breaking: renaming of classes

.gitignore

@@ -1,2 +1,3 @@
 build*/
-.cache/
+*.idx
+.cache/

CIValidations/Benchmark/CMakeLists.txt

@@ -3,6 +3,6 @@ foreach(TEST
     )
 
     add_executable(${TEST} ${TEST}.cpp)
-    target_link_libraries(${TEST} PRIVATE Catch2::Catch2WithMain MaCh3::All MaCh3Tutorial::samplePDFTutorial)
+    target_link_libraries(${TEST} PRIVATE Catch2::Catch2WithMain MaCh3::All MaCh3Tutorial::SamplesTutorial)
     catch_discover_tests(${TEST})
 endforeach()

CIValidations/Benchmark/MaCh3Benchmark.cpp

@@ -1,6 +1,6 @@
 // MaCh3 spline includes
-#include "mcmc/MaCh3Factory.h"
-#include "samplePDF/samplePDFTutorial.h"
+#include "Fitters/MaCh3Factory.h"
+#include "SamplesTutorial/SampleHandlerTutorial.h"
 
 #include "catch2/catch_test_macros.hpp"
 #include "catch2/benchmark/catch_benchmark.hpp"
@@ -10,44 +10,44 @@ TEST_CASE("Benchmark MaCh3") {
   auto FitManager = std::make_unique<manager>("TutorialConfigs/FitterConfig.yaml");
 
   // Initialise covariance class reasonable for Systematics
-  auto xsec = MaCh3CovarianceFactory<covarianceXsec>(FitManager.get(), "Xsec");
-  auto osc  = MaCh3CovarianceFactory<covarianceOsc>(FitManager.get(), "Osc");
+  auto xsec = MaCh3CovarianceFactory<ParameterHandlerGeneric>(FitManager.get(), "Xsec");
+  auto osc  = MaCh3CovarianceFactory<ParameterHandlerOsc>(FitManager.get(), "Osc");
 
-  std::vector<covarianceBase*> Covs;
+  std::vector<ParameterHandlerBase*> Covs;
   Covs.push_back(xsec.get());
   Covs.push_back(osc.get());
 
   // Initialise samplePDF
-  auto BeamSamples = MaCh3SamplePDFFactory<samplePDFTutorial>({"TutorialConfigs/Samples/SamplePDF_Tutorial.yaml"}, xsec.get(), osc.get());
-  auto ATMSamples = MaCh3SamplePDFFactory<samplePDFTutorial>({"TutorialConfigs/Samples/SamplePDF_Tutorial_ATM.yaml"}, xsec.get(), osc.get());
+  auto BeamSamples = MaCh3SampleHandlerFactory<SampleHandlerTutorial>({"TutorialConfigs/Samples/SampleHandler_Tutorial.yaml"}, xsec.get(), osc.get());
+  auto ATMSamples = MaCh3SampleHandlerFactory<SampleHandlerTutorial>({"TutorialConfigs/Samples/SampleHandler_Tutorial_ATM.yaml"}, xsec.get(), osc.get());
 
   BENCHMARK("Beam Reweight") {
     for (size_t s = 0; s < Covs.size(); ++s) {
-      Covs[s]->proposeStep();
-      Covs[s]->acceptStep();
+      Covs[s]->ProposeStep();
+      Covs[s]->AcceptStep();
       Covs[s]->GetLikelihood();
     }
     for(unsigned int ivs = 0; ivs < BeamSamples.size(); ivs++ ) {
-      BeamSamples[ivs]->reweight();
+      BeamSamples[ivs]->Reweight();
       BeamSamples[ivs]->GetLikelihood();
     }
   };
 
   BENCHMARK("Beam Reweight w/o Osc") {
     for(unsigned int ivs = 0; ivs < BeamSamples.size(); ivs++ ) {
-      BeamSamples[ivs]->reweight();
+      BeamSamples[ivs]->Reweight();
       BeamSamples[ivs]->GetLikelihood();
     }
   };
 
   BENCHMARK("ATM Reweight") {
     for (size_t s = 0; s < Covs.size(); ++s) {
-      Covs[s]->proposeStep();
-      Covs[s]->acceptStep();
+      Covs[s]->ProposeStep();
+      Covs[s]->AcceptStep();
       Covs[s]->GetLikelihood();
     }
     for(unsigned int ivs = 0; ivs < ATMSamples.size(); ivs++ ) {
-      ATMSamples[ivs]->reweight();
+      ATMSamples[ivs]->Reweight();
       ATMSamples[ivs]->GetLikelihood();
     }
   };

