const int iParam)
DB Pointer return to param position.
Definition covarianceBase.h:208
+
covarianceBase::retPointer
const double * retPointer(const int iParam)
DB Pointer return to param position.
Definition covarianceBase.h:209
samplePDFFDBase::CalcXsecNormsBins
void CalcXsecNormsBins(int iSample)
Definition samplePDFFDBase.cpp:717
@@ -3088,9 +3088,9 @@

679 return;
680}
covarianceXsec::GetNormParsFromDetID
const std::vector< XsecNorms4 > GetNormParsFromDetID(const int DetID)
DB Get norm/func parameters depending on given DetID.
Definition covarianceXsec.cpp:302
-
covarianceXsec::GetFuncParsNamesFromDetID
const std::vector< std::string > GetFuncParsNamesFromDetID(const int DetID)
DB Grab the Functional parameter names for the relevant DetID.
Definition covarianceXsec.h:87
-
covarianceXsec::GetFuncParsIndexFromDetID
const std::vector< int > GetFuncParsIndexFromDetID(const int DetID)
DB Grab the Functional parameter indices for the relevant DetID.
Definition covarianceXsec.h:89
-
covarianceXsec::GetNumFuncParamsFromDetID
int GetNumFuncParamsFromDetID(const int DetID)
DB Grab the number of Normalisation parameters for the relevant DetID.
Definition covarianceXsec.h:85
+
covarianceXsec::GetFuncParsNamesFromDetID
const std::vector< std::string > GetFuncParsNamesFromDetID(const int DetID)
DB Grab the Functional parameter names for the relevant DetID.
Definition covarianceXsec.h:86
+
covarianceXsec::GetFuncParsIndexFromDetID
const std::vector< int > GetFuncParsIndexFromDetID(const int DetID)
DB Grab the Functional parameter indices for the relevant DetID.
Definition covarianceXsec.h:88
+
covarianceXsec::GetNumFuncParamsFromDetID
int GetNumFuncParamsFromDetID(const int DetID)
DB Grab the number of Normalisation parameters for the relevant DetID.
Definition covarianceXsec.h:84
samplePDFFDBase::funcParsNames
std::vector< std::string > funcParsNames
Definition samplePDFFDBase.h:246
samplePDFFDBase::funcParsIndex
std::vector< int > funcParsIndex
Definition samplePDFFDBase.h:247
@@ -3140,7 +3140,7 @@

1429 throw;
1430 }
1431}
-
MACH3LOG_ERROR
#define MACH3LOG_ERROR
Definition MaCh3Logger.h:15
+
MACH3LOG_ERROR
#define MACH3LOG_ERROR
Definition MaCh3Logger.h:18
CUDAProb_nu
CUDAProb_nu
Definition Structs.h:445
e_t
@ e_t
Definition Structs.h:448
m_m
@ m_m
Definition Structs.h:450
diff --git a/classsplineFDBase.html b/classsplineFDBase.html index 96db88001..88fb6869b 100644 --- a/classsplineFDBase.html +++ b/classsplineFDBase.html @@ -270,7 +270,7 @@

14 MonolithIndex=0; //Keeps track of the monolith index we're on when filling arrays (declared here so we can have multiple FillSampleArray calls)
15 CoeffIndex=0; //Keeps track of our indexing the coefficient arrays [x, ybcd]
16}
-
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:18
+
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:21
SplineBase::SplineBase
SplineBase()
Constructor.
Definition SplineBase.cpp:5
splineFDBase::xsec
covarianceXsec * xsec
Definition splineFDBase.h:83
@@ -392,8 +392,8 @@

65}
covarianceXsec::GetSplineModeVecFromDetID
const std::vector< std::vector< int > > GetSplineModeVecFromDetID(const int DetID)
DB Grab the Spline Modes for the relevant DetID.
Definition covarianceXsec.cpp:202
covarianceXsec::GetFDSplineFileParsNamesFromDetID
const std::vector< std::string > GetFDSplineFileParsNamesFromDetID(const int DetID)
ETA - what does this even do?
Definition covarianceXsec.cpp:133
-
covarianceXsec::GetSplineParsIndexFromDetID
const std::vector< int > GetSplineParsIndexFromDetID(const int DetID)
DB Grab the Spline Indices for the relevant DetID.
Definition covarianceXsec.h:76
-
covarianceXsec::GetNumSplineParamsFromDetID
int GetNumSplineParamsFromDetID(const int DetID)
DB Grab the Number of splines for the relevant DetID.
Definition covarianceXsec.h:79
+
covarianceXsec::GetSplineParsIndexFromDetID
const std::vector< int > GetSplineParsIndexFromDetID(const int DetID)
DB Grab the Spline Indices for the relevant DetID.
Definition covarianceXsec.h:75
+
covarianceXsec::GetNumSplineParamsFromDetID
int GetNumSplineParamsFromDetID(const int DetID)
DB Grab the Number of splines for the relevant DetID.
Definition covarianceXsec.h:78
splineFDBase::FindSplineBinning
std::vector< TAxis * > FindSplineBinning(std::string FileName, std::string SampleName)
Definition splineFDBase.cpp:356
splineFDBase::SplineParsIndex
std::vector< std::vector< int > > SplineParsIndex
Definition splineFDBase.h:93
splineFDBase::SplineFileParPrefixNames
std::vector< std::vector< std::string > > SplineFileParPrefixNames
Definition splineFDBase.h:95
@@ -1030,7 +1030,7 @@

