Merge pull request #183 from mach3-software/feature_RemoveGarbage

Remove Garbage

covariance/covarianceBase.cpp

@@ -1,15 +1,15 @@
 #include "covariance/covarianceBase.h"
 
 // ********************************************
-covarianceBase::covarianceBase(const char *name, const char *file) : inputFile(std::string(file)), pca(false) {
+covarianceBase::covarianceBase(std::string name, std::string file) : inputFile(std::string(file)), pca(false) {
 // ********************************************
   MACH3LOG_INFO("Constructing instance of covarianceBase");
   init(name, file);
   FirstPCAdpar = -999;
   LastPCAdpar = -999;
 }
 // ********************************************
-covarianceBase::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) {
+covarianceBase::covarianceBase(const std::vector<std::string>& YAMLFile, std::string name, double threshold, int FirstPCA, int LastPCA) : inputFile(YAMLFile[0].c_str()), matrixName(name), pca(true), eigen_threshold(threshold), FirstPCAdpar(FirstPCA), LastPCAdpar(LastPCA) {
 // ********************************************
 
   MACH3LOG_INFO("Constructing instance of covarianceBase using ");
@@ -105,19 +105,19 @@ void covarianceBase::ConstructPCA() {
 }
 
 // ********************************************
-void covarianceBase::init(const char *name, const char *file) {
+void covarianceBase::init(std::string name, std::string file) {
 // ********************************************
 
   // Set the covariance matrix from input ROOT file (e.g. flux, ND280, NIWG)
-  TFile *infile = new TFile(file, "READ");
+  TFile *infile = new TFile(file.c_str(), "READ");
   if (infile->IsZombie()) {
     MACH3LOG_ERROR("Could not open input covariance ROOT file {} !!!", file);
     MACH3LOG_ERROR("Was about to retrieve matrix with name {}", name);
     throw MaCh3Exception(__FILE__ , __LINE__ );
   }
 
   // Should put in a 
-  TMatrixDSym *CovMat = (TMatrixDSym*)(infile->Get(name));
+  TMatrixDSym *CovMat = (TMatrixDSym*)(infile->Get(name.c_str()));
   if (CovMat == nullptr) {
     MACH3LOG_ERROR("Could not find covariance matrix name {} in file {}", name, file);
     MACH3LOG_ERROR("Are you really sure {} exists in the file?", name);
@@ -1319,7 +1319,7 @@ std::vector<double> covarianceBase::getNominalArray() {
 // KS: Convert covariance matrix to correlation matrix and return TH2D which can be used for fancy plotting
 TH2D* covarianceBase::GetCorrelationMatrix() {
 // ********************************************
-  TH2D* hMatrix = new TH2D(getName(), getName(), _fNumPar, 0.0, _fNumPar, _fNumPar, 0.0, _fNumPar);
+  TH2D* hMatrix = new TH2D(getName().c_str(), getName().c_str(), _fNumPar, 0.0, _fNumPar, _fNumPar, 0.0, _fNumPar);
 
   for(int i = 0; i < _fNumPar; i++)
   {

covariance/covarianceBase.h

@@ -22,11 +22,11 @@ class covarianceBase {
   /// @param threshold PCA threshold from 0 to 1. Default is -1 and means no PCA
   /// @param FirstPCAdpar First PCA parameter that will be decomposed.
   /// @param LastPCAdpar First PCA parameter that will be decomposed.
-  covarianceBase(const std::vector<std::string>& YAMLFile, const char *name, double threshold = -1, int FirstPCAdpar = -999, int LastPCAdpar = -999);
+  covarianceBase(const std::vector<std::string>& YAMLFile, std::string name, double threshold = -1, int FirstPCAdpar = -999, int LastPCAdpar = -999);
   /// @brief "Usual" constructors from root file
   /// @param name Matrix name
   /// @param file Path to matrix root file
-  covarianceBase(const char *name, const char *file);
+  covarianceBase(std::string name, std::string file);
 
