App->CIValidaitions and some tweaks to NuMCMC Tools

Apps/CMakeLists.txt → CIValidations/CMakeLists.txt

@@ -17,9 +17,10 @@ install(PROGRAMS
     NuMCMCvalidations.sh
     TestNuMCMC.py
 
-    DESTINATION Apps)
+    DESTINATION CIValidations)
 
 install(DIRECTORY
     TestOutputs
+    Scripts
 
-    DESTINATION Apps)
+    DESTINATION CIValidations)

CIValidations/NuMCMCconversion.cpp

@@ -0,0 +1,144 @@
+#include <iostream>
+
+#include "TChain.h"
+#include "TFile.h"
+#include "TTree.h"
+#include "TNamed.h"
+#include "TObjString.h"
+
+#include "mcmc/MaCh3Factory.h"
+
+int main(int argc, char *argv[])
+{
+  if (argc != 3)
+  {
+    return 1;
+  }
+
+  double t_sin2th_23;
+  double t_sin2th_13;
+  double t_sin2th_12;
+  double t_delm2_23;
+  double t_delm2_12;
+  double t_delta_cp;
+
+  TChain* myChain = new TChain("posteriors","");
+  myChain->Add(argv[1]);
+
+  std::map<std::string, std::string> branch_map = {
+    {"sin2th_23", "Theta23"},
+    {"sin2th_13", "Theta13"},
+    {"sin2th_12", "Theta12"},
+    {"delm2_12",  "Deltam2_21"},
+    {"delm2_23",  "Deltam2_32"},
+    {"delta_cp",  "DeltaCP"}
+  };
+
+  // Map for pointers to the original branches
+  std::map<std::string, double*> branch_pointers = {
+    {"sin2th_23", &t_sin2th_23},
+    {"sin2th_13", &t_sin2th_13},
+    {"sin2th_12", &t_sin2th_12},
+    {"delm2_12",  &t_delm2_12},
+    {"delm2_23",  &t_delm2_23},
+    {"delta_cp",  &t_delta_cp}
+  };
+
+  // Disable all branches by default
+  myChain->SetBranchStatus("*", 0);
+
+  // Enable branches based on map and set their addresses
+  for (const auto& [old_name, new_name] : branch_map) {
+    myChain->SetBranchStatus(old_name.c_str(), 1);
+    myChain->SetBranchAddress(old_name.c_str(), branch_pointers[old_name]);
+  }
+
+  /// Load cov osc
+  TFile *TempFile = new TFile(argv[1], "open");
+  TDirectory* CovarianceFolder = (TDirectory*)TempFile->Get("CovarianceFolder");
+
+  TMacro *OscConfig = (TMacro*)(CovarianceFolder->Get("Config_osc_cov"));
+
+  YAML::Node OscSettings = TMacroToYAML(*OscConfig);
+
+  // Create the new file and tree
+  TFile* newfile = new TFile(argv[2], "recreate");
+  TTree* newtree = new TTree("mcmc", "mcmc");
+
+  // Create new branches in new tree with the mapped names
+  for (const auto& [old_name, new_name] : branch_map) {
+    newtree->Branch(new_name.c_str(), branch_pointers[old_name], (new_name + "/D").c_str());
+  }
+
+  for (int i = 0; i < myChain->GetEntries(); ++i)
+  {
+    if (i % 10000 == 0) std::cout << i << std::endl;
+    myChain->GetEntry(i);
+
+    t_sin2th_23 = std::asin(std::sqrt(t_sin2th_23));
+    t_sin2th_13 = std::asin(std::sqrt(t_sin2th_13));
+    t_sin2th_12 = std::asin(std::sqrt(t_sin2th_12));
+
+    newtree->Fill();
+  }
+
+  newtree->Print();
+  newtree->AutoSave();
+
+  // List of parameter names and corresponding titles
+  std::vector<std::pair<std::string, std::string>> params;
+
+  // Iterate over each systematic entry in the YAML
+
+  for (auto const &entry : OscSettings["Systematics"])
+  {
+    std::string param_name = entry["Systematic"]["Names"]["ParameterName"].as<std::string>();
+    bool flat_prior = entry["Systematic"]["FlatPrior"].as<bool>();
+    std::string mapped_name = branch_map[param_name];  // Get the mapped name
+    if(mapped_name == "") continue;
+    std::string distribution;
+
+    if (param_name.rfind("sin", 0) == 0) {
+      if (flat_prior) {
+        distribution = "Uniform:sin^2(" + mapped_name + ")";
+      } else {
+        double prefit_value = entry["Systematic"]["ParameterValues"]["PreFitValue"].as<double>();
+        double error = entry["Systematic"]["Error"].as<double>();
+        distribution = "Gaussian(" + std::to_string(prefit_value) + ", " + std::to_string(error) + "):sin^2(" + mapped_name + ")";
+      }
+    } else {
+      if (flat_prior) {
+        distribution = "Uniform:" + mapped_name;
+      } else {
+        double prefit_value = entry["Systematic"]["ParameterValues"]["PreFitValue"].as<double>();
+        double error = entry["Systematic"]["Error"].as<double>();
+        distribution = "Gaussian(" + std::to_string(prefit_value) + ", " + std::to_string(error) + "):" + mapped_name;
+      }
+    }
+    params.emplace_back(mapped_name, distribution);
+  }
+
+  // Create a TList to hold the TNamed objects
+  TList *paramList = new TList();
+
+  // Create TNamed objects for each parameter and add them to the list
+  for (const auto& param : params) {
+    TNamed *namedParam = new TNamed(param.first.c_str(), param.second.c_str());
+    paramList->Add(namedParam);  // Add to TList
+  }
+
+  // Write the TList to the directory
+  paramList->Write("priors", TObject::kSingleKey);
+
+
+  TObjString doi("https://doi.org/10.5281/zenodo.13642670");
+
+  doi.Write("citation");
+
+  // Close the file
+  newfile->Close();
+
+  delete newfile;
+
+  return 0;
+}