269 }
270 // std::cout << "#----------------------------------------------------------------------------------------------------------------------------------#" << std::endl;
271}
-
covarianceBase::calcReWeight
double calcReWeight(const int bin)
What parameter Gets reweighted by what amount according to MCMC.
Definition covarianceBase.h:190
+
covarianceBase::calcReWeight
double calcReWeight(const int bin)
What parameter Gets reweighted by what amount according to MCMC.
Definition covarianceBase.h:191
splineFDBase::UniqueSystNKnots
std::vector< int > UniqueSystNKnots
Definition splineFDBase.h:104
splineFDBase::UniqueSystIndices
std::vector< int > UniqueSystIndices
Definition splineFDBase.h:103
diff --git a/covarianceBase_8cpp_source.html b/covarianceBase_8cpp_source.html index ddb2bf6ee..368e1720d 100644 --- a/covarianceBase_8cpp_source.html +++ b/covarianceBase_8cpp_source.html @@ -84,30 +84,30 @@
Go to the documentation of this file.
1#include "covarianceBase.h"
-
2// ********************************************
-
-
3covarianceBase::covarianceBase(const char *name, const char *file) : inputFile(std::string(file)), pca(false) {
-
4// ********************************************
-
5
+
2
+
3// ********************************************
+
+
4covarianceBase::covarianceBase(const char *name, const char *file) : inputFile(std::string(file)), pca(false) {
+
5// ********************************************
6 MACH3LOG_INFO("Constructing instance of covarianceBase");
-
7 init(name, file);
+
7 init(name, file);
8 FirstPCAdpar = -999;
9 LastPCAdpar = -999;
10}
11// ********************************************
-
12covarianceBase::covarianceBase(const std::vector<std::string>& YAMLFile, const char *name, double threshold, int FirstPCA, int LastPCA) : inputFile(YAMLFile[0].c_str()), matrixName(name), pca(true), eigen_threshold(threshold), FirstPCAdpar(FirstPCA), LastPCAdpar(LastPCA) {
+
12covarianceBase::covarianceBase(const std::vector<std::string>& YAMLFile, const char *name, double threshold, int FirstPCA, int LastPCA) : inputFile(YAMLFile[0].c_str()), matrixName(name), pca(true), eigen_threshold(threshold), FirstPCAdpar(FirstPCA), LastPCAdpar(LastPCA) {
13// ********************************************
14
15 MACH3LOG_INFO("Constructing instance of covarianceBase using ");
-
16 for(unsigned int i = 0; i < YAMLFile.size(); i++)
+
16 for(unsigned int i = 0; i < YAMLFile.size(); i++)
17 {
-
18 MACH3LOG_INFO("{}", YAMLFile[i]);
+
18 MACH3LOG_INFO("{}", YAMLFile[i]);
19 }
20 MACH3LOG_INFO("as an input");
21
-
22 if (threshold < 0 || threshold >= 1) {
+
22 if (threshold < 0 || threshold >= 1) {
23 MACH3LOG_INFO("Principal component analysis but given the threshold for the principal components to be less than 0, or greater than (or equal to) 1. This will not work");
24 MACH3LOG_INFO("Please specify a number between 0 and 1");
25 MACH3LOG_INFO("You specified: ");
@@ -115,7 +115,7 @@
27 pca = false;
28 }
29
-
30 init(YAMLFile);
+
30 init(YAMLFile);
31 // Call the innocent helper function
32 if (pca) ConstructPCA();
33}
@@ -123,20 +123,20 @@
34
35// ********************************************
-
36covarianceBase::covarianceBase(const char *name, const char *file, int seed) : inputFile(std::string(file)), pca(false) {
+
36covarianceBase::covarianceBase(const char *name, const char *file, int seed) : inputFile(std::string(file)), pca(false) {
37// ********************************************
38
39 #ifdef MULTITHREAD
-
40 if(seed != 0)
+
40 if(seed != 0)
41 {
-
42 MACH3LOG_WARN("You have set seed to {}", seed);
+
42 MACH3LOG_WARN("You have set seed to {}", seed);
43 MACH3LOG_WARN("And you are running with MULTITHREAD");
44 MACH3LOG_WARN("TRandom for each thread will have same seed");
45 MACH3LOG_WARN("This is fine if this was your intention");
46 }
47 #endif
48
-
49 init(name, file);
+
49 init(name, file);
50 FirstPCAdpar = -999;
51 LastPCAdpar = -999;
52}
@@ -144,11 +144,11 @@
53
54// ********************************************
-
55covarianceBase::covarianceBase(const char *name, const char *file, int seed, double threshold, int firstpcapar, int lastpcapar) : inputFile(std::string(file)), pca(true), eigen_threshold(threshold), FirstPCAdpar(firstpcapar), LastPCAdpar(lastpcapar) {
+
55covarianceBase::covarianceBase(const char *name, const char *file, int seed, double threshold, int firstpcapar, int lastpcapar) : inputFile(std::string(file)), pca(true), eigen_threshold(threshold), FirstPCAdpar(firstpcapar), LastPCAdpar(lastpcapar) {
56// ********************************************
57
-
58 if (threshold < 0 || threshold >= 1) {
-
59 MACH3LOG_INFO("NOTE: {} {}", name, file);
+
58 if (threshold < 0 || threshold >= 1) {
+
59 MACH3LOG_INFO("NOTE: {} {}", name, file);
60 MACH3LOG_INFO("Principal component analysis but given the threshold for the principal components to be less than 0, or greater than (or equal to) 1. This will not work");
61 MACH3LOG_INFO("Please specify a number between 0 and 1");
62 MACH3LOG_INFO("You specified: ");
@@ -156,16 +156,16 @@
64 pca = false;
65 }
66#ifdef MULTITHREAD
-
67 if(seed != 0)
+
67 if(seed != 0)
68 {
-
69 MACH3LOG_WARN("You have set seed to {}", seed);
+
69 MACH3LOG_WARN("You have set seed to {}", seed);
70 MACH3LOG_WARN("And you are running with MULTITHREAD");
71 MACH3LOG_WARN("TRandom for each thread will have same seed");
72 MACH3LOG_WARN("This is fine if this was your intention");
73 }
74#endif
75 MACH3LOG_INFO("Constructing instance of covarianceBase");
-
76 init(name, file);
+
76 init(name, file);
77 // Call the innocent helper function
78 if (pca) ConstructPCA();
79}
@@ -189,1237 +189,1237 @@
95 delete[] randParams;
96 delete[] corr_throw;
97
-
98 if (covMatrix != NULL) delete covMatrix;
-
99 if (invCovMatrix != NULL) delete invCovMatrix;
-
100 if (throwMatrix_CholDecomp != NULL) delete throwMatrix_CholDecomp;
+
98 if (covMatrix != NULL) delete covMatrix;
+
99 if (invCovMatrix != NULL) delete invCovMatrix;
+
100 if (throwMatrix_CholDecomp != NULL) delete throwMatrix_CholDecomp;
101
-
102 for(int i = 0; i < _fNumPar; i++)
+
102 for(int i = 0; i < _fNumPar; i++)
103 {
-
104 delete[] InvertCovMatrix[i];
-
105 delete[] throwMatrixCholDecomp[i];
+
104 delete[] InvertCovMatrix[i];
+
105 delete[] throwMatrixCholDecomp[i];
106 }
107 delete[] InvertCovMatrix;
108 delete[] throwMatrixCholDecomp;
109
-
110 const int nThreads = MaCh3Utils::GetNThreads();
-
111 for (int iThread = 0;iThread < nThreads; iThread++) delete random_number[iThread];
+
110 const int nThreads = MaCh3Utils::GetNThreads();
+
111 for (int iThread = 0;iThread < nThreads; iThread++) delete random_number[iThread];
112 delete[] random_number;
-
113 if (throwMatrix != NULL) delete throwMatrix;
-
114
-
115 if(adaption_struct.adaptive_covariance != nullptr){
-
116 delete adaption_struct.adaptive_covariance;
-
117 }
-
118
-
119}
-
-
120
-
121// ********************************************
-
-
122void covarianceBase::ConstructPCA() {
-
123// ********************************************
-
124
-
125 // Check that covariance matrix exists
-
126 if (covMatrix == NULL) {
-
127 MACH3LOG_ERROR("Covariance matrix for {} has not yet been set", matrixName);
-
128 MACH3LOG_ERROR("Can not construct PCA until it is set");
-
129 throw;
-
130 }
-
131
-
132 //Check whether first and last pcadpar are set and if not just PCA everything
-
133 if(FirstPCAdpar == -999 || LastPCAdpar == -999){
-
134 if(FirstPCAdpar == -999 && LastPCAdpar == -999){
-
135 FirstPCAdpar = 0;
-
136 LastPCAdpar = covMatrix->GetNrows()-1;
-
137 }
-
138 else{
-
139 MACH3LOG_ERROR("You must either leave FirstPCAdpar and LastPCAdpar at -999 or set them both to something");
-
140 throw;
-
141 }
+
113 if (throwMatrix != NULL) delete throwMatrix;
+
114}
+
+
115
+
116// ********************************************
+
+
117void covarianceBase::ConstructPCA() {
+
118// ********************************************
+
119
+
120 // Check that covariance matrix exists
+
121 if (covMatrix == NULL) {
+
122 MACH3LOG_ERROR("Covariance matrix for {} has not yet been set", matrixName);
+
123 MACH3LOG_ERROR("Can not construct PCA until it is set");
+
124 throw;
+
125 }
+
126
+
127 //Check whether first and last pcadpar are set and if not just PCA everything
+
128 if(FirstPCAdpar == -999 || LastPCAdpar == -999){
+
129 if(FirstPCAdpar == -999 && LastPCAdpar == -999){
+
130 FirstPCAdpar = 0;
+
131 LastPCAdpar = covMatrix->GetNrows()-1;
+
132 }
+
133 else{
+
134 MACH3LOG_ERROR("You must either leave FirstPCAdpar and LastPCAdpar at -999 or set them both to something");
+
135 throw;
+
136 }
+
137 }
+
138 if(FirstPCAdpar > covMatrix->GetNrows()-1 || LastPCAdpar>covMatrix->GetNrows()-1){
+
139 MACH3LOG_ERROR("FirstPCAdpar and LastPCAdpar are higher than the number of parameters");
+
140 MACH3LOG_ERROR("first: {} last: {}, params: {}", FirstPCAdpar, LastPCAdpar, covMatrix->GetNrows()-1);
+
141 throw;
142 }
-
143 if(FirstPCAdpar > covMatrix->GetNrows()-1 || LastPCAdpar>covMatrix->GetNrows()-1){
-
144 MACH3LOG_ERROR("FirstPCAdpar and LastPCAdpar are higher than the number of parameters");
-
145 MACH3LOG_ERROR("first: {} last: {}, params: {}", FirstPCAdpar, LastPCAdpar, covMatrix->GetNrows()-1);
+
143 if(FirstPCAdpar < 0 || LastPCAdpar < 0){
+
144 MACH3LOG_ERROR("FirstPCAdpar and LastPCAdpar are less than 0 but not default -999");
+
145 MACH3LOG_ERROR("first: {} last: {}", FirstPCAdpar, LastPCAdpar);
146 throw;
147 }
-
148 if(FirstPCAdpar < 0 || LastPCAdpar < 0){
-
149 MACH3LOG_ERROR("FirstPCAdpar and LastPCAdpar are less than 0 but not default -999");
-
150 MACH3LOG_ERROR("first: {} last: {}", FirstPCAdpar, LastPCAdpar);
-
151 throw;
-
152 }
+
148
+
149 MACH3LOG_INFO("PCAing parameters {} through {} inclusive", FirstPCAdpar, LastPCAdpar);
+
150 int numunpcadpars = covMatrix->GetNrows()-(LastPCAdpar-FirstPCAdpar+1);
+
151
+
152 TMatrixDSym submat(covMatrix->GetSub(FirstPCAdpar,LastPCAdpar,FirstPCAdpar,LastPCAdpar));
153
-
154 MACH3LOG_INFO("PCAing parameters {} through {} inclusive", FirstPCAdpar, LastPCAdpar);
-
155 int numunpcadpars = covMatrix->GetNrows()-(LastPCAdpar-FirstPCAdpar+1);
-
156
-
157 TMatrixDSym submat(covMatrix->GetSub(FirstPCAdpar,LastPCAdpar,FirstPCAdpar,LastPCAdpar));
-
158
-
159 //CW: Calculate how many eigen values this threshold corresponds to
-
160 TMatrixDSymEigen eigen(submat);
-
161 eigen_values.ResizeTo(eigen.GetEigenValues());
-
162 eigen_vectors.ResizeTo(eigen.GetEigenVectors());
-
163 eigen_values = eigen.GetEigenValues();
-
164 eigen_vectors = eigen.GetEigenVectors();
-
165 double sum = 0;
-
166 // Loop over eigen values and sum them up
-
167 for (int i = 0; i < eigen_values.GetNrows(); ++i) {
-
168 sum += eigen_values(i);
-
169 }
-
170 nKeptPCApars = eigen_values.GetNrows();
-
171 //CW: Now go through again and see how many eigen values correspond to threshold
-
172 for (int i = 0; i < eigen_values.GetNrows(); ++i) {
-
173 // Get the relative size of the eigen value
-
174 double sig = eigen_values(i)/sum;
-
175 // Check against the threshold
-
176 if (sig < eigen_threshold) {
-
177 nKeptPCApars = i;
-
178 break;
-
179 }
-
180 }
-
181 _fNumParPCA = numunpcadpars+nKeptPCApars;
-
182 MACH3LOG_INFO("Threshold of {} on eigen values relative sum of eigen value ({}) generates {} eigen vectors, plus we have {} unpcad pars, for a total of {}", eigen_threshold, sum, nKeptPCApars, numunpcadpars, _fNumParPCA);
-
183
-
184 //DB Create array of correct size so eigen_values can be used in CorrelateSteps
-
185 eigen_values_master = std::vector<double>(_fNumParPCA, 1.0);
-
186 for (int i = FirstPCAdpar; i < FirstPCAdpar+nKeptPCApars; ++i) {eigen_values_master[i] = eigen_values(i-FirstPCAdpar);}
+
154 //CW: Calculate how many eigen values this threshold corresponds to
+
155 TMatrixDSymEigen eigen(submat);
+
156 eigen_values.ResizeTo(eigen.GetEigenValues());
+
157 eigen_vectors.ResizeTo(eigen.GetEigenVectors());
+
158 eigen_values = eigen.GetEigenValues();
+
159 eigen_vectors = eigen.GetEigenVectors();
+
160 double sum = 0;
+
161 // Loop over eigen values and sum them up
+
162 for (int i = 0; i < eigen_values.GetNrows(); ++i) {
+
163 sum += eigen_values(i);
+
164 }
+
165 nKeptPCApars = eigen_values.GetNrows();
+
166 //CW: Now go through again and see how many eigen values correspond to threshold
+
167 for (int i = 0; i < eigen_values.GetNrows(); ++i) {
+
168 // Get the relative size of the eigen value
+
169 double sig = eigen_values(i)/sum;
+
170 // Check against the threshold
+
171 if (sig < eigen_threshold) {
+
172 nKeptPCApars = i;
+
173 break;
+
174 }
+
175 }
+
176 _fNumParPCA = numunpcadpars+nKeptPCApars;
+
177 MACH3LOG_INFO("Threshold of {} on eigen values relative sum of eigen value ({}) generates {} eigen vectors, plus we have {} unpcad pars, for a total of {}", eigen_threshold, sum, nKeptPCApars, numunpcadpars, _fNumParPCA);
+
178
+
179 //DB Create array of correct size so eigen_values can be used in CorrelateSteps
+
180 eigen_values_master = std::vector<double>(_fNumParPCA, 1.0);
+
181 for (int i = FirstPCAdpar; i < FirstPCAdpar+nKeptPCApars; ++i) {eigen_values_master[i] = eigen_values(i-FirstPCAdpar);}
+
182
+
183 // Now construct the transfer matrices
+
184 //These matrices will be as big as number of unPCAd pars plus number of eigenvalues kept
+
185 TransferMat.ResizeTo(covMatrix->GetNrows(), _fNumParPCA);
+
186 TransferMatT.ResizeTo(covMatrix->GetNrows(), _fNumParPCA);
187
-
188 // Now construct the transfer matrices
-
189 //These matrices will be as big as number of unPCAd pars plus number of eigenvalues kept
-
190 TransferMat.ResizeTo(covMatrix->GetNrows(), _fNumParPCA);
-
191 TransferMatT.ResizeTo(covMatrix->GetNrows(), _fNumParPCA);
-
192
-
193 // Get a subset of the eigen vector matrix
-
194 TMatrixD temp(eigen_vectors.GetSub(0, eigen_vectors.GetNrows()-1, 0, nKeptPCApars-1));
-
195
-
196 //Make transfer matrix which is two blocks of identity with a block of the PCA transfer matrix in between
-
197 TMatrixD temp2;
-
198 temp2.ResizeTo(covMatrix->GetNrows(), _fNumParPCA);
-
199
-
200 //First set the whole thing to 0
-
201 for(int iRow = 0; iRow < covMatrix->GetNrows(); iRow++){
-
202 for(int iCol = 0; iCol < _fNumParPCA; iCol++){
-
203 temp2[iRow][iCol] = 0;
-
204 }
-
205 }
-
206 //Set the first identity block
-
207 if(FirstPCAdpar != 0){
-
208 for(int iRow = 0; iRow < FirstPCAdpar; iRow++){
-
209 temp2[iRow][iRow] = 1;
-
210 }
-
211 }
-
212
-
213 //Set the transfer matrix block for the PCAd pars
-
214 temp2.SetSub(FirstPCAdpar,FirstPCAdpar,temp);
-
215
-
216 //Set the second identity block
-
217 if(LastPCAdpar != covMatrix->GetNrows()-1){
-
218 for(int iRow = 0;iRow < (covMatrix->GetNrows()-1)-LastPCAdpar; iRow++){
-
219 temp2[LastPCAdpar+1+iRow][FirstPCAdpar+nKeptPCApars+iRow] = 1;
-
220 }
-
221 }
-
222
-
223 TransferMat = temp2;
-
224 // Copy the contents
-
225 TransferMatT = TransferMat;
-
226 // And then transpose
-
227 TransferMatT.T();
-
228
-
229 // Make a note that we have now done PCA
-
230 pca = true;
+
188 // Get a subset of the eigen vector matrix
+
189 TMatrixD temp(eigen_vectors.GetSub(0, eigen_vectors.GetNrows()-1, 0, nKeptPCApars-1));
+
190
+
191 //Make transfer matrix which is two blocks of identity with a block of the PCA transfer matrix in between
+
192 TMatrixD temp2;
+
193 temp2.ResizeTo(covMatrix->GetNrows(), _fNumParPCA);
+
194
+
195 //First set the whole thing to 0
+
196 for(int iRow = 0; iRow < covMatrix->GetNrows(); iRow++){
+
197 for(int iCol = 0; iCol < _fNumParPCA; iCol++){
+
198 temp2[iRow][iCol] = 0;
+
199 }
+
200 }
+
201 //Set the first identity block
+
202 if(FirstPCAdpar != 0){
+
203 for(int iRow = 0; iRow < FirstPCAdpar; iRow++){
+
204 temp2[iRow][iRow] = 1;
+
205 }
+
206 }
+
207
+
208 //Set the transfer matrix block for the PCAd pars
+
209 temp2.SetSub(FirstPCAdpar,FirstPCAdpar,temp);
+
210
+
211 //Set the second identity block
+
212 if(LastPCAdpar != covMatrix->GetNrows()-1){
+
213 for(int iRow = 0;iRow < (covMatrix->GetNrows()-1)-LastPCAdpar; iRow++){
+
214 temp2[LastPCAdpar+1+iRow][FirstPCAdpar+nKeptPCApars+iRow] = 1;
+
215 }
+
216 }
+
217
+
218 TransferMat = temp2;
+
219 // Copy the contents
+
220 TransferMatT = TransferMat;
+
221 // And then transpose
+
222 TransferMatT.T();
+
223
+
224 // Make a note that we have now done PCA
+
225 pca = true;
+
226
+
227 // Make the PCA parameter arrays
+
228 fParCurr_PCA.ResizeTo(_fNumParPCA);
+
229 fParProp_PCA.ResizeTo(_fNumParPCA);
+
230 _fPreFitValue_PCA.resize(_fNumParPCA);
231
-
232 // Make the PCA parameter arrays
-
233 fParCurr_PCA.ResizeTo(_fNumParPCA);
-
234 fParProp_PCA.ResizeTo(_fNumParPCA);
-
235 _fPreFitValue_PCA.resize(_fNumParPCA);
-
236
-
237 //KS: make easy map so we could easily find un-decomposed parameters
-
238 isDecomposed_PCA.resize(_fNumParPCA);
-
239 fParSigma_PCA.resize(_fNumParPCA);
-
240 for (int i = 0; i < _fNumParPCA; ++i)
-
241 {
-
242 fParSigma_PCA[i] = 1;
-
243 isDecomposed_PCA[i] = -1;
-
244 }
-
245 for (int i = 0; i < FirstPCAdpar; ++i) isDecomposed_PCA[i] = i;
-
246
-
247 for (int i = FirstPCAdpar+nKeptPCApars+1; i < _fNumParPCA; ++i) isDecomposed_PCA[i] = i+(size-_fNumParPCA);
-
248
-
249 #ifdef DEBUG_PCA
-
250 //KS: Let's dump all useful matrices to properly validate PCA
-
251 DebugPCA(sum, temp, submat);
-
252 #endif
-
253}
-
-
254
-
255// ********************************************
-
-
256void covarianceBase::init(const char *name, const char *file) {
-
257// ********************************************
-
258
-
259 // Set the covariance matrix from input ROOT file (e.g. flux, ND280, NIWG)
-
260 TFile *infile = new TFile(file, "READ");
-
261 if (infile->IsZombie()) {
-
262 MACH3LOG_ERROR("Could not open input covariance ROOT file {} !!!", file);
-
263 MACH3LOG_ERROR("Was about to retrieve matrix with name {}", name);
-
264 throw;
-
265 }
-
266
-
267 // Should put in a
-
268 TMatrixDSym *CovMat = (TMatrixDSym*)(infile->Get(name));
-
269 if (CovMat == NULL) {
-
270 MACH3LOG_ERROR("Could not find covariance matrix name {} in file {}", name, file);
-
271 MACH3LOG_ERROR("Are you really sure {} exists in the file?", name);
-
272 throw MaCh3Exception(__FILE__ , __LINE__ );
-
273 }
-
274
-
275 PrintLength = 35;
-
276
-
277 const int nThreads = MaCh3Utils::GetNThreads();
-
278 //KS: set Random numbers for each thread so each thread has different seed
-
279 //or for one thread if without MULTITHREAD
-
280 random_number = new TRandom3*[nThreads]();
-
281 for (int iThread = 0; iThread < nThreads; iThread++) {
-
282 random_number[iThread] = new TRandom3(0);
-
283 }
-
284
-
285 // Not using adaptive by default
-
286 setAdaptionDefaults();
-
287 // Set the covariance matrix
-
288 size = CovMat->GetNrows();
-
289 _fNumPar = size;
-
290
-
291 InvertCovMatrix = new double*[_fNumPar]();
-
292 throwMatrixCholDecomp = new double*[_fNumPar]();
-
293 // Set the defaults to true
-
294 for(int i = 0; i < _fNumPar; i++)
-
295 {
-
296 InvertCovMatrix[i] = new double[_fNumPar]();
-
297 throwMatrixCholDecomp[i] = new double[_fNumPar]();
-
298 for (int j = 0; j < _fNumPar; j++)
-
299 {
-
300 InvertCovMatrix[i][j] = 0.;
-
301 throwMatrixCholDecomp[i][j] = 0.;
-
302 }
-
303 }
-
304
-
305 setName(name);
-
306 MakePosDef(CovMat);
-
307 setCovMatrix(CovMat);
-
308
-
309 if (_fNumPar <= 0) {
-
310 MACH3LOG_CRITICAL("Covariance matrix {} has {} entries!", getName(), _fNumPar);
-
311 throw;
-
312 }
-
313 _fNumParPCA = _fNumPar;
-
314
-
315 ReserveMemory(_fNumPar);
+
232 //KS: make easy map so we could easily find un-decomposed parameters
+
233 isDecomposed_PCA.resize(_fNumParPCA);
+
234 fParSigma_PCA.resize(_fNumParPCA);
+
235 for (int i = 0; i < _fNumParPCA; ++i)
+
236 {
+
237 fParSigma_PCA[i] = 1;
+
238 isDecomposed_PCA[i] = -1;
+
239 }
+
240 for (int i = 0; i < FirstPCAdpar; ++i) isDecomposed_PCA[i] = i;
+
241
+
242 for (int i = FirstPCAdpar+nKeptPCApars+1; i < _fNumParPCA; ++i) isDecomposed_PCA[i] = i+(size-_fNumParPCA);
+
243
+
244 #ifdef DEBUG_PCA
+
245 //KS: Let's dump all useful matrices to properly validate PCA
+
246 DebugPCA(sum, temp, submat);
+
247 #endif
+
248}
+
+
249
+
250// ********************************************
+
+
251void covarianceBase::init(const char *name, const char *file) {
+
252// ********************************************
+
253
+
254 // Set the covariance matrix from input ROOT file (e.g. flux, ND280, NIWG)
+
255 TFile *infile = new TFile(file, "READ");
+
256 if (infile->IsZombie()) {
+
257 MACH3LOG_ERROR("Could not open input covariance ROOT file {} !!!", file);
+
258 MACH3LOG_ERROR("Was about to retrieve matrix with name {}", name);
+
259 throw;
+
260 }
+
261
+
262 // Should put in a
+
263 TMatrixDSym *CovMat = (TMatrixDSym*)(infile->Get(name));
+
264 if (CovMat == NULL) {
+
265 MACH3LOG_ERROR("Could not find covariance matrix name {} in file {}", name, file);
+
266 MACH3LOG_ERROR("Are you really sure {} exists in the file?", name);
+
267 throw MaCh3Exception(__FILE__ , __LINE__ );
+
268 }
+
269
+
270 PrintLength = 35;
+
271
+
272 const int nThreads = MaCh3Utils::GetNThreads();
+
273 //KS: set Random numbers for each thread so each thread has different seed
+
274 //or for one thread if without MULTITHREAD
+
275 random_number = new TRandom3*[nThreads]();
+
276 for (int iThread = 0; iThread < nThreads; iThread++) {
+
277 random_number[iThread] = new TRandom3(0);
+
278 }
+
279
+
280 // Not using adaptive by default
+
281 setAdaptionDefaults();
+
282 // Set the covariance matrix
+
283 size = CovMat->GetNrows();
+
284 _fNumPar = size;
+
285
+
286 InvertCovMatrix = new double*[_fNumPar]();
+
287 throwMatrixCholDecomp = new double*[_fNumPar]();
+
288 // Set the defaults to true
+
289 for(int i = 0; i < _fNumPar; i++)
+
290 {
+
291 InvertCovMatrix[i] = new double[_fNumPar]();
+
292 throwMatrixCholDecomp[i] = new double[_fNumPar]();
+
293 for (int j = 0; j < _fNumPar; j++)
+
294 {
+
295 InvertCovMatrix[i][j] = 0.;
+
296 throwMatrixCholDecomp[i][j] = 0.;
+
297 }
+
298 }
+
299
+
300 setName(name);
+
301 MakePosDef(CovMat);
+
302 setCovMatrix(CovMat);
+
303
+
304 if (_fNumPar <= 0) {
+
305 MACH3LOG_CRITICAL("Covariance matrix {} has {} entries!", getName(), _fNumPar);
+
306 throw;
+
307 }
+
308 _fNumParPCA = _fNumPar;
+
309
+
310 ReserveMemory(_fNumPar);
+
311
+
312 infile->Close();
+
313
+
314 MACH3LOG_INFO("Created covariance matrix named: {}", getName());
+
315 MACH3LOG_INFO("from file: {}", file);
316
-
317 infile->Close();
-
318
-
319 MACH3LOG_INFO("Created covariance matrix named: {}", getName());
-
320 MACH3LOG_INFO("from file: {}", file);
-
321
-
322 delete infile;
-
323}
-
-
324
-
325// ********************************************
-
326// ETA
-
327// An init function for the YAML constructor
-
328// All you really need from the YAML file is the number of Systematics
-
329// Then get all the info from the YAML file in the covarianceXsec::ParseYAML function
-
-
330void covarianceBase::init(const std::vector<std::string>& YAMLFile) {
-
331// ********************************************
-
332 _fYAMLDoc["Systematics"] = YAML::Node(YAML::NodeType::Sequence);
-
333 for(unsigned int i = 0; i < YAMLFile.size(); i++)
-
334 {
-
335 YAML::Node YAMLDocTemp = YAML::LoadFile(YAMLFile[i]);
-
336 for (const auto& item : YAMLDocTemp["Systematics"]) {
-
337 _fYAMLDoc["Systematics"].push_back(item);
-
338 }
-
339 }
-
340
-
341 const int nThreads = MaCh3Utils::GetNThreads();
-
342 //KS: set Random numbers for each thread so each thread has different seed
-
343 //or for one thread if without MULTITHREAD
-
344 random_number = new TRandom3*[nThreads]();
-
345 for (int iThread = 0; iThread < nThreads; iThread++) {
-
346 random_number[iThread] = new TRandom3(0);
-
347 }
-
348
-
349 PrintLength = 35;
+
317 delete infile;
+
318}
+
+
319
+
320// ********************************************
+
321// ETA
+
322// An init function for the YAML constructor
+
323// All you really need from the YAML file is the number of Systematics
+
324// Then get all the info from the YAML file in the covarianceXsec::ParseYAML function
+
+
325void covarianceBase::init(const std::vector<std::string>& YAMLFile) {
+
326// ********************************************
+
327 _fYAMLDoc["Systematics"] = YAML::Node(YAML::NodeType::Sequence);
+
328 for(unsigned int i = 0; i < YAMLFile.size(); i++)
+
329 {
+
330 YAML::Node YAMLDocTemp = YAML::LoadFile(YAMLFile[i]);
+
331 for (const auto& item : YAMLDocTemp["Systematics"]) {
+
332 _fYAMLDoc["Systematics"].push_back(item);
+
333 }
+
334 }
+
335
+
336 const int nThreads = MaCh3Utils::GetNThreads();
+
337 //KS: set Random numbers for each thread so each thread has different seed
+
338 //or for one thread if without MULTITHREAD
+
339 random_number = new TRandom3*[nThreads]();
+
340 for (int iThread = 0; iThread < nThreads; iThread++) {
+
341 random_number[iThread] = new TRandom3(0);
+
342 }
+
343
+
344 PrintLength = 35;
+
345
+
346
+
347 // Set the covariance matrix
+
348 _fNumPar = _fYAMLDoc["Systematics"].size();
+
349 size = _fNumPar;
350
-
351
-
352 // Set the covariance matrix
-
353 _fNumPar = _fYAMLDoc["Systematics"].size();
-
354 size = _fNumPar;
-
355
-
356 setAdaptionDefaults();
-
357
-
358 InvertCovMatrix = new double*[_fNumPar]();
-
359 throwMatrixCholDecomp = new double*[_fNumPar]();
-
360 // Set the defaults to true
-
361 for(int i = 0; i < _fNumPar; i++)
-
362 {
-
363 InvertCovMatrix[i] = new double[_fNumPar]();
-
364 throwMatrixCholDecomp[i] = new double[_fNumPar]();
-
365 for (int j = 0; j < _fNumPar; j++)
-
366 {
-
367 InvertCovMatrix[i][j] = 0.;
-
368 throwMatrixCholDecomp[i][j] = 0.;
-
369 }
-
370 }
+
351 setAdaptionDefaults();
+
352
+
353 InvertCovMatrix = new double*[_fNumPar]();
+
354 throwMatrixCholDecomp = new double*[_fNumPar]();
+
355 // Set the defaults to true
+
356 for(int i = 0; i < _fNumPar; i++)
+
357 {
+
358 InvertCovMatrix[i] = new double[_fNumPar]();
+
359 throwMatrixCholDecomp[i] = new double[_fNumPar]();
+
360 for (int j = 0; j < _fNumPar; j++)
+
361 {
+
362 InvertCovMatrix[i][j] = 0.;
+
363 throwMatrixCholDecomp[i][j] = 0.;
+
364 }
+
365 }
+
366
+
367 ReserveMemory(_fNumPar);
+
368
+
369 TMatrixDSym* _fCovMatrix = new TMatrixDSym(_fNumPar);
+
370 //_fDetString = std::vector<std::string>(_fNumPar);
371
-
372 ReserveMemory(_fNumPar);
-
373
-
374 TMatrixDSym* _fCovMatrix = new TMatrixDSym(_fNumPar);
-
375 //_fDetString = std::vector<std::string>(_fNumPar);
-
376
-
377 int i = 0;
-
378 std::vector<std::map<std::string,double>> Correlations(_fNumPar);
-
379 std::map<std::string, int> CorrNamesMap;
-
380
-
381 //ETA - read in the systematics. Would be good to add in some checks to make sure
-
382 //that there are the correct number of entries i.e. are the _fNumPar for Names,
-
383 //PreFitValues etc etc.
-
384 for (auto const &param : _fYAMLDoc["Systematics"])
-
385 {
-
386 _fFancyNames[i] = (param["Systematic"]["Names"]["FancyName"].as<std::string>());
-
387 _fPreFitValue[i] = (param["Systematic"]["ParameterValues"]["PreFitValue"].as<double>());
-
388 _fGenerated[i] = (param["Systematic"]["ParameterValues"]["Generated"].as<double>());
-
389 _fIndivStepScale[i] = (param["Systematic"]["StepScale"]["MCMC"].as<double>());
-
390 _fError[i] = (param["Systematic"]["Error"].as<double>());
+
372 int i = 0;
+
373 std::vector<std::map<std::string,double>> Correlations(_fNumPar);
+
374 std::map<std::string, int> CorrNamesMap;
+
375
+
376 //ETA - read in the systematics. Would be good to add in some checks to make sure
+
377 //that there are the correct number of entries i.e. are the _fNumPar for Names,
+
378 //PreFitValues etc etc.
+
379 for (auto const &param : _fYAMLDoc["Systematics"])
+
380 {
+
381 _fFancyNames[i] = (param["Systematic"]["Names"]["FancyName"].as<std::string>());
+
382 _fPreFitValue[i] = (param["Systematic"]["ParameterValues"]["PreFitValue"].as<double>());
+
383 _fGenerated[i] = (param["Systematic"]["ParameterValues"]["Generated"].as<double>());
+
384 _fIndivStepScale[i] = (param["Systematic"]["StepScale"]["MCMC"].as<double>());
+
385 _fError[i] = (param["Systematic"]["Error"].as<double>());
+
386
+
387 //ETA - a bit of a fudge but works
+
388 std::vector<double> TempBoundsVec = param["Systematic"]["ParameterBounds"].as<std::vector<double>>();
+
389 _fLowBound[i] = TempBoundsVec[0];
+
390 _fUpBound[i] = TempBoundsVec[1];
391
-
392 //ETA - a bit of a fudge but works
-
393 std::vector<double> TempBoundsVec = param["Systematic"]["ParameterBounds"].as<std::vector<double>>();
-
394 _fLowBound[i] = TempBoundsVec[0];
-
395 _fUpBound[i] = TempBoundsVec[1];
-
396
-
397 //ETA - now for parameters which are optional and have default values
-
398 _fFlatPrior[i] = GetFromManager<bool>(param["Systematic"]["FlatPrior"], false);
-
399
-
400 //Fill the map to get the correlations later as well
-
401 CorrNamesMap[param["Systematic"]["Names"]["FancyName"].as<std::string>()]=i;
-
402
-
403 //Also loop through the correlations
-
404 if(param["Systematic"]["Correlations"]) {
-
405 for(unsigned int Corr_i = 0; Corr_i < param["Systematic"]["Correlations"].size(); ++Corr_i){
-
406 for (YAML::const_iterator it=param["Systematic"]["Correlations"][Corr_i].begin();it!=param["Systematic"]["Correlations"][Corr_i].end();++it) {
-
407 Correlations[i][it->first.as<std::string>()] = it->second.as<double>();
-
408 }
-
409 }
-
410 }
-
411 i++;
-
412 }
-
413
-
414 //ETA
-
415 //Now that we've been through all systematic let's fill the covmatrix
-
416 //This makes the root TCov from YAML
-
417 for(int j = 0; j < _fNumPar;j++) {
-
418 (*_fCovMatrix)(j, j)=_fError[j]*_fError[j];
-
419 //Get the map of parameter name to correlation from the Correlations object
-
420 for (auto const& pair : Correlations[j]) {
-
421 auto const& key = pair.first;
-
422 auto const& val = pair.second;
-
423 int index = -1;
-
424 //If you found the parameter name then get the index
-
425 if (CorrNamesMap.find(key) != CorrNamesMap.end()) {
-
426 index = CorrNamesMap[key];
-
427 }
-
428 else {
-
429 MACH3LOG_ERROR("Parameter {} not in list! Check your spelling?", key);
-
430 throw MaCh3Exception(__FILE__ , __LINE__ );
-
431 }
-
432 double Corr1 = val;
-
433 double Corr2 = 0;
-
434 if(Correlations[index].find(_fFancyNames[j]) != Correlations[index].end()) {
-
435 Corr2 = Correlations[index][_fFancyNames[j]];
-
436 //Do they agree to better than float precision?
-
437 if(std::abs(Corr2 - Corr1) > FLT_EPSILON) {
-
438 MACH3LOG_ERROR("Correlations are not equal between {} and {}", _fFancyNames[j], key);
-
439 MACH3LOG_ERROR("Got : {} and {}", Corr2, Corr1);
-
440 throw MaCh3Exception(__FILE__ , __LINE__ );
-
441 }
-
442 } else {
-
443 MACH3LOG_ERROR("Correlation does not appear reciprocally between {} and {}", _fFancyNames[j], key);
-
444 throw MaCh3Exception(__FILE__ , __LINE__ );
-
445 }
-
446 (*_fCovMatrix)(j, index)= (*_fCovMatrix)(index, j) = Corr1*_fError[j]*_fError[index];
-
447 }
-
448 }
-
449
-
450 //Now make positive definite
-
451 MakePosDef(_fCovMatrix);
-
452 setCovMatrix(_fCovMatrix);
-
453
-
454 if (_fNumPar <= 0) {
-
455 MACH3LOG_ERROR("Covariance object has {} systematics!", _fNumPar);
-
456 throw;
-
457 }
-
458 _fNumParPCA = _fNumPar;
-
459
-
460 MACH3LOG_INFO("Created covariance matrix from files: ");
-
461 for(const auto &file : YAMLFile){
-
462 MACH3LOG_INFO("{} ", file);
-
463 }
-
464 MACH3LOG_INFO("----------------");
-
465 MACH3LOG_INFO("Found {} systematics parameters in total", _fNumPar);
-
466 MACH3LOG_INFO("----------------");
-
467
-
468 return;
-
469}
-
-
470
-
471// ********************************************
-
-
472void covarianceBase::init(TMatrixDSym* covMat) {
-
473// ********************************************
-
474 size = covMat->GetNrows();
-
475 _fNumPar = size;
-
476 InvertCovMatrix = new double*[_fNumPar]();
-
477 throwMatrixCholDecomp = new double*[_fNumPar]();
-
478 // Set the defaults to true
-
479 for(int i = 0; i < _fNumPar; i++)
-
480 {
-
481 InvertCovMatrix[i] = new double[_fNumPar]();
-
482 throwMatrixCholDecomp[i] = new double[_fNumPar]();
-
483 for (int j = 0; j < _fNumPar; j++)
-
484 {
-
485 InvertCovMatrix[i][j] = 0.;
-
486 throwMatrixCholDecomp[i][j] = 0.;
-
487 }
-
488 }
+
392 //ETA - now for parameters which are optional and have default values
+
393 _fFlatPrior[i] = GetFromManager<bool>(param["Systematic"]["FlatPrior"], false);
+
394
+
395 //Fill the map to get the correlations later as well
+
396 CorrNamesMap[param["Systematic"]["Names"]["FancyName"].as<std::string>()]=i;
+
397
+
398 //Also loop through the correlations
+
399 if(param["Systematic"]["Correlations"]) {
+
400 for(unsigned int Corr_i = 0; Corr_i < param["Systematic"]["Correlations"].size(); ++Corr_i){
+
401 for (YAML::const_iterator it=param["Systematic"]["Correlations"][Corr_i].begin();it!=param["Systematic"]["Correlations"][Corr_i].end();++it) {
+
402 Correlations[i][it->first.as<std::string>()] = it->second.as<double>();
+
403 }
+
404 }
+
405 }
+
406 i++;
+
407 }
+
408
+
409 //ETA
+
410 //Now that we've been through all systematic let's fill the covmatrix
+
411 //This makes the root TCov from YAML
+
412 for(int j = 0; j < _fNumPar;j++) {
+
413 (*_fCovMatrix)(j, j)=_fError[j]*_fError[j];
+
414 //Get the map of parameter name to correlation from the Correlations object
+
415 for (auto const& pair : Correlations[j]) {
+
416 auto const& key = pair.first;
+
417 auto const& val = pair.second;
+
418 int index = -1;
+
419 //If you found the parameter name then get the index
+
420 if (CorrNamesMap.find(key) != CorrNamesMap.end()) {
+
421 index = CorrNamesMap[key];
+
422 }
+
423 else {
+
424 MACH3LOG_ERROR("Parameter {} not in list! Check your spelling?", key);
+
425 throw MaCh3Exception(__FILE__ , __LINE__ );
+
426 }
+
427 double Corr1 = val;
+
428 double Corr2 = 0;
+
429 if(Correlations[index].find(_fFancyNames[j]) != Correlations[index].end()) {
+
430 Corr2 = Correlations[index][_fFancyNames[j]];
+
431 //Do they agree to better than float precision?
+
432 if(std::abs(Corr2 - Corr1) > FLT_EPSILON) {
+
433 MACH3LOG_ERROR("Correlations are not equal between {} and {}", _fFancyNames[j], key);
+
434 MACH3LOG_ERROR("Got : {} and {}", Corr2, Corr1);
+
435 throw MaCh3Exception(__FILE__ , __LINE__ );
+
436 }
+
437 } else {
+
438 MACH3LOG_ERROR("Correlation does not appear reciprocally between {} and {}", _fFancyNames[j], key);
+
439 throw MaCh3Exception(__FILE__ , __LINE__ );
+
440 }
+
441 (*_fCovMatrix)(j, index)= (*_fCovMatrix)(index, j) = Corr1*_fError[j]*_fError[index];
+
442 }
+
443 }
+
444
+
445 //Now make positive definite
+
446 MakePosDef(_fCovMatrix);
+
447 setCovMatrix(_fCovMatrix);
+
448
+
449 if (_fNumPar <= 0) {
+
450 MACH3LOG_ERROR("Covariance object has {} systematics!", _fNumPar);
+
451 throw;
+
452 }
+
453 _fNumParPCA = _fNumPar;
+
454
+
455 MACH3LOG_INFO("Created covariance matrix from files: ");
+
456 for(const auto &file : YAMLFile){
+
457 MACH3LOG_INFO("{} ", file);
+
458 }
+
459 MACH3LOG_INFO("----------------");
+
460 MACH3LOG_INFO("Found {} systematics parameters in total", _fNumPar);
+
461 MACH3LOG_INFO("----------------");
+
462
+
463 return;
+
464}
+
+
465
+
466// ********************************************
+
+
467void covarianceBase::init(TMatrixDSym* covMat) {
+
468// ********************************************
+
469 size = covMat->GetNrows();
+
470 _fNumPar = size;
+
471 InvertCovMatrix = new double*[_fNumPar]();
+
472 throwMatrixCholDecomp = new double*[_fNumPar]();
+
473 // Set the defaults to true
+
474 for(int i = 0; i < _fNumPar; i++)
+
475 {
+
476 InvertCovMatrix[i] = new double[_fNumPar]();
+
477 throwMatrixCholDecomp[i] = new double[_fNumPar]();
+
478 for (int j = 0; j < _fNumPar; j++)
+
479 {
+
480 InvertCovMatrix[i][j] = 0.;
+
481 throwMatrixCholDecomp[i][j] = 0.;
+
482 }
+
483 }
+
484
+
485 setAdaptionDefaults();
+
486 setCovMatrix(covMat);
+
487
+
488 ReserveMemory(_fNumPar);
489
-
490 setAdaptionDefaults();
-
491 setCovMatrix(covMat);
-
492
-
493 ReserveMemory(_fNumPar);
-
494
-
495 MACH3LOG_INFO("Created covariance matrix named: {}", getName());
-
496}
-
-
497
-
498// ********************************************
-
499// Set the covariance matrix for this class
-
-
500void covarianceBase::setCovMatrix(TMatrixDSym *cov) {
-
501// ********************************************
-
502 if (cov == NULL) {
-
503 MACH3LOG_ERROR("Could not find covariance matrix you provided to setCovMatrix");
-
504 throw MaCh3Exception(__FILE__ , __LINE__ );
-
505 }
-
506 covMatrix = cov;
-
507 invCovMatrix = (TMatrixDSym*)cov->Clone();
-
508 invCovMatrix->Invert();
-
509 //KS: ROOT has bad memory management, using standard double means we can decrease most operation by factor 2 simply due to cache hits
-
510 for (int i = 0; i < _fNumPar; i++)
-
511 {
-
512 for (int j = 0; j < _fNumPar; ++j)
-
513 {
-
514 InvertCovMatrix[i][j] = (*invCovMatrix)(i,j);
-
515 }
-
516 }
-
517
-
518 setThrowMatrix(cov);
-
519}
-
-
520
-
-
521void covarianceBase::ReserveMemory(const int SizeVec) {
-
522
-
523 _fNames = std::vector<std::string>(SizeVec);
-
524 _fFancyNames = std::vector<std::string>(SizeVec);
-
525 _fGenerated = std::vector<double>(SizeVec);
-
526 _fPreFitValue = std::vector<double>(SizeVec);
-
527 _fError = std::vector<double>(SizeVec);
-
528 _fCurrVal = std::vector<double>(SizeVec);
-
529 _fPropVal = std::vector<double>(SizeVec);
-
530 _fLowBound = std::vector<double>(SizeVec);
-
531 _fUpBound = std::vector<double>(SizeVec);
-
532 _fFlatPrior = std::vector<bool>(SizeVec);
-
533 _fIndivStepScale = std::vector<double>(SizeVec);
-
534
-
535 corr_throw = new double[SizeVec]();
-
536 // set random parameter vector (for correlated steps)
-
537 randParams = new double[SizeVec];
-
538
-
539 // Set the defaults to true
-
540 for(int i = 0; i < SizeVec; i++) {
-
541 _fGenerated.at(i) = 1.;
-
542 _fPreFitValue.at(i) = 1.;
-
543 _fError.at(i) = 0.;
-
544 _fCurrVal.at(i) = 0.;
-
545 _fPropVal.at(i) = 0.;
-
546 _fLowBound.at(i) = -999.99;
-
547 _fUpBound.at(i) = 999.99;
-
548 _fFlatPrior.at(i) = false;
-
549 _fIndivStepScale.at(i) = 1.;
-
550 corr_throw[i] = 0.0;
-
551 }
-
552
-
553 _fGlobalStepScale = 1.0;
-
554}
-
-
555
-
556// Set all the covariance matrix parameters to a user-defined value
-
557// Might want to split this
-
-
558void covarianceBase::setPar(int i , double val) {
-
559 MACH3LOG_INFO("Over-riding {}: ", GetParName(i));
-
560 MACH3LOG_INFO("_fPropVal ({}), _fCurrVal ({}), _fPreFitValue ({}) to ({})", _fPropVal[i], _fCurrVal[i], _fPreFitValue[i], val);
-
561
-
562 _fPropVal[i] = val;
-
563 _fCurrVal[i] = val;
-
564 _fPreFitValue[i] = val;
-
565
-
566 // Transfer the parameter values to the PCA basis
-
567 if (pca) TransferToPCA();
-
568}
-
-
569
-
570// Transfer a parameter variation in the parameter basis to the eigen basis
-
-
571void covarianceBase::TransferToPCA() {
-
572 if (!pca) {
-
573 MACH3LOG_ERROR("Can not transfer to PCA if PCA isn't enabled");
-
574 throw MaCh3Exception(__FILE__ , __LINE__ );
-
575 }
-
576 // Make the temporary vectors
-
577 TVectorD fParCurr_vec(_fNumPar);
-
578 TVectorD fParProp_vec(_fNumPar);
-
579 for (int i = 0; i < _fNumPar; ++i) {
-
580 fParCurr_vec(i) = _fCurrVal[i];
-
581 fParProp_vec(i) = _fPropVal[i];
-
582 }
-
583
-
584 fParCurr_PCA = TransferMatT*fParCurr_vec;
-
585 fParProp_PCA = TransferMatT*fParProp_vec;
-
586}
-
-
587
-
588// Transfer a parameter variation in the eigen basis to the parameter basis
-
-
589void covarianceBase::TransferToParam() {
-
590 if (!pca) {
-
591 MACH3LOG_ERROR("Can not transfer to PCA if PCA isn't enabled");
-
592 throw MaCh3Exception(__FILE__ , __LINE__ );
-
593 }
-
594
-
595 // Make the temporary vectors
-
596 TVectorD fParProp_vec = TransferMat*fParProp_PCA;
-
597 TVectorD fParCurr_vec = TransferMat*fParCurr_PCA;
-
598#ifdef MULTITHREAD
-
599#pragma omp parallel for
-
600#endif
-
601 for (int i = 0; i < _fNumPar; ++i) {
-
602 _fPropVal[i] = fParProp_vec(i);
-
603 _fCurrVal[i] = fParCurr_vec(i);
-
604 }
-
605}
-
-
606// ********************************************
-
-
607std::vector<double> covarianceBase::getProposed() const {
-
608// ********************************************
-
609 std::vector<double> props(_fNumPar);
-
610 for (int i = 0; i < _fNumPar; ++i) props[i] = _fPropVal[i];
-
611 return props;
-
612}
-
-
613
-
614// Throw nominal values
-
-
615void covarianceBase::throwNominal(bool nomValues, int seed) {
-
616 TVectorD* vec = new TVectorD(_fNumPar);
-
617 for (int i = 0; i < _fNumPar; i++) {
-
618 (*vec)(i) = 1.0;
-
619 }
-
620
-
621 ThrowParms* nom_throws = new ThrowParms(*vec, (*covMatrix));
-
622 nom_throws->SetSeed(seed);
-
623 std::vector<double> nominal = getNominalArray();
-
624 nominal.clear();
-
625 nominal.resize(_fNumPar);
-
626
-
627 // If we want to put the nominals somewhere else than user specified
-
628 // Don't fully understand this though: won't we have to reweight the MC somehow?
-
629 // nominal[i] is used in GetLikelihood() as the penalty term, so we're essentially setting a random parameter penalty term?
-
630 if (!nomValues)
-
631 {
-
632 bool throw_again = true;
-
633
-
634 while(throw_again == true)
-
635 {
-
636 throw_again = false;
-
637 MACH3LOG_INFO("Setting {} nominal values to random throws.", getName());
-
638 nom_throws->ThrowSet(nominal);
-
639
-
640 for (int i = 0; i < _fNumPar; i++)
-
641 {
-
642 // if parameter is fixed, dont throw
-
643 if (_fError[i] < 0) {
-
644 nominal[i] = 1.0;
-
645 continue;
-
646 }
-
647
-
648 if (nominal[i] < 0) {
-
649 nominal[i] = 0.0;
-
650 throw_again = true;
-
651 }
-
652 }
-
653 }
-
654 } else {
-
655 // If we want nominal values, set all entries to 1 (defined as nominal in MaCh3)
-
656 for (int i = 0; i < int(nominal.size()); i++) {
-
657 nominal[i] = 1.0;
-
658 }
-
659 }
-
660
-
661 delete nom_throws;
-
662 delete vec;
-
663}
-
-
664
-
665// *************************************
-
666// Throw the parameters according to the covariance matrix
-
667// This shouldn't be used in MCMC code ase it can break Detailed Balance;
-
-
668void covarianceBase::throwParameters() {
-
669// *************************************
-
670
-
671 // First draw new randParams
-
672 randomize();
-
673
-
674 if (!pca) {
-
675 MatrixVectorMulti(corr_throw, throwMatrixCholDecomp, randParams, _fNumPar);
-
676
-
677#ifdef MULTITHREAD
-
678#pragma omp parallel for
-
679#endif
-
680 for (int i = 0; i < _fNumPar; ++i) {
-
681 // Check if parameter is fixed first: if so don't randomly throw
-
682 if (isParameterFixed(i)) continue;
-
683
-
684 _fPropVal[i] = _fPreFitValue[i] + corr_throw[i];
-
685 int throws = 0;
-
686 // Try again if we the initial parameter proposal falls outside of the range of the parameter
-
687 while (_fPropVal[i] > _fUpBound[i] || _fPropVal[i] < _fLowBound[i]) {
-
688#ifdef MULTITHREAD
-
689 randParams[i] = random_number[omp_get_thread_num()]->Gaus(0, 1);
-
690#else
-
691 randParams[i] = random_number[0]->Gaus(0,1);
-
692#endif
-
693 const double corr_throw_single = MatrixVectorMultiSingle(throwMatrixCholDecomp, randParams, _fNumPar, i);
-
694 _fPropVal[i] = _fPreFitValue[i] + corr_throw_single;
-
695 if (throws > 10000)
-
696 {
-
697 //KS: Since we are multithreading there is danger that those messages
-
698 //will be all over the place, small price to pay for faster code
-
699 MACH3LOG_WARN("Tried {} times to throw parameter {} but failed", throws, i);
-
700 MACH3LOG_WARN("Matrix: {}", matrixName);
-
701 MACH3LOG_WARN("Param: {}", _fNames[i]);
-
702 MACH3LOG_WARN("Setting _fPropVal: {} to {}", _fPropVal[i], _fPreFitValue[i]);
-
703 MACH3LOG_WARN("I live at {}:{}", __FILE__, __LINE__);
-
704 _fPropVal[i] = _fPreFitValue[i];
-
705 //throw;
-
706 }
-
707 throws++;
-
708 }
-
709 _fCurrVal[i] = _fPropVal[i];
-
710 }
-
711 }
-
712 else
-
713 {
-
714 MACH3LOG_CRITICAL("Hold on, you are trying to run Prior Predicitve Code with PCA, which is wrong");
-
715 MACH3LOG_CRITICAL("Sorry I have to kill you, I mean your job");
-
716 throw;
-
717 }
-
718}
+
490 MACH3LOG_INFO("Created covariance matrix named: {}", getName());
+
491}
-
719
-
720// *************************************
-
721// Throw each parameter within their 1 sigma range
-
722// Used to start the chain in different states
-
-
723void covarianceBase::RandomConfiguration() {
-
724 // *************************************
-
725 // Have the 1 sigma for each parameter in each covariance class, sweet!
-
726 // Don't want to change the nominal array because that's what determines our likelihood
-
727 // Want to change the fParProp, fParCurr, fParInit
-
728 // fParInit and the others will already be set
-
729 for (int i = 0; i < _fNumPar; ++i) {
-
730 // Check if parameter is fixed first: if so don't randomly throw
-
731 if (isParameterFixed(i)) continue;
-
732 // Check that the sigma range is larger than the parameter range
-
733 // If not, throw in the valid parameter range instead
-
734 const double paramrange = _fUpBound[i] - _fLowBound[i];
-
735 const double sigma = sqrt((*covMatrix)(i,i));
-
736 double throwrange = sigma;
-
737 if (paramrange < sigma) throwrange = paramrange;
-
738
-
739 _fPropVal[i] = _fPreFitValue[i] + random_number[0]->Gaus(0, 1)*throwrange;
-
740 // Try again if we the initial parameter proposal falls outside of the range of the parameter
-
741 // Really only relevant for the xsec parameters; the flux and ND280 have -999 and 999 set to the limits!
-
742 int throws = 0;
-
743 while (_fPropVal[i] > _fUpBound[i] || _fPropVal[i] < _fLowBound[i]) {
-
744 if (throws > 1000) {
-
745 MACH3LOG_WARN("Tried {} times to throw parameter {} but failed", throws, i);
-
746 MACH3LOG_WARN("Matrix: {}", matrixName);
-
747 MACH3LOG_WARN("Param: {}", _fNames[i]);
-
748 throw MaCh3Exception(__FILE__ , __LINE__ );
-
749 }
-
750 _fPropVal[i] = _fPreFitValue[i] + random_number[0]->Gaus(0, 1)*throwrange;
-
751 throws++;
-
752 }
-
753 MACH3LOG_INFO("Setting current step in {} param {} = {} from {}", matrixName, i, _fPropVal[i], _fCurrVal[i]);
-
754 _fCurrVal[i] = _fPropVal[i];
-
755 }
-
756 if (pca) TransferToPCA();
-
757}
-
-
758
-
759// *************************************
-
760// Set a single parameter
-
-
761void covarianceBase::setSingleParameter(const int parNo, const double parVal) {
-
762 // *************************************
-
763 _fPropVal[parNo] = parVal;
-
764 _fCurrVal[parNo] = parVal;
-
765 MACH3LOG_DEBUG("Setting {}(parameter {}) to {}", GetParName(parNo), parNo, parVal);
-
766
-
767 if (pca) TransferToPCA();
-
768}
-
-
769
-
-
770void covarianceBase::setParCurrProp(const int parNo, const double parVal) {
-
771 _fPropVal[parNo] = parVal;
-
772 _fCurrVal[parNo] = parVal;
-
773 MACH3LOG_DEBUG("Setting {}(parameter {}) to {}", GetParName(parNo), parNo, parVal);
-
774
-
775 if (pca) TransferToPCA();
-
776}
-
-
777
+
492
+
493// ********************************************
+
494// Set the covariance matrix for this class
+
+
495void covarianceBase::setCovMatrix(TMatrixDSym *cov) {
+
496// ********************************************
+
497 if (cov == NULL) {
+
498 MACH3LOG_ERROR("Could not find covariance matrix you provided to setCovMatrix");
+
499 throw MaCh3Exception(__FILE__ , __LINE__ );
+
500 }
+
501 covMatrix = cov;
+
502 invCovMatrix = (TMatrixDSym*)cov->Clone();
+
503 invCovMatrix->Invert();
+
504 //KS: ROOT has bad memory management, using standard double means we can decrease most operation by factor 2 simply due to cache hits
+
505 for (int i = 0; i < _fNumPar; i++)
+
506 {
+
507 for (int j = 0; j < _fNumPar; ++j)
+
508 {
+
509 InvertCovMatrix[i][j] = (*invCovMatrix)(i,j);
+
510 }
+
511 }
+
512
+
513 setThrowMatrix(cov);
+
514}
+
+
515// ********************************************
+
+
516void covarianceBase::ReserveMemory(const int SizeVec) {
+
517// ********************************************
+
518 _fNames = std::vector<std::string>(SizeVec);
+
519 _fFancyNames = std::vector<std::string>(SizeVec);
+
520 _fGenerated = std::vector<double>(SizeVec);
+
521 _fPreFitValue = std::vector<double>(SizeVec);
+
522 _fError = std::vector<double>(SizeVec);
+
523 _fCurrVal = std::vector<double>(SizeVec);
+
524 _fPropVal = std::vector<double>(SizeVec);
+
525 _fLowBound = std::vector<double>(SizeVec);
+
526 _fUpBound = std::vector<double>(SizeVec);
+
527 _fFlatPrior = std::vector<bool>(SizeVec);
+
528 _fIndivStepScale = std::vector<double>(SizeVec);
+
529
+
530 corr_throw = new double[SizeVec]();
+
531 // set random parameter vector (for correlated steps)
+
532 randParams = new double[SizeVec];
+
533
+
534 // Set the defaults to true
+
535 for(int i = 0; i < SizeVec; i++) {
+
536 _fGenerated.at(i) = 1.;
+
537 _fPreFitValue.at(i) = 1.;
+
538 _fError.at(i) = 0.;
+
539 _fCurrVal.at(i) = 0.;
+
540 _fPropVal.at(i) = 0.;
+
541 _fLowBound.at(i) = -999.99;
+
542 _fUpBound.at(i) = 999.99;
+
543 _fFlatPrior.at(i) = false;
+
544 _fIndivStepScale.at(i) = 1.;
+
545 corr_throw[i] = 0.0;
+
546 }
+
547
+
548 _fGlobalStepScale = 1.0;
+
549}
+
+
550
+
551// ********************************************
+
552// Set all the covariance matrix parameters to a user-defined value
+
553// Might want to split this
+
+
554void covarianceBase::setPar(int i , double val) {
+
555// ********************************************
+
556 MACH3LOG_INFO("Over-riding {}: ", GetParName(i));
+
557 MACH3LOG_INFO("_fPropVal ({}), _fCurrVal ({}), _fPreFitValue ({}) to ({})", _fPropVal[i], _fCurrVal[i], _fPreFitValue[i], val);
+
558
+
559 _fPropVal[i] = val;
+
560 _fCurrVal[i] = val;
+
561 _fPreFitValue[i] = val;
+
562
+
563 // Transfer the parameter values to the PCA basis
+
564 if (pca) TransferToPCA();
+
565}
+
+
566
+
567// Transfer a parameter variation in the parameter basis to the eigen basis
+
+
568void covarianceBase::TransferToPCA() {
+
569 if (!pca) {
+
570 MACH3LOG_ERROR("Can not transfer to PCA if PCA isn't enabled");
+
571 throw MaCh3Exception(__FILE__ , __LINE__ );
+
572 }
+
573 // Make the temporary vectors
+
574 TVectorD fParCurr_vec(_fNumPar);
+
575 TVectorD fParProp_vec(_fNumPar);
+
576 for (int i = 0; i < _fNumPar; ++i) {
+
577 fParCurr_vec(i) = _fCurrVal[i];
+
578 fParProp_vec(i) = _fPropVal[i];
+
579 }
+
580
+
581 fParCurr_PCA = TransferMatT*fParCurr_vec;
+
582 fParProp_PCA = TransferMatT*fParProp_vec;
+
583}
+
+
584
+
585// ********************************************
+
586// Transfer a parameter variation in the eigen basis to the parameter basis
+
+
587void covarianceBase::TransferToParam() {
+
588// ********************************************
+
589 if (!pca) {
+
590 MACH3LOG_ERROR("Can not transfer to PCA if PCA isn't enabled");
+
591 throw MaCh3Exception(__FILE__ , __LINE__ );
+
592 }
+
593
+
594 // Make the temporary vectors
+
595 TVectorD fParProp_vec = TransferMat*fParProp_PCA;
+
596 TVectorD fParCurr_vec = TransferMat*fParCurr_PCA;
+
597 #ifdef MULTITHREAD
+
598 #pragma omp parallel for
+
599 #endif
+
600 for (int i = 0; i < _fNumPar; ++i) {
+
601 _fPropVal[i] = fParProp_vec(i);
+
602 _fCurrVal[i] = fParCurr_vec(i);
+
603 }
+
604}
+
+
605// ********************************************
+
+
606std::vector<double> covarianceBase::getProposed() const {
+
607// ********************************************
+
608 std::vector<double> props(_fNumPar);
+
609 for (int i = 0; i < _fNumPar; ++i) props[i] = _fPropVal[i];
+
610 return props;
+
611}
+
+
612
+
613// Throw nominal values
+
+
614void covarianceBase::throwNominal(bool nomValues, int seed) {
+
615 TVectorD* vec = new TVectorD(_fNumPar);
+
616 for (int i = 0; i < _fNumPar; i++) {
+
617 (*vec)(i) = 1.0;
+
618 }
+
619
+
620 ThrowParms* nom_throws = new ThrowParms(*vec, (*covMatrix));
+
621 nom_throws->SetSeed(seed);
+
622 std::vector<double> nominal = getNominalArray();
+
623 nominal.clear();
+
624 nominal.resize(_fNumPar);
+
625
+
626 // If we want to put the nominals somewhere else than user specified
+
627 // Don't fully understand this though: won't we have to reweight the MC somehow?
+
628 // nominal[i] is used in GetLikelihood() as the penalty term, so we're essentially setting a random parameter penalty term?
+
629 if (!nomValues)
+
630 {
+
631 bool throw_again = true;
+
632
+
633 while(throw_again == true)
+
634 {
+
635 throw_again = false;
+
636 MACH3LOG_INFO("Setting {} nominal values to random throws.", getName());
+
637 nom_throws->ThrowSet(nominal);
+
638
+
639 for (int i = 0; i < _fNumPar; i++)
+
640 {
+
641 // if parameter is fixed, dont throw
+
642 if (_fError[i] < 0) {
+
643 nominal[i] = 1.0;
+
644 continue;
+
645 }
+
646
+
647 if (nominal[i] < 0) {
+
648 nominal[i] = 0.0;
+
649 throw_again = true;
+
650 }
+
651 }
+
652 }
+
653 } else {
+
654 // If we want nominal values, set all entries to 1 (defined as nominal in MaCh3)
+
655 for (int i = 0; i < int(nominal.size()); i++) {
+
656 nominal[i] = 1.0;
+
657 }
+
658 }
+
659
+
660 delete nom_throws;
+
661 delete vec;
+
662}
+
+
663
+
664// *************************************
+
665// Throw the parameters according to the covariance matrix
+
666// This shouldn't be used in MCMC code ase it can break Detailed Balance;
+
+
667void covarianceBase::throwParameters() {
+
668// *************************************
+
669 // First draw new randParams
+
670 randomize();
+
671
+
672 if (!pca) {
+
673 MatrixVectorMulti(corr_throw, throwMatrixCholDecomp, randParams, _fNumPar);
+
674
+
675 #ifdef MULTITHREAD
+
676 #pragma omp parallel for
+
677 #endif
+
678 for (int i = 0; i < _fNumPar; ++i) {
+
679 // Check if parameter is fixed first: if so don't randomly throw
+
680 if (isParameterFixed(i)) continue;
+
681
+
682 _fPropVal[i] = _fPreFitValue[i] + corr_throw[i];
+
683 int throws = 0;
+
684 // Try again if we the initial parameter proposal falls outside of the range of the parameter
+
685 while (_fPropVal[i] > _fUpBound[i] || _fPropVal[i] < _fLowBound[i]) {
+
686#ifdef MULTITHREAD
+
687 randParams[i] = random_number[omp_get_thread_num()]->Gaus(0, 1);
+
688#else
+
689 randParams[i] = random_number[0]->Gaus(0,1);
+
690#endif
+
691 const double corr_throw_single = MatrixVectorMultiSingle(throwMatrixCholDecomp, randParams, _fNumPar, i);
+
692 _fPropVal[i] = _fPreFitValue[i] + corr_throw_single;
+
693 if (throws > 10000)
+
694 {
+
695 //KS: Since we are multithreading there is danger that those messages
+
696 //will be all over the place, small price to pay for faster code
+
697 MACH3LOG_WARN("Tried {} times to throw parameter {} but failed", throws, i);
+
698 MACH3LOG_WARN("Matrix: {}", matrixName);
+
699 MACH3LOG_WARN("Param: {}", _fNames[i]);
+
700 MACH3LOG_WARN("Setting _fPropVal: {} to {}", _fPropVal[i], _fPreFitValue[i]);
+
701 MACH3LOG_WARN("I live at {}:{}", __FILE__, __LINE__);
+
702 _fPropVal[i] = _fPreFitValue[i];
+
703 //throw;
+
704 }
+
705 throws++;
+
706 }
+
707 _fCurrVal[i] = _fPropVal[i];
+
708 }
+
709 }
+
710 else
+
711 {
+
712 MACH3LOG_CRITICAL("Hold on, you are trying to run Prior Predicitve Code with PCA, which is wrong");
+
713 MACH3LOG_CRITICAL("Sorry I have to kill you, I mean your job");
+
714 throw;
+
715 }
+
716}
+
+
717
+
718// *************************************
+
719// Throw each parameter within their 1 sigma range
+
720// Used to start the chain in different states
+
+
721void covarianceBase::RandomConfiguration() {
+
722// *************************************
+
723 // Have the 1 sigma for each parameter in each covariance class, sweet!
+
724 // Don't want to change the nominal array because that's what determines our likelihood
+
725 // Want to change the fParProp, fParCurr, fParInit
+
726 // fParInit and the others will already be set
+
727 for (int i = 0; i < _fNumPar; ++i) {
+
728 // Check if parameter is fixed first: if so don't randomly throw
+
729 if (isParameterFixed(i)) continue;
+
730 // Check that the sigma range is larger than the parameter range
+
731 // If not, throw in the valid parameter range instead
+
732 const double paramrange = _fUpBound[i] - _fLowBound[i];
+
733 const double sigma = sqrt((*covMatrix)(i,i));
+
734 double throwrange = sigma;
+
735 if (paramrange < sigma) throwrange = paramrange;
+
736
+
737 _fPropVal[i] = _fPreFitValue[i] + random_number[0]->Gaus(0, 1)*throwrange;
+
738 // Try again if we the initial parameter proposal falls outside of the range of the parameter
+
739 // Really only relevant for the xsec parameters; the flux and ND280 have -999 and 999 set to the limits!
+
740 int throws = 0;
+
741 while (_fPropVal[i] > _fUpBound[i] || _fPropVal[i] < _fLowBound[i]) {
+
742 if (throws > 1000) {
+
743 MACH3LOG_WARN("Tried {} times to throw parameter {} but failed", throws, i);
+
744 MACH3LOG_WARN("Matrix: {}", matrixName);
+
745 MACH3LOG_WARN("Param: {}", _fNames[i]);
+
746 throw MaCh3Exception(__FILE__ , __LINE__ );
+
747 }
+
748 _fPropVal[i] = _fPreFitValue[i] + random_number[0]->Gaus(0, 1)*throwrange;
+
749 throws++;
+
750 }
+
751 MACH3LOG_INFO("Setting current step in {} param {} = {} from {}", matrixName, i, _fPropVal[i], _fCurrVal[i]);
+
752 _fCurrVal[i] = _fPropVal[i];
+
753 }
+
754 if (pca) TransferToPCA();
+
755}
+
+
756
+
757// *************************************
+
758// Set a single parameter
+
+
759void covarianceBase::setSingleParameter(const int parNo, const double parVal) {
+
760// *************************************
+
761 _fPropVal[parNo] = parVal;
+
762 _fCurrVal[parNo] = parVal;
+
763 MACH3LOG_DEBUG("Setting {}(parameter {}) to {}", GetParName(parNo), parNo, parVal);
+
764
+
765 if (pca) TransferToPCA();
+
766}
+
+
767// ********************************************
+
+
768void covarianceBase::setParCurrProp(const int parNo, const double parVal) {
+
769// ********************************************
+
770 _fPropVal[parNo] = parVal;
+
771 _fCurrVal[parNo] = parVal;
+
772 MACH3LOG_DEBUG("Setting {}(parameter {}) to {}", GetParName(parNo), parNo, parVal);
+
773
+
774 if (pca) TransferToPCA();
+
775}
+
+
776
+
777// ************************************************
778// Propose a step for the set of systematics parameters this covariance class holds
779void covarianceBase::proposeStep() {
-
780 // Make the random numbers for the step proposal
-
781 randomize();
-
782 CorrelateSteps();
-
783 if(use_adaptive){
-
784 updateAdaptiveCovariance();
-
785 total_steps++;
-
786 }
-
787}
-
-
788
-
789// ************************************************
-
790// "Randomize" the parameters in the covariance class for the proposed step
-
791// Used the proposal kernel and the current parameter value to set proposed step
-
792// Also get a new random number for the randParams
-
-
793void covarianceBase::randomize() {
-
794// ************************************************
-
795 if (!pca) {
-
796//KS: By multithreading here we gain at least factor 2 with 8 threads with ND only fit
-
797#ifdef MULTITHREAD
-
798#pragma omp parallel for
-
799#endif
-
800 for (int i = 0; i < _fNumPar; ++i) {
-
801 // If parameter isn't fixed
-
802 if (_fError[i] > 0.0) {
-
803#ifdef MULTITHREAD
-
804 randParams[i] = random_number[omp_get_thread_num()]->Gaus(0, 1);
-
805#else
-
806 randParams[i] = random_number[0]->Gaus(0, 1);
-
807#endif
-
808 // If parameter IS fixed
-
809 } else {
-
810 randParams[i] = 0.0;
-
811 }
-
812 } // end for
-
813 // If we're in the PCA basis we instead throw parameters there (only _fNumParPCA parameter)
-
814 } else {
-
815 // Scale the random parameters by the sqrt of eigen values for the throw
-
816#ifdef MULTITHREAD
-
817#pragma omp parallel for
-
818#endif
-
819 for (int i = 0; i < _fNumPar; ++i)
-
820 {
-
821 if (fParSigma_PCA[i] > 0. && i < _fNumParPCA)
-
822 {
-
823#ifdef MULTITHREAD
-
824 randParams[i] = random_number[omp_get_thread_num()]->Gaus(0,1);
-
825#else
-
826 randParams[i] = random_number[0]->Gaus(0,1);
-
827#endif
-
828 } else { // If parameter IS fixed or out od bounds
-
829 randParams[i] = 0.0;
-
830 }
-
831 }
-
832 }
-
833}
+
780// ************************************************
+
781 // Make the random numbers for the step proposal
+
782 randomize();
+
783 CorrelateSteps();
+
784 if(use_adaptive){
+
785 updateAdaptiveCovariance();
+
786 total_steps++;
+
787 }
+
788}
+
+
789
+
790// ************************************************
+
791// "Randomize" the parameters in the covariance class for the proposed step
+
792// Used the proposal kernel and the current parameter value to set proposed step
+
793// Also get a new random number for the randParams
+
+
794void covarianceBase::randomize() {
+
795// ************************************************
+
796 if (!pca) {
+
797//KS: By multithreading here we gain at least factor 2 with 8 threads with ND only fit
+
798 #ifdef MULTITHREAD
+
799 #pragma omp parallel for
+
800 #endif
+
801 for (int i = 0; i < _fNumPar; ++i) {
+
802 // If parameter isn't fixed
+
803 if (_fError[i] > 0.0) {
+
804#ifdef MULTITHREAD
+
805 randParams[i] = random_number[omp_get_thread_num()]->Gaus(0, 1);
+
806#else
+
807 randParams[i] = random_number[0]->Gaus(0, 1);
+
808#endif
+
809 // If parameter IS fixed
+
810 } else {
+
811 randParams[i] = 0.0;
+
812 }
+
813 } // end for
+
814 // If we're in the PCA basis we instead throw parameters there (only _fNumParPCA parameter)
+
815 } else {
+
816 // Scale the random parameters by the sqrt of eigen values for the throw
+
817 #ifdef MULTITHREAD
+
818 #pragma omp parallel for
+
819 #endif
+
820 for (int i = 0; i < _fNumPar; ++i)
+
821 {
+
822 if (fParSigma_PCA[i] > 0. && i < _fNumParPCA)
+
823 {
+
824#ifdef MULTITHREAD
+
825 randParams[i] = random_number[omp_get_thread_num()]->Gaus(0,1);
+
826#else
+
827 randParams[i] = random_number[0]->Gaus(0,1);
+
828#endif
+
829 } else { // If parameter IS fixed or out od bounds
+
830 randParams[i] = 0.0;
+
831 }
+
832 }
+
833 }
+
834}
-
834
835
-
836// ************************************************
-
837// Correlate the steps by setting the proposed step of a parameter to its current value + some correlated throw
-
-
838void covarianceBase::CorrelateSteps() {
-
839// ************************************************
-
840 //KS: Using custom function compared to ROOT one with 8 threads we have almost factor 2 performance increase, by replacing TMatrix with just double we increase it even more
-
841 MatrixVectorMulti(corr_throw, throwMatrixCholDecomp, randParams, _fNumPar);
-
842
-
843 // If not doing PCA
-
844 if (!pca) {
-
845#ifdef MULTITHREAD
-
846#pragma omp parallel for
-
847#endif
-
848 for (int i = 0; i < _fNumPar; ++i) {
-
849 if (_fError[i] > 0.) {
-
850 _fPropVal[i] = _fCurrVal[i] + corr_throw[i]*_fGlobalStepScale*_fIndivStepScale[i];
-
851 }
-
852 }
-
853 // If doing PCA throw uncorrelated in PCA basis (orthogonal basis by definition)
-
854 } else {
-
855 // Throw around the current step
-
856#ifdef MULTITHREAD
-
857#pragma omp parallel for
-
858#endif
-
859 for (int i = 0; i < _fNumParPCA; ++i)
-
860 {
-
861 if (fParSigma_PCA[i] > 0.)
-
862 {
-
863 double IndStepScale = 1.;
-
864 //KS: If undecomposed parameter apply individual step scale and Cholesky for better acceptance rate
-
865 if(isDecomposed_PCA[i] >= 0)
-
866 {
-
867 IndStepScale *= _fIndivStepScale[isDecomposed_PCA[i]];
-
868 IndStepScale *= corr_throw[isDecomposed_PCA[i]];
-
869 }
-
870 //If decomposed apply only random number
-
871 else
-
872 {
-
873 IndStepScale *= randParams[i];
-
874 //KS: All PCA-ed parameters have the same step scale
-
875 IndStepScale *= _fIndivStepScale[FirstPCAdpar];
-
876 }
-
877 fParProp_PCA(i) = fParCurr_PCA(i)+_fGlobalStepScale*IndStepScale*eigen_values_master[i];
-
878 }
-
879 }
-
880 // Then update the parameter basis
-
881 TransferToParam();
-
882 }
-
883}
-
-
884
-
885// Update so that current step becomes the previously proposed step
-
-
886void covarianceBase::acceptStep() {
-
887 if (!pca) {
-
888#ifdef MULTITHREAD
-
889#pragma omp parallel for
-
890#endif
-
891 for (int i = 0; i < _fNumPar; ++i) {
-
892 // Update state so that current state is proposed state
-
893 _fCurrVal[i] = _fPropVal[i];
-
894 }
-
895 } else {
-
896 // Update the book-keeping for the output
-
897#ifdef MULTITHREAD
-
898#pragma omp parallel for
-
899#endif
-
900 for (int i = 0; i < _fNumParPCA; ++i) {
-
901 fParCurr_PCA(i) = fParProp_PCA(i);
-
902 }
-
903 // Then update the parameter basis
-
904 TransferToParam();
-
905 }
-
906}
-
-
907
-
908// Throw the proposed parameter by mag sigma
-
909// Should really just have the user specify this throw by having argument double
-
-
910void covarianceBase::throwParProp(const double mag) {
-
911 randomize();
-
912 if (!pca) {
-
913 // Make the correlated throw
-
914 MatrixVectorMulti(corr_throw, throwMatrixCholDecomp, randParams, _fNumPar);
-
915 // Number of sigmas we throw
-
916 for (int i = 0; i < _fNumPar; i++) {
-
917 if (_fError[i] > 0.)
-
918 _fPropVal[i] = _fCurrVal[i] + corr_throw[i]*mag;
-
919 }
-
920 } else {
-
921 for (int i = 0; i < _fNumPar; i++) {
-
922 fParProp_PCA(i) = fParCurr_PCA(i)+mag*randParams[i];
-
923 }
-
924 // And update the fParCurr in the basis
-
925 // Then update the fParProp in the parameter basis using the transfer matrix, so likelihood is evaluated correctly
-
926 TVectorD proposed = TransferMat*fParProp_PCA;
-
927 for (int i = 0; i < _fNumPar; ++i) {
-
928 if (fParSigma_PCA[i] > 0.) {
-
929 _fPropVal[i] = proposed(i);
-
930 }
-
931 }
-
932 }
-
933}
-
-
934
-
935// Helper function to throw the current parameter by mag sigmas
-
936// Can study bias in MCMC with this; put different starting parameters
-
-
937void covarianceBase::throwParCurr(const double mag)
-
938{
-
939 randomize();
-
940 if (!pca) {
-
941 // Get the correlated throw vector
-
942 MatrixVectorMulti(corr_throw, throwMatrixCholDecomp, randParams, _fNumPar);
-
943 // The number of sigmas to throw
-
944 // Should probably have this as a default parameter input to the function instead
-
945 for (int i = 0; i < _fNumPar; i++) {
-
946 if (_fError[i] > 0.){
-
947 _fCurrVal[i] = corr_throw[i]*mag;
-
948 }
-
949 }
-
950 } else {
-
951 for (int i = 0; i < _fNumPar; i++) {
-
952 fParProp_PCA(i) = mag*randParams[i];
-
953 }
-
954 // And update the fParCurr in the basis
-
955 // Then update the fParProp in the parameter basis using the transfer matrix, so likelihood is evaluated correctly
-
956 TVectorD current = TransferMat*fParCurr_PCA;
-
957 for (int i = 0; i < _fNumPar; ++i) {
-
958 if (fParSigma_PCA[i] > 0.) {
-
959 _fCurrVal[i] = current(i);
-
960 }
-
961 }
-
962 }
-
963}
-
-
964
-
965// Function to print the nominal values
-
-
966void covarianceBase::printNominal() {
-
967 MACH3LOG_INFO("Prior values for {} covarianceBase:", getName());
-
968 for (int i = 0; i < _fNumPar; i++) {
-
969 MACH3LOG_INFO(" {} {} ", GetParFancyName(i), getParInit(i));
-
970 }
-
971}
-
-
972
-
973
-
974// ********************************************
-
975// Function to print the nominal, current and proposed values
-
-
976void covarianceBase::printNominalCurrProp() {
+
836
+
837// ************************************************
+
838// Correlate the steps by setting the proposed step of a parameter to its current value + some correlated throw
+
+
839void covarianceBase::CorrelateSteps() {
+
840// ************************************************
+
841 //KS: Using custom function compared to ROOT one with 8 threads we have almost factor 2 performance increase, by replacing TMatrix with just double we increase it even more
+
842 MatrixVectorMulti(corr_throw, throwMatrixCholDecomp, randParams, _fNumPar);
+
843
+
844 // If not doing PCA
+
845 if (!pca) {
+
846 #ifdef MULTITHREAD
+
847 #pragma omp parallel for
+
848 #endif
+
849 for (int i = 0; i < _fNumPar; ++i) {
+
850 if (_fError[i] > 0.) {
+
851 _fPropVal[i] = _fCurrVal[i] + corr_throw[i]*_fGlobalStepScale*_fIndivStepScale[i];
+
852 }
+
853 }
+
854 // If doing PCA throw uncorrelated in PCA basis (orthogonal basis by definition)
+
855 } else {
+
856 // Throw around the current step
+
857 #ifdef MULTITHREAD
+
858 #pragma omp parallel for
+
859 #endif
+
860 for (int i = 0; i < _fNumParPCA; ++i)
+
861 {
+
862 if (fParSigma_PCA[i] > 0.)
+
863 {
+
864 double IndStepScale = 1.;
+
865 //KS: If undecomposed parameter apply individual step scale and Cholesky for better acceptance rate
+
866 if(isDecomposed_PCA[i] >= 0)
+
867 {
+
868 IndStepScale *= _fIndivStepScale[isDecomposed_PCA[i]];
+
869 IndStepScale *= corr_throw[isDecomposed_PCA[i]];
+
870 }
+
871 //If decomposed apply only random number
+
872 else
+
873 {
+
874 IndStepScale *= randParams[i];
+
875 //KS: All PCA-ed parameters have the same step scale
+
876 IndStepScale *= _fIndivStepScale[FirstPCAdpar];
+
877 }
+
878 fParProp_PCA(i) = fParCurr_PCA(i)+_fGlobalStepScale*IndStepScale*eigen_values_master[i];
+
879 }
+
880 }
+
881 // Then update the parameter basis
+
882 TransferToParam();
+
883 }
+
884}
+
+
885// ********************************************
+
886// Update so that current step becomes the previously proposed step
+
+
887void covarianceBase::acceptStep() {
+
888// ********************************************
+
889 if (!pca) {
+
890 #ifdef MULTITHREAD
+
891 #pragma omp parallel for
+
892 #endif
+
893 for (int i = 0; i < _fNumPar; ++i) {
+
894 // Update state so that current state is proposed state
+
895 _fCurrVal[i] = _fPropVal[i];
+
896 }
+
897 } else {
+
898 // Update the book-keeping for the output
+
899 #ifdef MULTITHREAD
+
900 #pragma omp parallel for
+
901 #endif
+
902 for (int i = 0; i < _fNumParPCA; ++i) {
+
903 fParCurr_PCA(i) = fParProp_PCA(i);
+
904 }
+
905 // Then update the parameter basis
+
906 TransferToParam();
+
907 }
+
908}
+
+
909// ********************************************
+
910// Throw the proposed parameter by mag sigma
+
911// Should really just have the user specify this throw by having argument double
+
+
912void covarianceBase::throwParProp(const double mag) {
+
913// ********************************************
+
914 randomize();
+
915 if (!pca) {
+
916 // Make the correlated throw
+
917 MatrixVectorMulti(corr_throw, throwMatrixCholDecomp, randParams, _fNumPar);
+
918 // Number of sigmas we throw
+
919 for (int i = 0; i < _fNumPar; i++) {
+
920 if (_fError[i] > 0.)
+
921 _fPropVal[i] = _fCurrVal[i] + corr_throw[i]*mag;
+
922 }
+
923 } else {
+
924 for (int i = 0; i < _fNumPar; i++) {
+
925 fParProp_PCA(i) = fParCurr_PCA(i)+mag*randParams[i];
+
926 }
+
927 // And update the fParCurr in the basis
+
928 // Then update the fParProp in the parameter basis using the transfer matrix, so likelihood is evaluated correctly
+
929 TVectorD proposed = TransferMat*fParProp_PCA;
+
930 for (int i = 0; i < _fNumPar; ++i) {
+
931 if (fParSigma_PCA[i] > 0.) {
+
932 _fPropVal[i] = proposed(i);
+
933 }
+
934 }
+
935 }
+
936}
+
+
937
+
938// Helper function to throw the current parameter by mag sigmas
+
939// Can study bias in MCMC with this; put different starting parameters
+
+
940void covarianceBase::throwParCurr(const double mag)
+
941{
+
942 randomize();
+
943 if (!pca) {
+
944 // Get the correlated throw vector
+
945 MatrixVectorMulti(corr_throw, throwMatrixCholDecomp, randParams, _fNumPar);
+
946 // The number of sigmas to throw
+
947 // Should probably have this as a default parameter input to the function instead
+
948 for (int i = 0; i < _fNumPar; i++) {
+
949 if (_fError[i] > 0.){
+
950 _fCurrVal[i] = corr_throw[i]*mag;
+
951 }
+
952 }
+
953 } else {
+
954 for (int i = 0; i < _fNumPar; i++) {
+
955 fParProp_PCA(i) = mag*randParams[i];
+
956 }
+
957 // And update the fParCurr in the basis
+
958 // Then update the fParProp in the parameter basis using the transfer matrix, so likelihood is evaluated correctly
+
959 TVectorD current = TransferMat*fParCurr_PCA;
+
960 for (int i = 0; i < _fNumPar; ++i) {
+
961 if (fParSigma_PCA[i] > 0.) {
+
962 _fCurrVal[i] = current(i);
+
963 }
+
964 }
+
965 }
+
966}
+
+
967
+
968// Function to print the nominal values
+
+
969void covarianceBase::printNominal() {
+
970 MACH3LOG_INFO("Prior values for {} covarianceBase:", getName());
+
971 for (int i = 0; i < _fNumPar; i++) {
+
972 MACH3LOG_INFO(" {} {} ", GetParFancyName(i), getParInit(i));
+
973 }
+
974}
+
+
975
+
976
977// ********************************************
-
978 MACH3LOG_INFO("Printing parameters for {}", getName());
-
979 // Dump out the PCA parameters too
-
980 if (pca) {
-
981 MACH3LOG_INFO("PCA:");
-
982 for (int i = 0; i < _fNumParPCA; ++i) {
-
983 MACH3LOG_INFO("PCA {:<2} Current: {:<10.2f} Proposed: {:<10.2f}", i, fParCurr_PCA(i), fParProp_PCA(i));
-
984 }
-
985 }
-
986 MACH3LOG_INFO("{:<30} {:<10} {:<10} {:<10}", "Name", "Prior", "Current", "Proposed");
-
987 for (int i = 0; i < _fNumPar; ++i) {
-
988 MACH3LOG_INFO("{:<30} {:<10.2f} {:<10.2f} {:<10.2f}", GetParFancyName(i), _fPreFitValue[i], _fCurrVal[i], _fPropVal[i]);
-
989 }
-
990 //KS: "\n" is faster performance wise, keep std::endl at the end to flush just in case, also looks pretty
-
991 //std::cout << std::endl;
-
992}
-
-
993
-
994// ********************************************
-
995// Get the likelihood in the case where we want to include priors on the parameters
-
996// fParEvalLikelihood stores if we want to evaluate the likelihood for the given parameter
-
997// true = evaluate likelihood (so run with a prior)
-
998// false = don't evaluate likelihood (so run without a prior)
-
-
999double covarianceBase::CalcLikelihood() {
-
1000// ********************************************
-
1001
-
1002 double logL = 0.0;
-
1003 #ifdef MULTITHREAD
-
1004 #pragma omp parallel for reduction(+:logL)
-
1005 #endif
-
1006 for(int i = 0; i < _fNumPar; ++i){
-
1007 for (int j = 0; j <= i; ++j) {
-
1008 if (!_fFlatPrior[i] && !_fFlatPrior[j]) {
-
1009 //KS: Since matrix is symmetric we can calculate non diagonal elements only once and multiply by 2, can bring up to factor speed decrease.
-
1010 short int scale = (i != j) ? 2 : 1;
-
1011 logL += scale * 0.5*(_fPropVal[i] - _fPreFitValue[i])*(_fPropVal[j] - _fPreFitValue[j])*InvertCovMatrix[i][j];
-
1012 }
-
1013 }
-
1014 }
-
1015 return logL;
-
1016}
-
-
1017
-
1018// ********************************************
-
-
1019int covarianceBase::CheckBounds() {
-
1020// ********************************************
-
1021
-
1022 int NOutside = 0;
-
1023 #ifdef MULTITHREAD
-
1024 #pragma omp parallel for reduction(+:NOutside)
-
1025 #endif
-
1026 for (int i = 0; i < _fNumPar; ++i){
-
1027 if(_fPropVal[i] > _fUpBound[i] || _fPropVal[i] < _fLowBound[i]){
-
1028 NOutside++;
-
1029 }
-
1030 }
-
1031 return NOutside;
-
1032}
-
-
1033// ********************************************
-
-
1034double covarianceBase::GetLikelihood() {
-
1035// ********************************************
-
1036
-
1037 // Checkbounds and calclikelihood are virtual
-
1038 // Default behaviour is to reject negative values + do std llh calculation
-
1039 const int NOutside = CheckBounds();
-
1040
-
1041 if(NOutside > 0)
-
1042 return NOutside*_LARGE_LOGL_;
-
1043
-
1044 return CalcLikelihood();
-
1045}
-
-
1046
-
1047// ********************************************
-
-
1048void covarianceBase::printPars() {
+
978// Function to print the nominal, current and proposed values
+
+
979void covarianceBase::printNominalCurrProp() {
+
980// ********************************************
+
981 MACH3LOG_INFO("Printing parameters for {}", getName());
+
982 // Dump out the PCA parameters too
+
983 if (pca) {
+
984 MACH3LOG_INFO("PCA:");
+
985 for (int i = 0; i < _fNumParPCA; ++i) {
+
986 MACH3LOG_INFO("PCA {:<2} Current: {:<10.2f} Proposed: {:<10.2f}", i, fParCurr_PCA(i), fParProp_PCA(i));
+
987 }
+
988 }
+
989 MACH3LOG_INFO("{:<30} {:<10} {:<10} {:<10}", "Name", "Prior", "Current", "Proposed");
+
990 for (int i = 0; i < _fNumPar; ++i) {
+
991 MACH3LOG_INFO("{:<30} {:<10.2f} {:<10.2f} {:<10.2f}", GetParFancyName(i), _fPreFitValue[i], _fCurrVal[i], _fPropVal[i]);
+
992 }
+
993 //KS: "\n" is faster performance wise, keep std::endl at the end to flush just in case, also looks pretty
+
994 //std::cout << std::endl;
+
995}
+
+
996
+
997// ********************************************
+
998// Get the likelihood in the case where we want to include priors on the parameters
+
999// fParEvalLikelihood stores if we want to evaluate the likelihood for the given parameter
+
1000// true = evaluate likelihood (so run with a prior)
+
1001// false = don't evaluate likelihood (so run without a prior)
+
+
1002double covarianceBase::CalcLikelihood() {
+
1003// ********************************************
+
1004
+
1005 double logL = 0.0;
+
1006 #ifdef MULTITHREAD
+
1007 #pragma omp parallel for reduction(+:logL)
+
1008 #endif
+
1009 for(int i = 0; i < _fNumPar; ++i){
+
1010 for (int j = 0; j <= i; ++j) {
+
1011 if (!_fFlatPrior[i] && !_fFlatPrior[j]) {
+
1012 //KS: Since matrix is symmetric we can calculate non diagonal elements only once and multiply by 2, can bring up to factor speed decrease.
+
1013 short int scale = (i != j) ? 2 : 1;
+
1014 logL += scale * 0.5*(_fPropVal[i] - _fPreFitValue[i])*(_fPropVal[j] - _fPreFitValue[j])*InvertCovMatrix[i][j];
+
1015 }
+
1016 }
+
1017 }
+
1018 return logL;
+
1019}
+
+
1020
+
1021// ********************************************
+
+
1022int covarianceBase::CheckBounds() {
+
1023// ********************************************
+
1024
+
1025 int NOutside = 0;
+
1026 #ifdef MULTITHREAD
+
1027 #pragma omp parallel for reduction(+:NOutside)
+
1028 #endif
+
1029 for (int i = 0; i < _fNumPar; ++i){
+
1030 if(_fPropVal[i] > _fUpBound[i] || _fPropVal[i] < _fLowBound[i]){
+
1031 NOutside++;
+
1032 }
+
1033 }
+
1034 return NOutside;
+
1035}
+
+
1036// ********************************************
+
+
1037double covarianceBase::GetLikelihood() {
+
1038// ********************************************
+
1039 // Checkbounds and calclikelihood are virtual
+
1040 // Default behaviour is to reject negative values + do std llh calculation
+
1041 const int NOutside = CheckBounds();
+
1042
+
1043 if(NOutside > 0)
+
1044 return NOutside*_LARGE_LOGL_;
+
1045
+
1046 return CalcLikelihood();
+
1047}
+
+
1048
1049// ********************************************
-
1050 MACH3LOG_INFO("Number of pars: {}", _fNumPar);
-
1051 MACH3LOG_INFO("Current {} parameters:", matrixName);
-
1052 for(int i = 0; i < _fNumPar; i++) {
-
1053 std::cout << std::fixed << std::setprecision(5) << _fNames[i].c_str() << " current: \t" << _fCurrVal[i] << " \tproposed: \t" << _fPropVal[i] << std::endl;
-
1054 }
-
1055 return;
-
1056}
-
-
1057
-
1058// ********************************************
-
1059// Sets the proposed parameters to the nominal values
-
-
1060void covarianceBase::setParameters(const std::vector<double>& pars) {
-
1061// ********************************************
-
1062 // If empty, set the proposed to nominal
-
1063 if (pars.empty()) {
-
1064 // For xsec this means setting to the prior (because nominal is the prior)
-
1065 for (int i = 0; i < _fNumPar; i++) {
-
1066 _fPropVal[i] = _fPreFitValue[i];
-
1067 }
-
1068 // If not empty, set the parameters to the specified
-
1069 } else {
-
1070 if (pars.size() != size_t(_fNumPar)) {
-
1071 MACH3LOG_ERROR("Warning: parameter arrays of incompatible size! Not changing parameters! {} has size {} but was expecting {}", matrixName, pars.size(), _fNumPar);
-
1072 throw;
-
1073 }
-
1074
-
1075 unsigned int parsSize = pars.size();
-
1076 for (unsigned int i = 0; i < parsSize; i++) {
-
1077 //Make sure that you are actually passing a number to set the parameter to
-
1078 if(std::isnan(pars[i])) {
-
1079 std::cerr << "Error: trying to set parameter value to a nan for parameter " << GetParName(i) << " in matrix " << matrixName << ". This will not go well!" << std::endl;
-
1080 throw;
-
1081 } else {
-
1082 _fPropVal[i] = pars[i];
-
1083 }
-
1084 }
-
1085 }
-
1086
-
1087 // And if pca make the transfer
-
1088 if (pca) {
-
1089 TransferToPCA();
-
1090 TransferToParam();
-
1091 }
-
1092 return;
-
1093}
-
-
1094
-
1095// ********************************************
-
-
1096void covarianceBase::SetBranches(TTree &tree, bool SaveProposal) {
+
+
1050void covarianceBase::printPars() {
+
1051// ********************************************
+
1052 MACH3LOG_INFO("Number of pars: {}", _fNumPar);
+
1053 MACH3LOG_INFO("Current {} parameters:", matrixName);
+
1054 for(int i = 0; i < _fNumPar; i++) {
+
1055 std::cout << std::fixed << std::setprecision(5) << _fNames[i].c_str() << " current: \t" << _fCurrVal[i] << " \tproposed: \t" << _fPropVal[i] << std::endl;
+
1056 }
+
1057 return;
+
1058}
+
+
1059
+
1060// ********************************************
+
1061// Sets the proposed parameters to the nominal values
+
+
1062void covarianceBase::setParameters(const std::vector<double>& pars) {
+
1063// ********************************************
+
1064 // If empty, set the proposed to nominal
+
1065 if (pars.empty()) {
+
1066 // For xsec this means setting to the prior (because nominal is the prior)
+
1067 for (int i = 0; i < _fNumPar; i++) {
+
1068 _fPropVal[i] = _fPreFitValue[i];
+
1069 }
+
1070 // If not empty, set the parameters to the specified
+
1071 } else {
+
1072 if (pars.size() != size_t(_fNumPar)) {
+
1073 MACH3LOG_ERROR("Warning: parameter arrays of incompatible size! Not changing parameters! {} has size {} but was expecting {}", matrixName, pars.size(), _fNumPar);
+
1074 throw;
+
1075 }
+
1076
+
1077 unsigned int parsSize = pars.size();
+
1078 for (unsigned int i = 0; i < parsSize; i++) {
+
1079 //Make sure that you are actually passing a number to set the parameter to
+
1080 if(std::isnan(pars[i])) {
+
1081 std::cerr << "Error: trying to set parameter value to a nan for parameter " << GetParName(i) << " in matrix " << matrixName << ". This will not go well!" << std::endl;
+
1082 throw;
+
1083 } else {
+
1084 _fPropVal[i] = pars[i];
+
1085 }
+
1086 }
+
1087 }
+
1088
+
1089 // And if pca make the transfer
+
1090 if (pca) {
+
1091 TransferToPCA();
+
1092 TransferToParam();
+
1093 }
+
1094 return;
+
1095}
+
+
1096
1097// ********************************************
-
1098
-
1099 // loop over parameters and set a branch
-
1100 for (int i = 0; i < _fNumPar; ++i) {
-
1101 tree.Branch(_fNames[i].c_str(), &_fCurrVal[i], Form("%s/D", _fNames[i].c_str()));
-
1102 }
-
1103 // When running PCA, also save PCA parameters
-
1104 if (pca) {
-
1105 for (int i = 0; i < _fNumParPCA; ++i) {
-
1106 tree.Branch(Form("%s_PCA", _fNames[i].c_str()), (double*)&(fParCurr_PCA.GetMatrixArray()[i]), Form("%s_PCA/D", _fNames[i].c_str()));
-
1107 }
-
1108 }
-
1109 if(SaveProposal)
-
1110 {
-
1111 // loop over parameters and set a branch
-
1112 for (int i = 0; i < _fNumPar; ++i) {
-
1113 tree.Branch(Form("%s_Prop", _fNames[i].c_str()), &_fPropVal[i], Form("%s_Prop/D", _fNames[i].c_str()));
-
1114 }
-
1115 // When running PCA, also save PCA parameters
-
1116 if (pca) {
-
1117 for (int i = 0; i < _fNumParPCA; ++i) {
-
1118 tree.Branch(Form("%s_PCA_Prop", _fNames[i].c_str()), (double*)&(fParProp_PCA.GetMatrixArray()[i]), Form("%s_PCA_Prop/D", _fNames[i].c_str()));
-
1119 }
-
1120 }
-
1121 }
-
1122}
+
+
1098void covarianceBase::SetBranches(TTree &tree, bool SaveProposal) {
+
1099// ********************************************
+
1100
+
1101 // loop over parameters and set a branch
+
1102 for (int i = 0; i < _fNumPar; ++i) {
+
1103 tree.Branch(_fNames[i].c_str(), &_fCurrVal[i], Form("%s/D", _fNames[i].c_str()));
+
1104 }
+
1105 // When running PCA, also save PCA parameters
+
1106 if (pca) {
+
1107 for (int i = 0; i < _fNumParPCA; ++i) {
+
1108 tree.Branch(Form("%s_PCA", _fNames[i].c_str()), (double*)&(fParCurr_PCA.GetMatrixArray()[i]), Form("%s_PCA/D", _fNames[i].c_str()));
+
1109 }
+
1110 }
+
1111 if(SaveProposal)
+
1112 {
+
1113 // loop over parameters and set a branch
+
1114 for (int i = 0; i < _fNumPar; ++i) {
+
1115 tree.Branch(Form("%s_Prop", _fNames[i].c_str()), &_fPropVal[i], Form("%s_Prop/D", _fNames[i].c_str()));
+
1116 }
+
1117 // When running PCA, also save PCA parameters
+
1118 if (pca) {
+
1119 for (int i = 0; i < _fNumParPCA; ++i) {
+
1120 tree.Branch(Form("%s_PCA_Prop", _fNames[i].c_str()), (double*)&(fParProp_PCA.GetMatrixArray()[i]), Form("%s_PCA_Prop/D", _fNames[i].c_str()));
+
1121 }
+
1122 }
+
1123 }
+
1124}
-
1123// ********************************************
-
-
1124void covarianceBase::setStepScale(const double scale) {
1125// ********************************************
-
1126 if(scale == 0)
-
1127 {
-
1128 MACH3LOG_ERROR("You are trying so set StepScale to 0 this will not work");
-
1129 throw;
-
1130 }
-
1131 MACH3LOG_INFO("{} setStepScale() = {}", getName(), scale);
-
1132 _fGlobalStepScale = scale;
-
1133}
-
-
1134
-
1135// ********************************************
-
-
1136void covarianceBase::toggleFixAllParameters() {
+
+
1126void covarianceBase::setStepScale(const double scale) {
+
1127// ********************************************
+
1128 if(scale == 0)
+
1129 {
+
1130 MACH3LOG_ERROR("You are trying so set StepScale to 0 this will not work");
+
1131 throw;
+
1132 }
+
1133 MACH3LOG_INFO("{} setStepScale() = {}", getName(), scale);
+
1134 _fGlobalStepScale = scale;
+
1135}
+
+
1136
1137// ********************************************
-
1138 // fix or unfix all parameters by multiplying by -1
-
1139 if(!pca)
-
1140 {
-
1141 for (int i = 0; i < _fNumPar; i++) _fError[i] *= -1.0;
-
1142 } else{
-
1143 for (int i = 0; i < _fNumParPCA; i++) fParSigma_PCA[i] *= -1.0;
-
1144 }
-
1145 return;
-
1146}
-
-
1147
-
1148// ********************************************
-
-
1149void covarianceBase::toggleFixParameter(const int i) {
+
+
1138void covarianceBase::toggleFixAllParameters() {
+
1139// ********************************************
+
1140 // fix or unfix all parameters by multiplying by -1
+
1141 if(!pca)
+
1142 {
+
1143 for (int i = 0; i < _fNumPar; i++) _fError[i] *= -1.0;
+
1144 } else{
+
1145 for (int i = 0; i < _fNumParPCA; i++) fParSigma_PCA[i] *= -1.0;
+
1146 }
+
1147 return;
+
1148}
+
+
1149
1150// ********************************************
-
1151 if(!pca) {
-
1152 if (i > _fNumPar) {
-
1153 MACH3LOG_ERROR("Can't toggleFixParameter for parameter {} because size of covariance ={}", i, _fNumPar);
-
1154 MACH3LOG_ERROR("Fix this in your config file please!");
-
1155 throw;
-
1156 } else {
-
1157 _fError[i] *= -1.0;
-
1158 MACH3LOG_INFO("Setting {}(parameter {}) to fixed at {}", GetParFancyName(i), i, _fCurrVal[i]);
-
1159 }
-
1160 } else {
-
1161 int isDecom = -1;
-
1162 for (int im = 0; im < _fNumParPCA; ++im) {
-
1163 if(isDecomposed_PCA[im] == i) {isDecom = im;}
-
1164 }
-
1165 if(isDecom < 0) {
-
1166 MACH3LOG_ERROR("Parameter {} is PCA decomposed can't fix this", GetParName(i));
-
1167 //throw;
-
1168 } else {
-
1169 fParSigma_PCA[isDecom] *= -1.0;
-
1170 MACH3LOG_INFO("Setting un-decomposed {}(parameter {}/{} in PCA base) to fixed at {}", GetParName(i), i, isDecom, _fCurrVal[i]);
-
1171 }
-
1172 }
-
1173
-
1174 return;
-
1175}
-
-
1176
-
1177// ********************************************
-
-
1178void covarianceBase::toggleFixParameter(const std::string& name) {
-
1179// ********************************************
-
1180 for (int i = 0; i <_fNumPar; ++i) {
-
1181 if(name == _fFancyNames[i]) {
-
1182 toggleFixParameter(i);
-
1183 return;
-
1184 }
-
1185 }
-
1186 MACH3LOG_WARN("I couldn't find parameter with name {}, therefore will not fix it", name);
-
1187}
-
-
1188
-
1189// ********************************************
-
-
1190bool covarianceBase::isParameterFixed(const std::string& name) {
-
1191// ********************************************
-
1192 for (int i = 0; i <_fNumPar; ++i) {
-
1193 if(name == _fFancyNames[i]) {
-
1194 return isParameterFixed(i);
-
1195 }
-
1196 }
-
1197 MACH3LOG_WARN("I couldn't find parameter with name {}, therefore will not fix it", name);
-
1198 return false;
-
1199}
-
-
1200
-
1201// ********************************************
-
-
1202void covarianceBase::setFlatPrior(const int i, const bool eL) {
-
1203// ********************************************
-
1204 if (i > _fNumPar) {
-
1205 MACH3LOG_INFO("Can't setEvalLikelihood for Cov={}/Param={} because size of Covariance = {}", getName(), i, _fNumPar);
-
1206 MACH3LOG_ERROR("Fix this in your config file please!");
-
1207 throw;
-
1208 } else {
-
1209 if(eL){
-
1210 MACH3LOG_INFO("Setting {} (parameter {}) to flat prior", GetParName(i), i);
-
1211 }
-
1212 else{
-
1213 // HW :: This is useful
-
1214 MACH3LOG_INFO("Setting {} (parameter {}) to non-flat prior", GetParName(i), i);
-
1215 }
-
1216 _fFlatPrior[i] = eL;
-
1217 }
-
1218}
-
-
1219
-
1220// ********************************************
-
1221//KS: Custom function to perform multiplication of matrix and vector with multithreading
-
-
1222void covarianceBase::MatrixVectorMulti(double* _restrict_ VecMulti, double** _restrict_ matrix, const double* _restrict_ vector, const int n) {
-
1223// ********************************************
-
1224 #ifdef MULTITHREAD
-
1225 #pragma omp parallel for
-
1226 #endif
-
1227 for (int i = 0; i < n; ++i)
-
1228 {
-
1229 double result = 0.0;
-
1230 for (int j = 0; j < n; ++j)
-
1231 {
-
1232 result += matrix[i][j]*vector[j];
-
1233 }
-
1234 VecMulti[i] = result;
-
1235 }
-
1236}
-
-
1237
-
1238// ********************************************
-
-
1239double covarianceBase::MatrixVectorMultiSingle(double** _restrict_ matrix, const double* _restrict_ vector, const int Length, const int i) {
-
1240// ********************************************
-
1241
-
1242 double Element = 0.0;
-
1243 for (int j = 0; j < Length; ++j) {
-
1244 Element += matrix[i][j]*vector[j];
-
1245 }
-
1246 return Element;
-
1247}
-
-
1248
-
1249// ********************************************
-
-
1250void covarianceBase::setIndivStepScale(const std::vector<double>& stepscale) {
-
1251// ********************************************
-
1252
+
+
1151void covarianceBase::toggleFixParameter(const int i) {
+
1152// ********************************************
+
1153 if(!pca) {
+
1154 if (i > _fNumPar) {
+
1155 MACH3LOG_ERROR("Can't toggleFixParameter for parameter {} because size of covariance ={}", i, _fNumPar);
+
1156 MACH3LOG_ERROR("Fix this in your config file please!");
+
1157 throw;
+
1158 } else {
+
1159 _fError[i] *= -1.0;
+
1160 MACH3LOG_INFO("Setting {}(parameter {}) to fixed at {}", GetParFancyName(i), i, _fCurrVal[i]);
+
1161 }
+
1162 } else {
+
1163 int isDecom = -1;
+
1164 for (int im = 0; im < _fNumParPCA; ++im) {
+
1165 if(isDecomposed_PCA[im] == i) {isDecom = im;}
+
1166 }
+
1167 if(isDecom < 0) {
+
1168 MACH3LOG_ERROR("Parameter {} is PCA decomposed can't fix this", GetParName(i));
+
1169 //throw;
+
1170 } else {
+
1171 fParSigma_PCA[isDecom] *= -1.0;
+
1172 MACH3LOG_INFO("Setting un-decomposed {}(parameter {}/{} in PCA base) to fixed at {}", GetParName(i), i, isDecom, _fCurrVal[i]);
+
1173 }
+
1174 }
+
1175 return;
+
1176}
+
+
1177
+
1178// ********************************************
+
+
1179void covarianceBase::toggleFixParameter(const std::string& name) {
+
1180// ********************************************
+
1181 for (int i = 0; i <_fNumPar; ++i) {
+
1182 if(name == _fFancyNames[i]) {
+
1183 toggleFixParameter(i);
+
1184 return;
+
1185 }
+
1186 }
+
1187 MACH3LOG_WARN("I couldn't find parameter with name {}, therefore will not fix it", name);
+
1188}
+
+
1189
+
1190// ********************************************
+
+
1191bool covarianceBase::isParameterFixed(const std::string& name) {
+
1192// ********************************************
+
1193 for (int i = 0; i <_fNumPar; ++i) {
+
1194 if(name == _fFancyNames[i]) {
+
1195 return isParameterFixed(i);
+
1196 }
+
1197 }
+
1198 MACH3LOG_WARN("I couldn't find parameter with name {}, therefore will not fix it", name);
+
1199 return false;
+
1200}
+
+
1201
+
1202// ********************************************
+
+
1203void covarianceBase::setFlatPrior(const int i, const bool eL) {
+
1204// ********************************************
+
1205 if (i > _fNumPar) {
+
1206 MACH3LOG_INFO("Can't setEvalLikelihood for Cov={}/Param={} because size of Covariance = {}", getName(), i, _fNumPar);
+
1207 MACH3LOG_ERROR("Fix this in your config file please!");
+
1208 throw;
+
1209 } else {
+
1210 if(eL){
+
1211 MACH3LOG_INFO("Setting {} (parameter {}) to flat prior", GetParName(i), i);
+
1212 }
+
1213 else{
+
1214 // HW :: This is useful
+
1215 MACH3LOG_INFO("Setting {} (parameter {}) to non-flat prior", GetParName(i), i);
+
1216 }
+
1217 _fFlatPrior[i] = eL;
+
1218 }
+
1219}
+
+
1220
+
1221// ********************************************
+
1222//KS: Custom function to perform multiplication of matrix and vector with multithreading
+
+
1223void covarianceBase::MatrixVectorMulti(double* _restrict_ VecMulti, double** _restrict_ matrix, const double* _restrict_ vector, const int n) {
+
1224// ********************************************
+
1225 #ifdef MULTITHREAD
+
1226 #pragma omp parallel for
+
1227 #endif
+
1228 for (int i = 0; i < n; ++i)
+
1229 {
+
1230 double result = 0.0;
+
1231 for (int j = 0; j < n; ++j)
+
1232 {
+
1233 result += matrix[i][j]*vector[j];
+
1234 }
+
1235 VecMulti[i] = result;
+
1236 }
+
1237}
+
+
1238
+
1239// ********************************************
+
+
1240double covarianceBase::MatrixVectorMultiSingle(double** _restrict_ matrix, const double* _restrict_ vector, const int Length, const int i) {
+
1241// ********************************************
+
1242
+
1243 double Element = 0.0;
+
1244 for (int j = 0; j < Length; ++j) {
+
1245 Element += matrix[i][j]*vector[j];
+
1246 }
+
1247 return Element;
+
1248}
+
+
1249
+
1250// ********************************************
+
+
1251void covarianceBase::setIndivStepScale(const std::vector<double>& stepscale) {
+
1252// ********************************************
1253 if ((int)stepscale.size() != _fNumPar)
1254 {
1255 MACH3LOG_WARN("Stepscale vector not equal to number of parameters. Quitting..");
@@ -1450,952 +1450,755 @@
1278 std::cout << "============================================================" << std::endl;
1279}
-
1280
+
1280// ********************************************
1281//Makes sure that matrix is positive-definite (so no error is thrown when
1282//throwNominal() is called) by adding a small number to on-diagonal elements
1283void covarianceBase::MakePosDef(TMatrixDSym *cov) {
-
1284 //DB Save original warning state and then increase it in this function to suppress 'matrix not positive definite' messages
-
1285 //Means we no longer need to overload
-
1286 if(cov == nullptr){
-
1287 cov = &*covMatrix;
-
1288 }
-
1289
-
1290 int originalErrorWarning = gErrorIgnoreLevel;
-
1291 gErrorIgnoreLevel = kFatal;
-
1292
-
1293 //DB Loop 1000 times adding 1e-9 which tops out at 1e-6 shift on the diagonal before throwing error
-
1294 int MaxAttempts = 1e5;
-
1295 int iAttempt = 0;
-
1296 bool CanDecomp = false;
-
1297 TDecompChol chdcmp;
-
1298
-
1299 for (iAttempt = 0; iAttempt < MaxAttempts; iAttempt++) {
-
1300 chdcmp = TDecompChol(*cov);
-
1301 if (chdcmp.Decompose()) {
-
1302 CanDecomp = true;
-
1303 break;
-
1304 } else {
-
1305#ifdef MULTITHREAD
-
1306#pragma omp parallel for
-
1307#endif
-
