Removed using namespace std from header files and fix errors

inc/TRestRawAFTERToSignalProcess.h

@@ -38,7 +38,6 @@ struct EventHeader {
     // uint16_t dummy;
 };
 
-
 // ATENTION!!!!!
 // New verison of the DaqT2K (2.x)
 // added 30th July 2012 (JuanAn)

inc/TRestRawCommonNoiseReductionProcess.h

@@ -24,6 +24,7 @@
 #define RestCore_TRestRawCommonNoiseReductionProcess
 
 #include <TRestRawSignalEvent.h>
+
 #include "TRestEventProcess.h"
 #include "TRestRawSignal.h"
 

inc/TRestRawFEUDreamToSignalProcess.h

@@ -23,17 +23,6 @@
 #ifndef RestCore_TRestFEUDreamToSignalProcess
 #define RestCore_TRestFEUDreamToSignalProcess
 
-#include "TRestRawSignalEvent.h"
-#include "TRestRawToSignalProcess.h"
-
-#include <arpa/inet.h>
-#include <signal.h>
-#include <stdint.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
-#include <time.h>
-
 #include <TError.h>
 #include <TF1.h>
 #include <TH1D.h>
@@ -42,13 +31,22 @@
 #include <TROOT.h>
 #include <TSystem.h>
 #include <TTree.h>
-
 #include <arpa/inet.h>
+#include <signal.h>
+#include <stdint.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include <time.h>
+
 #include <iostream>
 #include <list>
 #include <map>
 #include <string>
 #include <vector>
+
+#include "TRestRawSignalEvent.h"
+#include "TRestRawToSignalProcess.h"
 #include "math.h"
 
 //! An process to read binary data from FEUDream electronics

inc/TRestRawFFT.h

@@ -18,13 +18,12 @@
 #ifndef RestCore_TRestRawFFT
 #define RestCore_TRestRawFFT
 
-#include <iostream>
-
 #include <TArrayD.h>
 #include <TObject.h>
-
 #include <TRestRawSignal.h>
 
+#include <iostream>
+
 class TRestRawFFT : public TObject {
    protected:
     Int_t fNfft;

inc/TRestRawFindResponseSignalProcess.h

@@ -48,7 +48,7 @@ class TRestRawFindResponseSignalProcess : public TRestEventProcess {
     TRestEvent* ProcessEvent(TRestEvent* eventInput);
     void EndProcess();
 
-    void LoadConfig(std::string cfgFilename, string name = "");
+    void LoadConfig(std::string cfgFilename, std::string name = "");
 
     void PrintMetadata() {
         BeginPrintProcess();

inc/TRestRawMultiCoBoAsAdToSignalProcess.h

@@ -24,6 +24,7 @@
 #define RestCore_TRestRawMultiCoBoAsAdToSignalProcess
 
 #include <map>
+
 #include "TRestRawSignalEvent.h"
 #include "TRestRawToSignalProcess.h"
 
@@ -72,20 +73,20 @@ struct CoBoHeaderFrame {
     // int fEveTimeNanoSec;
 
     void Show() {
-        cout << "------ Frame Header ------" << endl;
-        cout << "frameSize " << frameSize << endl;
-
-        cout << "frameType " << frameType << endl;
-        cout << "revision " << revision << endl;
-        cout << "headerSize " << headerSize << endl;
-        cout << "itemSize " << itemSize << endl;
-        cout << "nItems " << nItems << endl;
-        cout << "eventTime " << eventTime << endl;
-        cout << "eventIdx " << eventIdx << endl;
-
-        cout << "asadIdx " << asadIdx << endl;
-        cout << "readOffset " << readOffset << endl;
-        cout << "status " << status << endl;
+        std::cout << "------ Frame Header ------" << endl;
+        std::cout << "frameSize " << frameSize << endl;
+
+        std::cout << "frameType " << frameType << endl;
+        std::cout << "revision " << revision << endl;
+        std::cout << "headerSize " << headerSize << endl;
+        std::cout << "itemSize " << itemSize << endl;
+        std::cout << "nItems " << nItems << endl;
+        std::cout << "eventTime " << eventTime << endl;
+        std::cout << "eventIdx " << eventIdx << endl;
+
+        std::cout << "asadIdx " << asadIdx << endl;
+        std::cout << "readOffset " << readOffset << endl;
+        std::cout << "status " << status << endl;
     }
 };
 