CIValidations/CMakeLists.txt

@@ -14,7 +14,7 @@ foreach(app
     )
 
     add_executable(${app} ${app}.cpp)
-    target_link_libraries(${app} MaCh3Tutorial::ValidationsUtils MaCh3Tutorial::samplePDFTutorial)
+    target_link_libraries(${app} MaCh3Tutorial::ValidationsUtils MaCh3Tutorial::SamplesTutorial)
     if(MaCh3Tutorial_Coverage_ENABLED)
       target_compile_options(${app} PRIVATE --coverage)
       target_link_options(${app} PRIVATE --coverage)

CIValidations/CovarianceValidations.cpp

@@ -1,7 +1,7 @@
 // MaCh3 spline includes
 #include "Utils/Comparison.h"
-#include "covariance/covarianceXsec.h"
-#include "covariance/covarianceOsc.h"
+#include "Parameters/ParameterHandlerGeneric.h"
+#include "Parameters/ParameterHandlerOsc.h"
 
 
 int main(int argc, char *argv[])
@@ -14,12 +14,12 @@ int main(int argc, char *argv[])
   }
 
 ////////////// Normal Xsec //////////////
-  std::vector<std::string> xsecCovMatrixFile = {"TutorialConfigs/CovObjs/SystematicModel.yaml"};
-  auto xsec = std::make_unique<covarianceXsec>(xsecCovMatrixFile, "xsec_cov");
+  std::vector<std::string> ParameterMatrixFile = {"TutorialConfigs/CovObjs/SystematicModel.yaml"};
+  auto xsec = std::make_unique<ParameterHandlerGeneric>(ParameterMatrixFile, "xsec_cov");
 
   std::vector<double> ParProp = {1.05, 0.90, 1.10, 1.05, 1.05, 1.05, 1.05, 1.05, 0., 0.2};
-  xsec->setParameters(ParProp);
-  xsec->printNominalCurrProp();
+  xsec->SetParameters(ParProp);
+  xsec->PrintNominalCurrProp();
 
   xsec->DumpMatrixToFile("xsec_2024a_flux_21bv2.root");
 
@@ -35,10 +35,10 @@ int main(int argc, char *argv[])
     if (i % (Ntoys/10) == 0) {
       MaCh3Utils::PrintProgressBar(i, Ntoys);
     }
-    xsec->throwParameters();
+    xsec->ThrowParameters();
   }
-  xsec->setParameters(ParProp);
-  xsec->acceptStep();
+  xsec->SetParameters(ParProp);
+  xsec->AcceptStep();
   ///// Test Params from DetId /////
   const std::vector<std::string> AffectedSamples = {"Tutorial Beam", "Tutorial ATM", "tutorial beam", "blarb" "ATM"};
   for (size_t id = 0; id < AffectedSamples.size(); ++id)
@@ -87,36 +87,36 @@ int main(int argc, char *argv[])
 
   // Make sure we can reproduce parameter proposal
   for (int i = 0; i < xsec->GetNumParams(); ++i) {
-    outFile << "Proposed Step for param " << i  << " is equal to=" << xsec->getParProp(i) << std::endl;
+    outFile << "Proposed Step for param " << i  << " is equal to=" << xsec->GetParProp(i) << std::endl;
   }
 
 ////////////// Now PCA //////////////
   MACH3LOG_INFO("Testing PCA matrix");
-  xsecCovMatrixFile = {"TutorialConfigs/CovObjs/PCATest.yaml"};
-  auto PCA = std::make_shared<covarianceXsec>(xsecCovMatrixFile, "xsec_cov", 0.001);
-  std::vector<double>  EigenVal = PCA->getEigenValuesMaster();
+  ParameterMatrixFile = {"TutorialConfigs/CovObjs/PCATest.yaml"};
+  auto PCA = std::make_shared<ParameterHandlerGeneric>(ParameterMatrixFile, "xsec_cov", 0.001);
+  std::vector<double>  EigenVal = PCA->GetEigenValuesMaster();
   for(size_t i = 0; i < EigenVal.size(); i++) {
     outFile << "Eigen Value " << i << " = " << EigenVal[i] << std::endl;
   }
 
-  TVectorD eigen_values = PCA->getEigenValues();
+  TVectorD eigen_values = PCA->GetEigenValues();
   double sum = 0;
   for(int i = 0; i < eigen_values.GetNrows(); i++){
     sum += eigen_values(i);
   }
   outFile << "Sum of Eigen Value: " << sum << std::endl;
 
