From 082a44a2d8b46935d00c924af8f14ca7f33b4807 Mon Sep 17 00:00:00 2001
From: Kamil Skwarczynski <skwarczynskikamil@gmail.com>
Date: Mon, 18 Nov 2024 12:35:24 +0000
Subject: [PATCH] minor tweaks to factory

---
 mcmc/MaCh3Factory.cpp | 61 +------------------------------------------
 mcmc/MaCh3Factory.h   | 58 +++++++++++++++++++++++++++++++++++-----
 2 files changed, 53 insertions(+), 66 deletions(-)

diff --git a/mcmc/MaCh3Factory.cpp b/mcmc/MaCh3Factory.cpp
index 56ef9fcb..e257bc58 100644
--- a/mcmc/MaCh3Factory.cpp
+++ b/mcmc/MaCh3Factory.cpp
@@ -3,7 +3,7 @@
 
 
 // ********************************************
-std::unique_ptr<FitterBase> MaCh3FitterFactory(manager *fitMan, std::vector<samplePDFBase*>& Samples, std::vector<covarianceBase*>& Covariances) {
+std::unique_ptr<FitterBase> MaCh3FitterFactory(manager *fitMan) {
 // ********************************************
   std::unique_ptr<FitterBase> MaCh3Fitter = nullptr;
 
@@ -24,68 +24,9 @@ std::unique_ptr<FitterBase> MaCh3FitterFactory(manager *fitMan, std::vector<samp
     MACH3LOG_ERROR("You want to use algorithm {}, I don't recognize it, sry", Algorithm);
     throw MaCh3Exception(__FILE__ , __LINE__ );
   }
-
-  //KS: Adding samples and covariances to the Fitter class could be in the factory
-  for(unsigned int i = 0; Samples.size(); i++)
-    MaCh3Fitter->addSamplePDF(Samples[i]);
-  for(unsigned int i = 0; Covariances.size(); i++)
-    MaCh3Fitter->addSystObj(Covariances[i]);
-
   return MaCh3Fitter;
 }
 
-// ********************************************
-template <typename CovType>
-CovType* MaCh3CovarianceFactory(manager *FitManager, const std::string& PreFix){
-// ********************************************
-
-  // config for our matrix
-  YAML::Node Settings = FitManager->raw()["General"]["Systematics"];
-  auto CovMatrixName = Settings[std::string(PreFix) + "CovName"].as<std::string>();
-  MACH3LOG_INFO("Initialising {} matrix", CovMatrixName);
-
-  // yaml files initialising out matrix
-  auto CovMatrixFile = Settings[std::string(PreFix) + "CovFile"].as<std::vector<std::string>>();
-
-  // PCA threshold, -1 means no pca
-  auto PCAThreshold = GetFromManager<int>(Settings[std::string(PreFix) + "PCAThreshold"], -1);
-  // do we pca whole matrix or only submatrix
-  auto PCAParamRegion = GetFromManager<std::vector<int>>(Settings[std::string(PreFix) + "PCAParams"], {-999, -999});
-
-  /// @todo this massive hack with "xsec_cov" is because we have const char * ... will have to fix it later...
-  CovType* CovObject = new CovType(CovMatrixFile, "xsec_cov", PCAThreshold, PCAParamRegion[0], PCAParamRegion[1]);
-
-  // Fill the parameter values with their nominal values
-  // should _ALWAYS_ be done before overriding with fix or flat
-  CovObject->setParameters();
-
-  auto FixParams = GetFromManager<std::vector<std::string>>(Settings[std::string(PreFix) + "FixParams"], {});
-
-  // Fixed CovObject parameters loop
-  if (FixParams.size() == 1 && FixParams.at(0) == "All") {
-    for (int j = 0; j < CovObject->GetNumParams(); j++) {
-      CovObject->toggleFixParameter(j);
-    }
-  } else {
-    for (unsigned int j = 0; j < FixParams.size(); j++) {
-      CovObject->toggleFixParameter(FixParams.at(j));
-    }
-  }
-  //Global step scale for matrix
-  auto StepScale = Settings[std::string(PreFix) + "StepScale"].as<double>();
-
-  CovObject->setStepScale(StepScale);
-
-  // Adaptive MCMC stuff
-  if(FitManager->raw()["AdaptionOptions"])
-    CovObject->initialiseAdaption(FitManager->raw());
-
-  MACH3LOG_INFO("Factory successful");
-
-  return CovObject;
-}
-
-
 // ********************************************
 covarianceXsec* MaCh3CovarianceFactory(manager *FitManager, const std::string& PreFix) {
 // ********************************************
diff --git a/mcmc/MaCh3Factory.h b/mcmc/MaCh3Factory.h
index 6d9276dd..0ce1be88 100644
--- a/mcmc/MaCh3Factory.h
+++ b/mcmc/MaCh3Factory.h
@@ -22,9 +22,13 @@
 /// @code
 /// General:
 ///   FittingAlgorithm: ["MCMC"]
-std::unique_ptr<FitterBase> MaCh3FitterFactory(manager *fitMan, std::vector<samplePDFBase>& Samples, std::vector<covarianceBase>& Covariances);
+std::unique_ptr<FitterBase> MaCh3FitterFactory(manager *fitMan);
 