   /// @brief Destructor
   virtual ~covarianceBase();
@@ -37,11 +37,11 @@ class covarianceBase {
   /// @param cov Covariance matrix which we set and will be used later for evaluation of penalty term
   void setCovMatrix(TMatrixDSym *cov);
   /// @brief Set matrix name
-  void setName(const char *name) { matrixName = name; }
+  void setName(std::string name) { matrixName = name; }
   /// @brief change parameter name
   /// @param i Parameter index
   /// @param name new name which will be set
-  void setParName(int i, char *name) { _fNames.at(i) = std::string(name); }
+  void setParName(int i, std::string name) { _fNames.at(i) = name; }
   void setSingleParameter(const int parNo, const double parVal);
   /// @brief Set all the covariance matrix parameters to a user-defined value
   /// @param i Parameter index
@@ -111,19 +111,13 @@ class covarianceBase {
   inline bool getFlatPrior(const int i) { return _fFlatPrior[i]; }
 
   /// @brief Get name of covariance
-  const char *getName() { return matrixName; }
+  std::string getName() { return matrixName; }
   /// @brief Get name of covariance
   /// @param i Parameter index
   std::string GetParName(const int i) {return _fNames[i];}
-  /// @brief Get name of the Parameter
-  /// @param i Parameter index
-  const char* GetParName(const int i) const { return _fNames[i].c_str(); }
   /// @brief Get fancy name of the Parameter
   /// @param i Parameter index
   std::string GetParFancyName(const int i) {return _fFancyNames[i];}
-  /// @brief Get fancy name of the Parameter
-  /// @param i Parameter index
-  const char* GetParFancyName(const int i) const { return _fFancyNames[i].c_str(); }
   /// @brief Get name of input file
   std::string getInputFile() const { return inputFile; }
 
@@ -351,7 +345,7 @@ class covarianceBase {
   YAML::Node GetConfig() const { return _fYAMLDoc; }
 protected:
   /// @brief Initialisation of the class using matrix from root file
-  void init(const char *name, const char *file);
+  void init(std::string name, std::string file);
   /// @brief Initialisation of the class using config
   /// @param YAMLFile A vector of strings representing the YAML files used for initialisation of matrix
   void init(const std::vector<std::string>& YAMLFile);
@@ -396,7 +390,7 @@ class covarianceBase {
   /// Total number of params, deprecated, please don't use it
   int size;
   /// Name of cov matrix
-  const char *matrixName;
+  std::string matrixName;
   /// The covariance matrix
   TMatrixDSym *covMatrix;
   /// The inverse covariance matrix

covariance/covarianceOsc.cpp

@@ -1,7 +1,7 @@
 #include "covariance/covarianceOsc.h"
 
 // *************************************
-covarianceOsc::covarianceOsc(const std::vector<std::string>& YAMLFile, const char *name, double threshold, int FirstPCA, int LastPCA)
+covarianceOsc::covarianceOsc(const std::vector<std::string>& YAMLFile, std::string name, double threshold, int FirstPCA, int LastPCA)
 : covarianceBase(YAMLFile, name, threshold, FirstPCA, LastPCA){
 // *************************************
 
@@ -25,12 +25,7 @@ covarianceOsc::covarianceOsc(const std::vector<std::string>& YAMLFile, const cha
     _fPropVal[io] = _fCurrVal[io];
   }
 
-  /// WARNING HARDCODED
-  MACH3LOG_CRITICAL("Fixing baseline and density, it is hardcoded sry");
-  toggleFixParameter("baseline");
-  toggleFixParameter("density");
-
-  /// @todo KS: Technically if we would like to use PCA we have ot initialise parts here...
+  /// @todo KS: Technically if we would like to use PCA we have to initialise parts here...
   flipdelM = false;
 
   randomize();

covariance/covarianceOsc.h

@@ -8,7 +8,7 @@ class covarianceOsc : public covarianceBase
 {
  public:
   /// @brief Constructor
-  covarianceOsc(const std::vector<std::string>& FileNames, const char *name = "osc_cov", double threshold = -1, int FirstPCAdpar = -999, int LastPCAdpar = -999);
+  covarianceOsc(const std::vector<std::string>& FileNames, std::string name = "osc_cov", double threshold = -1, int FirstPCAdpar = -999, int LastPCAdpar = -999);
   /// @brief Destructor
   virtual ~covarianceOsc();
   /// @brief Checks if parameter didn't go outside of physical bounds