@@ -101,7 +102,7 @@ class TRestRawMultiCoBoAsAdToSignalProcess : public TRestRawToSignalProcess {
 
     std::map<int, CoBoDataFrame> fDataFrame;  //!///asadId, dataframe
 
-    vector<CoBoHeaderFrame> fHeaderFrame;  //!///reserves a header frame for each file
+    std::vector<CoBoHeaderFrame> fHeaderFrame;  //!///reserves a header frame for each file
 
     int fCurrentEvent = -1;  //!
     int fNextEvent = -1;     //!
@@ -110,7 +111,7 @@ class TRestRawMultiCoBoAsAdToSignalProcess : public TRestRawToSignalProcess {
    public:
     void InitProcess();
 
-    Bool_t AddInputFile(string file);
+    Bool_t AddInputFile(std::string file);
 
     void Initialize();
 

inc/TRestRawSignal.h

@@ -23,13 +23,13 @@
 #ifndef RestCore_TRestRawSignal
 #define RestCore_TRestRawSignal
 
-#include <iostream>
-
 #include <TGraph.h>
 #include <TObject.h>
 #include <TString.h>
 #include <TVector2.h>
 
+#include <iostream>
+
 //! It defines a Short_t array with a physical parameter that evolves in time
 //! using a fixed time bin.
 class TRestRawSignal : public TObject {
@@ -52,7 +52,7 @@ class TRestRawSignal : public TObject {
     /// A TGraph pointer used to store the TRestRawSignal drawing
     TGraph* fGraph;  //!
 
-    /// A vector containing the index of points that are identified over
+    /// A std::vector containing the index of points that are identified over
     /// threshold.
     std::vector<Int_t> fPointsOverThreshold;  //!
 
@@ -89,7 +89,7 @@ class TRestRawSignal : public TObject {
     /// Returns the actual number of points, or size of the signal
     Int_t GetNumberOfPoints() { return fSignalData.size(); }
 
-    /// Returns a vector containing the indexes of data points over threshold
+    /// Returns a std::vector containing the indexes of data points over threshold
     std::vector<Int_t> GetPointsOverThreshold() { return fPointsOverThreshold; }
 
     /// Returns the maximum value found in the data points. It includes baseline

inc/TRestRawSignalAddNoiseProcess.h

@@ -50,7 +50,7 @@ class TRestRawSignalAddNoiseProcess : public TRestEventProcess {
     TRestEvent* ProcessEvent(TRestEvent* eventInput);
     void EndProcess();
 
-    void LoadConfig(std::string cfgFilename, string name = "");
+    void LoadConfig(std::string cfgFilename, std::string name = "");
 
     void PrintMetadata() {
         BeginPrintProcess();

inc/TRestRawSignalChannelActivityProcess.h

@@ -30,6 +30,7 @@
 #endif
 
 #include <TRestRawSignalEvent.h>
+
 #include "TRestEventProcess.h"
 
 //! A pure analysis process to generate histograms with detector channels

inc/TRestRawSignalEvent.h

@@ -23,8 +23,6 @@
 #ifndef RestDAQ_TRestRawSignalEvent
 #define RestDAQ_TRestRawSignalEvent
 
-#include <iostream>
-
 #include <TArrayD.h>
 #include <TAxis.h>
 #include <TGraph.h>
@@ -33,6 +31,8 @@
 #include <TPad.h>
 #include <TVector2.h>
 
+#include <iostream>
+
 #include "TRestEvent.h"
 #include "TRestRawSignal.h"
 