Apps/NuMCMCvalidations.sh → CIValidations/NuMCMCvalidations.sh

@@ -1,11 +1,11 @@
 ./bin/MCMCTutorial Inputs/ManagerTest.yaml
 
-./Apps/NuMCMCconversion Test.root NewChain.root
+./CIValidations/NuMCMCconversion Test.root NewChain.root
 
 pip install -r NuMCMCTools/requirements.txt
 
 export PYTHONPATH="$PYTHONPATH:/${MaCh3Tutorial_ROOT}/NuMCMCTools"
 
-cp NewChain.root Apps/NewChain.root
+cp NewChain.root CIValidations/NewChain.root
 
-python3 Apps/TestNuMCMC.py
+python3 CIValidations/TestNuMCMC.py

CMakeLists.txt

@@ -112,7 +112,7 @@ cmessage(STATUS "CMAKE CXX Standard: ${CMAKE_CXX_STANDARD}")
 
 ################################# Build MaCh3 ##################################
 add_subdirectory(Utils)
-add_subdirectory(Apps)
+add_subdirectory(CIValidations)
 add_subdirectory(Tutorial)
 
 configure_file(cmake/Templates/setup.MaCh3Tutorial.sh.in "${PROJECT_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/setup.MaCh3Tutorial.sh" @ONLY)
@@ -121,7 +121,6 @@ install(FILES "${PROJECT_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/setup.MaCh3Tutorial
 ############################  Install  ####################################
 install(DIRECTORY Inputs DESTINATION ${CMAKE_BINARY_DIR})
 install(DIRECTORY plotting DESTINATION ${CMAKE_BINARY_DIR})
-install(DIRECTORY Scripts DESTINATION ${CMAKE_BINARY_DIR})
 
 include(CMakePackageConfigHelpers)
 configure_package_config_file(