1308 for (int iVar = 0 ; iVar < _fNumPar; iVar++) {
-
1309 (*cov)(iVar,iVar) += pow(10,-9);
-
1310 }
-
1311 }
-
1312 }
-
1313
-
1314 if (!CanDecomp) {
-
1315 MACH3LOG_ERROR("Tried {} times to shift diagonal but still can not decompose the matrix", MaxAttempts);
-
1316 MACH3LOG_ERROR("This indicates that something is wrong with the input matrix");
-
1317 throw;
-
1318 }
-
1319 if(total_steps < 2) {
-
1320 MACH3LOG_INFO("Had to shift diagonal {} time(s) to allow the covariance matrix to be decomposed", iAttempt);
-
1321 }
-
1322 //DB Resetting warning level
-
1323 gErrorIgnoreLevel = originalErrorWarning;
-
1324
-
1325 return;
-
1326}
-
-
1327
-
-
1328void covarianceBase::resetIndivStepScale() {
-
1329 std::vector<double> stepScales(_fNumPar);
-
1330 for (int i = 0; i <_fNumPar; i++) {
-
1331 stepScales[i] = 1.;
-
1332 }
-
1333 _fGlobalStepScale = 1.0;
-
1334 setIndivStepScale(stepScales);
-
1335}
-
-
1336
-
1337// HW: Code for throwing from separate throw matrix, needs to be set after init to ensure pos-def
-
-
1338void covarianceBase::setThrowMatrix(TMatrixDSym *cov){
-
1339 if (cov == NULL) {
-
1340 MACH3LOG_ERROR("Could not find covariance matrix you provided to setThrowMatrix");
-
1341 throw MaCh3Exception(__FILE__ , __LINE__ );
-
1342 }
-
1343
-
1344 if (covMatrix->GetNrows() != cov->GetNrows()) {
-
1345 MACH3LOG_ERROR("Matrix given for throw Matrix is not the same size as the covariance matrix stored in object!");
-
1346 std::cerr << "Stored covariance matrix size:" << covMatrix->GetNrows() << std::endl;
-
1347 std::cerr << "Given matrix size:" << cov->GetNrows() << std::endl;
-
1348 throw MaCh3Exception(__FILE__ , __LINE__ );
-
1349 }
-
1350
-
1351 throwMatrix = (TMatrixDSym*)cov->Clone();
-
1352 if(use_adaptive && total_steps <= adaption_struct.start_adaptive_throw) makeClosestPosDef(throwMatrix);
-
1353 else MakePosDef(throwMatrix);
-
1354
-
1355 TDecompChol TDecompChol_throwMatrix(*throwMatrix);
+
1284// ********************************************
+
1285 //DB Save original warning state and then increase it in this function to suppress 'matrix not positive definite' messages
+
1286 //Means we no longer need to overload
+
1287 if(cov == nullptr){
+
1288 cov = &*covMatrix;
+
1289 }
+
1290
+
1291 int originalErrorWarning = gErrorIgnoreLevel;
+
1292 gErrorIgnoreLevel = kFatal;
+
1293
+
1294 //DB Loop 1000 times adding 1e-9 which tops out at 1e-6 shift on the diagonal before throwing error
+
1295 int MaxAttempts = 1e5;
+
1296 int iAttempt = 0;
+
1297 bool CanDecomp = false;
+
1298 TDecompChol chdcmp;
+
1299
+
1300 for (iAttempt = 0; iAttempt < MaxAttempts; iAttempt++) {
+
1301 chdcmp = TDecompChol(*cov);
+
1302 if (chdcmp.Decompose()) {
+
1303 CanDecomp = true;
+
1304 break;
+
1305 } else {
+
1306 #ifdef MULTITHREAD
+
1307 #pragma omp parallel for
+
1308 #endif
+
1309 for (int iVar = 0 ; iVar < _fNumPar; iVar++) {
+
1310 (*cov)(iVar,iVar) += pow(10,-9);
+
1311 }
+
1312 }
+
1313 }
+
1314
+
1315 if (!CanDecomp) {
+
1316 MACH3LOG_ERROR("Tried {} times to shift diagonal but still can not decompose the matrix", MaxAttempts);
+
1317 MACH3LOG_ERROR("This indicates that something is wrong with the input matrix");
+
1318 throw;
+
1319 }
+
1320 if(total_steps < 2) {
+
1321 MACH3LOG_INFO("Had to shift diagonal {} time(s) to allow the covariance matrix to be decomposed", iAttempt);
+
1322 }
+
1323 //DB Resetting warning level
+
1324 gErrorIgnoreLevel = originalErrorWarning;
+
1325
+
1326 return;
+
1327}
+
+
1328// ********************************************
+
+
1329void covarianceBase::resetIndivStepScale() {
+
1330// ********************************************
+
1331 std::vector<double> stepScales(_fNumPar);
+
1332 for (int i = 0; i <_fNumPar; i++) {
+
1333 stepScales[i] = 1.;
+
1334 }
+
1335 _fGlobalStepScale = 1.0;
+
1336 setIndivStepScale(stepScales);
+
1337}
+
+
1338
+
1339// HW: Code for throwing from separate throw matrix, needs to be set after init to ensure pos-def
+
+
1340void covarianceBase::setThrowMatrix(TMatrixDSym *cov){
+
1341 if (cov == NULL) {
+
1342 MACH3LOG_ERROR("Could not find covariance matrix you provided to setThrowMatrix");
+
1343 throw MaCh3Exception(__FILE__ , __LINE__ );
+
1344 }
+
1345
+
1346 if (covMatrix->GetNrows() != cov->GetNrows()) {
+
1347 MACH3LOG_ERROR("Matrix given for throw Matrix is not the same size as the covariance matrix stored in object!");
+
1348 std::cerr << "Stored covariance matrix size:" << covMatrix->GetNrows() << std::endl;
+
1349 std::cerr << "Given matrix size:" << cov->GetNrows() << std::endl;
+
1350 throw MaCh3Exception(__FILE__ , __LINE__ );
+
1351 }
+
1352
+
1353 throwMatrix = (TMatrixDSym*)cov->Clone();
+
1354 if(use_adaptive && total_steps <= AdaptiveHandler.start_adaptive_throw) makeClosestPosDef(throwMatrix);
+
1355 else MakePosDef(throwMatrix);
1356
-
1357 if(!TDecompChol_throwMatrix.Decompose()) {
-
1358 MACH3LOG_ERROR("Cholesky decomposition failed for {} trying to make positive definite", matrixName);
-
1359 throw MaCh3Exception(__FILE__ , __LINE__ );
-
1360 }
-
1361
-
1362 throwMatrix_CholDecomp = new TMatrixD(TDecompChol_throwMatrix.GetU());
-
1363 throwMatrix_CholDecomp->T();
-
1364
-
1365 //KS: ROOT has bad memory management, using standard double means we can decrease most operation by factor 2 simply due to cache hits
-
1366#ifdef MULTITHREAD
-
1367#pragma omp parallel for
-
1368#endif
-
1369 for (int i = 0; i < _fNumPar; ++i)
-
1370 {
-
1371 for (int j = 0; j < _fNumPar; ++j)
-
1372 {
-
1373 throwMatrixCholDecomp[i][j] = (*throwMatrix_CholDecomp)(i,j);
-
1374 }
-
1375 }
-
1376}
+
1357 TDecompChol TDecompChol_throwMatrix(*throwMatrix);
+
1358
+
1359 if(!TDecompChol_throwMatrix.Decompose()) {
+
1360 MACH3LOG_ERROR("Cholesky decomposition failed for {} trying to make positive definite", matrixName);
+
1361 throw MaCh3Exception(__FILE__ , __LINE__ );
+
1362 }
+
1363
+
1364 throwMatrix_CholDecomp = new TMatrixD(TDecompChol_throwMatrix.GetU());
+
1365 throwMatrix_CholDecomp->T();
+
1366
+
1367 //KS: ROOT has bad memory management, using standard double means we can decrease most operation by factor 2 simply due to cache hits
+
1368 #ifdef MULTITHREAD
+
1369 #pragma omp parallel for
+
1370 #endif
+
1371 for (int i = 0; i < _fNumPar; ++i)
+
1372 {
+
1373 for (int j = 0; j < _fNumPar; ++j)
+
1374 {
+
1375 throwMatrixCholDecomp[i][j] = (*throwMatrix_CholDecomp)(i,j);
+
1376 }
+
1377 }
+
1378}
-
1377// ********************************************
-
-
1378void covarianceBase::updateThrowMatrix(TMatrixDSym *cov){
1379// ********************************************
-
1380 delete throwMatrix;
-
1381 throwMatrix = NULL;
-
1382 delete throwMatrix_CholDecomp;
-
1383 throwMatrix_CholDecomp = NULL;
-
1384 setThrowMatrix(cov);
-
1385}
-
-
1386
-
1387// ********************************************
-
1388//HW: Truly adaptive MCMC!
-
-
1389void covarianceBase::saveAdaptiveToFile(const TString& outFileName, const TString& systematicName){
+
+
1380void covarianceBase::updateThrowMatrix(TMatrixDSym *cov){
+
1381// ********************************************
+
1382 delete throwMatrix;
+
1383 throwMatrix = NULL;
+
1384 delete throwMatrix_CholDecomp;
+
1385 throwMatrix_CholDecomp = NULL;
+
1386 setThrowMatrix(cov);
+
1387}
+
+
1388
+
1389
1390// ********************************************
-
1391 TFile* outFile = new TFile(outFileName, "UPDATE");
-
1392 if(outFile->IsZombie()){
-
1393 MACH3LOG_ERROR("Couldn't find {}", outFileName);
-
1394 throw;
-
1395 }
-
1396 TVectorD* outMeanVec = new TVectorD((int)adaption_struct.par_means.size());
-
1397 for(int i = 0; i < (int)adaption_struct.par_means.size(); i++){
-
1398 (*outMeanVec)(i)=adaption_struct.par_means[i];
-
1399 }
-
1400 outFile->cd();
-
1401 adaption_struct.adaptive_covariance->Write(systematicName+"_postfit_matrix");
-
1402 outMeanVec->Write(systematicName+"_mean_vec");
-
1403 outFile->Close();
-
1404 delete outMeanVec;
-
1405 delete outFile;
-
1406}
-
-
1407
-
1408
-
-
1409void covarianceBase::setAdaptionDefaults(){
-
1410 // Puts adaptive MCMC default attributes somewhere obvious
-
1411 use_adaptive = false;
-
1412 total_steps = 0;
-
1413 adaption_struct.start_adaptive_throw = 0;
-
1414 adaption_struct.start_adaptive_update = 0;
-
1415 adaption_struct.end_adaptive_update = 1;
-
1416 adaption_struct.adaptive_update_step = 1000;
-
1417
-
1418 adaption_struct.par_means = {};
-
1419 adaption_struct.adaptive_covariance = nullptr;
-
1420}
-
-
1421// ********************************************
-
1422// HW : Here be adaption
-
-
1423void covarianceBase::initialiseAdaption(const YAML::Node& adapt_manager){
-
1424// ********************************************
-
1425 /*
-
1426 HW: Idea is that adaption can simply read the YAML config
-
1427 Options :
-
1428 External Info:
-
1429 * UseExternalMatrix [bool] : Use an external matrix
-
1430 * ExternalMatrixFileName [str] : Name of file containing external info
-
1431 * ExternalMatrixName [str] : Name of external Matrix
-
1432 * ExternalMeansName [str] : Name of external means vector [for updates]
-
1433
-
1434 General Info:
-
1435 * DoAdaption [bool] : Do we want to do adaption?
-
1436 * AdaptionStartThrow [int] : Step we start throwing adaptive matrix from
-
1437 * AdaptionEndUpdate [int] : Step we stop updating adaptive matrix
-
1438 * AdaptionStartUpdate [int] : Do we skip the first N steps?
-
1439 * AdaptionUpdateStep [int] : Number of steps between matrix updates
-
1440 * Adaption blocks [vector<vector<int>>] : Splits the throw matrix into several block matrices
-
1441 */
-
1442
-
1443 // need to cast matrixName to string
-
1444 std::string matrix_name_str(matrixName);
-
1445
-
1446 // setAdaptionDefaults();
-
1447 if(GetFromManager<std::string>(adapt_manager["AdaptionOptions"]["Covariance"][matrix_name_str], "")==""){
-
1448 MACH3LOG_WARN("Adaptive Settings not found for {}, this is fine if you don't want adaptive MCMC", matrix_name_str);
-
1449 return;
-
1450 }
-
1451
-
1452 // We"re going to grab this info from the YAML manager
-
1453 if(GetFromManager<bool>(adapt_manager["AdaptionOptions"]["Covariance"][matrix_name_str]["DoAdaption"], false)) {
-
1454 MACH3LOG_INFO("Not using adaption for {}", matrix_name_str);
-
1455 return;
-
1456 }
-
1457
-
1458 // Now we read the general settings [these SHOULD be common across all matrices!]
-
1459 adaption_struct.start_adaptive_throw = GetFromManager<int>(adapt_manager["AdaptionOptions"]["Settings"]["AdaptionStartThrow"], 10);
-
1460 adaption_struct.start_adaptive_update = GetFromManager<int>(adapt_manager["AdaptionOptions"]["Settings"]["AdaptionStartUpdate"], 0);
-
1461 adaption_struct.end_adaptive_update = GetFromManager<int>(adapt_manager["AdaptionOptions"]["Settings"]["AdaptionEndUpdate"], 10000);
-
1462 adaption_struct.adaptive_update_step = GetFromManager<int>(adapt_manager["AdaptionOptions"]["Settings"]["AdaptionUpdateStep"], 100);
-
1463
-
1464 adaptive_mcmc::print_adaptive_struct(adaption_struct);
+
+
1391void covarianceBase::setAdaptionDefaults(){
+
1392// ********************************************
+
1393 // Puts adaptive MCMC default attributes somewhere obvious
+
1394 use_adaptive = false;
+
1395 total_steps = 0;
+
1396}
+
+
1397
+
1398// ********************************************
+
1399// HW : Here be adaption
+
+
1400void covarianceBase::initialiseAdaption(const YAML::Node& adapt_manager){
+
1401// ********************************************
+
1402 /*
+
1403 HW: Idea is that adaption can simply read the YAML config
+
1404 Options :
+
1405 External Info:
+
1406 * UseExternalMatrix [bool] : Use an external matrix
+
1407 * ExternalMatrixFileName [str] : Name of file containing external info
+
1408 * ExternalMatrixName [str] : Name of external Matrix
+
1409 * ExternalMeansName [str] : Name of external means vector [for updates]
+
1410
+
1411 General Info:
+
1412 * DoAdaption [bool] : Do we want to do adaption?
+
1413 * AdaptionStartThrow [int] : Step we start throwing adaptive matrix from
+
1414 * AdaptionEndUpdate [int] : Step we stop updating adaptive matrix
+
1415 * AdaptionStartUpdate [int] : Do we skip the first N steps?
+
1416 * AdaptionUpdateStep [int] : Number of steps between matrix updates
+
1417 * Adaption blocks [vector<vector<int>>] : Splits the throw matrix into several block matrices
+
1418 */
+
1419
+
1420 // need to cast matrixName to string
+
1421 std::string matrix_name_str(matrixName);
+
1422
+
1423 // Now we read the general settings [these SHOULD be common across all matrices!]
+
1424 AdaptiveHandler.InitFromConfig(adapt_manager, matrix_name_str, getNpars());
+
1425 AdaptiveHandler.Print();
+
1426
+
1427 // Next let"s check for external matrices
+
1428 // We"re going to grab this info from the YAML manager
+
1429 if(!GetFromManager<bool>(adapt_manager["AdaptionOptions"]["Covariance"][matrix_name_str]["UseExternalMatrix"], false)) {
+
1430 MACH3LOG_WARN("Not using external matrix for {}, initialising adaption from scratch", matrix_name_str);
+
1431 // If we don't have a covariance matrix to start from for adaptive tune we need to make one!
+
1432 use_adaptive = true;
+
1433 AdaptiveHandler.CreateNewAdaptiveCovariance(_fNumPar);
+
1434 return;
+
1435 }
+
1436
+
1437 // Finally, we accept that we want to read the matrix from a file!
+
1438 std::string external_file_name = GetFromManager<std::string>(adapt_manager["AdaptionOptions"]["Covariance"][matrix_name_str]["ExternalMatrixFileName"], "");
+
1439 std::string external_matrix_name = GetFromManager<std::string>(adapt_manager["AdaptionOptions"]["Covariance"][matrix_name_str]["ExternalMatrixName"], "");
+
1440 std::string external_mean_name = GetFromManager<std::string>(adapt_manager["AdaptionOptions"]["Covariance"][matrix_name_str]["ExternalMeansName"], "");
+
1441
+
1442 AdaptiveHandler.SetThrowMatrixFromFile(external_file_name, external_matrix_name, external_mean_name, use_adaptive, _fNumPar);
+
1443 setThrowMatrix(AdaptiveHandler.adaptive_covariance);
+
1444 MACH3LOG_INFO("Successfully Set External Throw Matrix Stored in {}", external_file_name);
+
1445}
+
+
1446
+
1447// ********************************************
+
1448// Truely adaptive MCMC!
+
+
1449void covarianceBase::updateAdaptiveCovariance(){
+
1450// ********************************************
+
1451 // Updates adaptive matrix
+
1452 // First we update the total means
+
1453
+
1454 // Skip this if we're at a large number of steps
+
1455 if(total_steps>AdaptiveHandler.end_adaptive_update || total_steps<AdaptiveHandler.start_adaptive_update) return;
+
1456
+
1457 int steps_post_burn = total_steps - AdaptiveHandler.start_adaptive_update;
+
1458 // Call main adaption function
+
1459 AdaptiveHandler.UpdateAdaptiveCovariance(_fCurrVal, steps_post_burn, _fNumPar);
+
1460
+
1461 //This is likely going to be the slow bit!
+
1462 if(total_steps == AdaptiveHandler.start_adaptive_throw) {
+
1463 resetIndivStepScale();
+
1464 }
1465
-
1466 // We also want to check for "blocks" by default all parameters "know" about each other
-
1467 // but we can split the matrix into independent block matrices
-
1468
-
1469 // We"ll set a dummy variable here
-
1470 auto matrix_blocks = GetFromManager<std::vector<std::vector<int>>>(adapt_manager["AdaptionOptions"]["Settings"][matrix_name_str]["AdaptionUpdateStep"], {{}});
-
1471
-
1472 setAdaptiveBlocks(matrix_blocks);
-
1473
-
1474 // Next let"s check for external matrices
-
1475 // We"re going to grab this info from the YAML manager
-
1476 if(!GetFromManager<bool>(adapt_manager["AdaptionOptions"]["Covariance"][matrix_name_str]["UseExternalMatrix"], false)) {
-
1477 MACH3LOG_INFO("Not using external matrix for {}, initialising adaption from scratch", matrix_name_str);
-
1478 createNewAdaptiveCovariance();
-
1479 return;
-
1480 }
-
1481
-
1482 // Finally, we accept that we want to read the matrix from a file!
-
1483 //
-
1484 std::string external_file_name = GetFromManager<std::string>(adapt_manager["AdaptionOptions"]["Covariance"][matrix_name_str]["ExternalMatrixFileName"], "");
-
1485 std::string external_matrix_name = GetFromManager<std::string>(adapt_manager["AdaptionOptions"]["Covariance"][matrix_name_str]["ExternalMatrixName"], "");
-
1486 std::string external_mean_name = GetFromManager<std::string>(adapt_manager["AdaptionOptions"]["Covariance"][matrix_name_str]["ExternalMeansName"], "");
-
1487
-
1488 setThrowMatrixFromFile(external_file_name, external_matrix_name, external_mean_name);
-
1489}
+
1466 if(total_steps>=AdaptiveHandler.start_adaptive_throw && (total_steps-AdaptiveHandler.start_adaptive_throw)%AdaptiveHandler.adaptive_update_step==0) {
+
1467 TMatrixDSym* update_matrix = static_cast<TMatrixDSym*>(AdaptiveHandler.adaptive_covariance->Clone());
+
1468 updateThrowMatrix(update_matrix); //Now we update and continue!
+
1469 }
+
1470}
-
1490
-
1491// HW : I would like this to be less painful to use!
-
1492// First things first we need setters
-
-
1493void covarianceBase::setThrowMatrixFromFile(const std::string& matrix_file_name, const std::string& matrix_name, const std::string& means_name){
-
1494 // Lets you set the throw matrix externally
-
1495 // Open file
-
1496 std::unique_ptr<TFile>matrix_file(new TFile(matrix_file_name.c_str()));
-
1497 use_adaptive = true;
-
1498
-
1499 if(matrix_file->IsZombie()){
-
1500 MACH3LOG_ERROR("Couldn't find {}", matrix_file_name);
-
1501 throw;
-
1502 }
-
1503
-
1504 // Next we grab our matrix
-
1505 adaption_struct.adaptive_covariance = static_cast<TMatrixDSym*>(matrix_file->Get(matrix_name.c_str()));
-
1506 if(!adaption_struct.adaptive_covariance){
-
1507 MACH3LOG_ERROR("Couldn't find {} in {}", matrix_name, matrix_file_name);
-
1508 throw;
-
1509 }
-
1510
-
1511 MACH3LOG_INFO("Succesfully Set External Throw Matrix Stored in {}", matrix_file_name);
-
1512
-
1513 setThrowMatrix(adaption_struct.adaptive_covariance);
-
1514
-
1515 // Finally we grab the means vector
-
1516 TVectorD* means_vector = static_cast<TVectorD*>(matrix_file->Get(means_name.c_str()));
-
1517
-
1518 // This is fine to not exist!
-
1519 if(means_vector){
-
1520 // Yay our vector exists! Let's loop and fill it
-
1521
-
1522 // Should check this is done
-
1523 if(means_vector->GetNrows()){
-
1524 MACH3LOG_ERROR("External means vec size ({}) != matrix size ({})", means_vector->GetNrows(), size);
-
1525 throw MaCh3Exception(__FILE__, __LINE__);
-
1526 }
-
1527
-
1528 adaption_struct.par_means = std::vector<double>(size);
-
1529 for(int i=0; i<size; i++){
-
1530 adaption_struct.par_means[i] = (*means_vector)(i);
-
1531 }
-
1532 MACH3LOG_INFO("Found Means in External File, Will be able to adapt");
-
1533
-
1534 }
-
1535 // Totally fine if it doesn't exist, we just can't do adaption
-
1536 else{
-
1537 // We don't need a means vector, set the adaption=false
-
1538 MACH3LOG_WARN("Cannot find means vector in {}, therefore I will not be able to adapt!", matrix_file_name);
-
1539 use_adaptive=false;
-
1540 }
-
1541
-
1542 matrix_file->Close();
-
1543
-
1544 std::cout<<"Set up matrix from external file"<<std::endl;
-
1545}
+
1471
+
1472// ********************************************
+
1473//HW: Finds closest possible positive definite matrix in Frobenius Norm ||.||_frob
+
1474// Where ||X||_frob=sqrt[sum_ij(x_ij^2)] (basically just turns an n,n matrix into vector in n^2 space
+
1475// then does Euclidean norm)
+
+
1476void covarianceBase::makeClosestPosDef(TMatrixDSym *cov) {
+
1477// ********************************************
+
1478
+
1479 // Want to get cov' = (cov_sym+cov_polar)/2
+
1480 // cov_sym=(cov+cov^T)/2
+
1481 // cov_polar-> SVD cov to cov=USV^T then cov_polar=VSV^T
+
1482
+
1483 //Get frob norm of cov
+
1484 // Double_t cov_norm=cov->E2Norm();
+
1485
+
1486 TMatrixDSym* cov_trans = cov;
+
1487 cov_trans->T();
+
1488 TMatrixDSym cov_sym = 0.5*(*cov+*cov_trans); //If cov is symmetric does nothing, otherwise just ensures symmetry
+
1489
+
1490 //Do SVD to get polar form
+
1491 TDecompSVD cov_sym_svd=TDecompSVD(cov_sym);
+
1492 if(!cov_sym_svd.Decompose()){
+
1493 MACH3LOG_ERROR("Cannot do SVD on input matrix!");
+
1494 throw;
+
1495 }
+
1496
+
1497 TMatrixD cov_sym_v = (TMatrixD)cov_sym_svd.GetV();
+
1498 TMatrixD cov_sym_vt = cov_sym_v;
+
1499 cov_sym_vt.T();
+
1500 //SVD returns as vector (grrr) so need to get into matrix form for multiplying!
+
1501 TVectorD cov_sym_sigvect = (TVectorD)cov_sym_svd.GetSig();
+
1502 const Int_t nCols = cov_sym_v.GetNcols(); //square so only need rows hence lack of cols
+
1503 TMatrixDSym cov_sym_sig(nCols);
+
1504 TMatrixDDiag cov_sym_sig_diag(cov_sym_sig);
+
1505 cov_sym_sig_diag=cov_sym_sigvect;
+
1506
+
1507 //Can finally get H=VSV
+
1508 TMatrixDSym cov_sym_polar = cov_sym_sig.SimilarityT(cov_sym_vt);//V*S*V^T (this took forver to find!)
+
1509
+
1510 //Now we can construct closest approximater Ahat=0.5*(B+H)
+
1511 TMatrixDSym cov_closest_approx = 0.5*(cov_sym+cov_sym_polar);//Not fully sure why this is even needed since symmetric B -> U=V
+
1512 //Get norm of transformed
+
1513 // Double_t approx_norm=cov_closest_approx.E2Norm();
+
1514 //std::cout<<"Initial Norm : "<<cov_norm<<" | Norm after transformation : "<<approx_norm<<" | Ratio : "<<cov_norm/approx_norm<<std::endl;
+
1515
+
1516 *cov = cov_closest_approx;
+
1517 //Now can just add a makeposdef!
+
1518 MakePosDef(cov);
+
1519}
+
+
1520
+
1521// ********************************************
+
+
1522std::vector<double> covarianceBase::getNominalArray() {
+
1523// ********************************************
+
1524
+
1525 std::vector<double> nominal(_fNumPar);
+
1526 for (int i = 0; i < _fNumPar; ++i)
+
1527 {
+
1528 nominal[i] = _fPreFitValue[i];
+
1529 }
+
1530 return nominal;
+
1531}
+
+
1532
+
1533// ********************************************
+
1534// KS: Convert covariance matrix to correlation matrix and return TH2D which can be used for fancy plotting
+
+
1535TH2D* covarianceBase::GetCorrelationMatrix() {
+
1536// ********************************************
+
1537 TH2D* hMatrix = new TH2D(getName(), getName(), _fNumPar, 0.0, _fNumPar, _fNumPar, 0.0, _fNumPar);
+
1538
+
1539 for(int i = 0; i < _fNumPar; i++)
+
1540 {
+
1541 hMatrix->SetBinContent(i+1, i+1, 1.);
+
1542 hMatrix->GetXaxis()->SetBinLabel(i+1, GetParFancyName(i).c_str());
+
1543 hMatrix->GetYaxis()->SetBinLabel(i+1, GetParFancyName(i).c_str());
+
1544 }
+
1545
+
1546 #ifdef MULTITHREAD
+
1547 #pragma omp parallel for
+
1548 #endif
+
1549 for(int i = 0; i < _fNumPar; i++)
+
1550 {
+
1551 for(int j = 0; j <= i; j++)
+
1552 {
+
1553 const double Corr = (*covMatrix)(i,j) / ( getDiagonalError(i) * getDiagonalError(j));
+
1554 hMatrix->SetBinContent(i+1, j+1, Corr);
+
1555 hMatrix->SetBinContent(j+1, i+1, Corr);
+
1556 }
+
1557 }
+
1558 return hMatrix;
+
1559}
-
1546
-
-
1547void covarianceBase::setAdaptiveBlocks(std::vector<std::vector<int>> block_indices){
-
1548 /*
-
1549 In order to adapt efficient we want to setup our throw matrix to be a serious of block-diagonal (ish) matrices
-
1550
-
1551 To do this we set sub-block in the config by parameter index. For example having
-
1552 [[0,4],[4, 6]] in your config will set up two blocks one with all indices 0<=i<4 and the other with 4<=i<6
-
1553 */
-
1554 // Set up block regions
-
1555 adaption_struct.adapt_block_matrix_indices = std::vector<int>(getNpars(), 0);
-
1556
-
1557 // Should also make a matrix of block sizes
-
1558 adaption_struct.adapt_block_sizes = std::vector<int>((int)block_indices.size()+1, 0);
-
1559 adaption_struct.adapt_block_sizes[0]=getNpars();
1560
-
1561 if(block_indices.size()==0 || block_indices[0].size()==0) return;
-
1562
-
1563
-
1564 // Now we loop over our blocks
-
1565 for(int iblock=0; iblock<(int)block_indices.size(); iblock++){
-
1566 // Loop over blocks in the block
-
1567 for(int isubblock=0; isubblock<(int)block_indices[iblock].size()-1; isubblock+=2){
-
1568 int block_lb = block_indices[iblock][isubblock];
-
1569 int block_ub = block_indices[iblock][isubblock+1];
-
1570
-
1571 // std::cout<<block_lb<<" "<<block_ub<<std::endl;
-
1572
-
1573 if(block_lb>getNpars() || block_ub>getNpars()){
-
1574 MACH3LOG_ERROR("Cannot set matrix block with edges {}, {} for matrix of size {}",
-
1575 block_lb, block_ub, getNpars());
-
1576 throw MaCh3Exception(__FILE__, __LINE__);;
-
1577 }
-
1578
-
1579 for(int ipar=block_lb; ipar<block_ub; ipar++){
-
1580 adaption_struct.adapt_block_matrix_indices[ipar]=iblock+1;
-
1581 adaption_struct.adapt_block_sizes[iblock+1]+=1;
-
1582 adaption_struct.adapt_block_sizes[0]-=1;
-
1583 }
-
1584
-
1585 }
-
1586 }
+
1561// ********************************************
+
1562// KS: After step scale, prefit etc. value were modified save this modified config.
+
+
1563void covarianceBase::SaveUpdatedMatrixConfig() {
+
1564// ********************************************
+
1565
+
1566 if (!_fYAMLDoc)
+
1567 {
+
1568 MACH3LOG_CRITICAL("Yaml node hasn't been initialised for matrix {}, something is not right", matrixName);
+
1569 MACH3LOG_CRITICAL("I am not throwing error but should be investigated");
+
1570 return;
+
1571 }
+
1572
+
1573 YAML::Node copyNode = _fYAMLDoc;
+
1574 int i = 0;
+
1575
+
1576 for (YAML::Node param : copyNode["Systematics"])
+
1577 {
+
1578 //KS: Feel free to update it, if you need updated prefit value etc
+
1579 param["Systematic"]["StepScale"]["MCMC"] = std::round(_fIndivStepScale[i] * 100.0) / 100.0; // Round to 2 decimal places
+
1580
+
1581 i++;
+
1582 }
+
1583 // Save the modified node to a file
+
1584 std::ofstream fout("Modified_Matrix.yaml");
+
1585 fout << copyNode;
+
1586 fout.close();
1587}
1588
-
1589// ********************************************
-
-
1590void covarianceBase::createNewAdaptiveCovariance(){
+
1589
+
1590#ifdef DEBUG_PCA
1591// ********************************************
-
1592 // If we don't have a covariance matrix to start from for adaptive tune we need to make one!
-
1593 use_adaptive=true;
-
1594 adaption_struct.adaptive_covariance = new TMatrixDSym(size);
-
1595 adaption_struct.adaptive_covariance->Zero();
-
1596 adaption_struct.par_means = std::vector<double>(size, 0);
-
1597}
-
+
1592//KS: Let's dump all useful matrices to properly validate PCA
+
1593void covarianceBase::DebugPCA(const double sum, TMatrixD temp, TMatrixDSym submat) {
+
1594// ********************************************
+
1595 (void)submat;//This is used if DEBUG_PCA==2, this hack is to avoid compiler warnings
+
1596 TFile *PCA_Debug = new TFile("Debug_PCA.root", "RECREATE");
+
1597 PCA_Debug->cd();
1598
-
1599// Truely adaptive MCMC!
-
-
1600void covarianceBase::updateAdaptiveCovariance(){
-
1601 // https://projecteuclid.org/journals/bernoulli/volume-7/issue-2/An-adaptive-Metropolis-algorithm/bj/1080222083.full
-
1602 // Updates adaptive matrix
-
1603 // First we update the total means
-
1604
-
1605 // Skip this if we're at a large number of steps
-
1606 if(total_steps>adaption_struct.end_adaptive_update || total_steps<adaption_struct.start_adaptive_update) return;
-
1607
-
1608 int steps_post_burn = total_steps - adaption_struct.start_adaptive_update;
-
1609
-
1610 std::vector<double> par_means_prev = adaption_struct.par_means;
-
1611
-
1612 #ifdef MULTITHREAD
-
1613 #pragma omp parallel for
-
1614 #endif
-
1615 for(int iRow=0; iRow<size; iRow++){
-
1616 adaption_struct.par_means[iRow]=(_fCurrVal[iRow]+adaption_struct.par_means[iRow]*steps_post_burn)/(steps_post_burn+1);
-
1617 }
-
1618
-
1619 //Now we update the covariances using cov(x,y)=E(xy)-E(x)E(y)
-
1620 #ifdef MULTITHREAD
-
1621 #pragma omp parallel for
-
1622 #endif
-
1623 for(int irow=0; irow<size; irow++){
-
1624 int block = adaption_struct.adapt_block_matrix_indices[irow];
-
1625 // int scale_factor = 5.76/double(adapt_block_sizes[block]);
-
1626 for(int icol=0; icol<=irow; icol++){
-
1627 double cov_val=0;
-
1628 // Not in the same blocks
-
1629 if(adaption_struct.adapt_block_matrix_indices[icol]==block){
-
1630 // Calculate Covariance for block
-
1631 // https://projecteuclid.org/journals/bernoulli/volume-7/issue-2/An-adaptive-Metropolis-algorithm/bj/1080222083.full
-
1632 cov_val = (*adaption_struct.adaptive_covariance)(irow, icol)*size/5.6644;
-
1633 cov_val += par_means_prev[irow]*par_means_prev[icol]; //First we remove the current means
-
1634 cov_val = (cov_val*steps_post_burn+_fCurrVal[irow]*_fCurrVal[icol])/(steps_post_burn+1); //Now get mean(iRow*iCol)
-
1635 cov_val -= adaption_struct.par_means[icol]*adaption_struct.par_means[irow];
-
1636 cov_val*=5.6644/size;
-
1637 }
+
1599 bool PlotText = true;
+
1600 //KS: If we have more than 200 plot becomes unreadable :(
+
1601 if(_fNumPar > 200) PlotText = false;
+
1602
+
1603 TH1D* heigen_values = new TH1D("eigen_values", "Eigen Values", (int)eigen_values.GetNrows(), 0.0, (int)eigen_values.GetNrows());
+
1604 TH1D* heigen_cumulative = new TH1D("heigen_cumulative", "heigen_cumulative", (int)eigen_values.GetNrows(), 0.0, (int)eigen_values.GetNrows());
+
1605 TH1D* heigen_frac = new TH1D("heigen_fractional", "heigen_fractional", (int)eigen_values.GetNrows(), 0.0, (int)eigen_values.GetNrows());
+
1606 heigen_values->GetXaxis()->SetTitle("Eigen Vector");
+
1607 heigen_values->GetYaxis()->SetTitle("Eigen Value");
+
1608
+
1609 double Cumulative = 0;
+
1610 for(int i = 0; i < eigen_values.GetNrows(); i++)
+
1611 {
+
1612 heigen_values->SetBinContent(i+1, (eigen_values)(i));
+
1613 heigen_cumulative->SetBinContent(i+1, (eigen_values)(i)/sum + Cumulative);
+
1614 heigen_frac->SetBinContent(i+1, (eigen_values)(i)/sum);
+
1615 Cumulative += (eigen_values)(i)/sum;
+
1616 }
+
1617 heigen_values->Write("heigen_values");
+
1618 eigen_values.Write("eigen_values");
+
1619 heigen_cumulative->Write("heigen_values_cumulative");
+
1620 heigen_frac->Write("heigen_values_frac");
+
1621
+
1622 TH2D* heigen_vectors = new TH2D(eigen_vectors);
+
1623 heigen_vectors->GetXaxis()->SetTitle("Parameter in Normal Base");
+
1624 heigen_vectors->GetYaxis()->SetTitle("Parameter in Decomposed Base");
+
1625 heigen_vectors->Write("heigen_vectors");
+
1626 eigen_vectors.Write("eigen_vectors");
+
1627
+
1628 TH2D* SubsetPCA = new TH2D(temp);
+
1629 SubsetPCA->GetXaxis()->SetTitle("Parameter in Normal Base");
+
1630 SubsetPCA->GetYaxis()->SetTitle("Parameter in Decomposed Base");
+
1631
+
1632 SubsetPCA->Write("hSubsetPCA");
+
1633 temp.Write("SubsetPCA");
+
1634 TH2D* hTransferMat = new TH2D(TransferMat);
+
1635 hTransferMat->GetXaxis()->SetTitle("Parameter in Normal Base");
+
1636 hTransferMat->GetYaxis()->SetTitle("Parameter in Decomposed Base");
+
1637 TH2D* hTransferMatT = new TH2D(TransferMatT);
1638
-
1639 (*adaption_struct.adaptive_covariance)(icol, irow) = cov_val;
-
1640 (*adaption_struct.adaptive_covariance)(irow, icol) = cov_val;
-
1641 }
-
1642 }
-
1643
-
1644 //This is likely going to be the slow bit!
-
1645 if(total_steps==adaption_struct.start_adaptive_throw)
-
1646 {
-
1647 resetIndivStepScale();
-
1648 }
-
1649
-
1650 if(total_steps>=adaption_struct.start_adaptive_throw && (total_steps-adaption_struct.start_adaptive_throw)%adaption_struct.adaptive_update_step==0) {
-
1651 TMatrixDSym* update_matrix = static_cast<TMatrixDSym*>(adaption_struct.adaptive_covariance->Clone());
-
1652 updateThrowMatrix(update_matrix); //Now we update and continue!
-
1653 }
-
1654}
-
-
1655
-
1656// ********************************************
-
1657//HW: Finds closest possible positive definite matrix in Frobenius Norm ||.||_frob
-
1658// Where ||X||_frob=sqrt[sum_ij(x_ij^2)] (basically just turns an n,n matrix into vector in n^2 space
-
1659// then does Euclidean norm)
-
-
1660void covarianceBase::makeClosestPosDef(TMatrixDSym *cov) {
-
1661// ********************************************
-
1662
-
1663 // Want to get cov' = (cov_sym+cov_polar)/2
-
1664 // cov_sym=(cov+cov^T)/2
-
1665 // cov_polar-> SVD cov to cov=USV^T then cov_polar=VSV^T
+
1639 hTransferMatT->GetXaxis()->SetTitle("Parameter in Decomposed Base");
+
1640 hTransferMatT->GetYaxis()->SetTitle("Parameter in Normal Base");
+
1641
+
1642 hTransferMat->Write("hTransferMat");
+
1643 TransferMat.Write("TransferMat");
+
1644 hTransferMatT->Write("hTransferMatT");
+
1645 TransferMatT.Write("TransferMatT");
+
1646
+
1647 TCanvas *c1 = new TCanvas("c1"," ", 0, 0, 1024, 1024);
+
1648 c1->SetBottomMargin(0.1);
+
1649 c1->SetTopMargin(0.05);
+
1650 c1->SetRightMargin(0.05);
+
1651 c1->SetLeftMargin(0.12);
+
1652 c1->SetGrid();
+
1653
+
1654 gStyle->SetPaintTextFormat("4.1f");
+
1655 gStyle->SetOptFit(0);
+
1656 gStyle->SetOptStat(0);
+
1657 // Make pretty correlation colors (red to blue)
+
1658 const int NRGBs = 5;
+
1659 TColor::InitializeColors();
+
1660 Double_t stops[NRGBs] = { 0.00, 0.25, 0.50, 0.75, 1.00 };
+
1661 Double_t red[NRGBs] = { 0.00, 0.25, 1.00, 1.00, 0.50 };
+
1662 Double_t green[NRGBs] = { 0.00, 0.25, 1.00, 0.25, 0.00 };
+
1663 Double_t blue[NRGBs] = { 0.50, 1.00, 1.00, 0.25, 0.00 };
+
1664 TColor::CreateGradientColorTable(5, stops, red, green, blue, 255);
+
1665 gStyle->SetNumberContours(255);
1666
-
1667 //Get frob norm of cov
-
1668// Double_t cov_norm=cov->E2Norm();
-
1669
-
1670 TMatrixDSym* cov_trans = cov;
-
1671 cov_trans->T();
-
1672 TMatrixDSym cov_sym = 0.5*(*cov+*cov_trans); //If cov is symmetric does nothing, otherwise just ensures symmetry
-
1673
-
1674 //Do SVD to get polar form
-
1675 TDecompSVD cov_sym_svd=TDecompSVD(cov_sym);
-
1676 if(!cov_sym_svd.Decompose()){
-
1677 MACH3LOG_ERROR("Cannot do SVD on input matrix!");
-
1678 throw;
-
1679 }
-
1680
-
1681 TMatrixD cov_sym_v = (TMatrixD)cov_sym_svd.GetV();
-
1682 TMatrixD cov_sym_vt = cov_sym_v;
-
1683 cov_sym_vt.T();
-
1684 //SVD returns as vector (grrr) so need to get into matrix form for multiplying!
-
1685 TVectorD cov_sym_sigvect = (TVectorD)cov_sym_svd.GetSig();
-
1686 const Int_t nCols = cov_sym_v.GetNcols(); //square so only need rows hence lack of cols
-
1687 TMatrixDSym cov_sym_sig(nCols);
-
1688 TMatrixDDiag cov_sym_sig_diag(cov_sym_sig);
-
1689 cov_sym_sig_diag=cov_sym_sigvect;
-
1690
-
1691
-
1692 //Can finally get H=VSV
-
1693 TMatrixDSym cov_sym_polar = cov_sym_sig.SimilarityT(cov_sym_vt);//V*S*V^T (this took forver to find!)
-
1694
-
1695 //Now we can construct closest approximater Ahat=0.5*(B+H)
-
1696 TMatrixDSym cov_closest_approx = 0.5*(cov_sym+cov_sym_polar);//Not fully sure why this is even needed since symmetric B -> U=V
-
1697 //Get norm of transformed
-
1698// Double_t approx_norm=cov_closest_approx.E2Norm();
-
1699
-
1700 //std::cout<<"Initial Norm : "<<cov_norm<<" | Norm after transformation : "<<approx_norm<<" | Ratio : "<<cov_norm/approx_norm<<std::endl;
-
1701
-
1702 *cov = cov_closest_approx;
-
1703 //Now can just add a makeposdef!
-
1704 MakePosDef(cov);
-
1705}
-
-
1706// ********************************************
-
-
1707std::vector<double> covarianceBase::getNominalArray() {
-
1708// ********************************************
-
1709
-
1710 std::vector<double> nominal(_fNumPar);
-
1711 for (int i = 0; i < _fNumPar; ++i)
-
1712 {
-
1713 nominal[i] = _fPreFitValue[i];
-
1714 }
-
1715 return nominal;
-
1716}
-
-
1717
-
1718// ********************************************
-
1719// KS: Convert covariance matrix to correlation matrix and return TH2D which can be used for fancy plotting
-
-
1720TH2D* covarianceBase::GetCorrelationMatrix() {
-
1721// ********************************************
-
1722
-
1723 TH2D* hMatrix = new TH2D(getName(), getName(), _fNumPar, 0.0, _fNumPar, _fNumPar, 0.0, _fNumPar);
-
1724
-
1725 for(int i = 0; i < _fNumPar; i++)
-
1726 {
-
1727 hMatrix->SetBinContent(i+1, i+1, 1.);
-
1728 hMatrix->GetXaxis()->SetBinLabel(i+1, GetParFancyName(i).c_str());
-
1729 hMatrix->GetYaxis()->SetBinLabel(i+1, GetParFancyName(i).c_str());
-
1730 }
+
1667 double maxz = 0;
+
1668 double minz = 0;
+
1669
+
1670 c1->Print("Debug_PCA.pdf[");
+
1671 TLine *EigenLine = new TLine(nKeptPCApars, 0, nKeptPCApars, heigen_cumulative->GetMaximum());
+
1672 EigenLine->SetLineColor(kPink);
+
1673 EigenLine->SetLineWidth(2);
+
1674 EigenLine->SetLineStyle(kSolid);
+
1675
+
1676 TText* text = new TText(0.5, 0.5, Form("Threshold = %g", eigen_threshold));
+
1677 text->SetTextFont (43);
+
1678 text->SetTextSize (40);
+
1679
+
1680 heigen_values->SetLineColor(kRed);
+
1681 heigen_values->SetLineWidth(2);
+
1682 heigen_cumulative->SetLineColor(kGreen);
+
1683 heigen_cumulative->SetLineWidth(2);
+
1684 heigen_frac->SetLineColor(kBlue);
+
1685 heigen_frac->SetLineWidth(2);
+
1686
+
1687 c1->SetLogy();
+
1688 heigen_values->SetMaximum(heigen_cumulative->GetMaximum()+heigen_cumulative->GetMaximum()*0.4);
+
1689 heigen_values->Draw();
+
1690 heigen_frac->Draw("SAME");
+
1691 heigen_cumulative->Draw("SAME");
+
1692 EigenLine->Draw("Same");
+
1693 text->DrawTextNDC(0.42, 0.84,Form("Threshold = %g", eigen_threshold));
+
1694
+
1695 TLegend *leg = new TLegend(0.2, 0.2, 0.6, 0.5);
+
1696 leg->SetTextSize(0.04);
+
1697 leg->AddEntry(heigen_values, "Absolute", "l");
+
1698 leg->AddEntry(heigen_frac, "Fractional", "l");
+
1699 leg->AddEntry(heigen_cumulative, "Cumulative", "l");
+
1700
+
1701 leg->SetLineColor(0);
+
1702 leg->SetLineStyle(0);
+
1703 leg->SetFillColor(0);
+
1704 leg->SetFillStyle(0);
+
1705 leg->Draw("Same");
+
1706
+
1707 c1->Print("Debug_PCA.pdf");
+
1708 c1->SetRightMargin(0.15);
+
1709 c1->SetLogy(0);
+
1710 delete EigenLine;
+
1711 delete leg;
+
1712 delete text;
+
1713 delete heigen_values;
+
1714 delete heigen_frac;
+
1715 delete heigen_cumulative;
+
1716
+
1717 heigen_vectors->SetMarkerSize(0.2);
+
1718 minz = heigen_vectors->GetMinimum();
+
1719 if (fabs(0-maxz)>fabs(0-minz)) heigen_vectors->GetZaxis()->SetRangeUser(0-fabs(0-maxz),0+fabs(0-maxz));
+
1720 else heigen_vectors->GetZaxis()->SetRangeUser(0-fabs(0-minz),0+fabs(0-minz));
+
1721 if(PlotText) heigen_vectors->Draw("COLZ TEXT");
+
1722 else heigen_vectors->Draw("COLZ");
+
1723
+
1724 TLine *Eigen_Line = new TLine(0, nKeptPCApars, LastPCAdpar-FirstPCAdpar, nKeptPCApars);
+
1725 Eigen_Line->SetLineColor(kGreen);
+
1726 Eigen_Line->SetLineWidth(2);
+
1727 Eigen_Line->SetLineStyle(kDotted);
+
1728 Eigen_Line->Draw("SAME");
+
1729 c1->Print("Debug_PCA.pdf");
+
1730 delete Eigen_Line;
1731
-
1732 #ifdef MULTITHREAD
-
1733 #pragma omp parallel for
-
1734 #endif
-
1735 for(int i = 0; i < _fNumPar; i++)
-
1736 {
-
1737 for(int j = 0; j <= i; j++)
-
1738 {
-
1739 const double Corr = (*covMatrix)(i,j) / ( getDiagonalError(i) * getDiagonalError(j));
-
1740 hMatrix->SetBinContent(i+1, j+1, Corr);
-
1741 hMatrix->SetBinContent(j+1, i+1, Corr);
-
1742 }
-
1743 }
-
1744 return hMatrix;
-
1745}
-
-
1746
-
1747// ********************************************
-
1748// KS: After step scale, prefit etc. value were modified save this modified config.
-
-
1749void covarianceBase::SaveUpdatedMatrixConfig() {
-
1750// ********************************************
-
1751
-
1752 if (!_fYAMLDoc)
-
1753 {
-
1754 MACH3LOG_CRITICAL("Yaml node hasn't been initialised for matrix {}, something is not right", matrixName);
-
1755 MACH3LOG_CRITICAL("I am not throwing error but should be investigated");
-
1756 return;
-
1757 }
+
1732 SubsetPCA->SetMarkerSize(0.2);
+
1733 minz = SubsetPCA->GetMinimum();
+
1734 if (fabs(0-maxz)>fabs(0-minz)) SubsetPCA->GetZaxis()->SetRangeUser(0-fabs(0-maxz),0+fabs(0-maxz));
+
1735 else SubsetPCA->GetZaxis()->SetRangeUser(0-fabs(0-minz),0+fabs(0-minz));
+
1736 if(PlotText) SubsetPCA->Draw("COLZ TEXT");
+
1737 else SubsetPCA->Draw("COLZ");
+
1738 c1->Print("Debug_PCA.pdf");
+
1739 delete SubsetPCA;
+
1740
+
1741 hTransferMat->SetMarkerSize(0.15);
+
1742 minz = hTransferMat->GetMinimum();
+
1743 if (fabs(0-maxz)>fabs(0-minz)) hTransferMat->GetZaxis()->SetRangeUser(0-fabs(0-maxz),0+fabs(0-maxz));
+
1744 else hTransferMat->GetZaxis()->SetRangeUser(0-fabs(0-minz),0+fabs(0-minz));
+
1745 if(PlotText) hTransferMat->Draw("COLZ TEXT");
+
1746 else hTransferMat->Draw("COLZ");
+
1747 c1->Print("Debug_PCA.pdf");
+
1748 delete hTransferMat;
+
1749
+
1750 hTransferMatT->SetMarkerSize(0.15);
+
1751 minz = hTransferMatT->GetMinimum();
+
1752 if (fabs(0-maxz)>fabs(0-minz)) hTransferMatT->GetZaxis()->SetRangeUser(0-fabs(0-maxz),0+fabs(0-maxz));
+
1753 else hTransferMatT->GetZaxis()->SetRangeUser(0-fabs(0-minz),0+fabs(0-minz));
+
1754 if(PlotText) hTransferMatT->Draw("COLZ TEXT");
+
1755 else hTransferMatT->Draw("COLZ");
+
1756 c1->Print( "Debug_PCA.pdf");
+
1757 delete hTransferMatT;
1758
-
1759 YAML::Node copyNode = _fYAMLDoc;
-
1760 int i = 0;
-
1761
-
1762 for (YAML::Node param : copyNode["Systematics"])
-
1763 {
-
1764 //KS: Feel free to update it, if you need updated prefit value etc
-
1765 param["Systematic"]["StepScale"]["MCMC"] = std::round(_fIndivStepScale[i] * 100.0) / 100.0; // Round to 2 decimal places
-
1766
-
1767 i++;
-
1768 }
-
1769 // Save the modified node to a file
-
1770 std::ofstream fout("Modified_Matrix.yaml");
-
1771 fout << copyNode;
-
1772 fout.close();
-
1773}
-
-
1774
-
1775
-
1776#ifdef DEBUG_PCA
-
1777// ********************************************
-
1778//KS: Let's dump all useful matrices to properly validate PCA
-
1779void covarianceBase::DebugPCA(const double sum, TMatrixD temp, TMatrixDSym submat) {
-
1780// ********************************************
-
1781 (void)submat;//This is used if DEBUG_PCA==2, this hack is to avoid compiler warnings
-
1782 TFile *PCA_Debug = new TFile("Debug_PCA.root", "RECREATE");
-
1783 PCA_Debug->cd();
-
1784
-
1785 bool PlotText = true;
-
1786 //KS: If we have more than 200 plot becomes unreadable :(
-
1787 if(_fNumPar > 200) PlotText = false;
-
1788
-
1789 TH1D* heigen_values = new TH1D("eigen_values", "Eigen Values", (int)eigen_values.GetNrows(), 0.0, (int)eigen_values.GetNrows());
-
1790 TH1D* heigen_cumulative = new TH1D("heigen_cumulative", "heigen_cumulative", (int)eigen_values.GetNrows(), 0.0, (int)eigen_values.GetNrows());
-
1791 TH1D* heigen_frac = new TH1D("heigen_fractional", "heigen_fractional", (int)eigen_values.GetNrows(), 0.0, (int)eigen_values.GetNrows());
-
1792 heigen_values->GetXaxis()->SetTitle("Eigen Vector");
-
1793 heigen_values->GetYaxis()->SetTitle("Eigen Value");
-
1794
-
1795 double Cumulative = 0;
-
1796 for(int i = 0; i < eigen_values.GetNrows(); i++)
-
1797 {
-
1798 heigen_values->SetBinContent(i+1, (eigen_values)(i));
-
1799 heigen_cumulative->SetBinContent(i+1, (eigen_values)(i)/sum + Cumulative);
-
1800 heigen_frac->SetBinContent(i+1, (eigen_values)(i)/sum);
-
1801 Cumulative += (eigen_values)(i)/sum;
-
1802 }
-
1803 heigen_values->Write("heigen_values");
-
1804 eigen_values.Write("eigen_values");
-
1805 heigen_cumulative->Write("heigen_values_cumulative");
-
1806 heigen_frac->Write("heigen_values_frac");
-
1807
-
1808 TH2D* heigen_vectors = new TH2D(eigen_vectors);
-
1809 heigen_vectors->GetXaxis()->SetTitle("Parameter in Normal Base");
-
1810 heigen_vectors->GetYaxis()->SetTitle("Parameter in Decomposed Base");
-
1811 heigen_vectors->Write("heigen_vectors");
-
1812 eigen_vectors.Write("eigen_vectors");
-
1813
-
1814 TH2D* SubsetPCA = new TH2D(temp);
-
1815 SubsetPCA->GetXaxis()->SetTitle("Parameter in Normal Base");
-
1816 SubsetPCA->GetYaxis()->SetTitle("Parameter in Decomposed Base");
-
1817
-
1818 SubsetPCA->Write("hSubsetPCA");
-
1819 temp.Write("SubsetPCA");
-
1820 TH2D* hTransferMat = new TH2D(TransferMat);
-
1821 hTransferMat->GetXaxis()->SetTitle("Parameter in Normal Base");
-
1822 hTransferMat->GetYaxis()->SetTitle("Parameter in Decomposed Base");
-
1823 TH2D* hTransferMatT = new TH2D(TransferMatT);
-
1824
-
1825 hTransferMatT->GetXaxis()->SetTitle("Parameter in Decomposed Base");
-
1826 hTransferMatT->GetYaxis()->SetTitle("Parameter in Normal Base");
-
1827
-
1828 hTransferMat->Write("hTransferMat");
-
1829 TransferMat.Write("TransferMat");
-
1830 hTransferMatT->Write("hTransferMatT");
-
1831 TransferMatT.Write("TransferMatT");
-
1832
-
1833 TCanvas *c1 = new TCanvas("c1"," ", 0, 0, 1024, 1024);
-
1834 c1->SetBottomMargin(0.1);
-
1835 c1->SetTopMargin(0.05);
-
1836 c1->SetRightMargin(0.05);
-
1837 c1->SetLeftMargin(0.12);
-
1838 c1->SetGrid();
-
1839
-
1840 gStyle->SetPaintTextFormat("4.1f");
-
1841 gStyle->SetOptFit(0);
-
1842 gStyle->SetOptStat(0);
-
1843 // Make pretty correlation colors (red to blue)
-
1844 const int NRGBs = 5;
-
1845 TColor::InitializeColors();
-
1846 Double_t stops[NRGBs] = { 0.00, 0.25, 0.50, 0.75, 1.00 };
-
1847 Double_t red[NRGBs] = { 0.00, 0.25, 1.00, 1.00, 0.50 };
-
1848 Double_t green[NRGBs] = { 0.00, 0.25, 1.00, 0.25, 0.00 };
-
1849 Double_t blue[NRGBs] = { 0.50, 1.00, 1.00, 0.25, 0.00 };
-
1850 TColor::CreateGradientColorTable(5, stops, red, green, blue, 255);
-
1851 gStyle->SetNumberContours(255);
-
1852
-
1853 double maxz = 0;
-
1854 double minz = 0;
-
1855
-
1856 c1->Print("Debug_PCA.pdf[");
-
1857 TLine *EigenLine = new TLine(nKeptPCApars, 0, nKeptPCApars, heigen_cumulative->GetMaximum());
-
1858 EigenLine->SetLineColor(kPink);
-
1859 EigenLine->SetLineWidth(2);
-
1860 EigenLine->SetLineStyle(kSolid);
-
1861
-
1862 TText* text = new TText(0.5, 0.5, Form("Threshold = %g", eigen_threshold));
-
1863 text->SetTextFont (43);
-
1864 text->SetTextSize (40);
-
1865
-
1866 heigen_values->SetLineColor(kRed);
-
1867 heigen_values->SetLineWidth(2);
-
1868 heigen_cumulative->SetLineColor(kGreen);
-
1869 heigen_cumulative->SetLineWidth(2);
-
1870 heigen_frac->SetLineColor(kBlue);
-
1871 heigen_frac->SetLineWidth(2);
+
1759
+
1760 //KS: Crosscheck against Eigen library
+
1761 #if DEBUG_PCA == 2
+
1762 Eigen::MatrixXd Submat_Eigen(submat.GetNrows(), submat.GetNcols());
+
1763
+
1764 #ifdef MULTITHREAD
+
1765 #pragma omp parallel for
+
1766 #endif
+
1767 for(int i = 0; i < submat.GetNrows(); i++)
+
1768 {
+
1769 for(int j = 0; j < submat.GetNcols(); j++)
+
1770 {
+
1771 Submat_Eigen(i,j) = (submat)(i,j);
+
1772 }
+
1773 }
+
1774 Eigen::EigenSolver<Eigen::MatrixXd> EigenSolver;
+
1775 EigenSolver.compute(Submat_Eigen);
+
1776 Eigen::VectorXd eigen_val = EigenSolver.eigenvalues().real();
+
1777 Eigen::MatrixXd eigen_vect = EigenSolver.eigenvectors().real();
+
1778 std::vector<std::tuple<double, Eigen::VectorXd>> eigen_vectors_and_values;
+
1779 double Sum_Eigen = 0;
+
1780 for(int i = 0; i < eigen_val.size(); i++)
+
1781 {
+
1782 std::tuple<double, Eigen::VectorXd> vec_and_val(eigen_val[i], eigen_vect.row(i));
+
1783 eigen_vectors_and_values.push_back(vec_and_val);
+
1784 Sum_Eigen += eigen_val[i];
+
1785 }
+
1786 std::sort(eigen_vectors_and_values.begin(), eigen_vectors_and_values.end(),
+
1787 [&](const std::tuple<double, Eigen::VectorXd>& a, const std::tuple<double, Eigen::VectorXd>& b) -> bool
+
1788 { return std::get<0>(a) > std::get<0>(b); } );
+
1789 int index = 0;
+
1790 for(auto const vect : eigen_vectors_and_values)
+
1791 {
+
1792 eigen_val(index) = std::get<0>(vect);
+
1793 eigen_vect.row(index) = std::get<1>(vect);
+
1794 index++;
+
1795 }
+
1796 TH1D* heigen_values_Eigen = new TH1D("eig_values", "Eigen Values", eigen_val.size(), 0.0, eigen_val.size());
+
1797 TH1D* heigen_cumulative_Eigen = new TH1D("eig_cumulative", "heigen_cumulative", eigen_val.size(), 0.0, eigen_val.size());
+
1798 TH1D* heigen_frac_Eigen = new TH1D("eig_fractional", "heigen_fractional", eigen_val.size(), 0.0, eigen_val.size());
+
1799 heigen_values_Eigen->GetXaxis()->SetTitle("Eigen Vector");
+
1800 heigen_values_Eigen->GetYaxis()->SetTitle("Eigen Value");
+
1801
+
1802 double Cumulative_Eigen = 0;
+
1803 for(int i = 0; i < eigen_val.size(); i++)
+
1804 {
+
1805 heigen_values_Eigen->SetBinContent(i+1, eigen_val(i));
+
1806 heigen_cumulative_Eigen->SetBinContent(i+1, eigen_val(i)/sum + Cumulative_Eigen);
+
1807 heigen_frac_Eigen->SetBinContent(i+1, eigen_val(i)/sum);
+
1808 Cumulative_Eigen += eigen_val(i)/sum;
+
1809 }
+
1810 heigen_values_Eigen->SetLineColor(kRed);
+
1811 heigen_values_Eigen->SetLineWidth(2);
+
1812 heigen_cumulative_Eigen->SetLineColor(kGreen);
+
1813 heigen_cumulative_Eigen->SetLineWidth(2);
+
1814 heigen_frac_Eigen->SetLineColor(kBlue);
+
1815 heigen_frac_Eigen->SetLineWidth(2);
+
1816
+
1817 c1->SetLogy();
+
1818 heigen_values_Eigen->SetMaximum(heigen_cumulative_Eigen->GetMaximum()+heigen_cumulative_Eigen->GetMaximum()*0.4);
+
1819 heigen_values_Eigen->Draw();
+
1820 heigen_cumulative_Eigen->Draw("SAME");
+
1821 heigen_frac_Eigen->Draw("SAME");
+
1822
+
1823 TLegend *leg_Eigen = new TLegend(0.2, 0.2, 0.6, 0.5);
+
1824 leg_Eigen->SetTextSize(0.04);
+
1825 leg_Eigen->AddEntry(heigen_values_Eigen, "Absolute", "l");
+
1826 leg_Eigen->AddEntry(heigen_frac_Eigen, "Fractional", "l");
+
1827 leg_Eigen->AddEntry(heigen_cumulative_Eigen, "Cumulative", "l");
+
1828
+
1829 leg_Eigen->SetLineColor(0);
+
1830 leg_Eigen->SetLineStyle(0);
+
1831 leg_Eigen->SetFillColor(0);
+
1832 leg_Eigen->SetFillStyle(0);
+
1833 leg_Eigen->Draw("Same");
+
1834
+
1835 c1->Print( "Debug_PCA.pdf");
+
1836 c1->SetLogy(0);
+
1837 delete heigen_values_Eigen;
+
1838 delete heigen_cumulative_Eigen;
+
1839 delete heigen_frac_Eigen;
+
1840 delete leg_Eigen;
+
1841
+
1842 TH2D* heigen_vectors_Eigen = new TH2D("Eigen_Vectors", "Eigen_Vectors", eigen_val.size(), 0.0, eigen_val.size(), eigen_val.size(), 0.0, eigen_val.size());
+
1843
+
1844 for(int i = 0; i < eigen_val.size(); i++)
+
1845 {
+
1846 for(int j = 0; j < eigen_val.size(); j++)
+
1847 {
+
1848 //KS: +1 because there is offset in histogram relative to TMatrix
+
1849 heigen_vectors_Eigen->SetBinContent(i+1,j+1, eigen_vect(i,j));
+
1850 }
+
1851 }
+
1852 heigen_vectors_Eigen->GetXaxis()->SetTitle("Parameter in Normal Base");
+
1853 heigen_vectors_Eigen->GetYaxis()->SetTitle("Parameter in Decomposed Base");
+
1854 heigen_vectors_Eigen->SetMarkerSize(0.15);
+
1855 minz = heigen_vectors_Eigen->GetMinimum();
+
1856 if (fabs(0-maxz)>fabs(0-minz)) heigen_vectors_Eigen->GetZaxis()->SetRangeUser(0-fabs(0-maxz),0+fabs(0-maxz));
+
1857 else heigen_vectors_Eigen->GetZaxis()->SetRangeUser(0-fabs(0-minz),0+fabs(0-minz));
+
1858
+
1859 if(PlotText) heigen_vectors_Eigen->Draw("COLZ TEXT");
+
1860 else heigen_vectors_Eigen->Draw("COLZ");
+
1861 c1->Print( "Debug_PCA.pdf");
+
1862
+
1863 heigen_vectors->SetTitle("ROOT minus Eigen");
+
1864 heigen_vectors->Add(heigen_vectors_Eigen, -1.);
+
1865 minz = heigen_vectors->GetMinimum();
+
1866 if (fabs(0-maxz)>fabs(0-minz)) heigen_vectors->GetZaxis()->SetRangeUser(0-fabs(0-maxz),0+fabs(0-maxz));
+
1867 else heigen_vectors->GetZaxis()->SetRangeUser(0-fabs(0-minz),0+fabs(0-minz));
+
1868 if(PlotText) heigen_vectors->Draw("COLZ TEXT");
+
1869 else heigen_vectors->Draw("COLZ");
+
1870 c1->Print( "Debug_PCA.pdf");
+
1871 delete heigen_vectors_Eigen;
1872
-
1873 c1->SetLogy();
-
1874 heigen_values->SetMaximum(heigen_cumulative->GetMaximum()+heigen_cumulative->GetMaximum()*0.4);
-
1875 heigen_values->Draw();
-
1876 heigen_frac->Draw("SAME");
-
1877 heigen_cumulative->Draw("SAME");
-
1878 EigenLine->Draw("Same");
-
1879 text->DrawTextNDC(0.42, 0.84,Form("Threshold = %g", eigen_threshold));
-
1880
-
1881 TLegend *leg = new TLegend(0.2, 0.2, 0.6, 0.5);
-
1882 leg->SetTextSize(0.04);
-
1883 leg->AddEntry(heigen_values, "Absolute", "l");
-
1884 leg->AddEntry(heigen_frac, "Fractional", "l");
-
1885 leg->AddEntry(heigen_cumulative, "Cumulative", "l");
-
1886
-
1887 leg->SetLineColor(0);
-
1888 leg->SetLineStyle(0);
-
1889 leg->SetFillColor(0);
-
1890 leg->SetFillStyle(0);
-
1891 leg->Draw("Same");
-
1892
-
1893 c1->Print("Debug_PCA.pdf");
-
1894 c1->SetRightMargin(0.15);
-
1895 c1->SetLogy(0);
-
1896 delete EigenLine;
-
1897 delete leg;
-
1898 delete text;
-
1899 delete heigen_values;
-
1900 delete heigen_frac;
-
1901 delete heigen_cumulative;
-
1902
-
1903 heigen_vectors->SetMarkerSize(0.2);
-
1904 minz = heigen_vectors->GetMinimum();
-
1905 if (fabs(0-maxz)>fabs(0-minz)) heigen_vectors->GetZaxis()->SetRangeUser(0-fabs(0-maxz),0+fabs(0-maxz));
-
1906 else heigen_vectors->GetZaxis()->SetRangeUser(0-fabs(0-minz),0+fabs(0-minz));
-
1907 if(PlotText) heigen_vectors->Draw("COLZ TEXT");
-
1908 else heigen_vectors->Draw("COLZ");
-
1909
-
1910 TLine *Eigen_Line = new TLine(0, nKeptPCApars, LastPCAdpar-FirstPCAdpar, nKeptPCApars);
-
1911 Eigen_Line->SetLineColor(kGreen);
-
1912 Eigen_Line->SetLineWidth(2);
-
1913 Eigen_Line->SetLineStyle(kDotted);
-
1914 Eigen_Line->Draw("SAME");
-
1915 c1->Print("Debug_PCA.pdf");
-
1916 delete Eigen_Line;
-
1917
-
1918 SubsetPCA->SetMarkerSize(0.2);
-
1919 minz = SubsetPCA->GetMinimum();
-
1920 if (fabs(0-maxz)>fabs(0-minz)) SubsetPCA->GetZaxis()->SetRangeUser(0-fabs(0-maxz),0+fabs(0-maxz));
-
1921 else SubsetPCA->GetZaxis()->SetRangeUser(0-fabs(0-minz),0+fabs(0-minz));
-
1922 if(PlotText) SubsetPCA->Draw("COLZ TEXT");
-
1923 else SubsetPCA->Draw("COLZ");
-
1924 c1->Print("Debug_PCA.pdf");
-
1925 delete SubsetPCA;
-
1926
-
1927 hTransferMat->SetMarkerSize(0.15);
-
1928 minz = hTransferMat->GetMinimum();
-
1929 if (fabs(0-maxz)>fabs(0-minz)) hTransferMat->GetZaxis()->SetRangeUser(0-fabs(0-maxz),0+fabs(0-maxz));
-
1930 else hTransferMat->GetZaxis()->SetRangeUser(0-fabs(0-minz),0+fabs(0-minz));
-
1931 if(PlotText) hTransferMat->Draw("COLZ TEXT");
-
1932 else hTransferMat->Draw("COLZ");
-
1933 c1->Print("Debug_PCA.pdf");
-
1934 delete hTransferMat;
-
1935
-
1936 hTransferMatT->SetMarkerSize(0.15);
-
1937 minz = hTransferMatT->GetMinimum();
-
1938 if (fabs(0-maxz)>fabs(0-minz)) hTransferMatT->GetZaxis()->SetRangeUser(0-fabs(0-maxz),0+fabs(0-maxz));
-
1939 else hTransferMatT->GetZaxis()->SetRangeUser(0-fabs(0-minz),0+fabs(0-minz));
-
1940 if(PlotText) hTransferMatT->Draw("COLZ TEXT");
-
1941 else hTransferMatT->Draw("COLZ");
-
1942 c1->Print( "Debug_PCA.pdf");
-
1943 delete hTransferMatT;
-
1944
-
1945
-
1946 //KS: Crosscheck against Eigen library
-
1947 #if DEBUG_PCA == 2
-
1948 Eigen::MatrixXd Submat_Eigen(submat.GetNrows(), submat.GetNcols());
-
1949
-
1950 #ifdef MULTITHREAD
-
1951 #pragma omp parallel for
-
1952 #endif
-
1953 for(int i = 0; i < submat.GetNrows(); i++)
-
1954 {
-
1955 for(int j = 0; j < submat.GetNcols(); j++)
-
1956 {
-
1957 Submat_Eigen(i,j) = (submat)(i,j);
-
1958 }
-
1959 }
-
1960 Eigen::EigenSolver<Eigen::MatrixXd> EigenSolver;
-
1961 EigenSolver.compute(Submat_Eigen);
-
1962 Eigen::VectorXd eigen_val = EigenSolver.eigenvalues().real();
-
1963 Eigen::MatrixXd eigen_vect = EigenSolver.eigenvectors().real();
-
1964 std::vector<std::tuple<double, Eigen::VectorXd>> eigen_vectors_and_values;
-
1965 double Sum_Eigen = 0;
-
1966 for(int i = 0; i < eigen_val.size(); i++)
-
1967 {
-
1968 std::tuple<double, Eigen::VectorXd> vec_and_val(eigen_val[i], eigen_vect.row(i));
-
1969 eigen_vectors_and_values.push_back(vec_and_val);
-
1970 Sum_Eigen += eigen_val[i];
-
1971 }
-
1972 std::sort(eigen_vectors_and_values.begin(), eigen_vectors_and_values.end(),
-
1973 [&](const std::tuple<double, Eigen::VectorXd>& a, const std::tuple<double, Eigen::VectorXd>& b) -> bool
-
1974 { return std::get<0>(a) > std::get<0>(b); } );
-
1975 int index = 0;
-
1976 for(auto const vect : eigen_vectors_and_values)
-
1977 {
-
1978 eigen_val(index) = std::get<0>(vect);
-
1979 eigen_vect.row(index) = std::get<1>(vect);
-
1980 index++;
-
1981 }
-
1982 TH1D* heigen_values_Eigen = new TH1D("eig_values", "Eigen Values", eigen_val.size(), 0.0, eigen_val.size());
-
1983 TH1D* heigen_cumulative_Eigen = new TH1D("eig_cumulative", "heigen_cumulative", eigen_val.size(), 0.0, eigen_val.size());
-
1984 TH1D* heigen_frac_Eigen = new TH1D("eig_fractional", "heigen_fractional", eigen_val.size(), 0.0, eigen_val.size());
-
1985 heigen_values_Eigen->GetXaxis()->SetTitle("Eigen Vector");
-
1986 heigen_values_Eigen->GetYaxis()->SetTitle("Eigen Value");
-
1987
-
1988 double Cumulative_Eigen = 0;
-
1989 for(int i = 0; i < eigen_val.size(); i++)
-
1990 {
-
1991 heigen_values_Eigen->SetBinContent(i+1, eigen_val(i));
-
1992 heigen_cumulative_Eigen->SetBinContent(i+1, eigen_val(i)/sum + Cumulative_Eigen);
-
1993 heigen_frac_Eigen->SetBinContent(i+1, eigen_val(i)/sum);
-
1994 Cumulative_Eigen += eigen_val(i)/sum;
-
1995 }
-
1996 heigen_values_Eigen->SetLineColor(kRed);
-
1997 heigen_values_Eigen->SetLineWidth(2);
-
1998 heigen_cumulative_Eigen->SetLineColor(kGreen);
-
1999 heigen_cumulative_Eigen->SetLineWidth(2);
-
2000 heigen_frac_Eigen->SetLineColor(kBlue);
-
2001 heigen_frac_Eigen->SetLineWidth(2);
-
2002
-
2003 c1->SetLogy();
-
2004 heigen_values_Eigen->SetMaximum(heigen_cumulative_Eigen->GetMaximum()+heigen_cumulative_Eigen->GetMaximum()*0.4);
-
2005 heigen_values_Eigen->Draw();
-
2006 heigen_cumulative_Eigen->Draw("SAME");
-
2007 heigen_frac_Eigen->Draw("SAME");
-
2008
-
2009 TLegend *leg_Eigen = new TLegend(0.2, 0.2, 0.6, 0.5);
-
2010 leg_Eigen->SetTextSize(0.04);
-
2011 leg_Eigen->AddEntry(heigen_values_Eigen, "Absolute", "l");
-
2012 leg_Eigen->AddEntry(heigen_frac_Eigen, "Fractional", "l");
-
2013 leg_Eigen->AddEntry(heigen_cumulative_Eigen, "Cumulative", "l");
-
2014
-
2015 leg_Eigen->SetLineColor(0);
-
2016 leg_Eigen->SetLineStyle(0);
-
2017 leg_Eigen->SetFillColor(0);
-
2018 leg_Eigen->SetFillStyle(0);
-
2019 leg_Eigen->Draw("Same");
-
2020
-
2021 c1->Print( "Debug_PCA.pdf");
-
2022 c1->SetLogy(0);
-
2023 delete heigen_values_Eigen;
-
2024 delete heigen_cumulative_Eigen;
-
2025 delete heigen_frac_Eigen;
-
2026 delete leg_Eigen;
-
2027
-
2028 TH2D* heigen_vectors_Eigen = new TH2D("Eigen_Vectors", "Eigen_Vectors", eigen_val.size(), 0.0, eigen_val.size(), eigen_val.size(), 0.0, eigen_val.size());
-
2029
-
2030 for(int i = 0; i < eigen_val.size(); i++)
-
2031 {
-
2032 for(int j = 0; j < eigen_val.size(); j++)
-
2033 {
-
2034 //KS: +1 because there is offset in histogram relative to TMatrix
-
2035 heigen_vectors_Eigen->SetBinContent(i+1,j+1, eigen_vect(i,j));
-
2036 }
-
2037 }
-
2038 heigen_vectors_Eigen->GetXaxis()->SetTitle("Parameter in Normal Base");
-
2039 heigen_vectors_Eigen->GetYaxis()->SetTitle("Parameter in Decomposed Base");
-
2040 heigen_vectors_Eigen->SetMarkerSize(0.15);
-
2041 minz = heigen_vectors_Eigen->GetMinimum();
-
2042 if (fabs(0-maxz)>fabs(0-minz)) heigen_vectors_Eigen->GetZaxis()->SetRangeUser(0-fabs(0-maxz),0+fabs(0-maxz));
-
2043 else heigen_vectors_Eigen->GetZaxis()->SetRangeUser(0-fabs(0-minz),0+fabs(0-minz));
-
2044
-
2045 if(PlotText) heigen_vectors_Eigen->Draw("COLZ TEXT");
-
2046 else heigen_vectors_Eigen->Draw("COLZ");
-
2047 c1->Print( "Debug_PCA.pdf");
-
2048
-
2049 heigen_vectors->SetTitle("ROOT minus Eigen");
-
2050 heigen_vectors->Add(heigen_vectors_Eigen, -1.);
-
2051 minz = heigen_vectors->GetMinimum();
-
2052 if (fabs(0-maxz)>fabs(0-minz)) heigen_vectors->GetZaxis()->SetRangeUser(0-fabs(0-maxz),0+fabs(0-maxz));
-
2053 else heigen_vectors->GetZaxis()->SetRangeUser(0-fabs(0-minz),0+fabs(0-minz));
-
2054 if(PlotText) heigen_vectors->Draw("COLZ TEXT");
-
2055 else heigen_vectors->Draw("COLZ");
-
2056 c1->Print( "Debug_PCA.pdf");
-
2057 delete heigen_vectors_Eigen;
-
2058
-
2059 #endif
-
2060 delete heigen_vectors;
-
2061
-
2062 c1->Print( "Debug_PCA.pdf]");
-
2063 delete c1;
-
2064 PCA_Debug->Close();
-
2065 delete PCA_Debug;
-
2066}
-
2067#endif
+
1873 #endif
+
1874 delete heigen_vectors;
+
1875
+
1876 c1->Print( "Debug_PCA.pdf]");
+
1877 delete c1;
+
1878 PCA_Debug->Close();
+
1879 delete PCA_Debug;
+
1880}
+
1881#endif
nominal
std::vector< int > nominal
Definition GetPenaltyTerm.cpp:38
-
MACH3LOG_CRITICAL
#define MACH3LOG_CRITICAL
Definition MaCh3Logger.h:16
-
MACH3LOG_DEBUG
#define MACH3LOG_DEBUG
Definition MaCh3Logger.h:12
-
MACH3LOG_ERROR
#define MACH3LOG_ERROR
Definition MaCh3Logger.h:15
-
MACH3LOG_INFO
#define MACH3LOG_INFO
Definition MaCh3Logger.h:13
-
MACH3LOG_WARN
#define MACH3LOG_WARN
Definition MaCh3Logger.h:14
+
MACH3LOG_CRITICAL
#define MACH3LOG_CRITICAL
Definition MaCh3Logger.h:19
+
MACH3LOG_DEBUG
#define MACH3LOG_DEBUG
Definition MaCh3Logger.h:15
+
MACH3LOG_ERROR
#define MACH3LOG_ERROR
Definition MaCh3Logger.h:18
+
MACH3LOG_INFO
#define MACH3LOG_INFO
Definition MaCh3Logger.h:16
+
MACH3LOG_WARN
#define MACH3LOG_WARN
Definition MaCh3Logger.h:17
_restrict_
#define _restrict_
KS: Using restrict limits the effects of pointer aliasing, aiding optimizations. While reading I foun...
Definition Structs.h:26
-
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:18
-
MaCh3Exception
Custom exception class for MaCh3 errors.
Definition MaCh3Exception.h:10
+
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:21
+
MaCh3Exception
Custom exception class for MaCh3 errors.
Definition MaCh3Exception.h:12
ThrowParms
No idea really...
Definition ThrowParms.h:19
-
covarianceBase::CalcLikelihood
double CalcLikelihood()
Calc penalty term based on inverted covariance matrix.
Definition covarianceBase.cpp:999
-
covarianceBase::_fGlobalStepScale
double _fGlobalStepScale
Global step scale applied ot all params in this class.
Definition covarianceBase.h:429
-
covarianceBase::getDiagonalError
double getDiagonalError(const int i)
Get diagonal error for ith parameter.
Definition covarianceBase.h:162
-
covarianceBase::GetParName
std::string GetParName(const int i)
Get name of covariance.
Definition covarianceBase.h:147
-
covarianceBase::resetIndivStepScale
void resetIndivStepScale()
Adaptive Step Tuning Stuff.
Definition covarianceBase.cpp:1328
-
covarianceBase::_fPropVal
std::vector< double > _fPropVal
Proposed value of the parameter.
Definition covarianceBase.h:447
-
covarianceBase::getParInit
double getParInit(const int i)
Get prior parameter value.
Definition covarianceBase.h:226
+
adaptive_mcmc::AdaptiveMCMCHandler::Print
void Print()
Print all class members.
Definition AdaptiveMCMCHandler.cpp:221
+
adaptive_mcmc::AdaptiveMCMCHandler::start_adaptive_update
int start_adaptive_update
When do we stop update the adaptive matrix.
Definition AdaptiveMCMCHandler.h:62
+
adaptive_mcmc::AdaptiveMCMCHandler::start_adaptive_throw
int start_adaptive_throw
Definition AdaptiveMCMCHandler.h:59
+
adaptive_mcmc::AdaptiveMCMCHandler::end_adaptive_update
int end_adaptive_update
Steps between changing throw matrix.
Definition AdaptiveMCMCHandler.h:65
+
adaptive_mcmc::AdaptiveMCMCHandler::UpdateAdaptiveCovariance
void UpdateAdaptiveCovariance(const std::vector< double > &_fCurrVal, const int steps_post_burn, const int Npars)
Method to update adaptive MCMC.
Definition AdaptiveMCMCHandler.cpp:184
+
adaptive_mcmc::AdaptiveMCMCHandler::adaptive_update_step
int adaptive_update_step
Steps between changing throw matrix.
Definition AdaptiveMCMCHandler.h:68
+
adaptive_mcmc::AdaptiveMCMCHandler::CreateNewAdaptiveCovariance
void CreateNewAdaptiveCovariance(const int Npars)
If we don't have a covariance matrix to start from for adaptive tune we need to make one!
Definition AdaptiveMCMCHandler.cpp:57
+
adaptive_mcmc::AdaptiveMCMCHandler::InitFromConfig
void InitFromConfig(const YAML::Node &adapt_manager, const std::string &matrix_name_str, const int Npars)
Read initial values from config file.
Definition AdaptiveMCMCHandler.cpp:27
+
adaptive_mcmc::AdaptiveMCMCHandler::SetThrowMatrixFromFile
void SetThrowMatrixFromFile(const std::string &matrix_file_name, const std::string &matrix_name, const std::string &means_name, bool &use_adaptive, const int Npars)
sets throw matrix from a file
Definition AdaptiveMCMCHandler.cpp:130
+
adaptive_mcmc::AdaptiveMCMCHandler::adaptive_covariance
TMatrixDSym * adaptive_covariance
Full adaptive covariance matrix.
Definition AdaptiveMCMCHandler.h:81
+
covarianceBase::CalcLikelihood
double CalcLikelihood()
Calc penalty term based on inverted covariance matrix.
Definition covarianceBase.cpp:1002
+
covarianceBase::_fGlobalStepScale
double _fGlobalStepScale
Global step scale applied ot all params in this class.
Definition covarianceBase.h:443
+
covarianceBase::getDiagonalError
double getDiagonalError(const int i)
Get diagonal error for ith parameter.
Definition covarianceBase.h:163
+
covarianceBase::GetParName
std::string GetParName(const int i)
Get name of covariance.
Definition covarianceBase.h:148
+
covarianceBase::resetIndivStepScale
void resetIndivStepScale()
Adaptive Step Tuning Stuff.
Definition covarianceBase.cpp:1329
+
covarianceBase::_fPropVal
std::vector< double > _fPropVal
Proposed value of the parameter.
Definition covarianceBase.h:461
+
covarianceBase::getParInit
double getParInit(const int i)
Get prior parameter value.
Definition covarianceBase.h:227
covarianceBase::~covarianceBase
virtual ~covarianceBase()
Destructor.
Definition covarianceBase.cpp:83
-
covarianceBase::setFlatPrior
void setFlatPrior(const int i, const bool eL)
Set if parameter should have flat prior or not.
Definition covarianceBase.cpp:1202
-
covarianceBase::setIndivStepScale
void setIndivStepScale(const int ParameterIndex, const double StepScale)
DB Function to set fIndivStepScale from a vector (Can be used from execs and inside covariance constr...
Definition covarianceBase.h:106
-
covarianceBase::isParameterFixed
bool isParameterFixed(const int i)
Is parameter fixed or not.
Definition covarianceBase.h:348
-
covarianceBase::getNpars
int getNpars()
Get number of params which will be different depending if using Eigen decomposition or not.
Definition covarianceBase.h:319
-
covarianceBase::fParProp_PCA
TVectorD fParProp_PCA
CW: Current parameter value in PCA base.
Definition covarianceBase.h:489
-
covarianceBase::_fUpBound
std::vector< double > _fUpBound
Upper physical bound, parameter will not be able to go beyond it.
Definition covarianceBase.h:455
-
covarianceBase::randomize
void randomize()
"Randomize" the parameters in the covariance class for the proposed step. Used the proposal kernel an...
Definition covarianceBase.cpp:793
-
covarianceBase::_fError
std::vector< double > _fError
Prior error on the parameter.
Definition covarianceBase.h:451
-
covarianceBase::invCovMatrix
TMatrixDSym * invCovMatrix
The inverse covariance matrix.
Definition covarianceBase.h:417
-
covarianceBase::nKeptPCApars
int nKeptPCApars
Total number that remained after applying PCA Threshold.
Definition covarianceBase.h:475
-
covarianceBase::_fIndivStepScale
std::vector< double > _fIndivStepScale
Individual step scale used by MCMC algorithm.
Definition covarianceBase.h:457
-
covarianceBase::_fNames
std::vector< std::string > _fNames
ETA _fNames is set automatically in the covariance class to be something like xsec_i,...
Definition covarianceBase.h:435
-
covarianceBase::matrixName
const char * matrixName
Name of cov matrix.
Definition covarianceBase.h:413
-
covarianceBase::InvertCovMatrix
double ** InvertCovMatrix
KS: Same as above but much faster as TMatrixDSym cache miss.
Definition covarianceBase.h:419
-
covarianceBase::throwParCurr
void throwParCurr(const double mag=1.)
Helper function to throw the current parameter by mag sigma. Can study bias in MCMC with this; put di...
Definition covarianceBase.cpp:937
+
covarianceBase::setFlatPrior
void setFlatPrior(const int i, const bool eL)
Set if parameter should have flat prior or not.
Definition covarianceBase.cpp:1203
+
covarianceBase::setIndivStepScale
void setIndivStepScale(const int ParameterIndex, const double StepScale)
DB Function to set fIndivStepScale from a vector (Can be used from execs and inside covariance constr...
Definition covarianceBase.h:107
+
covarianceBase::isParameterFixed
bool isParameterFixed(const int i)
Is parameter fixed or not.
Definition covarianceBase.h:349
+
covarianceBase::getNpars
int getNpars()
Get number of params which will be different depending if using Eigen decomposition or not.
Definition covarianceBase.h:320
+
covarianceBase::fParProp_PCA
TVectorD fParProp_PCA
CW: Current parameter value in PCA base.
Definition covarianceBase.h:503
+
covarianceBase::_fUpBound
std::vector< double > _fUpBound
Upper physical bound, parameter will not be able to go beyond it.
Definition covarianceBase.h:469
+
covarianceBase::randomize
void randomize()
"Randomize" the parameters in the covariance class for the proposed step. Used the proposal kernel an...
Definition covarianceBase.cpp:794
+
covarianceBase::_fError
std::vector< double > _fError
Prior error on the parameter.
Definition covarianceBase.h:465
+
covarianceBase::invCovMatrix
TMatrixDSym * invCovMatrix
The inverse covariance matrix.
Definition covarianceBase.h:431
+
covarianceBase::nKeptPCApars
int nKeptPCApars
Total number that remained after applying PCA Threshold.
Definition covarianceBase.h:489
+
covarianceBase::_fIndivStepScale
std::vector< double > _fIndivStepScale
Individual step scale used by MCMC algorithm.
Definition covarianceBase.h:471
+
covarianceBase::_fNames
std::vector< std::string > _fNames
ETA _fNames is set automatically in the covariance class to be something like xsec_i,...
Definition covarianceBase.h:449
+
covarianceBase::matrixName
const char * matrixName
Name of cov matrix.
Definition covarianceBase.h:427
+
covarianceBase::InvertCovMatrix
double ** InvertCovMatrix
KS: Same as above but much faster as TMatrixDSym cache miss.
Definition covarianceBase.h:433
+
covarianceBase::throwParCurr
void throwParCurr(const double mag=1.)
Helper function to throw the current parameter by mag sigma. Can study bias in MCMC with this; put di...
Definition covarianceBase.cpp:940
covarianceBase::covarianceBase
covarianceBase(const std::vector< std::string > &YAMLFile, const char *name, double threshold=-1, int FirstPCAdpar=-999, int LastPCAdpar=-999)
ETA - constructor for a YAML file.
Definition covarianceBase.cpp:12
-
covarianceBase::updateAdaptiveCovariance
void updateAdaptiveCovariance()
Method to update adaptive MCMC.
Definition covarianceBase.cpp:1600
-
covarianceBase::setThrowMatrixFromFile
void setThrowMatrixFromFile(const std::string &matrix_file_name, const std::string &matrix_name, const std::string &means_name)
sets throw matrix from a file
Definition covarianceBase.cpp:1493
-
covarianceBase::TransferMatT
TMatrixD TransferMatT
Matrix used to converting from normal base to PCA base.
Definition covarianceBase.h:487
-
covarianceBase::TransferMat
TMatrixD TransferMat
Matrix used to converting from PCA base to normal base.
Definition covarianceBase.h:485
-
covarianceBase::LastPCAdpar
int LastPCAdpar
Index of the last param that is being decomposed.
Definition covarianceBase.h:473
-
covarianceBase::setCovMatrix
void setCovMatrix(TMatrixDSym *cov)
Set covariance matrix.
Definition covarianceBase.cpp:500
-
covarianceBase::setName
void setName(const char *name)
Set matrix name.
Definition covarianceBase.h:68
-
covarianceBase::random_number
TRandom3 ** random_number
KS: Set Random numbers for each thread so each thread has different seed.
Definition covarianceBase.h:422
-
covarianceBase::getProposed
std::vector< double > getProposed() const
Get vector of all proposed parameter values.
Definition covarianceBase.cpp:607
-
covarianceBase::MatrixVectorMulti
void MatrixVectorMulti(double *_restrict_ VecMulti, double **_restrict_ matrix, const double *_restrict_ vector, const int n)
KS: Custom function to perform multiplication of matrix and vector with multithreading.
Definition covarianceBase.cpp:1222
-
covarianceBase::TransferToPCA
void TransferToPCA()
Transfer param values from normal base to PCA base.
Definition covarianceBase.cpp:571
-
covarianceBase::TransferToParam
void TransferToParam()
Transfer param values from PCA base to normal base.
Definition covarianceBase.cpp:589
-
covarianceBase::setParCurrProp
void setParCurrProp(const int i, const double val)
Set current parameter value.
Definition covarianceBase.cpp:770
-
covarianceBase::GetParFancyName
std::string GetParFancyName(const int i)
Get fancy name of the Parameter.
Definition covarianceBase.h:153
-
covarianceBase::adaption_struct
adaptive_mcmc::AdaptiveMCMCStruct adaption_struct
Struct containing information about adaption.
Definition covarianceBase.h:526
-
covarianceBase::covMatrix
TMatrixDSym * covMatrix
The covariance matrix.
Definition covarianceBase.h:415
-
covarianceBase::throwMatrix
TMatrixDSym * throwMatrix
Definition covarianceBase.h:498
-
covarianceBase::randParams
double * randParams
Random number taken from gaussian around prior error used for corr_throw.
Definition covarianceBase.h:425
-
covarianceBase::initialiseAdaption
void initialiseAdaption(const YAML::Node &adapt_manager)
Initialise adaptive MCMC.
Definition covarianceBase.cpp:1423
-
covarianceBase::printNominalCurrProp
void printNominalCurrProp()
Print nominal, current and proposed value for each parameter.
Definition covarianceBase.cpp:976
-
covarianceBase::getName
const char * getName()
Get name of covariance.
Definition covarianceBase.h:144
-
covarianceBase::_fPreFitValue
std::vector< double > _fPreFitValue
Parameter value dictated by the prior model. Based on it penalty term is calculated.
Definition covarianceBase.h:443
-
covarianceBase::ReserveMemory
void ReserveMemory(const int size)
Initialise vectors with parameters information.
Definition covarianceBase.cpp:521
-
covarianceBase::MatrixVectorMultiSingle
double MatrixVectorMultiSingle(double **_restrict_ matrix, const double *_restrict_ vector, const int Length, const int i)
KS: Custom function to perform multiplication of matrix and single element which is thread safe.
Definition covarianceBase.cpp:1239
-
covarianceBase::corr_throw
double * corr_throw
Result of multiplication of Cholesky matrix and randParams.
Definition covarianceBase.h:427
-
covarianceBase::fParSigma_PCA
std::vector< double > fParSigma_PCA
Tells if parameter is fixed in PCA base or not.
Definition covarianceBase.h:493
-
covarianceBase::size
int size
Total number of parmas, deprecated, please don't use it.
Definition covarianceBase.h:411
-
covarianceBase::updateThrowMatrix
void updateThrowMatrix(TMatrixDSym *cov)
Definition covarianceBase.cpp:1378
-
covarianceBase::setStepScale
void setStepScale(const double scale)
Set global step scale for covariance object.
Definition covarianceBase.cpp:1124
-
covarianceBase::use_adaptive
bool use_adaptive
Are we using AMCMC?
Definition covarianceBase.h:522
-
covarianceBase::RandomConfiguration
void RandomConfiguration()
Randomly throw the parameters in their 1 sigma range.
Definition covarianceBase.cpp:723
-
covarianceBase::makeClosestPosDef
void makeClosestPosDef(TMatrixDSym *cov)
HW: Finds closest possible positive definite matrix in Frobenius Norm ||.||_frob Where ||X||_frob=sqr...
Definition covarianceBase.cpp:1660
-
covarianceBase::createNewAdaptiveCovariance
void createNewAdaptiveCovariance()
method to create new throw matrix
Definition covarianceBase.cpp:1590
-
covarianceBase::ConstructPCA
void ConstructPCA()
CW: Calculate eigen values, prepare transition matrices and remove param based on defined threshold.
Definition covarianceBase.cpp:122
-
covarianceBase::_fLowBound
std::vector< double > _fLowBound
Lowest physical bound, parameter will not be able to go beyond it.
Definition covarianceBase.h:453
-
covarianceBase::_fYAMLDoc
YAML::Node _fYAMLDoc
Stores config describing systematics.
Definition covarianceBase.h:439
+
covarianceBase::updateAdaptiveCovariance
void updateAdaptiveCovariance()
Method to update adaptive MCMC.
Definition covarianceBase.cpp:1449
+
covarianceBase::TransferMatT
TMatrixD TransferMatT
Matrix used to converting from normal base to PCA base.
Definition covarianceBase.h:501
+
covarianceBase::TransferMat
TMatrixD TransferMat
Matrix used to converting from PCA base to normal base.
Definition covarianceBase.h:499
+
covarianceBase::LastPCAdpar
int LastPCAdpar
Index of the last param that is being decomposed.
Definition covarianceBase.h:487
+
covarianceBase::setCovMatrix
void setCovMatrix(TMatrixDSym *cov)
Set covariance matrix.
Definition covarianceBase.cpp:495
+
covarianceBase::setName
void setName(const char *name)
Set matrix name.
Definition covarianceBase.h:69
+
covarianceBase::random_number
TRandom3 ** random_number
KS: Set Random numbers for each thread so each thread has different seed.
Definition covarianceBase.h:436
+
covarianceBase::getProposed
std::vector< double > getProposed() const
Get vector of all proposed parameter values.
Definition covarianceBase.cpp:606
+
covarianceBase::MatrixVectorMulti
void MatrixVectorMulti(double *_restrict_ VecMulti, double **_restrict_ matrix, const double *_restrict_ vector, const int n)
KS: Custom function to perform multiplication of matrix and vector with multithreading.
Definition covarianceBase.cpp:1223
+
covarianceBase::TransferToPCA
void TransferToPCA()
Transfer param values from normal base to PCA base.
Definition covarianceBase.cpp:568
+
covarianceBase::TransferToParam
void TransferToParam()
Transfer param values from PCA base to normal base.
Definition covarianceBase.cpp:587
+
covarianceBase::setParCurrProp
void setParCurrProp(const int i, const double val)
Set current parameter value.
Definition covarianceBase.cpp:768
+
covarianceBase::GetParFancyName
std::string GetParFancyName(const int i)
Get fancy name of the Parameter.
Definition covarianceBase.h:154
+
covarianceBase::covMatrix
TMatrixDSym * covMatrix
The covariance matrix.
Definition covarianceBase.h:429
+
covarianceBase::throwMatrix
TMatrixDSym * throwMatrix
Matrix which we use for step proposal before Cholesky decomposition (not actually used for step propo...
Definition covarianceBase.h:512
+
covarianceBase::randParams
double * randParams
Random number taken from gaussian around prior error used for corr_throw.
Definition covarianceBase.h:439
+
covarianceBase::initialiseAdaption
void initialiseAdaption(const YAML::Node &adapt_manager)
Initialise adaptive MCMC.
Definition covarianceBase.cpp:1400
+
covarianceBase::printNominalCurrProp
void printNominalCurrProp()
Print nominal, current and proposed value for each parameter.
Definition covarianceBase.cpp:979
+
covarianceBase::getName
const char * getName()
Get name of covariance.
Definition covarianceBase.h:145
+
covarianceBase::_fPreFitValue
std::vector< double > _fPreFitValue
Parameter value dictated by the prior model. Based on it penalty term is calculated.
Definition covarianceBase.h:457
+
covarianceBase::ReserveMemory
void ReserveMemory(const int size)
Initialise vectors with parameters information.
Definition covarianceBase.cpp:516
+
covarianceBase::MatrixVectorMultiSingle
double MatrixVectorMultiSingle(double **_restrict_ matrix, const double *_restrict_ vector, const int Length, const int i)
KS: Custom function to perform multiplication of matrix and single element which is thread safe.
Definition covarianceBase.cpp:1240
+
covarianceBase::corr_throw
double * corr_throw
Result of multiplication of Cholesky matrix and randParams.
Definition covarianceBase.h:441
+
covarianceBase::fParSigma_PCA
std::vector< double > fParSigma_PCA
Tells if parameter is fixed in PCA base or not.
Definition covarianceBase.h:507
+
covarianceBase::size
int size
Total number of params, deprecated, please don't use it.
Definition covarianceBase.h:425
+
covarianceBase::updateThrowMatrix
void updateThrowMatrix(TMatrixDSym *cov)
Definition covarianceBase.cpp:1380
+
covarianceBase::setStepScale
void setStepScale(const double scale)
Set global step scale for covariance object.
Definition covarianceBase.cpp:1126
+
covarianceBase::use_adaptive
bool use_adaptive
Are we using AMCMC?
Definition covarianceBase.h:519
+
covarianceBase::RandomConfiguration
void RandomConfiguration()
Randomly throw the parameters in their 1 sigma range.
Definition covarianceBase.cpp:721
+
covarianceBase::makeClosestPosDef
void makeClosestPosDef(TMatrixDSym *cov)
HW: Finds closest possible positive definite matrix in Frobenius Norm ||.||_frob Where ||X||_frob=sqr...
Definition covarianceBase.cpp:1476
+
covarianceBase::ConstructPCA
void ConstructPCA()
CW: Calculate eigen values, prepare transition matrices and remove param based on defined threshold.
Definition covarianceBase.cpp:117
+
covarianceBase::_fLowBound
std::vector< double > _fLowBound
Lowest physical bound, parameter will not be able to go beyond it.
Definition covarianceBase.h:467
+
covarianceBase::_fYAMLDoc
YAML::Node _fYAMLDoc
Stores config describing systematics.
Definition covarianceBase.h:453
covarianceBase::proposeStep
virtual void proposeStep()
Generate a new proposed state.
Definition covarianceBase.cpp:779
-
covarianceBase::_fFancyNames
std::vector< std::string > _fFancyNames
Fancy name for example rather than xsec_0 it is MAQE, useful for human reading.
Definition covarianceBase.h:437
-
covarianceBase::setSingleParameter
void setSingleParameter(const int parNo, const double parVal)
Definition covarianceBase.cpp:761
-
covarianceBase::_fGenerated
std::vector< double > _fGenerated
Generated value of the parameter.
Definition covarianceBase.h:449
-
covarianceBase::GetLikelihood
virtual double GetLikelihood()
Return CalcLikelihood if some params were thrown out of boundary return LARGE_LOGL
Definition covarianceBase.cpp:1034
-
covarianceBase::PrintLength
unsigned int PrintLength
KS: This is used when printing parameters, sometimes we have super long parameters name,...
Definition covarianceBase.h:432
-
covarianceBase::acceptStep
void acceptStep()
Accepted this step.
Definition covarianceBase.cpp:886
-
covarianceBase::setParameters
void setParameters(const std::vector< double > &pars={})
Set parameter values using vector, it has to have same size as covariance class.
Definition covarianceBase.cpp:1060
-
covarianceBase::throwParameters
void throwParameters()
Throw the parameters according to the covariance matrix. This shouldn't be used in MCMC code ase it c...
Definition covarianceBase.cpp:668
-
covarianceBase::fParCurr_PCA
TVectorD fParCurr_PCA
CW: Proposed parameter value in PCA base.
Definition covarianceBase.h:491
-
covarianceBase::setPar
void setPar(const int i, const double val)
Set all the covariance matrix parameters to a user-defined value.
Definition covarianceBase.cpp:558
-
covarianceBase::SetBranches
void SetBranches(TTree &tree, bool SaveProposal=false)
set branches for output file
Definition covarianceBase.cpp:1096
-
covarianceBase::toggleFixParameter
void toggleFixParameter(const int i)
fix parameter at prior values
Definition covarianceBase.cpp:1149
-
covarianceBase::SaveUpdatedMatrixConfig
void SaveUpdatedMatrixConfig()
KS: After step scale, prefit etc. value were modified save this modified config.
Definition covarianceBase.cpp:1749
-
covarianceBase::pca
bool pca
perform PCA or not
Definition covarianceBase.h:465
-
covarianceBase::throwMatrix_CholDecomp
TMatrixD * throwMatrix_CholDecomp
Definition covarianceBase.h:499
-
covarianceBase::CorrelateSteps
void CorrelateSteps()
Use Cholesky throw matrix for better step proposal.
Definition covarianceBase.cpp:838
-
covarianceBase::FirstPCAdpar
int FirstPCAdpar
Index of the first param that is being decomposed.
Definition covarianceBase.h:471
-
covarianceBase::init
void init(const char *name, const char *file)
Definition covarianceBase.cpp:256
-
covarianceBase::GetCorrelationMatrix
TH2D * GetCorrelationMatrix()
KS: Convert covariance matrix to correlation matrix and return TH2D which can be used for fancy plott...
Definition covarianceBase.cpp:1720
- -
covarianceBase::CheckBounds
virtual int CheckBounds()
Check if parameters were proposed outside physical boundary.
Definition covarianceBase.cpp:1019
-
covarianceBase::_fNumParPCA
int _fNumParPCA
Number of parameters in PCA base.
Definition covarianceBase.h:469
-
covarianceBase::eigen_vectors
TMatrixD eigen_vectors
Eigen vectors only of params which are being decomposed.
Definition covarianceBase.h:479
-
covarianceBase::_fNumPar
int _fNumPar
Number of systematic parameters.
Definition covarianceBase.h:441
-
covarianceBase::throwMatrixCholDecomp
double ** throwMatrixCholDecomp
Throw matrix that is being used in the fit, much faster as TMatrixDSym cache miss.
Definition covarianceBase.h:501
-
covarianceBase::setAdaptiveBlocks
void setAdaptiveBlocks(std::vector< std::vector< int > > block_indices)
sets adaptive block matrix
Definition covarianceBase.cpp:1547
+
covarianceBase::_fFancyNames
std::vector< std::string > _fFancyNames
Fancy name for example rather than xsec_0 it is MAQE, useful for human reading.
Definition covarianceBase.h:451
+
covarianceBase::setSingleParameter
void setSingleParameter(const int parNo, const double parVal)
Definition covarianceBase.cpp:759
+
covarianceBase::_fGenerated
std::vector< double > _fGenerated
Generated value of the parameter.
Definition covarianceBase.h:463
+
covarianceBase::GetLikelihood
virtual double GetLikelihood()
Return CalcLikelihood if some params were thrown out of boundary return LARGE_LOGL
Definition covarianceBase.cpp:1037
+
covarianceBase::PrintLength
unsigned int PrintLength
KS: This is used when printing parameters, sometimes we have super long parameters name,...
Definition covarianceBase.h:446
+
covarianceBase::acceptStep
void acceptStep()
Accepted this step.
Definition covarianceBase.cpp:887
+
covarianceBase::setParameters
void setParameters(const std::vector< double > &pars={})
Set parameter values using vector, it has to have same size as covariance class.
Definition covarianceBase.cpp:1062
+
covarianceBase::throwParameters
void throwParameters()
Throw the parameters according to the covariance matrix. This shouldn't be used in MCMC code ase it c...
Definition covarianceBase.cpp:667
+
covarianceBase::fParCurr_PCA
TVectorD fParCurr_PCA
CW: Proposed parameter value in PCA base.
Definition covarianceBase.h:505
+
covarianceBase::setPar
void setPar(const int i, const double val)
Set all the covariance matrix parameters to a user-defined value.
Definition covarianceBase.cpp:554
+
covarianceBase::SetBranches
void SetBranches(TTree &tree, bool SaveProposal=false)
set branches for output file
Definition covarianceBase.cpp:1098
+
covarianceBase::toggleFixParameter
void toggleFixParameter(const int i)
fix parameter at prior values
Definition covarianceBase.cpp:1151
+
covarianceBase::SaveUpdatedMatrixConfig
void SaveUpdatedMatrixConfig()
KS: After step scale, prefit etc. value were modified save this modified config.
Definition covarianceBase.cpp:1563
+
covarianceBase::AdaptiveHandler
adaptive_mcmc::AdaptiveMCMCHandler AdaptiveHandler
Struct containing information about adaption.
Definition covarianceBase.h:524
+
covarianceBase::pca
bool pca
perform PCA or not
Definition covarianceBase.h:479
+
covarianceBase::throwMatrix_CholDecomp
TMatrixD * throwMatrix_CholDecomp
Matrix which we use for step proposal after Cholesky decomposition.
Definition covarianceBase.h:514
+
covarianceBase::CorrelateSteps
void CorrelateSteps()
Use Cholesky throw matrix for better step proposal.
Definition covarianceBase.cpp:839
+
covarianceBase::FirstPCAdpar
int FirstPCAdpar
Index of the first param that is being decomposed.
Definition covarianceBase.h:485
+
covarianceBase::init
void init(const char *name, const char *file)
Initialisation of the class using matrix from root file.
Definition covarianceBase.cpp:251
+
covarianceBase::GetCorrelationMatrix
TH2D * GetCorrelationMatrix()
KS: Convert covariance matrix to correlation matrix and return TH2D which can be used for fancy plott...
Definition covarianceBase.cpp:1535
+ +
covarianceBase::CheckBounds
virtual int CheckBounds()
Check if parameters were proposed outside physical boundary.
Definition covarianceBase.cpp:1022
+
covarianceBase::_fNumParPCA
int _fNumParPCA
Number of parameters in PCA base.
Definition covarianceBase.h:483
+
covarianceBase::eigen_vectors
TMatrixD eigen_vectors
Eigen vectors only of params which are being decomposed.
Definition covarianceBase.h:493
+
covarianceBase::_fNumPar
int _fNumPar
Number of systematic parameters.
Definition covarianceBase.h:455
+
covarianceBase::throwMatrixCholDecomp
double ** throwMatrixCholDecomp
Throw matrix that is being used in the fit, much faster as TMatrixDSym cache miss.
Definition covarianceBase.h:516
covarianceBase::printIndivStepScale
void printIndivStepScale()
Print step scale for each parameter.
Definition covarianceBase.cpp:1271
-
covarianceBase::eigen_values
TVectorD eigen_values
Eigen value only of particles which are being decomposed.
Definition covarianceBase.h:477
-
covarianceBase::_fFlatPrior
std::vector< bool > _fFlatPrior
Whether to apply flat prior or not.
Definition covarianceBase.h:459
-
covarianceBase::toggleFixAllParameters
void toggleFixAllParameters()
fix parameters at prior values
Definition covarianceBase.cpp:1136
-
covarianceBase::eigen_threshold
double eigen_threshold
CW: Threshold based on which we remove parameters in eigen base.
Definition covarianceBase.h:467
-
covarianceBase::getNominalArray
virtual std::vector< double > getNominalArray()
Definition covarianceBase.cpp:1707
+
covarianceBase::eigen_values
TVectorD eigen_values
Eigen value only of particles which are being decomposed.
Definition covarianceBase.h:491
+
covarianceBase::_fFlatPrior
std::vector< bool > _fFlatPrior
Whether to apply flat prior or not.
Definition covarianceBase.h:473
+
covarianceBase::toggleFixAllParameters
void toggleFixAllParameters()
fix parameters at prior values
Definition covarianceBase.cpp:1138
+
covarianceBase::eigen_threshold
double eigen_threshold
CW: Threshold based on which we remove parameters in eigen base.
Definition covarianceBase.h:481
+
covarianceBase::getNominalArray
virtual std::vector< double > getNominalArray()
Definition covarianceBase.cpp:1522
covarianceBase::MakePosDef
void MakePosDef(TMatrixDSym *cov=nullptr)
Make matrix positive definite by adding small values to diagonal, necessary for inverting matrix.
Definition covarianceBase.cpp:1283
-
covarianceBase::saveAdaptiveToFile
void saveAdaptiveToFile(const TString &outFileName, const TString &systematicName)
Save adaptive throw matrix to file.
Definition covarianceBase.cpp:1389
-
covarianceBase::setAdaptionDefaults
void setAdaptionDefaults()
sets default values for adaptive MCMC parameters
Definition covarianceBase.cpp:1409
-
covarianceBase::_fPreFitValue_PCA
std::vector< double > _fPreFitValue_PCA
Prefit value for PCA params.
Definition covarianceBase.h:483
-
covarianceBase::_fCurrVal
std::vector< double > _fCurrVal
Current value of the parameter.
Definition covarianceBase.h:445
-
covarianceBase::isDecomposed_PCA
std::vector< int > isDecomposed_PCA
If param is decomposed this will return -1, if not this will return enumerator to param in normal bas...
Definition covarianceBase.h:495
-
covarianceBase::eigen_values_master
std::vector< double > eigen_values_master
Eigen values which have dimension equal to _fNumParPCA, and can be used in CorrelateSteps.
Definition covarianceBase.h:481
-
covarianceBase::printNominal
void printNominal()
Print nominal value for every parameter.
Definition covarianceBase.cpp:966
-
covarianceBase::setThrowMatrix
void setThrowMatrix(TMatrixDSym *cov)
Definition covarianceBase.cpp:1338
-
covarianceBase::throwParProp
void throwParProp(const double mag=1.)
Throw the proposed parameter by mag sigma. Should really just have the user specify this throw by hav...
Definition covarianceBase.cpp:910
-
covarianceBase::throwNominal
void throwNominal(const bool nomValues=false, const int seed=0)
Throw nominal values.
Definition covarianceBase.cpp:615
- +
covarianceBase::setAdaptionDefaults
void setAdaptionDefaults()
sets default values for adaptive MCMC parameters
Definition covarianceBase.cpp:1391
+
covarianceBase::_fPreFitValue_PCA
std::vector< double > _fPreFitValue_PCA
Prefit value for PCA params.
Definition covarianceBase.h:497
+
covarianceBase::_fCurrVal
std::vector< double > _fCurrVal
Current value of the parameter.
Definition covarianceBase.h:459
+
covarianceBase::isDecomposed_PCA
std::vector< int > isDecomposed_PCA
If param is decomposed this will return -1, if not this will return enumerator to param in normal bas...
Definition covarianceBase.h:509
+
covarianceBase::eigen_values_master
std::vector< double > eigen_values_master
Eigen values which have dimension equal to _fNumParPCA, and can be used in CorrelateSteps.
Definition covarianceBase.h:495
+
covarianceBase::printNominal
void printNominal()
Print nominal value for every parameter.
Definition covarianceBase.cpp:969
+
covarianceBase::setThrowMatrix
void setThrowMatrix(TMatrixDSym *cov)
Use new throw matrix, used in adaptive MCMC.
Definition covarianceBase.cpp:1340
+
covarianceBase::throwParProp
void throwParProp(const double mag=1.)
Throw the proposed parameter by mag sigma. Should really just have the user specify this throw by hav...
Definition covarianceBase.cpp:912
+
covarianceBase::throwNominal
void throwNominal(const bool nomValues=false, const int seed=0)
Throw nominal values.
Definition covarianceBase.cpp:614
+
covarianceBase::total_steps
int total_steps
Total number of MCMC steps.
Definition covarianceBase.h:521
_LARGE_LOGL_
#define _LARGE_LOGL_
Large Likelihood is used it parameter go out of physical boundary, this indicates in MCMC that such s...
Definition covarianceBase.h:12
-
MaCh3Utils::GetNThreads
int GetNThreads()
number of threads which we need for example for TRandom3
Definition CovarianceUtils.h:32
-
adaptive_mcmc::print_adaptive_struct
void print_adaptive_struct(AdaptiveMCMCStruct adaptive_struct)
Basic printer method for AMCMC struct.
Definition adaptiveMCMCStruct.h:43
+
MaCh3Utils::GetNThreads
int GetNThreads()
number of threads which we need for example for TRandom3
Definition CovarianceUtils.h:28
im
#define im
Definition probGpu.cu:70
-
adaptive_mcmc::AdaptiveMCMCStruct::adaptive_covariance
TMatrixDSym * adaptive_covariance
Full adaptive covariance matrix.
Definition adaptiveMCMCStruct.h:38
-
adaptive_mcmc::AdaptiveMCMCStruct::par_means
std::vector< double > par_means
Mean values for all parameters.
Definition adaptiveMCMCStruct.h:36
-
adaptive_mcmc::AdaptiveMCMCStruct::adapt_block_sizes
std::vector< int > adapt_block_sizes
Size of blocks for adaption.
Definition adaptiveMCMCStruct.h:32
-
adaptive_mcmc::AdaptiveMCMCStruct::end_adaptive_update
int end_adaptive_update
Steps between changing throw matrix.
Definition adaptiveMCMCStruct.h:26
-
adaptive_mcmc::AdaptiveMCMCStruct::adaptive_update_step
int adaptive_update_step
Steps between changing throw matrix.
Definition adaptiveMCMCStruct.h:28
-
adaptive_mcmc::AdaptiveMCMCStruct::start_adaptive_throw
int start_adaptive_throw
When do we start throwing.
Definition adaptiveMCMCStruct.h:22
-
adaptive_mcmc::AdaptiveMCMCStruct::start_adaptive_update
int start_adaptive_update
When do we stop update the adaptive matrix.
Definition adaptiveMCMCStruct.h:24
-
adaptive_mcmc::AdaptiveMCMCStruct::adapt_block_matrix_indices
std::vector< int > adapt_block_matrix_indices
Indices for block-matrix adaption.
Definition adaptiveMCMCStruct.h:30
diff --git a/covarianceBase_8h.html b/covarianceBase_8h.html index f15b4a71a..a858aa249 100644 --- a/covarianceBase_8h.html +++ b/covarianceBase_8h.html @@ -85,7 +85,7 @@ #include "covariance/CovarianceUtils.h"
#include "covariance/ThrowParms.h"
#include "manager/manager.h"
-#include "covariance/adaptiveMCMCStruct.h"
+#include "covariance/AdaptiveMCMCHandler.h"