@@ -61,7 +61,7 @@ class TRestRawSignalEvent : public TRestEvent {
     }
 
     // Setters
-    void AddSignal(TRestRawSignal &s);
+    void AddSignal(TRestRawSignal& s);
 
     void RemoveSignalWithId(Int_t sId);
 
@@ -91,10 +91,10 @@ class TRestRawSignalEvent : public TRestEvent {
 
     void PrintSignalIds() {
         for (int n = 0; n < GetNumberOfSignals(); n++) {
-            if (n > 0) cout << " , ";
-            cout << GetSignal(n)->GetSignalID();
+            if (n > 0) std::cout << " , ";
+            std::cout << GetSignal(n)->GetSignalID();
         }
-        cout << endl;
+        std::cout << std::endl;
     }
 
     std::vector<int> GetSignalIds() {

inc/TRestRawSignalFitEventProcess.h

@@ -24,6 +24,7 @@
 #define RestCore_TRestRawSignalFitEventProcess
 
 #include <TRestRawSignalEvent.h>
+
 #include "TF1Convolution.h"
 #include "TH1D.h"
 #include "TMath.h"
@@ -112,7 +113,7 @@ class TRestRawSignalFitEventProcess : public TRestEventProcess {
         if (fAgetFit == false) {
             metadata << "Fitting mode : Convolution" << endl;
         }
-        
+
         if (fAddAllPulses == true) {
             metadata << "Adding all pulses in the event" << endl;
         }

inc/TRestRawSignalFittingProcess.h

@@ -39,7 +39,7 @@ class TRestRawSignalFittingProcess : public TRestEventProcess {
     void Initialize();
 
     void LoadDefaultConfig();
-    
+
     Double_t fShaping = 0;
     Double_t fStartPosition = 0;
     Double_t fBaseline = 0;
@@ -51,7 +51,7 @@ class TRestRawSignalFittingProcess : public TRestEventProcess {
    public:
     any GetInputEvent() { return fRawSignalEvent; }
     any GetOutputEvent() { return fRawSignalEvent; }
-    
+
     Double_t GetShaping() { return fShaping; }
     Double_t GetStartPosition() { return fStartPosition; }
     Double_t GetBaseline() { return fBaseline; }

inc/TRestRawSignalGeneralFitProcess.h

@@ -41,7 +41,7 @@ class TRestRawSignalGeneralFitProcess : public TRestEventProcess {
     void LoadDefaultConfig();
 
     TVector2 fFunctionRange = TVector2(0, 0);
-    string fFunction;
+    std::string fFunction;
 
     TF1* fFitFunc = nullptr;  //!
 
@@ -73,7 +73,7 @@ class TRestRawSignalGeneralFitProcess : public TRestEventProcess {
     void PrintMetadata() {
         BeginPrintProcess();
 
-        metadata << "Function string: " << fFunction << endl;
+        metadata << "Function std::string: " << fFunction << endl;
         metadata << "Range: ( " << fFunctionRange.X() << " , " << fFunctionRange.Y() << " ) " << endl;
 
         EndPrintProcess();

inc/TRestRawSignalRemoveChannelsProcess.h

@@ -55,7 +55,7 @@ class TRestRawSignalRemoveChannelsProcess : public TRestEventProcess {
 
     TRestEvent* ProcessEvent(TRestEvent* eventInput);
 
-    void LoadConfig(std::string cfgFilename, string name = "");
+    void LoadConfig(std::string cfgFilename, std::string name = "");
 
     /// It prints out the process parameters stored in the metadata structure
     void PrintMetadata() {

inc/TRestRawSignalViewerProcess.h

@@ -24,7 +24,6 @@
 #define RestCore_TRestRawSignalViewerProcess
 
 #include <TH1D.h>
-
 #include <TRestRawSignalEvent.h>
 
 #include "TRestEventProcess.h"
@@ -35,8 +34,8 @@ class TRestRawSignalViewerProcess : public TRestEventProcess {
    private:
     TRestRawSignalEvent* fSignalEvent;  //!
 