+/// @brief Factory function for creating a covariance class for systematic handling.
+covarianceXsec* MaCh3CovarianceFactory(manager *FitManager, const std::string& PreFix);
 
+
+// ********************************************
 /// @brief Factory function for creating a covariance class for systematic handling.
 ///
 /// @param fitMan Pointer to the manager class that holds the configuration settings.
@@ -51,12 +55,54 @@ std::unique_ptr<FitterBase> MaCh3FitterFactory(manager *fitMan, std::vector<samp
 ///
 /// @todo add adaptive stuff
 template <typename CovType>
-CovType* MaCh3CovarianceFactory(manager *FitManager, const std::string& PreFix);
+CovType* MaCh3CovarianceFactory(manager *FitManager, const std::string& PreFix){
+// ********************************************
+  // config for our matrix
+  YAML::Node Settings = FitManager->raw()["General"]["Systematics"];
+  auto CovMatrixName = Settings[std::string(PreFix) + "CovName"].as<std::string>();
+  MACH3LOG_INFO("Initialising {} matrix", CovMatrixName);
 
-/// @brief Factory function for creating a covariance class for systematic handling.
-covarianceXsec* MaCh3CovarianceFactory(manager *FitManager, const std::string& PreFix);
+  // yaml files initialising out matrix
+  auto CovMatrixFile = Settings[std::string(PreFix) + "CovFile"].as<std::vector<std::string>>();
+
+  // PCA threshold, -1 means no pca
+  auto PCAThreshold = GetFromManager<int>(Settings[std::string(PreFix) + "PCAThreshold"], -1);
+  // do we pca whole matrix or only submatrix
+  auto PCAParamRegion = GetFromManager<std::vector<int>>(Settings[std::string(PreFix) + "PCAParams"], {-999, -999});
+
+  CovType* CovObject = new CovType(CovMatrixFile, CovMatrixName, PCAThreshold, PCAParamRegion[0], PCAParamRegion[1]);
+
+  // Fill the parameter values with their nominal values
+  // should _ALWAYS_ be done before overriding with fix or flat
+  CovObject->setParameters();
 
+  auto FixParams = GetFromManager<std::vector<std::string>>(Settings[std::string(PreFix) + "FixParams"], {});
+
+  // Fixed CovObject parameters loop
+  if (FixParams.size() == 1 && FixParams.at(0) == "All") {
+    for (int j = 0; j < CovObject->GetNumParams(); j++) {
+      CovObject->toggleFixParameter(j);
+    }
+  } else {
+    for (unsigned int j = 0; j < FixParams.size(); j++) {
+      CovObject->toggleFixParameter(FixParams.at(j));
+    }
+  }
+  //Global step scale for matrix
+  auto StepScale = Settings[std::string(PreFix) + "StepScale"].as<double>();
+
+  CovObject->setStepScale(StepScale);
+
+  // Adaptive MCMC stuff
+  if(FitManager->raw()["AdaptionOptions"])
+    CovObject->initialiseAdaption(FitManager->raw());
+
+  MACH3LOG_INFO("Factory successful");
+
+  return CovObject;
+}
 
+// ********************************************
 /// @brief Factory function for creating SamplePDF and initialisation with systematic.
 ///
 /// @tparam SampleType The class type of the sample to create, e.g., `samplePDFTutorial`.
@@ -72,8 +118,8 @@ covarianceXsec* MaCh3CovarianceFactory(manager *FitManager, const std::string& P
 template <typename SampleType>
 std::vector<SampleType*> MaCh3SamplePDFFactory(const std::vector<std::string>& SampleConfig,
                                                covarianceXsec* xsec,
-                                               covarianceOsc* osc = nullptr)
-{
+                                               covarianceOsc* osc = nullptr) {
+// ********************************************
   std::vector<SampleType*> PDFs(SampleConfig.size());
   for (size_t i = 0; i < SampleConfig.size(); ++i)
   {