Go to the source code of this file.

const char * covarianceXsec::GetParamTypeString std::string covarianceXsec::GetParamTypeString ( const int  i)
 diff --git a/covarianceBase_8h_source.html b/covarianceBase_8h_source.html index 28d7f2296..9d2071ec1 100644 --- a/covarianceBase_8h_source.html +++ b/covarianceBase_8h_source.html @@ -90,7 +90,7 @@
5#include "covariance/CovarianceUtils.h"
6#include "covariance/ThrowParms.h"
7#include "manager/manager.h"
-
8#include "covariance/adaptiveMCMCStruct.h"
+
8#include "covariance/AdaptiveMCMCHandler.h"
9
10#ifndef _LARGE_LOGL_
12#define _LARGE_LOGL_ 1234567890.0
@@ -99,491 +99,483 @@
15//#define DEBUG_PCA 1
16#ifdef DEBUG_PCA
17//KS: When debugging we produce some fancy plots, but we don't need it during normal work flow
-
18#include "TROOT.h"
-
19#include "TStyle.h"
-
20#include "TColor.h"
-
21#include "TLine.h"
-
22#include "TText.h"
-
23#include "TLegend.h"
-
24
-
25#if DEBUG_PCA == 2
-
26#include "Eigen/Eigenvalues"
-
27#endif
-
28
-
29#endif
-
30
-
-
33class covarianceBase {
-
34 public:
-
41 covarianceBase(const std::vector<std::string>& YAMLFile, const char *name, double threshold = -1, int FirstPCAdpar = -999, int LastPCAdpar = -999);
-
45 covarianceBase(const char *name, const char *file);
-
50 covarianceBase(const char *name, const char *file, int seed);
-
58 covarianceBase(const char *name, const char *file, int seed, double threshold, int FirstPCAdpar, int LastPCAdpar);
-
60 virtual ~covarianceBase();
-
61
-
62 // Setters
-
63 // ETA - maybe need to add checks to index on the setters? i.e. if( i > _fPropVal.size()){throw;}
-
66 void setCovMatrix(TMatrixDSym *cov);
-
68 void setName(const char *name) { matrixName = name; }
-
72 void setParName(int i, char *name) { _fNames.at(i) = std::string(name); }
-
73 void setSingleParameter(const int parNo, const double parVal);
-
77 void setPar(const int i, const double val);
-
81 void setParCurrProp(const int i, const double val);
-
-
84 void setParProp(const int i, const double val) {
-
85 _fPropVal[i] = val;
-
86 if (pca) TransferToPCA();
-
87 }
+
18#include "TCanvas.h"
+
19#include "TROOT.h"
+
20#include "TStyle.h"
+
21#include "TColor.h"
+
22#include "TLine.h"
+
23#include "TText.h"
+
24#include "TLegend.h"
+
25
+
26#if DEBUG_PCA == 2
+
27#include "Eigen/Eigenvalues"
+
28#endif
+
29
+
30#endif
+
31
+
+
34class covarianceBase {
+
35 public:
+
42 covarianceBase(const std::vector<std::string>& YAMLFile, const char *name, double threshold = -1, int FirstPCAdpar = -999, int LastPCAdpar = -999);
+
46 covarianceBase(const char *name, const char *file);
+
51 covarianceBase(const char *name, const char *file, int seed);
+
59 covarianceBase(const char *name, const char *file, int seed, double threshold, int FirstPCAdpar, int LastPCAdpar);
+
61 virtual ~covarianceBase();
+
62
+
63 // Setters
+
64 // ETA - maybe need to add checks to index on the setters? i.e. if( i > _fPropVal.size()){throw;}
+
67 void setCovMatrix(TMatrixDSym *cov);
+
69 void setName(const char *name) { matrixName = name; }
+
73 void setParName(int i, char *name) { _fNames.at(i) = std::string(name); }
+
74 void setSingleParameter(const int parNo, const double parVal);
+
78 void setPar(const int i, const double val);
+
82 void setParCurrProp(const int i, const double val);
+
+
85 void setParProp(const int i, const double val) {
+
86 _fPropVal[i] = val;
+
87 if (pca) TransferToPCA();
+
88 }
-
90 void setParameters(const std::vector<double>& pars = {});
-
94 void setFlatPrior(const int i, const bool eL);
-
95
-
99 void SetBranches(TTree &tree, bool SaveProposal = false);
-
102 void setStepScale(const double scale);
-
106 void setIndivStepScale(const int ParameterIndex, const double StepScale){ _fIndivStepScale.at(ParameterIndex) = StepScale; }
-
109 void setIndivStepScale(const std::vector<double>& stepscale);
-
111 inline void setPrintLength(const unsigned int PriLen) { PrintLength = PriLen; }
-
112
-
114 void SaveUpdatedMatrixConfig();
-
115
-
117 void throwParProp(const double mag = 1.);
-
118
-
120 void throwParCurr(const double mag = 1.);
-
122 void throwParameters();
-
124 void throwNominal(const bool nomValues = false, const int seed = 0);
-
126 void RandomConfiguration();
-
127
-
129 virtual int CheckBounds();
-
131 double CalcLikelihood();
-
133 virtual double GetLikelihood();
-
134
-
136 TMatrixDSym *getCovMatrix() { return covMatrix; }
-
138 TMatrixDSym *getInvCovMatrix() { return invCovMatrix; }
-
141 inline bool getFlatPrior(const int i) { return _fFlatPrior[i]; }
-
142
-
144 const char *getName() { return matrixName; }
-
147 std::string GetParName(const int i) {return _fNames[i];}
-
150 const char* GetParName(const int i) const { return _fNames[i].c_str(); }
-
153 std::string GetParFancyName(const int i) {return _fFancyNames[i];}
-
156 const char* GetParFancyName(const int i) const { return _fFancyNames[i].c_str(); }
-
158 std::string getInputFile() const { return inputFile; }
-
159
-
162 inline double getDiagonalError(const int i) { return std::sqrt((*covMatrix)(i,i)); }
-
163
-
165 void resetIndivStepScale();
-
166
-
169 void initialiseAdaption(const YAML::Node& adapt_manager);
-
171 void saveAdaptiveToFile(const TString& outFileName, const TString& systematicName);
+
91 void setParameters(const std::vector<double>& pars = {});
+
95 void setFlatPrior(const int i, const bool eL);
+
96
+
100 void SetBranches(TTree &tree, bool SaveProposal = false);
+
103 void setStepScale(const double scale);
+
107 void setIndivStepScale(const int ParameterIndex, const double StepScale){ _fIndivStepScale.at(ParameterIndex) = StepScale; }
+
110 void setIndivStepScale(const std::vector<double>& stepscale);
+
112 inline void setPrintLength(const unsigned int PriLen) { PrintLength = PriLen; }
+
113
+
115 void SaveUpdatedMatrixConfig();
+
116
+
118 void throwParProp(const double mag = 1.);
+
119
+
121 void throwParCurr(const double mag = 1.);
+
123 void throwParameters();
+
125 void throwNominal(const bool nomValues = false, const int seed = 0);
+
127 void RandomConfiguration();
+
128
+
130 virtual int CheckBounds();
+
132 double CalcLikelihood();
+
134 virtual double GetLikelihood();
+
135
+
137 TMatrixDSym *getCovMatrix() { return covMatrix; }
+
139 TMatrixDSym *getInvCovMatrix() { return invCovMatrix; }
+
142 inline bool getFlatPrior(const int i) { return _fFlatPrior[i]; }
+
143
+
145 const char *getName() { return matrixName; }
+
148 std::string GetParName(const int i) {return _fNames[i];}
+
151 const char* GetParName(const int i) const { return _fNames[i].c_str(); }
+
154 std::string GetParFancyName(const int i) {return _fFancyNames[i];}
+
157 const char* GetParFancyName(const int i) const { return _fFancyNames[i].c_str(); }
+
159 std::string getInputFile() const { return inputFile; }
+
160
+
163 inline double getDiagonalError(const int i) { return std::sqrt((*covMatrix)(i,i)); }
+
164
+
166 void resetIndivStepScale();
+
167
+
170 void initialiseAdaption(const YAML::Node& adapt_manager);
+
171
173 bool getDoAdaption(){return use_adaptive;}
-
174
175 void setThrowMatrix(TMatrixDSym *cov);
176 void updateThrowMatrix(TMatrixDSym *cov);
-
-
177 inline void setNumberOfSteps(const int nsteps) {
-
178 total_steps = nsteps;
-
179 if(total_steps >= adaption_struct.start_adaptive_throw) resetIndivStepScale();
-
180 }
+ -
181
-
182 inline TMatrixDSym *getThrowMatrix(){return throwMatrix;}
-
183 inline TMatrixD *getThrowMatrix_CholDecomp(){return throwMatrix_CholDecomp;}
-
184 inline std::vector<double> getParameterMeans(){return adaption_struct.par_means;}
-
186 TH2D* GetCorrelationMatrix();
-
187
-
-
190 inline double calcReWeight(const int bin) {
-
191 if (bin >= 0 && bin < _fNumPar) {
-
192 return _fPropVal[bin];
-
193 } else {
-
194 MACH3LOG_WARN("Specified bin is <= 0 OR bin > npar!");
-
195 MACH3LOG_WARN("bin = {}, npar = {}", bin, _fNumPar);
-
196 MACH3LOG_WARN("This won't ruin much that this step in the MCMC, but does indicate something wrong in memory!");
-
197 return 1.0;
-
198 }
-
199 return 1.0;
-
200 }
+
182
+
183 inline TMatrixDSym *getThrowMatrix(){return throwMatrix;}
+
184 inline TMatrixD *getThrowMatrix_CholDecomp(){return throwMatrix_CholDecomp;}
+
185 inline std::vector<double> getParameterMeans(){return AdaptiveHandler.par_means;}
+
187 TH2D* GetCorrelationMatrix();
+
188
+
+
191 inline double calcReWeight(const int bin) {
+
192 if (bin >= 0 && bin < _fNumPar) {
+
193 return _fPropVal[bin];
+
194 } else {
+
195 MACH3LOG_WARN("Specified bin is <= 0 OR bin > npar!");
+
196 MACH3LOG_WARN("bin = {}, npar = {}", bin, _fNumPar);
+
197 MACH3LOG_WARN("This won't ruin much that this step in the MCMC, but does indicate something wrong in memory!");
+
198 return 1.0;
+
199 }
+
200 return 1.0;
+
201 }
-
201 //========
-
202 //ETA - This might be a bit squiffy? If the vector gots moved from say a
-
203 //push_back then the pointer is no longer valid... maybe need a better
-
204 //way to deal with this? It was fine before when the return was to an
-
205 //element of a new array. There must be a clever C++ way to be careful
-
206 //========
-
208 inline const double* retPointer(const int iParam) {return &(_fPropVal.data()[iParam]);}
-
209
-
210 //Some Getters
-
212 inline int GetNumParams() {return _fNumPar;}
-
213 virtual std::vector<double> getNominalArray();
-
214 std::vector<double> getPreFitValues(){return _fPreFitValue;}
-
215 std::vector<double> getGeneratedValues(){return _fGenerated;}
-
217 std::vector<double> getProposed() const;
-
220 inline double getParProp(const int i) { return _fPropVal[i]; }
-
223 inline double getParCurr(const int i) { return _fCurrVal[i]; }
-
226 inline double getParInit(const int i) { return _fPreFitValue[i]; }
-
229 virtual double getNominal(const int i) { return getParInit(i); }
-
232 inline double GetGenerated(const int i) { return _fGenerated[i];}
-
235 inline double GetUpperBound(const int i){ return _fUpBound[i];}
-
238 inline double GetLowerBound(const int i){ return _fLowBound[i]; }
-
241 inline double GetIndivStepScale(const int ParameterIndex){return _fIndivStepScale.at(ParameterIndex); }
-
-
244 inline double getParProp_PCA(const int i) {
-
245 if (!pca) { MACH3LOG_ERROR("Am not running in PCA mode"); throw; }
-
246 return fParProp_PCA(i);
-
247 }
+
202 //========
+
203 //ETA - This might be a bit squiffy? If the vector gots moved from say a
+
204 //push_back then the pointer is no longer valid... maybe need a better
+
205 //way to deal with this? It was fine before when the return was to an
+
206 //element of a new array. There must be a clever C++ way to be careful
+
207 //========
+
209 inline const double* retPointer(const int iParam) {return &(_fPropVal.data()[iParam]);}
+
210
+
211 //Some Getters
+
213 inline int GetNumParams() {return _fNumPar;}
+
214 virtual std::vector<double> getNominalArray();
+
215 std::vector<double> getPreFitValues(){return _fPreFitValue;}
+
216 std::vector<double> getGeneratedValues(){return _fGenerated;}
+
218 std::vector<double> getProposed() const;
+
221 inline double getParProp(const int i) { return _fPropVal[i]; }
+
224 inline double getParCurr(const int i) { return _fCurrVal[i]; }
+
227 inline double getParInit(const int i) { return _fPreFitValue[i]; }
+
230 virtual double getNominal(const int i) { return getParInit(i); }
+
233 inline double GetGenerated(const int i) { return _fGenerated[i];}
+
236 inline double GetUpperBound(const int i){ return _fUpBound[i];}
+
239 inline double GetLowerBound(const int i){ return _fLowBound[i]; }
+
242 inline double GetIndivStepScale(const int ParameterIndex){return _fIndivStepScale.at(ParameterIndex); }
+
+
245 inline double getParProp_PCA(const int i) {
+
246 if (!pca) { MACH3LOG_ERROR("Am not running in PCA mode"); throw; }
+
247 return fParProp_PCA(i);
+
248 }
-
248
-
-
251 inline double getParCurr_PCA(const int i) {
-
252 if (!pca) { MACH3LOG_ERROR("Am not running in PCA mode"); throw; }
-
253 return fParCurr_PCA(i);
-
254 }
+
249
+
+
252 inline double getParCurr_PCA(const int i) {
+
253 if (!pca) { MACH3LOG_ERROR("Am not running in PCA mode"); throw; }
+
254 return fParCurr_PCA(i);
+
255 }
-
255
-
-
258 inline bool isParameterFixedPCA(const int i) {
-
259 if (fParSigma_PCA[i] < 0) { return true; }
-
260 else { return false; }
-
261 }
+
256
+
+
259 inline bool isParameterFixedPCA(const int i) {
+
260 if (fParSigma_PCA[i] < 0) { return true; }
+
261 else { return false; }
+
262 }
-
-
263 inline const TMatrixD getTransferMatrix() {
-
264 if (!pca) { MACH3LOG_ERROR("Am not running in PCA mode"); throw; }
-
265 return TransferMat;
-
266 }
+
+
264 inline const TMatrixD getTransferMatrix() {
+
265 if (!pca) { MACH3LOG_ERROR("Am not running in PCA mode"); throw; }
+
266 return TransferMat;
+
267 }
-
-
268 inline const TMatrixD getEigenVectors() {
-
269 if (!pca) { MACH3LOG_ERROR("Am not running in PCA mode"); throw; }
-
270 return eigen_vectors;
-
271 }
+
+
269 inline const TMatrixD getEigenVectors() {
+
270 if (!pca) { MACH3LOG_ERROR("Am not running in PCA mode"); throw; }
+
271 return eigen_vectors;
+
272 }
-
-
273 inline const TVectorD getEigenValues() {
-
274 if (!pca) { MACH3LOG_ERROR("Am not running in PCA mode"); throw; }
-
275 return eigen_values;
-
276 }
+
+
274 inline const TVectorD getEigenValues() {
+
275 if (!pca) { MACH3LOG_ERROR("Am not running in PCA mode"); throw; }
+
276 return eigen_values;
+
277 }
-
-
278 inline const std::vector<double> getEigenValuesMaster() {
-
279 if (!pca) { MACH3LOG_ERROR("Am not running in PCA mode"); throw; }
-
280 return eigen_values_master;
-
281 }
+
+
279 inline const std::vector<double> getEigenValuesMaster() {
+
280 if (!pca) { MACH3LOG_ERROR("Am not running in PCA mode"); throw; }
+
281 return eigen_values_master;
+
282 }
-
-
285 inline void setParProp_PCA(const int i, const double value) {
-
286 if (!pca) { MACH3LOG_ERROR("Am not running in PCA mode"); throw; }
-
287 fParProp_PCA(i) = value;
-
288 // And then transfer back to the parameter basis
-
289 TransferToParam();
-
290 }
+
+
286 inline void setParProp_PCA(const int i, const double value) {
+
287 if (!pca) { MACH3LOG_ERROR("Am not running in PCA mode"); throw; }
+
288 fParProp_PCA(i) = value;
+
289 // And then transfer back to the parameter basis
+
290 TransferToParam();
+
291 }
-
-
294 inline void setParCurr_PCA(const int i, const double value) {
-
295 if (!pca) { MACH3LOG_ERROR("Am not running in PCA mode"); throw; }
-
296 fParCurr_PCA(i) = value;
-
297 // And then transfer back to the parameter basis
-
298 TransferToParam();
-
299 }
+
+
295 inline void setParCurr_PCA(const int i, const double value) {
+
296 if (!pca) { MACH3LOG_ERROR("Am not running in PCA mode"); throw; }
+
297 fParCurr_PCA(i) = value;
+
298 // And then transfer back to the parameter basis
+
299 TransferToParam();
+
300 }
-
300
-
-
303 inline void setParameters_PCA(const std::vector<double> &pars) {
-
304 if (!pca) { MACH3LOG_ERROR("Am not running in PCA mode"); throw; }
-
305 if (pars.size() != size_t(_fNumParPCA)) {
-
306 MACH3LOG_ERROR("Warning: parameter arrays of incompatible size! Not changing parameters! {} has size {} but was expecting {}", matrixName, pars.size(), _fNumPar);
-
307 throw;
-
308 }
-
309 unsigned int parsSize = pars.size();
-
310 for (unsigned int i = 0; i < parsSize; i++) {
-
311 fParProp_PCA(i) = pars[i];
-
312 }
-
313 //KS: Transfer to normal base
-
314 TransferToParam();
-
315 }
+
301
+
+
304 inline void setParameters_PCA(const std::vector<double> &pars) {
+
305 if (!pca) { MACH3LOG_ERROR("Am not running in PCA mode"); throw; }
+
306 if (pars.size() != size_t(_fNumParPCA)) {
+
307 MACH3LOG_ERROR("Warning: parameter arrays of incompatible size! Not changing parameters! {} has size {} but was expecting {}", matrixName, pars.size(), _fNumPar);
+
308 throw;
+
309 }
+
310 unsigned int parsSize = pars.size();
+
311 for (unsigned int i = 0; i < parsSize; i++) {
+
312 fParProp_PCA(i) = pars[i];
+
313 }
+
314 //KS: Transfer to normal base
+
315 TransferToParam();
+
316 }
-
317 inline int getSize() { return _fNumPar; }
-
-
319 inline int getNpars() {
-
320 if (pca) return _fNumParPCA;
-
321 else return _fNumPar;
-
322 }
+
318 inline int getSize() { return _fNumPar; }
+
+
320 inline int getNpars() {
+
321 if (pca) return _fNumParPCA;
+
322 else return _fNumPar;
+
323 }
-
323
-
325 void printNominal();
-
327 void printNominalCurrProp();
-
328 void printPars();
-
330 void printIndivStepScale();
-
331
-
333 virtual void proposeStep();
-
335 void acceptStep();
-
336
-
338 void toggleFixAllParameters();
-
341 void toggleFixParameter(const int i);
-
344 void toggleFixParameter(const std::string& name);
-
345
-
-
348 bool isParameterFixed(const int i) {
-
349 if (_fError[i] < 0) { return true; }
-
350 else { return false; }
-
351 }
+
324
+
326 void printNominal();
+
328 void printNominalCurrProp();
+
329 void printPars();
+
331 void printIndivStepScale();
+
332
+
334 virtual void proposeStep();
+
336 void acceptStep();
+
337
+
339 void toggleFixAllParameters();
+
342 void toggleFixParameter(const int i);
+
345 void toggleFixParameter(const std::string& name);
+
346
+
+
349 bool isParameterFixed(const int i) {
+
350 if (_fError[i] < 0) { return true; }
+
351 else { return false; }
+
352 }
-
354 bool isParameterFixed(const std::string& name);
-
355
-
358 void ConstructPCA();
-
359 #ifdef DEBUG_PCA
-
361 void DebugPCA(const double sum, TMatrixD temp, TMatrixDSym submat);
-
362 #endif
-
363
-
365 inline bool IsPCA() { return pca; }
-
366
-
372 inline void MatrixVectorMulti(double* _restrict_ VecMulti, double** _restrict_ matrix, const double* _restrict_ vector, const int n);
-
374 inline double MatrixVectorMultiSingle(double** _restrict_ matrix, const double* _restrict_ vector, const int Length, const int i);
-
375
-
376protected:
-
377
-
378 void init(const char *name, const char *file);
-
381 void init(const std::vector<std::string>& YAMLFile);
-
383 void init(TMatrixDSym* covMat);
-
386 void ReserveMemory(const int size);
-
387
-
389 void randomize();
-
391 void CorrelateSteps();
-
392
-
395 void MakePosDef(TMatrixDSym *cov = nullptr);
-
396
-
398 void makeClosestPosDef(TMatrixDSym *cov);
-
400 void TransferToPCA();
-
402 void TransferToParam();
-
403
-
405 const double* ReturnUnity(){return &Unity;}
-
406
-
408 const std::string inputFile;
-
409
-
411 int size;
-
413 const char *matrixName;
-
415 TMatrixDSym *covMatrix;
-
417 TMatrixDSym *invCovMatrix;
-
419 double **InvertCovMatrix;
-
420
-
422 TRandom3 **random_number;
+
355 bool isParameterFixed(const std::string& name);
+
356
+
359 void ConstructPCA();
+
360 #ifdef DEBUG_PCA
+
362 void DebugPCA(const double sum, TMatrixD temp, TMatrixDSym submat);
+
363 #endif
+
364
+
366 inline bool IsPCA() { return pca; }
+
367
+
373 inline void MatrixVectorMulti(double* _restrict_ VecMulti, double** _restrict_ matrix, const double* _restrict_ vector, const int n);
+
375 inline double MatrixVectorMultiSingle(double** _restrict_ matrix, const double* _restrict_ vector, const int Length, const int i);
+
376
+
377protected:
+
379 void init(const char *name, const char *file);
+
382 void init(const std::vector<std::string>& YAMLFile);
+
384 void init(TMatrixDSym* covMat);
+
387 void ReserveMemory(const int size);
+
388
+
390 void randomize();
+
392 void CorrelateSteps();
+
393
+
396 void MakePosDef(TMatrixDSym *cov = nullptr);
+
397
+
399 void makeClosestPosDef(TMatrixDSym *cov);
+
401 void TransferToPCA();
+
403 void TransferToParam();
+
404
+
406 const double* ReturnUnity(){return &Unity;}
+
407
+
409 void setAdaptionDefaults();
+
410
+
415 void setThrowMatrixFromFile(const std::string& matrix_file_name, const std::string& matrix_name, const std::string& means_name);
+
416
+
419 void updateAdaptiveCovariance();
+
420
+
422 const std::string inputFile;
423
-
425 double* randParams;
-
427 double* corr_throw;
-
429 double _fGlobalStepScale;
-
430
-
432 unsigned int PrintLength;
-
433
-
435 std::vector<std::string> _fNames;
-
437 std::vector<std::string> _fFancyNames;
-
439 YAML::Node _fYAMLDoc;
-
441 int _fNumPar;
-
443 std::vector<double> _fPreFitValue;
-
445 std::vector<double> _fCurrVal;
-
447 std::vector<double> _fPropVal;
-
449 std::vector<double> _fGenerated;
-
451 std::vector<double> _fError;
-
453 std::vector<double> _fLowBound;
-
455 std::vector<double> _fUpBound;
-
457 std::vector<double> _fIndivStepScale;
-
459 std::vector<bool> _fFlatPrior;
-
460
-
462 const double Unity = 1.0;
-
463
-
465 bool pca;
-
467 double eigen_threshold;
-
469 int _fNumParPCA;
-
471 int FirstPCAdpar;
-
473 int LastPCAdpar;
-
475 int nKeptPCApars;
-
477 TVectorD eigen_values;
-
479 TMatrixD eigen_vectors;
-
481 std::vector<double> eigen_values_master;
-
483 std::vector<double> _fPreFitValue_PCA;
-
485 TMatrixD TransferMat;
-
487 TMatrixD TransferMatT;
-
489 TVectorD fParProp_PCA;
-
491 TVectorD fParCurr_PCA;
-
493 std::vector<double> fParSigma_PCA;
-
495 std::vector<int> isDecomposed_PCA;
-
496
-
497 // Adaptive MCMC
-
498 TMatrixDSym* throwMatrix;
-
499 TMatrixD* throwMatrix_CholDecomp;
-
501 double **throwMatrixCholDecomp;
-
502
-
504 void setAdaptionDefaults();
-
505
-
508 void setAdaptiveBlocks(std::vector<std::vector<int>> block_indices);
-
509
-
514 void setThrowMatrixFromFile(const std::string& matrix_file_name, const std::string& matrix_name, const std::string& means_name);
-
515
-
517 void updateAdaptiveCovariance();
-
519 void createNewAdaptiveCovariance();
-
520
-
522 bool use_adaptive;
-
523 int total_steps;
-
524
-
526 adaptive_mcmc::AdaptiveMCMCStruct adaption_struct;
-
527};
+
425 int size;
+
427 const char *matrixName;
+
429 TMatrixDSym *covMatrix;
+
431 TMatrixDSym *invCovMatrix;
+
433 double **InvertCovMatrix;
+
434
+
436 TRandom3 **random_number;
+
437
+
439 double* randParams;
+
441 double* corr_throw;
+
443 double _fGlobalStepScale;
+
444
+
446 unsigned int PrintLength;
+
447
+
449 std::vector<std::string> _fNames;
+
451 std::vector<std::string> _fFancyNames;
+
453 YAML::Node _fYAMLDoc;
+
455 int _fNumPar;
+
457 std::vector<double> _fPreFitValue;
+
459 std::vector<double> _fCurrVal;
+
461 std::vector<double> _fPropVal;
+
463 std::vector<double> _fGenerated;
+
465 std::vector<double> _fError;
+
467 std::vector<double> _fLowBound;
+
469 std::vector<double> _fUpBound;
+
471 std::vector<double> _fIndivStepScale;
+
473 std::vector<bool> _fFlatPrior;
+
474
+
476 const double Unity = 1.0;
+
477
+
479 bool pca;
+
481 double eigen_threshold;
+
483 int _fNumParPCA;
+
485 int FirstPCAdpar;
+
487 int LastPCAdpar;
+
489 int nKeptPCApars;
+
491 TVectorD eigen_values;
+
493 TMatrixD eigen_vectors;
+
495 std::vector<double> eigen_values_master;
+
497 std::vector<double> _fPreFitValue_PCA;
+
499 TMatrixD TransferMat;
+
501 TMatrixD TransferMatT;
+
503 TVectorD fParProp_PCA;
+
505 TVectorD fParCurr_PCA;
+
507 std::vector<double> fParSigma_PCA;
+
509 std::vector<int> isDecomposed_PCA;
+
510
+
512 TMatrixDSym* throwMatrix;
+
514 TMatrixD* throwMatrix_CholDecomp;
+
516 double **throwMatrixCholDecomp;
+
517
+
519 bool use_adaptive;
+
521 int total_steps;
+
522
+
524 adaptive_mcmc::AdaptiveMCMCHandler AdaptiveHandler;
+
525};
+ -
MACH3LOG_ERROR
#define MACH3LOG_ERROR
Definition MaCh3Logger.h:15
-
MACH3LOG_WARN
#define MACH3LOG_WARN
Definition MaCh3Logger.h:14
+
MACH3LOG_ERROR
#define MACH3LOG_ERROR
Definition MaCh3Logger.h:18
+
MACH3LOG_WARN
#define MACH3LOG_WARN
Definition MaCh3Logger.h:17
_restrict_
#define _restrict_
KS: Using restrict limits the effects of pointer aliasing, aiding optimizations. While reading I foun...
Definition Structs.h:26
-
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:18
- -
covarianceBase
Base class responsible for handling of systematic error parameters. Capable of using PCA or using ada...
Definition covarianceBase.h:33
-
covarianceBase::CalcLikelihood
double CalcLikelihood()
Calc penalty term based on inverted covariance matrix.
Definition covarianceBase.cpp:999
-
covarianceBase::_fGlobalStepScale
double _fGlobalStepScale
Global step scale applied ot all params in this class.
Definition covarianceBase.h:429
-
covarianceBase::getDiagonalError
double getDiagonalError(const int i)
Get diagonal error for ith parameter.
Definition covarianceBase.h:162
-
covarianceBase::getFlatPrior
bool getFlatPrior(const int i)
Get if param has flat prior or not.
Definition covarianceBase.h:141
-
covarianceBase::GetParName
std::string GetParName(const int i)
Get name of covariance.
Definition covarianceBase.h:147
-
covarianceBase::getParCurr
double getParCurr(const int i)
Get current parameter value.
Definition covarianceBase.h:223
-
covarianceBase::resetIndivStepScale
void resetIndivStepScale()
Adaptive Step Tuning Stuff.
Definition covarianceBase.cpp:1328
-
covarianceBase::GetUpperBound
double GetUpperBound(const int i)
Get upper parameter bound in which it is physically valid.
Definition covarianceBase.h:235
-
covarianceBase::getEigenValuesMaster
const std::vector< double > getEigenValuesMaster()
Get eigen value of only decomposed parameters, if you want for all parameters use getEigenValues.
Definition covarianceBase.h:278
+
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:21
+
adaptive_mcmc::AdaptiveMCMCHandler
Contains information about adaptive covariance matrix.
Definition AdaptiveMCMCHandler.h:13
+
adaptive_mcmc::AdaptiveMCMCHandler::par_means
std::vector< double > par_means
Mean values for all parameters.
Definition AdaptiveMCMCHandler.h:78
+
adaptive_mcmc::AdaptiveMCMCHandler::start_adaptive_throw
int start_adaptive_throw
Definition AdaptiveMCMCHandler.h:59
+
covarianceBase
Base class responsible for handling of systematic error parameters. Capable of using PCA or using ada...
Definition covarianceBase.h:34
+
covarianceBase::CalcLikelihood
double CalcLikelihood()
Calc penalty term based on inverted covariance matrix.
Definition covarianceBase.cpp:1002
+
covarianceBase::_fGlobalStepScale
double _fGlobalStepScale
Global step scale applied ot all params in this class.
Definition covarianceBase.h:443
+
covarianceBase::getDiagonalError
double getDiagonalError(const int i)
Get diagonal error for ith parameter.
Definition covarianceBase.h:163
+
covarianceBase::getFlatPrior
bool getFlatPrior(const int i)
Get if param has flat prior or not.
Definition covarianceBase.h:142
+
covarianceBase::GetParName
std::string GetParName(const int i)
Get name of covariance.
Definition covarianceBase.h:148
+
covarianceBase::getParCurr
double getParCurr(const int i)
Get current parameter value.
Definition covarianceBase.h:224
+
covarianceBase::resetIndivStepScale
void resetIndivStepScale()
Adaptive Step Tuning Stuff.
Definition covarianceBase.cpp:1329
+
covarianceBase::GetUpperBound
double GetUpperBound(const int i)
Get upper parameter bound in which it is physically valid.
Definition covarianceBase.h:236
+
covarianceBase::getEigenValuesMaster
const std::vector< double > getEigenValuesMaster()
Get eigen value of only decomposed parameters, if you want for all parameters use getEigenValues.
Definition covarianceBase.h:279
covarianceBase::getDoAdaption
bool getDoAdaption()
Do we adapt or not.
Definition covarianceBase.h:173
-
covarianceBase::getInvCovMatrix
TMatrixDSym * getInvCovMatrix()
Return inverted covariance matrix.
Definition covarianceBase.h:138
-
covarianceBase::_fPropVal
std::vector< double > _fPropVal
Proposed value of the parameter.
Definition covarianceBase.h:447
-
covarianceBase::calcReWeight
double calcReWeight(const int bin)
What parameter Gets reweighted by what amount according to MCMC.
Definition covarianceBase.h:190
-
covarianceBase::getParInit
double getParInit(const int i)
Get prior parameter value.
Definition covarianceBase.h:226
-
covarianceBase::setNumberOfSteps
void setNumberOfSteps(const int nsteps)
Definition covarianceBase.h:177
+
covarianceBase::getInvCovMatrix
TMatrixDSym * getInvCovMatrix()
Return inverted covariance matrix.
Definition covarianceBase.h:139
+
covarianceBase::_fPropVal
std::vector< double > _fPropVal
Proposed value of the parameter.
Definition covarianceBase.h:461
+
covarianceBase::calcReWeight
double calcReWeight(const int bin)
What parameter Gets reweighted by what amount according to MCMC.
Definition covarianceBase.h:191
+
covarianceBase::getParInit
double getParInit(const int i)
Get prior parameter value.
Definition covarianceBase.h:227
+
covarianceBase::setNumberOfSteps
void setNumberOfSteps(const int nsteps)
Set number of MCMC step, when running adaptive MCMC it is updated with given frequency....
Definition covarianceBase.h:178
covarianceBase::~covarianceBase
virtual ~covarianceBase()
Destructor.
Definition covarianceBase.cpp:83
-
covarianceBase::setFlatPrior
void setFlatPrior(const int i, const bool eL)
Set if parameter should have flat prior or not.
Definition covarianceBase.cpp:1202
-
covarianceBase::setIndivStepScale
void setIndivStepScale(const int ParameterIndex, const double StepScale)
DB Function to set fIndivStepScale from a vector (Can be used from execs and inside covariance constr...
Definition covarianceBase.h:106
-
covarianceBase::isParameterFixed
bool isParameterFixed(const int i)
Is parameter fixed or not.
Definition covarianceBase.h:348
-
covarianceBase::getNpars
int getNpars()
Get number of params which will be different depending if using Eigen decomposition or not.
Definition covarianceBase.h:319
-
covarianceBase::GetParName
const char * GetParName(const int i) const
Get name of the Parameter.
Definition covarianceBase.h:150
-
covarianceBase::fParProp_PCA
TVectorD fParProp_PCA
CW: Current parameter value in PCA base.
Definition covarianceBase.h:489
-
covarianceBase::IsPCA
bool IsPCA()
is PCA, can use to query e.g. LLH scans
Definition covarianceBase.h:365
-
covarianceBase::_fUpBound
std::vector< double > _fUpBound
Upper physical bound, parameter will not be able to go beyond it.
Definition covarianceBase.h:455
-
covarianceBase::setPrintLength
void setPrintLength(const unsigned int PriLen)
KS: In case someone really want to change this.
Definition covarianceBase.h:111
-
covarianceBase::randomize
void randomize()
"Randomize" the parameters in the covariance class for the proposed step. Used the proposal kernel an...
Definition covarianceBase.cpp:793
-
covarianceBase::_fError
std::vector< double > _fError
Prior error on the parameter.
Definition covarianceBase.h:451
-
covarianceBase::invCovMatrix
TMatrixDSym * invCovMatrix
The inverse covariance matrix.
Definition covarianceBase.h:417
-
covarianceBase::nKeptPCApars
int nKeptPCApars
Total number that remained after applying PCA Threshold.
Definition covarianceBase.h:475
-
covarianceBase::getParProp
double getParProp(const int i)
Get proposed parameter value.
Definition covarianceBase.h:220
-
covarianceBase::_fIndivStepScale
std::vector< double > _fIndivStepScale
Individual step scale used by MCMC algorithm.
Definition covarianceBase.h:457
-
covarianceBase::GetGenerated
double GetGenerated(const int i)
Return generated value for a given parameter.
Definition covarianceBase.h:232
-
covarianceBase::GetNumParams
int GetNumParams()
Get total number of parameters.
Definition covarianceBase.h:212
-
covarianceBase::getParProp_PCA
double getParProp_PCA(const int i)
Get current parameter value using PCA.
Definition covarianceBase.h:244
-
covarianceBase::ReturnUnity
const double * ReturnUnity()
Handy function to return 1 for any systs.
Definition covarianceBase.h:405
-
covarianceBase::_fNames
std::vector< std::string > _fNames
ETA _fNames is set automatically in the covariance class to be something like xsec_i,...
Definition covarianceBase.h:435
-
covarianceBase::matrixName
const char * matrixName
Name of cov matrix.
Definition covarianceBase.h:413
-
covarianceBase::InvertCovMatrix
double ** InvertCovMatrix
KS: Same as above but much faster as TMatrixDSym cache miss.
Definition covarianceBase.h:419
-
covarianceBase::throwParCurr
void throwParCurr(const double mag=1.)
Helper function to throw the current parameter by mag sigma. Can study bias in MCMC with this; put di...
Definition covarianceBase.cpp:937
-
covarianceBase::updateAdaptiveCovariance
void updateAdaptiveCovariance()
Method to update adaptive MCMC.
Definition covarianceBase.cpp:1600
-
covarianceBase::GetParFancyName
const char * GetParFancyName(const int i) const
Get fancy name of the Parameter.
Definition covarianceBase.h:156
-
covarianceBase::inputFile
const std::string inputFile
The input root file we read in.
Definition covarianceBase.h:408
-
covarianceBase::getThrowMatrix_CholDecomp
TMatrixD * getThrowMatrix_CholDecomp()
Definition covarianceBase.h:183
-
covarianceBase::setParameters_PCA
void setParameters_PCA(const std::vector< double > &pars)
Set values for PCA parameters in PCA base.
Definition covarianceBase.h:303
-
covarianceBase::setParCurr_PCA
void setParCurr_PCA(const int i, const double value)
Set current value for parameter in PCA base.
Definition covarianceBase.h:294
-
covarianceBase::getCovMatrix
TMatrixDSym * getCovMatrix()
Return covariance matrix.
Definition covarianceBase.h:136
-
covarianceBase::setThrowMatrixFromFile
void setThrowMatrixFromFile(const std::string &matrix_file_name, const std::string &matrix_name, const std::string &means_name)
sets throw matrix from a file
Definition covarianceBase.cpp:1493
-
covarianceBase::getNominal
virtual double getNominal(const int i)
Return generated value, although is virtual so class inheriting might actual get nominal not generate...
Definition covarianceBase.h:229
-
covarianceBase::TransferMatT
TMatrixD TransferMatT
Matrix used to converting from normal base to PCA base.
Definition covarianceBase.h:487
-
covarianceBase::TransferMat
TMatrixD TransferMat
Matrix used to converting from PCA base to normal base.
Definition covarianceBase.h:485
-
covarianceBase::LastPCAdpar
int LastPCAdpar
Index of the last param that is being decomposed.
Definition covarianceBase.h:473
-
covarianceBase::setCovMatrix
void setCovMatrix(TMatrixDSym *cov)
Set covariance matrix.
Definition covarianceBase.cpp:500
-
covarianceBase::setName
void setName(const char *name)
Set matrix name.
Definition covarianceBase.h:68
-
covarianceBase::random_number
TRandom3 ** random_number
KS: Set Random numbers for each thread so each thread has different seed.
Definition covarianceBase.h:422
-
covarianceBase::GetLowerBound
double GetLowerBound(const int i)
Get lower parameter bound in which it is physically valid.
Definition covarianceBase.h:238
-
covarianceBase::getProposed
std::vector< double > getProposed() const
Get vector of all proposed parameter values.
Definition covarianceBase.cpp:607
-
covarianceBase::MatrixVectorMulti
void MatrixVectorMulti(double *_restrict_ VecMulti, double **_restrict_ matrix, const double *_restrict_ vector, const int n)
KS: Custom function to perform multiplication of matrix and vector with multithreading.
Definition covarianceBase.cpp:1222
-
covarianceBase::TransferToPCA
void TransferToPCA()
Transfer param values from normal base to PCA base.
Definition covarianceBase.cpp:571
-
covarianceBase::TransferToParam
void TransferToParam()
Transfer param values from PCA base to normal base.
Definition covarianceBase.cpp:589
-
covarianceBase::setParCurrProp
void setParCurrProp(const int i, const double val)
Set current parameter value.
Definition covarianceBase.cpp:770
-
covarianceBase::GetParFancyName
std::string GetParFancyName(const int i)
Get fancy name of the Parameter.
Definition covarianceBase.h:153
-
covarianceBase::adaption_struct
adaptive_mcmc::AdaptiveMCMCStruct adaption_struct
Struct containing information about adaption.
Definition covarianceBase.h:526
-
covarianceBase::covMatrix
TMatrixDSym * covMatrix
The covariance matrix.
Definition covarianceBase.h:415
-
covarianceBase::throwMatrix
TMatrixDSym * throwMatrix
Definition covarianceBase.h:498
-
covarianceBase::randParams
double * randParams
Random number taken from gaussian around prior error used for corr_throw.
Definition covarianceBase.h:425
-
covarianceBase::initialiseAdaption
void initialiseAdaption(const YAML::Node &adapt_manager)
Initialise adaptive MCMC.
Definition covarianceBase.cpp:1423
-
covarianceBase::getGeneratedValues
std::vector< double > getGeneratedValues()
Definition covarianceBase.h:215
-
covarianceBase::printNominalCurrProp
void printNominalCurrProp()
Print nominal, current and proposed value for each parameter.
Definition covarianceBase.cpp:976
-
covarianceBase::getName
const char * getName()
Get name of covariance.
Definition covarianceBase.h:144
-
covarianceBase::_fPreFitValue
std::vector< double > _fPreFitValue
Parameter value dictated by the prior model. Based on it penalty term is calculated.
Definition covarianceBase.h:443
-
covarianceBase::ReserveMemory
void ReserveMemory(const int size)
Initialise vectors with parameters information.
Definition covarianceBase.cpp:521
-
covarianceBase::MatrixVectorMultiSingle
double MatrixVectorMultiSingle(double **_restrict_ matrix, const double *_restrict_ vector, const int Length, const int i)
KS: Custom function to perform multiplication of matrix and single element which is thread safe.
Definition covarianceBase.cpp:1239
-
covarianceBase::Unity
const double Unity
Unity for null systs to point back to.
Definition covarianceBase.h:462
-
covarianceBase::corr_throw
double * corr_throw
Result of multiplication of Cholesky matrix and randParams.
Definition covarianceBase.h:427
-
covarianceBase::fParSigma_PCA
std::vector< double > fParSigma_PCA
Tells if parameter is fixed in PCA base or not.
Definition covarianceBase.h:493
-
covarianceBase::setParProp_PCA
void setParProp_PCA(const int i, const double value)
Set proposed value for parameter in PCA base.
Definition covarianceBase.h:285
-
covarianceBase::size
int size
Total number of parmas, deprecated, please don't use it.
Definition covarianceBase.h:411
-
covarianceBase::updateThrowMatrix
void updateThrowMatrix(TMatrixDSym *cov)
Definition covarianceBase.cpp:1378
-
covarianceBase::setStepScale
void setStepScale(const double scale)
Set global step scale for covariance object.
Definition covarianceBase.cpp:1124
-
covarianceBase::use_adaptive
bool use_adaptive
Are we using AMCMC?
Definition covarianceBase.h:522
-
covarianceBase::RandomConfiguration
void RandomConfiguration()
Randomly throw the parameters in their 1 sigma range.
Definition covarianceBase.cpp:723
-
covarianceBase::makeClosestPosDef
void makeClosestPosDef(TMatrixDSym *cov)
HW: Finds closest possible positive definite matrix in Frobenius Norm ||.||_frob Where ||X||_frob=sqr...
Definition covarianceBase.cpp:1660
-
covarianceBase::createNewAdaptiveCovariance
void createNewAdaptiveCovariance()
method to create new throw matrix
Definition covarianceBase.cpp:1590
-
covarianceBase::ConstructPCA
void ConstructPCA()
CW: Calculate eigen values, prepare transition matrices and remove param based on defined threshold.
Definition covarianceBase.cpp:122
-
covarianceBase::_fLowBound
std::vector< double > _fLowBound
Lowest physical bound, parameter will not be able to go beyond it.
Definition covarianceBase.h:453
-
covarianceBase::_fYAMLDoc
YAML::Node _fYAMLDoc
Stores config describing systematics.
Definition covarianceBase.h:439
+
covarianceBase::setFlatPrior
void setFlatPrior(const int i, const bool eL)
Set if parameter should have flat prior or not.
Definition covarianceBase.cpp:1203
+
covarianceBase::setIndivStepScale
void setIndivStepScale(const int ParameterIndex, const double StepScale)
DB Function to set fIndivStepScale from a vector (Can be used from execs and inside covariance constr...
Definition covarianceBase.h:107
+
covarianceBase::isParameterFixed
bool isParameterFixed(const int i)
Is parameter fixed or not.
Definition covarianceBase.h:349
+
covarianceBase::getNpars
int getNpars()
Get number of params which will be different depending if using Eigen decomposition or not.
Definition covarianceBase.h:320
+
covarianceBase::GetParName
const char * GetParName(const int i) const
Get name of the Parameter.
Definition covarianceBase.h:151
+
covarianceBase::fParProp_PCA
TVectorD fParProp_PCA
CW: Current parameter value in PCA base.
Definition covarianceBase.h:503
+
covarianceBase::IsPCA
bool IsPCA()
is PCA, can use to query e.g. LLH scans
Definition covarianceBase.h:366
+
covarianceBase::_fUpBound
std::vector< double > _fUpBound
Upper physical bound, parameter will not be able to go beyond it.
Definition covarianceBase.h:469
+
covarianceBase::setPrintLength
void setPrintLength(const unsigned int PriLen)
KS: In case someone really want to change this.
Definition covarianceBase.h:112
+
covarianceBase::randomize
void randomize()
"Randomize" the parameters in the covariance class for the proposed step. Used the proposal kernel an...
Definition covarianceBase.cpp:794
+
covarianceBase::_fError
std::vector< double > _fError
Prior error on the parameter.
Definition covarianceBase.h:465
+
covarianceBase::invCovMatrix
TMatrixDSym * invCovMatrix
The inverse covariance matrix.
Definition covarianceBase.h:431
+
covarianceBase::nKeptPCApars
int nKeptPCApars
Total number that remained after applying PCA Threshold.
Definition covarianceBase.h:489
+
covarianceBase::getParProp
double getParProp(const int i)
Get proposed parameter value.
Definition covarianceBase.h:221
+
covarianceBase::_fIndivStepScale
std::vector< double > _fIndivStepScale
Individual step scale used by MCMC algorithm.
Definition covarianceBase.h:471
+
covarianceBase::GetGenerated
double GetGenerated(const int i)
Return generated value for a given parameter.
Definition covarianceBase.h:233
+
covarianceBase::GetNumParams
int GetNumParams()
Get total number of parameters.
Definition covarianceBase.h:213
+
covarianceBase::getParProp_PCA
double getParProp_PCA(const int i)
Get current parameter value using PCA.
Definition covarianceBase.h:245
+
covarianceBase::ReturnUnity
const double * ReturnUnity()
Handy function to return 1 for any systs.
Definition covarianceBase.h:406
+
covarianceBase::_fNames
std::vector< std::string > _fNames
ETA _fNames is set automatically in the covariance class to be something like xsec_i,...
Definition covarianceBase.h:449
+
covarianceBase::matrixName
const char * matrixName
Name of cov matrix.
Definition covarianceBase.h:427
+
covarianceBase::InvertCovMatrix
double ** InvertCovMatrix
KS: Same as above but much faster as TMatrixDSym cache miss.
Definition covarianceBase.h:433
+
covarianceBase::throwParCurr
void throwParCurr(const double mag=1.)
Helper function to throw the current parameter by mag sigma. Can study bias in MCMC with this; put di...
Definition covarianceBase.cpp:940
+
covarianceBase::updateAdaptiveCovariance
void updateAdaptiveCovariance()
Method to update adaptive MCMC.
Definition covarianceBase.cpp:1449
+
covarianceBase::GetParFancyName
const char * GetParFancyName(const int i) const
Get fancy name of the Parameter.
Definition covarianceBase.h:157
+
covarianceBase::inputFile
const std::string inputFile
The input root file we read in.
Definition covarianceBase.h:422
+
covarianceBase::getThrowMatrix_CholDecomp
TMatrixD * getThrowMatrix_CholDecomp()
Definition covarianceBase.h:184
+
covarianceBase::setParameters_PCA
void setParameters_PCA(const std::vector< double > &pars)
Set values for PCA parameters in PCA base.
Definition covarianceBase.h:304
+
covarianceBase::setParCurr_PCA
void setParCurr_PCA(const int i, const double value)
Set current value for parameter in PCA base.
Definition covarianceBase.h:295
+
covarianceBase::getCovMatrix
TMatrixDSym * getCovMatrix()
Return covariance matrix.
Definition covarianceBase.h:137
+
covarianceBase::setThrowMatrixFromFile
void setThrowMatrixFromFile(const std::string &matrix_file_name, const std::string &matrix_name, const std::string &means_name)
sets throw matrix from a file
+
covarianceBase::getNominal
virtual double getNominal(const int i)
Return generated value, although is virtual so class inheriting might actual get nominal not generate...
Definition covarianceBase.h:230
+
covarianceBase::TransferMatT
TMatrixD TransferMatT
Matrix used to converting from normal base to PCA base.
Definition covarianceBase.h:501
+
covarianceBase::TransferMat
TMatrixD TransferMat
Matrix used to converting from PCA base to normal base.
Definition covarianceBase.h:499
+
covarianceBase::LastPCAdpar
int LastPCAdpar
Index of the last param that is being decomposed.
Definition covarianceBase.h:487
+
covarianceBase::setCovMatrix
void setCovMatrix(TMatrixDSym *cov)
Set covariance matrix.
Definition covarianceBase.cpp:495
+
covarianceBase::setName
void setName(const char *name)
Set matrix name.
Definition covarianceBase.h:69
+
covarianceBase::random_number
TRandom3 ** random_number
KS: Set Random numbers for each thread so each thread has different seed.
Definition covarianceBase.h:436
+
covarianceBase::GetLowerBound
double GetLowerBound(const int i)
Get lower parameter bound in which it is physically valid.
Definition covarianceBase.h:239
+
covarianceBase::getProposed
std::vector< double > getProposed() const
Get vector of all proposed parameter values.
Definition covarianceBase.cpp:606
+
covarianceBase::MatrixVectorMulti
void MatrixVectorMulti(double *_restrict_ VecMulti, double **_restrict_ matrix, const double *_restrict_ vector, const int n)
KS: Custom function to perform multiplication of matrix and vector with multithreading.
Definition covarianceBase.cpp:1223
+
covarianceBase::TransferToPCA
void TransferToPCA()
Transfer param values from normal base to PCA base.
Definition covarianceBase.cpp:568
+
covarianceBase::TransferToParam
void TransferToParam()
Transfer param values from PCA base to normal base.
Definition covarianceBase.cpp:587
+
covarianceBase::setParCurrProp
void setParCurrProp(const int i, const double val)
Set current parameter value.
Definition covarianceBase.cpp:768
+
covarianceBase::GetParFancyName
std::string GetParFancyName(const int i)
Get fancy name of the Parameter.
Definition covarianceBase.h:154
+
covarianceBase::covMatrix
TMatrixDSym * covMatrix
The covariance matrix.
Definition covarianceBase.h:429
+
covarianceBase::throwMatrix
TMatrixDSym * throwMatrix
Matrix which we use for step proposal before Cholesky decomposition (not actually used for step propo...
Definition covarianceBase.h:512
+
covarianceBase::randParams
double * randParams
Random number taken from gaussian around prior error used for corr_throw.
Definition covarianceBase.h:439
+
covarianceBase::initialiseAdaption
void initialiseAdaption(const YAML::Node &adapt_manager)
Initialise adaptive MCMC.
Definition covarianceBase.cpp:1400
+
covarianceBase::getGeneratedValues
std::vector< double > getGeneratedValues()
Definition covarianceBase.h:216
+
covarianceBase::printNominalCurrProp
void printNominalCurrProp()
Print nominal, current and proposed value for each parameter.
Definition covarianceBase.cpp:979
+
covarianceBase::getName
const char * getName()
Get name of covariance.
Definition covarianceBase.h:145
+
covarianceBase::_fPreFitValue
std::vector< double > _fPreFitValue
Parameter value dictated by the prior model. Based on it penalty term is calculated.
Definition covarianceBase.h:457
+
covarianceBase::ReserveMemory
void ReserveMemory(const int size)
Initialise vectors with parameters information.
Definition covarianceBase.cpp:516
+
covarianceBase::MatrixVectorMultiSingle
double MatrixVectorMultiSingle(double **_restrict_ matrix, const double *_restrict_ vector, const int Length, const int i)
KS: Custom function to perform multiplication of matrix and single element which is thread safe.
Definition covarianceBase.cpp:1240
+
covarianceBase::Unity
const double Unity
Unity for null systs to point back to.
Definition covarianceBase.h:476
+
covarianceBase::corr_throw
double * corr_throw
Result of multiplication of Cholesky matrix and randParams.
Definition covarianceBase.h:441
+
covarianceBase::fParSigma_PCA
std::vector< double > fParSigma_PCA
Tells if parameter is fixed in PCA base or not.
Definition covarianceBase.h:507
+
covarianceBase::setParProp_PCA
void setParProp_PCA(const int i, const double value)
Set proposed value for parameter in PCA base.
Definition covarianceBase.h:286
+
covarianceBase::size
int size
Total number of params, deprecated, please don't use it.
Definition covarianceBase.h:425
+
covarianceBase::updateThrowMatrix
void updateThrowMatrix(TMatrixDSym *cov)
Definition covarianceBase.cpp:1380
+
covarianceBase::setStepScale
void setStepScale(const double scale)
Set global step scale for covariance object.
Definition covarianceBase.cpp:1126
+
covarianceBase::use_adaptive
bool use_adaptive
Are we using AMCMC?
Definition covarianceBase.h:519
+
covarianceBase::RandomConfiguration
void RandomConfiguration()
Randomly throw the parameters in their 1 sigma range.
Definition covarianceBase.cpp:721
+
covarianceBase::makeClosestPosDef
void makeClosestPosDef(TMatrixDSym *cov)
HW: Finds closest possible positive definite matrix in Frobenius Norm ||.||_frob Where ||X||_frob=sqr...
Definition covarianceBase.cpp:1476
+
covarianceBase::ConstructPCA
void ConstructPCA()
CW: Calculate eigen values, prepare transition matrices and remove param based on defined threshold.
Definition covarianceBase.cpp:117
+
covarianceBase::_fLowBound
std::vector< double > _fLowBound
Lowest physical bound, parameter will not be able to go beyond it.
Definition covarianceBase.h:467
+
covarianceBase::_fYAMLDoc
YAML::Node _fYAMLDoc
Stores config describing systematics.
Definition covarianceBase.h:453
covarianceBase::proposeStep
virtual void proposeStep()
Generate a new proposed state.
Definition covarianceBase.cpp:779
-
covarianceBase::_fFancyNames
std::vector< std::string > _fFancyNames
Fancy name for example rather than xsec_0 it is MAQE, useful for human reading.
Definition covarianceBase.h:437
-
covarianceBase::setSingleParameter
void setSingleParameter(const int parNo, const double parVal)
Definition covarianceBase.cpp:761
-
covarianceBase::_fGenerated
std::vector< double > _fGenerated
Generated value of the parameter.
Definition covarianceBase.h:449
-
covarianceBase::GetLikelihood
virtual double GetLikelihood()
Return CalcLikelihood if some params were thrown out of boundary return LARGE_LOGL
Definition covarianceBase.cpp:1034
-
covarianceBase::PrintLength
unsigned int PrintLength
KS: This is used when printing parameters, sometimes we have super long parameters name,...
Definition covarianceBase.h:432
-
covarianceBase::setParProp
void setParProp(const int i, const double val)
Set proposed parameter value.
Definition covarianceBase.h:84
-
covarianceBase::acceptStep
void acceptStep()
Accepted this step.
Definition covarianceBase.cpp:886
-
covarianceBase::getThrowMatrix
TMatrixDSym * getThrowMatrix()
Definition covarianceBase.h:182
-
covarianceBase::setParameters
void setParameters(const std::vector< double > &pars={})
Set parameter values using vector, it has to have same size as covariance class.
Definition covarianceBase.cpp:1060
-
covarianceBase::getInputFile
std::string getInputFile() const
Get name of input file.
Definition covarianceBase.h:158
-
covarianceBase::throwParameters
void throwParameters()
Throw the parameters according to the covariance matrix. This shouldn't be used in MCMC code ase it c...
Definition covarianceBase.cpp:668
-
covarianceBase::fParCurr_PCA
TVectorD fParCurr_PCA
CW: Proposed parameter value in PCA base.
Definition covarianceBase.h:491
-
covarianceBase::retPointer
const double * retPointer(const int iParam)
DB Pointer return to param position.
Definition covarianceBase.h:208
-
covarianceBase::setPar
void setPar(const int i, const double val)
Set all the covariance matrix parameters to a user-defined value.
Definition covarianceBase.cpp:558
-
covarianceBase::SetBranches
void SetBranches(TTree &tree, bool SaveProposal=false)
set branches for output file
Definition covarianceBase.cpp:1096
-
covarianceBase::toggleFixParameter
void toggleFixParameter(const int i)
fix parameter at prior values
Definition covarianceBase.cpp:1149
-
covarianceBase::getPreFitValues
std::vector< double > getPreFitValues()
Definition covarianceBase.h:214
-
covarianceBase::SaveUpdatedMatrixConfig
void SaveUpdatedMatrixConfig()
KS: After step scale, prefit etc. value were modified save this modified config.
Definition covarianceBase.cpp:1749
-
covarianceBase::getSize
int getSize()
Get number of params in normal Base, if you want something which will work with PCA as well please us...
Definition covarianceBase.h:317
-
covarianceBase::pca
bool pca
perform PCA or not
Definition covarianceBase.h:465
-
covarianceBase::isParameterFixedPCA
bool isParameterFixedPCA(const int i)
Is parameter fixed in PCA base or not.
Definition covarianceBase.h:258
-
covarianceBase::getParameterMeans
std::vector< double > getParameterMeans()
Definition covarianceBase.h:184
-
covarianceBase::throwMatrix_CholDecomp
TMatrixD * throwMatrix_CholDecomp
Definition covarianceBase.h:499
-
covarianceBase::CorrelateSteps
void CorrelateSteps()
Use Cholesky throw matrix for better step proposal.
Definition covarianceBase.cpp:838
-
covarianceBase::FirstPCAdpar
int FirstPCAdpar
Index of the first param that is being decomposed.
Definition covarianceBase.h:471
-
covarianceBase::init
void init(const char *name, const char *file)
Definition covarianceBase.cpp:256
-
covarianceBase::GetCorrelationMatrix
TH2D * GetCorrelationMatrix()
KS: Convert covariance matrix to correlation matrix and return TH2D which can be used for fancy plott...
Definition covarianceBase.cpp:1720
- -
covarianceBase::CheckBounds
virtual int CheckBounds()
Check if parameters were proposed outside physical boundary.
Definition covarianceBase.cpp:1019
-
covarianceBase::_fNumParPCA
int _fNumParPCA
Number of parameters in PCA base.
Definition covarianceBase.h:469
-
covarianceBase::eigen_vectors
TMatrixD eigen_vectors
Eigen vectors only of params which are being decomposed.
Definition covarianceBase.h:479
-
covarianceBase::_fNumPar
int _fNumPar
Number of systematic parameters.
Definition covarianceBase.h:441
-
covarianceBase::throwMatrixCholDecomp
double ** throwMatrixCholDecomp
Throw matrix that is being used in the fit, much faster as TMatrixDSym cache miss.
Definition covarianceBase.h:501
-
covarianceBase::getTransferMatrix
const TMatrixD getTransferMatrix()
Get transfer matrix allowing to go from PCA base to normal base.
Definition covarianceBase.h:263
-
covarianceBase::setParName
void setParName(int i, char *name)
change parameter name
Definition covarianceBase.h:72
-
covarianceBase::setAdaptiveBlocks
void setAdaptiveBlocks(std::vector< std::vector< int > > block_indices)
sets adaptive block matrix
Definition covarianceBase.cpp:1547
-
covarianceBase::getEigenVectors
const TMatrixD getEigenVectors()
Get eigen vectors of covariance matrix, only works with PCA.
Definition covarianceBase.h:268
+
covarianceBase::_fFancyNames
std::vector< std::string > _fFancyNames
Fancy name for example rather than xsec_0 it is MAQE, useful for human reading.
Definition covarianceBase.h:451
+
covarianceBase::setSingleParameter
void setSingleParameter(const int parNo, const double parVal)
Definition covarianceBase.cpp:759
+
covarianceBase::_fGenerated
std::vector< double > _fGenerated
Generated value of the parameter.
Definition covarianceBase.h:463
+
covarianceBase::GetLikelihood
virtual double GetLikelihood()
Return CalcLikelihood if some params were thrown out of boundary return LARGE_LOGL
Definition covarianceBase.cpp:1037
+
covarianceBase::PrintLength
unsigned int PrintLength
KS: This is used when printing parameters, sometimes we have super long parameters name,...
Definition covarianceBase.h:446
+
covarianceBase::setParProp
void setParProp(const int i, const double val)
Set proposed parameter value.
Definition covarianceBase.h:85
+
covarianceBase::acceptStep
void acceptStep()
Accepted this step.
Definition covarianceBase.cpp:887
+
covarianceBase::getThrowMatrix
TMatrixDSym * getThrowMatrix()
Definition covarianceBase.h:183
+
covarianceBase::setParameters
void setParameters(const std::vector< double > &pars={})
Set parameter values using vector, it has to have same size as covariance class.
Definition covarianceBase.cpp:1062
+
covarianceBase::getInputFile
std::string getInputFile() const
Get name of input file.
Definition covarianceBase.h:159
+
covarianceBase::throwParameters
void throwParameters()
Throw the parameters according to the covariance matrix. This shouldn't be used in MCMC code ase it c...
Definition covarianceBase.cpp:667
+
covarianceBase::fParCurr_PCA
TVectorD fParCurr_PCA
CW: Proposed parameter value in PCA base.
Definition covarianceBase.h:505
+
covarianceBase::retPointer
const double * retPointer(const int iParam)
DB Pointer return to param position.
Definition covarianceBase.h:209
+
covarianceBase::setPar
void setPar(const int i, const double val)
Set all the covariance matrix parameters to a user-defined value.
Definition covarianceBase.cpp:554
+
covarianceBase::SetBranches
void SetBranches(TTree &tree, bool SaveProposal=false)
set branches for output file
Definition covarianceBase.cpp:1098
+
covarianceBase::toggleFixParameter
void toggleFixParameter(const int i)
fix parameter at prior values
Definition covarianceBase.cpp:1151
+
covarianceBase::getPreFitValues
std::vector< double > getPreFitValues()
Definition covarianceBase.h:215
+
covarianceBase::SaveUpdatedMatrixConfig
void SaveUpdatedMatrixConfig()
KS: After step scale, prefit etc. value were modified save this modified config.
Definition covarianceBase.cpp:1563
+
covarianceBase::AdaptiveHandler
adaptive_mcmc::AdaptiveMCMCHandler AdaptiveHandler
Struct containing information about adaption.
Definition covarianceBase.h:524
+
covarianceBase::getSize
int getSize()
Get number of params in normal Base, if you want something which will work with PCA as well please us...
Definition covarianceBase.h:318
+
covarianceBase::pca
bool pca
perform PCA or not
Definition covarianceBase.h:479
+
covarianceBase::isParameterFixedPCA
bool isParameterFixedPCA(const int i)
Is parameter fixed in PCA base or not.
Definition covarianceBase.h:259
+
covarianceBase::getParameterMeans
std::vector< double > getParameterMeans()
Definition covarianceBase.h:185
+
covarianceBase::throwMatrix_CholDecomp
TMatrixD * throwMatrix_CholDecomp
Matrix which we use for step proposal after Cholesky decomposition.
Definition covarianceBase.h:514
+
covarianceBase::CorrelateSteps
void CorrelateSteps()
Use Cholesky throw matrix for better step proposal.
Definition covarianceBase.cpp:839
+
covarianceBase::FirstPCAdpar
int FirstPCAdpar
Index of the first param that is being decomposed.
Definition covarianceBase.h:485
+
covarianceBase::init
void init(const char *name, const char *file)
Initialisation of the class using matrix from root file.
Definition covarianceBase.cpp:251
+
covarianceBase::GetCorrelationMatrix
TH2D * GetCorrelationMatrix()
KS: Convert covariance matrix to correlation matrix and return TH2D which can be used for fancy plott...
Definition covarianceBase.cpp:1535
+ +
covarianceBase::CheckBounds
virtual int CheckBounds()
Check if parameters were proposed outside physical boundary.
Definition covarianceBase.cpp:1022
+
covarianceBase::_fNumParPCA
int _fNumParPCA
Number of parameters in PCA base.
Definition covarianceBase.h:483
+
covarianceBase::eigen_vectors
TMatrixD eigen_vectors
Eigen vectors only of params which are being decomposed.
Definition covarianceBase.h:493
+
covarianceBase::_fNumPar
int _fNumPar
Number of systematic parameters.
Definition covarianceBase.h:455
+
covarianceBase::throwMatrixCholDecomp
double ** throwMatrixCholDecomp
Throw matrix that is being used in the fit, much faster as TMatrixDSym cache miss.
Definition covarianceBase.h:516
+
covarianceBase::getTransferMatrix
const TMatrixD getTransferMatrix()
Get transfer matrix allowing to go from PCA base to normal base.
Definition covarianceBase.h:264
+
covarianceBase::setParName
void setParName(int i, char *name)
change parameter name
Definition covarianceBase.h:73
+
covarianceBase::getEigenVectors
const TMatrixD getEigenVectors()
Get eigen vectors of covariance matrix, only works with PCA.
Definition covarianceBase.h:269
covarianceBase::printIndivStepScale
void printIndivStepScale()
Print step scale for each parameter.
Definition covarianceBase.cpp:1271
-
covarianceBase::eigen_values
TVectorD eigen_values
Eigen value only of particles which are being decomposed.
Definition covarianceBase.h:477
-
covarianceBase::GetIndivStepScale
double GetIndivStepScale(const int ParameterIndex)
Get individual step scale for selected parameter.
Definition covarianceBase.h:241
-
covarianceBase::_fFlatPrior
std::vector< bool > _fFlatPrior
Whether to apply flat prior or not.
Definition covarianceBase.h:459
-
covarianceBase::toggleFixAllParameters
void toggleFixAllParameters()
fix parameters at prior values
Definition covarianceBase.cpp:1136
-
covarianceBase::getEigenValues
const TVectorD getEigenValues()
Get eigen values for all parameters, if you want for decomposed only parameters use getEigenValuesMas...
Definition covarianceBase.h:273
-
covarianceBase::eigen_threshold
double eigen_threshold
CW: Threshold based on which we remove parameters in eigen base.
Definition covarianceBase.h:467
-
covarianceBase::getNominalArray
virtual std::vector< double > getNominalArray()
Definition covarianceBase.cpp:1707
+
covarianceBase::eigen_values
TVectorD eigen_values
Eigen value only of particles which are being decomposed.
Definition covarianceBase.h:491
+
covarianceBase::GetIndivStepScale
double GetIndivStepScale(const int ParameterIndex)
Get individual step scale for selected parameter.
Definition covarianceBase.h:242
+
covarianceBase::_fFlatPrior
std::vector< bool > _fFlatPrior
Whether to apply flat prior or not.
Definition covarianceBase.h:473
+
covarianceBase::toggleFixAllParameters
void toggleFixAllParameters()
fix parameters at prior values
Definition covarianceBase.cpp:1138
+
covarianceBase::getEigenValues
const TVectorD getEigenValues()
Get eigen values for all parameters, if you want for decomposed only parameters use getEigenValuesMas...
Definition covarianceBase.h:274
+
covarianceBase::eigen_threshold
double eigen_threshold
CW: Threshold based on which we remove parameters in eigen base.
Definition covarianceBase.h:481
+
covarianceBase::getNominalArray
virtual std::vector< double > getNominalArray()
Definition covarianceBase.cpp:1522
covarianceBase::MakePosDef
void MakePosDef(TMatrixDSym *cov=nullptr)
Make matrix positive definite by adding small values to diagonal, necessary for inverting matrix.
Definition covarianceBase.cpp:1283
-
covarianceBase::saveAdaptiveToFile
void saveAdaptiveToFile(const TString &outFileName, const TString &systematicName)
Save adaptive throw matrix to file.
Definition covarianceBase.cpp:1389
-
covarianceBase::setAdaptionDefaults
void setAdaptionDefaults()
sets default values for adaptive MCMC parameters
Definition covarianceBase.cpp:1409
-
covarianceBase::_fPreFitValue_PCA
std::vector< double > _fPreFitValue_PCA
Prefit value for PCA params.
Definition covarianceBase.h:483
-
covarianceBase::_fCurrVal
std::vector< double > _fCurrVal
Current value of the parameter.
Definition covarianceBase.h:445
-
covarianceBase::isDecomposed_PCA
std::vector< int > isDecomposed_PCA
If param is decomposed this will return -1, if not this will return enumerator to param in normal bas...
Definition covarianceBase.h:495
-
covarianceBase::eigen_values_master
std::vector< double > eigen_values_master
Eigen values which have dimension equal to _fNumParPCA, and can be used in CorrelateSteps.
Definition covarianceBase.h:481
-
covarianceBase::printNominal
void printNominal()
Print nominal value for every parameter.
Definition covarianceBase.cpp:966
-
covarianceBase::setThrowMatrix
void setThrowMatrix(TMatrixDSym *cov)
Definition covarianceBase.cpp:1338
-
covarianceBase::getParCurr_PCA
double getParCurr_PCA(const int i)
Get current parameter value using PCA.
Definition covarianceBase.h:251
-
covarianceBase::throwParProp
void throwParProp(const double mag=1.)
Throw the proposed parameter by mag sigma. Should really just have the user specify this throw by hav...
Definition covarianceBase.cpp:910
-
covarianceBase::throwNominal
void throwNominal(const bool nomValues=false, const int seed=0)
Throw nominal values.
Definition covarianceBase.cpp:615
- +
covarianceBase::setAdaptionDefaults
void setAdaptionDefaults()
sets default values for adaptive MCMC parameters
Definition covarianceBase.cpp:1391
+
covarianceBase::_fPreFitValue_PCA
std::vector< double > _fPreFitValue_PCA
Prefit value for PCA params.
Definition covarianceBase.h:497
+
covarianceBase::_fCurrVal
std::vector< double > _fCurrVal
Current value of the parameter.
Definition covarianceBase.h:459
+
covarianceBase::isDecomposed_PCA
std::vector< int > isDecomposed_PCA
If param is decomposed this will return -1, if not this will return enumerator to param in normal bas...
Definition covarianceBase.h:509
+
covarianceBase::eigen_values_master
std::vector< double > eigen_values_master
Eigen values which have dimension equal to _fNumParPCA, and can be used in CorrelateSteps.
Definition covarianceBase.h:495
+
covarianceBase::printNominal
void printNominal()
Print nominal value for every parameter.
Definition covarianceBase.cpp:969
+
covarianceBase::setThrowMatrix
void setThrowMatrix(TMatrixDSym *cov)
Use new throw matrix, used in adaptive MCMC.
Definition covarianceBase.cpp:1340
+
covarianceBase::getParCurr_PCA
double getParCurr_PCA(const int i)
Get current parameter value using PCA.
Definition covarianceBase.h:252
+
covarianceBase::throwParProp
void throwParProp(const double mag=1.)
Throw the proposed parameter by mag sigma. Should really just have the user specify this throw by hav...
Definition covarianceBase.cpp:912
+
covarianceBase::throwNominal
void throwNominal(const bool nomValues=false, const int seed=0)
Throw nominal values.
Definition covarianceBase.cpp:614
+
covarianceBase::total_steps
int total_steps
Total number of MCMC steps.
Definition covarianceBase.h:521
-
adaptive_mcmc::AdaptiveMCMCStruct
struct encapsulating all adaptive MCMC information
Definition adaptiveMCMCStruct.h:19
-
adaptive_mcmc::AdaptiveMCMCStruct::par_means
std::vector< double > par_means
Mean values for all parameters.
Definition adaptiveMCMCStruct.h:36
-
adaptive_mcmc::AdaptiveMCMCStruct::start_adaptive_throw
int start_adaptive_throw
When do we start throwing.
Definition adaptiveMCMCStruct.h:22
diff --git a/covarianceOsc_8cpp_source.html b/covarianceOsc_8cpp_source.html index 9d1ef2374..e226f3f7e 100644 --- a/covarianceOsc_8cpp_source.html +++ b/covarianceOsc_8cpp_source.html @@ -365,24 +365,24 @@
263 }
264}
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MACH3LOG_ERROR
#define MACH3LOG_ERROR
Definition MaCh3Logger.h:15
-
MACH3LOG_INFO
#define MACH3LOG_INFO
Definition MaCh3Logger.h:13
-
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:18
-
MaCh3Exception
Custom exception class for MaCh3 errors.
Definition MaCh3Exception.h:10
-
covarianceBase
Base class responsible for handling of systematic error parameters. Capable of using PCA or using ada...
Definition covarianceBase.h:33
-
covarianceBase::_fPropVal
std::vector< double > _fPropVal
Proposed value of the parameter.
Definition covarianceBase.h:447
-
covarianceBase::setFlatPrior
void setFlatPrior(const int i, const bool eL)
Set if parameter should have flat prior or not.
Definition covarianceBase.cpp:1202
-
covarianceBase::randomize
void randomize()
"Randomize" the parameters in the covariance class for the proposed step. Used the proposal kernel an...
Definition covarianceBase.cpp:793
-
covarianceBase::_fError
std::vector< double > _fError
Prior error on the parameter.
Definition covarianceBase.h:451
-
covarianceBase::_fIndivStepScale
std::vector< double > _fIndivStepScale
Individual step scale used by MCMC algorithm.
Definition covarianceBase.h:457
-
covarianceBase::_fNames
std::vector< std::string > _fNames
ETA _fNames is set automatically in the covariance class to be something like xsec_i,...
Definition covarianceBase.h:435
-
covarianceBase::matrixName
const char * matrixName
Name of cov matrix.
Definition covarianceBase.h:413
-
covarianceBase::random_number
TRandom3 ** random_number
KS: Set Random numbers for each thread so each thread has different seed.
Definition covarianceBase.h:422
-
covarianceBase::_fPreFitValue
std::vector< double > _fPreFitValue
Parameter value dictated by the prior model. Based on it penalty term is calculated.
Definition covarianceBase.h:443
+
MACH3LOG_ERROR
#define MACH3LOG_ERROR
Definition MaCh3Logger.h:18
+
MACH3LOG_INFO
#define MACH3LOG_INFO
Definition MaCh3Logger.h:16
+
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:21
+
MaCh3Exception
Custom exception class for MaCh3 errors.
Definition MaCh3Exception.h:12
+
covarianceBase
Base class responsible for handling of systematic error parameters. Capable of using PCA or using ada...
Definition covarianceBase.h:34
+
covarianceBase::_fPropVal
std::vector< double > _fPropVal
Proposed value of the parameter.
Definition covarianceBase.h:461
+
covarianceBase::setFlatPrior
void setFlatPrior(const int i, const bool eL)
Set if parameter should have flat prior or not.
Definition covarianceBase.cpp:1203
+
covarianceBase::randomize
void randomize()
"Randomize" the parameters in the covariance class for the proposed step. Used the proposal kernel an...
Definition covarianceBase.cpp:794
+
covarianceBase::_fError
std::vector< double > _fError
Prior error on the parameter.
Definition covarianceBase.h:465
+
covarianceBase::_fIndivStepScale
std::vector< double > _fIndivStepScale
Individual step scale used by MCMC algorithm.
Definition covarianceBase.h:471
+
covarianceBase::_fNames
std::vector< std::string > _fNames
ETA _fNames is set automatically in the covariance class to be something like xsec_i,...
Definition covarianceBase.h:449
+
covarianceBase::matrixName
const char * matrixName
Name of cov matrix.
Definition covarianceBase.h:427
+
covarianceBase::random_number
TRandom3 ** random_number
KS: Set Random numbers for each thread so each thread has different seed.
Definition covarianceBase.h:436
+
covarianceBase::_fPreFitValue
std::vector< double > _fPreFitValue
Parameter value dictated by the prior model. Based on it penalty term is calculated.
Definition covarianceBase.h:457
covarianceBase::proposeStep
virtual void proposeStep()
Generate a new proposed state.
Definition covarianceBase.cpp:779
-
covarianceBase::GetLikelihood
virtual double GetLikelihood()
Return CalcLikelihood if some params were thrown out of boundary return LARGE_LOGL
Definition covarianceBase.cpp:1034
-
covarianceBase::_fNumPar
int _fNumPar
Number of systematic parameters.
Definition covarianceBase.h:441
-
covarianceBase::_fCurrVal
std::vector< double > _fCurrVal
Current value of the parameter.
Definition covarianceBase.h:445
+
covarianceBase::GetLikelihood
virtual double GetLikelihood()
Return CalcLikelihood if some params were thrown out of boundary return LARGE_LOGL
Definition covarianceBase.cpp:1037
+
covarianceBase::_fNumPar
int _fNumPar
Number of systematic parameters.
Definition covarianceBase.h:455
+
covarianceBase::_fCurrVal
std::vector< double > _fCurrVal
Current value of the parameter.
Definition covarianceBase.h:459
covarianceOsc::flipBeta
bool flipBeta
Do we flip Beta or not.
Definition covarianceOsc.h:55
covarianceOsc::getPropPars
double * getPropPars()
Retrieves the proposed parameters.
Definition covarianceOsc.cpp:147
covarianceOsc::kDeltaM23
int kDeltaM23
There is special treatment for DeltaM23, therefore store enum keeping track when to apply special tre...
Definition covarianceOsc.h:64
diff --git a/covarianceOsc_8h_source.html b/covarianceOsc_8h_source.html index 32249cd30..a3dde6a64 100644 --- a/covarianceOsc_8h_source.html +++ b/covarianceOsc_8h_source.html @@ -125,8 +125,8 @@
69};
70
-
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:18
-
covarianceBase
Base class responsible for handling of systematic error parameters. Capable of using PCA or using ada...
Definition covarianceBase.h:33
+
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:21
+
covarianceBase
Base class responsible for handling of systematic error parameters. Capable of using PCA or using ada...
Definition covarianceBase.h:34
covarianceOsc
Class responsible for handling of neutrino oscillation parameters.
Definition covarianceOsc.h:8
covarianceOsc::GetPerformBetaStudy
bool GetPerformBetaStudy()
Check if we are performing beta study or not.
Definition covarianceOsc.h:39
covarianceOsc::flipBeta
bool flipBeta
Do we flip Beta or not.
Definition covarianceOsc.h:55
diff --git a/covarianceXsec_8cpp_source.html b/covarianceXsec_8cpp_source.html index bffc77172..804c3b781 100644 --- a/covarianceXsec_8cpp_source.html +++ b/covarianceXsec_8cpp_source.html @@ -658,10 +658,10 @@
536 }
537}
-
MACH3LOG_CRITICAL
#define MACH3LOG_CRITICAL
Definition MaCh3Logger.h:16
-
MACH3LOG_DEBUG
#define MACH3LOG_DEBUG
Definition MaCh3Logger.h:12
-
MACH3LOG_ERROR
#define MACH3LOG_ERROR
Definition MaCh3Logger.h:15
-
MACH3LOG_INFO
#define MACH3LOG_INFO
Definition MaCh3Logger.h:13
+
MACH3LOG_CRITICAL
#define MACH3LOG_CRITICAL
Definition MaCh3Logger.h:19
+
MACH3LOG_DEBUG
#define MACH3LOG_DEBUG
Definition MaCh3Logger.h:15
+
MACH3LOG_ERROR
#define MACH3LOG_ERROR
Definition MaCh3Logger.h:18
+
MACH3LOG_INFO
#define MACH3LOG_INFO
Definition MaCh3Logger.h:16
SplineInterpolation_ToString
std::string SplineInterpolation_ToString(const SplineInterpolation i)
Convert a LLH type to a string.
Definition Structs.h:122
SplineInterpolation
SplineInterpolation
Make an enum of the spline interpolation type.
Definition Structs.h:112
kTSpline3
@ kTSpline3
Definition Structs.h:113
@@ -672,62 +672,62 @@
kSpline
@ kSpline
Definition Structs.h:152
kSystTypes
@ kSystTypes
Definition Structs.h:154
kFunc
@ kFunc
Definition Structs.h:153
-
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:18
-
MaCh3Exception
Custom exception class for MaCh3 errors.
Definition MaCh3Exception.h:10
-
covarianceBase
Base class responsible for handling of systematic error parameters. Capable of using PCA or using ada...
Definition covarianceBase.h:33
-
covarianceBase::GetParName
std::string GetParName(const int i)
Get name of covariance.
Definition covarianceBase.h:147
-
covarianceBase::_fPropVal
std::vector< double > _fPropVal
Proposed value of the parameter.
Definition covarianceBase.h:447
-
covarianceBase::_fUpBound
std::vector< double > _fUpBound
Upper physical bound, parameter will not be able to go beyond it.
Definition covarianceBase.h:455
-
covarianceBase::randomize
void randomize()
"Randomize" the parameters in the covariance class for the proposed step. Used the proposal kernel an...
Definition covarianceBase.cpp:793
-
covarianceBase::_fError
std::vector< double > _fError
Prior error on the parameter.
Definition covarianceBase.h:451
-
covarianceBase::_fIndivStepScale
std::vector< double > _fIndivStepScale
Individual step scale used by MCMC algorithm.
Definition covarianceBase.h:457
-
covarianceBase::GetNumParams
int GetNumParams()
Get total number of parameters.
Definition covarianceBase.h:212
-
covarianceBase::_fNames
std::vector< std::string > _fNames
ETA _fNames is set automatically in the covariance class to be something like xsec_i,...
Definition covarianceBase.h:435
-
covarianceBase::LastPCAdpar
int LastPCAdpar
Index of the last param that is being decomposed.
Definition covarianceBase.h:473
-
covarianceBase::TransferToPCA
void TransferToPCA()
Transfer param values from normal base to PCA base.
Definition covarianceBase.cpp:571
-
covarianceBase::GetParFancyName
std::string GetParFancyName(const int i)
Get fancy name of the Parameter.
Definition covarianceBase.h:153
-
covarianceBase::_fPreFitValue
std::vector< double > _fPreFitValue
Parameter value dictated by the prior model. Based on it penalty term is calculated.
Definition covarianceBase.h:443
-
covarianceBase::_fLowBound
std::vector< double > _fLowBound
Lowest physical bound, parameter will not be able to go beyond it.
Definition covarianceBase.h:453
-
covarianceBase::_fYAMLDoc
YAML::Node _fYAMLDoc
Stores config describing systematics.
Definition covarianceBase.h:439
-
covarianceBase::_fFancyNames
std::vector< std::string > _fFancyNames
Fancy name for example rather than xsec_0 it is MAQE, useful for human reading.
Definition covarianceBase.h:437
-
covarianceBase::_fGenerated
std::vector< double > _fGenerated
Generated value of the parameter.
Definition covarianceBase.h:449
-
covarianceBase::PrintLength
unsigned int PrintLength
KS: This is used when printing parameters, sometimes we have super long parameters name,...
Definition covarianceBase.h:432
-
covarianceBase::fParCurr_PCA
TVectorD fParCurr_PCA
CW: Proposed parameter value in PCA base.
Definition covarianceBase.h:491
-
covarianceBase::pca
bool pca
perform PCA or not
Definition covarianceBase.h:465
-
covarianceBase::CorrelateSteps
void CorrelateSteps()
Use Cholesky throw matrix for better step proposal.
Definition covarianceBase.cpp:838
-
covarianceBase::FirstPCAdpar
int FirstPCAdpar
Index of the first param that is being decomposed.
Definition covarianceBase.h:471
-
covarianceBase::_fNumParPCA
int _fNumParPCA
Number of parameters in PCA base.
Definition covarianceBase.h:469
-
covarianceBase::_fNumPar
int _fNumPar
Number of systematic parameters.
Definition covarianceBase.h:441
-
covarianceBase::_fPreFitValue_PCA
std::vector< double > _fPreFitValue_PCA
Prefit value for PCA params.
Definition covarianceBase.h:483
-
covarianceBase::_fCurrVal
std::vector< double > _fCurrVal
Current value of the parameter.
Definition covarianceBase.h:445
+
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:21
+
MaCh3Exception
Custom exception class for MaCh3 errors.
Definition MaCh3Exception.h:12
+
covarianceBase
Base class responsible for handling of systematic error parameters. Capable of using PCA or using ada...
Definition covarianceBase.h:34
+
covarianceBase::GetParName
std::string GetParName(const int i)
Get name of covariance.
Definition covarianceBase.h:148
+
covarianceBase::_fPropVal
std::vector< double > _fPropVal
Proposed value of the parameter.
Definition covarianceBase.h:461
+
covarianceBase::_fUpBound
std::vector< double > _fUpBound
Upper physical bound, parameter will not be able to go beyond it.
Definition covarianceBase.h:469
+
covarianceBase::randomize
void randomize()
"Randomize" the parameters in the covariance class for the proposed step. Used the proposal kernel an...
Definition covarianceBase.cpp:794
+
covarianceBase::_fError
std::vector< double > _fError
Prior error on the parameter.
Definition covarianceBase.h:465
+
covarianceBase::_fIndivStepScale
std::vector< double > _fIndivStepScale
Individual step scale used by MCMC algorithm.
Definition covarianceBase.h:471
+
covarianceBase::GetNumParams
int GetNumParams()
Get total number of parameters.
Definition covarianceBase.h:213
+
covarianceBase::_fNames
std::vector< std::string > _fNames
ETA _fNames is set automatically in the covariance class to be something like xsec_i,...
Definition covarianceBase.h:449
+
covarianceBase::LastPCAdpar
int LastPCAdpar
Index of the last param that is being decomposed.
Definition covarianceBase.h:487
+
covarianceBase::TransferToPCA
void TransferToPCA()
Transfer param values from normal base to PCA base.
Definition covarianceBase.cpp:568
+
covarianceBase::GetParFancyName
std::string GetParFancyName(const int i)
Get fancy name of the Parameter.
Definition covarianceBase.h:154
+
covarianceBase::_fPreFitValue
std::vector< double > _fPreFitValue
Parameter value dictated by the prior model. Based on it penalty term is calculated.
Definition covarianceBase.h:457
+
covarianceBase::_fLowBound
std::vector< double > _fLowBound
Lowest physical bound, parameter will not be able to go beyond it.
Definition covarianceBase.h:467
+
covarianceBase::_fYAMLDoc
YAML::Node _fYAMLDoc
Stores config describing systematics.
Definition covarianceBase.h:453
+
covarianceBase::_fFancyNames
std::vector< std::string > _fFancyNames
Fancy name for example rather than xsec_0 it is MAQE, useful for human reading.
Definition covarianceBase.h:451
+
covarianceBase::_fGenerated
std::vector< double > _fGenerated
Generated value of the parameter.
Definition covarianceBase.h:463
+
covarianceBase::PrintLength
unsigned int PrintLength
KS: This is used when printing parameters, sometimes we have super long parameters name,...
Definition covarianceBase.h:446
+
covarianceBase::fParCurr_PCA
TVectorD fParCurr_PCA
CW: Proposed parameter value in PCA base.
Definition covarianceBase.h:505
+
covarianceBase::pca
bool pca
perform PCA or not
Definition covarianceBase.h:479
+
covarianceBase::CorrelateSteps
void CorrelateSteps()
Use Cholesky throw matrix for better step proposal.
Definition covarianceBase.cpp:839
+
covarianceBase::FirstPCAdpar
int FirstPCAdpar
Index of the first param that is being decomposed.
Definition covarianceBase.h:485
+
covarianceBase::_fNumParPCA
int _fNumParPCA
Number of parameters in PCA base.
Definition covarianceBase.h:483
+
covarianceBase::_fNumPar
int _fNumPar
Number of systematic parameters.
Definition covarianceBase.h:455
+
covarianceBase::_fPreFitValue_PCA
std::vector< double > _fPreFitValue_PCA
Prefit value for PCA params.
Definition covarianceBase.h:497
+
covarianceBase::_fCurrVal
std::vector< double > _fCurrVal
Current value of the parameter.
Definition covarianceBase.h:459
covarianceXsec::GetNumParamsFromDetID
int GetNumParamsFromDetID(const int DetID, const SystType Type)
DB Grab the number of parameters for the relevant DetID.
Definition covarianceXsec.cpp:324
covarianceXsec::setFluxOnlyParameters
void setFluxOnlyParameters()
KS Function to set to nominal flux parameters.
Definition covarianceXsec.cpp:513
-
covarianceXsec::_fFDSplineModes
std::vector< std::vector< int > > _fFDSplineModes
Definition covarianceXsec.h:140
-
covarianceXsec::_fDetID
std::vector< int > _fDetID
Tells to which samples object param should be applied.
Definition covarianceXsec.h:133
-
covarianceXsec::GetParamType
SystType GetParamType(const int i) const
Returns enum describing our param type.
Definition covarianceXsec.h:42
+
covarianceXsec::_fFDSplineModes
std::vector< std::vector< int > > _fFDSplineModes
Definition covarianceXsec.h:139
+
covarianceXsec::_fDetID
std::vector< int > _fDetID
Tells to which samples object param should be applied.
Definition covarianceXsec.h:132
+
covarianceXsec::GetParamType
SystType GetParamType(const int i) const
Returns enum describing our param type.
Definition covarianceXsec.h:41
covarianceXsec::GetSplineModeVecFromDetID
const std::vector< std::vector< int > > GetSplineModeVecFromDetID(const int DetID)
DB Grab the Spline Modes for the relevant DetID.
Definition covarianceXsec.cpp:202
covarianceXsec::CheckCorrectInitialisation
void CheckCorrectInitialisation()
KS: Check if matrix is correctly initialised.
Definition covarianceXsec.cpp:489
covarianceXsec::GetXsecNorm
XsecNorms4 GetXsecNorm(const YAML::Node &param, const int Index)
Get Norm params.
Definition covarianceXsec.cpp:222
-
covarianceXsec::GetParSplineInterpolation
SplineInterpolation GetParSplineInterpolation(const int i)
Get interpolation type for a given parameter.
Definition covarianceXsec.h:46
+
covarianceXsec::GetParSplineInterpolation
SplineInterpolation GetParSplineInterpolation(const int i)
Get interpolation type for a given parameter.
Definition covarianceXsec.h:45
covarianceXsec::GetFDSplineFileParsNamesFromDetID
const std::vector< std::string > GetFDSplineFileParsNamesFromDetID(const int DetID)
ETA - what does this even do?
Definition covarianceXsec.cpp:133
covarianceXsec::GetSplineParsNamesFromDetID
const std::vector< std::string > GetSplineParsNamesFromDetID(const int DetID)
DB Get spline parameters depending on given DetID.
Definition covarianceXsec.cpp:102
-
covarianceXsec::isFlux
std::vector< bool > isFlux
Definition covarianceXsec.h:130
+
covarianceXsec::isFlux
std::vector< bool > isFlux
Definition covarianceXsec.h:129
covarianceXsec::GetParsNamesFromDetID
const std::vector< std::string > GetParsNamesFromDetID(const int DetID, const SystType Type)
DB Grab the parameter names for the relevant DetID.
Definition covarianceXsec.cpp:340
-
covarianceXsec::_fFDSplineNames
std::vector< std::string > _fFDSplineNames
Definition covarianceXsec.h:139
+
covarianceXsec::_fFDSplineNames
std::vector< std::string > _fFDSplineNames
Definition covarianceXsec.h:138
covarianceXsec::InitXsecFromConfig
void InitXsecFromConfig()
ETA - trying out the yaml parsing.
Definition covarianceXsec.cpp:27
covarianceXsec::GetNormParsFromDetID
const std::vector< XsecNorms4 > GetNormParsFromDetID(const int DetID)
DB Get norm/func parameters depending on given DetID.
Definition covarianceXsec.cpp:302
-
covarianceXsec::GetParSplineKnotLowerBound
double GetParSplineKnotLowerBound(const int i)
EM: value at which we cap spline knot weight.
Definition covarianceXsec.h:53
+
covarianceXsec::GetParSplineKnotLowerBound
double GetParSplineKnotLowerBound(const int i)
EM: value at which we cap spline knot weight.
Definition covarianceXsec.h:52
covarianceXsec::GetParsIndexFromDetID
const std::vector< int > GetParsIndexFromDetID(const int DetID, const SystType Type)
DB Grab the parameter indices for the relevant DetID.
Definition covarianceXsec.cpp:356
covarianceXsec::GetNDSplineFileParsNamesFromDetID
const std::vector< std::string > GetNDSplineFileParsNamesFromDetID(const int DetID)
Definition covarianceXsec.cpp:155
-
covarianceXsec::GetParDetID
int GetParDetID(const int i) const
ETA - just return the int of the DetID, this can be removed to do a string comp at some point.
Definition covarianceXsec.h:36
-
covarianceXsec::_fParamType
std::vector< SystType > _fParamType
Type of parameter like norm, spline etc.
Definition covarianceXsec.h:135
-
covarianceXsec::_fNDSplineNames
std::vector< std::string > _fNDSplineNames
Definition covarianceXsec.h:138
-
covarianceXsec::GetParSplineKnotUpperBound
double GetParSplineKnotUpperBound(const int i)
EM: value at which we cap spline knot weight.
Definition covarianceXsec.h:50
-
covarianceXsec::NormParams
std::vector< XsecNorms4 > NormParams
Vector containing info for normalisation systematics.
Definition covarianceXsec.h:146
+
covarianceXsec::GetParDetID
int GetParDetID(const int i) const
ETA - just return the int of the DetID, this can be removed to do a string comp at some point.
Definition covarianceXsec.h:35
+
covarianceXsec::_fParamType
std::vector< SystType > _fParamType
Type of parameter like norm, spline etc.
Definition covarianceXsec.h:134
+
covarianceXsec::_fNDSplineNames
std::vector< std::string > _fNDSplineNames
Definition covarianceXsec.h:137
+
covarianceXsec::GetParSplineKnotUpperBound
double GetParSplineKnotUpperBound(const int i)
EM: value at which we cap spline knot weight.
Definition covarianceXsec.h:49
+
covarianceXsec::NormParams
std::vector< XsecNorms4 > NormParams
Vector containing info for normalisation systematics.
Definition covarianceXsec.h:145
covarianceXsec::GetXsecSpline
XsecSplines1 GetXsecSpline(const YAML::Node &param)
Get Spline params.
Definition covarianceXsec.cpp:278
covarianceXsec::GetSplineFileParsNamesFromDetID
const std::vector< std::string > GetSplineFileParsNamesFromDetID(const int DetID)
DB Get spline parameters depending on given DetID.
Definition covarianceXsec.cpp:175
covarianceXsec::Print
void Print()
Print information about the whole object once it is set.
Definition covarianceXsec.cpp:402
-
covarianceXsec::SplineParams
std::vector< XsecSplines1 > SplineParams
Vector containing info for normalisation systematics.
Definition covarianceXsec.h:143
+
covarianceXsec::SplineParams
std::vector< XsecSplines1 > SplineParams
Vector containing info for normalisation systematics.
Definition covarianceXsec.h:142
covarianceXsec::covarianceXsec
covarianceXsec(const std::vector< std::string > &FileNames, const char *name="xsec_cov", double threshold=-1, int FirstPCAdpar=-999, int LastPCAdpar=-999)
Constructor.
Definition covarianceXsec.cpp:7
covarianceXsec::initParams
void initParams()
Initialise CovarianceXsec.
Definition covarianceXsec.cpp:371
covarianceXsec::~covarianceXsec
~covarianceXsec()
Destructor.
Definition covarianceXsec.cpp:95
diff --git a/covarianceXsec_8h.html b/covarianceXsec_8h.html index ae07d760c..f3c453011 100644 --- a/covarianceXsec_8h.html +++ b/covarianceXsec_8h.html @@ -80,8 +80,7 @@
covarianceXsec.h File Reference
-
#include <math.h>
-#include <map>
+
#include <map>
#include "TList.h"
#include "covariance/covarianceBase.h"
diff --git a/covarianceXsec_8h_source.html b/covarianceXsec_8h_source.html index d9d088a1b..44f131609 100644 --- a/covarianceXsec_8h_source.html +++ b/covarianceXsec_8h_source.html @@ -86,90 +86,89 @@ Go to the documentation of this file.
1#pragma once
2
3// C++ includes
-
4#include <math.h>
-
5#include <map>
-
6
-
7// ROOT includes
-
8#include "TList.h"
-
9
-
10// MaCh3 includes
-
11#include "covariance/covarianceBase.h"
-
12
-
-
15class covarianceXsec : public covarianceBase {
-
16 public:
-
23 covarianceXsec(const std::vector<std::string>& FileNames, const char *name = "xsec_cov", double threshold = -1, int FirstPCAdpar = -999, int LastPCAdpar = -999);
-
25 ~covarianceXsec();
-
26
-
28 inline void Print();
-
29
-
31 void CheckCorrectInitialisation();
-
32
-
33 // General Getter functions not split by detector
-
36 inline int GetParDetID(const int i) const { return _fDetID[i];};
-
39 inline const char* GetParamTypeString(const int i) const {return SystType_ToString(_fParamType[i]).c_str();}
-
42 inline SystType GetParamType(const int i) const {return _fParamType[i];}
-
43
-
46 inline SplineInterpolation GetParSplineInterpolation(const int i) {return SplineParams.at(i).SplineInterpolationType;}
-
47
-
50 inline double GetParSplineKnotUpperBound(const int i) {return SplineParams.at(i).SplineKnotUpBound;}
-
53 inline double GetParSplineKnotLowerBound(const int i) {return SplineParams.at(i).SplineKnotLowBound;}
-
54
-
57 int GetNumParamsFromDetID(const int DetID, const SystType Type);
-
60 const std::vector<std::string> GetParsNamesFromDetID(const int DetID, const SystType Type);
-
63 const std::vector<int> GetParsIndexFromDetID(const int DetID, const SystType Type);
-
64
-
66 const std::vector<std::string> GetSplineParsNamesFromDetID(const int DetID);
-
68 const std::vector<std::string> GetSplineFileParsNamesFromDetID(const int DetID);
-
69
-
71 const std::vector<std::string> GetFDSplineFileParsNamesFromDetID(const int DetID);
-
72 const std::vector<std::string> GetNDSplineFileParsNamesFromDetID(const int DetID);
-
74 const std::vector< std::vector<int> > GetSplineModeVecFromDetID(const int DetID);
-
76 const std::vector<int> GetSplineParsIndexFromDetID(const int DetID){return GetParsIndexFromDetID(DetID, kSpline);}
-
77
-
79 int GetNumSplineParamsFromDetID(const int DetID){return GetNumParamsFromDetID(DetID, kSpline);}
-
80
-
82 const std::vector<XsecNorms4> GetNormParsFromDetID(const int DetID);
-
83
-
85 int GetNumFuncParamsFromDetID(const int DetID){return GetNumParamsFromDetID(DetID, kFunc);}
-
87 const std::vector<std::string> GetFuncParsNamesFromDetID(const int DetID){return GetParsNamesFromDetID(DetID, kFunc);}
-
89 const std::vector<int> GetFuncParsIndexFromDetID(const int DetID){return GetParsIndexFromDetID(DetID, kFunc);}
-
90
-
-
93 std::vector<double> getNominalArray() override
-
94 {
-
95 std::vector<double> nominal(_fNumPar);
-
96 for (int i = 0; i < _fNumPar; i++) {
-
97 nominal[i] = _fPreFitValue.at(i);
-
98 }
-
99 return nominal;
-
100 }
+
4#include <map>
+
5
+
6// ROOT includes
+
7#include "TList.h"
+
8
+
9// MaCh3 includes
+
10#include "covariance/covarianceBase.h"
+
11
+
+
14class covarianceXsec : public covarianceBase {
+
15 public:
+
22 covarianceXsec(const std::vector<std::string>& FileNames, const char *name = "xsec_cov", double threshold = -1, int FirstPCAdpar = -999, int LastPCAdpar = -999);
+
24 ~covarianceXsec();
+
25
+
27 inline void Print();
+
28
+
30 void CheckCorrectInitialisation();
+
31
+
32 // General Getter functions not split by detector
+
35 inline int GetParDetID(const int i) const { return _fDetID[i];};
+
38 inline std::string GetParamTypeString(const int i) const { return SystType_ToString(_fParamType[i]); }
+
41 inline SystType GetParamType(const int i) const {return _fParamType[i];}
+
42
+
45 inline SplineInterpolation GetParSplineInterpolation(const int i) {return SplineParams.at(i).SplineInterpolationType;}
+
46
+
49 inline double GetParSplineKnotUpperBound(const int i) {return SplineParams.at(i).SplineKnotUpBound;}
+
52 inline double GetParSplineKnotLowerBound(const int i) {return SplineParams.at(i).SplineKnotLowBound;}
+
53
+
56 int GetNumParamsFromDetID(const int DetID, const SystType Type);
+
59 const std::vector<std::string> GetParsNamesFromDetID(const int DetID, const SystType Type);
+
62 const std::vector<int> GetParsIndexFromDetID(const int DetID, const SystType Type);
+
63
+
65 const std::vector<std::string> GetSplineParsNamesFromDetID(const int DetID);
+
67 const std::vector<std::string> GetSplineFileParsNamesFromDetID(const int DetID);
+
68
+
70 const std::vector<std::string> GetFDSplineFileParsNamesFromDetID(const int DetID);
+
71 const std::vector<std::string> GetNDSplineFileParsNamesFromDetID(const int DetID);
+
73 const std::vector< std::vector<int> > GetSplineModeVecFromDetID(const int DetID);
+
75 const std::vector<int> GetSplineParsIndexFromDetID(const int DetID){return GetParsIndexFromDetID(DetID, kSpline);}
+
76
+
78 int GetNumSplineParamsFromDetID(const int DetID){return GetNumParamsFromDetID(DetID, kSpline);}
+
79
+
81 const std::vector<XsecNorms4> GetNormParsFromDetID(const int DetID);
+
82
+
84 int GetNumFuncParamsFromDetID(const int DetID){return GetNumParamsFromDetID(DetID, kFunc);}
+
86 const std::vector<std::string> GetFuncParsNamesFromDetID(const int DetID){return GetParsNamesFromDetID(DetID, kFunc);}
+
88 const std::vector<int> GetFuncParsIndexFromDetID(const int DetID){return GetParsIndexFromDetID(DetID, kFunc);}
+
89
+
+
92 std::vector<double> getNominalArray() override
+
93 {
+
94 std::vector<double> nominal(_fNumPar);
+
95 for (int i = 0; i < _fNumPar; i++) {
+
96 nominal[i] = _fPreFitValue.at(i);
+
97 }
+
98 return nominal;
+
99 }
-
103 inline double getNominal(const int i) override { return _fPreFitValue.at(i); };
-
107 inline bool IsParFlux(const int i){ return isFlux[i]; }
-
110 void setXsecOnlyParameters();
-
113 void setFluxOnlyParameters();
-
114
-
115 protected:
-
117 void initParams();
-
119 inline void InitXsecFromConfig();
-
123 inline XsecNorms4 GetXsecNorm(const YAML::Node& param, const int Index);
-
126 inline XsecSplines1 GetXsecSpline(const YAML::Node& param);
-
127
-
130 std::vector<bool> isFlux;
-
131
-
133 std::vector<int> _fDetID;
-
135 std::vector<SystType> _fParamType;
-
136
-
137 //Variables related to spline systematics
-
138 std::vector<std::string> _fNDSplineNames;
-
139 std::vector<std::string> _fFDSplineNames;
-
140 std::vector<std::vector<int>> _fFDSplineModes;
-
141
-
143 std::vector<XsecSplines1> SplineParams;
-
144
-
146 std::vector<XsecNorms4> NormParams;
-
147};
+
102 inline double getNominal(const int i) override { return _fPreFitValue.at(i); };
+
106 inline bool IsParFlux(const int i){ return isFlux[i]; }
+
109 void setXsecOnlyParameters();
+
112 void setFluxOnlyParameters();
+
113
+
114 protected:
+
116 void initParams();
+
118 inline void InitXsecFromConfig();
+
122 inline XsecNorms4 GetXsecNorm(const YAML::Node& param, const int Index);
+
125 inline XsecSplines1 GetXsecSpline(const YAML::Node& param);
+
126
+
129 std::vector<bool> isFlux;
+
130
+
132 std::vector<int> _fDetID;
+
134 std::vector<SystType> _fParamType;
+
135
+
136 //Variables related to spline systematics
+
137 std::vector<std::string> _fNDSplineNames;
+
138 std::vector<std::string> _fFDSplineNames;
+
139 std::vector<std::vector<int>> _fFDSplineModes;
+
140
+
142 std::vector<XsecSplines1> SplineParams;
+
143
+
145 std::vector<XsecNorms4> NormParams;
+
146};
nominal
std::vector< int > nominal
Definition GetPenaltyTerm.cpp:38
FileNames
std::vector< std::string > FileNames
Definition GetPostfitParamPlots.cpp:32
@@ -178,53 +177,53 @@
SystType
SystType
Make an enum of systematic type recognised by covariance class.
Definition Structs.h:150
kSpline
@ kSpline
Definition Structs.h:152
kFunc
@ kFunc
Definition Structs.h:153
-
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:18
-
covarianceBase
Base class responsible for handling of systematic error parameters. Capable of using PCA or using ada...
Definition covarianceBase.h:33
-
covarianceBase::LastPCAdpar
int LastPCAdpar
Index of the last param that is being decomposed.
Definition covarianceBase.h:473
-
covarianceBase::_fPreFitValue
std::vector< double > _fPreFitValue
Parameter value dictated by the prior model. Based on it penalty term is calculated.
Definition covarianceBase.h:443
-
covarianceBase::FirstPCAdpar
int FirstPCAdpar
Index of the first param that is being decomposed.
Definition covarianceBase.h:471
-
covarianceBase::_fNumPar
int _fNumPar
Number of systematic parameters.
Definition covarianceBase.h:441
-
covarianceXsec
Class responsible for handling of systematic error parameters with different types defined in the con...
Definition covarianceXsec.h:15
+
GetFromManager
Type GetFromManager(const YAML::Node &node, Type defval)
Get content of config file if node is not found take default value specified.
Definition YamlHelper.h:21
+
covarianceBase
Base class responsible for handling of systematic error parameters. Capable of using PCA or using ada...
Definition covarianceBase.h:34
+
covarianceBase::LastPCAdpar
int LastPCAdpar
Index of the last param that is being decomposed.
Definition covarianceBase.h:487
+
covarianceBase::_fPreFitValue
std::vector< double > _fPreFitValue
Parameter value dictated by the prior model. Based on it penalty term is calculated.
Definition covarianceBase.h:457
+
covarianceBase::FirstPCAdpar
int FirstPCAdpar
Index of the first param that is being decomposed.
Definition covarianceBase.h:485
+
covarianceBase::_fNumPar
int _fNumPar
Number of systematic parameters.
Definition covarianceBase.h:455
+
covarianceXsec
Class responsible for handling of systematic error parameters with different types defined in the con...
Definition covarianceXsec.h:14
covarianceXsec::GetNumParamsFromDetID
int GetNumParamsFromDetID(const int DetID, const SystType Type)
DB Grab the number of parameters for the relevant DetID.
Definition covarianceXsec.cpp:324
covarianceXsec::setFluxOnlyParameters
void setFluxOnlyParameters()
KS Function to set to nominal flux parameters.
Definition covarianceXsec.cpp:513
-
covarianceXsec::IsParFlux
bool IsParFlux(const int i)
Is parameter a flux param or not. This might become deprecated in future.
Definition covarianceXsec.h:107
-
covarianceXsec::_fFDSplineModes
std::vector< std::vector< int > > _fFDSplineModes
Definition covarianceXsec.h:140
-
covarianceXsec::_fDetID
std::vector< int > _fDetID
Tells to which samples object param should be applied.
Definition covarianceXsec.h:133
-
covarianceXsec::GetParamType
SystType GetParamType(const int i) const
Returns enum describing our param type.
Definition covarianceXsec.h:42
+
covarianceXsec::IsParFlux
bool IsParFlux(const int i)
Is parameter a flux param or not. This might become deprecated in future.
Definition covarianceXsec.h:106
+
covarianceXsec::_fFDSplineModes
std::vector< std::vector< int > > _fFDSplineModes
Definition covarianceXsec.h:139
+
covarianceXsec::_fDetID
std::vector< int > _fDetID
Tells to which samples object param should be applied.
Definition covarianceXsec.h:132
+
covarianceXsec::GetParamType
SystType GetParamType(const int i) const
Returns enum describing our param type.
Definition covarianceXsec.h:41
covarianceXsec::GetSplineModeVecFromDetID
const std::vector< std::vector< int > > GetSplineModeVecFromDetID(const int DetID)
DB Grab the Spline Modes for the relevant DetID.
Definition covarianceXsec.cpp:202
covarianceXsec::CheckCorrectInitialisation
void CheckCorrectInitialisation()
KS: Check if matrix is correctly initialised.
Definition covarianceXsec.cpp:489
covarianceXsec::GetXsecNorm
XsecNorms4 GetXsecNorm(const YAML::Node &param, const int Index)
Get Norm params.
Definition covarianceXsec.cpp:222
-
covarianceXsec::GetParSplineInterpolation
SplineInterpolation GetParSplineInterpolation(const int i)
Get interpolation type for a given parameter.
Definition covarianceXsec.h:46
+
covarianceXsec::GetParSplineInterpolation
SplineInterpolation GetParSplineInterpolation(const int i)
Get interpolation type for a given parameter.
Definition covarianceXsec.h:45
covarianceXsec::GetFDSplineFileParsNamesFromDetID
const std::vector< std::string > GetFDSplineFileParsNamesFromDetID(const int DetID)
ETA - what does this even do?
Definition covarianceXsec.cpp:133
covarianceXsec::GetSplineParsNamesFromDetID
const std::vector< std::string > GetSplineParsNamesFromDetID(const int DetID)
DB Get spline parameters depending on given DetID.
Definition covarianceXsec.cpp:102
-
covarianceXsec::isFlux
std::vector< bool > isFlux
Definition covarianceXsec.h:130
+
covarianceXsec::isFlux
std::vector< bool > isFlux
Definition covarianceXsec.h:129
covarianceXsec::GetParsNamesFromDetID
const std::vector< std::string > GetParsNamesFromDetID(const int DetID, const SystType Type)
DB Grab the parameter names for the relevant DetID.
Definition covarianceXsec.cpp:340
-
covarianceXsec::_fFDSplineNames
std::vector< std::string > _fFDSplineNames
Definition covarianceXsec.h:139
-
covarianceXsec::GetSplineParsIndexFromDetID
const std::vector< int > GetSplineParsIndexFromDetID(const int DetID)
DB Grab the Spline Indices for the relevant DetID.
Definition covarianceXsec.h:76
+
covarianceXsec::_fFDSplineNames
std::vector< std::string > _fFDSplineNames
Definition covarianceXsec.h:138
+
covarianceXsec::GetSplineParsIndexFromDetID
const std::vector< int > GetSplineParsIndexFromDetID(const int DetID)
DB Grab the Spline Indices for the relevant DetID.
Definition covarianceXsec.h:75
covarianceXsec::InitXsecFromConfig
void InitXsecFromConfig()
ETA - trying out the yaml parsing.
Definition covarianceXsec.cpp:27
+
covarianceXsec::GetParamTypeString
std::string GetParamTypeString(const int i) const
ETA - just return a string of "spline", "norm" or "functional".
Definition covarianceXsec.h:38
covarianceXsec::GetNormParsFromDetID
const std::vector< XsecNorms4 > GetNormParsFromDetID(const int DetID)
DB Get norm/func parameters depending on given DetID.
Definition covarianceXsec.cpp:302
-
covarianceXsec::getNominalArray
std::vector< double > getNominalArray() override
KS: For most covariances nominal and fparInit (prior) are the same, however for Xsec those can be dif...
Definition covarianceXsec.h:93
-
covarianceXsec::GetParSplineKnotLowerBound
double GetParSplineKnotLowerBound(const int i)
EM: value at which we cap spline knot weight.
Definition covarianceXsec.h:53
+
covarianceXsec::getNominalArray
std::vector< double > getNominalArray() override
KS: For most covariances nominal and fparInit (prior) are the same, however for Xsec those can be dif...
Definition covarianceXsec.h:92
+
covarianceXsec::GetParSplineKnotLowerBound
double GetParSplineKnotLowerBound(const int i)
EM: value at which we cap spline knot weight.
Definition covarianceXsec.h:52
covarianceXsec::GetParsIndexFromDetID
const std::vector< int > GetParsIndexFromDetID(const int DetID, const SystType Type)
DB Grab the parameter indices for the relevant DetID.
Definition covarianceXsec.cpp:356
covarianceXsec::GetNDSplineFileParsNamesFromDetID
const std::vector< std::string > GetNDSplineFileParsNamesFromDetID(const int DetID)
Definition covarianceXsec.cpp:155
-
covarianceXsec::GetParDetID
int GetParDetID(const int i) const
ETA - just return the int of the DetID, this can be removed to do a string comp at some point.
Definition covarianceXsec.h:36
-
covarianceXsec::_fParamType
std::vector< SystType > _fParamType
Type of parameter like norm, spline etc.
Definition covarianceXsec.h:135
-
covarianceXsec::_fNDSplineNames
std::vector< std::string > _fNDSplineNames
Definition covarianceXsec.h:138
-
covarianceXsec::GetParSplineKnotUpperBound
double GetParSplineKnotUpperBound(const int i)
EM: value at which we cap spline knot weight.
Definition covarianceXsec.h:50
-
covarianceXsec::GetParamTypeString
const char * GetParamTypeString(const int i) const
ETA - just return a string of "spline", "norm" or "functional".
Definition covarianceXsec.h:39
-
covarianceXsec::NormParams
std::vector< XsecNorms4 > NormParams
Vector containing info for normalisation systematics.
Definition covarianceXsec.h:146
+
covarianceXsec::GetParDetID
int GetParDetID(const int i) const
ETA - just return the int of the DetID, this can be removed to do a string comp at some point.
Definition covarianceXsec.h:35
+
covarianceXsec::_fParamType
std::vector< SystType > _fParamType
Type of parameter like norm, spline etc.
Definition covarianceXsec.h:134
+
covarianceXsec::_fNDSplineNames
std::vector< std::string > _fNDSplineNames
Definition covarianceXsec.h:137
+
covarianceXsec::GetParSplineKnotUpperBound
double GetParSplineKnotUpperBound(const int i)
EM: value at which we cap spline knot weight.
Definition covarianceXsec.h:49
+
covarianceXsec::NormParams
std::vector< XsecNorms4 > NormParams
Vector containing info for normalisation systematics.
Definition covarianceXsec.h:145
covarianceXsec::GetXsecSpline
XsecSplines1 GetXsecSpline(const YAML::Node &param)
Get Spline params.
Definition covarianceXsec.cpp:278
covarianceXsec::GetSplineFileParsNamesFromDetID
const std::vector< std::string > GetSplineFileParsNamesFromDetID(const int DetID)
DB Get spline parameters depending on given DetID.
Definition covarianceXsec.cpp:175
-
covarianceXsec::GetFuncParsNamesFromDetID
const std::vector< std::string > GetFuncParsNamesFromDetID(const int DetID)
DB Grab the Functional parameter names for the relevant DetID.
Definition covarianceXsec.h:87
+
covarianceXsec::GetFuncParsNamesFromDetID
const std::vector< std::string > GetFuncParsNamesFromDetID(const int DetID)
DB Grab the Functional parameter names for the relevant DetID.
Definition covarianceXsec.h:86
covarianceXsec::Print
void Print()
Print information about the whole object once it is set.
Definition covarianceXsec.cpp:402
-
covarianceXsec::GetFuncParsIndexFromDetID
const std::vector< int > GetFuncParsIndexFromDetID(const int DetID)
DB Grab the Functional parameter indices for the relevant DetID.
Definition covarianceXsec.h:89
-
covarianceXsec::SplineParams
std::vector< XsecSplines1 > SplineParams
Vector containing info for normalisation systematics.
Definition covarianceXsec.h:143
+
covarianceXsec::GetFuncParsIndexFromDetID
const std::vector< int > GetFuncParsIndexFromDetID(const int DetID)
DB Grab the Functional parameter indices for the relevant DetID.
Definition covarianceXsec.h:88
+
covarianceXsec::SplineParams
std::vector< XsecSplines1 > SplineParams
Vector containing info for normalisation systematics.
Definition covarianceXsec.h:142
covarianceXsec::initParams
void initParams()
Initialise CovarianceXsec.
Definition covarianceXsec.cpp:371
-
covarianceXsec::getNominal
double getNominal(const int i) override
Get nominal for a given param.
Definition covarianceXsec.h:103
-
covarianceXsec::GetNumFuncParamsFromDetID
int GetNumFuncParamsFromDetID(const int DetID)
DB Grab the number of Normalisation parameters for the relevant DetID.
Definition covarianceXsec.h:85
+
covarianceXsec::getNominal
double getNominal(const int i) override
Get nominal for a given param.
Definition covarianceXsec.h:102
+
covarianceXsec::GetNumFuncParamsFromDetID
int GetNumFuncParamsFromDetID(const int DetID)
DB Grab the number of Normalisation parameters for the relevant DetID.
Definition covarianceXsec.h:84
covarianceXsec::~covarianceXsec
~covarianceXsec()
Destructor.
Definition covarianceXsec.cpp:95
covarianceXsec::setXsecOnlyParameters
void setXsecOnlyParameters()
KS Function to set to nominal flux parameters.
Definition covarianceXsec.cpp:527
-
covarianceXsec::GetNumSplineParamsFromDetID
int GetNumSplineParamsFromDetID(const int DetID)
DB Grab the Number of splines for the relevant DetID.
Definition covarianceXsec.h:79
+
covarianceXsec::GetNumSplineParamsFromDetID
int GetNumSplineParamsFromDetID(const int DetID)
DB Grab the Number of splines for the relevant DetID.
Definition covarianceXsec.h:78
XsecNorms4
ETA - Normalisations for cross-section parameters Carrier for whether you want to apply a systematic ...
Definition Structs.h:80
XsecSplines1
KS: Struct holding info about Spline Systematics.
Definition Structs.h:160
diff --git a/dir_ad7582af392f69120f12d3a638849ade.html b/dir_ad7582af392f69120f12d3a638849ade.html index cf3da8acc..f15072bae 100644 --- a/dir_ad7582af392f69120f12d3a638849ade.html +++ b/dir_ad7582af392f69120f12d3a638849ade.html @@ -81,7 +81,9 @@
- + + + diff --git a/files.html b/files.html index 8a3214f18..568b1cf33 100644 --- a/files.html +++ b/files.html @@ -77,84 +77,85 @@
Here is a list of all files with brief descriptions:
[detail level 123]