-  outFile << "Num of PCA pars: " << PCA->getNpars() << std::endl;
-  for(int i = 0; i < PCA->getNpars(); i++){
-    outFile << "Param in PCA base: " << i << " = " << PCA->getParCurr_PCA(i) << std::endl;
+  outFile << "Num of PCA pars: " << PCA->GetNParameters() << std::endl;
+  for(int i = 0; i < PCA->GetNParameters(); i++){
+    outFile << "Param in PCA base: " << i << " = " << PCA->GetParCurrPCA(i) << std::endl;
   }
 
 ////////////// Now Osc //////////////
   std::vector<std::string> OscCovMatrixFile = {"TutorialConfigs/CovObjs/OscillationModel.yaml"};
-  auto osc = std::make_unique<covarianceOsc>(OscCovMatrixFile, "osc_cov");
+  auto osc = std::make_unique<ParameterHandlerOsc>(OscCovMatrixFile, "osc_cov");
   std::vector<double> OscParProp = {0.3, 0.5, 0.020, 7.53e-5, 2.494e-3, 0.0, 295, 2.6, 0.5, 15};
-  osc->setParameters(OscParProp);
-  osc->printNominalCurrProp();
+  osc->SetParameters(OscParProp);
+  osc->PrintNominalCurrProp();
   outFile << "Likelihood Osc=" << osc->GetLikelihood() << std::endl;
 
 ////////////// Now Adaptive //////////////
@@ -151,12 +151,12 @@ std::string yamlContent = R"(
   // Convert the string to a YAML node
   YAML::Node AdaptSetting = STRINGtoYAML(yamlContent);
   std::vector<std::string> AdaptiveCovMatrixFile = {"TutorialConfigs/CovObjs/SystematicModel.yaml", "TutorialConfigs/CovObjs/PCATest.yaml"};
-  auto Adapt = std::make_unique<covarianceXsec>(AdaptiveCovMatrixFile, "xsec_cov");
+  auto Adapt = std::make_unique<ParameterHandlerGeneric>(AdaptiveCovMatrixFile, "xsec_cov");
   //KS: Let's make Doctor Wallace proud
-  Adapt->initialiseAdaption(AdaptSetting);
+  Adapt->InitialiseAdaption(AdaptSetting);
 
   std::vector<double> ParAdapt = {1.05, 0.90, 1.10, 1.05, 1.05, 1.05, 1.05, 1.05, 0., 0.2, -0.1, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0};
-  Adapt->setParameters(ParAdapt);
+  Adapt->SetParameters(ParAdapt);
   bool increase = true;
   for(int i = 0; i < 50000; ++i ) {
 
@@ -168,10 +168,10 @@ std::string yamlContent = R"(
     for (double& param : ParAdapt) {
       param += (increase ? 0.001 : -0.001);
     }
-    Adapt->setParameters(ParAdapt);
-    Adapt->acceptStep();
+    Adapt->SetParameters(ParAdapt);
+    Adapt->AcceptStep();
   }
-  Adapt->saveAdaptiveToFile("Wacky.root", "xsec");
+  Adapt->SaveAdaptiveToFile("Wacky.root", "xsec");
 
   outFile.close();
   bool TheSame = CompareTwoFiles("CIValidations/TestOutputs/CovarianceOut.txt", "NewCovarianceOut.txt");

CIValidations/FitterValidations.cpp

@@ -1,8 +1,8 @@
 // MaCh3 spline includes
-#include "mcmc/MaCh3Factory.h"
-#include "covariance/covarianceXsec.h"
+#include "Fitters/MaCh3Factory.h"
+#include "Parameters/ParameterHandlerGeneric.h"
 #include "Utils/Comparison.h"
-#include "samplePDF/samplePDFTutorial.h"
+#include "SamplesTutorial/SampleHandlerTutorial.h"
 
 void FitVal(const std::string& Algo, bool MoreTests)
 {
@@ -11,8 +11,8 @@ void FitVal(const std::string& Algo, bool MoreTests)
 
   MACH3LOG_INFO("Testing {}", Algo);
 
-  auto xsec = MaCh3CovarianceFactory<covarianceXsec>(FitManager.get(), "Xsec");
-  auto osc  = MaCh3CovarianceFactory<covarianceOsc>(FitManager.get(), "Osc");
+  auto xsec = MaCh3CovarianceFactory<ParameterHandlerGeneric>(FitManager.get(), "Xsec");
+  auto osc  = MaCh3CovarianceFactory<ParameterHandlerOsc>(FitManager.get(), "Osc");
   std::unique_ptr<FitterBase> MaCh3Fitter = nullptr;
   if(Algo == "MCMC") {
     FitManager->OverrideSettings("General", "OutputFile", "MCMC_Test.root");
@@ -34,24 +34,24 @@ void FitVal(const std::string& Algo, bool MoreTests)
     throw MaCh3Exception(__FILE__ , __LINE__ );
   }
 