covariance/covarianceXsec.cpp

@@ -4,7 +4,7 @@
 // ETA - YAML constructor
 // this will replace the root file constructor but let's keep it in
 // to do some validations
-covarianceXsec::covarianceXsec(const std::vector<std::string>& YAMLFile, const char *name, double threshold, int FirstPCA, int LastPCA)
+covarianceXsec::covarianceXsec(const std::vector<std::string>& YAMLFile, std::string name, double threshold, int FirstPCA, int LastPCA)
                : covarianceBase(YAMLFile, name, threshold, FirstPCA, LastPCA){
 // ********************************************
   InitXsecFromConfig();

covariance/covarianceXsec.h

@@ -14,7 +14,7 @@ class covarianceXsec : public covarianceBase {
     /// @param threshold PCA threshold from 0 to 1. Default is -1 and means no PCA
     /// @param FirstPCAdpar First PCA parameter that will be decomposed.
     /// @param LastPCAdpar First PCA parameter that will be decomposed.
-    covarianceXsec(const std::vector<std::string>& FileNames, const char *name = "xsec_cov", double threshold = -1, int FirstPCAdpar = -999, int LastPCAdpar = -999);
+    covarianceXsec(const std::vector<std::string>& FileNames, std::string name = "xsec_cov", double threshold = -1, int FirstPCAdpar = -999, int LastPCAdpar = -999);
     /// @brief Destructor
     ~covarianceXsec();
 
@@ -62,27 +62,12 @@ class covarianceXsec : public covarianceBase {
 
     /// @brief DB Grab the Spline Modes for the relevant DetID
     const std::vector< std::vector<int> > GetSplineModeVecFromDetID(const int DetID);
-    /// @brief DB Grab the Spline Indices for the relevant DetID
-    const std::vector<int> GetSplineParsIndexFromDetID(const int DetID){return GetParsIndexFromDetID(DetID, SystType::kSpline);}
-    /// @brief ETA Grab the index of the spline relative to the _fSplineNames vector.
-    const std::vector<int> GetSplineSystIndexFromDetID(const int DetID){return GetSystIndexFromDetID(DetID, SystType::kSpline);};
     /// @brief Grab the index of the syst relative to global numbering.
     /// @param Type Type of syst, for example kNorm, kSpline etc
     const std::vector<int> GetSystIndexFromDetID(const int DetID, const SystType Type);
-
-    /// @brief DB Grab the Number of splines for the relevant DetID
-    int GetNumSplineParamsFromDetID(const int DetID){return GetNumParamsFromDetID(DetID, SystType::kSpline);}
-
     /// @brief DB Get norm/func parameters depending on given DetID
     const std::vector<XsecNorms4> GetNormParsFromDetID(const int DetID);
 
-    /// @brief DB Grab the number of Normalisation parameters for the relevant DetID
-    int GetNumFuncParamsFromDetID(const int DetID){return GetNumParamsFromDetID(DetID, SystType::kFunc);}
-    /// @brief DB Grab the Functional parameter names for the relevant DetID
-    const std::vector<std::string> GetFuncParsNamesFromDetID(const int DetID){return GetParsNamesFromDetID(DetID, SystType::kFunc);}
-    /// @brief DB Grab the Functional parameter indices for the relevant DetID
-    const std::vector<int> GetFuncParsIndexFromDetID(const int DetID){return GetParsIndexFromDetID(DetID, SystType::kFunc);}
-
     /// @brief KS: For most covariances nominal and fparInit (prior) are the same, however for Xsec those can be different
     /// For example Sigma Var are done around nominal in ND280, no idea why though...
     std::vector<double> getNominalArray() override

mcmc/FitterBase.cpp

@@ -66,7 +66,6 @@ FitterBase::FitterBase(manager * const man) : fitMan(man) {
   // Clear the samples and systematics
   samples.clear();
   systematics.clear();
-  osc = nullptr;
 
   sample_llh = nullptr;
   syst_llh = nullptr;
@@ -182,11 +181,6 @@ void FitterBase::PrepareOutput() {
       (*it)->SetBranches(*outTree, SaveProposal);
     }
 
