Merge pull request #98 from mach3-software/feature_NoThrowParms

Remove ThrowParms

Diagnostics/README.md

@@ -1,4 +1,4 @@
-### Plotting and Diagnostic
+### 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
 <ol>
 <li> Produce a covariance matrix with multithreading (which requires lots of RAM due to caching) </li>

covariance/AdaptiveMCMCHandler.h

@@ -1,7 +1,6 @@
 #pragma once
 
 // MaCh3 Includes
-#include "manager/MaCh3Logger.h"
 #include "manager/manager.h"
 #include "covariance/CovarianceUtils.h"
 

covariance/CMakeLists.txt

@@ -1,5 +1,4 @@
 set(HEADERS
-    ThrowParms.h
     CovarianceUtils.h
     covarianceBase.h
     covarianceOsc.h
@@ -9,7 +8,6 @@ set(HEADERS
 )
 
 add_library(Covariance SHARED
-    ThrowParms.cpp
     covarianceBase.cpp
     covarianceOsc.cpp
     covarianceXsec.cpp

covariance/PCAHandler.h

@@ -1,7 +1,6 @@
 #pragma once
 
 // MaCh3 Includes
-#include "manager/MaCh3Logger.h"
 #include "manager/manager.h"
 #include "covariance/CovarianceUtils.h"
 

covariance/covarianceBase.cpp

@@ -531,57 +531,6 @@ std::vector<double> covarianceBase::getProposed() const {
   return props;
 }
 
-// Throw nominal values
-void covarianceBase::throwNominal(bool nomValues, int seed) {
-  TVectorD* vec = new TVectorD(_fNumPar);
-  for (int i = 0; i < _fNumPar; i++) {
-    (*vec)(i) = 1.0;
-  }
-
-  ThrowParms* nom_throws = new ThrowParms(*vec, (*covMatrix));
-  nom_throws->SetSeed(seed);
-  std::vector<double> nominal = getNominalArray();
-  nominal.clear();
-  nominal.resize(_fNumPar);
-
-  // If we want to put the nominals somewhere else than user specified
-  // Don't fully understand this though: won't we have to reweight the MC somehow?
-  // nominal[i] is used in GetLikelihood() as the penalty term, so we're essentially setting a random parameter penalty term?
-  if (!nomValues)
-  {
-    bool throw_again = true;
-
-    while(throw_again == true)
-    {
-      throw_again = false;
-      MACH3LOG_INFO("Setting {} nominal values to random throws.", getName());
-      nom_throws->ThrowSet(nominal);
-
-      for (int i = 0; i < _fNumPar; i++)
-      {
-      // if parameter is fixed, dont throw
-        if (_fError[i] < 0) {
-          nominal[i] = 1.0;
-          continue;
-        }
-
-        if (nominal[i] < 0) {
-          nominal[i] = 0.0;
-          throw_again = true;
-        }
-      }
-    }
-  } else {
-    // If we want nominal values, set all entries to 1 (defined as nominal in MaCh3)
-    for (int i = 0; i < int(nominal.size()); i++) {
-      nominal[i] = 1.0;
-    }
-  }
-
-  delete nom_throws;
-  delete vec;
-}
-
 // *************************************
 // Throw the parameters according to the covariance matrix
 // This shouldn't be used in MCMC code ase it can break Detailed Balance;
@@ -995,16 +944,15 @@ void covarianceBase::setParameters(const std::vector<double>& pars) {
 
     unsigned int parsSize = pars.size();
     for (unsigned int i = 0; i < parsSize; i++) {
-	  //Make sure that you are actually passing a number to set the parameter to
-	  if(isnan(pars[i])) {
+      //Make sure that you are actually passing a number to set the parameter to
+      if(std::isnan(pars[i])) {
 	    MACH3LOG_ERROR("Error: trying to set parameter value to a nan for parameter {} in matrix {}. This will not go well!", GetParName(i), matrixName);
 		throw;
 	  } else {
 		_fPropVal[i] = pars[i];
 	  }
     }
   }
-
   // And if pca make the transfer
   if (pca) {
     TransferToPCA();
@@ -1199,8 +1147,7 @@ void covarianceBase::printIndivStepScale() {
   std::cout << "============================================================" << std::endl;
 }
 // ********************************************
-//Makes sure that matrix is positive-definite (so no error is thrown when
-//throwNominal() is called) by adding a small number to on-diagonal elements
+//Makes sure that matrix is positive-definite by adding a small number to on-diagonal elements
 void covarianceBase::MakePosDef(TMatrixDSym *cov) {
 // ********************************************
   //DB Save original warning state and then increase it in this function to suppress 'matrix not positive definite' messages