-  std::string SampleConfig = {"TutorialConfigs/Samples/SamplePDF_Tutorial.yaml"};
-  auto Sample = std::make_unique<samplePDFTutorial>(SampleConfig, xsec.get(), osc.get());
-  Sample->reweight();
+  std::string SampleConfig = {"TutorialConfigs/Samples/SampleHandler_Tutorial.yaml"};
+  auto Sample = std::make_unique<SampleHandlerTutorial>(SampleConfig, xsec.get(), osc.get());
+  Sample->Reweight();
   std::string name = Sample->GetTitle();
   TString NameTString = TString(name.c_str());
-  TH1D *SampleHistogramPrior = (TH1D*)Sample->get1DHist()->Clone(NameTString+"_Prior");
-  Sample->addData(SampleHistogramPrior);
+  TH1D *SampleHistogramPrior = (TH1D*)Sample->Get1DHist()->Clone(NameTString+"_Prior");
+  Sample->AddData(SampleHistogramPrior);
 
-  MaCh3Fitter->addSystObj(xsec.get());
-  MaCh3Fitter->addSamplePDF(Sample.get());
+  MaCh3Fitter->AddSystObj(xsec.get());
+  MaCh3Fitter->AddSampleHandler(Sample.get());
   if(MoreTests)
   {
     MaCh3Fitter->DragRace();
     MaCh3Fitter->RunLLHScan();
     MaCh3Fitter->Run2DLLHScan();
     MaCh3Fitter->GetStepScaleBasedOnLLHScan();
   }
-  MaCh3Fitter->runMCMC();
+  MaCh3Fitter->RunMCMC();
 }
 
 void StartFromPosteriorTest(const std::string& PreviousName)
@@ -61,13 +61,13 @@ void StartFromPosteriorTest(const std::string& PreviousName)
 
   FitManager->OverrideSettings("General", "OutputFile", "MCMC_Test_Start.root");
 
-  auto xsec = MaCh3CovarianceFactory<covarianceXsec>(FitManager.get(), "Xsec");
+  auto xsec = MaCh3CovarianceFactory<ParameterHandlerGeneric>(FitManager.get(), "Xsec");
   std::unique_ptr<mcmc> MarkovChain = std::make_unique<mcmc>(FitManager.get());
-  MarkovChain->addSystObj(xsec.get());
+  MarkovChain->AddSystObj(xsec.get());
 
   MarkovChain->StartFromPreviousFit(PreviousName);
 
-  MarkovChain->runMCMC();
+  MarkovChain->RunMCMC();
 }
 
 int main(int argc, char *argv[])

CIValidations/MaCh3ModeValidations.cpp

@@ -1,6 +1,6 @@
 // MaCh3 spline includes
 #include "Utils/Comparison.h"
-#include "manager/MaCh3Modes.h"
+#include "Manager/MaCh3Modes.h"
 
 /// Current tests include
 int main(int argc, char *argv[])

CIValidations/NuMCMCconversion.cpp

@@ -6,7 +6,7 @@
 #include "TNamed.h"
 #include "TObjString.h"
 
-#include "mcmc/MaCh3Factory.h"
+#include "Fitters/MaCh3Factory.h"
 
 int main(int argc, char *argv[])
 {

CIValidations/SamplePDFValidations.cpp

@@ -1,12 +1,12 @@
 // MaCh3 spline includes
 #include "Utils/Comparison.h"
-#include "samplePDF/samplePDFTutorial.h"
+#include "SamplesTutorial/SampleHandlerTutorial.h"
 
 _MaCh3_Safe_Include_Start_ //{
 #include "Oscillator/OscillatorFactory.h"
 _MaCh3_Safe_Include_End_ //}
 
-void SharedNuOscTest(const std::string& config, covarianceXsec* xsec, covarianceOsc* osc){
+void SharedNuOscTest(const std::string& config, ParameterHandlerGeneric* xsec, ParameterHandlerOsc* osc){
   OscillatorBase* OscillatorObj = nullptr;
   MACH3LOG_INFO("Utilising a shared NuOscillator object between all atmospheric samples");
 
@@ -17,8 +17,8 @@ void SharedNuOscTest(const std::string& config, covarianceXsec* xsec, covariance
   OscillatorObj->Setup();
   delete OscillFactory;
 