-    vector<TObject*> fDrawingObjects;  //!
-    Double_t fDrawRefresh;             //!
+    std::vector<TObject*> fDrawingObjects;  //!
+    Double_t fDrawRefresh;                  //!
 
     TVector2 fBaseLineRange;  //!
     int eveCounter = 0;       //!
@@ -67,7 +66,7 @@ class TRestRawSignalViewerProcess : public TRestEventProcess {
     void PrintMetadata() {
         BeginPrintProcess();
 
-        cout << "Refresh value : " << fDrawRefresh << endl;
+        std::cout << "Refresh value : " << fDrawRefresh << endl;
 
         EndPrintProcess();
     }

inc/TRestRawToSignalProcess.h

@@ -32,7 +32,7 @@ class TRestRawToSignalProcess : public TRestEventProcess {
     virtual void InitFromConfigFile();
     unsigned int payload;
     unsigned int frameBits;
-    string fElectronicsType;  // AFTER or AGET
+    std::string fElectronicsType;  // AFTER or AGET
     Int_t fMinPoints;
 
     Double_t tStart;
@@ -49,7 +49,7 @@ class TRestRawToSignalProcess : public TRestEventProcess {
     Int_t nFiles;                    //!
     Int_t iCurFile;                  //!
     std::vector<FILE*> fInputFiles;  //!
-    std::vector<string> fInputFileNames;
+    std::vector<std::string> fInputFileNames;
     bool fgKeepFileOpen;  //! true if need to open all raw files at the beginning
 
     Int_t fShowSamples;  //!
@@ -77,15 +77,15 @@ class TRestRawToSignalProcess : public TRestEventProcess {
 
     // Bool_t OpenInputBinFile(TString fName);
 
-    virtual Bool_t OpenInputFiles(vector<string> files);
-    virtual Bool_t AddInputFile(string file);
+    virtual Bool_t OpenInputFiles(std::vector<std::string> files);
+    virtual Bool_t AddInputFile(std::string file);
     Bool_t ResetEntry();
 
     virtual Long64_t GetTotalBytesReaded() { return totalBytesReaded; }
     virtual Long64_t GetTotalBytes() { return totalBytes; }
     //  Int_t GetRunNumber(){return fRunNumber;}
     //  Int_t GetRunIndex(){return fRunIndex;}
-    virtual string GetElectronicsType() { return fElectronicsType; }
+    virtual std::string GetElectronicsType() { return fElectronicsType; }
 
     Bool_t GoToNextFile();
 

inc/TRestRawUSTCToSignalProcess.h

@@ -24,6 +24,7 @@
 #define RestCore_TRestRawUSTCToSignalProcess
 
 #include <map>
+
 #include "TRestRawToSignalProcess.h"
 
 //#define V3_Readout_Format_Long
@@ -88,14 +89,14 @@ class TRestRawUSTCToSignalProcess : public TRestRawToSignalProcess {
     UChar_t fHeader[64];
     UChar_t fEnding[32];
 
-    vector<vector<USTCDataFrame>> fEventBuffer;  //!
-    int nBufferedEvent;                          //!
-    int fCurrentFile = 0;                        //!
-    int fCurrentEvent = -1;                      //!
-    int fCurrentBuffer = 0;                      //!
-    int fLastBufferedId = 0;                     //!
-    vector<int> errorevents;                     //!
-    int unknownerrors = 0;                       //!
+    std::vector<std::vector<USTCDataFrame>> fEventBuffer;  //!
+    int nBufferedEvent;                                    //!
+    int fCurrentFile = 0;                                  //!
+    int fCurrentEvent = -1;                                //!
+    int fCurrentBuffer = 0;                                //!
+    int fLastBufferedId = 0;                               //!
+    std::vector<int> errorevents;                          //!
+    int unknownerrors = 0;                                 //!
 
     Long64_t fTimeOffset = 0;
     std::set<int> fChannelOffset;