-    if (osc) {
-      osc->SetBranches(*outTree, SaveProposal);
-      outTree->Branch("LogL_osc", &osc_llh, "LogL_osc/D");
-    }
-
     outTree->Branch("LogL", &logLCurr, "LogL/D");
     outTree->Branch("accProb", &accProb, "accProb/D");
     outTree->Branch("step", &step, "step/I");
@@ -287,7 +281,7 @@ void FitterBase::addSystObj(covarianceBase * const cov) {
   t_vec.Write((std::string(cov->getName()) + "_prior").c_str());
   delete[] n_vec;
 
-  cov->getCovMatrix()->Write(cov->getName());
+  cov->getCovMatrix()->Write(cov->getName().c_str());
 
   TH2D* CorrMatrix = cov->GetCorrelationMatrix();
   CorrMatrix->Write((cov->getName() + std::string("_Corr")).c_str());
@@ -306,39 +300,6 @@ void FitterBase::addSystObj(covarianceBase * const cov) {
   return;
 }
 
-// *************************
-// Add an oscillation handler
-// Similar to systematic really, but handles the oscillation weights
-void FitterBase::addOscHandler(covarianceOsc * const oscf) {
-// *************************
-  osc = oscf;
-  if (save_nominal) {
-    CovFolder->cd();
-    std::vector<double> vec = oscf->getNominalArray();
-    size_t n = vec.size();
-    double *n_vec = new double[n];
-    for (size_t i = 0; i < n; ++i) {
-      n_vec[i] = vec[i];
-    }
-    TVectorT<double> t_vec(n, n_vec);
-    TString nameof = TString(oscf->getName());
-    nameof = nameof.Append("_nom");
-    t_vec.Write(nameof);
-    delete[] n_vec;
-    outputFile->cd();
-  }
-
-  // If we have yaml config file for covariance let's save it
-  YAML::Node Config = oscf->GetConfig();
-  if(!Config.IsNull())
-  {
-    TMacro ConfigSave = YAMLtoTMacro(Config, (std::string("Config_") + oscf->getName()));
-    ConfigSave.Write();
-  }
-  return;
-}
-
-
 // *******************
 // Process the MCMC output to get postfit etc
 void FitterBase::ProcessMCMC() {

mcmc/FitterBase.h

@@ -8,7 +8,6 @@
 // MaCh3 Includes
 #include "samplePDF/samplePDFBase.h"
 #include "covariance/covarianceBase.h"
-#include "covariance/covarianceOsc.h"
 #include "manager/manager.h"
 #include "mcmc/MCMCProcessor.h"
 
@@ -37,10 +36,6 @@ class FitterBase {
   /// @param cov A pointer to a Covariance object derived from covarianceBase.
   void addSystObj(covarianceBase* cov);
 
-  /// @brief Adds an oscillation handler for covariance objects.
-  /// @param oscf A pointer to a covarianceOsc object for forward oscillations.
-  void addOscHandler(covarianceOsc* oscf);
-
   /// @brief The specific fitting algorithm implemented in this function depends on the derived class. It could be Markov Chain Monte Carlo (MCMC), MinuitFit, or another algorithm.
   virtual void runMCMC() = 0;
 
@@ -102,9 +97,6 @@ class FitterBase {
   /// counts accepted steps
   int accCount;
 
-  /// LLH for samples/syst objects
-  /// oscillation covariance llh
-  double osc_llh;
   /// store the llh breakdowns
   double *sample_llh;
   /// systematic llh breakdowns
@@ -118,9 +110,6 @@ class FitterBase {
   /// Systematic holder
   std::vector<covarianceBase*> systematics;
 