-  samplePDFTutorial *Sample1 = new samplePDFTutorial(config, xsec, osc, OscillatorObj);
-  samplePDFTutorial *Sample2 = new samplePDFTutorial(config, xsec, osc, OscillatorObj);
+  SampleHandlerTutorial *Sample1 = new SampleHandlerTutorial(config, xsec, osc, OscillatorObj);
+  SampleHandlerTutorial *Sample2 = new SampleHandlerTutorial(config, xsec, osc, OscillatorObj);
 
   delete Sample1;
   delete Sample2;
@@ -35,25 +35,25 @@ int main(int argc, char *argv[])
   }
 
   std::vector<std::string> xsecCovMatrixFile = {"TutorialConfigs/CovObjs/SystematicModel.yaml"};
-  covarianceXsec* xsec = new covarianceXsec(xsecCovMatrixFile, "xsec_cov");
+  ParameterHandlerGeneric* xsec = new ParameterHandlerGeneric(xsecCovMatrixFile, "xsec_cov");
 
   std::vector<std::string> OscCovMatrixFile = {"TutorialConfigs/CovObjs/OscillationModel.yaml"};
-  covarianceOsc* osc = new covarianceOsc(OscCovMatrixFile, "osc_cov");
-  osc->setParameters();
+  ParameterHandlerOsc* osc = new ParameterHandlerOsc(OscCovMatrixFile, "osc_cov");
+  osc->SetParameters();
 
   // Open a file in write mode
   std::ofstream outFile("NewSampleOut.txt");
-  std::vector<std::string> SampleConfig = {"TutorialConfigs/Samples/SamplePDF_Tutorial.yaml", "TutorialConfigs/Samples/SamplePDF_Tutorial_ATM.yaml"};
+  std::vector<std::string> SampleConfig = {"TutorialConfigs/Samples/SampleHandler_Tutorial.yaml", "TutorialConfigs/Samples/SampleHandler_Tutorial_ATM.yaml"};
   for (const auto& configPath : SampleConfig) {
-    samplePDFTutorial *Sample = new samplePDFTutorial({configPath}, xsec, osc);
+    SampleHandlerTutorial *Sample = new SampleHandlerTutorial({configPath}, xsec, osc);
 
     std::string name = Sample->GetTitle();
     TString NameTString = TString(name.c_str());
 
     // Reweight and process prior histogram
-    Sample->reweight();
-    TH1D *SampleHistogramPrior = (TH1D*)Sample->get1DHist()->Clone(NameTString + "_Prior");
-    Sample->addData(SampleHistogramPrior);
+    Sample->Reweight();
+    TH1D *SampleHistogramPrior = (TH1D*)Sample->Get1DHist()->Clone(NameTString + "_Prior");
+    Sample->AddData(SampleHistogramPrior);
 
     // Write initial info to file
     outFile << "Info for sample: " << NameTString << std::endl;
@@ -62,17 +62,17 @@ int main(int argc, char *argv[])
 
     // Set oscillation parameters and reweight for posterior
     std::vector<double> OscParProp = {0.3, 0.5, 0.020, 7.53e-5, 2.494e-3, 0.0, 295, 2.6, 0.5, 15};
-    osc->setParameters(OscParProp);
-    Sample->reweight();
+    osc->SetParameters(OscParProp);
+    Sample->Reweight();
 
     // Process posterior histogram
-    TH1D *SampleHistogramPost = (TH1D*)Sample->get1DHist()->Clone(NameTString + "_Post");
+    TH1D *SampleHistogramPost = (TH1D*)Sample->Get1DHist()->Clone(NameTString + "_Post");
     outFile << "Rates Post:" << SampleHistogramPrior->Integral() << std::endl;
     outFile << "Likelihood:" << std::fabs(Sample->GetLikelihood()) << std::endl;
 
     MACH3LOG_INFO("Now trying to compare each weight individually");
-    for (int iSample = 0; iSample < Sample->getNMCSamples(); ++iSample) {
-      for (int iEntry = 0; iEntry < Sample->getNEventsInSample(iSample); ++iEntry) {
+    for (int iSample = 0; iSample < Sample->GetNMCSamples(); ++iSample) {
+      for (int iEntry = 0; iEntry < Sample->GetNEventsInSample(iSample); ++iEntry) {
         double weight = Sample->GetEventWeight(iSample, iEntry);
         outFile<< "Sample: "<< NameTString << " Channel: "<< iSample<<" Event: " << iEntry <<" weight: " << weight << std::endl;
       }