Files

 adaptiveMCMCStruct.h
 AdaptiveMCMCHandler.cpp
 
 AdaptiveMCMCHandler.h
 
 covarianceBase.cpp
 
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
 ▼ covariance
 adaptiveMCMCStruct.h
 covarianceBase.cpp
 covarianceBase.h
 covarianceOsc.cpp
 covarianceOsc.h
 CovarianceUtils.h
 covarianceXsec.cpp
 covarianceXsec.h
 ThrowParms.cpp
 ThrowParms.h
 ▼ Diagnostics
 ▼ Diagnostics_utils
 PlotAutoCorrelations.C
 PlotMCMC_Diagnosis.cpp
 CombineMaCh3Chains.cpp
 DiagMCMC.cpp
 GetPenaltyTerm.cpp
 GetPostfitParamPlots.cpp
 PlotLLH.cpp
 ProcessMCMC.cpp
 RHat.cpp
 ▼ manager
 gpuUtils.cu
 gpuUtils.cuh
 MaCh3Exception.h
 MaCh3Logger.h
 MaCh3Modes.cpp
 MaCh3Modes.h
 manager.cpp
 manager.h
 Monitor.cpp
 Monitor.h
 YamlHelper.h
 ▼ mcmc
 FitterBase.cpp
 FitterBase.h
 gpuMCMCProcessorUtils.cu
 gpuMCMCProcessorUtils.cuh
 LikelihoodFit.cpp
 LikelihoodFit.h
 MaCh3Factory.cpp
 MaCh3Factory.h
 mcmc.cpp
 mcmc.h
 MCMCProcessor.cpp
 MCMCProcessor.h
 MinuitFit.cpp
 MinuitFit.h
 PSO.cpp
 PSO.h
 SampleSummary.cpp
 SampleSummary.h
 StatisticalUtils.h
 ▼ OscClass
 OscClass_CUDAProb3.cpp
 OscClass_CUDAProb3.h
 ▼ samplePDF
 FDMCStruct.h
 kdeGpu.cu
 kdeGpu2.cu
 probGpu.cu
 samplePDFBase.cpp
 samplePDFBase.h
 samplePDFFDBase.cpp
 samplePDFFDBase.h
 ShiftFunctors.h
 Structs.cpp
 Structs.h
 ▼ splines
 gpuSplineUtils.cu
 SplineBase.cpp
 SplineBase.h
 SplineCommon.h
 splineFDBase.cpp
 splineFDBase.h
 SplineMonolith.cpp
 SplineMonolith.h
 SplineStructs.h
 AdaptiveMCMCHandler.cpp
 AdaptiveMCMCHandler.h
 covarianceBase.cpp
 covarianceBase.h
 covarianceOsc.cpp
 covarianceOsc.h
 CovarianceUtils.h
 covarianceXsec.cpp
 covarianceXsec.h
 ThrowParms.cpp
 ThrowParms.h
 ▼ Diagnostics
 ▼ Diagnostics_utils
 PlotAutoCorrelations.C
 PlotMCMC_Diagnosis.cpp
 CombineMaCh3Chains.cpp
 DiagMCMC.cpp
 GetPenaltyTerm.cpp
 GetPostfitParamPlots.cpp
 PlotLLH.cpp
 ProcessMCMC.cpp
 RHat.cpp
 ▼ manager
 gpuUtils.cu
 gpuUtils.cuh
 MaCh3Exception.h
 MaCh3Logger.h
 MaCh3Modes.cpp
 MaCh3Modes.h
 manager.cpp
 manager.h
 Monitor.cpp
 Monitor.h
 YamlHelper.h
 ▼ mcmc
 FitterBase.cpp
 FitterBase.h
 gpuMCMCProcessorUtils.cu
 gpuMCMCProcessorUtils.cuh
 LikelihoodFit.cpp
 LikelihoodFit.h
 MaCh3Factory.cpp
 MaCh3Factory.h
 mcmc.cpp
 mcmc.h
 MCMCProcessor.cpp
 MCMCProcessor.h
 MinuitFit.cpp
 MinuitFit.h
 PSO.cpp
 PSO.h
 SampleSummary.cpp
 SampleSummary.h
 StatisticalUtils.h
 ▼ OscClass
 OscClass_CUDAProb3.cpp
 OscClass_CUDAProb3.h
 ▼ samplePDF
 FDMCStruct.h
 kdeGpu.cu
 kdeGpu2.cu
 probGpu.cu
 samplePDFBase.cpp
 samplePDFBase.h
 samplePDFFDBase.cpp
 samplePDFFDBase.h
 ShiftFunctors.h
 Structs.cpp
 Structs.h
 ▼ splines
 gpuSplineUtils.cu
 SplineBase.cpp
 SplineBase.h
 SplineCommon.h
 splineFDBase.cpp
 splineFDBase.h
 SplineMonolith.cpp
 SplineMonolith.h
 SplineStructs.h

diff --git a/functions_a.html b/functions_a.html index f7d6b8e3b..b94dd181b 100644 --- a/functions_a.html +++ b/functions_a.html @@ -80,12 +80,13 @@

- a -

  • accProb : FitterBase
  • AccProbBatchedAverages : MCMCProcessor
  • AccProbValues : MCMCProcessor
    • -
  • adapt_block_matrix_indices : adaptive_mcmc::AdaptiveMCMCStruct
    • -
  • adapt_block_sizes : adaptive_mcmc::AdaptiveMCMCStruct
    • -
  • adaption_struct : covarianceBase
    • -
  • adaptive_covariance : adaptive_mcmc::AdaptiveMCMCStruct
    • -
  • adaptive_update_step : adaptive_mcmc::AdaptiveMCMCStruct
    • -
  • addData() : samplePDFBase, samplePDFFDBase
    • +
  • adapt_block_matrix_indices : adaptive_mcmc::AdaptiveMCMCHandler
    • +
  • adapt_block_sizes : adaptive_mcmc::AdaptiveMCMCHandler
    • +
  • adaptive_covariance : adaptive_mcmc::AdaptiveMCMCHandler
    • +
  • adaptive_update_step : adaptive_mcmc::AdaptiveMCMCHandler
    • +
  • AdaptiveHandler : covarianceBase
    • +
  • AdaptiveMCMCHandler() : adaptive_mcmc::AdaptiveMCMCHandler
    • +
  • addData() : samplePDFBase, samplePDFFDBase
  • AddData() : SampleSummary
  • AddNominal() : SampleSummary
  • addOscHandler() : FitterBase
    • diff --git a/functions_c.html b/functions_c.html index 1c5505f70..2d9eee57b 100644 --- a/functions_c.html +++ b/functions_c.html @@ -130,7 +130,7 @@

    - c -

    diff --git a/functions_e.html b/functions_e.html index 8a6d91d16..00e7a7e7e 100644 --- a/functions_e.html +++ b/functions_e.html @@ -79,7 +79,7 @@

    - e -

    • eigen_values : covarianceBase
    • eigen_values_master : covarianceBase
    • eigen_vectors : covarianceBase
      • -
    • end_adaptive_update : adaptive_mcmc::AdaptiveMCMCStruct
      • +
    • end_adaptive_update : adaptive_mcmc::AdaptiveMCMCHandler
    • EnergyScale() : EnergyScale
    • EnsureModeNameRegistered() : MaCh3Modes
    • errbuf : samplePDFBase
      • diff --git a/functions_func.html b/functions_func.html index be6f7ffbd..8af8c8bee 100644 --- a/functions_func.html +++ b/functions_func.html @@ -76,6 +76,7 @@

      - a -

      • AcceptanceProbabilities() : MCMCProcessor
      • acceptStep() : covarianceBase
        • +
      • AdaptiveMCMCHandler() : adaptive_mcmc::AdaptiveMCMCHandler
      • addData() : samplePDFBase, samplePDFFDBase
      • AddData() : SampleSummary
      • AddNominal() : SampleSummary
        • diff --git a/functions_func_c.html b/functions_func_c.html index 6174af84b..96657263c 100644 --- a/functions_func_c.html +++ b/functions_func_c.html @@ -103,7 +103,7 @@

        - c -

        diff --git a/functions_func_g.html b/functions_func_g.html index 566f4ee49..b25b3afc5 100644 --- a/functions_func_g.html +++ b/functions_func_g.html @@ -134,7 +134,7 @@

        - g -

        • GetMaCh3ModeName() : MaCh3Modes
        • GetMaCh3Modes() : manager, samplePDFBase
        • GetMCStatLLH() : manager
          • -
        • GetMode() : MaCh3Modes
          • +
        • GetMode() : MaCh3Modes
        • GetModeError() : SampleSummary
        • GetModeFromGenerator() : MaCh3Modes
        • GetModeName() : samplePDFBase
          • @@ -172,9 +172,9 @@

          - g -

          • GetOscillogramNBins() : Oscillator
          • GetParameter() : TF1_red
          • getParameterMeans() : covarianceBase
            • -
          • GetParamIndexFromName() : MCMCProcessor
            • +
          • GetParamIndexFromName() : MCMCProcessor
          • GetParamType() : covarianceXsec
            • -
          • GetParamTypeString() : covarianceXsec
            • +
          • GetParamTypeString() : covarianceXsec
          • getParCurr() : covarianceBase
          • getParCurr_PCA() : covarianceBase
          • GetParDetID() : covarianceXsec
            • diff --git a/functions_func_i.html b/functions_func_i.html index 60a8640cf..89113cd76 100644 --- a/functions_func_i.html +++ b/functions_func_i.html @@ -75,6 +75,7 @@

            - i -

            • init() : covarianceBase, PSO, samplePDFBase
              • +
            • InitFromConfig() : adaptive_mcmc::AdaptiveMCMCHandler
            • Initialise() : MCMCProcessor, SMonolith
            • initialiseAdaption() : covarianceBase
            • InitialiseHistograms() : Oscillator
              • diff --git a/functions_func_p.html b/functions_func_p.html index c44127de0..272849d55 100644 --- a/functions_func_p.html +++ b/functions_func_p.html @@ -88,7 +88,7 @@

              - p -

              • PrepareSplineFile() : SMonolith
              • PrepForReweight() : splineFDBase
              • PrepFunctionalParameters() : samplePDFFDBase
                • -
              • Print() : covarianceOsc, covarianceXsec, MaCh3Modes, manager, TF1_red, XSecStruct< T >
                • +
              • Print() : adaptive_mcmc::AdaptiveMCMCHandler, covarianceOsc, covarianceXsec, MaCh3Modes, manager, TF1_red, XSecStruct< T >
              • PrintArrayDetails() : splineFDBase
              • PrintArrayDimension() : splineFDBase
              • PrintBinning() : Oscillator, splineFDBase
                • diff --git a/functions_func_s.html b/functions_func_s.html index 171f6a66c..dd60ad393 100644 --- a/functions_func_s.html +++ b/functions_func_s.html @@ -77,7 +77,7 @@

                - s -

                • samplePDFBase() : samplePDFBase
                • samplePDFFDBase() : samplePDFFDBase
                • SampleSummary() : SampleSummary
                  • -
                • saveAdaptiveToFile() : covarianceBase
                  • +
                • SaveAdaptiveToFile() : adaptive_mcmc::AdaptiveMCMCHandler
                • SaveOscillogramsToFile() : Oscillator
                • SaveOutput() : FitterBase
                • SaveParams() : Oscillator
                  • @@ -95,7 +95,7 @@

                  - s -

                  • set_value() : particle
                  • set_velocity() : particle
                  • setAdaptionDefaults() : covarianceBase
                    • -
                  • setAdaptiveBlocks() : covarianceBase
                    • +
                  • SetAdaptiveBlocks() : adaptive_mcmc::AdaptiveMCMCHandler
                  • SetBranches() : covarianceBase
                  • setChainLength() : mcmc
                  • setCovMatrix() : covarianceBase
                    • @@ -149,6 +149,7 @@

                    - s -

                    • SetStepCut() : MCMCProcessor
                    • setStepScale() : covarianceBase
                    • setThrowMatrix() : covarianceBase
                      • +
                    • SetThrowMatrixFromFile() : adaptive_mcmc::AdaptiveMCMCHandler
                    • setThrowMatrixFromFile() : covarianceBase
                    • SetUncertainty() : BaseFuncPar
                    • setup() : BaseFuncPar
                      • diff --git a/functions_func_u.html b/functions_func_u.html index 582a130cc..4745e20a9 100644 --- a/functions_func_u.html +++ b/functions_func_u.html @@ -75,6 +75,7 @@

                      - u -

                      • uncertainty_check() : PSO
                        • +
                      • UpdateAdaptiveCovariance() : adaptive_mcmc::AdaptiveMCMCHandler
                      • updateAdaptiveCovariance() : covarianceBase
                      • updateThrowMatrix() : covarianceBase
                      • UseBinnedOscReweighting() : samplePDFFDBase
                        • diff --git a/functions_func_~.html b/functions_func_~.html index 2d0f2c056..ec0d0df19 100644 --- a/functions_func_~.html +++ b/functions_func_~.html @@ -74,6 +74,7 @@
                        Here is a list of all functions with links to the classes they belong to:

                        - ~ -

                          +
                        • ~AdaptiveMCMCHandler() : adaptive_mcmc::AdaptiveMCMCHandler
                        • ~BaseFuncPar() : BaseFuncPar
                        • ~covarianceBase() : covarianceBase
                        • ~covarianceOsc() : covarianceOsc
                          • diff --git a/functions_g.html b/functions_g.html index d1ebf2401..8572ab2b1 100644 --- a/functions_g.html +++ b/functions_g.html @@ -137,7 +137,7 @@

                          - g -

                          • GetMaCh3ModeName() : MaCh3Modes
                          • GetMaCh3Modes() : manager, samplePDFBase
                          • GetMCStatLLH() : manager
                            • -
                          • GetMode() : MaCh3Modes
                            • +
                          • GetMode() : MaCh3Modes
                          • GetModeError() : SampleSummary
                          • GetModeFromGenerator() : MaCh3Modes
                          • GetModeName() : samplePDFBase
                            • @@ -175,9 +175,9 @@

                            - g -

                            • GetOscillogramNBins() : Oscillator
                            • GetParameter() : TF1_red
                            • getParameterMeans() : covarianceBase
                              • -
                            • GetParamIndexFromName() : MCMCProcessor
                              • +
                            • GetParamIndexFromName() : MCMCProcessor
                            • GetParamType() : covarianceXsec
                              • -
                            • GetParamTypeString() : covarianceXsec
                              • +
                            • GetParamTypeString() : covarianceXsec
                            • getParCurr() : covarianceBase
                            • getParCurr_PCA() : covarianceBase
                            • GetParDetID() : covarianceXsec
                              • diff --git a/functions_i.html b/functions_i.html index 2480d4678..3ef8570ca 100644 --- a/functions_i.html +++ b/functions_i.html @@ -79,6 +79,7 @@

                              - i -

                              • index_cpu : SMonolith
                              • indexvec : splineFDBase
                              • init() : covarianceBase, PSO, samplePDFBase
                                • +
                              • InitFromConfig() : adaptive_mcmc::AdaptiveMCMCHandler
                              • Initialise() : MCMCProcessor, SMonolith
                              • initialiseAdaption() : covarianceBase
                              • InitialiseHistograms() : Oscillator
                                • @@ -97,8 +98,8 @@

                                - i -

                                • isFlat() : SMonolith
                                • isflatarray : splineFDBase
                                • isFlux : covarianceXsec
                                  • -
                                • IsLinear : Oscillator
                                • isLinear() : Oscillator
                                  • +
                                • IsLinear : Oscillator
                                • IsMode() : MaCh3ModeInfo
                                • isNC : fdmc_base
                                • isParameterFixed() : covarianceBase
                                  • diff --git a/functions_p.html b/functions_p.html index e6b97faea..03202b388 100644 --- a/functions_p.html +++ b/functions_p.html @@ -76,7 +76,7 @@

                                  - p -

                                  • par : PSO
                                  • Par : TF1_red, TSpline3_red
                                    • -
                                  • par_means : adaptive_mcmc::AdaptiveMCMCStruct
                                    • +
                                  • par_means : adaptive_mcmc::AdaptiveMCMCHandler
                                  • Param_pos : BaseFuncPar
                                  • ParamCentral : MCMCProcessor
                                  • ParamErrors : MCMCProcessor
                                    • @@ -129,7 +129,7 @@

                                    - p -

                                    • PrimaryXBinEvalPoints : Oscillator
                                    • PrimaryYBinEdges : Oscillator
                                    • PrimaryYBinEvalPoints : Oscillator
                                      • -
                                    • Print() : covarianceOsc, covarianceXsec, MaCh3Modes, manager, TF1_red, XSecStruct< T >
                                      • +
                                    • Print() : adaptive_mcmc::AdaptiveMCMCHandler, covarianceOsc, covarianceXsec, MaCh3Modes, manager, TF1_red, XSecStruct< T >
                                    • PrintArrayDetails() : splineFDBase
                                    • PrintArrayDimension() : splineFDBase
                                    • PrintBinning() : Oscillator, splineFDBase
                                      • diff --git a/functions_s.html b/functions_s.html index 5f56b3832..c84cc4c70 100644 --- a/functions_s.html +++ b/functions_s.html @@ -90,7 +90,7 @@

                                      - s -

                                      • SampleSummary() : SampleSummary
                                      • SampleValues : MCMCProcessor
                                      • save_nominal : FitterBase
                                        • -
                                      • saveAdaptiveToFile() : covarianceBase
                                        • +
                                      • SaveAdaptiveToFile() : adaptive_mcmc::AdaptiveMCMCHandler
                                      • SaveOscillogramsToFile() : Oscillator
                                      • SaveOutput() : FitterBase
                                      • SaveParams() : Oscillator
                                        • @@ -121,7 +121,7 @@

                                        - s -

                                        • set_value() : particle
                                        • set_velocity() : particle
                                        • setAdaptionDefaults() : covarianceBase
                                          • -
                                        • setAdaptiveBlocks() : covarianceBase
                                          • +
                                        • SetAdaptiveBlocks() : adaptive_mcmc::AdaptiveMCMCHandler
                                        • SetBranches() : covarianceBase
                                        • setChainLength() : mcmc
                                        • setCovMatrix() : covarianceBase
                                          • @@ -172,9 +172,10 @@

                                          - s -

                                          • SetSmoothing() : MCMCProcessor
                                          • SetSplineNumber() : XSecStruct< T >
                                          • setSplinePointers() : SMonolith
                                            • -
                                          • SetStepCut() : MCMCProcessor
                                            • +
                                          • SetStepCut() : MCMCProcessor
                                          • setStepScale() : covarianceBase
                                          • setThrowMatrix() : covarianceBase
                                            • +
                                          • SetThrowMatrixFromFile() : adaptive_mcmc::AdaptiveMCMCHandler
                                          • setThrowMatrixFromFile() : covarianceBase
                                          • SettingsSaved : FitterBase
                                          • SetUncertainty() : BaseFuncPar
                                            • @@ -208,8 +209,8 @@

                                            - s -

                                            • splineParsPointer : FastSplineInfo, SMonolith
                                            • splinevec_Monolith : splineFDBase
                                            • StandardFluctuation : SampleSummary
                                              • -
                                            • start_adaptive_throw : adaptive_mcmc::AdaptiveMCMCStruct
                                              • -
                                            • start_adaptive_update : adaptive_mcmc::AdaptiveMCMCStruct
                                              • +
                                            • start_adaptive_throw : adaptive_mcmc::AdaptiveMCMCHandler
                                              • +
                                            • start_adaptive_update : adaptive_mcmc::AdaptiveMCMCHandler
                                            • StdNormRand() : ThrowParms
                                            • step : FitterBase
                                            • stepClock : FitterBase
                                              • diff --git a/functions_u.html b/functions_u.html index ad6e4a7ca..e211fa13e 100644 --- a/functions_u.html +++ b/functions_u.html @@ -84,6 +84,7 @@

                                              - u -

                                              • UniqueSystNKnots : splineFDBase
                                              • UniqueSystXPts : splineFDBase
                                              • Unity : covarianceBase, fdmc_base
                                                • +
                                              • UpdateAdaptiveCovariance() : adaptive_mcmc::AdaptiveMCMCHandler
                                              • updateAdaptiveCovariance() : covarianceBase
                                              • updateThrowMatrix() : covarianceBase
                                              • UpperCut : MCMCProcessor
                                                • diff --git a/functions_vars_a.html b/functions_vars_a.html index 01f11850a..1e60fed68 100644 --- a/functions_vars_a.html +++ b/functions_vars_a.html @@ -78,11 +78,11 @@

                                                - a -

                                                • accProb : FitterBase
                                                • AccProbBatchedAverages : MCMCProcessor
                                                • AccProbValues : MCMCProcessor
                                                  • -
                                                • adapt_block_matrix_indices : adaptive_mcmc::AdaptiveMCMCStruct
                                                  • -
                                                • adapt_block_sizes : adaptive_mcmc::AdaptiveMCMCStruct
                                                  • -
                                                • adaption_struct : covarianceBase
                                                  • -
                                                • adaptive_covariance : adaptive_mcmc::AdaptiveMCMCStruct
                                                  • -
                                                • adaptive_update_step : adaptive_mcmc::AdaptiveMCMCStruct
                                                  • +
                                                • adapt_block_matrix_indices : adaptive_mcmc::AdaptiveMCMCHandler
                                                  • +
                                                • adapt_block_sizes : adaptive_mcmc::AdaptiveMCMCHandler
                                                  • +
                                                • adaptive_covariance : adaptive_mcmc::AdaptiveMCMCHandler
                                                  • +
                                                • adaptive_update_step : adaptive_mcmc::AdaptiveMCMCHandler
                                                  • +
                                                • AdaptiveHandler : covarianceBase
                                                • anneal : mcmc
                                                • AnnealTemp : mcmc
                                                • ApplySmoothing : MCMCProcessor
                                                  • diff --git a/functions_vars_e.html b/functions_vars_e.html index 9e4fcece3..09009c8bb 100644 --- a/functions_vars_e.html +++ b/functions_vars_e.html @@ -79,7 +79,7 @@

                                                  - e -

                                                  • eigen_values : covarianceBase
                                                  • eigen_values_master : covarianceBase
                                                  • eigen_vectors : covarianceBase
                                                    • -
                                                  • end_adaptive_update : adaptive_mcmc::AdaptiveMCMCStruct
                                                    • +
                                                  • end_adaptive_update : adaptive_mcmc::AdaptiveMCMCHandler
                                                  • errbuf : samplePDFBase
                                                  • errorMessage : MaCh3Exception
                                                  • Errors : MCMCProcessor
                                                    • diff --git a/functions_vars_p.html b/functions_vars_p.html index 65164846f..eaa11eb98 100644 --- a/functions_vars_p.html +++ b/functions_vars_p.html @@ -76,7 +76,7 @@

                                                    - p -

                                                    • par : PSO
                                                    • Par : TF1_red, TSpline3_red
                                                      • -
                                                    • par_means : adaptive_mcmc::AdaptiveMCMCStruct
                                                      • +
                                                    • par_means : adaptive_mcmc::AdaptiveMCMCHandler
                                                    • Param_pos : BaseFuncPar
                                                    • ParamCentral : MCMCProcessor
                                                    • ParamErrors : MCMCProcessor
                                                      • diff --git a/functions_vars_s.html b/functions_vars_s.html index 68d68a9c8..fa4f79988 100644 --- a/functions_vars_s.html +++ b/functions_vars_s.html @@ -117,8 +117,8 @@

                                                      - s -

                                                      • splineParsPointer : FastSplineInfo, SMonolith
                                                      • splinevec_Monolith : splineFDBase
                                                      • StandardFluctuation : SampleSummary
                                                        • -
                                                      • start_adaptive_throw : adaptive_mcmc::AdaptiveMCMCStruct
                                                        • -
                                                      • start_adaptive_update : adaptive_mcmc::AdaptiveMCMCStruct
                                                        • +
                                                      • start_adaptive_throw : adaptive_mcmc::AdaptiveMCMCHandler
                                                        • +
                                                      • start_adaptive_update : adaptive_mcmc::AdaptiveMCMCHandler
                                                      • step : FitterBase
                                                      • stepClock : FitterBase
                                                      • StepCut : MCMCProcessor
                                                        • diff --git a/functions_~.html b/functions_~.html index 5617c78b6..c4c70ae15 100644 --- a/functions_~.html +++ b/functions_~.html @@ -74,6 +74,7 @@
                                                        Here is a list of all class members with links to the classes they belong to:

                                                        - ~ -

                                                          +
                                                        • ~AdaptiveMCMCHandler() : adaptive_mcmc::AdaptiveMCMCHandler
                                                        • ~BaseFuncPar() : BaseFuncPar
                                                        • ~covarianceBase() : covarianceBase
                                                        • ~covarianceOsc() : covarianceOsc
                                                          • diff --git a/gpuMCMCProcessorUtils_8cu.html b/gpuMCMCProcessorUtils_8cu.html index d830647af..bc4b24814 100644 --- a/gpuMCMCProcessorUtils_8cu.html +++ b/gpuMCMCProcessorUtils_8cu.html @@ -158,6 +158,15 @@

                                                          KS: free memory on gpu.

                                                          +
                                                          Parameters
                                                          + + + + + +
                                                          ParStep_gpuParameter value at each step
                                                          NumeratorSum_gpuSum used for nominator of autocorrelation calculations
                                                          ParamSums_gpuOverall sum for each parameter over all steps
                                                          DenomSum_gpuSum used for denominator of autocorrelation calculations
                                                          +
                                                          +

                                                          Definition at line 201 of file gpuMCMCProcessorUtils.cu.

                                                          205 {
                                                          @@ -170,7 +179,7 @@

                                                          212 printf(" Cleared memory at GPU, I am free \n");

                                                          213 return;
                                                          214}
                                                          -
                                                          GetFromManager
                                                          Type GetFromManager(const YAML::Node &node, Type defval)
                                                          Get content of config file if node is not found take default value specified.
                                                          Definition YamlHelper.h:18
                                                          +
                                                          GetFromManager
                                                          Type GetFromManager(const YAML::Node &node, Type defval)
                                                          Get content of config file if node is not found take default value specified.
                                                          Definition YamlHelper.h:21
                                                          @@ -237,6 +246,19 @@

                                                          KS: Copy necessary variables from CPU to GPU.

                                                          +
                                                          Parameters
                                                          + + + + + + + + + +
                                                          ParStep_cpuParameter value at each step
                                                          NumeratorSum_cpuSum used for nominator of autocorrelation calculations
                                                          ParamSums_cpuOverall sum for each parameter over all steps
                                                          DenomSum_cpuSum used for denominator of autocorrelation calculations
                                                          ParStep_gpuParameter value at each step
                                                          NumeratorSum_gpuSum used for nominator of autocorrelation calculations
                                                          ParamSums_gpuOverall sum for each parameter over all steps
                                                          DenomSum_gpuSum used for denominator of autocorrelation calculations
                                                          +
                                                          +

                                                          Definition at line 76 of file gpuMCMCProcessorUtils.cu.

                                                          86 {
                                                          @@ -303,6 +325,15 @@

                                                          Eval autocorrelations based on Box and Jenkins.

                                                          +
                                                          Parameters
                                                          + + + + + +
                                                          ParStep_gpuParameter value at each step
                                                          NumeratorSum_gpuSum used for nominator of autocorrelation calculations
                                                          ParamSums_gpuOverall sum for each parameter over all steps
                                                          DenomSum_gpuSum used for denominator of autocorrelation calculations
                                                          +
                                                          +

                                                          Definition at line 112 of file gpuMCMCProcessorUtils.cu.

                                                          116 {
                                                          @@ -413,6 +444,18 @@

                                                          KS: Initialiser, here we allocate memory for variables and copy constants.

                                                          +
                                                          Parameters
                                                          + + + + + + + + +
                                                          ParStep_gpuParameter value at each step
                                                          NumeratorSum_gpuSum used for nominator of autocorrelation calculations
                                                          ParamSums_gpuOverall sum for each parameter over all steps
                                                          DenomSum_gpuSum used for denominator of autocorrelation calculations
                                                          n_EntriesTotal number of entries in mcmc chain
                                                          n_ParsNumber of relevant parameters
                                                          n_LagsValue of Lag in autocreation calculation
                                                          +
                                                          +

                                                          Definition at line 23 of file gpuMCMCProcessorUtils.cu.

                                                          32 {
                                                          @@ -506,6 +549,17 @@

                                                          KS: This call the main kernel responsible for calculating LagL and later copy results back to CPU.

                                                          +
                                                          Parameters
                                                          + + + + + + + +
                                                          ParStep_gpuParameter value at each step
                                                          NumeratorSum_gpuSum used for nominator of autocorrelation calculations
                                                          ParamSums_gpuOverall sum for each parameter over all steps
                                                          DenomSum_gpuSum used for denominator of autocorrelation calculations
                                                          NumeratorSum_cpuSum used for nominator of autocorrelation calculations
                                                          DenomSum_cpuSum used for denominator of autocorrelation calculations
                                                          +
                                                          +

                                                          Definition at line 163 of file gpuMCMCProcessorUtils.cu.

                                                          169 {
                                                          diff --git a/gpuMCMCProcessorUtils_8cu_source.html b/gpuMCMCProcessorUtils_8cu_source.html index 333dcee34..850e26708 100644 --- a/gpuMCMCProcessorUtils_8cu_source.html +++ b/gpuMCMCProcessorUtils_8cu_source.html @@ -302,7 +302,7 @@
                                                          213 return;
                                                          214}
                                                          -
                                                          GetFromManager
                                                          Type GetFromManager(const YAML::Node &node, Type defval)
                                                          Get content of config file if node is not found take default value specified.
                                                          Definition YamlHelper.h:18
                                                          +
                                                          GetFromManager
                                                          Type GetFromManager(const YAML::Node &node, Type defval)
                                                          Get content of config file if node is not found take default value specified.
                                                          Definition YamlHelper.h:21
                                                          d_nEntries
                                                          __device__ __constant__ int d_nEntries
                                                          Definition gpuMCMCProcessorUtils.cu:10
                                                          EvalOnGPU_AutoCorr
                                                          __global__ void EvalOnGPU_AutoCorr(const float *__restrict__ ParStep_gpu, const float *__restrict__ ParamSums_gpu, float *NumeratorSum_gpu, float *DenomSum_gpu)
                                                          Eval autocorrelations based on Box and Jenkins.
                                                          Definition gpuMCMCProcessorUtils.cu:112
                                                          h_nLag
                                                          static int h_nLag
                                                          Definition gpuMCMCProcessorUtils.cu:13
                                                          diff --git a/gpuMCMCProcessorUtils_8cuh.html b/gpuMCMCProcessorUtils_8cuh.html index 46b91bf89..471b83e86 100644 --- a/gpuMCMCProcessorUtils_8cuh.html +++ b/gpuMCMCProcessorUtils_8cuh.html @@ -142,6 +142,15 @@

                                                          KS: free memory on gpu.

                                                          +
                                                          Parameters
                                                          + + + + + +
                                                          ParStep_gpuParameter value at each step
                                                          NumeratorSum_gpuSum used for nominator of autocorrelation calculations
                                                          ParamSums_gpuOverall sum for each parameter over all steps
                                                          DenomSum_gpuSum used for denominator of autocorrelation calculations
                                                          +
                                                          +

                                                          Definition at line 201 of file gpuMCMCProcessorUtils.cu.

                                                          205 {
                                                          @@ -154,7 +163,7 @@

                                                          212 printf(" Cleared memory at GPU, I am free \n");

                                                          213 return;
                                                          214}
                                                          -
                                                          GetFromManager
                                                          Type GetFromManager(const YAML::Node &node, Type defval)
                                                          Get content of config file if node is not found take default value specified.
                                                          Definition YamlHelper.h:18
                                                          +
                                                          GetFromManager
                                                          Type GetFromManager(const YAML::Node &node, Type defval)
                                                          Get content of config file if node is not found take default value specified.
                                                          Definition YamlHelper.h:21

                                                          @@ -221,6 +230,19 @@

                                                          KS: Copy necessary variables from CPU to GPU.

                                                          +
                                                          Parameters
                                                          + + + + + + + + + +
                                                          ParStep_cpuParameter value at each step
                                                          NumeratorSum_cpuSum used for nominator of autocorrelation calculations
                                                          ParamSums_cpuOverall sum for each parameter over all steps
                                                          DenomSum_cpuSum used for denominator of autocorrelation calculations
                                                          ParStep_gpuParameter value at each step
                                                          NumeratorSum_gpuSum used for nominator of autocorrelation calculations
                                                          ParamSums_gpuOverall sum for each parameter over all steps
                                                          DenomSum_gpuSum used for denominator of autocorrelation calculations
                                                          +
                                                          +

                                                          Definition at line 76 of file gpuMCMCProcessorUtils.cu.

                                                          86 {
                                                          @@ -287,6 +309,15 @@

                                                          Eval autocorrelations based on Box and Jenkins.

                                                          +
                                                          Parameters
                                                          + + + + + +
                                                          ParStep_gpuParameter value at each step
                                                          NumeratorSum_gpuSum used for nominator of autocorrelation calculations
                                                          ParamSums_gpuOverall sum for each parameter over all steps
                                                          DenomSum_gpuSum used for denominator of autocorrelation calculations
                                                          +
                                                          +

                                                          Definition at line 112 of file gpuMCMCProcessorUtils.cu.

                                                          116 {
                                                          @@ -397,6 +428,18 @@

                                                          KS: Initialiser, here we allocate memory for variables and copy constants.

                                                          +
                                                          Parameters
                                                          + + + + + + + + +
                                                          ParStep_gpuParameter value at each step
                                                          NumeratorSum_gpuSum used for nominator of autocorrelation calculations
                                                          ParamSums_gpuOverall sum for each parameter over all steps
                                                          DenomSum_gpuSum used for denominator of autocorrelation calculations
                                                          n_EntriesTotal number of entries in mcmc chain
                                                          n_ParsNumber of relevant parameters
                                                          n_LagsValue of Lag in autocreation calculation
                                                          +
                                                          +

                                                          Definition at line 23 of file gpuMCMCProcessorUtils.cu.

                                                          32 {
                                                          @@ -490,6 +533,17 @@

                                                          KS: This call the main kernel responsible for calculating LagL and later copy results back to CPU.

                                                          +
                                                          Parameters
                                                          + + + + + + + +
                                                          ParStep_gpuParameter value at each step
                                                          NumeratorSum_gpuSum used for nominator of autocorrelation calculations
                                                          ParamSums_gpuOverall sum for each parameter over all steps
                                                          DenomSum_gpuSum used for denominator of autocorrelation calculations
                                                          NumeratorSum_cpuSum used for nominator of autocorrelation calculations
                                                          DenomSum_cpuSum used for denominator of autocorrelation calculations
                                                          +
                                                          +

                                                          Definition at line 163 of file gpuMCMCProcessorUtils.cu.

                                                          169 {
                                                          diff --git a/gpuMCMCProcessorUtils_8cuh_source.html b/gpuMCMCProcessorUtils_8cuh_source.html index e8a7d1d1d..546a5024e 100644 --- a/gpuMCMCProcessorUtils_8cuh_source.html +++ b/gpuMCMCProcessorUtils_8cuh_source.html @@ -98,48 +98,48 @@
                                                          13// INITIALISE GPU
                                                          14// *******************************************
                                                          15
                                                          -
                                                          17__host__ void InitGPU_AutoCorr(
                                                          -
                                                          18 float **ParStep_gpu,
                                                          -
                                                          19 float **NumeratorSum_gpu,
                                                          -
                                                          20 float **ParamSums_gpu,
                                                          -
                                                          21 float **DenomSum_gpu,
                                                          -
                                                          22
                                                          -
                                                          23 int n_Entries,
                                                          -
                                                          24 int n_Pars,
                                                          -
                                                          25 const int n_Lags);
                                                          -
                                                          26
                                                          -
                                                          28__host__ void CopyToGPU_AutoCorr(
                                                          -
                                                          29 float *ParStep_cpu,
                                                          -
                                                          30 float *NumeratorSum_cpu,
                                                          -
                                                          31 float *ParamSums_cpu,
                                                          -
                                                          32 float *DenomSum_cpu,
                                                          +
                                                          24__host__ void InitGPU_AutoCorr(
                                                          +
                                                          25 float **ParStep_gpu,
                                                          +
                                                          26 float **NumeratorSum_gpu,
                                                          +
                                                          27 float **ParamSums_gpu,
                                                          +
                                                          28 float **DenomSum_gpu,
                                                          +
                                                          29
                                                          +
                                                          30 int n_Entries,
                                                          +
                                                          31 int n_Pars,
                                                          +
                                                          32 const int n_Lags);
                                                          33
                                                          -
                                                          34 float *ParStep_gpu,
                                                          -
                                                          35 float *NumeratorSum_gpu,
                                                          -
                                                          36 float *ParamSums_gpu,
                                                          -
                                                          37 float *DenomSum_gpu);
                                                          -
                                                          38
                                                          -
                                                          39
                                                          -
                                                          41__global__ void EvalOnGPU_AutoCorr(
                                                          -
                                                          42 const float* __restrict__ ParStep_gpu,
                                                          -
                                                          43 const float* __restrict__ ParamSums_gpu,
                                                          -
                                                          44 float* NumeratorSum_gpu,
                                                          -
                                                          45 float* DenomSum_gpu);
                                                          -
                                                          46
                                                          -
                                                          48__host__ void RunGPU_AutoCorr(
                                                          -
                                                          49 float* ParStep_gpu,
                                                          -
                                                          50 float* ParamSums_gpu,
                                                          -
                                                          51 float* NumeratorSum_gpu,
                                                          -
                                                          52 float* DenomSum_gpu,
                                                          -
                                                          53 float* NumeratorSum_cpu,
                                                          -
                                                          54 float* DenomSum_cpu);
                                                          -
                                                          55
                                                          -
                                                          57__host__ void CleanupGPU_AutoCorr(
                                                          -
                                                          58 float *ParStep_gpu,
                                                          -
                                                          59 float *NumeratorSum_gpu,
                                                          -
                                                          60 float *ParamSums_gpu,
                                                          -
                                                          61 float *DenomSum_gpu);
                                                          -
                                                          GetFromManager
                                                          Type GetFromManager(const YAML::Node &node, Type defval)
                                                          Get content of config file if node is not found take default value specified.
                                                          Definition YamlHelper.h:18
                                                          +
                                                          43__host__ void CopyToGPU_AutoCorr(
                                                          +
                                                          44 float *ParStep_cpu,
                                                          +
                                                          45 float *NumeratorSum_cpu,
                                                          +
                                                          46 float *ParamSums_cpu,
                                                          +
                                                          47 float *DenomSum_cpu,
                                                          +
                                                          48
                                                          +
                                                          49 float *ParStep_gpu,
                                                          +
                                                          50 float *NumeratorSum_gpu,
                                                          +
                                                          51 float *ParamSums_gpu,
                                                          +
                                                          52 float *DenomSum_gpu);
                                                          +
                                                          53
                                                          +
                                                          54
                                                          +
                                                          60__global__ void EvalOnGPU_AutoCorr(
                                                          +
                                                          61 const float* __restrict__ ParStep_gpu,
                                                          +
                                                          62 const float* __restrict__ ParamSums_gpu,
                                                          +
                                                          63 float* NumeratorSum_gpu,
                                                          +
                                                          64 float* DenomSum_gpu);
                                                          +
                                                          65
                                                          +
                                                          73__host__ void RunGPU_AutoCorr(
                                                          +
                                                          74 float* ParStep_gpu,
                                                          +
                                                          75 float* ParamSums_gpu,
                                                          +
                                                          76 float* NumeratorSum_gpu,
                                                          +
                                                          77 float* DenomSum_gpu,
                                                          +
                                                          78 float* NumeratorSum_cpu,
                                                          +
                                                          79 float* DenomSum_cpu);
                                                          +
                                                          80
                                                          +
                                                          86__host__ void CleanupGPU_AutoCorr(
                                                          +
                                                          87 float *ParStep_gpu,
                                                          +
                                                          88 float *NumeratorSum_gpu,
                                                          +
                                                          89 float *ParamSums_gpu,
                                                          +
                                                          90 float *DenomSum_gpu);
                                                          +
                                                          GetFromManager
                                                          Type GetFromManager(const YAML::Node &node, Type defval)
                                                          Get content of config file if node is not found take default value specified.
                                                          Definition YamlHelper.h:21
                                                          EvalOnGPU_AutoCorr
                                                          __global__ void EvalOnGPU_AutoCorr(const float *__restrict__ ParStep_gpu, const float *__restrict__ ParamSums_gpu, float *NumeratorSum_gpu, float *DenomSum_gpu)
                                                          Eval autocorrelations based on Box and Jenkins.
                                                          Definition gpuMCMCProcessorUtils.cu:112
                                                          InitGPU_AutoCorr
                                                          __host__ void InitGPU_AutoCorr(float **ParStep_gpu, float **NumeratorSum_gpu, float **ParamSums_gpu, float **DenomSum_gpu, int n_Entries, int n_Pars, const int n_Lags)
                                                          KS: Initialiser, here we allocate memory for variables and copy constants.
                                                          Definition gpuMCMCProcessorUtils.cu:23
                                                          CopyToGPU_AutoCorr
                                                          __host__ void CopyToGPU_AutoCorr(float *ParStep_cpu, float *NumeratorSum_cpu, float *ParamSums_cpu, float *DenomSum_cpu, float *ParStep_gpu, float *NumeratorSum_gpu, float *ParamSums_gpu, float *DenomSum_gpu)
                                                          KS: Copy necessary variables from CPU to GPU.
                                                          Definition gpuMCMCProcessorUtils.cu:76
                                                          diff --git a/gpuSplineUtils_8cu.html b/gpuSplineUtils_8cu.html index 2709b3224..5891f52f8 100644 --- a/gpuSplineUtils_8cu.html +++ b/gpuSplineUtils_8cu.html @@ -101,6 +101,7 @@  Initialiser when using the x array and combined y,b,c,d array.
                                                            __host__ void InitGPU_Segments (short int **segment) + Allocate memory for spline segments.
                                                            __host__ void InitGPU_Vals (float **vals)   @@ -111,6 +112,7 @@  Copy to GPU for x array and separate ybcd array.
                                                            __global__ void EvalOnGPU_SepMany (const short int *__restrict__ gpu_paramNo_arr, const unsigned int *__restrict__ gpu_nKnots_arr, const float *__restrict__ gpu_coeff_many, float *gpu_weights, const cudaTextureObject_t __restrict__ text_coeff_x) + Evaluate the spline on the GPU Using one {y,b,c,d} array and one {x} array Should be most efficient at cache hitting and memory coalescence But using spline segments rather than the parameter value: avoids doing binary search on GPU.
                                                            __global__ void EvalOnGPU_TF1 (const float *__restrict__ gpu_coeffs, const short int *__restrict__ gpu_paramNo_arr, const short int *__restrict__ gpu_nPoints_arr, float *gpu_weights)  Evaluate the TF1 on the GPU Using 5th order polynomial.
                                                          @@ -119,6 +121,7 @@  KS: Evaluate the total spline event weight on the GPU, as in most cases GPU is faster, even more this significant reduce memory transfer from GPU to CPU.
                                                            __host__ void RunGPU_SepMany (const short int *gpu_paramNo_arr, const unsigned int *gpu_nKnots_arr, const float *gpu_coeff_many, float *gpu_weights, float *gpu_total_weights, float *cpu_total_weights, float *vals, short int *segment, const unsigned int h_n_splines) + Run the GPU code for the separate many arrays. As in separate {x}, {y,b,c,d} arrays Pass the segment and the parameter values (binary search already performed in samplePDFND::FindSplineSegment()
                                                            __host__ void RunGPU_TF1 (const float *gpu_coeffs, const short int *gpu_paramNo_arr, const short int *gpu_nPoints_arr, float *gpu_weights, float *gpu_total_weights, float *cpu_total_weights, float *vals, const unsigned int h_n_splines)  Run the GPU code for the TF1.
                                                          @@ -139,10 +142,13 @@

                                                          Variables

                                                          __device__ __constant__ unsigned int d_n_splines + Number of splines living on GPU.
                                                            __device__ __constant__ short int d_spline_size + Size of splines living on GPU.
                                                            __device__ __constant__ int d_n_events + Number of events living on GPU.
                                                            __device__ __constant__ float val_gpu [_N_SPLINES_]  CW: Constant memory needs to be hard-coded on compile time. Could make this texture memory instead, but don't care enough right now...
                                                          @@ -150,14 +156,19 @@ __device__ __constant__ short int segment_gpu [_N_SPLINES_]   static short int h_spline_size = -1 + Number of splines living on CPU.
                                                            static int h_n_params = -1 + Number of params living on CPU.
                                                            static int h_n_events = -1 + Number of events living on CPU.
                                                            cudaTextureObject_t text_coeff_x = 0 + KS: Textures are L1 cache variables which are well optimised for fetching. Make texture only for variables you often access but rarely overwrite. There are limits on texture memory so don't use huge arrays.
                                                            cudaTextureObject_t text_nParamPerEvent = 0 + KS: Map keeping track how many parameters applies to each event, we keep two numbers here {number of splines per event, index where splines start for a given event}.
                                                           

                                                          Macro Definition Documentation

                                                          @@ -172,6 +183,7 @@

                                                          +

                                                          Hard code the number of splines Not entirely necessary: only used for val_gpu and segment_gpu being device constants. Could move them to not being device constants EM: for OA2022:

                                                          Definition at line 20 of file gpuSplineUtils.cu.

                                                          @@ -206,18 +218,18 @@

                                                          Definition at line 841 of file gpuSplineUtils.cu.

                                                          -
                                                          841 {
                                                          -
                                                          842// *******************************************
                                                          -
                                                          843 cudaFreeHost(segment);
                                                          -
                                                          844 cudaFreeHost(vals);
                                                          -
                                                          845
                                                          -
                                                          846 segment = nullptr;
                                                          -
                                                          847 vals = nullptr;
                                                          -
                                                          848
                                                          -
                                                          849 return;
                                                          -
                                                          850}
                                                          -
                                                          GetFromManager
                                                          Type GetFromManager(const YAML::Node &node, Type defval)
                                                          Get content of config file if node is not found take default value specified.
                                                          Definition YamlHelper.h:18
                                                          +

                                                          Definition at line 843 of file gpuSplineUtils.cu.

                                                          +
                                                          843 {
                                                          +
                                                          844// *******************************************
                                                          +
                                                          845 cudaFreeHost(segment);
                                                          +
                                                          846 cudaFreeHost(vals);
                                                          +
                                                          847
                                                          +
                                                          848 segment = nullptr;
                                                          +
                                                          849 vals = nullptr;
                                                          +
                                                          850
                                                          +
                                                          851 return;
                                                          +
                                                          852}
                                                          +
                                                          GetFromManager
                                                          Type GetFromManager(const YAML::Node &node, Type defval)
                                                          Get content of config file if node is not found take default value specified.
                                                          Definition YamlHelper.h:21

                                                          @@ -285,31 +297,31 @@

                                                          Definition at line 805 of file gpuSplineUtils.cu.

                                                          -
                                                          816 {
                                                          -
                                                          817// *********************************
                                                          -
                                                          818 cudaFree(gpu_paramNo_arr);
                                                          -
                                                          819 cudaFree(gpu_nKnots_arr);
                                                          -
                                                          820
                                                          -
                                                          821 // free the coefficient arrays
                                                          -
                                                          822 cudaDestroyTextureObject(text_coeff_x);
                                                          -
                                                          823 cudaFree(gpu_x_array);
                                                          -
                                                          824 cudaFree(gpu_many_array);
                                                          -
                                                          825
                                                          -
                                                          826 // free weights on the gpu
                                                          -
                                                          827 cudaFree(gpu_weights);
                                                          -
                                                          828#ifndef Weight_On_SplineBySpline_Basis
                                                          -
                                                          829 cudaFree(gpu_total_weights);
                                                          -
                                                          830 //KS: Before removing variable let's destroy texture
                                                          -
                                                          831 cudaDestroyTextureObject(text_nParamPerEvent);
                                                          -
                                                          832 cudaFree(gpu_nParamPerEvent);
                                                          -
                                                          833 cudaFreeHost(cpu_total_weights);
                                                          -
                                                          834 cpu_total_weights = nullptr;
                                                          -
                                                          835#endif
                                                          -
                                                          836 return;
                                                          -
                                                          837}
                                                          -
                                                          text_coeff_x
                                                          cudaTextureObject_t text_coeff_x
                                                          Definition gpuSplineUtils.cu:93
                                                          -
                                                          text_nParamPerEvent
                                                          cudaTextureObject_t text_nParamPerEvent
                                                          Definition gpuSplineUtils.cu:96
                                                          +

                                                          Definition at line 807 of file gpuSplineUtils.cu.

                                                          +
                                                          818 {
                                                          +
                                                          819// *********************************
                                                          +
                                                          820 cudaFree(gpu_paramNo_arr);
                                                          +
                                                          821 cudaFree(gpu_nKnots_arr);
                                                          +
                                                          822
                                                          +
                                                          823 // free the coefficient arrays
                                                          +
                                                          824 cudaDestroyTextureObject(text_coeff_x);
                                                          +
                                                          825 cudaFree(gpu_x_array);
                                                          +
                                                          826 cudaFree(gpu_many_array);
                                                          +
                                                          827
                                                          +
                                                          828 // free weights on the gpu
                                                          +
                                                          829 cudaFree(gpu_weights);
                                                          +
                                                          830#ifndef Weight_On_SplineBySpline_Basis
                                                          +
                                                          831 cudaFree(gpu_total_weights);
                                                          +
                                                          832 //KS: Before removing variable let's destroy texture
                                                          +
                                                          833 cudaDestroyTextureObject(text_nParamPerEvent);
                                                          +
                                                          834 cudaFree(gpu_nParamPerEvent);
                                                          +
                                                          835 cudaFreeHost(cpu_total_weights);
                                                          +
                                                          836 cpu_total_weights = nullptr;
                                                          +
                                                          837#endif
                                                          +
                                                          838 return;
                                                          +
                                                          839}
                                                          +
                                                          text_coeff_x
                                                          cudaTextureObject_t text_coeff_x
                                                          KS: Textures are L1 cache variables which are well optimised for fetching. Make texture only for vari...
                                                          Definition gpuSplineUtils.cu:99
                                                          +
                                                          text_nParamPerEvent
                                                          cudaTextureObject_t text_nParamPerEvent
                                                          KS: Map keeping track how many parameters applies to each event, we keep two numbers here {number of ...
                                                          Definition gpuSplineUtils.cu:102

                                                          @@ -365,20 +377,20 @@

                                                          Definition at line 854 of file gpuSplineUtils.cu.

                                                          -
                                                          863 {
                                                          -
                                                          864// *********************************
                                                          -
                                                          865 cudaFree(gpu_coeffs);
                                                          -
                                                          866 cudaFree(gpu_paramNo_arr);
                                                          -
                                                          867 cudaFree(gpu_nPoints_arr);
                                                          -
                                                          868 cudaFree(gpu_weights);
                                                          -
                                                          869#ifndef Weight_On_SplineBySpline_Basis
                                                          -
                                                          870 cudaFree(gpu_total_weights);
                                                          -
                                                          871 cudaFreeHost(cpu_total_weights);
                                                          -
                                                          872#endif
                                                          -
                                                          873
                                                          -
                                                          874 return;
                                                          -
                                                          875}
                                                          +

                                                          Definition at line 856 of file gpuSplineUtils.cu.

                                                          +
                                                          865 {
                                                          +
                                                          866// *********************************
                                                          +
                                                          867 cudaFree(gpu_coeffs);
                                                          +
                                                          868 cudaFree(gpu_paramNo_arr);
                                                          +
                                                          869 cudaFree(gpu_nPoints_arr);
                                                          +
                                                          870 cudaFree(gpu_weights);
                                                          +
                                                          871#ifndef Weight_On_SplineBySpline_Basis
                                                          +
                                                          872 cudaFree(gpu_total_weights);
                                                          +
                                                          873 cudaFreeHost(cpu_total_weights);
                                                          +
                                                          874#endif
                                                          +
                                                          875
                                                          +
                                                          876 return;
                                                          +
                                                          877}

                                                          @@ -488,98 +500,98 @@

                                                          Definition at line 251 of file gpuSplineUtils.cu.

                                                          -
                                                          271 {
                                                          -
                                                          272 if (n_params != _N_SPLINES_) {
                                                          -
                                                          273 printf("Number of splines not equal to %i, GPU code for event-by-event splines will fail\n", _N_SPLINES_);
                                                          -
                                                          274 printf("n_params = %i\n", n_params);
                                                          -
                                                          275 printf("%s : %i\n", __FILE__, __LINE__);
                                                          -
                                                          276 exit(-1);
                                                          -
                                                          277 }
                                                          -
                                                          278
                                                          -
                                                          279 // Write to the global statics (h_* denotes host stored variable)
                                                          -
                                                          280 h_n_params = n_params;
                                                          -
                                                          281 h_spline_size = spline_size;
                                                          -
                                                          282#ifndef Weight_On_SplineBySpline_Basis
                                                          -
                                                          283 h_n_events = n_events;
                                                          -
                                                          284#endif
                                                          -
                                                          285 // Copy the constants
                                                          -
                                                          286 // Total number of valid splines for all loaded events
                                                          -
                                                          287 cudaMemcpyToSymbol(d_n_splines, &n_splines, sizeof(n_splines));
                                                          -
                                                          288 CudaCheckError();
                                                          -
                                                          289 // Total spline size per spline; i.e. just the number of points or knots in the spline
                                                          -
                                                          290 cudaMemcpyToSymbol(d_spline_size, &h_spline_size, sizeof(h_spline_size));
                                                          -
                                                          291 CudaCheckError();
                                                          -
                                                          292#ifndef Weight_On_SplineBySpline_Basis
                                                          -
                                                          293 // Number of events
                                                          -
                                                          294 cudaMemcpyToSymbol(d_n_events, &h_n_events, sizeof(h_n_events));
                                                          -
                                                          295 CudaCheckError();
                                                          -
                                                          296#endif
                                                          -
                                                          297 // Copy the coefficient arrays to the GPU; this only happens once per entire Markov Chain so is OK to do multiple extensive memory copies
                                                          -
                                                          298 cudaMemcpy(gpu_many_array, cpu_many_array.data(), sizeof(float)*sizeof_array*_nCoeff_, cudaMemcpyHostToDevice);
                                                          -
                                                          299 CudaCheckError();
                                                          -
                                                          300
                                                          -
                                                          301 cudaMemcpy(gpu_x_array, cpu_x_array.data(), sizeof(float)*spline_size*n_params, cudaMemcpyHostToDevice);
                                                          -
                                                          302 CudaCheckError();
                                                          -
                                                          303
                                                          -
                                                          304 //KS: Bind our texture with the GPU variable
                                                          -
                                                          305 //KS: Tried also moving gpu_many_array to texture memory it only worked with restricted number of MC runs, most likely hit texture memory limit :(
                                                          -
                                                          306 struct cudaResourceDesc resDesc_coeff_x;
                                                          -
                                                          307 memset(&resDesc_coeff_x, 0, sizeof(resDesc_coeff_x));
                                                          -
                                                          308 resDesc_coeff_x.resType = cudaResourceTypeLinear;
                                                          -
                                                          309 resDesc_coeff_x.res.linear.devPtr = gpu_x_array;
                                                          -
                                                          310 resDesc_coeff_x.res.linear.desc = cudaCreateChannelDesc<float>();
                                                          -
                                                          311 resDesc_coeff_x.res.linear.sizeInBytes = sizeof(float)*spline_size*n_params;
                                                          -
                                                          312
                                                          -
                                                          313 // Specify texture object parameters
                                                          -
                                                          314 struct cudaTextureDesc texDesc_coeff_x;
                                                          -
                                                          315 memset(&texDesc_coeff_x, 0, sizeof(texDesc_coeff_x));
                                                          -
                                                          316 texDesc_coeff_x.readMode = cudaReadModeElementType;
                                                          +

                                                          Definition at line 256 of file gpuSplineUtils.cu.

                                                          +
                                                          276 {
                                                          +
                                                          277 if (n_params != _N_SPLINES_) {
                                                          +
                                                          278 printf("Number of splines not equal to %i, GPU code for event-by-event splines will fail\n", _N_SPLINES_);
                                                          +
                                                          279 printf("n_params = %i\n", n_params);
                                                          +
                                                          280 printf("%s : %i\n", __FILE__, __LINE__);
                                                          +
                                                          281 exit(-1);
                                                          +
                                                          282 }
                                                          +
                                                          283
                                                          +
                                                          284 // Write to the global statics (h_* denotes host stored variable)
                                                          +
                                                          285 h_n_params = n_params;
                                                          +
                                                          286 h_spline_size = spline_size;
                                                          +
                                                          287#ifndef Weight_On_SplineBySpline_Basis
                                                          +
                                                          288 h_n_events = n_events;
                                                          +
                                                          289#endif
                                                          +
                                                          290 // Copy the constants
                                                          +
                                                          291 // Total number of valid splines for all loaded events
                                                          +
                                                          292 cudaMemcpyToSymbol(d_n_splines, &n_splines, sizeof(n_splines));
                                                          +
                                                          293 CudaCheckError();
                                                          +
                                                          294 // Total spline size per spline; i.e. just the number of points or knots in the spline
                                                          +
                                                          295 cudaMemcpyToSymbol(d_spline_size, &h_spline_size, sizeof(h_spline_size));
                                                          +
                                                          296 CudaCheckError();
                                                          +
                                                          297#ifndef Weight_On_SplineBySpline_Basis
                                                          +
                                                          298 // Number of events
                                                          +
                                                          299 cudaMemcpyToSymbol(d_n_events, &h_n_events, sizeof(h_n_events));
                                                          +
                                                          300 CudaCheckError();
                                                          +
                                                          301#endif
                                                          +
                                                          302 // Copy the coefficient arrays to the GPU; this only happens once per entire Markov Chain so is OK to do multiple extensive memory copies
                                                          +
                                                          303 cudaMemcpy(gpu_many_array, cpu_many_array.data(), sizeof(float)*sizeof_array*_nCoeff_, cudaMemcpyHostToDevice);
                                                          +
                                                          304 CudaCheckError();
                                                          +
                                                          305
                                                          +
                                                          306 cudaMemcpy(gpu_x_array, cpu_x_array.data(), sizeof(float)*spline_size*n_params, cudaMemcpyHostToDevice);
                                                          +
                                                          307 CudaCheckError();
                                                          +
                                                          308
                                                          +
                                                          309 //KS: Bind our texture with the GPU variable
                                                          +
                                                          310 //KS: Tried also moving gpu_many_array to texture memory it only worked with restricted number of MC runs, most likely hit texture memory limit :(
                                                          +
                                                          311 struct cudaResourceDesc resDesc_coeff_x;
                                                          +
                                                          312 memset(&resDesc_coeff_x, 0, sizeof(resDesc_coeff_x));
                                                          +
                                                          313 resDesc_coeff_x.resType = cudaResourceTypeLinear;
                                                          +
                                                          314 resDesc_coeff_x.res.linear.devPtr = gpu_x_array;
                                                          +
                                                          315 resDesc_coeff_x.res.linear.desc = cudaCreateChannelDesc<float>();
                                                          +
                                                          316 resDesc_coeff_x.res.linear.sizeInBytes = sizeof(float)*spline_size*n_params;
                                                          317
                                                          -
                                                          318 // Create texture object
                                                          -
                                                          319 cudaCreateTextureObject(&text_coeff_x, &resDesc_coeff_x, &texDesc_coeff_x, NULL);
                                                          -
                                                          320 CudaCheckError();
                                                          -
                                                          321
                                                          -
                                                          322 // Also copy the parameter number for each spline onto the GPU; i.e. what spline parameter are we calculating right now
                                                          -
                                                          323 cudaMemcpy(gpu_paramNo_arr, paramNo_arr.data(), n_splines*sizeof(short int), cudaMemcpyHostToDevice);
                                                          -
                                                          324 CudaCheckError();
                                                          -
                                                          325
                                                          -
                                                          326 // Also copy the knot map for each spline onto the GPU;
                                                          -
                                                          327 cudaMemcpy(gpu_nKnots_arr, nKnots_arr.data(), n_splines*sizeof(unsigned int), cudaMemcpyHostToDevice);
                                                          -
                                                          328 CudaCheckError();
                                                          -
                                                          329
                                                          -
                                                          330 #ifndef Weight_On_SplineBySpline_Basis
                                                          -
                                                          331 //KS: Keep track how much splines each event has
                                                          -
                                                          332 cudaMemcpy(gpu_nParamPerEvent, cpu_nParamPerEvent.data(), 2*n_events*sizeof(unsigned int), cudaMemcpyHostToDevice);
                                                          +
                                                          318 // Specify texture object parameters
                                                          +
                                                          319 struct cudaTextureDesc texDesc_coeff_x;
                                                          +
                                                          320 memset(&texDesc_coeff_x, 0, sizeof(texDesc_coeff_x));
                                                          +
                                                          321 texDesc_coeff_x.readMode = cudaReadModeElementType;
                                                          +
                                                          322
                                                          +
                                                          323 // Create texture object
                                                          +
                                                          324 cudaCreateTextureObject(&text_coeff_x, &resDesc_coeff_x, &texDesc_coeff_x, NULL);
                                                          +
                                                          325 CudaCheckError();
                                                          +
                                                          326
                                                          +
                                                          327 // Also copy the parameter number for each spline onto the GPU; i.e. what spline parameter are we calculating right now
                                                          +
                                                          328 cudaMemcpy(gpu_paramNo_arr, paramNo_arr.data(), n_splines*sizeof(short int), cudaMemcpyHostToDevice);
                                                          +
                                                          329 CudaCheckError();
                                                          +
                                                          330
                                                          +
                                                          331 // Also copy the knot map for each spline onto the GPU;
                                                          +
                                                          332 cudaMemcpy(gpu_nKnots_arr, nKnots_arr.data(), n_splines*sizeof(unsigned int), cudaMemcpyHostToDevice);
                                                          333 CudaCheckError();
                                                          -
                                                          334
                                                          -
                                                          335 //KS: Bind our texture with the GPU variable
                                                          -
                                                          336 // create a resource descriptor based on device pointers
                                                          -
                                                          337 struct cudaResourceDesc resDesc_nParamPerEvent;
                                                          -
                                                          338 memset(&resDesc_nParamPerEvent, 0, sizeof(resDesc_nParamPerEvent));
                                                          -
                                                          339 resDesc_nParamPerEvent.resType = cudaResourceTypeLinear;
                                                          -
                                                          340 resDesc_nParamPerEvent.res.linear.devPtr = gpu_nParamPerEvent;
                                                          -
                                                          341 resDesc_nParamPerEvent.res.linear.desc = cudaCreateChannelDesc<unsigned int>();
                                                          -
                                                          342 resDesc_nParamPerEvent.res.linear.sizeInBytes = 2*n_events*sizeof(unsigned int);
                                                          -
                                                          343
                                                          -
                                                          344 // Specify texture object parameters
                                                          -
                                                          345 struct cudaTextureDesc texDesc_nParamPerEvent;
                                                          -
                                                          346 memset(&texDesc_nParamPerEvent, 0, sizeof(texDesc_nParamPerEvent));
                                                          -
                                                          347 texDesc_nParamPerEvent.readMode = cudaReadModeElementType;
                                                          +
                                                          334
                                                          +
                                                          335 #ifndef Weight_On_SplineBySpline_Basis
                                                          +
                                                          336 //KS: Keep track how much splines each event has
                                                          +
                                                          337 cudaMemcpy(gpu_nParamPerEvent, cpu_nParamPerEvent.data(), 2*n_events*sizeof(unsigned int), cudaMemcpyHostToDevice);
                                                          +
                                                          338 CudaCheckError();
                                                          +
                                                          339
                                                          +
                                                          340 //KS: Bind our texture with the GPU variable
                                                          +
                                                          341 // create a resource descriptor based on device pointers
                                                          +
                                                          342 struct cudaResourceDesc resDesc_nParamPerEvent;
                                                          +
                                                          343 memset(&resDesc_nParamPerEvent, 0, sizeof(resDesc_nParamPerEvent));
                                                          +
                                                          344 resDesc_nParamPerEvent.resType = cudaResourceTypeLinear;
                                                          +
                                                          345 resDesc_nParamPerEvent.res.linear.devPtr = gpu_nParamPerEvent;
                                                          +
                                                          346 resDesc_nParamPerEvent.res.linear.desc = cudaCreateChannelDesc<unsigned int>();
                                                          +
                                                          347 resDesc_nParamPerEvent.res.linear.sizeInBytes = 2*n_events*sizeof(unsigned int);
                                                          348
                                                          -
                                                          349 //Finally create texture object
                                                          -
                                                          350 cudaCreateTextureObject(&text_nParamPerEvent, &resDesc_nParamPerEvent, &texDesc_nParamPerEvent, NULL);
                                                          -
                                                          351 CudaCheckError();
                                                          -
                                                          352 #endif
                                                          -
                                                          353}
                                                          +
                                                          349 // Specify texture object parameters
                                                          +
                                                          350 struct cudaTextureDesc texDesc_nParamPerEvent;
                                                          +
                                                          351 memset(&texDesc_nParamPerEvent, 0, sizeof(texDesc_nParamPerEvent));
                                                          +
                                                          352 texDesc_nParamPerEvent.readMode = cudaReadModeElementType;
                                                          +
                                                          353
                                                          +
                                                          354 //Finally create texture object
                                                          +
                                                          355 cudaCreateTextureObject(&text_nParamPerEvent, &resDesc_nParamPerEvent, &texDesc_nParamPerEvent, NULL);
                                                          +
                                                          356 CudaCheckError();
                                                          +
                                                          357 #endif
                                                          +
                                                          358}
                                                          _nCoeff_
                                                          #define _nCoeff_
                                                          KS: We store coefficients {y,b,c,d} in one array one by one, this is only to define it once rather th...
                                                          Definition SplineCommon.h:8
                                                          -
                                                          h_n_params
                                                          static int h_n_params
                                                          Definition gpuSplineUtils.cu:84
                                                          -
                                                          h_spline_size
                                                          static short int h_spline_size
                                                          Definition gpuSplineUtils.cu:83
                                                          +
                                                          h_n_params
                                                          static int h_n_params
                                                          Number of params living on CPU.
                                                          Definition gpuSplineUtils.cu:89
                                                          +
                                                          h_spline_size
                                                          static short int h_spline_size
                                                          Number of splines living on CPU.
                                                          Definition gpuSplineUtils.cu:87
                                                          _N_SPLINES_
                                                          #define _N_SPLINES_
                                                          Definition gpuSplineUtils.cu:20
                                                          -
                                                          d_n_splines
                                                          __device__ __constant__ unsigned int d_n_splines
                                                          Definition gpuSplineUtils.cu:73
                                                          -
                                                          h_n_events
                                                          static int h_n_events
                                                          Definition gpuSplineUtils.cu:86
                                                          -
                                                          d_n_events
                                                          __device__ __constant__ int d_n_events
                                                          Definition gpuSplineUtils.cu:76
                                                          -
                                                          d_spline_size
                                                          __device__ __constant__ short int d_spline_size
                                                          Definition gpuSplineUtils.cu:74
                                                          +
                                                          d_n_splines
                                                          __device__ __constant__ unsigned int d_n_splines
                                                          Number of splines living on GPU.
                                                          Definition gpuSplineUtils.cu:74
                                                          +
                                                          h_n_events
                                                          static int h_n_events
                                                          Number of events living on CPU.
                                                          Definition gpuSplineUtils.cu:92
                                                          +
                                                          d_n_events
                                                          __device__ __constant__ int d_n_events
                                                          Number of events living on GPU.
                                                          Definition gpuSplineUtils.cu:79
                                                          +
                                                          d_spline_size
                                                          __device__ __constant__ short int d_spline_size
                                                          Size of splines living on GPU.
                                                          Definition gpuSplineUtils.cu:76
                                                          CudaCheckError
                                                          #define CudaCheckError()
                                                          Definition gpuUtils.cuh:18
                                                          @@ -672,70 +684,70 @@

                                                          Definition at line 357 of file gpuSplineUtils.cu.

                                                          -
                                                          374 {
                                                          -
                                                          375
                                                          -
                                                          376 if (n_params != _N_SPLINES_) {
                                                          -
                                                          377 printf("Number of splines not equal to %i, GPU code for event-by-event splines will fail\n", _N_SPLINES_);
                                                          -
                                                          378 printf("n_params = %i\n", n_params);
                                                          -
                                                          379 printf("%s : %i\n", __FILE__, __LINE__);
                                                          -
                                                          380 exit(-1);
                                                          -
                                                          381 }
                                                          -
                                                          382
                                                          -
                                                          383 // Write to the global statics (h_* denotes host stored variable)
                                                          -
                                                          384 h_n_params = n_params;
                                                          -
                                                          385 h_spline_size = _max_knots;
                                                          -
                                                          386#ifndef Weight_On_SplineBySpline_Basis
                                                          -
                                                          387 h_n_events = n_events;
                                                          -
                                                          388#endif
                                                          -
                                                          389 // Copy the constants
                                                          -
                                                          390 // Total number of valid splines for all loaded events
                                                          -
                                                          391 cudaMemcpyToSymbol(d_n_splines, &n_splines, sizeof(n_splines));
                                                          -
                                                          392 CudaCheckError();
                                                          -
                                                          393 // Total spline size per spline; i.e. just the number of points or knots in the spline
                                                          -
                                                          394 cudaMemcpyToSymbol(d_spline_size, &h_spline_size, sizeof(h_spline_size));
                                                          -
                                                          395 CudaCheckError();
                                                          -
                                                          396
                                                          -
                                                          397#ifndef Weight_On_SplineBySpline_Basis
                                                          -
                                                          398 // Number of events
                                                          -
                                                          399 cudaMemcpyToSymbol(d_n_events, &h_n_events, sizeof(h_n_events));
                                                          +

                                                          Definition at line 362 of file gpuSplineUtils.cu.

                                                          +
                                                          379 {
                                                          +
                                                          380
                                                          +
                                                          381 if (n_params != _N_SPLINES_) {
                                                          +
                                                          382 printf("Number of splines not equal to %i, GPU code for event-by-event splines will fail\n", _N_SPLINES_);
                                                          +
                                                          383 printf("n_params = %i\n", n_params);
                                                          +
                                                          384 printf("%s : %i\n", __FILE__, __LINE__);
                                                          +
                                                          385 exit(-1);
                                                          +
                                                          386 }
                                                          +
                                                          387
                                                          +
                                                          388 // Write to the global statics (h_* denotes host stored variable)
                                                          +
                                                          389 h_n_params = n_params;
                                                          +
                                                          390 h_spline_size = _max_knots;
                                                          +
                                                          391#ifndef Weight_On_SplineBySpline_Basis
                                                          +
                                                          392 h_n_events = n_events;
                                                          +
                                                          393#endif
                                                          +
                                                          394 // Copy the constants
                                                          +
                                                          395 // Total number of valid splines for all loaded events
                                                          +
                                                          396 cudaMemcpyToSymbol(d_n_splines, &n_splines, sizeof(n_splines));
                                                          +
                                                          397 CudaCheckError();
                                                          +
                                                          398 // Total spline size per spline; i.e. just the number of points or knots in the spline
                                                          +
                                                          399 cudaMemcpyToSymbol(d_spline_size, &h_spline_size, sizeof(h_spline_size));
                                                          400 CudaCheckError();
                                                          -
                                                          401#endif
                                                          -
                                                          402 // Move the coefficients
                                                          -
                                                          403 cudaMemcpy(gpu_coeffs, cpu_coeffs.data(), n_splines*5*sizeof(float), cudaMemcpyHostToDevice);
                                                          -
                                                          404 CudaCheckError();
                                                          -
                                                          405
                                                          -
                                                          406 // Also copy the parameter number for each spline onto the GPU; i.e. what spline parameter are we calculating right now
                                                          -
                                                          407 cudaMemcpy(gpu_paramNo_arr, paramNo_arr.data(), n_splines*sizeof(short int), cudaMemcpyHostToDevice);
                                                          -
                                                          408 CudaCheckError();
                                                          -
                                                          409
                                                          -
                                                          410 cudaMemcpy(gpu_nPoints_arr, nPoints_arr.data(), n_splines*sizeof(short int), cudaMemcpyHostToDevice);
                                                          -
                                                          411 CudaCheckError();
                                                          -
                                                          412
                                                          -
                                                          413 #ifndef Weight_On_SplineBySpline_Basis
                                                          -
                                                          414 //KS: Keep track how much splines each event has
                                                          -
                                                          415 cudaMemcpy(gpu_nParamPerEvent, cpu_nParamPerEvent.data(), 2*n_events*sizeof(unsigned int), cudaMemcpyHostToDevice);
                                                          +
                                                          401
                                                          +
                                                          402#ifndef Weight_On_SplineBySpline_Basis
                                                          +
                                                          403 // Number of events
                                                          +
                                                          404 cudaMemcpyToSymbol(d_n_events, &h_n_events, sizeof(h_n_events));
                                                          +
                                                          405 CudaCheckError();
                                                          +
                                                          406#endif
                                                          +
                                                          407 // Move the coefficients
                                                          +
                                                          408 cudaMemcpy(gpu_coeffs, cpu_coeffs.data(), n_splines*5*sizeof(float), cudaMemcpyHostToDevice);
                                                          +
                                                          409 CudaCheckError();
                                                          +
                                                          410
                                                          +
                                                          411 // Also copy the parameter number for each spline onto the GPU; i.e. what spline parameter are we calculating right now
                                                          +
                                                          412 cudaMemcpy(gpu_paramNo_arr, paramNo_arr.data(), n_splines*sizeof(short int), cudaMemcpyHostToDevice);
                                                          +
                                                          413 CudaCheckError();
                                                          +
                                                          414
                                                          +
                                                          415 cudaMemcpy(gpu_nPoints_arr, nPoints_arr.data(), n_splines*sizeof(short int), cudaMemcpyHostToDevice);
                                                          416 CudaCheckError();
                                                          -
                                                          417
                                                          -
                                                          418 //KS: Bind our texture with the GPU variable
                                                          -
                                                          419 // create a resource descriptor based on device pointers
                                                          -
                                                          420 struct cudaResourceDesc resDesc_nParamPerEvent;
                                                          -
                                                          421 memset(&resDesc_nParamPerEvent, 0, sizeof(resDesc_nParamPerEvent));
                                                          -
                                                          422 resDesc_nParamPerEvent.resType = cudaResourceTypeLinear;
                                                          -
                                                          423 resDesc_nParamPerEvent.res.linear.devPtr = gpu_nParamPerEvent;
                                                          -
                                                          424 resDesc_nParamPerEvent.res.linear.desc = cudaCreateChannelDesc<float>();
                                                          -
                                                          425 resDesc_nParamPerEvent.res.linear.sizeInBytes = 2*n_events*sizeof(unsigned int);
                                                          -
                                                          426
                                                          -
                                                          427 // Specify texture object parameters
                                                          -
                                                          428 struct cudaTextureDesc texDesc_nParamPerEvent;
                                                          -
                                                          429 memset(&texDesc_nParamPerEvent, 0, sizeof(texDesc_nParamPerEvent));
                                                          -
                                                          430 texDesc_nParamPerEvent.readMode = cudaReadModeElementType;
                                                          +
                                                          417
                                                          +
                                                          418 #ifndef Weight_On_SplineBySpline_Basis
                                                          +
                                                          419 //KS: Keep track how much splines each event has
                                                          +
                                                          420 cudaMemcpy(gpu_nParamPerEvent, cpu_nParamPerEvent.data(), 2*n_events*sizeof(unsigned int), cudaMemcpyHostToDevice);
                                                          +
                                                          421 CudaCheckError();
                                                          +
                                                          422
                                                          +
                                                          423 //KS: Bind our texture with the GPU variable
                                                          +
                                                          424 // create a resource descriptor based on device pointers
                                                          +
                                                          425 struct cudaResourceDesc resDesc_nParamPerEvent;
                                                          +
                                                          426 memset(&resDesc_nParamPerEvent, 0, sizeof(resDesc_nParamPerEvent));
                                                          +
                                                          427 resDesc_nParamPerEvent.resType = cudaResourceTypeLinear;
                                                          +
                                                          428 resDesc_nParamPerEvent.res.linear.devPtr = gpu_nParamPerEvent;
                                                          +
                                                          429 resDesc_nParamPerEvent.res.linear.desc = cudaCreateChannelDesc<float>();
                                                          +
                                                          430 resDesc_nParamPerEvent.res.linear.sizeInBytes = 2*n_events*sizeof(unsigned int);
                                                          431
                                                          -
                                                          432 //Lastly create texture object
                                                          -
                                                          433 cudaCreateTextureObject(&text_nParamPerEvent, &resDesc_nParamPerEvent, &texDesc_nParamPerEvent, NULL);
                                                          -
                                                          434 CudaCheckError();
                                                          -
                                                          435 #endif
                                                          -
                                                          436}
                                                          +
                                                          432 // Specify texture object parameters
                                                          +
                                                          433 struct cudaTextureDesc texDesc_nParamPerEvent;
                                                          +
                                                          434 memset(&texDesc_nParamPerEvent, 0, sizeof(texDesc_nParamPerEvent));
                                                          +
                                                          435 texDesc_nParamPerEvent.readMode = cudaReadModeElementType;
                                                          +
                                                          436
                                                          +
                                                          437 //Lastly create texture object
                                                          +
                                                          438 cudaCreateTextureObject(&text_nParamPerEvent, &resDesc_nParamPerEvent, &texDesc_nParamPerEvent, NULL);
                                                          +
                                                          439 CudaCheckError();
                                                          +
                                                          440 #endif
                                                          +
                                                          441}

                                                          @@ -783,59 +795,61 @@

                                                          -

                                                          Definition at line 451 of file gpuSplineUtils.cu.

                                                          -
                                                          456 {
                                                          -
                                                          457//*********************************************************
                                                          -
                                                          458
                                                          -
                                                          459 // points per spline is the offset to skip in the index to move between splines
                                                          -
                                                          460 const unsigned int splineNum = (blockIdx.x * blockDim.x + threadIdx.x);
                                                          +

                                                          Evaluate the spline on the GPU Using one {y,b,c,d} array and one {x} array Should be most efficient at cache hitting and memory coalescence But using spline segments rather than the parameter value: avoids doing binary search on GPU.