covariance/covarianceBase.h

@@ -4,11 +4,9 @@
 #include "manager/manager.h"
 #include "samplePDF/Structs.h"
 #include "covariance/CovarianceUtils.h"
-#include "covariance/ThrowParms.h"
 #include "covariance/AdaptiveMCMCHandler.h"
 #include "covariance/PCAHandler.h"
 
-
 #ifndef _LARGE_LOGL_
 /// Large Likelihood is used it parameter go out of physical boundary, this indicates in MCMC that such step should eb removed
 #define _LARGE_LOGL_ 1234567890.0

covariance/covarianceXsec.h

@@ -9,9 +9,6 @@
 // MaCh3 includes
 #include "covariance/covarianceBase.h"
 #include "samplePDF/Structs.h"
-#include "manager/YamlHelper.h"
-
-#include "yaml-cpp/yaml.h"
 
 /// @brief Class responsible for handling of systematic error parameters with different types defined in the config. Like spline, normalisation parameters etc.
 /// @see For more details, visit the [Wiki](https://github.com/mach3-software/MaCh3/wiki/02.-Implementation-of-Systematic).

manager/manager.h

@@ -1,17 +1,5 @@
 #pragma once
 
-// C++ includes
-#include <iostream>
-#include <fstream>
-#include <string>
-#include <vector>
-#include <cstdlib>
-
-// ROOT include
-#include "TTree.h"
-#include "TBranch.h"
-#include "TMacro.h"
-
 // MaCh3 Includes
 #include "manager/MaCh3Logger.h"
 #include "samplePDF/Structs.h"

plotting/plottingUtils/plottingUtils.cpp

@@ -36,7 +36,7 @@ TH1D TGraphToTH1D(TGraph graph, std::string newName, std::string newTitle) {
   }
 
   // get the bin edges
-  Double_t binEdges[nPoints + 1];
+  std::vector<double> binEdges(nPoints + 1);
   binEdges[0] = pointsX[0] - (pointsX[1] - pointsX[0]) / 2.0;
   binEdges[nPoints] = pointsX[nPoints - 1] + (pointsX[nPoints - 1] - pointsX[nPoints - 2]) / 2.0;
 
@@ -46,7 +46,7 @@ TH1D TGraphToTH1D(TGraph graph, std::string newName, std::string newTitle) {
     binEdges[pointId] = (pointsX[pointId] + pointsX[pointId - 1]) / 2.0;
   }
 
-  TH1D retHist = TH1D(name.c_str(), title.c_str(), nPoints, binEdges);
+  TH1D retHist = TH1D(name.c_str(), title.c_str(), nPoints, binEdges.data());
 
   for (int binId = 0; binId < nPoints; binId++)
   {
@@ -80,4 +80,4 @@ std::vector<std::vector<float>> TGraphToVector(TGraph graph) {
   return ret;
 }
 
-} // namespace MaCh3Plotting 
+} // namespace MaCh3Plotting 

samplePDF/ShiftFunctors.h

@@ -1,6 +1,6 @@
 #pragma once
 
-#include "samplePDFFDBase.h"
+#include "samplePDF/Structs.h"
 
 class BaseFuncPar{
   public:

samplePDF/Structs.cpp

@@ -1,4 +1,4 @@
-#include "Structs.h"
+#include "samplePDF/Structs.h"
 
 #include "TList.h"
 #include "TObjArray.h"

samplePDF/samplePDFBase.h

@@ -1,10 +1,7 @@
 #pragma once
 
 //C++ includes
-#include <iostream>
-#include <vector>
 #include <assert.h>
-#include <stdexcept>
 
 //ROOT includes
 #include "TTree.h"
@@ -13,11 +10,8 @@
 #include "TMath.h"
 #include "TFile.h"
 #include "TROOT.h"
-#include "TRandom.h"
-#include "TSpline.h"
 #include "TRandom3.h"
 #include "TString.h"
-#include "TMath.h"
 
 //MaCh3 includes
 #include "samplePDF/Structs.h"