-  /// handles oscillation parameters
-  covarianceOsc *osc;
-
   /// tells global time how long fit took
   TStopwatch* clock;
   /// tells how long single step/fit iteration took

mcmc/LikelihoodFit.cpp

@@ -32,10 +32,6 @@ void LikelihoodFit::PrepareFit() {
     NParsPCA += systematics[s]->getNpars();
   }
 
-  if (osc) {
-    std::cerr<<" Osc not supported "<<std::endl;
-    throw;
-  }
   //KS: If PCA is note enabled NParsPCA == NPars
   MACH3LOG_INFO("Total number of parameters {}", NParsPCA);
 }
@@ -112,13 +108,7 @@ double LikelihoodFit::CalcChi2(const double* x) {
   // But since sample reweight is multi-threaded it's probably better to do that
   for (size_t i = 0; i < samples.size(); i++)
   {
-    // If we're running with different oscillation parameters for neutrino and anti-neutrino
-    if (osc) {
-      samples[i]->reweight();
-      // If we aren't using any oscillation
-      } else {
-        samples[i]->reweight();
-    }
+    samples[i]->reweight();
   }
 
   //DB for atmospheric event by event sample migration, need to fully reweight all samples to allow event passing prior to likelihood evaluation

mcmc/mcmc.cpp

@@ -60,10 +60,6 @@ void mcmc::CheckStep() {
   if (accept && !reject) {
     logLCurr = logLProp;
 
-    if (osc) {
-      osc->acceptStep();
-    }
-
     // Loop over systematics and accept
     for (size_t s = 0; s < systematics.size(); ++s) {
       systematics[s]->acceptStep();
@@ -136,21 +132,6 @@ void mcmc::ProposeStep() {
   // Initiate to false
   reject = false;
 
-  // Propose steps for the oscillation handlers
-  if (osc) {
-    osc->proposeStep();
-
-    // Now get the likelihoods for the oscillation
-    osc_llh = osc->GetLikelihood();
-
-    // Add the oscillation likelihoods to the reconfigure likelihoods
-    llh += osc_llh;
-
-    #ifdef DEBUG
-    if (debug) debugFile << "LLH for oscillation handler: " << llh << std::endl;
-    #endif
-  }
-
   // Loop over the systematics and propose the initial step
   for (size_t s = 0; s < systematics.size(); ++s) {
     // Could throw the initial value here to do MCMC stability studies

python/fitter.cpp

@@ -128,14 +128,6 @@ void initFitter(py::module &m){
             py::arg("cov")
         )
 
-        .def(
-            "add_osc_handler",
-            py::overload_cast<covarianceOsc *>(&FitterBase::addOscHandler),
-            " Adds an oscillation handler for covariance objects. \n"
-            " :param oscf: An oscillation handler object for dealing with neutrino oscillation calculations. ",
-            py::arg("osc")
-        )
-
     ; // End of FitterBase class binding
 
     py::class_<mcmc, FitterBase>(m_fitter, "MCMC")
@@ -193,4 +185,4 @@ void initFitter(py::module &m){
 
     ; // end of PSO class binding
 
-}
+}

samplePDF/samplePDFFDBase.cpp

@@ -741,9 +741,9 @@ void samplePDFFDBase::SetXsecCov(covarianceXsec *xsec){
 
   //DB Now get this information using the DetID from the config
   xsec_norms = XsecCov->GetNormParsFromDetID(SampleDetID);
-  nFuncParams = XsecCov->GetNumFuncParamsFromDetID(SampleDetID);
-  funcParsNames = XsecCov->GetFuncParsNamesFromDetID(SampleDetID);
-  funcParsIndex = XsecCov->GetFuncParsIndexFromDetID(SampleDetID);
+  nFuncParams = XsecCov->GetNumParamsFromDetID(SampleDetID, SystType::kFunc);
+  funcParsNames = XsecCov->GetParsNamesFromDetID(SampleDetID, SystType::kFunc);
+  funcParsIndex = XsecCov->GetParsIndexFromDetID(SampleDetID, SystType::kFunc);
 
   return;
 }