                                                          + +

                                                          Definition at line 454 of file gpuSplineUtils.cu.

                                                          +
                                                          459 {
                                                          +
                                                          460//*********************************************************
                                                          461
                                                          -
                                                          462 // Note, the new arrays are arranged as:
                                                          -
                                                          463 // gpu_paramNo_arr has length = spln_counter (keeps track of which parameter we're using on this thread)
                                                          -
                                                          464 // gpu_nKnots_arrhas length = spln_counter (keeps track where current spline starts)
                                                          -
                                                          465 // text_coeff_x has length = n_params * spline_size
                                                          -
                                                          466 // gpu_coeff_many has length = nKnots * 4
                                                          -
                                                          467 // ...
                                                          -
                                                          468 // gpu_weights has length = spln_counter * spline_size
                                                          -
                                                          469
                                                          -
                                                          470 // this is the stopping condition!
                                                          -
                                                          471 if (splineNum < d_n_splines) {
                                                          -
                                                          472 // This is the segment we want for this parameter variation
                                                          -
                                                          473 // for this particular splineNum; 0 = MACCQE, 1 = pFC, 2 = EBC, etc
                                                          -
                                                          474
                                                          -
                                                          475 //CW: Which Parameter we are accesing
                                                          -
                                                          476 const short int Param = gpu_paramNo_arr[splineNum];
                                                          +
                                                          462 // points per spline is the offset to skip in the index to move between splines
                                                          +
                                                          463 const unsigned int splineNum = (blockIdx.x * blockDim.x + threadIdx.x);
                                                          +
                                                          464
                                                          +
                                                          465 // Note, the new arrays are arranged as:
                                                          +
                                                          466 // gpu_paramNo_arr has length = spln_counter (keeps track of which parameter we're using on this thread)
                                                          +
                                                          467 // gpu_nKnots_arrhas length = spln_counter (keeps track where current spline starts)
                                                          +
                                                          468 // text_coeff_x has length = n_params * spline_size
                                                          +
                                                          469 // gpu_coeff_many has length = nKnots * 4
                                                          +
                                                          470 // ...
                                                          +
                                                          471 // gpu_weights has length = spln_counter * spline_size
                                                          +
                                                          472
                                                          +
                                                          473 // this is the stopping condition!
                                                          +
                                                          474 if (splineNum < d_n_splines) {
                                                          +
                                                          475 // This is the segment we want for this parameter variation
                                                          +
                                                          476 // for this particular splineNum; 0 = MACCQE, 1 = pFC, 2 = EBC, etc
                                                          477
                                                          -
                                                          478 //CW: Avoids doing costly binary search on GPU
                                                          -
                                                          479 const short int segment = segment_gpu[Param];
                                                          +
                                                          478 //CW: Which Parameter we are accesing
                                                          +
                                                          479 const short int Param = gpu_paramNo_arr[splineNum];
                                                          480
                                                          -
                                                          481 //KS: Segment for coeff_x is simply parameter*max knots + segment as each parmeters has the same spacing
                                                          -
                                                          482 const short int segment_X = Param*d_spline_size+segment;
                                                          +
                                                          481 //CW: Avoids doing costly binary search on GPU
                                                          +
                                                          482 const short int segment = segment_gpu[Param];
                                                          483
                                                          -
                                                          484 //KS: Find knot position in out monolitical structure
                                                          -
                                                          485 const unsigned int CurrentKnotPos = gpu_nKnots_arr[splineNum]*_nCoeff_+segment*_nCoeff_;
                                                          +
                                                          484 //KS: Segment for coeff_x is simply parameter*max knots + segment as each parmeters has the same spacing
                                                          +
                                                          485 const short int segment_X = Param*d_spline_size+segment;
                                                          486
                                                          -
                                                          487 // We've read the segment straight from CPU and is saved in segment_gpu
                                                          -
                                                          488 // polynomial parameters from the monolithic splineMonolith
                                                          -
                                                          489 const float fY = gpu_coeff_many[CurrentKnotPos];
                                                          -
                                                          490 const float fB = gpu_coeff_many[CurrentKnotPos+1];
                                                          -
                                                          491 const float fC = gpu_coeff_many[CurrentKnotPos+2];
                                                          -
                                                          492 const float fD = gpu_coeff_many[CurrentKnotPos+3];
                                                          -
                                                          493 // The is the variation itself (needed to evaluate variation - stored spline point = dx)
                                                          -
                                                          494 const float dx = val_gpu[Param] - tex1Dfetch<float>(text_coeff_x, segment_X);
                                                          -
                                                          495
                                                          -
                                                          496 //CW: Wooow, let's use some fancy intrinsics and pull down the processing time by <1% from normal multiplication! HURRAY
                                                          -
                                                          497 gpu_weights[splineNum] = fmaf(dx, fmaf(dx, fmaf(dx, fD, fC), fB), fY);
                                                          -
                                                          498 // Or for the more "easy to read" version:
                                                          -
                                                          499 //gpu_weights[splineNum] = (fY+dx*(fB+dx*(fC+dx*fD)));
                                                          -
                                                          500
                                                          -
                                                          501#ifdef DEBUG
                                                          -
                                                          502 printf("splineNum = %i/%i, paramNo = %i, variation = %f, segment = %i, fX = %f, fX+1 = %f, dx = %f, d_n_splines = %i, d_spline_size = %i, weight = %f \n", splineNum, d_n_splines, gpu_paramNo_arr[splineNum], val_gpu[Param], segment, tex1Dfetch<float>(text_coeff_x, segment_X), tex1Dfetch<float>(text_coeff_x, segment_X+1), dx, d_n_splines, d_spline_size, gpu_weights[splineNum]);
                                                          -
                                                          503#endif
                                                          -
                                                          504 }
                                                          -
                                                          505}
                                                          -
                                                          segment_gpu
                                                          __device__ __constant__ short int segment_gpu[_N_SPLINES_]
                                                          Definition gpuSplineUtils.cu:80
                                                          -
                                                          val_gpu
                                                          __device__ __constant__ float val_gpu[_N_SPLINES_]
                                                          CW: Constant memory needs to be hard-coded on compile time. Could make this texture memory instead,...
                                                          Definition gpuSplineUtils.cu:79
                                                          +
                                                          487 //KS: Find knot position in out monolitical structure
                                                          +
                                                          488 const unsigned int CurrentKnotPos = gpu_nKnots_arr[splineNum]*_nCoeff_+segment*_nCoeff_;
                                                          +
                                                          489
                                                          +
                                                          490 // We've read the segment straight from CPU and is saved in segment_gpu
                                                          +
                                                          491 // polynomial parameters from the monolithic splineMonolith
                                                          +
                                                          492 const float fY = gpu_coeff_many[CurrentKnotPos];
                                                          +
                                                          493 const float fB = gpu_coeff_many[CurrentKnotPos+1];
                                                          +
                                                          494 const float fC = gpu_coeff_many[CurrentKnotPos+2];
                                                          +
                                                          495 const float fD = gpu_coeff_many[CurrentKnotPos+3];
                                                          +
                                                          496 // The is the variation itself (needed to evaluate variation - stored spline point = dx)
                                                          +
                                                          497 const float dx = val_gpu[Param] - tex1Dfetch<float>(text_coeff_x, segment_X);
                                                          +
                                                          498
                                                          +
                                                          499 //CW: Wooow, let's use some fancy intrinsics and pull down the processing time by <1% from normal multiplication! HURRAY
                                                          +
                                                          500 gpu_weights[splineNum] = fmaf(dx, fmaf(dx, fmaf(dx, fD, fC), fB), fY);
                                                          +
                                                          501 // Or for the more "easy to read" version:
                                                          +
                                                          502 //gpu_weights[splineNum] = (fY+dx*(fB+dx*(fC+dx*fD)));
                                                          +
                                                          503
                                                          +
                                                          504#ifdef DEBUG
                                                          +
                                                          505 printf("splineNum = %i/%i, paramNo = %i, variation = %f, segment = %i, fX = %f, fX+1 = %f, dx = %f, d_n_splines = %i, d_spline_size = %i, weight = %f \n", splineNum, d_n_splines, gpu_paramNo_arr[splineNum], val_gpu[Param], segment, tex1Dfetch<float>(text_coeff_x, segment_X), tex1Dfetch<float>(text_coeff_x, segment_X+1), dx, d_n_splines, d_spline_size, gpu_weights[splineNum]);
                                                          +
                                                          506#endif
                                                          +
                                                          507 }
                                                          +
                                                          508}
                                                          +
                                                          segment_gpu
                                                          __device__ __constant__ short int segment_gpu[_N_SPLINES_]
                                                          Definition gpuSplineUtils.cu:83
                                                          +
                                                          val_gpu
                                                          __device__ __constant__ float val_gpu[_N_SPLINES_]
                                                          CW: Constant memory needs to be hard-coded on compile time. Could make this texture memory instead,...
                                                          Definition gpuSplineUtils.cu:82
                                                          @@ -879,49 +893,49 @@

                                                          Definition at line 509 of file gpuSplineUtils.cu.

                                                          -
                                                          513 {
                                                          -
                                                          514//*********************************************************
                                                          -
                                                          515
                                                          -
                                                          516 // points per spline is the offset to skip in the index to move between splines
                                                          -
                                                          517 const unsigned int splineNum = (blockIdx.x * blockDim.x + threadIdx.x);
                                                          +

                                                          Definition at line 512 of file gpuSplineUtils.cu.

                                                          +
                                                          516 {
                                                          +
                                                          517//*********************************************************
                                                          518
                                                          -
                                                          519 // Note, the new arrays are arranged as:
                                                          -
                                                          520 // gpu_paramNo_arr has length = spln_counter (keeps track of which parameter we're using on this thread)
                                                          -
                                                          521 // gpu_coeff_x has length = n_params * spline_size
                                                          -
                                                          522 // gpu_coeff_many has length = spln_counter * spline_size * 4
                                                          -
                                                          523 // ...
                                                          -
                                                          524 // gpu_weights has length = spln_counter * spline_size
                                                          -
                                                          525
                                                          -
                                                          526 if (splineNum < d_n_splines) {
                                                          -
                                                          527 // The is the variation itself (needed to evaluate variation - stored spline point = dx)
                                                          -
                                                          528 const float x = val_gpu[gpu_paramNo_arr[splineNum]];
                                                          -
                                                          529
                                                          -
                                                          530 // Read the coefficients
                                                          -
                                                          531 const float a = gpu_coeffs[splineNum*d_spline_size];
                                                          -
                                                          532 const float b = gpu_coeffs[splineNum*d_spline_size+1];
                                                          -
                                                          533 const float c = gpu_coeffs[splineNum*d_spline_size+2];
                                                          -
                                                          534 const float d = gpu_coeffs[splineNum*d_spline_size+3];
                                                          -
                                                          535 const float e = gpu_coeffs[splineNum*d_spline_size+4];
                                                          -
                                                          536
                                                          -
                                                          537 // Match these with form in SetSplines
                                                          -
                                                          538 // Might not be great to have this if statement: maybe split two kernels?
                                                          -
                                                          539 if (gpu_nPoints_arr[splineNum] == 5) {
                                                          -
                                                          540 gpu_weights[splineNum] = 1 + a*x + b*x*x + c*x*x*x + d*x*x*x*x + e*x*x*x*x*x;
                                                          -
                                                          541 } else if (gpu_nPoints_arr[splineNum] == 2) {
                                                          -
                                                          542 gpu_weights[splineNum] = (x<=0)*(1+a*x) + (x>0)*(1+b*x);
                                                          -
                                                          543 } else {
                                                          -
                                                          544 printf("Big problems, I found a nPoints array which is not 5 or 2 on GPU!\n");
                                                          -
                                                          545 }
                                                          -
                                                          546
                                                          -
                                                          547#ifdef DEBUG
                                                          -
                                                          548 //if (splineNum < 200) {
                                                          -
                                                          549 if (gpu_nPoints_arr[splineNum] == 2) {
                                                          -
                                                          550 printf("splineNum = %i, spline_size=%i, paramNo = %i, variation = %f, a = %f, b = %f, c = %f, d = %f, e = %f, weight = %f\n", splineNum, d_spline_size, gpu_paramNo_arr[splineNum], x, a, b, c, d, e, gpu_weights[splineNum] );
                                                          -
                                                          551 }
                                                          -
                                                          552#endif
                                                          -
                                                          553 }
                                                          -
                                                          554}
                                                          +
                                                          519 // points per spline is the offset to skip in the index to move between splines
                                                          +
                                                          520 const unsigned int splineNum = (blockIdx.x * blockDim.x + threadIdx.x);
                                                          +
                                                          521
                                                          +
                                                          522 // Note, the new arrays are arranged as:
                                                          +
                                                          523 // gpu_paramNo_arr has length = spln_counter (keeps track of which parameter we're using on this thread)
                                                          +
                                                          524 // gpu_coeff_x has length = n_params * spline_size
                                                          +
                                                          525 // gpu_coeff_many has length = spln_counter * spline_size * 4
                                                          +
                                                          526 // ...
                                                          +
                                                          527 // gpu_weights has length = spln_counter * spline_size
                                                          +
                                                          528
                                                          +
                                                          529 if (splineNum < d_n_splines) {
                                                          +
                                                          530 // The is the variation itself (needed to evaluate variation - stored spline point = dx)
                                                          +
                                                          531 const float x = val_gpu[gpu_paramNo_arr[splineNum]];
                                                          +
                                                          532
                                                          +
                                                          533 // Read the coefficients
                                                          +
                                                          534 const float a = gpu_coeffs[splineNum*d_spline_size];
                                                          +
                                                          535 const float b = gpu_coeffs[splineNum*d_spline_size+1];
                                                          +
                                                          536 const float c = gpu_coeffs[splineNum*d_spline_size+2];
                                                          +
                                                          537 const float d = gpu_coeffs[splineNum*d_spline_size+3];
                                                          +
                                                          538 const float e = gpu_coeffs[splineNum*d_spline_size+4];
                                                          +
                                                          539
                                                          +
                                                          540 // Match these with form in SetSplines
                                                          +
                                                          541 // Might not be great to have this if statement: maybe split two kernels?
                                                          +
                                                          542 if (gpu_nPoints_arr[splineNum] == 5) {
                                                          +
                                                          543 gpu_weights[splineNum] = 1 + a*x + b*x*x + c*x*x*x + d*x*x*x*x + e*x*x*x*x*x;
                                                          +
                                                          544 } else if (gpu_nPoints_arr[splineNum] == 2) {
                                                          +
                                                          545 gpu_weights[splineNum] = (x<=0)*(1+a*x) + (x>0)*(1+b*x);
                                                          +
                                                          546 } else {
                                                          +
                                                          547 printf("Big problems, I found a nPoints array which is not 5 or 2 on GPU!\n");
                                                          +
                                                          548 }
                                                          +
                                                          549
                                                          +
                                                          550#ifdef DEBUG
                                                          +
                                                          551 //if (splineNum < 200) {
                                                          +
                                                          552 if (gpu_nPoints_arr[splineNum] == 2) {
                                                          +
                                                          553 printf("splineNum = %i, spline_size=%i, paramNo = %i, variation = %f, a = %f, b = %f, c = %f, d = %f, e = %f, weight = %f\n", splineNum, d_spline_size, gpu_paramNo_arr[splineNum], x, a, b, c, d, e, gpu_weights[splineNum] );
                                                          +
                                                          554 }
                                                          +
                                                          555#endif
                                                          +
                                                          556 }
                                                          +
                                                          557}
                                                          @@ -959,27 +973,27 @@

                                                          Definition at line 559 of file gpuSplineUtils.cu.

                                                          -
                                                          562 {
                                                          -
                                                          563//*********************************************************
                                                          -
                                                          564 const unsigned int EventNum = (blockIdx.x * blockDim.x + threadIdx.x);
                                                          -
                                                          565 //KS: Accessing shared memory is much much faster than global memory hence we use shared memory for calculation and then write to global memory
                                                          -
                                                          566 __shared__ float shared_total_weights[_BlockSize_];
                                                          -
                                                          567 if(EventNum < d_n_events) //stopping condition
                                                          -
                                                          568 {
                                                          -
                                                          569 shared_total_weights[threadIdx.x] = 1.f;
                                                          -
                                                          570 const unsigned int EventOffset = 2*EventNum;
                                                          -
                                                          571 for (unsigned int id = 0; id < tex1Dfetch<unsigned int>(text_nParamPerEvent, EventOffset); ++id)
                                                          -
                                                          572 {
                                                          -
                                                          573 shared_total_weights[threadIdx.x] *= gpu_weights[tex1Dfetch<unsigned int>(text_nParamPerEvent, EventOffset+1) + id];
                                                          -
                                                          574 #ifdef DEBUG
                                                          -
                                                          575 printf("Event = %i, Spline_Num = %i, gpu_weights = %f \n",
                                                          -
                                                          576 EventNum, tex1Dfetch<unsigned int>(text_nParamPerEvent, 2*EventNum+1) + id, gpu_weights[tex1Dfetch<unsigned int>(text_nParamPerEvent, 2*EventNum+1) + id];
                                                          -
                                                          577 #endif
                                                          -
                                                          578 }
                                                          -
                                                          579 gpu_total_weights[EventNum] = shared_total_weights[threadIdx.x];
                                                          -
                                                          580 }
                                                          -
                                                          581}
                                                          +

                                                          Definition at line 562 of file gpuSplineUtils.cu.

                                                          +
                                                          565 {
                                                          +
                                                          566//*********************************************************
                                                          +
                                                          567 const unsigned int EventNum = (blockIdx.x * blockDim.x + threadIdx.x);
                                                          +
                                                          568 //KS: Accessing shared memory is much much faster than global memory hence we use shared memory for calculation and then write to global memory
                                                          +
                                                          569 __shared__ float shared_total_weights[_BlockSize_];
                                                          +
                                                          570 if(EventNum < d_n_events) //stopping condition
                                                          +
                                                          571 {
                                                          +
                                                          572 shared_total_weights[threadIdx.x] = 1.f;
                                                          +
                                                          573 const unsigned int EventOffset = 2*EventNum;
                                                          +
                                                          574 for (unsigned int id = 0; id < tex1Dfetch<unsigned int>(text_nParamPerEvent, EventOffset); ++id)
                                                          +
                                                          575 {
                                                          +
                                                          576 shared_total_weights[threadIdx.x] *= gpu_weights[tex1Dfetch<unsigned int>(text_nParamPerEvent, EventOffset+1) + id];
                                                          +
                                                          577 #ifdef DEBUG
                                                          +
                                                          578 printf("Event = %i, Spline_Num = %i, gpu_weights = %f \n",
                                                          +
                                                          579 EventNum, tex1Dfetch<unsigned int>(text_nParamPerEvent, 2*EventNum+1) + id, gpu_weights[tex1Dfetch<unsigned int>(text_nParamPerEvent, 2*EventNum+1) + id];
                                                          +
                                                          580 #endif
                                                          +
                                                          581 }
                                                          +
                                                          582 gpu_total_weights[EventNum] = shared_total_weights[threadIdx.x];
                                                          +
                                                          583 }
                                                          +
                                                          584}
                                                          _BlockSize_
                                                          #define _BlockSize_
                                                          KS: Need it for shared memory, there is way to use dynamic shared memory but I am lazy right now.
                                                          Definition gpuUtils.cuh:21
                                                          @@ -1000,14 +1014,15 @@

                                                          -

                                                          Definition at line 226 of file gpuSplineUtils.cu.

                                                          -
                                                          226 {
                                                          -
                                                          227// *******************************************
                                                          -
                                                          228
                                                          -
                                                          229 //KS: Rather than allocate memory in standard way this fancy cuda tool allows to pin host memory which make memory transfer faster
                                                          -
                                                          230 cudaMallocHost((void **) segment, _N_SPLINES_*sizeof(short int));
                                                          -
                                                          231 CudaCheckError();
                                                          -
                                                          232}
                                                          +

                                                          Allocate memory for spline segments.

                                                          + +

                                                          Definition at line 232 of file gpuSplineUtils.cu.

                                                          +
                                                          232 {
                                                          +
                                                          233// *******************************************
                                                          +
                                                          234 //KS: Rather than allocate memory in standard way this fancy cuda tool allows to pin host memory which make memory transfer faster
                                                          +
                                                          235 cudaMallocHost((void **) segment, _N_SPLINES_*sizeof(short int));
                                                          +
                                                          236 CudaCheckError();
                                                          +
                                                          237}
                                                          @@ -1099,49 +1114,49 @@

                                                          Definition at line 106 of file gpuSplineUtils.cu.

                                                          -
                                                          123 {
                                                          -
                                                          124
                                                          -
                                                          125 // Allocate chunks of memory to GPU
                                                          -
                                                          126 cudaMalloc((void **) gpu_paramNo_arr, n_splines*sizeof(short int));
                                                          -
                                                          127 CudaCheckError();
                                                          -
                                                          128
                                                          -
                                                          129 cudaMalloc((void **) gpu_nKnots_arr, n_splines*sizeof(unsigned int));
                                                          -
                                                          130 CudaCheckError();
                                                          -
                                                          131
                                                          -
                                                          132 cudaMalloc((void **) gpu_x_array, Eve_size*sizeof(float));
                                                          +

                                                          Definition at line 112 of file gpuSplineUtils.cu.

                                                          +
                                                          129 {
                                                          +
                                                          130
                                                          +
                                                          131 // Allocate chunks of memory to GPU
                                                          +
                                                          132 cudaMalloc((void **) gpu_paramNo_arr, n_splines*sizeof(short int));
                                                          133 CudaCheckError();
                                                          134
                                                          -
                                                          135 cudaMalloc((void **) gpu_many_array, _nCoeff_*sizeof_array*sizeof(float));
                                                          +
                                                          135 cudaMalloc((void **) gpu_nKnots_arr, n_splines*sizeof(unsigned int));
                                                          136 CudaCheckError();
                                                          137
                                                          -
                                                          138 // Allocate memory for the array of weights to be returned to CPU
                                                          -
                                                          139 cudaMalloc((void **) gpu_weights, n_splines*sizeof(float));
                                                          -
                                                          140 CudaCheckError();
                                                          -
                                                          141#ifndef Weight_On_SplineBySpline_Basis
                                                          -
                                                          142 //KS: Rather than allocate memory in standard way this fancy cuda tool allows to pin host memory which make memory transfer faster
                                                          -
                                                          143 cudaMallocHost((void **) cpu_total_weights, n_events*sizeof(float));
                                                          -
                                                          144 CudaCheckError();
                                                          -
                                                          145
                                                          -
                                                          146 //KS: Allocate memory for the array of total weights to be returned to CPU
                                                          -
                                                          147 cudaMalloc((void **) gpu_total_weights, n_events*sizeof(float));
                                                          -
                                                          148 CudaCheckError();
                                                          -
                                                          149
                                                          -
                                                          150 //KS: Allocate memory for the map keeping track how many splines each parameter has
                                                          -
                                                          151 cudaMalloc((void **) gpu_nParamPerEvent, 2*n_events*sizeof(unsigned int));
                                                          -
                                                          152 CudaCheckError();
                                                          -
                                                          153
                                                          -
                                                          154#endif
                                                          +
                                                          138 cudaMalloc((void **) gpu_x_array, Eve_size*sizeof(float));
                                                          +
                                                          139 CudaCheckError();
                                                          +
                                                          140
                                                          +
                                                          141 cudaMalloc((void **) gpu_many_array, _nCoeff_*sizeof_array*sizeof(float));
                                                          +
                                                          142 CudaCheckError();
                                                          +
                                                          143
                                                          +
                                                          144 // Allocate memory for the array of weights to be returned to CPU
                                                          +
                                                          145 cudaMalloc((void **) gpu_weights, n_splines*sizeof(float));
                                                          +
                                                          146 CudaCheckError();
                                                          +
                                                          147#ifndef Weight_On_SplineBySpline_Basis
                                                          +
                                                          148 //KS: Rather than allocate memory in standard way this fancy cuda tool allows to pin host memory which make memory transfer faster
                                                          +
                                                          149 cudaMallocHost((void **) cpu_total_weights, n_events*sizeof(float));
                                                          +
                                                          150 CudaCheckError();
                                                          +
                                                          151
                                                          +
                                                          152 //KS: Allocate memory for the array of total weights to be returned to CPU
                                                          +
                                                          153 cudaMalloc((void **) gpu_total_weights, n_events*sizeof(float));
                                                          +
                                                          154 CudaCheckError();
                                                          155
                                                          -
                                                          156 // Print allocation info to user
                                                          -
                                                          157 printf(" Allocated %i entries for paramNo and nKnots arrays, size = %f MB\n", n_splines, double(sizeof(short int)*n_splines+sizeof(unsigned int)*n_splines)/1.E6);
                                                          -
                                                          158 printf(" Allocated %i entries for x coeff arrays, size = %f MB\n", Eve_size, double(sizeof(float)*Eve_size)/1.E6);
                                                          -
                                                          159 printf(" Allocated %i entries for {ybcd} coeff arrays, size = %f MB\n", _nCoeff_*sizeof_array, double(sizeof(float)*_nCoeff_*sizeof_array)/1.E6);
                                                          -
                                                          160
                                                          -
                                                          161 //KS: Ask CUDA about memory usage
                                                          -
                                                          162 checkGpuMem();
                                                          -
                                                          163 PrintNdevices();
                                                          -
                                                          164}
                                                          +
                                                          156 //KS: Allocate memory for the map keeping track how many splines each parameter has
                                                          +
                                                          157 cudaMalloc((void **) gpu_nParamPerEvent, 2*n_events*sizeof(unsigned int));
                                                          +
                                                          158 CudaCheckError();
                                                          +
                                                          159
                                                          +
                                                          160#endif
                                                          +
                                                          161
                                                          +
                                                          162 // Print allocation info to user
                                                          +
                                                          163 printf(" Allocated %i entries for paramNo and nKnots arrays, size = %f MB\n", n_splines, double(sizeof(short int)*n_splines+sizeof(unsigned int)*n_splines)/1.E6);
                                                          +
                                                          164 printf(" Allocated %i entries for x coeff arrays, size = %f MB\n", Eve_size, double(sizeof(float)*Eve_size)/1.E6);
                                                          +
                                                          165 printf(" Allocated %i entries for {ybcd} coeff arrays, size = %f MB\n", _nCoeff_*sizeof_array, double(sizeof(float)*_nCoeff_*sizeof_array)/1.E6);
                                                          +
                                                          166
                                                          +
                                                          167 //KS: Ask CUDA about memory usage
                                                          +
                                                          168 checkGpuMem();
                                                          +
                                                          169 PrintNdevices();
                                                          +
                                                          170}
                                                          checkGpuMem
                                                          void checkGpuMem()
                                                          KS: Get some fancy info about VRAM usage.
                                                          Definition gpuUtils.cu:45
                                                          PrintNdevices
                                                          void PrintNdevices()
                                                          KS: Get some fancy info about GPU.
                                                          Definition gpuUtils.cu:63
                                                          @@ -1217,47 +1232,47 @@

                                                          Definition at line 168 of file gpuSplineUtils.cu.

                                                          -
                                                          182 {
                                                          -
                                                          183
                                                          -
                                                          184 // Holds the parameter number
                                                          -
                                                          185 cudaMalloc((void **) gpu_paramNo_arr, n_splines*sizeof(short int));
                                                          -
                                                          186 CudaCheckError();
                                                          -
                                                          187
                                                          -
                                                          188 // Holds the number of points
                                                          -
                                                          189 cudaMalloc((void **) gpu_nPoints_arr, n_splines*sizeof(short int));
                                                          -
                                                          190 CudaCheckError();
                                                          -
                                                          191
                                                          -
                                                          192 // Holds the coefficients (5th order polynomial and constant term == 1) -> 5
                                                          -
                                                          193 cudaMalloc((void **) gpu_coeffs, 5*n_splines*sizeof(float));
                                                          -
                                                          194 CudaCheckError();
                                                          -
                                                          195
                                                          -
                                                          196 // Allocate memory for the array of weights to be returned to CPU
                                                          -
                                                          197 cudaMalloc((void **) gpu_weights, n_splines*sizeof(float));
                                                          -
                                                          198 CudaCheckError();
                                                          -
                                                          199
                                                          -
                                                          200#ifndef Weight_On_SplineBySpline_Basis
                                                          -
                                                          201 //KS: Rather than allocate memory in standard way this fancy cuda tool allows to pin host memory which make memory transfer faster
                                                          -
                                                          202 cudaMallocHost((void **) cpu_total_weights, n_events*sizeof(float));
                                                          -
                                                          203 CudaCheckError();
                                                          -
                                                          204
                                                          -
                                                          205 //KS: Allocate memory for the array of total weights to be returned to CPU
                                                          -
                                                          206 cudaMalloc((void **) gpu_total_weights, n_events*sizeof(float));
                                                          -
                                                          207 CudaCheckError();
                                                          -
                                                          208
                                                          -
                                                          209 //KS: Allocate memory for the map keeping track how many splines each parameter has
                                                          -
                                                          210 cudaMalloc((void **) gpu_nParamPerEvent, 2*n_events*sizeof(unsigned int));
                                                          -
                                                          211 CudaCheckError();
                                                          -
                                                          212#endif
                                                          -
                                                          213
                                                          -
                                                          214 // Print allocation info to user
                                                          -
                                                          215 printf(" Allocated %i entries for paramNo and nPoints arrays, size = %f MB\n", n_splines, double(2.0*sizeof(int)*n_splines)/1.E6);
                                                          -
                                                          216 printf(" Allocated %i entries for coefficient arrays, size = %f MB\n", 5*n_splines, double(sizeof(float)*5*n_splines)/1.E6);
                                                          -
                                                          217
                                                          -
                                                          218 //KS: Ask CUDA about memory usage
                                                          -
                                                          219 checkGpuMem();
                                                          -
                                                          220 PrintNdevices();
                                                          -
                                                          221}
                                                          +

                                                          Definition at line 174 of file gpuSplineUtils.cu.

                                                          +
                                                          188 {
                                                          +
                                                          189
                                                          +
                                                          190 // Holds the parameter number
                                                          +
                                                          191 cudaMalloc((void **) gpu_paramNo_arr, n_splines*sizeof(short int));
                                                          +
                                                          192 CudaCheckError();
                                                          +
                                                          193
                                                          +
                                                          194 // Holds the number of points
                                                          +
                                                          195 cudaMalloc((void **) gpu_nPoints_arr, n_splines*sizeof(short int));
                                                          +
                                                          196 CudaCheckError();
                                                          +
                                                          197
                                                          +
                                                          198 // Holds the coefficients (5th order polynomial and constant term == 1) -> 5
                                                          +
                                                          199 cudaMalloc((void **) gpu_coeffs, 5*n_splines*sizeof(float));
                                                          +
                                                          200 CudaCheckError();
                                                          +
                                                          201
                                                          +
                                                          202 // Allocate memory for the array of weights to be returned to CPU
                                                          +
                                                          203 cudaMalloc((void **) gpu_weights, n_splines*sizeof(float));
                                                          +
                                                          204 CudaCheckError();
                                                          +
                                                          205
                                                          +
                                                          206#ifndef Weight_On_SplineBySpline_Basis
                                                          +
                                                          207 //KS: Rather than allocate memory in standard way this fancy cuda tool allows to pin host memory which make memory transfer faster
                                                          +
                                                          208 cudaMallocHost((void **) cpu_total_weights, n_events*sizeof(float));
                                                          +
                                                          209 CudaCheckError();
                                                          +
                                                          210
                                                          +
                                                          211 //KS: Allocate memory for the array of total weights to be returned to CPU
                                                          +
                                                          212 cudaMalloc((void **) gpu_total_weights, n_events*sizeof(float));
                                                          +
                                                          213 CudaCheckError();
                                                          +
                                                          214
                                                          +
                                                          215 //KS: Allocate memory for the map keeping track how many splines each parameter has
                                                          +
                                                          216 cudaMalloc((void **) gpu_nParamPerEvent, 2*n_events*sizeof(unsigned int));
                                                          +
                                                          217 CudaCheckError();
                                                          +
                                                          218#endif
                                                          +
                                                          219
                                                          +
                                                          220 // Print allocation info to user
                                                          +
                                                          221 printf(" Allocated %i entries for paramNo and nPoints arrays, size = %f MB\n", n_splines, double(2.0*sizeof(int)*n_splines)/1.E6);
                                                          +
                                                          222 printf(" Allocated %i entries for coefficient arrays, size = %f MB\n", 5*n_splines, double(sizeof(float)*5*n_splines)/1.E6);
                                                          +
                                                          223
                                                          +
                                                          224 //KS: Ask CUDA about memory usage
                                                          +
                                                          225 checkGpuMem();
                                                          +
                                                          226 PrintNdevices();
                                                          +
                                                          227}

                                                          @@ -1277,14 +1292,14 @@

                                                          -

                                                          Definition at line 236 of file gpuSplineUtils.cu.

                                                          -
                                                          236 {
                                                          -
                                                          237// *******************************************
                                                          -
                                                          238
                                                          -
                                                          239 //KS: Rather than allocate memory in standard way this fancy cuda tool allows to pin host memory which make memory transfer faster
                                                          -
                                                          240 cudaMallocHost((void **) vals, _N_SPLINES_*sizeof(float));
                                                          -
                                                          241 CudaCheckError();
                                                          -
                                                          242}
                                                          +

                                                          Definition at line 241 of file gpuSplineUtils.cu.

                                                          +
                                                          241 {
                                                          +
                                                          242// *******************************************
                                                          +
                                                          243
                                                          +
                                                          244 //KS: Rather than allocate memory in standard way this fancy cuda tool allows to pin host memory which make memory transfer faster
                                                          +
                                                          245 cudaMallocHost((void **) vals, _N_SPLINES_*sizeof(float));
                                                          +
                                                          246 CudaCheckError();
                                                          +
                                                          247}
                                                          @@ -1356,94 +1371,96 @@

                                                          -

                                                          Definition at line 589 of file gpuSplineUtils.cu.

                                                          -
                                                          606 {
                                                          -
                                                          607// *****************************************
                                                          -
                                                          608
                                                          -
                                                          609 dim3 block_size;
                                                          -
                                                          610 dim3 grid_size;
                                                          -
                                                          611
                                                          -
                                                          612 block_size.x = _BlockSize_;
                                                          -
                                                          613 grid_size.x = (h_n_splines / block_size.x) + 1;
                                                          -
                                                          614
                                                          -
                                                          615 // Copy the segment values to the GPU (segment_gpu), which is h_n_params long
                                                          -
                                                          616 cudaMemcpyToSymbol(segment_gpu, segment, h_n_params*sizeof(short int));
                                                          -
                                                          617 CudaCheckError();
                                                          -
                                                          618
                                                          -
                                                          619 // Copy the parameter values values to the GPU (vals_gpu), which is h_n_params long
                                                          -
                                                          620 cudaMemcpyToSymbol(val_gpu, vals, h_n_params*sizeof(float));
                                                          -
                                                          621 CudaCheckError();
                                                          -
                                                          622
                                                          -
                                                          623#ifdef DEBUG
                                                          -
                                                          624 printf("\n***********************\nGPU DEBUGGING ENABLED\n***********************\n");
                                                          -
                                                          625 printf("block_size.x = %i, grid_size.x = %i \n", block_size.x, grid_size.x);
                                                          -
                                                          626 printf("RunGPU_SepMany segments\n");
                                                          -
                                                          627 for (int i = 0; i < h_n_params; i++) {
                                                          -
                                                          628 printf("val[%i] = %f in segment %i\n", i, vals[i], segment[i]);
                                                          -
                                                          629 }
                                                          -
                                                          630 printf("nParams = %i, n_splines = %i", h_n_params, h_n_splines);
                                                          -
                                                          631 printf("\n***********************\nAM NOW CALLING KERNEL\n***********************\n");
                                                          -
                                                          632#endif
                                                          -
                                                          633
                                                          -
                                                          634 // Set the cache config to prefer L1 for the kernel
                                                          -
                                                          635 //cudaFuncSetCacheConfig(EvalOnGPU_SepMany, cudaFuncCachePreferL1);
                                                          -
                                                          636 EvalOnGPU_SepMany<<<grid_size, block_size>>>(
                                                          -
                                                          637 gpu_paramNo_arr,
                                                          -
                                                          638 gpu_nKnots_arr,
                                                          -
                                                          639
                                                          -
                                                          640 gpu_coeff_many,
                                                          +

                                                          Run the GPU code for the separate many arrays. As in separate {x}, {y,b,c,d} arrays Pass the segment and the parameter values (binary search already performed in samplePDFND::FindSplineSegment()

                                                          + +

                                                          Definition at line 591 of file gpuSplineUtils.cu.

                                                          +
                                                          608 {
                                                          +
                                                          609// *****************************************
                                                          +
                                                          610
                                                          +
                                                          611 dim3 block_size;
                                                          +
                                                          612 dim3 grid_size;
                                                          +
                                                          613
                                                          +
                                                          614 block_size.x = _BlockSize_;
                                                          +
                                                          615 grid_size.x = (h_n_splines / block_size.x) + 1;
                                                          +
                                                          616
                                                          +
                                                          617 // Copy the segment values to the GPU (segment_gpu), which is h_n_params long
                                                          +
                                                          618 cudaMemcpyToSymbol(segment_gpu, segment, h_n_params*sizeof(short int));
                                                          +
                                                          619 CudaCheckError();
                                                          +
                                                          620
                                                          +
                                                          621 // Copy the parameter values values to the GPU (vals_gpu), which is h_n_params long
                                                          +
                                                          622 cudaMemcpyToSymbol(val_gpu, vals, h_n_params*sizeof(float));
                                                          +
                                                          623 CudaCheckError();
                                                          +
                                                          624
                                                          +
                                                          625#ifdef DEBUG
                                                          +
                                                          626 printf("\n***********************\nGPU DEBUGGING ENABLED\n***********************\n");
                                                          +
                                                          627 printf("block_size.x = %i, grid_size.x = %i \n", block_size.x, grid_size.x);
                                                          +
                                                          628 printf("RunGPU_SepMany segments\n");
                                                          +
                                                          629 for (int i = 0; i < h_n_params; i++) {
                                                          +
                                                          630 printf("val[%i] = %f in segment %i\n", i, vals[i], segment[i]);
                                                          +
                                                          631 }
                                                          +
                                                          632 printf("nParams = %i, n_splines = %i", h_n_params, h_n_splines);
                                                          +
                                                          633 printf("\n***********************\nAM NOW CALLING KERNEL\n***********************\n");
                                                          +
                                                          634#endif
                                                          +
                                                          635
                                                          +
                                                          636 // Set the cache config to prefer L1 for the kernel
                                                          +
                                                          637 //cudaFuncSetCacheConfig(EvalOnGPU_SepMany, cudaFuncCachePreferL1);
                                                          +
                                                          638 EvalOnGPU_SepMany<<<grid_size, block_size>>>(
                                                          +
                                                          639 gpu_paramNo_arr,
                                                          +
                                                          640 gpu_nKnots_arr,
                                                          641
                                                          -
                                                          642 gpu_weights,
                                                          -
                                                          643 text_coeff_x
                                                          -
                                                          644 );
                                                          -
                                                          645 CudaCheckError();
                                                          -
                                                          646
                                                          -
                                                          647#ifdef DEBUG
                                                          -
                                                          648 printf("Evaluated kernel with SUCCESS (drink beer)\n");
                                                          -
                                                          649#endif
                                                          -
                                                          650
                                                          -
                                                          651//KS: We can either copy gpu_weight and calculate total weight in reweighting loop, or not copy and calculate total weight stall at GPU, which means less memory transfer
                                                          -
                                                          652#ifdef Weight_On_SplineBySpline_Basis
                                                          -
                                                          653 // Here we have to make a somewhat large GPU->CPU transfer because it's all the splines' response
                                                          -
                                                          654 cudaMemcpy(cpu_weights, gpu_weights, h_n_splines*sizeof(float), cudaMemcpyDeviceToHost);
                                                          -
                                                          655 CudaCheckError();
                                                          -
                                                          656 #ifdef DEBUG
                                                          -
                                                          657 printf("Copied GPU weights to CPU with SUCCESS (drink more beer)\n");
                                                          -
                                                          658 printf("Released calculated response from GPU with SUCCESS (drink most beer)\n");
                                                          -
                                                          659 #endif
                                                          -
                                                          660
                                                          -
                                                          661//KS: Else calculate Total Weight
                                                          -
                                                          662#else
                                                          -
                                                          663 grid_size.x = (h_n_events / block_size.x) + 1;
                                                          -
                                                          664
                                                          -
                                                          665 #ifdef DEBUG
                                                          -
                                                          666 printf("\n***********************\nGPU DEBUGGING ENABLED\n***********************\n");
                                                          -
                                                          667 printf("block_size.x = %i, grid_size.x = %i \n", block_size.x, grid_size.x);
                                                          -
                                                          668 printf("RunGPU_TotWeight\n");
                                                          -
                                                          669
                                                          -
                                                          670 printf("nEvents = %i, n_splines = %i, d_n_params", h_n_events, h_n_splines, h_n_params);
                                                          -
                                                          671 printf("\n***********************\nI AM NOW CALLING KERNEL\n***********************\n");
                                                          -
                                                          672 #endif
                                                          -
                                                          673 EvalOnGPU_TotWeight<<<grid_size, block_size>>>(
                                                          -
                                                          674 gpu_weights,
                                                          -
                                                          675 gpu_total_weights,
                                                          -
                                                          676 text_nParamPerEvent
                                                          -
                                                          677 );
                                                          -
                                                          678 #ifdef DEBUG
                                                          -
                                                          679 CudaCheckError();
                                                          -
                                                          680 printf("Evaluated kernel with SUCCESS (drink tea)\n");
                                                          -
                                                          681 #endif
                                                          -
                                                          682 //KS: Here we have to make a somewhat large GPU->CPU transfer because it is proportional to number of events
                                                          -
                                                          683 //KS: Normally code wait for memory transfer to finish before moving further cudaMemcpyAsync means we will continue to execute code and in a meantime keep copying stuff.
                                                          -
                                                          684 cudaMemcpyAsync(cpu_total_weights, gpu_total_weights, h_n_events * sizeof(float), cudaMemcpyDeviceToHost, 0);
                                                          -
                                                          685
                                                          -
                                                          686 #ifdef DEBUG
                                                          -
                                                          687 CudaCheckError();
                                                          -
                                                          688 printf("Copied GPU total weights to CPU with SUCCESS (drink moar tea)\n");
                                                          -
                                                          689 printf("Released calculated response from GPU with SUCCESS (drink most tea)\n");
                                                          -
                                                          690 #endif
                                                          -
                                                          691#endif
                                                          -
                                                          692}
                                                          +
                                                          642 gpu_coeff_many,
                                                          +
                                                          643
                                                          +
                                                          644 gpu_weights,
                                                          +
                                                          645 text_coeff_x
                                                          +
                                                          646 );
                                                          +
                                                          647 CudaCheckError();
                                                          +
                                                          648
                                                          +
                                                          649#ifdef DEBUG
                                                          +
                                                          650 printf("Evaluated kernel with SUCCESS (drink beer)\n");
                                                          +
                                                          651#endif
                                                          +
                                                          652
                                                          +
                                                          653//KS: We can either copy gpu_weight and calculate total weight in reweighting loop, or not copy and calculate total weight stall at GPU, which means less memory transfer
                                                          +
                                                          654#ifdef Weight_On_SplineBySpline_Basis
                                                          +
                                                          655 // Here we have to make a somewhat large GPU->CPU transfer because it's all the splines' response
                                                          +
                                                          656 cudaMemcpy(cpu_weights, gpu_weights, h_n_splines*sizeof(float), cudaMemcpyDeviceToHost);
                                                          +
                                                          657 CudaCheckError();
                                                          +
                                                          658 #ifdef DEBUG
                                                          +
                                                          659 printf("Copied GPU weights to CPU with SUCCESS (drink more beer)\n");
                                                          +
                                                          660 printf("Released calculated response from GPU with SUCCESS (drink most beer)\n");
                                                          +
                                                          661 #endif
                                                          +
                                                          662
                                                          +
                                                          663//KS: Else calculate Total Weight
                                                          +
                                                          664#else
                                                          +
                                                          665 grid_size.x = (h_n_events / block_size.x) + 1;
                                                          +
                                                          666
                                                          +
                                                          667 #ifdef DEBUG
                                                          +
                                                          668 printf("\n***********************\nGPU DEBUGGING ENABLED\n***********************\n");
                                                          +
                                                          669 printf("block_size.x = %i, grid_size.x = %i \n", block_size.x, grid_size.x);
                                                          +
                                                          670 printf("RunGPU_TotWeight\n");
                                                          +
                                                          671
                                                          +
                                                          672 printf("nEvents = %i, n_splines = %i, d_n_params", h_n_events, h_n_splines, h_n_params);
                                                          +
                                                          673 printf("\n***********************\nI AM NOW CALLING KERNEL\n***********************\n");
                                                          +
                                                          674 #endif
                                                          +
                                                          675 EvalOnGPU_TotWeight<<<grid_size, block_size>>>(
                                                          +
                                                          676 gpu_weights,
                                                          +
                                                          677 gpu_total_weights,
                                                          +
                                                          678 text_nParamPerEvent
                                                          +
                                                          679 );
                                                          +
                                                          680 #ifdef DEBUG
                                                          +
                                                          681 CudaCheckError();
                                                          +
                                                          682 printf("Evaluated kernel with SUCCESS (drink tea)\n");
                                                          +
                                                          683 #endif
                                                          +
                                                          684 //KS: Here we have to make a somewhat large GPU->CPU transfer because it is proportional to number of events
                                                          +
                                                          685 //KS: Normally code wait for memory transfer to finish before moving further cudaMemcpyAsync means we will continue to execute code and in a meantime keep copying stuff.
                                                          +
                                                          686 cudaMemcpyAsync(cpu_total_weights, gpu_total_weights, h_n_events * sizeof(float), cudaMemcpyDeviceToHost, 0);
                                                          +
                                                          687
                                                          +
                                                          688 #ifdef DEBUG
                                                          +
                                                          689 CudaCheckError();
                                                          +
                                                          690 printf("Copied GPU total weights to CPU with SUCCESS (drink moar tea)\n");
                                                          +
                                                          691 printf("Released calculated response from GPU with SUCCESS (drink most tea)\n");
                                                          +
                                                          692 #endif
                                                          +
                                                          693#endif
                                                          +
                                                          694}
                                                          @@ -1511,88 +1528,88 @@

                                                          Definition at line 696 of file gpuSplineUtils.cu.

                                                          -
                                                          711 {
                                                          -
                                                          712// *****************************************
                                                          -
                                                          713
                                                          -
                                                          714 dim3 block_size;
                                                          -
                                                          715 dim3 grid_size;
                                                          -
                                                          716
                                                          -
                                                          717 block_size.x = _BlockSize_;
                                                          -
                                                          718 grid_size.x = (h_n_splines / block_size.x) + 1;
                                                          -
                                                          719
                                                          -
                                                          720 // Copy the parameter values values to the GPU (vals_gpu), which is h_n_params long
                                                          -
                                                          721 cudaMemcpyToSymbol(val_gpu, vals, h_n_params*sizeof(float));
                                                          -
                                                          722 CudaCheckError();
                                                          -
                                                          723
                                                          -
                                                          724#ifdef DEBUG
                                                          -
                                                          725 printf("\n***********************\nGPU DEBUGGING ENABLED\n***********************\n");
                                                          -
                                                          726 printf("block_size.x = %i, grid_size.x = %i \n", block_size.x, grid_size.x);
                                                          -
                                                          727 printf("RunGPU_TF1 segments\n");
                                                          -
                                                          728 for (int i = 0; i < h_n_params; i++) {
                                                          -
                                                          729 printf("val[%i] = %f \n", i, vals[i]);
                                                          -
                                                          730 }
                                                          -
                                                          731 printf("nParams = %i, n_splines = %i", h_n_params, h_n_splines);
                                                          -
                                                          732 printf("\n***********************\nAM NOW CALLING KERNEL\n***********************\n");
                                                          -
                                                          733#endif
                                                          -
                                                          734
                                                          -
                                                          735 // Set the cache config to prefer L1 for the kernel
                                                          -
                                                          736 //cudaFuncSetCacheConfig(EvalOnGPU_TF1, cudaFuncCachePreferL1);
                                                          -
                                                          737 EvalOnGPU_TF1<<<grid_size, block_size>>>(
                                                          -
                                                          738 gpu_coeffs,
                                                          -
                                                          739 gpu_paramNo_arr,
                                                          -
                                                          740 gpu_nPoints_arr,
                                                          -
                                                          741
                                                          -
                                                          742 gpu_weights
                                                          -
                                                          743 );
                                                          -
                                                          744 CudaCheckError();
                                                          -
                                                          745
                                                          -
                                                          746#ifdef DEBUG
                                                          -
                                                          747 printf("Evaluated TF1 kernel with SUCCESS (drink beer)\n");
                                                          -
                                                          748#endif
                                                          -
                                                          749
                                                          -
                                                          750//KS: We can either copy gpu_weight and calculate total weight in reweighting loop, or not copy and calculate total weight stall at GPU, which means less memory transfer
                                                          -
                                                          751#ifdef Weight_On_SplineBySpline_Basis
                                                          -
                                                          752 // Here we have to make a somewhat large GPU->CPU transfer because it's all the splines' response
                                                          -
                                                          753 cudaMemcpy(cpu_weights, gpu_weights, h_n_splines*sizeof(float), cudaMemcpyDeviceToHost);
                                                          -
                                                          754 CudaCheckError();
                                                          -
                                                          755
                                                          -
                                                          756 #ifdef DEBUG
                                                          -
                                                          757 printf("Copied TF1 GPU weights to CPU with SUCCESS (drink moar beer)\n");
                                                          -
                                                          758 printf("Released TF1 calculated response from GPU with SUCCESS (drink most beer)\n");
                                                          -
                                                          759 #endif
                                                          -
                                                          760
                                                          -
                                                          761//KS: Else calculate Total Weight
                                                          -
                                                          762#else
                                                          -
                                                          763 grid_size.x = (h_n_events / block_size.x) + 1;
                                                          -
                                                          764
                                                          -
                                                          765 #ifdef DEBUG
                                                          -
                                                          766 printf("\n***********************\nGPU DEBUGGING ENABLED\n***********************\n");
                                                          -
                                                          767 printf("block_size.x = %i, grid_size.x = %i \n", block_size.x, grid_size.x);
                                                          -
                                                          768 printf("RunGPU_TotWeight\n");
                                                          -
                                                          769
                                                          -
                                                          770 printf("nEvents = %i, n_splines = %i, d_n_params", h_n_events, h_n_splines, h_n_params);
                                                          -
                                                          771 printf("\n***********************\nI AM NOW CALLING KERNEL\n***********************\n");
                                                          -
                                                          772 #endif
                                                          -
                                                          773 EvalOnGPU_TotWeight<<<grid_size, block_size>>>(
                                                          -
                                                          774 gpu_weights,
                                                          -
                                                          775 gpu_total_weights,
                                                          -
                                                          776 text_nParamPerEvent
                                                          -
                                                          777 );
                                                          -
                                                          778 #ifdef DEBUG
                                                          -
                                                          779 CudaCheckError();
                                                          -
                                                          780 printf("Evaluated kernel with SUCCESS (drink tea)\n");
                                                          -
                                                          781 #endif
                                                          -
                                                          782 //KS: Here we have to make a somewhat large GPU->CPU transfer because it is proportional to number of events
                                                          -
                                                          783 //KS: In the future it might be worth to calculate only weight for events which have splines, this should reduce memory transfer
                                                          -
                                                          784 cudaMemcpy(cpu_total_weights, gpu_total_weights, h_n_events*sizeof(float), cudaMemcpyDeviceToHost);
                                                          -
                                                          785 #ifdef DEBUG
                                                          -
                                                          786 CudaCheckError();
                                                          -
                                                          787 printf("Copied GPU total weights to CPU with SUCCESS (drink moar tea)\n");
                                                          -
                                                          788 printf("Released calculated response from GPU with SUCCESS (drink most tea)\n");
                                                          -
                                                          789 #endif
                                                          -
                                                          790#endif
                                                          -
                                                          791}
                                                          +

                                                          Definition at line 698 of file gpuSplineUtils.cu.

                                                          +
                                                          713 {
                                                          +
                                                          714// *****************************************
                                                          +
                                                          715
                                                          +
                                                          716 dim3 block_size;
                                                          +
                                                          717 dim3 grid_size;
                                                          +
                                                          718
                                                          +
                                                          719 block_size.x = _BlockSize_;
                                                          +
                                                          720 grid_size.x = (h_n_splines / block_size.x) + 1;
                                                          +
                                                          721
                                                          +
                                                          722 // Copy the parameter values values to the GPU (vals_gpu), which is h_n_params long
                                                          +
                                                          723 cudaMemcpyToSymbol(val_gpu, vals, h_n_params*sizeof(float));
                                                          +
                                                          724 CudaCheckError();
                                                          +
                                                          725
                                                          +
                                                          726#ifdef DEBUG
                                                          +
                                                          727 printf("\n***********************\nGPU DEBUGGING ENABLED\n***********************\n");
                                                          +
                                                          728 printf("block_size.x = %i, grid_size.x = %i \n", block_size.x, grid_size.x);
                                                          +
                                                          729 printf("RunGPU_TF1 segments\n");
                                                          +
                                                          730 for (int i = 0; i < h_n_params; i++) {
                                                          +
                                                          731 printf("val[%i] = %f \n", i, vals[i]);
                                                          +
                                                          732 }
                                                          +
                                                          733 printf("nParams = %i, n_splines = %i", h_n_params, h_n_splines);
                                                          +
                                                          734 printf("\n***********************\nAM NOW CALLING KERNEL\n***********************\n");
                                                          +
                                                          735#endif
                                                          +
                                                          736
                                                          +
                                                          737 // Set the cache config to prefer L1 for the kernel
                                                          +
                                                          738 //cudaFuncSetCacheConfig(EvalOnGPU_TF1, cudaFuncCachePreferL1);
                                                          +
                                                          739 EvalOnGPU_TF1<<<grid_size, block_size>>>(
                                                          +
                                                          740 gpu_coeffs,
                                                          +
                                                          741 gpu_paramNo_arr,
                                                          +
                                                          742 gpu_nPoints_arr,
                                                          +
                                                          743
                                                          +
                                                          744 gpu_weights
                                                          +
                                                          745 );
                                                          +
                                                          746 CudaCheckError();
                                                          +
                                                          747
                                                          +
                                                          748#ifdef DEBUG
                                                          +
                                                          749 printf("Evaluated TF1 kernel with SUCCESS (drink beer)\n");
                                                          +
                                                          750#endif
                                                          +
                                                          751
                                                          +
                                                          752//KS: We can either copy gpu_weight and calculate total weight in reweighting loop, or not copy and calculate total weight stall at GPU, which means less memory transfer
                                                          +
                                                          753#ifdef Weight_On_SplineBySpline_Basis
                                                          +
                                                          754 // Here we have to make a somewhat large GPU->CPU transfer because it's all the splines' response
                                                          +
                                                          755 cudaMemcpy(cpu_weights, gpu_weights, h_n_splines*sizeof(float), cudaMemcpyDeviceToHost);
                                                          +
                                                          756 CudaCheckError();
                                                          +
                                                          757
                                                          +
                                                          758 #ifdef DEBUG
                                                          +
                                                          759 printf("Copied TF1 GPU weights to CPU with SUCCESS (drink moar beer)\n");
                                                          +
                                                          760 printf("Released TF1 calculated response from GPU with SUCCESS (drink most beer)\n");
                                                          +
                                                          761 #endif
                                                          +
                                                          762
                                                          +
                                                          763//KS: Else calculate Total Weight
                                                          +
                                                          764#else
                                                          +
                                                          765 grid_size.x = (h_n_events / block_size.x) + 1;
                                                          +
                                                          766
                                                          +
                                                          767 #ifdef DEBUG
                                                          +
                                                          768 printf("\n***********************\nGPU DEBUGGING ENABLED\n***********************\n");
                                                          +
                                                          769 printf("block_size.x = %i, grid_size.x = %i \n", block_size.x, grid_size.x);
                                                          +
                                                          770 printf("RunGPU_TotWeight\n");
                                                          +
                                                          771
                                                          +
                                                          772 printf("nEvents = %i, n_splines = %i, d_n_params", h_n_events, h_n_splines, h_n_params);
                                                          +
                                                          773 printf("\n***********************\nI AM NOW CALLING KERNEL\n***********************\n");
                                                          +
                                                          774 #endif
                                                          +
                                                          775 EvalOnGPU_TotWeight<<<grid_size, block_size>>>(
                                                          +
                                                          776 gpu_weights,
                                                          +
                                                          777 gpu_total_weights,
                                                          +
                                                          778 text_nParamPerEvent
                                                          +
                                                          779 );
                                                          +
                                                          780 #ifdef DEBUG
                                                          +
                                                          781 CudaCheckError();
                                                          +
                                                          782 printf("Evaluated kernel with SUCCESS (drink tea)\n");
                                                          +
                                                          783 #endif
                                                          +
                                                          784 //KS: Here we have to make a somewhat large GPU->CPU transfer because it is proportional to number of events
                                                          +
                                                          785 //KS: In the future it might be worth to calculate only weight for events which have splines, this should reduce memory transfer
                                                          +
                                                          786 cudaMemcpy(cpu_total_weights, gpu_total_weights, h_n_events*sizeof(float), cudaMemcpyDeviceToHost);
                                                          +
                                                          787 #ifdef DEBUG
                                                          +
                                                          788 CudaCheckError();
                                                          +
                                                          789 printf("Copied GPU total weights to CPU with SUCCESS (drink moar tea)\n");
                                                          +
                                                          790 printf("Released calculated response from GPU with SUCCESS (drink most tea)\n");
                                                          +
                                                          791 #endif
                                                          +
                                                          792#endif
                                                          +
                                                          793}
                                                          @@ -1613,10 +1630,10 @@

                                                          Definition at line 795 of file gpuSplineUtils.cu.

                                                          -
                                                          795 {
                                                          -
                                                          796 cudaDeviceSynchronize();
                                                          -
                                                          797}
                                                          +

                                                          Definition at line 797 of file gpuSplineUtils.cu.

                                                          +
                                                          797 {
                                                          +
                                                          798 cudaDeviceSynchronize();
                                                          +
                                                          799}
                                                          @@ -1633,7 +1650,9 @@

                                                          -

                                                          Definition at line 76 of file gpuSplineUtils.cu.

                                                          +

                                                          Number of events living on GPU.

                                                          + +

                                                          Definition at line 79 of file gpuSplineUtils.cu.

                                                          @@ -1649,7 +1668,9 @@

                                                          -

                                                          Definition at line 73 of file gpuSplineUtils.cu.

                                                          +

                                                          Number of splines living on GPU.

                                                          + +

                                                          Definition at line 74 of file gpuSplineUtils.cu.

                                                          @@ -1665,7 +1686,9 @@

                                                          -

                                                          Definition at line 74 of file gpuSplineUtils.cu.

                                                          +

                                                          Size of splines living on GPU.

                                                          + +

                                                          Definition at line 76 of file gpuSplineUtils.cu.

                                                          @@ -1689,7 +1712,9 @@

                                                          -

                                                          Definition at line 86 of file gpuSplineUtils.cu.

                                                          +

                                                          Number of events living on CPU.

                                                          + +

                                                          Definition at line 92 of file gpuSplineUtils.cu.

                                                          @@ -1713,7 +1738,9 @@

                                                          -

                                                          Definition at line 84 of file gpuSplineUtils.cu.

                                                          +

                                                          Number of params living on CPU.

                                                          + +

                                                          Definition at line 89 of file gpuSplineUtils.cu.

                                                          @@ -1737,7 +1764,9 @@

                                                          -

                                                          Definition at line 83 of file gpuSplineUtils.cu.

                                                          +

                                                          Number of splines living on CPU.

                                                          + +

                                                          Definition at line 87 of file gpuSplineUtils.cu.

                                                          @@ -1753,7 +1782,7 @@

                                                          -

                                                          Definition at line 80 of file gpuSplineUtils.cu.

                                                          +

                                                          Definition at line 83 of file gpuSplineUtils.cu.

                                                          @@ -1769,7 +1798,9 @@

                                                          -

                                                          Definition at line 93 of file gpuSplineUtils.cu.

                                                          +

                                                          KS: Textures are L1 cache variables which are well optimised for fetching. Make texture only for variables you often access but rarely overwrite. There are limits on texture memory so don't use huge arrays.

                                                          + +

                                                          Definition at line 99 of file gpuSplineUtils.cu.

                                                          @@ -1785,7 +1816,9 @@

                                                          -

                                                          Definition at line 96 of file gpuSplineUtils.cu.

                                                          +

                                                          KS: Map keeping track how many parameters applies to each event, we keep two numbers here {number of splines per event, index where splines start for a given event}.

                                                          + +

                                                          Definition at line 102 of file gpuSplineUtils.cu.

                                                          @@ -1803,7 +1836,7 @@

                                                          Definition at line 79 of file gpuSplineUtils.cu.

                                                          +

                                                          Definition at line 82 of file gpuSplineUtils.cu.

                                                          diff --git a/gpuSplineUtils_8cu_source.html b/gpuSplineUtils_8cu_source.html index e695b2804..5e3c7a1d2 100644 --- a/gpuSplineUtils_8cu_source.html +++ b/gpuSplineUtils_8cu_source.html @@ -94,9 +94,6 @@
                                                          9#include "manager/gpuUtils.cuh"
                                                          10#include "splines/SplineCommon.h"
                                                          11
                                                          -
                                                          12// Hard code the number of splines
                                                          -
                                                          13// Not entirely necessary: only used for val_gpu and segment_gpu being device constants. Could move them to not being device constants
                                                          -
                                                          14// EM: for OA2022:
                                                          15#ifdef NSPLINES_ND280
                                                          16#pragma message("using User Specified N splines")
                                                          17#define _N_SPLINES_ NSPLINES_ND280
                                                          @@ -155,856 +152,843 @@
                                                          70// ******************************************
                                                          71
                                                          72// d_NAME declares DEVICE constants (live on GPU)
                                                          -
                                                          73__device__ __constant__ unsigned int d_n_splines;
                                                          -
                                                          74__device__ __constant__ short int d_spline_size;
                                                          -
                                                          75#ifndef Weight_On_SplineBySpline_Basis
                                                          -
                                                          76__device__ __constant__ int d_n_events;
                                                          -
                                                          77#endif
                                                          -
                                                          79__device__ __constant__ float val_gpu[_N_SPLINES_];
                                                          -
                                                          80__device__ __constant__ short int segment_gpu[_N_SPLINES_];
                                                          -
                                                          81
                                                          -
                                                          82// h_NAME declares HOST constants (live on CPU)
                                                          -
                                                          83static short int h_spline_size = -1;
                                                          -
                                                          84static int h_n_params = -1;
                                                          -
                                                          85#ifndef Weight_On_SplineBySpline_Basis
                                                          -
                                                          86static int h_n_events = -1;
                                                          -
                                                          87#endif
                                                          -
                                                          88
                                                          -
                                                          89// ******************************************
                                                          -
                                                          90// TEXTURES
                                                          -
                                                          91// ******************************************
                                                          -
                                                          92//KS: Textures are L1 cache variables which are well optimised for fetching. Make texture only for variables you often access but rarely overwrite. There are limits on texture memory so don't use huge arrays
                                                          -
                                                          93cudaTextureObject_t text_coeff_x = 0;
                                                          -
                                                          94#ifndef Weight_On_SplineBySpline_Basis
                                                          -
                                                          95//KS: Map keeping track how many parameters applies to each event, we keep two numbers here {number of splines per event, index where splines start for a given event}
                                                          -
                                                          96cudaTextureObject_t text_nParamPerEvent = 0;
                                                          -
                                                          97#endif
                                                          -
                                                          98
                                                          -
                                                          99
                                                          -
                                                          100// *******************************************
                                                          -
                                                          101// INITIALISE GPU
                                                          -
                                                          102// *******************************************
                                                          -
                                                          103
                                                          -
                                                          104// *******************************************
                                                          -
                                                          -
                                                          106__host__ void InitGPU_SepMany(
                                                          -
                                                          107// *******************************************
                                                          -
                                                          108 float **gpu_x_array,
                                                          -
                                                          109 float **gpu_many_array,
                                                          -
                                                          110 float **gpu_weights,
                                                          -
                                                          111
                                                          -
                                                          112 short int** gpu_paramNo_arr,
                                                          -
                                                          113 unsigned int** gpu_nKnots_arr,
                                                          -
                                                          114
                                                          -
                                                          115 #ifndef Weight_On_SplineBySpline_Basis
                                                          -
                                                          116 float **cpu_total_weights,
                                                          -
                                                          117 float **gpu_total_weights,
                                                          -
                                                          118 int n_events,
                                                          -
                                                          119 unsigned int** gpu_nParamPerEvent,
                                                          -
                                                          120 #endif
                                                          -
                                                          121 unsigned int sizeof_array,
                                                          -
                                                          122 unsigned int n_splines,
                                                          -
                                                          123 int Eve_size) {
                                                          -
                                                          124
                                                          -
                                                          125 // Allocate chunks of memory to GPU
                                                          -
                                                          126 cudaMalloc((void **) gpu_paramNo_arr, n_splines*sizeof(short int));
                                                          -
                                                          127 CudaCheckError();
                                                          -
                                                          128
                                                          -
                                                          129 cudaMalloc((void **) gpu_nKnots_arr, n_splines*sizeof(unsigned int));
                                                          -
                                                          130 CudaCheckError();
                                                          -
                                                          131
                                                          -
                                                          132 cudaMalloc((void **) gpu_x_array, Eve_size*sizeof(float));
                                                          +
                                                          74__device__ __constant__ unsigned int d_n_splines;
                                                          +
                                                          76__device__ __constant__ short int d_spline_size;
                                                          +
                                                          77#ifndef Weight_On_SplineBySpline_Basis
                                                          +
                                                          79__device__ __constant__ int d_n_events;
                                                          +
                                                          80#endif
                                                          +
                                                          82__device__ __constant__ float val_gpu[_N_SPLINES_];
                                                          +
                                                          83__device__ __constant__ short int segment_gpu[_N_SPLINES_];
                                                          +
                                                          84
                                                          +
                                                          85// h_NAME declares HOST constants (live on CPU)
                                                          +
                                                          87static short int h_spline_size = -1;
                                                          +
                                                          89static int h_n_params = -1;
                                                          +
                                                          90#ifndef Weight_On_SplineBySpline_Basis
                                                          +
                                                          92static int h_n_events = -1;
                                                          +
                                                          93#endif
                                                          +
                                                          94
                                                          +
                                                          95// ******************************************
                                                          +
                                                          96// TEXTURES
                                                          +
                                                          97// ******************************************
                                                          +
                                                          99cudaTextureObject_t text_coeff_x = 0;
                                                          +
                                                          100#ifndef Weight_On_SplineBySpline_Basis
                                                          +
                                                          102cudaTextureObject_t text_nParamPerEvent = 0;
                                                          +
                                                          103#endif
                                                          +
                                                          104
                                                          +
                                                          105
                                                          +
                                                          106// *******************************************
                                                          +
                                                          107// INITIALISE GPU
                                                          +
                                                          108// *******************************************
                                                          +
                                                          109
                                                          +
                                                          110// *******************************************
                                                          +
                                                          +
                                                          112__host__ void InitGPU_SepMany(
                                                          +
                                                          113// *******************************************
                                                          +
                                                          114 float **gpu_x_array,
                                                          +
                                                          115 float **gpu_many_array,
                                                          +
                                                          116 float **gpu_weights,
                                                          +
                                                          117
                                                          +
                                                          118 short int** gpu_paramNo_arr,
                                                          +
                                                          119 unsigned int** gpu_nKnots_arr,
                                                          +
                                                          120
                                                          +
                                                          121 #ifndef Weight_On_SplineBySpline_Basis
                                                          +
                                                          122 float **cpu_total_weights,
                                                          +
                                                          123 float **gpu_total_weights,
                                                          +
                                                          124 int n_events,
                                                          +
                                                          125 unsigned int** gpu_nParamPerEvent,
                                                          +
                                                          126 #endif
                                                          +
                                                          127 unsigned int sizeof_array,
                                                          +
                                                          128 unsigned int n_splines,
                                                          +
                                                          129 int Eve_size) {
                                                          +
                                                          130
                                                          +
                                                          131 // Allocate chunks of memory to GPU
                                                          +
                                                          132 cudaMalloc((void **) gpu_paramNo_arr, n_splines*sizeof(short int));
                                                          133 CudaCheckError();
                                                          134
                                                          -
                                                          135 cudaMalloc((void **) gpu_many_array, _nCoeff_*sizeof_array*sizeof(float));
                                                          +
                                                          135 cudaMalloc((void **) gpu_nKnots_arr, n_splines*sizeof(unsigned int));
                                                          136 CudaCheckError();
                                                          137
                                                          -
                                                          138 // Allocate memory for the array of weights to be returned to CPU
                                                          -
                                                          139 cudaMalloc((void **) gpu_weights, n_splines*sizeof(float));
                                                          -
                                                          140 CudaCheckError();
                                                          -
                                                          141#ifndef Weight_On_SplineBySpline_Basis
                                                          -
                                                          142 //KS: Rather than allocate memory in standard way this fancy cuda tool allows to pin host memory which make memory transfer faster
                                                          -
                                                          143 cudaMallocHost((void **) cpu_total_weights, n_events*sizeof(float));
                                                          -
                                                          144 CudaCheckError();
                                                          -
                                                          145
                                                          -
                                                          146 //KS: Allocate memory for the array of total weights to be returned to CPU
                                                          -
                                                          147 cudaMalloc((void **) gpu_total_weights, n_events*sizeof(float));
                                                          -
                                                          148 CudaCheckError();
                                                          -
                                                          149
                                                          -
                                                          150 //KS: Allocate memory for the map keeping track how many splines each parameter has
                                                          -
                                                          151 cudaMalloc((void **) gpu_nParamPerEvent, 2*n_events*sizeof(unsigned int));
                                                          -
                                                          152 CudaCheckError();
                                                          -
                                                          153
                                                          -
                                                          154#endif
                                                          +
                                                          138 cudaMalloc((void **) gpu_x_array, Eve_size*sizeof(float));
                                                          +
                                                          139 CudaCheckError();
                                                          +
                                                          140
                                                          +
                                                          141 cudaMalloc((void **) gpu_many_array, _nCoeff_*sizeof_array*sizeof(float));
                                                          +
                                                          142 CudaCheckError();
                                                          +
                                                          143
                                                          +
                                                          144 // Allocate memory for the array of weights to be returned to CPU
                                                          +
                                                          145 cudaMalloc((void **) gpu_weights, n_splines*sizeof(float));
                                                          +
                                                          146 CudaCheckError();
                                                          +
                                                          147#ifndef Weight_On_SplineBySpline_Basis
                                                          +
                                                          148 //KS: Rather than allocate memory in standard way this fancy cuda tool allows to pin host memory which make memory transfer faster
                                                          +
                                                          149 cudaMallocHost((void **) cpu_total_weights, n_events*sizeof(float));
                                                          +
                                                          150 CudaCheckError();
                                                          +
                                                          151
                                                          +
                                                          152 //KS: Allocate memory for the array of total weights to be returned to CPU
                                                          +
                                                          153 cudaMalloc((void **) gpu_total_weights, n_events*sizeof(float));
                                                          +
                                                          154 CudaCheckError();
                                                          155
                                                          -
                                                          156 // Print allocation info to user
                                                          -
                                                          157 printf(" Allocated %i entries for paramNo and nKnots arrays, size = %f MB\n", n_splines, double(sizeof(short int)*n_splines+sizeof(unsigned int)*n_splines)/1.E6);
                                                          -
                                                          158 printf(" Allocated %i entries for x coeff arrays, size = %f MB\n", Eve_size, double(sizeof(float)*Eve_size)/1.E6);
                                                          -
                                                          159 printf(" Allocated %i entries for {ybcd} coeff arrays, size = %f MB\n", _nCoeff_*sizeof_array, double(sizeof(float)*_nCoeff_*sizeof_array)/1.E6);
                                                          -
                                                          160
                                                          -
                                                          161 //KS: Ask CUDA about memory usage
                                                          -
                                                          162 checkGpuMem();
                                                          -
                                                          163 PrintNdevices();
                                                          -
                                                          164}
                                                          +
                                                          156 //KS: Allocate memory for the map keeping track how many splines each parameter has
                                                          +
                                                          157 cudaMalloc((void **) gpu_nParamPerEvent, 2*n_events*sizeof(unsigned int));
                                                          +
                                                          158 CudaCheckError();
                                                          +
                                                          159
                                                          +
                                                          160#endif
                                                          +
                                                          161
                                                          +
                                                          162 // Print allocation info to user
                                                          +
                                                          163 printf(" Allocated %i entries for paramNo and nKnots arrays, size = %f MB\n", n_splines, double(sizeof(short int)*n_splines+sizeof(unsigned int)*n_splines)/1.E6);
                                                          +
                                                          164 printf(" Allocated %i entries for x coeff arrays, size = %f MB\n", Eve_size, double(sizeof(float)*Eve_size)/1.E6);
                                                          +
                                                          165 printf(" Allocated %i entries for {ybcd} coeff arrays, size = %f MB\n", _nCoeff_*sizeof_array, double(sizeof(float)*_nCoeff_*sizeof_array)/1.E6);
                                                          +
                                                          166
                                                          +
                                                          167 //KS: Ask CUDA about memory usage
                                                          +
                                                          168 checkGpuMem();
                                                          +
                                                          169 PrintNdevices();
                                                          +
                                                          170}
                                                          -
                                                          165
                                                          -
                                                          166// *******************************************
                                                          -
                                                          -
                                                          168__host__ void InitGPU_TF1(
                                                          -
                                                          169// *******************************************
                                                          -
                                                          170 float **gpu_coeffs,
                                                          -
                                                          171 short int** gpu_paramNo_arr,
                                                          -
                                                          172 short int** gpu_nPoints_arr,
                                                          -
                                                          173 float **gpu_weights,
                                                          -
                                                          174
                                                          -
                                                          175 #ifndef Weight_On_SplineBySpline_Basis
                                                          -
                                                          176 float **cpu_total_weights,
                                                          -
                                                          177 float **gpu_total_weights,
                                                          -
                                                          178 int n_events,
                                                          -
                                                          179
                                                          -
                                                          180 unsigned int** gpu_nParamPerEvent,
                                                          -
                                                          181 #endif
                                                          -
                                                          182 unsigned int n_splines) {
                                                          -
                                                          183
                                                          -
                                                          184 // Holds the parameter number
                                                          -
                                                          185 cudaMalloc((void **) gpu_paramNo_arr, n_splines*sizeof(short int));
                                                          -
                                                          186 CudaCheckError();
                                                          -
                                                          187
                                                          -
                                                          188 // Holds the number of points
                                                          -
                                                          189 cudaMalloc((void **) gpu_nPoints_arr, n_splines*sizeof(short int));
                                                          -
                                                          190 CudaCheckError();
                                                          -
                                                          191
                                                          -
                                                          192 // Holds the coefficients (5th order polynomial and constant term == 1) -> 5
                                                          -
                                                          193 cudaMalloc((void **) gpu_coeffs, 5*n_splines*sizeof(float));
                                                          -
                                                          194 CudaCheckError();
                                                          -
                                                          195
                                                          -
                                                          196 // Allocate memory for the array of weights to be returned to CPU
                                                          -
                                                          197 cudaMalloc((void **) gpu_weights, n_splines*sizeof(float));
                                                          -
                                                          198 CudaCheckError();
                                                          -
                                                          199
                                                          -
                                                          200#ifndef Weight_On_SplineBySpline_Basis
                                                          -
                                                          201 //KS: Rather than allocate memory in standard way this fancy cuda tool allows to pin host memory which make memory transfer faster
                                                          -
                                                          202 cudaMallocHost((void **) cpu_total_weights, n_events*sizeof(float));
                                                          -
                                                          203 CudaCheckError();
                                                          -
                                                          204
                                                          -
                                                          205 //KS: Allocate memory for the array of total weights to be returned to CPU
                                                          -
                                                          206 cudaMalloc((void **) gpu_total_weights, n_events*sizeof(float));
                                                          -
                                                          207 CudaCheckError();
                                                          -
                                                          208
                                                          -
                                                          209 //KS: Allocate memory for the map keeping track how many splines each parameter has
                                                          -
                                                          210 cudaMalloc((void **) gpu_nParamPerEvent, 2*n_events*sizeof(unsigned int));
                                                          -
                                                          211 CudaCheckError();
                                                          -
                                                          212#endif
                                                          -
                                                          213
                                                          -
                                                          214 // Print allocation info to user
                                                          -
                                                          215 printf(" Allocated %i entries for paramNo and nPoints arrays, size = %f MB\n", n_splines, double(2.0*sizeof(int)*n_splines)/1.E6);
                                                          -
                                                          216 printf(" Allocated %i entries for coefficient arrays, size = %f MB\n", 5*n_splines, double(sizeof(float)*5*n_splines)/1.E6);
                                                          -
                                                          217
                                                          -
                                                          218 //KS: Ask CUDA about memory usage
                                                          -
                                                          219 checkGpuMem();
                                                          -
                                                          220 PrintNdevices();
                                                          -
                                                          221}
                                                          -
                                                          -
                                                          222
                                                          +
                                                          171
                                                          +
                                                          172// *******************************************
                                                          +
                                                          +
                                                          174__host__ void InitGPU_TF1(
                                                          +
                                                          175// *******************************************
                                                          +
                                                          176 float **gpu_coeffs,
                                                          +
                                                          177 short int** gpu_paramNo_arr,
                                                          +
                                                          178 short int** gpu_nPoints_arr,
                                                          +
                                                          179 float **gpu_weights,
                                                          +
                                                          180
                                                          +
                                                          181 #ifndef Weight_On_SplineBySpline_Basis
                                                          +
                                                          182 float **cpu_total_weights,
                                                          +
                                                          183 float **gpu_total_weights,
                                                          +
                                                          184 int n_events,
                                                          +
                                                          185
                                                          +
                                                          186 unsigned int** gpu_nParamPerEvent,
                                                          +
                                                          187 #endif
                                                          +
                                                          188 unsigned int n_splines) {
                                                          +
                                                          189
                                                          +
                                                          190 // Holds the parameter number
                                                          +
                                                          191 cudaMalloc((void **) gpu_paramNo_arr, n_splines*sizeof(short int));
                                                          +
                                                          192 CudaCheckError();
                                                          +
                                                          193
                                                          +
                                                          194 // Holds the number of points
                                                          +
                                                          195 cudaMalloc((void **) gpu_nPoints_arr, n_splines*sizeof(short int));
                                                          +
                                                          196 CudaCheckError();
                                                          +
                                                          197
                                                          +
                                                          198 // Holds the coefficients (5th order polynomial and constant term == 1) -> 5
                                                          +
                                                          199 cudaMalloc((void **) gpu_coeffs, 5*n_splines*sizeof(float));
                                                          +
                                                          200 CudaCheckError();
                                                          +
                                                          201
                                                          +
                                                          202 // Allocate memory for the array of weights to be returned to CPU
                                                          +
                                                          203 cudaMalloc((void **) gpu_weights, n_splines*sizeof(float));
                                                          +
                                                          204 CudaCheckError();
                                                          +
                                                          205
                                                          +
                                                          206#ifndef Weight_On_SplineBySpline_Basis
                                                          +
                                                          207 //KS: Rather than allocate memory in standard way this fancy cuda tool allows to pin host memory which make memory transfer faster
                                                          +
                                                          208 cudaMallocHost((void **) cpu_total_weights, n_events*sizeof(float));
                                                          +
                                                          209 CudaCheckError();
                                                          +
                                                          210
                                                          +
                                                          211 //KS: Allocate memory for the array of total weights to be returned to CPU
                                                          +
                                                          212 cudaMalloc((void **) gpu_total_weights, n_events*sizeof(float));
                                                          +
                                                          213 CudaCheckError();
                                                          +
                                                          214
                                                          +
                                                          215 //KS: Allocate memory for the map keeping track how many splines each parameter has
                                                          +
                                                          216 cudaMalloc((void **) gpu_nParamPerEvent, 2*n_events*sizeof(unsigned int));
                                                          +
                                                          217 CudaCheckError();
                                                          +
                                                          218#endif
                                                          +
                                                          219
                                                          +
                                                          220 // Print allocation info to user
                                                          +
                                                          221 printf(" Allocated %i entries for paramNo and nPoints arrays, size = %f MB\n", n_splines, double(2.0*sizeof(int)*n_splines)/1.E6);
                                                          +
                                                          222 printf(" Allocated %i entries for coefficient arrays, size = %f MB\n", 5*n_splines, double(sizeof(float)*5*n_splines)/1.E6);
                                                          223
                                                          -
                                                          224// *******************************************
                                                          -
                                                          225// Allocate memory for spline segments
                                                          -
                                                          -
                                                          226__host__ void InitGPU_Segments(short int **segment) {
                                                          -
                                                          227// *******************************************
                                                          +
                                                          224 //KS: Ask CUDA about memory usage
                                                          +
                                                          225 checkGpuMem();
                                                          +
                                                          226 PrintNdevices();
                                                          +
                                                          227}
                                                          +
                                                          228
                                                          -
                                                          229 //KS: Rather than allocate memory in standard way this fancy cuda tool allows to pin host memory which make memory transfer faster
                                                          -
                                                          230 cudaMallocHost((void **) segment, _N_SPLINES_*sizeof(short int));
                                                          -
                                                          231 CudaCheckError();
                                                          -
                                                          232}
                                                          +
                                                          229
                                                          +
                                                          230// *******************************************
                                                          +
                                                          +
                                                          232__host__ void InitGPU_Segments(short int **segment) {
                                                          +
                                                          233// *******************************************
                                                          +
                                                          234 //KS: Rather than allocate memory in standard way this fancy cuda tool allows to pin host memory which make memory transfer faster
                                                          +
                                                          235 cudaMallocHost((void **) segment, _N_SPLINES_*sizeof(short int));
                                                          +
                                                          236 CudaCheckError();
                                                          +
                                                          237}
                                                          -
                                                          233
                                                          -
                                                          234// *******************************************
                                                          -
                                                          235// Allocate memory for spline segments
                                                          -
                                                          -
                                                          236__host__ void InitGPU_Vals(float **vals) {
                                                          -
                                                          237// *******************************************
                                                          238
                                                          -
                                                          239 //KS: Rather than allocate memory in standard way this fancy cuda tool allows to pin host memory which make memory transfer faster
                                                          -
                                                          240 cudaMallocHost((void **) vals, _N_SPLINES_*sizeof(float));
                                                          -
                                                          241 CudaCheckError();
                                                          -
                                                          242}
                                                          -
                                                          +
                                                          239// *******************************************
                                                          +
                                                          240// Allocate memory for spline segments
                                                          +
                                                          +
                                                          241__host__ void InitGPU_Vals(float **vals) {
                                                          +
                                                          242// *******************************************
                                                          243
                                                          -
                                                          244
                                                          -
                                                          245// ******************************************************
                                                          -
                                                          246// START COPY TO GPU
                                                          -
                                                          247// ******************************************************
                                                          +
                                                          244 //KS: Rather than allocate memory in standard way this fancy cuda tool allows to pin host memory which make memory transfer faster
                                                          +
                                                          245 cudaMallocHost((void **) vals, _N_SPLINES_*sizeof(float));
                                                          +
                                                          246 CudaCheckError();
                                                          +
                                                          247}
                                                          +
                                                          248
                                                          -
                                                          249// ******************************************************
                                                          -
                                                          -
                                                          251__host__ void CopyToGPU_SepMany(
                                                          +
                                                          249
                                                          +
                                                          250// ******************************************************
                                                          +
                                                          251// START COPY TO GPU
                                                          252// ******************************************************
                                                          -
                                                          253 short int *gpu_paramNo_arr,
                                                          -
                                                          254 unsigned int *gpu_nKnots_arr,
                                                          -
                                                          255 float *gpu_x_array,
                                                          -
                                                          256 float *gpu_many_array,
                                                          -
                                                          257
                                                          -
                                                          258 std::vector<short int> paramNo_arr,
                                                          -
                                                          259 std::vector<unsigned int> nKnots_arr,
                                                          -
                                                          260 std::vector<float> cpu_x_array,
                                                          -
                                                          261 std::vector<float> cpu_many_array,
                                                          +
                                                          253
                                                          +
                                                          254// ******************************************************
                                                          +
                                                          +
                                                          256__host__ void CopyToGPU_SepMany(
                                                          +
                                                          257// ******************************************************
                                                          +
                                                          258 short int *gpu_paramNo_arr,
                                                          +
                                                          259 unsigned int *gpu_nKnots_arr,
                                                          +
                                                          260 float *gpu_x_array,
                                                          +
                                                          261 float *gpu_many_array,
                                                          262
                                                          -
                                                          263 #ifndef Weight_On_SplineBySpline_Basis
                                                          -
                                                          264 int n_events,
                                                          -
                                                          265 std::vector<unsigned int> cpu_nParamPerEvent,
                                                          -
                                                          266 unsigned int *gpu_nParamPerEvent,
                                                          -
                                                          267 #endif
                                                          -
                                                          268 int n_params,
                                                          -
                                                          269 unsigned int n_splines,
                                                          -
                                                          270 short int spline_size,
                                                          -
                                                          271 unsigned int sizeof_array) {
                                                          -
                                                          272 if (n_params != _N_SPLINES_) {
                                                          -
                                                          273 printf("Number of splines not equal to %i, GPU code for event-by-event splines will fail\n", _N_SPLINES_);
                                                          -
                                                          274 printf("n_params = %i\n", n_params);
                                                          -
                                                          275 printf("%s : %i\n", __FILE__, __LINE__);
                                                          -
                                                          276 exit(-1);
                                                          -
                                                          277 }
                                                          -
                                                          278
                                                          -
                                                          279 // Write to the global statics (h_* denotes host stored variable)
                                                          -
                                                          280 h_n_params = n_params;
                                                          -
                                                          281 h_spline_size = spline_size;
                                                          -
                                                          282#ifndef Weight_On_SplineBySpline_Basis
                                                          -
                                                          283 h_n_events = n_events;
                                                          -
                                                          284#endif
                                                          -
                                                          285 // Copy the constants
                                                          -
                                                          286 // Total number of valid splines for all loaded events
                                                          -
                                                          287 cudaMemcpyToSymbol(d_n_splines, &n_splines, sizeof(n_splines));
                                                          -
                                                          288 CudaCheckError();
                                                          -
                                                          289 // Total spline size per spline; i.e. just the number of points or knots in the spline
                                                          -
                                                          290 cudaMemcpyToSymbol(d_spline_size, &h_spline_size, sizeof(h_spline_size));
                                                          -
                                                          291 CudaCheckError();
                                                          -
                                                          292#ifndef Weight_On_SplineBySpline_Basis
                                                          -
                                                          293 // Number of events
                                                          -
                                                          294 cudaMemcpyToSymbol(d_n_events, &h_n_events, sizeof(h_n_events));
                                                          -
                                                          295 CudaCheckError();
                                                          -
                                                          296#endif
                                                          -
                                                          297 // Copy the coefficient arrays to the GPU; this only happens once per entire Markov Chain so is OK to do multiple extensive memory copies
                                                          -
                                                          298 cudaMemcpy(gpu_many_array, cpu_many_array.data(), sizeof(float)*sizeof_array*_nCoeff_, cudaMemcpyHostToDevice);
                                                          -
                                                          299 CudaCheckError();
                                                          -
                                                          300
                                                          -
                                                          301 cudaMemcpy(gpu_x_array, cpu_x_array.data(), sizeof(float)*spline_size*n_params, cudaMemcpyHostToDevice);
                                                          -
                                                          302 CudaCheckError();
                                                          -
                                                          303
                                                          -
                                                          304 //KS: Bind our texture with the GPU variable
                                                          -
                                                          305 //KS: Tried also moving gpu_many_array to texture memory it only worked with restricted number of MC runs, most likely hit texture memory limit :(
                                                          -
                                                          306 struct cudaResourceDesc resDesc_coeff_x;
                                                          -
                                                          307 memset(&resDesc_coeff_x, 0, sizeof(resDesc_coeff_x));
                                                          -
                                                          308 resDesc_coeff_x.resType = cudaResourceTypeLinear;
                                                          -
                                                          309 resDesc_coeff_x.res.linear.devPtr = gpu_x_array;
                                                          -
                                                          310 resDesc_coeff_x.res.linear.desc = cudaCreateChannelDesc<float>();
                                                          -
                                                          311 resDesc_coeff_x.res.linear.sizeInBytes = sizeof(float)*spline_size*n_params;
                                                          -
                                                          312
                                                          -
                                                          313 // Specify texture object parameters
                                                          -
                                                          314 struct cudaTextureDesc texDesc_coeff_x;
                                                          -
                                                          315 memset(&texDesc_coeff_x, 0, sizeof(texDesc_coeff_x));
                                                          -
                                                          316 texDesc_coeff_x.readMode = cudaReadModeElementType;
                                                          +
                                                          263 std::vector<short int> paramNo_arr,
                                                          +
                                                          264 std::vector<unsigned int> nKnots_arr,
                                                          +
                                                          265 std::vector<float> cpu_x_array,
                                                          +
                                                          266 std::vector<float> cpu_many_array,
                                                          +
                                                          267
                                                          +
                                                          268 #ifndef Weight_On_SplineBySpline_Basis
                                                          +
                                                          269 int n_events,
                                                          +
                                                          270 std::vector<unsigned int> cpu_nParamPerEvent,
                                                          +
                                                          271 unsigned int *gpu_nParamPerEvent,
                                                          +
                                                          272 #endif
                                                          +
                                                          273 int n_params,
                                                          +
                                                          274 unsigned int n_splines,
                                                          +
                                                          275 short int spline_size,
                                                          +
                                                          276 unsigned int sizeof_array) {
                                                          +
                                                          277 if (n_params != _N_SPLINES_) {
                                                          +
                                                          278 printf("Number of splines not equal to %i, GPU code for event-by-event splines will fail\n", _N_SPLINES_);
                                                          +
                                                          279 printf("n_params = %i\n", n_params);
                                                          +
                                                          280 printf("%s : %i\n", __FILE__, __LINE__);
                                                          +
                                                          281 exit(-1);
                                                          +
                                                          282 }
                                                          +
                                                          283
                                                          +
                                                          284 // Write to the global statics (h_* denotes host stored variable)
                                                          +
                                                          285 h_n_params = n_params;
                                                          +
                                                          286 h_spline_size = spline_size;
                                                          +
                                                          287#ifndef Weight_On_SplineBySpline_Basis
                                                          +
                                                          288 h_n_events = n_events;
                                                          +
                                                          289#endif
                                                          +
                                                          290 // Copy the constants
                                                          +
                                                          291 // Total number of valid splines for all loaded events
                                                          +
                                                          292 cudaMemcpyToSymbol(d_n_splines, &n_splines, sizeof(n_splines));
                                                          +
                                                          293 CudaCheckError();
                                                          +
                                                          294 // Total spline size per spline; i.e. just the number of points or knots in the spline
                                                          +
                                                          295 cudaMemcpyToSymbol(d_spline_size, &h_spline_size, sizeof(h_spline_size));
                                                          +
                                                          296 CudaCheckError();
                                                          +
                                                          297#ifndef Weight_On_SplineBySpline_Basis
                                                          +
                                                          298 // Number of events
                                                          +
                                                          299 cudaMemcpyToSymbol(d_n_events, &h_n_events, sizeof(h_n_events));
                                                          +
                                                          300 CudaCheckError();
                                                          +
                                                          301#endif
                                                          +
                                                          302 // Copy the coefficient arrays to the GPU; this only happens once per entire Markov Chain so is OK to do multiple extensive memory copies
                                                          +
                                                          303 cudaMemcpy(gpu_many_array, cpu_many_array.data(), sizeof(float)*sizeof_array*_nCoeff_, cudaMemcpyHostToDevice);
                                                          +
                                                          304 CudaCheckError();
                                                          +
                                                          305
                                                          +
                                                          306 cudaMemcpy(gpu_x_array, cpu_x_array.data(), sizeof(float)*spline_size*n_params, cudaMemcpyHostToDevice);
                                                          +
                                                          307 CudaCheckError();
                                                          +
                                                          308
                                                          +
                                                          309 //KS: Bind our texture with the GPU variable
                                                          +
                                                          310 //KS: Tried also moving gpu_many_array to texture memory it only worked with restricted number of MC runs, most likely hit texture memory limit :(
                                                          +
                                                          311 struct cudaResourceDesc resDesc_coeff_x;
                                                          +
                                                          312 memset(&resDesc_coeff_x, 0, sizeof(resDesc_coeff_x));
                                                          +
                                                          313 resDesc_coeff_x.resType = cudaResourceTypeLinear;
                                                          +
                                                          314 resDesc_coeff_x.res.linear.devPtr = gpu_x_array;
                                                          +
                                                          315 resDesc_coeff_x.res.linear.desc = cudaCreateChannelDesc<float>();
                                                          +
                                                          316 resDesc_coeff_x.res.linear.sizeInBytes = sizeof(float)*spline_size*n_params;
                                                          317
                                                          -
                                                          318 // Create texture object
                                                          -
                                                          319 cudaCreateTextureObject(&text_coeff_x, &resDesc_coeff_x, &texDesc_coeff_x, NULL);
                                                          -
                                                          320 CudaCheckError();
                                                          -
                                                          321
                                                          -
                                                          322 // Also copy the parameter number for each spline onto the GPU; i.e. what spline parameter are we calculating right now
                                                          -
                                                          323 cudaMemcpy(gpu_paramNo_arr, paramNo_arr.data(), n_splines*sizeof(short int), cudaMemcpyHostToDevice);
                                                          -
                                                          324 CudaCheckError();
                                                          -
                                                          325
                                                          -
                                                          326 // Also copy the knot map for each spline onto the GPU;
                                                          -
                                                          327 cudaMemcpy(gpu_nKnots_arr, nKnots_arr.data(), n_splines*sizeof(unsigned int), cudaMemcpyHostToDevice);
                                                          -
                                                          328 CudaCheckError();
                                                          -
                                                          329
                                                          -
                                                          330 #ifndef Weight_On_SplineBySpline_Basis
                                                          -
                                                          331 //KS: Keep track how much splines each event has
                                                          -
                                                          332 cudaMemcpy(gpu_nParamPerEvent, cpu_nParamPerEvent.data(), 2*n_events*sizeof(unsigned int), cudaMemcpyHostToDevice);
                                                          +
                                                          318 // Specify texture object parameters
                                                          +
                                                          319 struct cudaTextureDesc texDesc_coeff_x;
                                                          +
                                                          320 memset(&texDesc_coeff_x, 0, sizeof(texDesc_coeff_x));
                                                          +
                                                          321 texDesc_coeff_x.readMode = cudaReadModeElementType;
                                                          +
                                                          322
                                                          +
                                                          323 // Create texture object
                                                          +
                                                          324 cudaCreateTextureObject(&text_coeff_x, &resDesc_coeff_x, &texDesc_coeff_x, NULL);
                                                          +
                                                          325 CudaCheckError();
                                                          +
                                                          326
                                                          +
                                                          327 // Also copy the parameter number for each spline onto the GPU; i.e. what spline parameter are we calculating right now
                                                          +
                                                          328 cudaMemcpy(gpu_paramNo_arr, paramNo_arr.data(), n_splines*sizeof(short int), cudaMemcpyHostToDevice);
                                                          +
                                                          329 CudaCheckError();
                                                          +
                                                          330
                                                          +
                                                          331 // Also copy the knot map for each spline onto the GPU;
                                                          +
                                                          332 cudaMemcpy(gpu_nKnots_arr, nKnots_arr.data(), n_splines*sizeof(unsigned int), cudaMemcpyHostToDevice);
                                                          333 CudaCheckError();
                                                          -
                                                          334
                                                          -
                                                          335 //KS: Bind our texture with the GPU variable
                                                          -
                                                          336 // create a resource descriptor based on device pointers
                                                          -
                                                          337 struct cudaResourceDesc resDesc_nParamPerEvent;
                                                          -
                                                          338 memset(&resDesc_nParamPerEvent, 0, sizeof(resDesc_nParamPerEvent));
                                                          -
                                                          339 resDesc_nParamPerEvent.resType = cudaResourceTypeLinear;
                                                          -
                                                          340 resDesc_nParamPerEvent.res.linear.devPtr = gpu_nParamPerEvent;
                                                          -
                                                          341 resDesc_nParamPerEvent.res.linear.desc = cudaCreateChannelDesc<unsigned int>();
                                                          -
                                                          342 resDesc_nParamPerEvent.res.linear.sizeInBytes = 2*n_events*sizeof(unsigned int);
                                                          -
                                                          343
                                                          -
                                                          344 // Specify texture object parameters
                                                          -
                                                          345 struct cudaTextureDesc texDesc_nParamPerEvent;
                                                          -
                                                          346 memset(&texDesc_nParamPerEvent, 0, sizeof(texDesc_nParamPerEvent));
                                                          -
                                                          347 texDesc_nParamPerEvent.readMode = cudaReadModeElementType;
                                                          +
                                                          334
                                                          +
                                                          335 #ifndef Weight_On_SplineBySpline_Basis
                                                          +
                                                          336 //KS: Keep track how much splines each event has
                                                          +
                                                          337 cudaMemcpy(gpu_nParamPerEvent, cpu_nParamPerEvent.data(), 2*n_events*sizeof(unsigned int), cudaMemcpyHostToDevice);
                                                          +
                                                          338 CudaCheckError();
                                                          +
                                                          339
                                                          +
                                                          340 //KS: Bind our texture with the GPU variable
                                                          +
                                                          341 // create a resource descriptor based on device pointers
                                                          +
                                                          342 struct cudaResourceDesc resDesc_nParamPerEvent;
                                                          +
                                                          343 memset(&resDesc_nParamPerEvent, 0, sizeof(resDesc_nParamPerEvent));
                                                          +
                                                          344 resDesc_nParamPerEvent.resType = cudaResourceTypeLinear;
                                                          +
                                                          345 resDesc_nParamPerEvent.res.linear.devPtr = gpu_nParamPerEvent;
                                                          +
                                                          346 resDesc_nParamPerEvent.res.linear.desc = cudaCreateChannelDesc<unsigned int>();
                                                          +
                                                          347 resDesc_nParamPerEvent.res.linear.sizeInBytes = 2*n_events*sizeof(unsigned int);
                                                          348
                                                          -
                                                          349 //Finally create texture object
                                                          -
                                                          350 cudaCreateTextureObject(&text_nParamPerEvent, &resDesc_nParamPerEvent, &texDesc_nParamPerEvent, NULL);
                                                          -
                                                          351 CudaCheckError();
                                                          -
                                                          352 #endif
                                                          -
                                                          353}
                                                          +
                                                          349 // Specify texture object parameters
                                                          +
                                                          350 struct cudaTextureDesc texDesc_nParamPerEvent;
                                                          +
                                                          351 memset(&texDesc_nParamPerEvent, 0, sizeof(texDesc_nParamPerEvent));
                                                          +
                                                          352 texDesc_nParamPerEvent.readMode = cudaReadModeElementType;
                                                          +
                                                          353
                                                          +
                                                          354 //Finally create texture object
                                                          +
                                                          355 cudaCreateTextureObject(&text_nParamPerEvent, &resDesc_nParamPerEvent, &texDesc_nParamPerEvent, NULL);
                                                          +
                                                          356 CudaCheckError();
                                                          +
                                                          357 #endif
                                                          +
                                                          358}
                                                          -
                                                          354
                                                          -
                                                          355// ******************************************************
                                                          -
                                                          -
                                                          357__host__ void CopyToGPU_TF1(
                                                          -
                                                          358// ******************************************************
                                                          -
                                                          359 float *gpu_coeffs,
                                                          -
                                                          360 short int *gpu_paramNo_arr,
                                                          -
                                                          361 short int *gpu_nPoints_arr,
                                                          -
                                                          362
                                                          -
                                                          363 std::vector<float> cpu_coeffs,
                                                          -
                                                          364 std::vector<short int> paramNo_arr,
                                                          -
                                                          365 std::vector<short int> nPoints_arr,
                                                          -
                                                          366
                                                          -
                                                          367 #ifndef Weight_On_SplineBySpline_Basis
                                                          -
                                                          368 int n_events,
                                                          -
                                                          369 std::vector<unsigned int> cpu_nParamPerEvent,
                                                          -
                                                          370 unsigned int *gpu_nParamPerEvent,
                                                          -
                                                          371 #endif
                                                          -
                                                          372 int n_params,
                                                          -
                                                          373 unsigned int n_splines,
                                                          -
                                                          374 short int _max_knots) {
                                                          -
                                                          375
                                                          -
                                                          376 if (n_params != _N_SPLINES_) {
                                                          -
                                                          377 printf("Number of splines not equal to %i, GPU code for event-by-event splines will fail\n", _N_SPLINES_);
                                                          -
                                                          378 printf("n_params = %i\n", n_params);
                                                          -
                                                          379 printf("%s : %i\n", __FILE__, __LINE__);
                                                          -
                                                          380 exit(-1);
                                                          -
                                                          381 }
                                                          -
                                                          382
                                                          -
                                                          383 // Write to the global statics (h_* denotes host stored variable)
                                                          -
                                                          384 h_n_params = n_params;
                                                          -
                                                          385 h_spline_size = _max_knots;
                                                          -
                                                          386#ifndef Weight_On_SplineBySpline_Basis
                                                          -
                                                          387 h_n_events = n_events;
                                                          -
                                                          388#endif
                                                          -
                                                          389 // Copy the constants
                                                          -
                                                          390 // Total number of valid splines for all loaded events
                                                          -
                                                          391 cudaMemcpyToSymbol(d_n_splines, &n_splines, sizeof(n_splines));
                                                          -
                                                          392 CudaCheckError();
                                                          -
                                                          393 // Total spline size per spline; i.e. just the number of points or knots in the spline
                                                          -
                                                          394 cudaMemcpyToSymbol(d_spline_size, &h_spline_size, sizeof(h_spline_size));
                                                          -
                                                          395 CudaCheckError();
                                                          -
                                                          396
                                                          -
                                                          397#ifndef Weight_On_SplineBySpline_Basis
                                                          -
                                                          398 // Number of events
                                                          -
                                                          399 cudaMemcpyToSymbol(d_n_events, &h_n_events, sizeof(h_n_events));
                                                          +
                                                          359
                                                          +
                                                          360// ******************************************************
                                                          +
                                                          +
                                                          362__host__ void CopyToGPU_TF1(
                                                          +
                                                          363// ******************************************************
                                                          +
                                                          364 float *gpu_coeffs,
                                                          +
                                                          365 short int *gpu_paramNo_arr,
                                                          +
                                                          366 short int *gpu_nPoints_arr,
                                                          +
                                                          367
                                                          +
                                                          368 std::vector<float> cpu_coeffs,
                                                          +
                                                          369 std::vector<short int> paramNo_arr,
                                                          +
                                                          370 std::vector<short int> nPoints_arr,
                                                          +
                                                          371
                                                          +
                                                          372 #ifndef Weight_On_SplineBySpline_Basis
                                                          +
                                                          373 int n_events,
                                                          +
                                                          374 std::vector<unsigned int> cpu_nParamPerEvent,
                                                          +
                                                          375 unsigned int *gpu_nParamPerEvent,
                                                          +
                                                          376 #endif
                                                          +
                                                          377 int n_params,
                                                          +
                                                          378 unsigned int n_splines,
                                                          +
                                                          379 short int _max_knots) {
                                                          +
                                                          380
                                                          +
                                                          381 if (n_params != _N_SPLINES_) {
                                                          +
                                                          382 printf("Number of splines not equal to %i, GPU code for event-by-event splines will fail\n", _N_SPLINES_);
                                                          +
                                                          383 printf("n_params = %i\n", n_params);
                                                          +
                                                          384 printf("%s : %i\n", __FILE__, __LINE__);
                                                          +
                                                          385 exit(-1);
                                                          +
                                                          386 }
                                                          +
                                                          387
                                                          +
                                                          388 // Write to the global statics (h_* denotes host stored variable)
                                                          +
                                                          389 h_n_params = n_params;
                                                          +
                                                          390 h_spline_size = _max_knots;
                                                          +
                                                          391#ifndef Weight_On_SplineBySpline_Basis
                                                          +
                                                          392 h_n_events = n_events;
                                                          +
                                                          393#endif
                                                          +
                                                          394 // Copy the constants
                                                          +
                                                          395 // Total number of valid splines for all loaded events
                                                          +
                                                          396 cudaMemcpyToSymbol(d_n_splines, &n_splines, sizeof(n_splines));
                                                          +
                                                          397 CudaCheckError();
                                                          +
                                                          398 // Total spline size per spline; i.e. just the number of points or knots in the spline
                                                          +
                                                          399 cudaMemcpyToSymbol(d_spline_size, &h_spline_size, sizeof(h_spline_size));
                                                          400 CudaCheckError();
                                                          -
                                                          401#endif
                                                          -
                                                          402 // Move the coefficients
                                                          -
                                                          403 cudaMemcpy(gpu_coeffs, cpu_coeffs.data(), n_splines*5*sizeof(float), cudaMemcpyHostToDevice);
                                                          -
                                                          404 CudaCheckError();
                                                          -
                                                          405
                                                          -
                                                          406 // Also copy the parameter number for each spline onto the GPU; i.e. what spline parameter are we calculating right now
                                                          -
                                                          407 cudaMemcpy(gpu_paramNo_arr, paramNo_arr.data(), n_splines*sizeof(short int), cudaMemcpyHostToDevice);
                                                          -
                                                          408 CudaCheckError();
                                                          -
                                                          409
                                                          -
                                                          410 cudaMemcpy(gpu_nPoints_arr, nPoints_arr.data(), n_splines*sizeof(short int), cudaMemcpyHostToDevice);
                                                          -
                                                          411 CudaCheckError();
                                                          -
                                                          412
                                                          -
                                                          413 #ifndef Weight_On_SplineBySpline_Basis
                                                          -
                                                          414 //KS: Keep track how much splines each event has
                                                          -
                                                          415 cudaMemcpy(gpu_nParamPerEvent, cpu_nParamPerEvent.data(), 2*n_events*sizeof(unsigned int), cudaMemcpyHostToDevice);
                                                          +
                                                          401
                                                          +
                                                          402#ifndef Weight_On_SplineBySpline_Basis
                                                          +
                                                          403 // Number of events
                                                          +
                                                          404 cudaMemcpyToSymbol(d_n_events, &h_n_events, sizeof(h_n_events));
                                                          +
                                                          405 CudaCheckError();
                                                          +
                                                          406#endif
                                                          +
                                                          407 // Move the coefficients
                                                          +
                                                          408 cudaMemcpy(gpu_coeffs, cpu_coeffs.data(), n_splines*5*sizeof(float), cudaMemcpyHostToDevice);
                                                          +
                                                          409 CudaCheckError();
                                                          +
                                                          410
                                                          +
                                                          411 // Also copy the parameter number for each spline onto the GPU; i.e. what spline parameter are we calculating right now
                                                          +
                                                          412 cudaMemcpy(gpu_paramNo_arr, paramNo_arr.data(), n_splines*sizeof(short int), cudaMemcpyHostToDevice);
                                                          +
                                                          413 CudaCheckError();
                                                          +
                                                          414
                                                          +
                                                          415 cudaMemcpy(gpu_nPoints_arr, nPoints_arr.data(), n_splines*sizeof(short int), cudaMemcpyHostToDevice);
                                                          416 CudaCheckError();
                                                          -
                                                          417
                                                          -
                                                          418 //KS: Bind our texture with the GPU variable
                                                          -
                                                          419 // create a resource descriptor based on device pointers
                                                          -
                                                          420 struct cudaResourceDesc resDesc_nParamPerEvent;
                                                          -
                                                          421 memset(&resDesc_nParamPerEvent, 0, sizeof(resDesc_nParamPerEvent));
                                                          -
                                                          422 resDesc_nParamPerEvent.resType = cudaResourceTypeLinear;
                                                          -
                                                          423 resDesc_nParamPerEvent.res.linear.devPtr = gpu_nParamPerEvent;
                                                          -
                                                          424 resDesc_nParamPerEvent.res.linear.desc = cudaCreateChannelDesc<float>();
                                                          -
                                                          425 resDesc_nParamPerEvent.res.linear.sizeInBytes = 2*n_events*sizeof(unsigned int);
                                                          -
                                                          426
                                                          -
                                                          427 // Specify texture object parameters
                                                          -
                                                          428 struct cudaTextureDesc texDesc_nParamPerEvent;
                                                          -
                                                          429 memset(&texDesc_nParamPerEvent, 0, sizeof(texDesc_nParamPerEvent));
                                                          -
                                                          430 texDesc_nParamPerEvent.readMode = cudaReadModeElementType;
                                                          +
                                                          417
                                                          +
                                                          418 #ifndef Weight_On_SplineBySpline_Basis
                                                          +
                                                          419 //KS: Keep track how much splines each event has
                                                          +
                                                          420 cudaMemcpy(gpu_nParamPerEvent, cpu_nParamPerEvent.data(), 2*n_events*sizeof(unsigned int), cudaMemcpyHostToDevice);
                                                          +
                                                          421 CudaCheckError();
                                                          +
                                                          422
                                                          +
                                                          423 //KS: Bind our texture with the GPU variable
                                                          +
                                                          424 // create a resource descriptor based on device pointers
                                                          +
                                                          425 struct cudaResourceDesc resDesc_nParamPerEvent;
                                                          +
                                                          426 memset(&resDesc_nParamPerEvent, 0, sizeof(resDesc_nParamPerEvent));
                                                          +
                                                          427 resDesc_nParamPerEvent.resType = cudaResourceTypeLinear;
                                                          +
                                                          428 resDesc_nParamPerEvent.res.linear.devPtr = gpu_nParamPerEvent;
                                                          +
                                                          429 resDesc_nParamPerEvent.res.linear.desc = cudaCreateChannelDesc<float>();
                                                          +
                                                          430 resDesc_nParamPerEvent.res.linear.sizeInBytes = 2*n_events*sizeof(unsigned int);
                                                          431
                                                          -
                                                          432 //Lastly create texture object
                                                          -
                                                          433 cudaCreateTextureObject(&text_nParamPerEvent, &resDesc_nParamPerEvent, &texDesc_nParamPerEvent, NULL);
                                                          -
                                                          434 CudaCheckError();
                                                          -
                                                          435 #endif
                                                          -
                                                          436}
                                                          +
                                                          432 // Specify texture object parameters
                                                          +
                                                          433 struct cudaTextureDesc texDesc_nParamPerEvent;
                                                          +
                                                          434 memset(&texDesc_nParamPerEvent, 0, sizeof(texDesc_nParamPerEvent));
                                                          +
                                                          435 texDesc_nParamPerEvent.readMode = cudaReadModeElementType;
                                                          +
                                                          436
                                                          +
                                                          437 //Lastly create texture object
                                                          +
                                                          438 cudaCreateTextureObject(&text_nParamPerEvent, &resDesc_nParamPerEvent, &texDesc_nParamPerEvent, NULL);
                                                          +
                                                          439 CudaCheckError();
                                                          +
                                                          440 #endif
                                                          +
                                                          441}
                                                          -
                                                          437
                                                          -
                                                          438// ********************************************************
                                                          -
                                                          439// START GPU KERNELS
                                                          -
                                                          440//*********************************************************
                                                          -
                                                          441// All the GPU kernels have similar tasks but different implementations
                                                          -
                                                          442// Essentially they perform a binary search to find which TSpline3 point is nearest to our parameter variation
                                                          -
                                                          443// Once it knows this, we simply extract the pre-computed coefficients for that spline point and multiply together to get a weight
                                                          -
                                                          444
                                                          +
                                                          442
                                                          +
                                                          443// ********************************************************
                                                          +
                                                          444// START GPU KERNELS
                                                          445//*********************************************************
                                                          -
                                                          446// Evaluate the spline on the GPU
                                                          -
                                                          447// Using one {y,b,c,d} array
                                                          -
                                                          448// And one {x} array
                                                          -
                                                          449// Should be most efficient at cache hitting and memory coalescence
                                                          -
                                                          450// But using spline segments rather than the parameter value: avoids doing binary search on GPU
                                                          -
                                                          -
                                                          451__global__ void EvalOnGPU_SepMany(
                                                          -
                                                          452 const short int* __restrict__ gpu_paramNo_arr,
                                                          -
                                                          453 const unsigned int* __restrict__ gpu_nKnots_arr,
                                                          -
                                                          454 const float* __restrict__ gpu_coeff_many,
                                                          -
                                                          455 float *gpu_weights,
                                                          -
                                                          456 const cudaTextureObject_t __restrict__ text_coeff_x) {
                                                          -
                                                          457//*********************************************************
                                                          -
                                                          458
                                                          -
                                                          459 // points per spline is the offset to skip in the index to move between splines
                                                          -
                                                          460 const unsigned int splineNum = (blockIdx.x * blockDim.x + threadIdx.x);
                                                          +
                                                          446// All the GPU kernels have similar tasks but different implementations
                                                          +
                                                          447// Essentially they perform a binary search to find which TSpline3 point is nearest to our parameter variation
                                                          +
                                                          448// Once it knows this, we simply extract the pre-computed coefficients for that spline point and multiply together to get a weight
                                                          +
                                                          449
                                                          +
                                                          450//*********************************************************
                                                          +
                                                          +
                                                          454__global__ void EvalOnGPU_SepMany(
                                                          +
                                                          455 const short int* __restrict__ gpu_paramNo_arr,
                                                          +
                                                          456 const unsigned int* __restrict__ gpu_nKnots_arr,
                                                          +
                                                          457 const float* __restrict__ gpu_coeff_many,
                                                          +
                                                          458 float *gpu_weights,
                                                          +
                                                          459 const cudaTextureObject_t __restrict__ text_coeff_x) {
                                                          +
                                                          460//*********************************************************
                                                          461
                                                          -
                                                          462 // Note, the new arrays are arranged as:
                                                          -
                                                          463 // gpu_paramNo_arr has length = spln_counter (keeps track of which parameter we're using on this thread)
                                                          -
                                                          464 // gpu_nKnots_arrhas length = spln_counter (keeps track where current spline starts)
                                                          -
                                                          465 // text_coeff_x has length = n_params * spline_size
                                                          -
                                                          466 // gpu_coeff_many has length = nKnots * 4
                                                          -
                                                          467 // ...
                                                          -
                                                          468 // gpu_weights has length = spln_counter * spline_size
                                                          -
                                                          469
                                                          -
                                                          470 // this is the stopping condition!
                                                          -
                                                          471 if (splineNum < d_n_splines) {
                                                          -
                                                          472 // This is the segment we want for this parameter variation
                                                          -
                                                          473 // for this particular splineNum; 0 = MACCQE, 1 = pFC, 2 = EBC, etc
                                                          -
                                                          474
                                                          -
                                                          475 //CW: Which Parameter we are accesing
                                                          -
                                                          476 const short int Param = gpu_paramNo_arr[splineNum];
                                                          +
                                                          462 // points per spline is the offset to skip in the index to move between splines
                                                          +
                                                          463 const unsigned int splineNum = (blockIdx.x * blockDim.x + threadIdx.x);
                                                          +
                                                          464
                                                          +
                                                          465 // Note, the new arrays are arranged as:
                                                          +
                                                          466 // gpu_paramNo_arr has length = spln_counter (keeps track of which parameter we're using on this thread)
                                                          +
                                                          467 // gpu_nKnots_arrhas length = spln_counter (keeps track where current spline starts)
                                                          +
                                                          468 // text_coeff_x has length = n_params * spline_size
                                                          +
                                                          469 // gpu_coeff_many has length = nKnots * 4
                                                          +
                                                          470 // ...
                                                          +
                                                          471 // gpu_weights has length = spln_counter * spline_size
                                                          +
                                                          472
                                                          +
                                                          473 // this is the stopping condition!
                                                          +
                                                          474 if (splineNum < d_n_splines) {
                                                          +
                                                          475 // This is the segment we want for this parameter variation
                                                          +
                                                          476 // for this particular splineNum; 0 = MACCQE, 1 = pFC, 2 = EBC, etc
                                                          477
                                                          -
                                                          478 //CW: Avoids doing costly binary search on GPU
                                                          -
                                                          479 const short int segment = segment_gpu[Param];
                                                          +
                                                          478 //CW: Which Parameter we are accesing
                                                          +
                                                          479 const short int Param = gpu_paramNo_arr[splineNum];
                                                          480
                                                          -
                                                          481 //KS: Segment for coeff_x is simply parameter*max knots + segment as each parmeters has the same spacing
                                                          -
                                                          482 const short int segment_X = Param*d_spline_size+segment;
                                                          +
                                                          481 //CW: Avoids doing costly binary search on GPU
                                                          +
                                                          482 const short int segment = segment_gpu[Param];
                                                          483
                                                          -
                                                          484 //KS: Find knot position in out monolitical structure
                                                          -
                                                          485 const unsigned int CurrentKnotPos = gpu_nKnots_arr[splineNum]*_nCoeff_+segment*_nCoeff_;
                                                          +
                                                          484 //KS: Segment for coeff_x is simply parameter*max knots + segment as each parmeters has the same spacing
                                                          +
                                                          485 const short int segment_X = Param*d_spline_size+segment;
                                                          486
                                                          -
                                                          487 // We've read the segment straight from CPU and is saved in segment_gpu
                                                          -
                                                          488 // polynomial parameters from the monolithic splineMonolith
                                                          -
                                                          489 const float fY = gpu_coeff_many[CurrentKnotPos];
                                                          -
                                                          490 const float fB = gpu_coeff_many[CurrentKnotPos+1];
                                                          -
                                                          491 const float fC = gpu_coeff_many[CurrentKnotPos+2];
                                                          -
                                                          492 const float fD = gpu_coeff_many[CurrentKnotPos+3];
                                                          -
                                                          493 // The is the variation itself (needed to evaluate variation - stored spline point = dx)
                                                          -
                                                          494 const float dx = val_gpu[Param] - tex1Dfetch<float>(text_coeff_x, segment_X);
                                                          -
                                                          495
                                                          -
                                                          496 //CW: Wooow, let's use some fancy intrinsics and pull down the processing time by <1% from normal multiplication! HURRAY
                                                          -
                                                          497 gpu_weights[splineNum] = fmaf(dx, fmaf(dx, fmaf(dx, fD, fC), fB), fY);
                                                          -
                                                          498 // Or for the more "easy to read" version:
                                                          -
                                                          499 //gpu_weights[splineNum] = (fY+dx*(fB+dx*(fC+dx*fD)));
                                                          -
                                                          500
                                                          -
                                                          501#ifdef DEBUG
                                                          -
                                                          502 printf("splineNum = %i/%i, paramNo = %i, variation = %f, segment = %i, fX = %f, fX+1 = %f, dx = %f, d_n_splines = %i, d_spline_size = %i, weight = %f \n", splineNum, d_n_splines, gpu_paramNo_arr[splineNum], val_gpu[Param], segment, tex1Dfetch<float>(text_coeff_x, segment_X), tex1Dfetch<float>(text_coeff_x, segment_X+1), dx, d_n_splines, d_spline_size, gpu_weights[splineNum]);
                                                          -
                                                          503#endif
                                                          -
                                                          504 }
                                                          -
                                                          505}
                                                          +
                                                          487 //KS: Find knot position in out monolitical structure
                                                          +
                                                          488 const unsigned int CurrentKnotPos = gpu_nKnots_arr[splineNum]*_nCoeff_+segment*_nCoeff_;
                                                          +
                                                          489
                                                          +
                                                          490 // We've read the segment straight from CPU and is saved in segment_gpu
                                                          +
                                                          491 // polynomial parameters from the monolithic splineMonolith
                                                          +
                                                          492 const float fY = gpu_coeff_many[CurrentKnotPos];
                                                          +
                                                          493 const float fB = gpu_coeff_many[CurrentKnotPos+1];
                                                          +
                                                          494 const float fC = gpu_coeff_many[CurrentKnotPos+2];
                                                          +
                                                          495 const float fD = gpu_coeff_many[CurrentKnotPos+3];
                                                          +
                                                          496 // The is the variation itself (needed to evaluate variation - stored spline point = dx)
                                                          +
                                                          497 const float dx = val_gpu[Param] - tex1Dfetch<float>(text_coeff_x, segment_X);
                                                          +
                                                          498
                                                          +
                                                          499 //CW: Wooow, let's use some fancy intrinsics and pull down the processing time by <1% from normal multiplication! HURRAY
                                                          +
                                                          500 gpu_weights[splineNum] = fmaf(dx, fmaf(dx, fmaf(dx, fD, fC), fB), fY);
                                                          +
                                                          501 // Or for the more "easy to read" version:
                                                          +
                                                          502 //gpu_weights[splineNum] = (fY+dx*(fB+dx*(fC+dx*fD)));
                                                          +
                                                          503
                                                          +
                                                          504#ifdef DEBUG
                                                          +
                                                          505 printf("splineNum = %i/%i, paramNo = %i, variation = %f, segment = %i, fX = %f, fX+1 = %f, dx = %f, d_n_splines = %i, d_spline_size = %i, weight = %f \n", splineNum, d_n_splines, gpu_paramNo_arr[splineNum], val_gpu[Param], segment, tex1Dfetch<float>(text_coeff_x, segment_X), tex1Dfetch<float>(text_coeff_x, segment_X+1), dx, d_n_splines, d_spline_size, gpu_weights[splineNum]);
                                                          +
                                                          506#endif
                                                          +
                                                          507 }
                                                          +
                                                          508}
                                                          -
                                                          506
                                                          -
                                                          507//*********************************************************
                                                          -
                                                          -
                                                          509__global__ void EvalOnGPU_TF1(
                                                          -
                                                          510 const float* __restrict__ gpu_coeffs,
                                                          -
                                                          511 const short int* __restrict__ gpu_paramNo_arr,
                                                          -
                                                          512 const short int* __restrict__ gpu_nPoints_arr,
                                                          -
                                                          513 float *gpu_weights) {
                                                          -
                                                          514//*********************************************************
                                                          -
                                                          515
                                                          -
                                                          516 // points per spline is the offset to skip in the index to move between splines
                                                          -
                                                          517 const unsigned int splineNum = (blockIdx.x * blockDim.x + threadIdx.x);
                                                          +
                                                          509
                                                          +
                                                          510//*********************************************************
                                                          +
                                                          +
                                                          512__global__ void EvalOnGPU_TF1(
                                                          +
                                                          513 const float* __restrict__ gpu_coeffs,
                                                          +
                                                          514 const short int* __restrict__ gpu_paramNo_arr,
                                                          +
                                                          515 const short int* __restrict__ gpu_nPoints_arr,
                                                          +
                                                          516 float *gpu_weights) {
                                                          +
                                                          517//*********************************************************
                                                          518
                                                          -
                                                          519 // Note, the new arrays are arranged as:
                                                          -
                                                          520 // gpu_paramNo_arr has length = spln_counter (keeps track of which parameter we're using on this thread)
                                                          -
                                                          521 // gpu_coeff_x has length = n_params * spline_size
                                                          -
                                                          522 // gpu_coeff_many has length = spln_counter * spline_size * 4
                                                          -
                                                          523 // ...
                                                          -
                                                          524 // gpu_weights has length = spln_counter * spline_size
                                                          -
                                                          525
                                                          -
                                                          526 if (splineNum < d_n_splines) {
                                                          -
                                                          527 // The is the variation itself (needed to evaluate variation - stored spline point = dx)
                                                          -
                                                          528 const float x = val_gpu[gpu_paramNo_arr[splineNum]];
                                                          -
                                                          529
                                                          -
                                                          530 // Read the coefficients
                                                          -
                                                          531 const float a = gpu_coeffs[splineNum*d_spline_size];
                                                          -
                                                          532 const float b = gpu_coeffs[splineNum*d_spline_size+1];
                                                          -
                                                          533 const float c = gpu_coeffs[splineNum*d_spline_size+2];
                                                          -
                                                          534 const float d = gpu_coeffs[splineNum*d_spline_size+3];
                                                          -
                                                          535 const float e = gpu_coeffs[splineNum*d_spline_size+4];
                                                          -
                                                          536
                                                          -
                                                          537 // Match these with form in SetSplines
                                                          -
                                                          538 // Might not be great to have this if statement: maybe split two kernels?
                                                          -
                                                          539 if (gpu_nPoints_arr[splineNum] == 5) {
                                                          -
                                                          540 gpu_weights[splineNum] = 1 + a*x + b*x*x + c*x*x*x + d*x*x*x*x + e*x*x*x*x*x;
                                                          -
                                                          541 } else if (gpu_nPoints_arr[splineNum] == 2) {
                                                          -
                                                          542 gpu_weights[splineNum] = (x<=0)*(1+a*x) + (x>0)*(1+b*x);
                                                          -
                                                          543 } else {
                                                          -
                                                          544 printf("Big problems, I found a nPoints array which is not 5 or 2 on GPU!\n");
                                                          -
                                                          545 }
                                                          -
                                                          546
                                                          -
                                                          547#ifdef DEBUG
                                                          -
                                                          548 //if (splineNum < 200) {
                                                          -
                                                          549 if (gpu_nPoints_arr[splineNum] == 2) {
                                                          -
                                                          550 printf("splineNum = %i, spline_size=%i, paramNo = %i, variation = %f, a = %f, b = %f, c = %f, d = %f, e = %f, weight = %f\n", splineNum, d_spline_size, gpu_paramNo_arr[splineNum], x, a, b, c, d, e, gpu_weights[splineNum] );
                                                          -
                                                          551 }
                                                          -
                                                          552#endif
                                                          -
                                                          553 }
                                                          -
                                                          554}
                                                          +
                                                          519 // points per spline is the offset to skip in the index to move between splines
                                                          +
                                                          520 const unsigned int splineNum = (blockIdx.x * blockDim.x + threadIdx.x);
                                                          +
                                                          521
                                                          +
                                                          522 // Note, the new arrays are arranged as:
                                                          +
                                                          523 // gpu_paramNo_arr has length = spln_counter (keeps track of which parameter we're using on this thread)
                                                          +
                                                          524 // gpu_coeff_x has length = n_params * spline_size
                                                          +
                                                          525 // gpu_coeff_many has length = spln_counter * spline_size * 4
                                                          +
                                                          526 // ...
                                                          +
                                                          527 // gpu_weights has length = spln_counter * spline_size
                                                          +
                                                          528
                                                          +
                                                          529 if (splineNum < d_n_splines) {
                                                          +
                                                          530 // The is the variation itself (needed to evaluate variation - stored spline point = dx)
                                                          +
                                                          531 const float x = val_gpu[gpu_paramNo_arr[splineNum]];
                                                          +
                                                          532
                                                          +
                                                          533 // Read the coefficients
                                                          +
                                                          534 const float a = gpu_coeffs[splineNum*d_spline_size];
                                                          +
                                                          535 const float b = gpu_coeffs[splineNum*d_spline_size+1];
                                                          +
                                                          536 const float c = gpu_coeffs[splineNum*d_spline_size+2];
                                                          +
                                                          537 const float d = gpu_coeffs[splineNum*d_spline_size+3];
                                                          +
                                                          538 const float e = gpu_coeffs[splineNum*d_spline_size+4];
                                                          +
                                                          539
                                                          +
                                                          540 // Match these with form in SetSplines
                                                          +
                                                          541 // Might not be great to have this if statement: maybe split two kernels?
                                                          +
                                                          542 if (gpu_nPoints_arr[splineNum] == 5) {
                                                          +
                                                          543 gpu_weights[splineNum] = 1 + a*x + b*x*x + c*x*x*x + d*x*x*x*x + e*x*x*x*x*x;
                                                          +
                                                          544 } else if (gpu_nPoints_arr[splineNum] == 2) {
                                                          +
                                                          545 gpu_weights[splineNum] = (x<=0)*(1+a*x) + (x>0)*(1+b*x);
                                                          +
                                                          546 } else {
                                                          +
                                                          547 printf("Big problems, I found a nPoints array which is not 5 or 2 on GPU!\n");
                                                          +
                                                          548 }
                                                          +
                                                          549
                                                          +
                                                          550#ifdef DEBUG
                                                          +
                                                          551 //if (splineNum < 200) {
                                                          +
                                                          552 if (gpu_nPoints_arr[splineNum] == 2) {
                                                          +
                                                          553 printf("splineNum = %i, spline_size=%i, paramNo = %i, variation = %f, a = %f, b = %f, c = %f, d = %f, e = %f, weight = %f\n", splineNum, d_spline_size, gpu_paramNo_arr[splineNum], x, a, b, c, d, e, gpu_weights[splineNum] );
                                                          +
                                                          554 }
                                                          +
                                                          555#endif
                                                          +
                                                          556 }
                                                          +
                                                          557}
                                                          -
                                                          555
                                                          -
                                                          556#ifndef Weight_On_SplineBySpline_Basis
                                                          -
                                                          557//*********************************************************
                                                          -
                                                          -
                                                          559__global__ void EvalOnGPU_TotWeight(
                                                          -
                                                          560 const float* __restrict__ gpu_weights,
                                                          -
                                                          561 float *gpu_total_weights,
                                                          -
                                                          562 const cudaTextureObject_t __restrict__ text_nParamPerEvent) {
                                                          -
                                                          563//*********************************************************
                                                          -
                                                          564 const unsigned int EventNum = (blockIdx.x * blockDim.x + threadIdx.x);
                                                          -
                                                          565 //KS: Accessing shared memory is much much faster than global memory hence we use shared memory for calculation and then write to global memory
                                                          -
                                                          566 __shared__ float shared_total_weights[_BlockSize_];
                                                          -
                                                          567 if(EventNum < d_n_events) //stopping condition
                                                          -
                                                          568 {
                                                          -
                                                          569 shared_total_weights[threadIdx.x] = 1.f;
                                                          -
                                                          570 const unsigned int EventOffset = 2*EventNum;
                                                          -
                                                          571 for (unsigned int id = 0; id < tex1Dfetch<unsigned int>(text_nParamPerEvent, EventOffset); ++id)
                                                          -
                                                          572 {
                                                          -
                                                          573 shared_total_weights[threadIdx.x] *= gpu_weights[tex1Dfetch<unsigned int>(text_nParamPerEvent, EventOffset+1) + id];
                                                          -
                                                          574 #ifdef DEBUG
                                                          -
                                                          575 printf("Event = %i, Spline_Num = %i, gpu_weights = %f \n",
                                                          -
                                                          576 EventNum, tex1Dfetch<unsigned int>(text_nParamPerEvent, 2*EventNum+1) + id, gpu_weights[tex1Dfetch<unsigned int>(text_nParamPerEvent, 2*EventNum+1) + id];
                                                          -
                                                          577 #endif
                                                          -
                                                          578 }
                                                          -
                                                          579 gpu_total_weights[EventNum] = shared_total_weights[threadIdx.x];
                                                          -
                                                          580 }
                                                          -
                                                          581}
                                                          +
                                                          558
                                                          +
                                                          559#ifndef Weight_On_SplineBySpline_Basis
                                                          +
                                                          560//*********************************************************
                                                          +
                                                          +
                                                          562__global__ void EvalOnGPU_TotWeight(
                                                          +
                                                          563 const float* __restrict__ gpu_weights,
                                                          +
                                                          564 float *gpu_total_weights,
                                                          +
                                                          565 const cudaTextureObject_t __restrict__ text_nParamPerEvent) {
                                                          +
                                                          566//*********************************************************
                                                          +
                                                          567 const unsigned int EventNum = (blockIdx.x * blockDim.x + threadIdx.x);
                                                          +
                                                          568 //KS: Accessing shared memory is much much faster than global memory hence we use shared memory for calculation and then write to global memory
                                                          +
                                                          569 __shared__ float shared_total_weights[_BlockSize_];
                                                          +
                                                          570 if(EventNum < d_n_events) //stopping condition
                                                          +
                                                          571 {
                                                          +
                                                          572 shared_total_weights[threadIdx.x] = 1.f;
                                                          +
                                                          573 const unsigned int EventOffset = 2*EventNum;
                                                          +
                                                          574 for (unsigned int id = 0; id < tex1Dfetch<unsigned int>(text_nParamPerEvent, EventOffset); ++id)
                                                          +
                                                          575 {
                                                          +
                                                          576 shared_total_weights[threadIdx.x] *= gpu_weights[tex1Dfetch<unsigned int>(text_nParamPerEvent, EventOffset+1) + id];
                                                          +
                                                          577 #ifdef DEBUG
                                                          +
                                                          578 printf("Event = %i, Spline_Num = %i, gpu_weights = %f \n",
                                                          +
                                                          579 EventNum, tex1Dfetch<unsigned int>(text_nParamPerEvent, 2*EventNum+1) + id, gpu_weights[tex1Dfetch<unsigned int>(text_nParamPerEvent, 2*EventNum+1) + id];
                                                          +
                                                          580 #endif
                                                          +
                                                          581 }
                                                          +
                                                          582 gpu_total_weights[EventNum] = shared_total_weights[threadIdx.x];
                                                          +
                                                          583 }
                                                          +
                                                          584}
                                                          -
                                                          582#endif
                                                          -
                                                          583
                                                          -
                                                          584// *****************************************
                                                          -
                                                          585// Run the GPU code for the separate many arrays
                                                          -
                                                          586// As in separate {x}, {y,b,c,d} arrays
                                                          -
                                                          587// Pass the segment and the parameter values
                                                          -
                                                          588// (binary search already performed in samplePDFND::FindSplineSegment()
                                                          -
                                                          -
                                                          589__host__ void RunGPU_SepMany(
                                                          -
                                                          590 const short int* gpu_paramNo_arr,
                                                          -
                                                          591 const unsigned int* gpu_nKnots_arr,
                                                          -
                                                          592
                                                          -
                                                          593 const float *gpu_coeff_many,
                                                          +
                                                          585#endif
                                                          +
                                                          586
                                                          +
                                                          587// *****************************************
                                                          +
                                                          +
                                                          591__host__ void RunGPU_SepMany(
                                                          +
                                                          592 const short int* gpu_paramNo_arr,
                                                          +
                                                          593 const unsigned int* gpu_nKnots_arr,
                                                          594
                                                          -
                                                          595 float* gpu_weights,
                                                          -
                                                          596#ifdef Weight_On_SplineBySpline_Basis
                                                          -
                                                          597 float* cpu_weights,
                                                          -
                                                          598#else
                                                          -
                                                          599 float* gpu_total_weights,
                                                          -
                                                          600 float* cpu_total_weights,
                                                          -
                                                          601#endif
                                                          -
                                                          602 // Holds the changes in parameters
                                                          -
                                                          603 float *vals,
                                                          -
                                                          604 // Holds the segments for parameters
                                                          -
                                                          605 short int *segment,
                                                          -
                                                          606 const unsigned int h_n_splines) {
                                                          -
                                                          607// *****************************************
                                                          -
                                                          608
                                                          -
                                                          609 dim3 block_size;
                                                          -
                                                          610 dim3 grid_size;
                                                          -
                                                          611
                                                          -
                                                          612 block_size.x = _BlockSize_;
                                                          -
                                                          613 grid_size.x = (h_n_splines / block_size.x) + 1;
                                                          -
                                                          614
                                                          -
                                                          615 // Copy the segment values to the GPU (segment_gpu), which is h_n_params long
                                                          -
                                                          616 cudaMemcpyToSymbol(segment_gpu, segment, h_n_params*sizeof(short int));
                                                          -
                                                          617 CudaCheckError();
                                                          -
                                                          618
                                                          -
                                                          619 // Copy the parameter values values to the GPU (vals_gpu), which is h_n_params long
                                                          -
                                                          620 cudaMemcpyToSymbol(val_gpu, vals, h_n_params*sizeof(float));
                                                          -
                                                          621 CudaCheckError();
                                                          -
                                                          622
                                                          -
                                                          623#ifdef DEBUG
                                                          -
                                                          624 printf("\n***********************\nGPU DEBUGGING ENABLED\n***********************\n");
                                                          -
                                                          625 printf("block_size.x = %i, grid_size.x = %i \n", block_size.x, grid_size.x);
                                                          -
                                                          626 printf("RunGPU_SepMany segments\n");
                                                          -
                                                          627 for (int i = 0; i < h_n_params; i++) {
                                                          -
                                                          628 printf("val[%i] = %f in segment %i\n", i, vals[i], segment[i]);
                                                          -
                                                          629 }
                                                          -
                                                          630 printf("nParams = %i, n_splines = %i", h_n_params, h_n_splines);
                                                          -
                                                          631 printf("\n***********************\nAM NOW CALLING KERNEL\n***********************\n");
                                                          -
                                                          632#endif
                                                          -
                                                          633
                                                          -
                                                          634 // Set the cache config to prefer L1 for the kernel
                                                          -
                                                          635 //cudaFuncSetCacheConfig(EvalOnGPU_SepMany, cudaFuncCachePreferL1);
                                                          -
                                                          636 EvalOnGPU_SepMany<<<grid_size, block_size>>>(
                                                          -
                                                          637 gpu_paramNo_arr,
                                                          -
                                                          638 gpu_nKnots_arr,
                                                          -
                                                          639
                                                          -
                                                          640 gpu_coeff_many,
                                                          +
                                                          595 const float *gpu_coeff_many,
                                                          +
                                                          596
                                                          +
                                                          597 float* gpu_weights,
                                                          +
                                                          598#ifdef Weight_On_SplineBySpline_Basis
                                                          +
                                                          599 float* cpu_weights,
                                                          +
                                                          600#else
                                                          +
                                                          601 float* gpu_total_weights,
                                                          +
                                                          602 float* cpu_total_weights,
                                                          +
                                                          603#endif
                                                          +
                                                          604 // Holds the changes in parameters
                                                          +
                                                          605 float *vals,
                                                          +
                                                          606 // Holds the segments for parameters
                                                          +
                                                          607 short int *segment,
                                                          +
                                                          608 const unsigned int h_n_splines) {
                                                          +
                                                          609// *****************************************
                                                          +
                                                          610
                                                          +
                                                          611 dim3 block_size;
                                                          +
                                                          612 dim3 grid_size;
                                                          +
                                                          613
                                                          +
                                                          614 block_size.x = _BlockSize_;
                                                          +
                                                          615 grid_size.x = (h_n_splines / block_size.x) + 1;
                                                          +
                                                          616
                                                          +
                                                          617 // Copy the segment values to the GPU (segment_gpu), which is h_n_params long
                                                          +
                                                          618 cudaMemcpyToSymbol(segment_gpu, segment, h_n_params*sizeof(short int));
                                                          +
                                                          619 CudaCheckError();
                                                          +
                                                          620
                                                          +
                                                          621 // Copy the parameter values values to the GPU (vals_gpu), which is h_n_params long
                                                          +
                                                          622 cudaMemcpyToSymbol(val_gpu, vals, h_n_params*sizeof(float));
                                                          +
                                                          623 CudaCheckError();
                                                          +
                                                          624
                                                          +
                                                          625#ifdef DEBUG
                                                          +
                                                          626 printf("\n***********************\nGPU DEBUGGING ENABLED\n***********************\n");
                                                          +
                                                          627 printf("block_size.x = %i, grid_size.x = %i \n", block_size.x, grid_size.x);
                                                          +
                                                          628 printf("RunGPU_SepMany segments\n");
                                                          +
                                                          629 for (int i = 0; i < h_n_params; i++) {
                                                          +
                                                          630 printf("val[%i] = %f in segment %i\n", i, vals[i], segment[i]);
                                                          +
                                                          631 }
                                                          +
                                                          632 printf("nParams = %i, n_splines = %i", h_n_params, h_n_splines);
                                                          +
                                                          633 printf("\n***********************\nAM NOW CALLING KERNEL\n***********************\n");
                                                          +
                                                          634#endif
                                                          +
                                                          635
                                                          +
                                                          636 // Set the cache config to prefer L1 for the kernel
                                                          +
                                                          637 //cudaFuncSetCacheConfig(EvalOnGPU_SepMany, cudaFuncCachePreferL1);
                                                          +
                                                          638 EvalOnGPU_SepMany<<<grid_size, block_size>>>(
                                                          +
                                                          639 gpu_paramNo_arr,
                                                          +
                                                          640 gpu_nKnots_arr,
                                                          641
                                                          -
                                                          642 gpu_weights,
                                                          -
                                                          643 text_coeff_x
                                                          -
                                                          644 );
                                                          -
                                                          645 CudaCheckError();
                                                          -
                                                          646
                                                          -
                                                          647#ifdef DEBUG
                                                          -
                                                          648 printf("Evaluated kernel with SUCCESS (drink beer)\n");
                                                          -
                                                          649#endif
                                                          -
                                                          650
                                                          -
                                                          651//KS: We can either copy gpu_weight and calculate total weight in reweighting loop, or not copy and calculate total weight stall at GPU, which means less memory transfer
                                                          -
                                                          652#ifdef Weight_On_SplineBySpline_Basis
                                                          -
                                                          653 // Here we have to make a somewhat large GPU->CPU transfer because it's all the splines' response
                                                          -
                                                          654 cudaMemcpy(cpu_weights, gpu_weights, h_n_splines*sizeof(float), cudaMemcpyDeviceToHost);
                                                          -
                                                          655 CudaCheckError();
                                                          -
                                                          656 #ifdef DEBUG
                                                          -
                                                          657 printf("Copied GPU weights to CPU with SUCCESS (drink more beer)\n");
                                                          -
                                                          658 printf("Released calculated response from GPU with SUCCESS (drink most beer)\n");
                                                          -
                                                          659 #endif
                                                          -
                                                          660
                                                          -
                                                          661//KS: Else calculate Total Weight
                                                          -
                                                          662#else
                                                          -
                                                          663 grid_size.x = (h_n_events / block_size.x) + 1;
                                                          -
                                                          664
                                                          -
                                                          665 #ifdef DEBUG
                                                          -
                                                          666 printf("\n***********************\nGPU DEBUGGING ENABLED\n***********************\n");
                                                          -
                                                          667 printf("block_size.x = %i, grid_size.x = %i \n", block_size.x, grid_size.x);
                                                          -
                                                          668 printf("RunGPU_TotWeight\n");
                                                          -
                                                          669
                                                          -
                                                          670 printf("nEvents = %i, n_splines = %i, d_n_params", h_n_events, h_n_splines, h_n_params);
                                                          -
                                                          671 printf("\n***********************\nI AM NOW CALLING KERNEL\n***********************\n");
                                                          -
                                                          672 #endif
                                                          -
                                                          673 EvalOnGPU_TotWeight<<<grid_size, block_size>>>(
                                                          -
                                                          674 gpu_weights,
                                                          -
                                                          675 gpu_total_weights,
                                                          -
                                                          676 text_nParamPerEvent
                                                          -
                                                          677 );
                                                          -
                                                          678 #ifdef DEBUG
                                                          -
                                                          679 CudaCheckError();
                                                          -
                                                          680 printf("Evaluated kernel with SUCCESS (drink tea)\n");
                                                          -
                                                          681 #endif
                                                          -
                                                          682 //KS: Here we have to make a somewhat large GPU->CPU transfer because it is proportional to number of events
                                                          -
                                                          683 //KS: Normally code wait for memory transfer to finish before moving further cudaMemcpyAsync means we will continue to execute code and in a meantime keep copying stuff.
                                                          -
                                                          684 cudaMemcpyAsync(cpu_total_weights, gpu_total_weights, h_n_events * sizeof(float), cudaMemcpyDeviceToHost, 0);
                                                          -
                                                          685
                                                          -
                                                          686 #ifdef DEBUG
                                                          -
                                                          687 CudaCheckError();
                                                          -
                                                          688 printf("Copied GPU total weights to CPU with SUCCESS (drink moar tea)\n");
                                                          -
                                                          689 printf("Released calculated response from GPU with SUCCESS (drink most tea)\n");
                                                          -
                                                          690 #endif
                                                          -
                                                          691#endif
                                                          -
                                                          692}
                                                          +
                                                          642 gpu_coeff_many,
                                                          +
                                                          643
                                                          +
                                                          644 gpu_weights,
                                                          +
                                                          645 text_coeff_x
                                                          +
                                                          646 );
                                                          +
                                                          647 CudaCheckError();
                                                          +
                                                          648
                                                          +
                                                          649#ifdef DEBUG
                                                          +
                                                          650 printf("Evaluated kernel with SUCCESS (drink beer)\n");
                                                          +
                                                          651#endif
                                                          +
                                                          652
                                                          +
                                                          653//KS: We can either copy gpu_weight and calculate total weight in reweighting loop, or not copy and calculate total weight stall at GPU, which means less memory transfer
                                                          +
                                                          654#ifdef Weight_On_SplineBySpline_Basis
                                                          +
                                                          655 // Here we have to make a somewhat large GPU->CPU transfer because it's all the splines' response
                                                          +
                                                          656 cudaMemcpy(cpu_weights, gpu_weights, h_n_splines*sizeof(float), cudaMemcpyDeviceToHost);
                                                          +
                                                          657 CudaCheckError();
                                                          +
                                                          658 #ifdef DEBUG
                                                          +
                                                          659 printf("Copied GPU weights to CPU with SUCCESS (drink more beer)\n");
                                                          +
                                                          660 printf("Released calculated response from GPU with SUCCESS (drink most beer)\n");
                                                          +
                                                          661 #endif
                                                          +
                                                          662
                                                          +
                                                          663//KS: Else calculate Total Weight
                                                          +
                                                          664#else
                                                          +
                                                          665 grid_size.x = (h_n_events / block_size.x) + 1;
                                                          +
                                                          666
                                                          +
                                                          667 #ifdef DEBUG
                                                          +
                                                          668 printf("\n***********************\nGPU DEBUGGING ENABLED\n***********************\n");
                                                          +
                                                          669 printf("block_size.x = %i, grid_size.x = %i \n", block_size.x, grid_size.x);
                                                          +
                                                          670 printf("RunGPU_TotWeight\n");
                                                          +
                                                          671
                                                          +
                                                          672 printf("nEvents = %i, n_splines = %i, d_n_params", h_n_events, h_n_splines, h_n_params);
                                                          +
                                                          673 printf("\n***********************\nI AM NOW CALLING KERNEL\n***********************\n");
                                                          +
                                                          674 #endif
                                                          +
                                                          675 EvalOnGPU_TotWeight<<<grid_size, block_size>>>(
                                                          +
                                                          676 gpu_weights,
                                                          +
                                                          677 gpu_total_weights,
                                                          +
                                                          678 text_nParamPerEvent
                                                          +
                                                          679 );
                                                          +
                                                          680 #ifdef DEBUG
                                                          +
                                                          681 CudaCheckError();
                                                          +
                                                          682 printf("Evaluated kernel with SUCCESS (drink tea)\n");
                                                          +
                                                          683 #endif
                                                          +
                                                          684 //KS: Here we have to make a somewhat large GPU->CPU transfer because it is proportional to number of events
                                                          +
                                                          685 //KS: Normally code wait for memory transfer to finish before moving further cudaMemcpyAsync means we will continue to execute code and in a meantime keep copying stuff.
                                                          +
                                                          686 cudaMemcpyAsync(cpu_total_weights, gpu_total_weights, h_n_events * sizeof(float), cudaMemcpyDeviceToHost, 0);
                                                          +
                                                          687
                                                          +
                                                          688 #ifdef DEBUG
                                                          +
                                                          689 CudaCheckError();
                                                          +
                                                          690 printf("Copied GPU total weights to CPU with SUCCESS (drink moar tea)\n");
                                                          +
                                                          691 printf("Released calculated response from GPU with SUCCESS (drink most tea)\n");
                                                          +
                                                          692 #endif
                                                          +
                                                          693#endif
                                                          +
                                                          694}
                                                          -
                                                          693
                                                          -
                                                          694// *****************************************
                                                          -
                                                          -
                                                          696__host__ void RunGPU_TF1(
                                                          -
                                                          697 const float *gpu_coeffs,
                                                          -
                                                          698 const short int* gpu_paramNo_arr,
                                                          -
                                                          699 const short int* gpu_nPoints_arr,
                                                          -
                                                          700
                                                          -
                                                          701 float* gpu_weights,
                                                          -
                                                          702#ifdef Weight_On_SplineBySpline_Basis
                                                          -
                                                          703 float* cpu_weights,
                                                          -
                                                          704#else
                                                          -
                                                          705 float* gpu_total_weights,
                                                          -
                                                          706 float* cpu_total_weights,
                                                          -
                                                          707#endif
                                                          -
                                                          708
                                                          -
                                                          709 // Holds the changes in parameters
                                                          -
                                                          710 float *vals,
                                                          -
                                                          711 const unsigned int h_n_splines) {
                                                          -
                                                          712// *****************************************
                                                          -
                                                          713
                                                          -
                                                          714 dim3 block_size;
                                                          -
                                                          715 dim3 grid_size;
                                                          -
                                                          716
                                                          -
                                                          717 block_size.x = _BlockSize_;
                                                          -
                                                          718 grid_size.x = (h_n_splines / block_size.x) + 1;
                                                          -
                                                          719
                                                          -
                                                          720 // Copy the parameter values values to the GPU (vals_gpu), which is h_n_params long
                                                          -
                                                          721 cudaMemcpyToSymbol(val_gpu, vals, h_n_params*sizeof(float));
                                                          -
                                                          722 CudaCheckError();
                                                          -
                                                          723
                                                          -
                                                          724#ifdef DEBUG
                                                          -
                                                          725 printf("\n***********************\nGPU DEBUGGING ENABLED\n***********************\n");
                                                          -
                                                          726 printf("block_size.x = %i, grid_size.x = %i \n", block_size.x, grid_size.x);
                                                          -
                                                          727 printf("RunGPU_TF1 segments\n");
                                                          -
                                                          728 for (int i = 0; i < h_n_params; i++) {
                                                          -
                                                          729 printf("val[%i] = %f \n", i, vals[i]);
                                                          -
                                                          730 }
                                                          -
                                                          731 printf("nParams = %i, n_splines = %i", h_n_params, h_n_splines);
                                                          -
                                                          732 printf("\n***********************\nAM NOW CALLING KERNEL\n***********************\n");
                                                          -
                                                          733#endif
                                                          -
                                                          734
                                                          -
                                                          735 // Set the cache config to prefer L1 for the kernel
                                                          -
                                                          736 //cudaFuncSetCacheConfig(EvalOnGPU_TF1, cudaFuncCachePreferL1);
                                                          -
                                                          737 EvalOnGPU_TF1<<<grid_size, block_size>>>(
                                                          -
                                                          738 gpu_coeffs,
                                                          -
                                                          739 gpu_paramNo_arr,
                                                          -
                                                          740 gpu_nPoints_arr,
                                                          -
                                                          741
                                                          -
                                                          742 gpu_weights
                                                          -
                                                          743 );
                                                          -
                                                          744 CudaCheckError();
                                                          -
                                                          745
                                                          -
                                                          746#ifdef DEBUG
                                                          -
                                                          747 printf("Evaluated TF1 kernel with SUCCESS (drink beer)\n");
                                                          -
                                                          748#endif
                                                          -
                                                          749
                                                          -
                                                          750//KS: We can either copy gpu_weight and calculate total weight in reweighting loop, or not copy and calculate total weight stall at GPU, which means less memory transfer
                                                          -
                                                          751#ifdef Weight_On_SplineBySpline_Basis
                                                          -
                                                          752 // Here we have to make a somewhat large GPU->CPU transfer because it's all the splines' response
                                                          -
                                                          753 cudaMemcpy(cpu_weights, gpu_weights, h_n_splines*sizeof(float), cudaMemcpyDeviceToHost);
                                                          -
                                                          754 CudaCheckError();
                                                          -
                                                          755
                                                          -
                                                          756 #ifdef DEBUG
                                                          -
                                                          757 printf("Copied TF1 GPU weights to CPU with SUCCESS (drink moar beer)\n");
                                                          -
                                                          758 printf("Released TF1 calculated response from GPU with SUCCESS (drink most beer)\n");
                                                          -
                                                          759 #endif
                                                          -
                                                          760
                                                          -
                                                          761//KS: Else calculate Total Weight
                                                          -
                                                          762#else
                                                          -
                                                          763 grid_size.x = (h_n_events / block_size.x) + 1;
                                                          -
                                                          764
                                                          -
                                                          765 #ifdef DEBUG
                                                          -
                                                          766 printf("\n***********************\nGPU DEBUGGING ENABLED\n***********************\n");
                                                          -
                                                          767 printf("block_size.x = %i, grid_size.x = %i \n", block_size.x, grid_size.x);
                                                          -
                                                          768 printf("RunGPU_TotWeight\n");
                                                          -
                                                          769
                                                          -
                                                          770 printf("nEvents = %i, n_splines = %i, d_n_params", h_n_events, h_n_splines, h_n_params);
                                                          -
                                                          771 printf("\n***********************\nI AM NOW CALLING KERNEL\n***********************\n");
                                                          -
                                                          772 #endif
                                                          -
                                                          773 EvalOnGPU_TotWeight<<<grid_size, block_size>>>(
                                                          -
                                                          774 gpu_weights,
                                                          -
                                                          775 gpu_total_weights,
                                                          -
                                                          776 text_nParamPerEvent
                                                          -
                                                          777 );
                                                          -
                                                          778 #ifdef DEBUG
                                                          -
                                                          779 CudaCheckError();
                                                          -
                                                          780 printf("Evaluated kernel with SUCCESS (drink tea)\n");
                                                          -
                                                          781 #endif
                                                          -
                                                          782 //KS: Here we have to make a somewhat large GPU->CPU transfer because it is proportional to number of events
                                                          -
                                                          783 //KS: In the future it might be worth to calculate only weight for events which have splines, this should reduce memory transfer
                                                          -
                                                          784 cudaMemcpy(cpu_total_weights, gpu_total_weights, h_n_events*sizeof(float), cudaMemcpyDeviceToHost);
                                                          -
                                                          785 #ifdef DEBUG
                                                          -
                                                          786 CudaCheckError();
                                                          -
                                                          787 printf("Copied GPU total weights to CPU with SUCCESS (drink moar tea)\n");
                                                          -
                                                          788 printf("Released calculated response from GPU with SUCCESS (drink most tea)\n");
                                                          -
                                                          789 #endif
                                                          -
                                                          790#endif
                                                          -
                                                          791}
                                                          +
                                                          695
                                                          +
                                                          696// *****************************************
                                                          +
                                                          +
                                                          698__host__ void RunGPU_TF1(
                                                          +
                                                          699 const float *gpu_coeffs,
                                                          +
                                                          700 const short int* gpu_paramNo_arr,
                                                          +
                                                          701 const short int* gpu_nPoints_arr,
                                                          +
                                                          702
                                                          +
                                                          703 float* gpu_weights,
                                                          +
                                                          704#ifdef Weight_On_SplineBySpline_Basis
                                                          +
                                                          705 float* cpu_weights,
                                                          +
                                                          706#else
                                                          +
                                                          707 float* gpu_total_weights,
                                                          +
                                                          708 float* cpu_total_weights,
                                                          +
                                                          709#endif
                                                          +
                                                          710
                                                          +
                                                          711 // Holds the changes in parameters
                                                          +
                                                          712 float *vals,
                                                          +
                                                          713 const unsigned int h_n_splines) {
                                                          +
                                                          714// *****************************************
                                                          +
                                                          715
                                                          +
                                                          716 dim3 block_size;
                                                          +
                                                          717 dim3 grid_size;
                                                          +
                                                          718
                                                          +
                                                          719 block_size.x = _BlockSize_;
                                                          +
                                                          720 grid_size.x = (h_n_splines / block_size.x) + 1;
                                                          +
                                                          721
                                                          +
                                                          722 // Copy the parameter values values to the GPU (vals_gpu), which is h_n_params long
                                                          +
                                                          723 cudaMemcpyToSymbol(val_gpu, vals, h_n_params*sizeof(float));
                                                          +
                                                          724 CudaCheckError();
                                                          +
                                                          725
                                                          +
                                                          726#ifdef DEBUG
                                                          +
                                                          727 printf("\n***********************\nGPU DEBUGGING ENABLED\n***********************\n");
                                                          +
                                                          728 printf("block_size.x = %i, grid_size.x = %i \n", block_size.x, grid_size.x);
                                                          +
                                                          729 printf("RunGPU_TF1 segments\n");
                                                          +
                                                          730 for (int i = 0; i < h_n_params; i++) {
                                                          +
                                                          731 printf("val[%i] = %f \n", i, vals[i]);
                                                          +
                                                          732 }
                                                          +
                                                          733 printf("nParams = %i, n_splines = %i", h_n_params, h_n_splines);
                                                          +
                                                          734 printf("\n***********************\nAM NOW CALLING KERNEL\n***********************\n");
                                                          +
                                                          735#endif
                                                          +
                                                          736
                                                          +
                                                          737 // Set the cache config to prefer L1 for the kernel
                                                          +
                                                          738 //cudaFuncSetCacheConfig(EvalOnGPU_TF1, cudaFuncCachePreferL1);
                                                          +
                                                          739 EvalOnGPU_TF1<<<grid_size, block_size>>>(
                                                          +
                                                          740 gpu_coeffs,
                                                          +
                                                          741 gpu_paramNo_arr,
                                                          +
                                                          742 gpu_nPoints_arr,
                                                          +
                                                          743
                                                          +
                                                          744 gpu_weights
                                                          +
                                                          745 );
                                                          +
                                                          746 CudaCheckError();
                                                          +
                                                          747
                                                          +
                                                          748#ifdef DEBUG
                                                          +
                                                          749 printf("Evaluated TF1 kernel with SUCCESS (drink beer)\n");
                                                          +
                                                          750#endif
                                                          +
                                                          751
                                                          +
                                                          752//KS: We can either copy gpu_weight and calculate total weight in reweighting loop, or not copy and calculate total weight stall at GPU, which means less memory transfer
                                                          +
                                                          753#ifdef Weight_On_SplineBySpline_Basis
                                                          +
                                                          754 // Here we have to make a somewhat large GPU->CPU transfer because it's all the splines' response
                                                          +
                                                          755 cudaMemcpy(cpu_weights, gpu_weights, h_n_splines*sizeof(float), cudaMemcpyDeviceToHost);
                                                          +
                                                          756 CudaCheckError();
                                                          +
                                                          757
                                                          +
                                                          758 #ifdef DEBUG
                                                          +
                                                          759 printf("Copied TF1 GPU weights to CPU with SUCCESS (drink moar beer)\n");
                                                          +
                                                          760 printf("Released TF1 calculated response from GPU with SUCCESS (drink most beer)\n");
                                                          +
                                                          761 #endif
                                                          +
                                                          762
                                                          +
                                                          763//KS: Else calculate Total Weight
                                                          +
                                                          764#else
                                                          +
                                                          765 grid_size.x = (h_n_events / block_size.x) + 1;
                                                          +
                                                          766
                                                          +
                                                          767 #ifdef DEBUG
                                                          +
                                                          768 printf("\n***********************\nGPU DEBUGGING ENABLED\n***********************\n");
                                                          +
                                                          769 printf("block_size.x = %i, grid_size.x = %i \n", block_size.x, grid_size.x);
                                                          +
                                                          770 printf("RunGPU_TotWeight\n");
                                                          +
                                                          771
                                                          +
                                                          772 printf("nEvents = %i, n_splines = %i, d_n_params", h_n_events, h_n_splines, h_n_params);
                                                          +
                                                          773 printf("\n***********************\nI AM NOW CALLING KERNEL\n***********************\n");
                                                          +
                                                          774 #endif
                                                          +
                                                          775 EvalOnGPU_TotWeight<<<grid_size, block_size>>>(
                                                          +
                                                          776 gpu_weights,
                                                          +
                                                          777 gpu_total_weights,
                                                          +
                                                          778 text_nParamPerEvent
                                                          +
                                                          779 );
                                                          +
                                                          780 #ifdef DEBUG
                                                          +
                                                          781 CudaCheckError();
                                                          +
                                                          782 printf("Evaluated kernel with SUCCESS (drink tea)\n");
                                                          +
                                                          783 #endif
                                                          +
                                                          784 //KS: Here we have to make a somewhat large GPU->CPU transfer because it is proportional to number of events
                                                          +
                                                          785 //KS: In the future it might be worth to calculate only weight for events which have splines, this should reduce memory transfer
                                                          +
                                                          786 cudaMemcpy(cpu_total_weights, gpu_total_weights, h_n_events*sizeof(float), cudaMemcpyDeviceToHost);
                                                          +
                                                          787 #ifdef DEBUG
                                                          +
                                                          788 CudaCheckError();
                                                          +
                                                          789 printf("Copied GPU total weights to CPU with SUCCESS (drink moar tea)\n");
                                                          +
                                                          790 printf("Released calculated response from GPU with SUCCESS (drink most tea)\n");
                                                          +
                                                          791 #endif
                                                          +
                                                          792#endif
                                                          +
                                                          793}
                                                          -
                                                          792
                                                          -
                                                          793// *****************************************
                                                          -
                                                          -
                                                          795__host__ void SynchroniseSplines() {
                                                          -
                                                          796 cudaDeviceSynchronize();
                                                          -
                                                          797}
                                                          +
                                                          794
                                                          +
                                                          795// *****************************************
                                                          + -
                                                          798
                                                          -
                                                          799// *********************************
                                                          -
                                                          800// CLEANING
                                                          +
                                                          800
                                                          801// *********************************
                                                          -
                                                          802
                                                          +
                                                          802// CLEANING
                                                          803// *********************************
                                                          -
                                                          -
                                                          805__host__ void CleanupGPU_SepMany(
                                                          -
                                                          806 short int *gpu_paramNo_arr,
                                                          -
                                                          807 unsigned int *gpu_nKnots_arr,
                                                          -
                                                          808
                                                          -
                                                          809 float *gpu_x_array,
                                                          -
                                                          810 float *gpu_many_array,
                                                          -
                                                          811#ifndef Weight_On_SplineBySpline_Basis
                                                          -
                                                          812 float *gpu_total_weights,
                                                          -
                                                          813 unsigned int *gpu_nParamPerEvent,
                                                          -
                                                          814 float *cpu_total_weights,
                                                          -
                                                          815#endif
                                                          -
                                                          816 float *gpu_weights) {
                                                          -
                                                          817// *********************************
                                                          -
                                                          818 cudaFree(gpu_paramNo_arr);
                                                          -
                                                          819 cudaFree(gpu_nKnots_arr);
                                                          -
                                                          820
                                                          -
                                                          821 // free the coefficient arrays
                                                          -
                                                          822 cudaDestroyTextureObject(text_coeff_x);
                                                          -
                                                          823 cudaFree(gpu_x_array);
                                                          -
                                                          824 cudaFree(gpu_many_array);
                                                          -
                                                          825
                                                          -
                                                          826 // free weights on the gpu
                                                          -
                                                          827 cudaFree(gpu_weights);
                                                          -
                                                          828#ifndef Weight_On_SplineBySpline_Basis
                                                          -
                                                          829 cudaFree(gpu_total_weights);
                                                          -
                                                          830 //KS: Before removing variable let's destroy texture
                                                          -
                                                          831 cudaDestroyTextureObject(text_nParamPerEvent);
                                                          -
                                                          832 cudaFree(gpu_nParamPerEvent);
                                                          -
                                                          833 cudaFreeHost(cpu_total_weights);
                                                          -
                                                          834 cpu_total_weights = nullptr;
                                                          -
                                                          835#endif
                                                          -
                                                          836 return;
                                                          -
                                                          837}
                                                          +
                                                          804
                                                          +
                                                          805// *********************************
                                                          +
                                                          +
                                                          807__host__ void CleanupGPU_SepMany(
                                                          +
                                                          808 short int *gpu_paramNo_arr,
                                                          +
                                                          809 unsigned int *gpu_nKnots_arr,
                                                          +
                                                          810
                                                          +
                                                          811 float *gpu_x_array,
                                                          +
                                                          812 float *gpu_many_array,
                                                          +
                                                          813#ifndef Weight_On_SplineBySpline_Basis
                                                          +
                                                          814 float *gpu_total_weights,
                                                          +
                                                          815 unsigned int *gpu_nParamPerEvent,
                                                          +
                                                          816 float *cpu_total_weights,
                                                          +
                                                          817#endif
                                                          +
                                                          818 float *gpu_weights) {
                                                          +
                                                          819// *********************************
                                                          +
                                                          820 cudaFree(gpu_paramNo_arr);
                                                          +
                                                          821 cudaFree(gpu_nKnots_arr);
                                                          +
                                                          822
                                                          +
                                                          823 // free the coefficient arrays
                                                          +
                                                          824 cudaDestroyTextureObject(text_coeff_x);
                                                          +
                                                          825 cudaFree(gpu_x_array);
                                                          +
                                                          826 cudaFree(gpu_many_array);
                                                          +
                                                          827
                                                          +
                                                          828 // free weights on the gpu
                                                          +
                                                          829 cudaFree(gpu_weights);
                                                          +
                                                          830#ifndef Weight_On_SplineBySpline_Basis
                                                          +
                                                          831 cudaFree(gpu_total_weights);
                                                          +
                                                          832 //KS: Before removing variable let's destroy texture
                                                          +
                                                          833 cudaDestroyTextureObject(text_nParamPerEvent);
                                                          +
                                                          834 cudaFree(gpu_nParamPerEvent);
                                                          +
                                                          835 cudaFreeHost(cpu_total_weights);
                                                          +
                                                          836 cpu_total_weights = nullptr;
                                                          +
                                                          837#endif
                                                          +
                                                          838 return;
                                                          +
                                                          839}
                                                          -
                                                          838
                                                          -
                                                          839// *******************************************
                                                          -
                                                          -
                                                          841__host__ void CleanupGPU_Segments(short int *segment, float *vals) {
                                                          -
                                                          842// *******************************************
                                                          -
                                                          843 cudaFreeHost(segment);
                                                          -
                                                          844 cudaFreeHost(vals);
                                                          -
                                                          845
                                                          -
                                                          846 segment = nullptr;
                                                          -
                                                          847 vals = nullptr;
                                                          -
                                                          848
                                                          -
                                                          849 return;
                                                          -
                                                          850}
                                                          +
                                                          840
                                                          +
                                                          841// *******************************************
                                                          +
                                                          +
                                                          843__host__ void CleanupGPU_Segments(short int *segment, float *vals) {
                                                          +
                                                          844// *******************************************
                                                          +
                                                          845 cudaFreeHost(segment);
                                                          +
                                                          846 cudaFreeHost(vals);
                                                          +
                                                          847
                                                          +
                                                          848 segment = nullptr;
                                                          +
                                                          849 vals = nullptr;
                                                          +
                                                          850
                                                          +
                                                          851 return;
                                                          +
                                                          852}
                                                          -
                                                          851
                                                          -
                                                          852// *********************************
                                                          -
                                                          -
                                                          854__host__ void CleanupGPU_TF1(
                                                          -
                                                          855 float *gpu_coeffs,
                                                          -
                                                          856 short int *gpu_paramNo_arr,
                                                          -
                                                          857 short int *gpu_nPoints_arr,
                                                          -
                                                          858
                                                          -
                                                          859#ifndef Weight_On_SplineBySpline_Basis
                                                          -
                                                          860 float *gpu_total_weights,
                                                          -
                                                          861 float *cpu_total_weights,
                                                          -
                                                          862#endif
                                                          -
                                                          863 float *gpu_weights) {
                                                          -
                                                          864// *********************************
                                                          -
                                                          865 cudaFree(gpu_coeffs);
                                                          -
                                                          866 cudaFree(gpu_paramNo_arr);
                                                          -
                                                          867 cudaFree(gpu_nPoints_arr);
                                                          -
                                                          868 cudaFree(gpu_weights);
                                                          -
                                                          869#ifndef Weight_On_SplineBySpline_Basis
                                                          -
                                                          870 cudaFree(gpu_total_weights);
                                                          -
                                                          871 cudaFreeHost(cpu_total_weights);
                                                          -
                                                          872#endif
                                                          -
                                                          873
                                                          -
                                                          874 return;
                                                          -
                                                          875}
                                                          +
                                                          853
                                                          +
                                                          854// *********************************
                                                          +
                                                          +
                                                          856__host__ void CleanupGPU_TF1(
                                                          +
                                                          857 float *gpu_coeffs,
                                                          +
                                                          858 short int *gpu_paramNo_arr,
                                                          +
                                                          859 short int *gpu_nPoints_arr,
                                                          +
                                                          860
                                                          +
                                                          861#ifndef Weight_On_SplineBySpline_Basis
                                                          +
                                                          862 float *gpu_total_weights,
                                                          +
                                                          863 float *cpu_total_weights,
                                                          +
                                                          864#endif
                                                          +
                                                          865 float *gpu_weights) {
                                                          +
                                                          866// *********************************
                                                          +
                                                          867 cudaFree(gpu_coeffs);
                                                          +
                                                          868 cudaFree(gpu_paramNo_arr);
                                                          +
                                                          869 cudaFree(gpu_nPoints_arr);
                                                          +
                                                          870 cudaFree(gpu_weights);
                                                          +
                                                          871#ifndef Weight_On_SplineBySpline_Basis
                                                          +
                                                          872 cudaFree(gpu_total_weights);
                                                          +
                                                          873 cudaFreeHost(cpu_total_weights);
                                                          +
                                                          874#endif
                                                          +
                                                          875
                                                          +
                                                          876 return;
                                                          +
                                                          877}
                                                          _nCoeff_
                                                          #define _nCoeff_
                                                          KS: We store coefficients {y,b,c,d} in one array one by one, this is only to define it once rather th...
                                                          Definition SplineCommon.h:8
                                                          -
                                                          GetFromManager
                                                          Type GetFromManager(const YAML::Node &node, Type defval)
                                                          Get content of config file if node is not found take default value specified.
                                                          Definition YamlHelper.h:18
                                                          -
                                                          CopyToGPU_SepMany
                                                          __host__ void CopyToGPU_SepMany(short int *gpu_paramNo_arr, unsigned int *gpu_nKnots_arr, float *gpu_x_array, float *gpu_many_array, std::vector< short int > paramNo_arr, std::vector< unsigned int > nKnots_arr, std::vector< float > cpu_x_array, std::vector< float > cpu_many_array, int n_events, std::vector< unsigned int > cpu_nParamPerEvent, unsigned int *gpu_nParamPerEvent, int n_params, unsigned int n_splines, short int spline_size, unsigned int sizeof_array)
                                                          Copy to GPU for x array and separate ybcd array.
                                                          Definition gpuSplineUtils.cu:251
                                                          -
                                                          InitGPU_SepMany
                                                          __host__ void InitGPU_SepMany(float **gpu_x_array, float **gpu_many_array, float **gpu_weights, short int **gpu_paramNo_arr, unsigned int **gpu_nKnots_arr, float **cpu_total_weights, float **gpu_total_weights, int n_events, unsigned int **gpu_nParamPerEvent, unsigned int sizeof_array, unsigned int n_splines, int Eve_size)
                                                          Initialiser when using the x array and combined y,b,c,d array.
                                                          Definition gpuSplineUtils.cu:106
                                                          -
                                                          text_coeff_x
                                                          cudaTextureObject_t text_coeff_x
                                                          Definition gpuSplineUtils.cu:93
                                                          -
                                                          h_n_params
                                                          static int h_n_params
                                                          Definition gpuSplineUtils.cu:84
                                                          -
                                                          h_spline_size
                                                          static short int h_spline_size
                                                          Definition gpuSplineUtils.cu:83
                                                          -
                                                          CopyToGPU_TF1
                                                          __host__ void CopyToGPU_TF1(float *gpu_coeffs, short int *gpu_paramNo_arr, short int *gpu_nPoints_arr, std::vector< float > cpu_coeffs, std::vector< short int > paramNo_arr, std::vector< short int > nPoints_arr, int n_events, std::vector< unsigned int > cpu_nParamPerEvent, unsigned int *gpu_nParamPerEvent, int n_params, unsigned int n_splines, short int _max_knots)
                                                          Copy to GPU for x array and separate ybcd array.
                                                          Definition gpuSplineUtils.cu:357
                                                          +
                                                          GetFromManager
                                                          Type GetFromManager(const YAML::Node &node, Type defval)
                                                          Get content of config file if node is not found take default value specified.
                                                          Definition YamlHelper.h:21
                                                          +
                                                          CopyToGPU_SepMany
                                                          __host__ void CopyToGPU_SepMany(short int *gpu_paramNo_arr, unsigned int *gpu_nKnots_arr, float *gpu_x_array, float *gpu_many_array, std::vector< short int > paramNo_arr, std::vector< unsigned int > nKnots_arr, std::vector< float > cpu_x_array, std::vector< float > cpu_many_array, int n_events, std::vector< unsigned int > cpu_nParamPerEvent, unsigned int *gpu_nParamPerEvent, int n_params, unsigned int n_splines, short int spline_size, unsigned int sizeof_array)
                                                          Copy to GPU for x array and separate ybcd array.
                                                          Definition gpuSplineUtils.cu:256
                                                          +
                                                          InitGPU_SepMany
                                                          __host__ void InitGPU_SepMany(float **gpu_x_array, float **gpu_many_array, float **gpu_weights, short int **gpu_paramNo_arr, unsigned int **gpu_nKnots_arr, float **cpu_total_weights, float **gpu_total_weights, int n_events, unsigned int **gpu_nParamPerEvent, unsigned int sizeof_array, unsigned int n_splines, int Eve_size)
                                                          Initialiser when using the x array and combined y,b,c,d array.
                                                          Definition gpuSplineUtils.cu:112
                                                          +
                                                          text_coeff_x
                                                          cudaTextureObject_t text_coeff_x
                                                          KS: Textures are L1 cache variables which are well optimised for fetching. Make texture only for vari...
                                                          Definition gpuSplineUtils.cu:99
                                                          +
                                                          h_n_params
                                                          static int h_n_params
                                                          Number of params living on CPU.
                                                          Definition gpuSplineUtils.cu:89
                                                          +
                                                          h_spline_size
                                                          static short int h_spline_size
                                                          Number of splines living on CPU.
                                                          Definition gpuSplineUtils.cu:87
                                                          +
                                                          CopyToGPU_TF1
                                                          __host__ void CopyToGPU_TF1(float *gpu_coeffs, short int *gpu_paramNo_arr, short int *gpu_nPoints_arr, std::vector< float > cpu_coeffs, std::vector< short int > paramNo_arr, std::vector< short int > nPoints_arr, int n_events, std::vector< unsigned int > cpu_nParamPerEvent, unsigned int *gpu_nParamPerEvent, int n_params, unsigned int n_splines, short int _max_knots)
                                                          Copy to GPU for x array and separate ybcd array.
                                                          Definition gpuSplineUtils.cu:362
                                                          _N_SPLINES_
                                                          #define _N_SPLINES_
                                                          Definition gpuSplineUtils.cu:20
                                                          -
                                                          InitGPU_TF1
                                                          __host__ void InitGPU_TF1(float **gpu_coeffs, short int **gpu_paramNo_arr, short int **gpu_nPoints_arr, float **gpu_weights, float **cpu_total_weights, float **gpu_total_weights, int n_events, unsigned int **gpu_nParamPerEvent, unsigned int n_splines)
                                                          Initialiser when using the x array and combined y,b,c,d array.
                                                          Definition gpuSplineUtils.cu:168
                                                          -
                                                          EvalOnGPU_TF1
                                                          __global__ void EvalOnGPU_TF1(const float *__restrict__ gpu_coeffs, const short int *__restrict__ gpu_paramNo_arr, const short int *__restrict__ gpu_nPoints_arr, float *gpu_weights)
                                                          Evaluate the TF1 on the GPU Using 5th order polynomial.
                                                          Definition gpuSplineUtils.cu:509
                                                          -
                                                          InitGPU_Segments
                                                          __host__ void InitGPU_Segments(short int **segment)
                                                          Definition gpuSplineUtils.cu:226
                                                          -
                                                          RunGPU_TF1
                                                          __host__ void RunGPU_TF1(const float *gpu_coeffs, const short int *gpu_paramNo_arr, const short int *gpu_nPoints_arr, float *gpu_weights, float *gpu_total_weights, float *cpu_total_weights, float *vals, const unsigned int h_n_splines)
                                                          Run the GPU code for the TF1.
                                                          Definition gpuSplineUtils.cu:696
                                                          -
                                                          d_n_splines
                                                          __device__ __constant__ unsigned int d_n_splines
                                                          Definition gpuSplineUtils.cu:73
                                                          -
                                                          SynchroniseSplines
                                                          __host__ void SynchroniseSplines()
                                                          Make sure all Cuda threads finished execution.
                                                          Definition gpuSplineUtils.cu:795
                                                          -
                                                          h_n_events
                                                          static int h_n_events
                                                          Definition gpuSplineUtils.cu:86
                                                          -
                                                          segment_gpu
                                                          __device__ __constant__ short int segment_gpu[_N_SPLINES_]
                                                          Definition gpuSplineUtils.cu:80
                                                          -
                                                          CleanupGPU_SepMany
                                                          __host__ void CleanupGPU_SepMany(short int *gpu_paramNo_arr, unsigned int *gpu_nKnots_arr, float *gpu_x_array, float *gpu_many_array, float *gpu_total_weights, unsigned int *gpu_nParamPerEvent, float *cpu_total_weights, float *gpu_weights)
                                                          Clean up the {x},{ybcd} arrays.
                                                          Definition gpuSplineUtils.cu:805
                                                          -
                                                          InitGPU_Vals
                                                          __host__ void InitGPU_Vals(float **vals)
                                                          Definition gpuSplineUtils.cu:236
                                                          -
                                                          d_n_events
                                                          __device__ __constant__ int d_n_events
                                                          Definition gpuSplineUtils.cu:76
                                                          -
                                                          EvalOnGPU_TotWeight
                                                          __global__ void EvalOnGPU_TotWeight(const float *__restrict__ gpu_weights, float *gpu_total_weights, const cudaTextureObject_t __restrict__ text_nParamPerEvent)
                                                          KS: Evaluate the total spline event weight on the GPU, as in most cases GPU is faster,...
                                                          Definition gpuSplineUtils.cu:559
                                                          -
                                                          d_spline_size
                                                          __device__ __constant__ short int d_spline_size
                                                          Definition gpuSplineUtils.cu:74
                                                          -
                                                          CleanupGPU_Segments
                                                          __host__ void CleanupGPU_Segments(short int *segment, float *vals)
                                                          Clean up pinned variables at CPU.
                                                          Definition gpuSplineUtils.cu:841
                                                          -
                                                          val_gpu
                                                          __device__ __constant__ float val_gpu[_N_SPLINES_]
                                                          CW: Constant memory needs to be hard-coded on compile time. Could make this texture memory instead,...
                                                          Definition gpuSplineUtils.cu:79
                                                          -
                                                          RunGPU_SepMany
                                                          __host__ void RunGPU_SepMany(const short int *gpu_paramNo_arr, const unsigned int *gpu_nKnots_arr, const float *gpu_coeff_many, float *gpu_weights, float *gpu_total_weights, float *cpu_total_weights, float *vals, short int *segment, const unsigned int h_n_splines)
                                                          Definition gpuSplineUtils.cu:589
                                                          -
                                                          EvalOnGPU_SepMany
                                                          __global__ void EvalOnGPU_SepMany(const short int *__restrict__ gpu_paramNo_arr, const unsigned int *__restrict__ gpu_nKnots_arr, const float *__restrict__ gpu_coeff_many, float *gpu_weights, const cudaTextureObject_t __restrict__ text_coeff_x)
                                                          Definition gpuSplineUtils.cu:451
                                                          -
                                                          text_nParamPerEvent
                                                          cudaTextureObject_t text_nParamPerEvent
                                                          Definition gpuSplineUtils.cu:96
                                                          -
                                                          CleanupGPU_TF1
                                                          __host__ void CleanupGPU_TF1(float *gpu_coeffs, short int *gpu_paramNo_arr, short int *gpu_nPoints_arr, float *gpu_total_weights, float *cpu_total_weights, float *gpu_weights)
                                                          Clean up the TF1 arrays.
                                                          Definition gpuSplineUtils.cu:854
                                                          +
                                                          InitGPU_TF1
                                                          __host__ void InitGPU_TF1(float **gpu_coeffs, short int **gpu_paramNo_arr, short int **gpu_nPoints_arr, float **gpu_weights, float **cpu_total_weights, float **gpu_total_weights, int n_events, unsigned int **gpu_nParamPerEvent, unsigned int n_splines)
                                                          Initialiser when using the x array and combined y,b,c,d array.
                                                          Definition gpuSplineUtils.cu:174
                                                          +
                                                          EvalOnGPU_TF1
                                                          __global__ void EvalOnGPU_TF1(const float *__restrict__ gpu_coeffs, const short int *__restrict__ gpu_paramNo_arr, const short int *__restrict__ gpu_nPoints_arr, float *gpu_weights)
                                                          Evaluate the TF1 on the GPU Using 5th order polynomial.
                                                          Definition gpuSplineUtils.cu:512
                                                          +
                                                          InitGPU_Segments
                                                          __host__ void InitGPU_Segments(short int **segment)
                                                          Allocate memory for spline segments.
                                                          Definition gpuSplineUtils.cu:232
                                                          +
                                                          RunGPU_TF1
                                                          __host__ void RunGPU_TF1(const float *gpu_coeffs, const short int *gpu_paramNo_arr, const short int *gpu_nPoints_arr, float *gpu_weights, float *gpu_total_weights, float *cpu_total_weights, float *vals, const unsigned int h_n_splines)
                                                          Run the GPU code for the TF1.
                                                          Definition gpuSplineUtils.cu:698
                                                          +
                                                          d_n_splines
                                                          __device__ __constant__ unsigned int d_n_splines
                                                          Number of splines living on GPU.
                                                          Definition gpuSplineUtils.cu:74
                                                          +
                                                          SynchroniseSplines
                                                          __host__ void SynchroniseSplines()
                                                          Make sure all Cuda threads finished execution.
                                                          Definition gpuSplineUtils.cu:797
                                                          +
                                                          h_n_events
                                                          static int h_n_events
                                                          Number of events living on CPU.
                                                          Definition gpuSplineUtils.cu:92
                                                          +
                                                          segment_gpu
                                                          __device__ __constant__ short int segment_gpu[_N_SPLINES_]
                                                          Definition gpuSplineUtils.cu:83
                                                          +
                                                          CleanupGPU_SepMany
                                                          __host__ void CleanupGPU_SepMany(short int *gpu_paramNo_arr, unsigned int *gpu_nKnots_arr, float *gpu_x_array, float *gpu_many_array, float *gpu_total_weights, unsigned int *gpu_nParamPerEvent, float *cpu_total_weights, float *gpu_weights)
                                                          Clean up the {x},{ybcd} arrays.
                                                          Definition gpuSplineUtils.cu:807
                                                          +
                                                          InitGPU_Vals
                                                          __host__ void InitGPU_Vals(float **vals)
                                                          Definition gpuSplineUtils.cu:241
                                                          +
                                                          d_n_events
                                                          __device__ __constant__ int d_n_events
                                                          Number of events living on GPU.
                                                          Definition gpuSplineUtils.cu:79
                                                          +
                                                          EvalOnGPU_TotWeight
                                                          __global__ void EvalOnGPU_TotWeight(const float *__restrict__ gpu_weights, float *gpu_total_weights, const cudaTextureObject_t __restrict__ text_nParamPerEvent)
                                                          KS: Evaluate the total spline event weight on the GPU, as in most cases GPU is faster,...
                                                          Definition gpuSplineUtils.cu:562
                                                          +
                                                          d_spline_size
                                                          __device__ __constant__ short int d_spline_size
                                                          Size of splines living on GPU.
                                                          Definition gpuSplineUtils.cu:76
                                                          +
                                                          CleanupGPU_Segments
                                                          __host__ void CleanupGPU_Segments(short int *segment, float *vals)
                                                          Clean up pinned variables at CPU.
                                                          Definition gpuSplineUtils.cu:843
                                                          +
                                                          val_gpu
                                                          __device__ __constant__ float val_gpu[_N_SPLINES_]
                                                          CW: Constant memory needs to be hard-coded on compile time. Could make this texture memory instead,...
                                                          Definition gpuSplineUtils.cu:82
                                                          +
                                                          RunGPU_SepMany
                                                          __host__ void RunGPU_SepMany(const short int *gpu_paramNo_arr, const unsigned int *gpu_nKnots_arr, const float *gpu_coeff_many, float *gpu_weights, float *gpu_total_weights, float *cpu_total_weights, float *vals, short int *segment, const unsigned int h_n_splines)
                                                          Run the GPU code for the separate many arrays. As in separate {x}, {y,b,c,d} arrays Pass the segment ...
                                                          Definition gpuSplineUtils.cu:591
                                                          +
                                                          EvalOnGPU_SepMany
                                                          __global__ void EvalOnGPU_SepMany(const short int *__restrict__ gpu_paramNo_arr, const unsigned int *__restrict__ gpu_nKnots_arr, const float *__restrict__ gpu_coeff_many, float *gpu_weights, const cudaTextureObject_t __restrict__ text_coeff_x)
                                                          Evaluate the spline on the GPU Using one {y,b,c,d} array and one {x} array Should be most efficient a...
                                                          Definition gpuSplineUtils.cu:454
                                                          +
                                                          text_nParamPerEvent
                                                          cudaTextureObject_t text_nParamPerEvent
                                                          KS: Map keeping track how many parameters applies to each event, we keep two numbers here {number of ...
                                                          Definition gpuSplineUtils.cu:102
                                                          +
                                                          CleanupGPU_TF1
                                                          __host__ void CleanupGPU_TF1(float *gpu_coeffs, short int *gpu_paramNo_arr, short int *gpu_nPoints_arr, float *gpu_total_weights, float *cpu_total_weights, float *gpu_weights)
                                                          Clean up the TF1 arrays.
                                                          Definition gpuSplineUtils.cu:856
                                                          checkGpuMem
                                                          void checkGpuMem()
                                                          KS: Get some fancy info about VRAM usage.
                                                          Definition gpuUtils.cu:45
                                                          PrintNdevices
                                                          void PrintNdevices()
                                                          KS: Get some fancy info about GPU.
                                                          Definition gpuUtils.cu:63
                                                          diff --git a/gpuUtils_8cu.html b/gpuUtils_8cu.html index 7c96944c0..40e03ff23 100644 --- a/gpuUtils_8cu.html +++ b/gpuUtils_8cu.html @@ -136,6 +136,13 @@

                                                          Check if there's been an error.

                                                          +

                                                          This function checks if there has been any CUDA runtime API error and reports it.

                                                          Parameters
                                                          + + + +
                                                          fileThe file name where the error occurred.
                                                          lineThe line number where the error occurred.
                                                          +
                                                          +

                                                          Definition at line 19 of file gpuUtils.cu.

                                                          19 {
                                                          @@ -157,7 +164,7 @@

                                                          35#endif

                                                          36 return;
                                                          37}
                                                          -
                                                          GetFromManager
                                                          Type GetFromManager(const YAML::Node &node, Type defval)
                                                          Get content of config file if node is not found take default value specified.
                                                          Definition YamlHelper.h:18
                                                          +
                                                          GetFromManager
                                                          Type GetFromManager(const YAML::Node &node, Type defval)
                                                          Get content of config file if node is not found take default value specified.
                                                          Definition YamlHelper.h:21

                                                          @@ -194,6 +201,14 @@

                                                          Check for a safe call on GPU.

                                                          +

                                                          This function checks the error status returned by CUDA runtime API functions and reports any errors.

                                                          Parameters
                                                          + + + + +
                                                          errThe CUDA error code.
                                                          fileThe file name where the error occurred.
                                                          lineThe line number where the error occurred.
                                                          +
                                                          +

                                                          Definition at line 6 of file gpuUtils.cu.

                                                          6 {
                                                          @@ -256,13 +271,20 @@

                                                          int GetNumGPUThreads ( const int  - Device) + Device = 0)

                                                          KS: Get number of GPU threads for currently used GPU.

                                                          +
                                                          Parameters
                                                          + + +
                                                          DeviceThe ID of the device. Defaults to 0.
                                                          +
                                                          +
                                                          +
                                                          Returns
                                                          The number of GPU threads.

                                                          Definition at line 110 of file gpuUtils.cu.

                                                          110 {
                                                          diff --git a/gpuUtils_8cu_source.html b/gpuUtils_8cu_source.html index 9a6785516..11e3b07cc 100644 --- a/gpuUtils_8cu_source.html +++ b/gpuUtils_8cu_source.html @@ -224,7 +224,7 @@
                                                          127 return nThreadsBlocks;
                                                          128}
                                                          -
                                                          GetFromManager
                                                          Type GetFromManager(const YAML::Node &node, Type defval)
                                                          Get content of config file if node is not found take default value specified.
                                                          Definition YamlHelper.h:18
                                                          +
                                                          GetFromManager
                                                          Type GetFromManager(const YAML::Node &node, Type defval)
                                                          Get content of config file if node is not found take default value specified.
                                                          Definition YamlHelper.h:21
                                                          __cudaCheckError
                                                          void __cudaCheckError(const char *file, const int line)
                                                          Check if there's been an error.
                                                          Definition gpuUtils.cu:19
                                                          SetDevice
                                                          void SetDevice(const int deviceId)
                                                          Only useful if using multiple GPU.
                                                          Definition gpuUtils.cu:91
                                                          ResetDevice
                                                          void ResetDevice()
                                                          KS: Completely clean GPU, this is time consuming and may lead to unexpected behaviour.
                                                          Definition gpuUtils.cu:81
                                                          diff --git a/gpuUtils_8cuh.html b/gpuUtils_8cuh.html index 3f9b7f9c5..cd3f01e03 100644 --- a/gpuUtils_8cuh.html +++ b/gpuUtils_8cuh.html @@ -215,6 +215,13 @@

                                                          Check if there's been an error.

                                                          +

                                                          This function checks if there has been any CUDA runtime API error and reports it.

                                                          Parameters
                                                          + + + +
                                                          fileThe file name where the error occurred.
                                                          lineThe line number where the error occurred.
                                                          +
                                                          +

                                                          Definition at line 19 of file gpuUtils.cu.

                                                          19 {
                                                          @@ -236,7 +243,7 @@

                                                          35#endif

                                                          36 return;
                                                          37}
                                                          -
                                                          GetFromManager
                                                          Type GetFromManager(const YAML::Node &node, Type defval)
                                                          Get content of config file if node is not found take default value specified.
                                                          Definition YamlHelper.h:18
                                                          +
                                                          GetFromManager
                                                          Type GetFromManager(const YAML::Node &node, Type defval)
                                                          Get content of config file if node is not found take default value specified.
                                                          Definition YamlHelper.h:21

                                                          @@ -281,6 +288,14 @@

                                                          Check for a safe call on GPU.

                                                          +

                                                          This function checks the error status returned by CUDA runtime API functions and reports any errors.

                                                          Parameters
                                                          + + + + +
                                                          errThe CUDA error code.
                                                          fileThe file name where the error occurred.
                                                          lineThe line number where the error occurred.
                                                          +
                                                          +

                                                          Definition at line 6 of file gpuUtils.cu.

                                                          6 {
                                                          @@ -350,6 +365,13 @@

                                                          KS: Get number of GPU threads for currently used GPU.

                                                          +
                                                          Parameters
                                                          + + +
                                                          DeviceThe ID of the device. Defaults to 0.
                                                          +
                                                          +
                                                          +
                                                          Returns
                                                          The number of GPU threads.

                                                          Definition at line 110 of file gpuUtils.cu.

                                                          110 {
                                                          @@ -453,6 +475,12 @@

                                                          KS: Only useful if using multiple GPU.

                                                          +
                                                          Parameters
                                                          + + +
                                                          deviceIdThe ID of the device to be set as active.
                                                          +
                                                          +

                                                          KS: Only useful if using multiple GPU.

                                                          Definition at line 91 of file gpuUtils.cu.

                                                          diff --git a/gpuUtils_8cuh_source.html b/gpuUtils_8cuh_source.html index c1aa948f9..8c153a09d 100644 --- a/gpuUtils_8cuh_source.html +++ b/gpuUtils_8cuh_source.html @@ -116,25 +116,25 @@
                                                          32// Also exist in helper_cuda.h
                                                          33// **************************************************
                                                          34
                                                          -
                                                          36void __cudaSafeCall( cudaError err, const char *file, const int line );
                                                          -
                                                          37
                                                          -
                                                          39void __cudaCheckError( const char *file, const int line );
                                                          -
                                                          40
                                                          -
                                                          41// *******************************************
                                                          -
                                                          42// Utils
                                                          -
                                                          43// *******************************************
                                                          -
                                                          44
                                                          -
                                                          45// *******************************************
                                                          -
                                                          47void checkGpuMem();
                                                          -
                                                          48
                                                          -
                                                          50void PrintNdevices();
                                                          +
                                                          40void __cudaSafeCall( cudaError err, const char *file, const int line );
                                                          +
                                                          41
                                                          +
                                                          46void __cudaCheckError( const char *file, const int line );
                                                          +
                                                          47
                                                          +
                                                          48// *******************************************
                                                          +
                                                          49// Utils
                                                          +
                                                          50// *******************************************
                                                          51
                                                          -
                                                          53void ResetDevice();
                                                          -
                                                          54
                                                          -
                                                          56void SetDevice(const int deviceId);
                                                          -
                                                          57
                                                          -
                                                          59int GetNumGPUThreads(const int Device = 0);
                                                          -
                                                          GetFromManager
                                                          Type GetFromManager(const YAML::Node &node, Type defval)
                                                          Get content of config file if node is not found take default value specified.
                                                          Definition YamlHelper.h:18
                                                          +
                                                          52// *******************************************
                                                          +
                                                          54void checkGpuMem();
                                                          +
                                                          55
                                                          +
                                                          57void PrintNdevices();
                                                          +
                                                          58
                                                          +
                                                          60void ResetDevice();
                                                          +
                                                          61
                                                          +
                                                          64void SetDevice(const int deviceId);
                                                          +
                                                          65
                                                          +
                                                          69int GetNumGPUThreads(const int Device = 0);
                                                          +
                                                          GetFromManager
                                                          Type GetFromManager(const YAML::Node &node, Type defval)
                                                          Get content of config file if node is not found take default value specified.
                                                          Definition YamlHelper.h:21
                                                          __cudaCheckError
                                                          void __cudaCheckError(const char *file, const int line)
                                                          Check if there's been an error.
                                                          Definition gpuUtils.cu:19
                                                          SetDevice
                                                          void SetDevice(const int deviceId)
                                                          KS: Only useful if using multiple GPU.
                                                          Definition gpuUtils.cu:91
                                                          ResetDevice
                                                          void ResetDevice()
                                                          KS: Completely clean GPU, this is time consuming and may lead to unexpected behaviour.
                                                          Definition gpuUtils.cu:81
                                                          diff --git a/hierarchy.html b/hierarchy.html index 98ff6af2d..7a19f78ad 100644 --- a/hierarchy.html +++ b/hierarchy.html @@ -76,7 +76,7 @@
                                                          This inheritance list is sorted roughly, but not completely, alphabetically:
                                                          [detail level 123]
                                                          - + diff --git a/kdeGpu2_8cu.html b/kdeGpu2_8cu.html index 0f1a625c2..db3283fbc 100644 --- a/kdeGpu2_8cu.html +++ b/kdeGpu2_8cu.html @@ -327,7 +327,7 @@

                                                          116 }
                                                          117 return;
                                                          118}
                                                          -
                                                          GetFromManager
                                                          Type GetFromManager(const YAML::Node &node, Type defval)
                                                          Get content of config file if node is not found take default value specified.
                                                          Definition YamlHelper.h:18
                                                          +
                                                          GetFromManager
                                                          Type GetFromManager(const YAML::Node &node, Type defval)
                                                          Get content of config file if node is not found take default value specified.
                                                          Definition YamlHelper.h:21
                                                          MULTI_DATA
                                                          #define MULTI_DATA
                                                          Definition kdeGpu2.cu:4
                                                          BLOCK_SIZE
                                                          #define BLOCK_SIZE
                                                          Definition kdeGpu2.cu:2
                                                          diff --git a/kdeGpu2_8cu_source.html b/kdeGpu2_8cu_source.html index 25b3cdff3..8e3435aa1 100644 --- a/kdeGpu2_8cu_source.html +++ b/kdeGpu2_8cu_source.html @@ -353,7 +353,7 @@
                                                          263}
                                                          264
                                                          -
                                                          GetFromManager
                                                          Type GetFromManager(const YAML::Node &node, Type defval)
                                                          Get content of config file if node is not found take default value specified.
                                                          Definition YamlHelper.h:18
                                                          +
                                                          GetFromManager
                                                          Type GetFromManager(const YAML::Node &node, Type defval)
                                                          Get content of config file if node is not found take default value specified.
                                                          Definition YamlHelper.h:21
                                                          CudaCheckError
                                                          #define CudaCheckError()
                                                          Definition gpuUtils.cuh:18
                                                          GRID_SIZE
                                                          #define GRID_SIZE
                                                          Definition kdeGpu2.cu:3
                                                          diff --git a/kdeGpu_8cu.html b/kdeGpu_8cu.html index 23d171dd8..c3d4a8a73 100644 --- a/kdeGpu_8cu.html +++ b/kdeGpu_8cu.html @@ -185,7 +185,7 @@

                                                          38 }
                                                          39 return;
                                                          40}
                                                          -
                                                          GetFromManager
                                                          Type GetFromManager(const YAML::Node &node, Type defval)
                                                          Get content of config file if node is not found take default value specified.
                                                          Definition YamlHelper.h:18
                                                          +
                                                          GetFromManager
                                                          Type GetFromManager(const YAML::Node &node, Type defval)
                                                          Get content of config file if node is not found take default value specified.
                                                          Definition YamlHelper.h:21
                                                          c_data_x
                                                          __constant__ double c_data_x[1000]
                                                          Definition kdeGpu.cu:10
                                                          diff --git a/kdeGpu_8cu_source.html b/kdeGpu_8cu_source.html index 2fb081cb6..891311138 100644 --- a/kdeGpu_8cu_source.html +++ b/kdeGpu_8cu_source.html @@ -217,7 +217,7 @@
                                                          127}
                                                          128
                                                          -
                                                          GetFromManager
                                                          Type GetFromManager(const YAML::Node &node, Type defval)
                                                          Get content of config file if node is not found take default value specified.
                                                          Definition YamlHelper.h:18
                                                          +
                                                          GetFromManager
                                                          Type GetFromManager(const YAML::Node &node, Type defval)
                                                          Get content of config file if node is not found take default value specified.
                                                          Definition YamlHelper.h:21
                                                          c_data_x
                                                          __constant__ double c_data_x[1000]
                                                          Definition kdeGpu.cu:10
                                                          calcPdfAtData
                                                          __global__ void calcPdfAtData(int n_data, int n_mc, double sigma, double *d_datamcweights, double *d_pdfatdata)
                                                          Definition kdeGpu.cu:42
                                                          diff --git a/manager_8cpp_source.html b/manager_8cpp_source.html index 5659e79f8..ef0090b9f 100644 --- a/manager_8cpp_source.html +++ b/manager_8cpp_source.html @@ -200,9 +200,9 @@
                                                          108}
                                                          config
                                                          YAML::Node config
                                                          Definition GetPostfitParamPlots.cpp:30
                                                          -
                                                          MACH3LOG_ERROR
                                                          #define MACH3LOG_ERROR
                                                          Definition MaCh3Logger.h:15
                                                          -
                                                          MACH3LOG_INFO
                                                          #define MACH3LOG_INFO
                                                          Definition MaCh3Logger.h:13
                                                          -
                                                          SetMaCh3LoggerFormat
                                                          void SetMaCh3LoggerFormat()
                                                          Set messaging format of the logger.
                                                          Definition MaCh3Logger.h:20
                                                          +
                                                          MACH3LOG_ERROR
                                                          #define MACH3LOG_ERROR
                                                          Definition MaCh3Logger.h:18
                                                          +
                                                          MACH3LOG_INFO
                                                          #define MACH3LOG_INFO
                                                          Definition MaCh3Logger.h:16
                                                          +
                                                          SetMaCh3LoggerFormat
                                                          void SetMaCh3LoggerFormat()
                                                          Set messaging format of the logger.
                                                          Definition MaCh3Logger.h:23
                                                          TestStatistic
                                                          TestStatistic
                                                          Make an enum of the test statistic that we're using.
                                                          Definition Structs.h:353
                                                          kNTestStatistics
                                                          @ kNTestStatistics
                                                          Definition Structs.h:359
                                                          kPearson
                                                          @ kPearson
                                                          Definition Structs.h:357
                                                          @@ -211,9 +211,9 @@
                                                          kDembinskiAbdelmottele
                                                          @ kDembinskiAbdelmottele
                                                          Definition Structs.h:358
                                                          kPoisson
                                                          @ kPoisson
                                                          Definition Structs.h:354
                                                          TestStatistic_ToString
                                                          std::string TestStatistic_ToString(TestStatistic i)
                                                          Convert a LLH type to a string.
                                                          Definition Structs.h:364
                                                          -
                                                          GetFromManager
                                                          Type GetFromManager(const YAML::Node &node, Type defval)
                                                          Get content of config file if node is not found take default value specified.
                                                          Definition YamlHelper.h:18
                                                          -
                                                          MaCh3Exception
                                                          Custom exception class for MaCh3 errors.
                                                          Definition MaCh3Exception.h:10
                                                          -
                                                          MaCh3Modes
                                                          KS: Class describing MaCh3 modes used in the analysis, it is being initialised from config.
                                                          Definition MaCh3Modes.h:32
                                                          +
                                                          GetFromManager
                                                          Type GetFromManager(const YAML::Node &node, Type defval)
                                                          Get content of config file if node is not found take default value specified.
                                                          Definition YamlHelper.h:21
                                                          +
                                                          MaCh3Exception
                                                          Custom exception class for MaCh3 errors.
                                                          Definition MaCh3Exception.h:12
                                                          +
                                                          MaCh3Modes
                                                          KS: Class describing MaCh3 modes used in the analysis, it is being initialised from config.
                                                          Definition MaCh3Modes.h:33
                                                          manager::SaveSettings
                                                          void SaveSettings(TFile *const OutputFile)
                                                          Add manager useful information's to TFile, in most cases to Fitter.
                                                          Definition manager.cpp:58
                                                          manager::FileName
                                                          std::string FileName
                                                          The name of the configuration file.
                                                          Definition manager.h:57
                                                          manager::Print
                                                          void Print()
                                                          Print currently used config.
                                                          Definition manager.cpp:102
                                                          diff --git a/manager_8h_source.html b/manager_8h_source.html index 7816e6994..5c581b36a 100644 --- a/manager_8h_source.html +++ b/manager_8h_source.html @@ -97,8 +97,8 @@
                                                          12#include "TBranch.h"
                                                          13#include "TMacro.h"
                                                          14
                                                          -
                                                          15#include "manager/MaCh3Logger.h"
                                                          -
                                                          16
                                                          +
                                                          15// MaCh3 Includes
                                                          +
                                                          16#include "manager/MaCh3Logger.h"
                                                          17#include "samplePDF/Structs.h"
                                                          18#include "manager/YamlHelper.h"
                                                          19#include "manager/Monitor.h"
                                                          @@ -136,8 +136,8 @@ -
                                                          GetFromManager
                                                          Type GetFromManager(const YAML::Node &node, Type defval)
                                                          Get content of config file if node is not found take default value specified.
                                                          Definition YamlHelper.h:18
                                                          -
                                                          MaCh3Modes
                                                          KS: Class describing MaCh3 modes used in the analysis, it is being initialised from config.
                                                          Definition MaCh3Modes.h:32
                                                          +
                                                          GetFromManager
                                                          Type GetFromManager(const YAML::Node &node, Type defval)
                                                          Get content of config file if node is not found take default value specified.
                                                          Definition YamlHelper.h:21
                                                          +
                                                          MaCh3Modes
                                                          KS: Class describing MaCh3 modes used in the analysis, it is being initialised from config.
                                                          Definition MaCh3Modes.h:33
                                                          manager
                                                          The manager class is responsible for managing configurations and settings.
                                                          Definition manager.h:28
                                                          manager::SaveSettings
                                                          void SaveSettings(TFile *const OutputFile)
                                                          Add manager useful information's to TFile, in most cases to Fitter.
                                                          Definition manager.cpp:58
                                                          manager::FileName
                                                          std::string FileName
                                                          The name of the configuration file.
                                                          Definition manager.h:57
                                                          diff --git a/mcmc_8cpp_source.html b/mcmc_8cpp_source.html index c264e4a0f..dc784acf7 100644 --- a/mcmc_8cpp_source.html +++ b/mcmc_8cpp_source.html @@ -369,31 +369,31 @@
                                                          271 #endif
                                                          272}
                                                          -
                                                          MACH3LOG_INFO
                                                          #define MACH3LOG_INFO
                                                          Definition MaCh3Logger.h:13
                                                          -
                                                          GetFromManager
                                                          Type GetFromManager(const YAML::Node &node, Type defval)
                                                          Get content of config file if node is not found take default value specified.
                                                          Definition YamlHelper.h:18
                                                          -
                                                          FitterBase
                                                          Base class for implementing fitting algorithms.
                                                          Definition FitterBase.h:23
                                                          -
                                                          FitterBase::osc
                                                          covarianceOsc * osc
                                                          handles oscillation parameters
                                                          Definition FitterBase.h:125
                                                          -
                                                          FitterBase::logLProp
                                                          double logLProp
                                                          proposed likelihood
                                                          Definition FitterBase.h:102
                                                          +
                                                          MACH3LOG_INFO
                                                          #define MACH3LOG_INFO
                                                          Definition MaCh3Logger.h:16
                                                          +
                                                          GetFromManager
                                                          Type GetFromManager(const YAML::Node &node, Type defval)
                                                          Get content of config file if node is not found take default value specified.
                                                          Definition YamlHelper.h:21
                                                          +
                                                          FitterBase
                                                          Base class for implementing fitting algorithms.
                                                          Definition FitterBase.h:24
                                                          +
                                                          FitterBase::osc
                                                          covarianceOsc * osc
                                                          handles oscillation parameters
                                                          Definition FitterBase.h:126
                                                          +
                                                          FitterBase::logLProp
                                                          double logLProp
                                                          proposed likelihood
                                                          Definition FitterBase.h:103
                                                          FitterBase::ProcessMCMC
                                                          void ProcessMCMC()
                                                          Process MCMC output.
                                                          Definition FitterBase.cpp:373
                                                          -
                                                          FitterBase::stepClock
                                                          TStopwatch * stepClock
                                                          tells how long single step/fit iteration took
                                                          Definition FitterBase.h:132
                                                          -
                                                          FitterBase::accCount
                                                          int accCount
                                                          counts accepted steps
                                                          Definition FitterBase.h:106
                                                          -
                                                          FitterBase::random
                                                          TRandom3 * random
                                                          Random number.
                                                          Definition FitterBase.h:137
                                                          -
                                                          FitterBase::systematics
                                                          std::vector< covarianceBase * > systematics
                                                          Systematic holder.
                                                          Definition FitterBase.h:122
                                                          +
                                                          FitterBase::stepClock
                                                          TStopwatch * stepClock
                                                          tells how long single step/fit iteration took
                                                          Definition FitterBase.h:133
                                                          +
                                                          FitterBase::accCount
                                                          int accCount
                                                          counts accepted steps
                                                          Definition FitterBase.h:107
                                                          +
                                                          FitterBase::random
                                                          TRandom3 * random
                                                          Random number.
                                                          Definition FitterBase.h:138
                                                          +
                                                          FitterBase::systematics
                                                          std::vector< covarianceBase * > systematics
                                                          Systematic holder.
                                                          Definition FitterBase.h:123
                                                          FitterBase::SaveOutput
                                                          void SaveOutput()
                                                          Save output and close files.
                                                          Definition FitterBase.cpp:241
                                                          FitterBase::SaveSettings
                                                          void SaveSettings()
                                                          Save the settings that the MCMC was run with.
                                                          Definition FitterBase.cpp:103
                                                          -
                                                          FitterBase::fitMan
                                                          manager * fitMan
                                                          The manager.
                                                          Definition FitterBase.h:92
                                                          -
                                                          FitterBase::step
                                                          unsigned int step
                                                          current state
                                                          Definition FitterBase.h:98
                                                          +
                                                          FitterBase::fitMan
                                                          manager * fitMan
                                                          The manager.
                                                          Definition FitterBase.h:93
                                                          +
                                                          FitterBase::step
                                                          unsigned int step
                                                          current state
                                                          Definition FitterBase.h:99
                                                          FitterBase::PrepareOutput
                                                          void PrepareOutput()
                                                          Prepare the output file.
                                                          Definition FitterBase.cpp:169
                                                          -
                                                          FitterBase::accProb
                                                          double accProb
                                                          current acceptance prob
                                                          Definition FitterBase.h:104
                                                          -
                                                          FitterBase::sample_llh
                                                          double * sample_llh
                                                          store the llh breakdowns
                                                          Definition FitterBase.h:112
                                                          -
                                                          FitterBase::stepTime
                                                          double stepTime
                                                          Time of single step.
                                                          Definition FitterBase.h:134
                                                          -
                                                          FitterBase::logLCurr
                                                          double logLCurr
                                                          current likelihood
                                                          Definition FitterBase.h:100
                                                          -
                                                          FitterBase::osc_llh
                                                          double osc_llh
                                                          Definition FitterBase.h:110
                                                          -
                                                          FitterBase::syst_llh
                                                          double * syst_llh
                                                          systematic llh breakdowns
                                                          Definition FitterBase.h:114
                                                          -
                                                          FitterBase::auto_save
                                                          int auto_save
                                                          auto save every N steps
                                                          Definition FitterBase.h:146
                                                          -
                                                          FitterBase::outTree
                                                          TTree * outTree
                                                          Output tree with posteriors.
                                                          Definition FitterBase.h:144
                                                          -
                                                          FitterBase::samples
                                                          std::vector< samplePDFBase * > samples
                                                          Sample holder.
                                                          Definition FitterBase.h:117
                                                          -
                                                          covarianceBase::acceptStep
                                                          void acceptStep()
                                                          Accepted this step.
                                                          Definition covarianceBase.cpp:886
                                                          +
                                                          FitterBase::accProb
                                                          double accProb
                                                          current acceptance prob
                                                          Definition FitterBase.h:105
                                                          +
                                                          FitterBase::sample_llh
                                                          double * sample_llh
                                                          store the llh breakdowns
                                                          Definition FitterBase.h:113
                                                          +
                                                          FitterBase::stepTime
                                                          double stepTime
                                                          Time of single step.
                                                          Definition FitterBase.h:135
                                                          +
                                                          FitterBase::logLCurr
                                                          double logLCurr
                                                          current likelihood
                                                          Definition FitterBase.h:101
                                                          +
                                                          FitterBase::osc_llh
                                                          double osc_llh
                                                          Definition FitterBase.h:111
                                                          +
                                                          FitterBase::syst_llh
                                                          double * syst_llh
                                                          systematic llh breakdowns
                                                          Definition FitterBase.h:115
                                                          +
                                                          FitterBase::auto_save
                                                          int auto_save
                                                          auto save every N steps
                                                          Definition FitterBase.h:147
                                                          +
                                                          FitterBase::outTree
                                                          TTree * outTree
                                                          Output tree with posteriors.
                                                          Definition FitterBase.h:145
                                                          +
                                                          FitterBase::samples
                                                          std::vector< samplePDFBase * > samples
                                                          Sample holder.
                                                          Definition FitterBase.h:118
                                                          +
                                                          covarianceBase::acceptStep
                                                          void acceptStep()
                                                          Accepted this step.
                                                          Definition covarianceBase.cpp:887
                                                          covarianceOsc::getPropPars
                                                          double * getPropPars()
                                                          Retrieves the proposed parameters.
                                                          Definition covarianceOsc.cpp:147
                                                          covarianceOsc::GetLikelihood
                                                          double GetLikelihood() override
                                                          Same implementation as in base class but accounts for applying reactor prior.
                                                          Definition covarianceOsc.cpp:109
                                                          covarianceOsc::proposeStep
                                                          void proposeStep() override
                                                          Propose MCMC step, including mass flipping.
                                                          Definition covarianceOsc.cpp:165
                                                          diff --git a/mcmc_8h_source.html b/mcmc_8h_source.html index fc74b502f..86ed79477 100644 --- a/mcmc_8h_source.html +++ b/mcmc_8h_source.html @@ -120,9 +120,9 @@
                                                          51
                                                          -
                                                          GetFromManager
                                                          Type GetFromManager(const YAML::Node &node, Type defval)
                                                          Get content of config file if node is not found take default value specified.
                                                          Definition YamlHelper.h:18
                                                          -
                                                          FitterBase
                                                          Base class for implementing fitting algorithms.
                                                          Definition FitterBase.h:23
                                                          -
                                                          FitterBase::fitMan
                                                          manager * fitMan
                                                          The manager.
                                                          Definition FitterBase.h:92
                                                          +
                                                          GetFromManager
                                                          Type GetFromManager(const YAML::Node &node, Type defval)
                                                          Get content of config file if node is not found take default value specified.
                                                          Definition YamlHelper.h:21
                                                          +
                                                          FitterBase
                                                          Base class for implementing fitting algorithms.
                                                          Definition FitterBase.h:24
                                                          +
                                                          FitterBase::fitMan
                                                          manager * fitMan
                                                          The manager.
                                                          Definition FitterBase.h:93
                                                          manager
                                                          The manager class is responsible for managing configurations and settings.
                                                          Definition manager.h:28
                                                          mcmc
                                                          Implementation of MR2T2 algorithm.
                                                          Definition mcmc.h:6
                                                          mcmc::GetName
                                                          std::string GetName() const
                                                          Get name of class.
                                                          Definition mcmc.h:24
                                                          diff --git a/md__2github_2workspace_2Diagnostics_2README.html b/md__2github_2workspace_2Diagnostics_2README.html index 9f547c4a2..94a57294a 100644 --- a/md__2github_2workspace_2Diagnostics_2README.html +++ b/md__2github_2workspace_2Diagnostics_2README.html @@ -74,7 +74,7 @@
                                                          Plotting and Diagnostic
                                                          -

                                                          ProcessMCMC - The main app you want to use for analysing the ND280 chain. It prints posterior distribution after burn-in the cut. Moreover, you can compare two/three different chains. There are a few options you can modify easily inside the app like selection, burn-in cut, and whether to plot xse+flux or only flux. Other functionality

                                                            +

                                                            ProcessMCMC - The main app you want to use for analysing the ND280 chain. It prints posterior distribution after burn-in the cut. Moreover, you can compare two/three different chains. There are a few options you can modify easily inside the app like selection, burn-in cut, and whether to plot xse+flux or only flux. Other functionality

                                                            1. Produce a covariance matrix with multithreading (which requires lots of RAM due to caching)
                                                            2. diff --git a/md__2github_2workspace_2SECURITY.html b/md__2github_2workspace_2SECURITY.html new file mode 100644 index 000000000..a0e7684d2 --- /dev/null +++ b/md__2github_2workspace_2SECURITY.html @@ -0,0 +1,93 @@ + + + + + + + +MaCh3: Security Policy + + + + + + + + + +
                                                              +
                                                              +

                                                           Cadaptive_mcmc::AdaptiveMCMCStructStruct encapsulating all adaptive MCMC information
                                                           Cadaptive_mcmc::AdaptiveMCMCHandlerContains information about adaptive covariance matrix
                                                           ▼CBaseFuncPar
                                                           CEnergyScale
                                                           CSKEScale
                                                          + + + + + + +
                                                          +
                                                          MaCh3 1.1.0 +
                                                          +
                                                          Reference Guide
                                                          +
                                                          +
                                                          + + + + + + + + +
                                                          +
                                                          + + +
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                                                          +
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                                                          +
                                                          +
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                                                          +
                                                          + +
                                                          +
                                                          +
                                                          Security Policy
                                                          +
                                                          +
                                                          +

                                                          +

                                                          +Supported Versions

                                                          +

                                                          Security updates are applied only to the latest release.

                                                          +

                                                          +Reporting a Vulnerability

                                                          +

                                                          If you have discovered a security vulnerability in this project, please report it privately. Do not disclose it as a public issue. This gives us time to work with you to fix the issue before public exposure, reducing the chance that the exploit will be used before a patch is released.

                                                          +

                                                          Please disclose it at security advisory.

                                                          +

                                                          This project is maintained by a team of volunteers on a reasonable-effort basis. As such, vulnerabilities will be disclosed in a best effort base.

                                                          +
                                                          +
                                                          + +
                                                          +Generated by doxygen 1.9.8 +
                                                          + + diff --git a/namespaceMaCh3Utils.html b/namespaceMaCh3Utils.html index 07a93c11e..6b74fd4ef 100644 --- a/namespaceMaCh3Utils.html +++ b/namespaceMaCh3Utils.html @@ -186,8 +186,8 @@

                                                          185

                                                          186 MACH3LOG_INFO("Data transfer: {} B, rate: {:.2f} MB/s", bytesProcessed, dataRateMBps);
                                                          187}
                                                          -
                                                          MACH3LOG_INFO
                                                          #define MACH3LOG_INFO
                                                          Definition MaCh3Logger.h:13
                                                          -
                                                          GetFromManager
                                                          Type GetFromManager(const YAML::Node &node, Type defval)
                                                          Get content of config file if node is not found take default value specified.
                                                          Definition YamlHelper.h:18
                                                          +
                                                          MACH3LOG_INFO
                                                          #define MACH3LOG_INFO
                                                          Definition MaCh3Logger.h:16
                                                          +
                                                          GetFromManager
                                                          Type GetFromManager(const YAML::Node &node, Type defval)
                                                          Get content of config file if node is not found take default value specified.
                                                          Definition YamlHelper.h:21

                                                          @@ -354,7 +354,7 @@

                                                          79

                                                          80 return MaCh3_VERSION;
                                                          81}
                                                          -
                                                          MACH3LOG_ERROR
                                                          #define MACH3LOG_ERROR
                                                          Definition MaCh3Logger.h:15
                                                          +
                                                          MACH3LOG_ERROR
                                                          #define MACH3LOG_ERROR
                                                          Definition MaCh3Logger.h:18
                                                          @@ -468,16 +468,16 @@

                                                          Definition at line 32 of file CovarianceUtils.h.

                                                          -
                                                          33 {
                                                          -
                                                          34 #ifdef MULTITHREAD
                                                          -
                                                          35 int nThreads = omp_get_max_threads();
                                                          -
                                                          36 #else
                                                          -
                                                          37 int nThreads = 1;
                                                          -
                                                          38 #endif
                                                          -
                                                          39
                                                          -
                                                          40 return nThreads;
                                                          -
                                                          41 }
                                                          +

                                                          Definition at line 28 of file CovarianceUtils.h.

                                                          +
                                                          29 {
                                                          +
                                                          30 #ifdef MULTITHREAD
                                                          +
                                                          31 int nThreads = omp_get_max_threads();
                                                          +
                                                          32 #else
                                                          +
                                                          33 int nThreads = 1;
                                                          +
                                                          34 #endif
                                                          +
                                                          35
                                                          +
                                                          36 return nThreads;
                                                          +
                                                          37 }

                                                          @@ -700,42 +700,42 @@

                                                          Definition at line 76 of file CovarianceUtils.h.

                                                          -
                                                          76 {
                                                          -
                                                          77 // First make into monolithic array
                                                          -
                                                          78 double *A_mon = new double[n*n];
                                                          -
                                                          79 double *B_mon = new double[n*n];
                                                          -
                                                          80
                                                          -
                                                          81 #ifdef MULTITHREAD
                                                          -
                                                          82 #pragma omp parallel for
                                                          -
                                                          83 #endif
                                                          -
                                                          84 for (int i = 0; i < n; ++i) {
                                                          -
                                                          85 for (int j = 0; j < n; ++j) {
                                                          -
                                                          86 A_mon[i*n+j] = A[i][j];
                                                          -
                                                          87 B_mon[i*n+j] = B[i][j];
                                                          -
                                                          88 }
                                                          -
                                                          89 }
                                                          -
                                                          90 //CW: Now call the monolithic calculator
                                                          -
                                                          91 double *C_mon = MatrixMult(A_mon, B_mon, n);
                                                          -
                                                          92 delete A_mon;
                                                          -
                                                          93 delete B_mon;
                                                          -
                                                          94
                                                          -
                                                          95 // Return the double pointer
                                                          -
                                                          96 double **C = new double*[n];
                                                          -
                                                          97 #ifdef MULTITHREAD
                                                          -
                                                          98 #pragma omp parallel for
                                                          -
                                                          99 #endif
                                                          -
                                                          100 for (int i = 0; i < n; ++i) {
                                                          -
                                                          101 C[i] = new double[n];
                                                          -
                                                          102 for (int j = 0; j < n; ++j) {
                                                          -
                                                          103 C[i][j] = C_mon[i*n+j];
                                                          -
                                                          104 }
                                                          -
                                                          105 }
                                                          -
                                                          106 delete C_mon;
                                                          -
                                                          107
                                                          -
                                                          108 return C;
                                                          -
                                                          109 }
                                                          -
                                                          MaCh3Utils::MatrixMult
                                                          double * MatrixMult(double *A, double *B, int n)
                                                          CW: Multi-threaded matrix multiplication.
                                                          Definition CovarianceUtils.h:44
                                                          +

                                                          Definition at line 72 of file CovarianceUtils.h.

                                                          +
                                                          72 {
                                                          +
                                                          73 // First make into monolithic array
                                                          +
                                                          74 double *A_mon = new double[n*n];
                                                          +
                                                          75 double *B_mon = new double[n*n];
                                                          +
                                                          76
                                                          +
                                                          77 #ifdef MULTITHREAD
                                                          +
                                                          78 #pragma omp parallel for
                                                          +
                                                          79 #endif
                                                          +
                                                          80 for (int i = 0; i < n; ++i) {
                                                          +
                                                          81 for (int j = 0; j < n; ++j) {
                                                          +
                                                          82 A_mon[i*n+j] = A[i][j];
                                                          +
                                                          83 B_mon[i*n+j] = B[i][j];
                                                          +
                                                          84 }
                                                          +
                                                          85 }
                                                          +
                                                          86 //CW: Now call the monolithic calculator
                                                          +
                                                          87 double *C_mon = MatrixMult(A_mon, B_mon, n);
                                                          +
                                                          88 delete A_mon;
                                                          +
                                                          89 delete B_mon;
                                                          +
                                                          90
                                                          +
                                                          91 // Return the double pointer
                                                          +
                                                          92 double **C = new double*[n];
                                                          +
                                                          93 #ifdef MULTITHREAD
                                                          +
                                                          94 #pragma omp parallel for
                                                          +
                                                          95 #endif
                                                          +
                                                          96 for (int i = 0; i < n; ++i) {
                                                          +
                                                          97 C[i] = new double[n];
                                                          +
                                                          98 for (int j = 0; j < n; ++j) {
                                                          +
                                                          99 C[i][j] = C_mon[i*n+j];
                                                          +
                                                          100 }
                                                          +
                                                          101 }
                                                          +
                                                          102 delete C_mon;
                                                          +
                                                          103
                                                          +
                                                          104 return C;
                                                          +
                                                          105 }
                                                          +
                                                          MaCh3Utils::MatrixMult
                                                          double * MatrixMult(double *A, double *B, int n)
                                                          CW: Multi-threaded matrix multiplication.
                                                          Definition CovarianceUtils.h:40

                                                          @@ -781,37 +781,37 @@

                                                          Definition at line 44 of file CovarianceUtils.h.

                                                          -
                                                          44 {
                                                          -
                                                          45 //CW: First transpose to increse cache hits
                                                          -
                                                          46 double *BT = new double[n*n];
                                                          -
                                                          47 #ifdef MULTITHREAD
                                                          -
                                                          48 #pragma omp parallel for
                                                          -
                                                          49 #endif
                                                          -
                                                          50 for (int i = 0; i < n; i++) {
                                                          -
                                                          51 for (int j = 0; j < n; j++) {
                                                          -
                                                          52 BT[j*n+i] = B[i*n+j];
                                                          -
                                                          53 }
                                                          -
                                                          54 }
                                                          -
                                                          55
                                                          -
                                                          56 // Now multiply
                                                          -
                                                          57 double *C = new double[n*n];
                                                          -
                                                          58 #ifdef MULTITHREAD
                                                          -
                                                          59 #pragma omp parallel for
                                                          -
                                                          60 #endif
                                                          -
                                                          61 for (int i = 0; i < n; i++) {
                                                          -
                                                          62 for (int j = 0; j < n; j++) {
                                                          -
                                                          63 double sum = 0;
                                                          -
                                                          64 for (int k = 0; k < n; k++) {
                                                          -
                                                          65 sum += A[i*n+k]*BT[j*n+k];
                                                          -
                                                          66 }
                                                          -
                                                          67 C[i*n+j] = sum;
                                                          -
                                                          68 }
                                                          -
                                                          69 }
                                                          -
                                                          70 delete BT;
                                                          -
                                                          71
                                                          -
                                                          72 return C;
                                                          -
                                                          73 }
                                                          +

                                                          Definition at line 40 of file CovarianceUtils.h.

                                                          +
                                                          40 {
                                                          +
                                                          41 //CW: First transpose to increse cache hits
                                                          +
                                                          42 double *BT = new double[n*n];
                                                          +
                                                          43 #ifdef MULTITHREAD
                                                          +
                                                          44 #pragma omp parallel for
                                                          +
                                                          45 #endif
                                                          +
                                                          46 for (int i = 0; i < n; i++) {
                                                          +
                                                          47 for (int j = 0; j < n; j++) {
                                                          +
                                                          48 BT[j*n+i] = B[i*n+j];
                                                          +
                                                          49 }
                                                          +
                                                          50 }
                                                          +
                                                          51
                                                          +
                                                          52 // Now multiply
                                                          +
                                                          53 double *C = new double[n*n];
                                                          +
                                                          54 #ifdef MULTITHREAD
                                                          +
                                                          55 #pragma omp parallel for
                                                          +
                                                          56 #endif
                                                          +
                                                          57 for (int i = 0; i < n; i++) {
                                                          +
                                                          58 for (int j = 0; j < n; j++) {
                                                          +
                                                          59 double sum = 0;
                                                          +
                                                          60 for (int k = 0; k < n; k++) {
                                                          +
                                                          61 sum += A[i*n+k]*BT[j*n+k];
                                                          +
                                                          62 }
                                                          +
                                                          63 C[i*n+j] = sum;
                                                          +
                                                          64 }
                                                          +
                                                          65 }
                                                          +
                                                          66 delete BT;
                                                          +
                                                          67
                                                          +
                                                          68 return C;
                                                          +
                                                          69 }
                                                          @@ -851,13 +851,13 @@

                                                          Definition at line 112 of file CovarianceUtils.h.

                                                          -
                                                          113 {
                                                          -
                                                          114 double *C_mon = MatrixMult(A.GetMatrixArray(), B.GetMatrixArray(), A.GetNcols());
                                                          -
                                                          115 TMatrixD C;
                                                          -
                                                          116 C.Use(A.GetNcols(), A.GetNrows(), C_mon);
                                                          -
                                                          117 return C;
                                                          -
                                                          118 }
                                                          +

                                                          Definition at line 108 of file CovarianceUtils.h.

                                                          +
                                                          109 {
                                                          +
                                                          110 double *C_mon = MatrixMult(A.GetMatrixArray(), B.GetMatrixArray(), A.GetNcols());
                                                          +
                                                          111 TMatrixD C;
                                                          +
                                                          112 C.Use(A.GetNcols(), A.GetNrows(), C_mon);
                                                          +
                                                          113 return C;
                                                          +
                                                          114 }
                                                          diff --git a/namespaceadaptive__mcmc.html b/namespaceadaptive__mcmc.html index 97ad65c0d..58c21dc0b 100644 --- a/namespaceadaptive__mcmc.html +++ b/namespaceadaptive__mcmc.html @@ -72,70 +72,17 @@
                                                          -Classes | -Functions
                                                          +Classes
                                                          adaptive_mcmc Namespace Reference
                                                          - -

                                                          Contains information about adaptive covariance matrix. -More...

                                                          - - + + -

                                                          Classes

                                                          struct  AdaptiveMCMCStruct
                                                           struct encapsulating all adaptive MCMC information More...
                                                          class  AdaptiveMCMCHandler
                                                           Contains information about adaptive covariance matrix. More...
                                                           
                                                          - - - - -

                                                          -Functions

                                                          void print_adaptive_struct (AdaptiveMCMCStruct adaptive_struct)
                                                           Basic printer method for AMCMC struct.
                                                           
                                                          -

                                                          Detailed Description

                                                          -

                                                          Contains information about adaptive covariance matrix.

                                                          -
                                                          See also
                                                          An adaptive Metropolis algorithm, H.Haario et al., 2001 for more info!
                                                          -

                                                          Function Documentation

                                                          - -

                                                          ◆ print_adaptive_struct()

                                                          - -
                                                          -
                                                          - - - - -
                                                          - - - - - - - - -
                                                          void adaptive_mcmc::print_adaptive_struct (AdaptiveMCMCStruct adaptive_struct)
                                                          -                                                           		-inline
                                                          -
                                                          - -

                                                          Basic printer method for AMCMC struct.

                                                          - -

                                                          Definition at line 43 of file adaptiveMCMCStruct.h.

                                                          -
                                                          43 {
                                                          -
                                                          44 MACH3LOG_INFO("Adaptive MCMC Info:");
                                                          -
                                                          45 MACH3LOG_INFO("Throwing from New Matrix from Step : {}", adaptive_struct.start_adaptive_throw);
                                                          -
                                                          46 MACH3LOG_INFO("Adaption Matrix Start Update : {}", adaptive_struct.start_adaptive_update);
                                                          -
                                                          47 MACH3LOG_INFO("Adaption Matrix Ending Updates : {}", adaptive_struct.end_adaptive_update);
                                                          -
                                                          48 MACH3LOG_INFO("Steps Between Updates : {}", adaptive_struct.adaptive_update_step);
                                                          -
                                                          49}
                                                          -
                                                          MACH3LOG_INFO
                                                          #define MACH3LOG_INFO
                                                          Definition MaCh3Logger.h:13
                                                          -
                                                          GetFromManager
                                                          Type GetFromManager(const YAML::Node &node, Type defval)
                                                          Get content of config file if node is not found take default value specified.
                                                          Definition YamlHelper.h:18
                                                          -
                                                          -
                                                          -
                                                          diff --git a/namespacemembers.html b/namespacemembers.html index e8d434961..325f375df 100644 --- a/namespacemembers.html +++ b/namespacemembers.html @@ -86,7 +86,6 @@
                                                        • MatrixMult() : MaCh3Utils
                                                        • nKnownDetIDs : MaCh3Utils
                                                        • parseLine() : MaCh3Utils
                                                          • -
                                                        • print_adaptive_struct() : adaptive_mcmc
                                                        • PrintConfig() : MaCh3Utils
                                                        • PrintProgressBar() : MaCh3Utils
                                                        • TerminalToString() : MaCh3Utils
                                                          • diff --git a/namespacemembers_func.html b/namespacemembers_func.html index ab42cefb7..e9e8fc4ca 100644 --- a/namespacemembers_func.html +++ b/namespacemembers_func.html @@ -85,7 +85,6 @@
                                                        • MaCh3Welcome() : MaCh3Utils
                                                        • MatrixMult() : MaCh3Utils
                                                        • parseLine() : MaCh3Utils
                                                          • -
                                                        • print_adaptive_struct() : adaptive_mcmc
                                                        • PrintConfig() : MaCh3Utils
                                                        • PrintProgressBar() : MaCh3Utils
                                                        • TerminalToString() : MaCh3Utils
                                                          • diff --git a/namespaces.html b/namespaces.html index d542cb294..4539fbc3e 100644 --- a/namespaces.html +++ b/namespaces.html @@ -76,8 +76,8 @@
                                                          Here is a list of all namespaces with brief descriptions:
                                                          [detail level 12]
                                                          - - + +
                                                           ▼Nadaptive_mcmcContains information about adaptive covariance matrix
                                                           CAdaptiveMCMCStructStruct encapsulating all adaptive MCMC information
                                                           ▼Nadaptive_mcmc
                                                           CAdaptiveMCMCHandlerContains information about adaptive covariance matrix
                                                           NMaCh3Utils
                                                          diff --git a/pages.html b/pages.html index 38704b63f..fde43183d 100644 --- a/pages.html +++ b/pages.html @@ -78,7 +78,8 @@ - + +
                                                           How to Contribute Code to MaCh3
                                                           MaCh3 <img src="Doc/mach3logo.png" alt="MaCh3" align="center" width="100"/>
                                                           Plotting and Diagnostic
                                                           Security Policy
                                                           Plotting and Diagnostic
                                                          diff --git a/probGpu_8cu.html b/probGpu_8cu.html index c1db90308..7c8df95bf 100644 --- a/probGpu_8cu.html +++ b/probGpu_8cu.html @@ -583,6 +583,13 @@

                                                          Check if there's been an error.

                                                          +

                                                          This function checks if there has been any CUDA runtime API error and reports it.

                                                          Parameters
                                                          + + + +
                                                          fileThe file name where the error occurred.
                                                          lineThe line number where the error occurred.
                                                          +
                                                          +

                                                          Definition at line 39 of file probGpu.cu.

                                                          40{
                                                          @@ -608,7 +615,7 @@

                                                          60

                                                          61 return;
                                                          62}
                                                          -
                                                          GetFromManager
                                                          Type GetFromManager(const YAML::Node &node, Type defval)
                                                          Get content of config file if node is not found take default value specified.
                                                          Definition YamlHelper.h:18
                                                          +
                                                          GetFromManager
                                                          Type GetFromManager(const YAML::Node &node, Type defval)
                                                          Get content of config file if node is not found take default value specified.
                                                          Definition YamlHelper.h:21
                                                          @@ -653,6 +660,14 @@

                                                          Check for a safe call on GPU.

                                                          +

                                                          This function checks the error status returned by CUDA runtime API functions and reports any errors.

                                                          Parameters
                                                          + + + + +
                                                          errThe CUDA error code.
                                                          fileThe file name where the error occurred.
                                                          lineThe line number where the error occurred.
                                                          +
                                                          +

                                                          Definition at line 25 of file probGpu.cu.

                                                          26{
                                                          diff --git a/probGpu_8cu_source.html b/probGpu_8cu_source.html index 86a99eaa2..ab47a8b97 100644 --- a/probGpu_8cu_source.html +++ b/probGpu_8cu_source.html @@ -1709,7 +1709,7 @@
                                                          1561
                                                          size
                                                          int size
                                                          Definition GetPenaltyTerm.cpp:42
                                                          -
                                                          GetFromManager
                                                          Type GetFromManager(const YAML::Node &node, Type defval)
                                                          Get content of config file if node is not found take default value specified.
                                                          Definition YamlHelper.h:18
                                                          +
                                                          GetFromManager
                                                          Type GetFromManager(const YAML::Node &node, Type defval)
                                                          Get content of config file if node is not found take default value specified.
                                                          Definition YamlHelper.h:21
                                                          SetDensityProfile
                                                          __device__ void SetDensityProfile(double CosineZ, double PathLength, double ProductionHeight, int &Layers, double *_TraverseRhos, double *_TraverseDistance, double *_TraverseYpMap)
                                                          Definition probGpu.cu:1251
                                                          CudaCheckError
                                                          #define CudaCheckError()
                                                          Definition probGpu.cu:23
                                                          matrix_type
                                                          matrix_type
                                                          Definition probGpu.cu:80
                                                          diff --git a/samplePDFBase_8cpp_source.html b/samplePDFBase_8cpp_source.html index 246b28095..c23d5e337 100644 --- a/samplePDFBase_8cpp_source.html +++ b/samplePDFBase_8cpp_source.html @@ -604,8 +604,8 @@
                                                          kIceCube
                                                          @ kIceCube
                                                          Definition Structs.h:356
                                                          kDembinskiAbdelmottele
                                                          @ kDembinskiAbdelmottele
                                                          Definition Structs.h:358
                                                          kPoisson
                                                          @ kPoisson
                                                          Definition Structs.h:354
                                                          -
                                                          GetFromManager
                                                          Type GetFromManager(const YAML::Node &node, Type defval)
                                                          Get content of config file if node is not found take default value specified.
                                                          Definition YamlHelper.h:18
                                                          -
                                                          MaCh3Modes::GetNModes
                                                          int GetNModes()
                                                          KS: Get number of modes, keep in mind actual number is +1 greater due to unknown category.
                                                          Definition MaCh3Modes.h:43
                                                          +
                                                          GetFromManager
                                                          Type GetFromManager(const YAML::Node &node, Type defval)
                                                          Get content of config file if node is not found take default value specified.
                                                          Definition YamlHelper.h:21
                                                          +
                                                          MaCh3Modes::GetNModes
                                                          int GetNModes()
                                                          KS: Get number of modes, keep in mind actual number is +1 greater due to unknown category.
                                                          Definition MaCh3Modes.h:44
                                                          MaCh3Modes::GetMaCh3ModeName
                                                          std::string GetMaCh3ModeName(const int Index)
                                                          KS: Get normal name of mode, if mode not known you will get UNKNOWN_BAD.
                                                          Definition MaCh3Modes.cpp:124
                                                          samplePDFBase::GetModeName
                                                          void GetModeName(std::vector< std::string > &modeNameVect)
                                                          Definition samplePDFBase.cpp:431
                                                          samplePDFBase::rnd
                                                          TRandom3 * rnd
                                                          Definition samplePDFBase.h:136
                                                          diff --git a/samplePDFBase_8h_source.html b/samplePDFBase_8h_source.html index bafbfbcc0..5ca37bffd 100644 --- a/samplePDFBase_8h_source.html +++ b/samplePDFBase_8h_source.html @@ -217,9 +217,9 @@
                                                          _int_
                                                          #define _int_
                                                          Definition Structs.h:12
                                                          TestStatistic
                                                          TestStatistic
                                                          Make an enum of the test statistic that we're using.
                                                          Definition Structs.h:353
                                                          -
                                                          GetFromManager
                                                          Type GetFromManager(const YAML::Node &node, Type defval)
                                                          Get content of config file if node is not found take default value specified.
                                                          Definition YamlHelper.h:18
                                                          -
                                                          MaCh3Exception
                                                          Custom exception class for MaCh3 errors.
                                                          Definition MaCh3Exception.h:10
                                                          -
                                                          MaCh3Modes
                                                          KS: Class describing MaCh3 modes used in the analysis, it is being initialised from config.
                                                          Definition MaCh3Modes.h:32
                                                          +
                                                          GetFromManager
                                                          Type GetFromManager(const YAML::Node &node, Type defval)
                                                          Get content of config file if node is not found take default value specified.
                                                          Definition YamlHelper.h:21
                                                          +
                                                          MaCh3Exception
                                                          Custom exception class for MaCh3 errors.
                                                          Definition MaCh3Exception.h:12
                                                          +
                                                          MaCh3Modes
                                                          KS: Class describing MaCh3 modes used in the analysis, it is being initialised from config.
                                                          Definition MaCh3Modes.h:33
                                                          samplePDFBase
                                                          Class responsible for handling implementation of samples used in analysis, reweighting and returning ...
                                                          Definition samplePDFBase.h:28
                                                          samplePDFBase::GetModeName
                                                          void GetModeName(std::vector< std::string > &modeNameVect)
                                                          Definition samplePDFBase.cpp:431
                                                          samplePDFBase::rnd
                                                          TRandom3 * rnd
                                                          Definition samplePDFBase.h:136
                                                          diff --git a/samplePDFFDBase_8cpp_source.html b/samplePDFFDBase_8cpp_source.html index 02c656d8c..3a84312be 100644 --- a/samplePDFFDBase_8cpp_source.html +++ b/samplePDFFDBase_8cpp_source.html @@ -1591,7 +1591,7 @@
                                                          1432#endif
                                                          1433
                                                          -
                                                          MACH3LOG_ERROR
                                                          #define MACH3LOG_ERROR
                                                          Definition MaCh3Logger.h:15
                                                          +
                                                          MACH3LOG_ERROR
                                                          #define MACH3LOG_ERROR
                                                          Definition MaCh3Logger.h:18
                                                          GetCUDAProbFlavour
                                                          CUDAProb_nu GetCUDAProbFlavour(int nu_i, int nu_f)
                                                          Get CUDAProb3 flavour from intital and final states.
                                                          Definition Structs.h:460
                                                          kPoisson
                                                          @ kPoisson
                                                          Definition Structs.h:354
                                                          _DEFAULT_RETURN_VAL_
                                                          #define _DEFAULT_RETURN_VAL_
                                                          Definition Structs.h:38
                                                          @@ -1605,17 +1605,17 @@
                                                          e_e
                                                          @ e_e
                                                          Definition Structs.h:446
                                                          t_m
                                                          @ t_m
                                                          Definition Structs.h:453
                                                          m_t
                                                          @ m_t
                                                          Definition Structs.h:451
                                                          -
                                                          GetFromManager
                                                          Type GetFromManager(const YAML::Node &node, Type defval)
                                                          Get content of config file if node is not found take default value specified.
                                                          Definition YamlHelper.h:18
                                                          +
                                                          GetFromManager
                                                          Type GetFromManager(const YAML::Node &node, Type defval)
                                                          Get content of config file if node is not found take default value specified.
                                                          Definition YamlHelper.h:21
                                                          Oscillator::FillOscillogram
                                                          void FillOscillogram(double *oscpar, double prodH, double Yp_Val=0.468)
                                                          Definition OscClass_CUDAProb3.cpp:955
                                                          Oscillator::retPointer
                                                          const double * retPointer(int GenNeutrinoFlavour, int DetNeutrinoFlavour, double NeutrinoEnergy, double TrueCZ)
                                                          Definition OscClass_CUDAProb3.cpp:1247
                                                          -
                                                          covarianceBase::retPointer
                                                          const double * retPointer(const int iParam)
                                                          DB Pointer return to param position.
                                                          Definition covarianceBase.h:208
                                                          -
                                                          covarianceXsec
                                                          Class responsible for handling of systematic error parameters with different types defined in the con...
                                                          Definition covarianceXsec.h:15
                                                          +
                                                          covarianceBase::retPointer
                                                          const double * retPointer(const int iParam)
                                                          DB Pointer return to param position.
                                                          Definition covarianceBase.h:209
                                                          +
                                                          covarianceXsec
                                                          Class responsible for handling of systematic error parameters with different types defined in the con...
                                                          Definition covarianceXsec.h:14
                                                          covarianceXsec::GetNormParsFromDetID
                                                          const std::vector< XsecNorms4 > GetNormParsFromDetID(const int DetID)
                                                          DB Get norm/func parameters depending on given DetID.
                                                          Definition covarianceXsec.cpp:302
                                                          -
                                                          covarianceXsec::GetParDetID
                                                          int GetParDetID(const int i) const
                                                          ETA - just return the int of the DetID, this can be removed to do a string comp at some point.
                                                          Definition covarianceXsec.h:36
                                                          -
                                                          covarianceXsec::GetFuncParsNamesFromDetID
                                                          const std::vector< std::string > GetFuncParsNamesFromDetID(const int DetID)
                                                          DB Grab the Functional parameter names for the relevant DetID.
                                                          Definition covarianceXsec.h:87
                                                          -
                                                          covarianceXsec::GetFuncParsIndexFromDetID
                                                          const std::vector< int > GetFuncParsIndexFromDetID(const int DetID)
                                                          DB Grab the Functional parameter indices for the relevant DetID.
                                                          Definition covarianceXsec.h:89
                                                          -
                                                          covarianceXsec::GetNumFuncParamsFromDetID
                                                          int GetNumFuncParamsFromDetID(const int DetID)
                                                          DB Grab the number of Normalisation parameters for the relevant DetID.
                                                          Definition covarianceXsec.h:85
                                                          +
                                                          covarianceXsec::GetParDetID
                                                          int GetParDetID(const int i) const
                                                          ETA - just return the int of the DetID, this can be removed to do a string comp at some point.
                                                          Definition covarianceXsec.h:35
                                                          +
                                                          covarianceXsec::GetFuncParsNamesFromDetID
                                                          const std::vector< std::string > GetFuncParsNamesFromDetID(const int DetID)
                                                          DB Grab the Functional parameter names for the relevant DetID.
                                                          Definition covarianceXsec.h:86
                                                          +
                                                          covarianceXsec::GetFuncParsIndexFromDetID
                                                          const std::vector< int > GetFuncParsIndexFromDetID(const int DetID)
                                                          DB Grab the Functional parameter indices for the relevant DetID.
                                                          Definition covarianceXsec.h:88
                                                          +
                                                          covarianceXsec::GetNumFuncParamsFromDetID
                                                          int GetNumFuncParamsFromDetID(const int DetID)
                                                          DB Grab the number of Normalisation parameters for the relevant DetID.
                                                          Definition covarianceXsec.h:84
                                                          samplePDFBase
                                                          Class responsible for handling implementation of samples used in analysis, reweighting and returning ...
                                                          Definition samplePDFBase.h:28
                                                          samplePDFBase::SampleName
                                                          std::vector< std::string > SampleName
                                                          Name of Sample.
                                                          Definition samplePDFBase.h:124
                                                          diff --git a/samplePDFFDBase_8h_source.html b/samplePDFFDBase_8h_source.html index 359f9065d..c86043128 100644 --- a/samplePDFFDBase_8h_source.html +++ b/samplePDFFDBase_8h_source.html @@ -360,9 +360,9 @@
                                                          OscClass_CUDAProb3.h
                                                          CUDAProb_nu
                                                          CUDAProb_nu
                                                          Definition Structs.h:445
                                                          -
                                                          GetFromManager
                                                          Type GetFromManager(const YAML::Node &node, Type defval)
                                                          Get content of config file if node is not found take default value specified.
                                                          Definition YamlHelper.h:18
                                                          +
                                                          GetFromManager
                                                          Type GetFromManager(const YAML::Node &node, Type defval)
                                                          Get content of config file if node is not found take default value specified.
                                                          Definition YamlHelper.h:21
                                                          -
                                                          covarianceXsec
                                                          Class responsible for handling of systematic error parameters with different types defined in the con...
                                                          Definition covarianceXsec.h:15
                                                          +
                                                          covarianceXsec
                                                          Class responsible for handling of systematic error parameters with different types defined in the con...
                                                          Definition covarianceXsec.h:14
                                                          samplePDFBase
                                                          Class responsible for handling implementation of samples used in analysis, reweighting and returning ...
                                                          Definition samplePDFBase.h:28
                                                          samplePDFFDBase::SelectionBounds
                                                          std::vector< std::vector< double > > SelectionBounds
                                                          Definition samplePDFFDBase.h:257
                                                          diff --git a/search/all_10.js b/search/all_10.js index 46215836e..50316834f 100644 --- a/search/all_10.js +++ b/search/all_10.js @@ -4,8 +4,8 @@ var searchData= ['p2_1',['p2',['../GetPostfitParamPlots_8cpp.html#afcf736152a1c6e4f65d2d41b7335136c',1,'GetPostfitParamPlots.cpp']]], ['p3_2',['p3',['../GetPostfitParamPlots_8cpp.html#a814cbca1b36d9e3f622031e0e9634ce0',1,'GetPostfitParamPlots.cpp']]], ['p4_3',['p4',['../GetPostfitParamPlots_8cpp.html#ac577141e2ab46a432ac74c34d18d0739',1,'GetPostfitParamPlots.cpp']]], - ['par_4',['par',['../classTF1__red.html#a37ad3ad0f1a93e8f17f1c6bf06058b59',1,'TF1_red::Par'],['../classTSpline3__red.html#a5864d7f83769639e0fbe5f417bee5dfe',1,'TSpline3_red::Par'],['../classPSO.html#ae5eff2b0193e0d7c9c221edbc14118bd',1,'PSO::par']]], - ['par_5fmeans_5',['par_means',['../structadaptive__mcmc_1_1AdaptiveMCMCStruct.html#a41c1966053923eca5cd268770b2416d1',1,'adaptive_mcmc::AdaptiveMCMCStruct']]], + 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index 4a481091f..52f31678b 100644 --- a/splineFDBase_8cpp_source.html +++ b/splineFDBase_8cpp_source.html @@ -1164,14 +1164,14 @@
                                                          kCoeffY
                                                          @ kCoeffY
                                                          Definition SplineCommon.h:15
                                                          kCoeffC
                                                          @ kCoeffC
                                                          Definition SplineCommon.h:17
                                                          _float_
                                                          #define _float_
                                                          Definition Structs.h:11
                                                          -
                                                          GetFromManager
                                                          Type GetFromManager(const YAML::Node &node, Type defval)
                                                          Get content of config file if node is not found take default value specified.
                                                          Definition YamlHelper.h:18
                                                          +
                                                          GetFromManager
                                                          Type GetFromManager(const YAML::Node &node, Type defval)
                                                          Get content of config file if node is not found take default value specified.
                                                          Definition YamlHelper.h:21
                                                          SplineBase
                                                          Base class for calculating weight from spline.
                                                          Definition SplineBase.h:28
                                                          -
                                                          covarianceBase::calcReWeight
                                                          double calcReWeight(const int bin)
                                                          What parameter Gets reweighted by what amount according to MCMC.
                                                          Definition covarianceBase.h:190
                                                          -
                                                          covarianceXsec
                                                          Class responsible for handling of systematic error parameters with different types defined in the con...
                                                          Definition covarianceXsec.h:15
                                                          +
                                                          covarianceBase::calcReWeight
                                                          double calcReWeight(const int bin)
                                                          What parameter Gets reweighted by what amount according to MCMC.
                                                          Definition covarianceBase.h:191
                                                          +
                                                          covarianceXsec
                                                          Class responsible for handling of systematic error parameters with different types defined in the con...
                                                          Definition covarianceXsec.h:14
                                                          covarianceXsec::GetSplineModeVecFromDetID
                                                          const std::vector< std::vector< int > > GetSplineModeVecFromDetID(const int DetID)
                                                          DB Grab the Spline Modes for the relevant DetID.
                                                          Definition covarianceXsec.cpp:202
                                                          covarianceXsec::GetFDSplineFileParsNamesFromDetID
                                                          const std::vector< std::string > GetFDSplineFileParsNamesFromDetID(const int DetID)
                                                          ETA - what does this even do?
                                                          Definition covarianceXsec.cpp:133
                                                          -
                                                          covarianceXsec::GetSplineParsIndexFromDetID
                                                          const std::vector< int > GetSplineParsIndexFromDetID(const int DetID)
                                                          DB Grab the Spline Indices for the relevant DetID.
                                                          Definition covarianceXsec.h:76
                                                          -
                                                          covarianceXsec::GetNumSplineParamsFromDetID
                                                          int GetNumSplineParamsFromDetID(const int DetID)
                                                          DB Grab the Number of splines for the relevant DetID.
                                                          Definition covarianceXsec.h:79
                                                          +
                                                          covarianceXsec::GetSplineParsIndexFromDetID
                                                          const std::vector< int > GetSplineParsIndexFromDetID(const int DetID)
                                                          DB Grab the Spline Indices for the relevant DetID.
                                                          Definition covarianceXsec.h:75
                                                          +
                                                          covarianceXsec::GetNumSplineParamsFromDetID
                                                          int GetNumSplineParamsFromDetID(const int DetID)
                                                          DB Grab the Number of splines for the relevant DetID.
                                                          Definition covarianceXsec.h:78
                                                          splineFDBase::FindSplineBinning
                                                          std::vector< TAxis * > FindSplineBinning(std::string FileName, std::string SampleName)
                                                          Definition splineFDBase.cpp:356
                                                          splineFDBase::getDimLabel
                                                          TString getDimLabel(int BinningOpt, int Axis)
                                                          Definition splineFDBase.cpp:791
                                                          splineFDBase::SplineParsIndex
                                                          std::vector< std::vector< int > > SplineParsIndex
                                                          Definition splineFDBase.h:93
                                                          diff --git a/splineFDBase_8h_source.html b/splineFDBase_8h_source.html index 81ad0f539..c4302cdba 100644 --- a/splineFDBase_8h_source.html +++ b/splineFDBase_8h_source.html @@ -215,9 +215,9 @@
                                                          _float_
                                                          #define _float_
                                                          Definition Structs.h:11
                                                          -
                                                          GetFromManager
                                                          Type GetFromManager(const YAML::Node &node, Type defval)
                                                          Get content of config file if node is not found take default value specified.
                                                          Definition YamlHelper.h:18
                                                          +
                                                          GetFromManager
                                                          Type GetFromManager(const YAML::Node &node, Type defval)
                                                          Get content of config file if node is not found take default value specified.
                                                          Definition YamlHelper.h:21
                                                          SplineBase
                                                          Base class for calculating weight from spline.
                                                          Definition SplineBase.h:28
                                                          -
                                                          covarianceXsec
                                                          Class responsible for handling of systematic error parameters with different types defined in the con...
                                                          Definition covarianceXsec.h:15
                                                          +
                                                          covarianceXsec
                                                          Class responsible for handling of systematic error parameters with different types defined in the con...
                                                          Definition covarianceXsec.h:14
                                                          splineFDBase
                                                          Bin-by-bin class calculating response for spline parameters.
                                                          Definition splineFDBase.h:11
                                                          splineFDBase::FindSplineBinning
                                                          std::vector< TAxis * > FindSplineBinning(std::string FileName, std::string SampleName)
                                                          Definition splineFDBase.cpp:356
                                                          splineFDBase::FindUniqueModes
                                                          void FindUniqueModes()
                                                          diff --git a/structMaCh3ModeInfo.html b/structMaCh3ModeInfo.html index 42b554e4b..805f61a10 100644 --- a/structMaCh3ModeInfo.html +++ b/structMaCh3ModeInfo.html @@ -105,7 +105,7 @@

                                                          Detailed Description

                                                          KS: Class containing information for a single MaCh3Mode.

                                                          -

                                                          Definition at line 16 of file MaCh3Modes.h.

                                                          +

                                                          Definition at line 17 of file MaCh3Modes.h.

                                                          Member Function Documentation

                                                          ◆ IsMode()

                                                          @@ -133,13 +133,13 @@

                                                          Definition at line 24 of file MaCh3Modes.h.

                                                          -
                                                          24 {
                                                          -
                                                          25 bool exists = std::find(GeneratorMaping.begin(), GeneratorMaping.end(), GenMode) != GeneratorMaping.end();
                                                          -
                                                          26 return exists;
                                                          -
                                                          27 }
                                                          -
                                                          GetFromManager
                                                          Type GetFromManager(const YAML::Node &node, Type defval)
                                                          Get content of config file if node is not found take default value specified.
                                                          Definition YamlHelper.h:18
                                                          -
                                                          MaCh3ModeInfo::GeneratorMaping
                                                          std::vector< int > GeneratorMaping
                                                          Mapping between mode and generator integers.
                                                          Definition MaCh3Modes.h:22
                                                          +

                                                          Definition at line 25 of file MaCh3Modes.h.

                                                          +
                                                          25 {
                                                          +
                                                          26 bool exists = std::find(GeneratorMaping.begin(), GeneratorMaping.end(), GenMode) != GeneratorMaping.end();
                                                          +
                                                          27 return exists;
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                                                          GetFromManager
                                                          Type GetFromManager(const YAML::Node &node, Type defval)
                                                          Get content of config file if node is not found take default value specified.
                                                          Definition YamlHelper.h:21
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                                                          MaCh3ModeInfo::GeneratorMaping
                                                          std::vector< int > GeneratorMaping
                                                          Mapping between mode and generator integers.
                                                          Definition MaCh3Modes.h:23
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                                                          Definition at line 19 of file MaCh3Modes.h.

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                                                          adaptive_mcmc::AdaptiveMCMCStruct Member List
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                                                          This is the complete list of members for adaptive_mcmc::AdaptiveMCMCStruct, including all inherited members.

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                                                          adapt_block_matrix_indicesadaptive_mcmc::AdaptiveMCMCStruct
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                                                          par_meansadaptive_mcmc::AdaptiveMCMCStruct
                                                          start_adaptive_throwadaptive_mcmc::AdaptiveMCMCStruct
                                                          start_adaptive_updateadaptive_mcmc::AdaptiveMCMCStruct
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                                                          adaptive_mcmc::AdaptiveMCMCStruct Struct Reference
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                                                          struct encapsulating all adaptive MCMC information - More...

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                                                          #include <adaptiveMCMCStruct.h>

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                                                          int start_adaptive_throw
                                                           When do we start throwing.
                                                           
                                                          int start_adaptive_update
                                                           When do we stop update the adaptive matrix.
                                                           
                                                          int end_adaptive_update
                                                           Steps between changing throw matrix.
                                                           
                                                          int adaptive_update_step
                                                           Steps between changing throw matrix.
                                                           
                                                          std::vector< int > adapt_block_matrix_indices
                                                           Indices for block-matrix adaption.
                                                           
                                                          std::vector< int > adapt_block_sizes
                                                           Size of blocks for adaption.
                                                           
                                                          std::vector< double > par_means
                                                           Mean values for all parameters.
                                                           
                                                          TMatrixDSym * adaptive_covariance
                                                           Full adaptive covariance matrix.
                                                           
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                                                          Detailed Description

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                                                          struct encapsulating all adaptive MCMC information

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                                                          Definition at line 19 of file adaptiveMCMCStruct.h.

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                                                          ◆ adapt_block_matrix_indices

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                                                          std::vector<int> adaptive_mcmc::AdaptiveMCMCStruct::adapt_block_matrix_indices
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                                                          Indices for block-matrix adaption.

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                                                          Definition at line 30 of file adaptiveMCMCStruct.h.

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                                                          ◆ adapt_block_sizes

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                                                          std::vector<int> adaptive_mcmc::AdaptiveMCMCStruct::adapt_block_sizes
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                                                          Size of blocks for adaption.

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                                                          Definition at line 32 of file adaptiveMCMCStruct.h.

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                                                          ◆ adaptive_covariance

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                                                          TMatrixDSym* adaptive_mcmc::AdaptiveMCMCStruct::adaptive_covariance
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                                                          Full adaptive covariance matrix.

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                                                          Definition at line 38 of file adaptiveMCMCStruct.h.

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                                                          ◆ adaptive_update_step

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                                                          int adaptive_mcmc::AdaptiveMCMCStruct::adaptive_update_step
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                                                          Steps between changing throw matrix.

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                                                          Definition at line 28 of file adaptiveMCMCStruct.h.

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                                                          ◆ end_adaptive_update

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                                                          int adaptive_mcmc::AdaptiveMCMCStruct::end_adaptive_update
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                                                          Steps between changing throw matrix.

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                                                          Definition at line 26 of file adaptiveMCMCStruct.h.

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                                                          ◆ par_means

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                                                          std::vector<double> adaptive_mcmc::AdaptiveMCMCStruct::par_means
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                                                          Mean values for all parameters.

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                                                          Definition at line 36 of file adaptiveMCMCStruct.h.

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                                                          ◆ start_adaptive_throw

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                                                          int adaptive_mcmc::AdaptiveMCMCStruct::start_adaptive_throw
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                                                          When do we start throwing.

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                                                          Definition at line 22 of file adaptiveMCMCStruct.h.

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                                                          ◆ start_adaptive_update

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                                                          int adaptive_mcmc::AdaptiveMCMCStruct::start_adaptive_update
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                                                          When do we stop update the adaptive matrix.

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                                                          Definition at line 24 of file adaptiveMCMCStruct.h.

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