Some Fixes

.github/workflows/CIPythonValidations.yml

@@ -39,5 +39,5 @@ jobs:
         export PYTHONPATH=$PYTHONPATH:$PWD/python-test-modules/
         export MACH3=$PWD
 
-        python3 -m pytest --config Inputs/ManagerTest.yaml CIValidations/PythonTests
+        python3 -m pytest --config Inputs/FitterConfig.yaml CIValidations/PythonTests
 

CMakeLists.txt

@@ -3,7 +3,7 @@ set(CMAKE_VERBOSE_MAKEFILE ON)
 # CMake version check
 cmake_minimum_required(VERSION 3.14 FATAL_ERROR)
 
-project(MaCh3 VERSION 1.2.0 LANGUAGES CXX)
+project(MaCh3 VERSION 1.2.1 LANGUAGES CXX)
 set(MaCh3_VERSION ${PROJECT_VERSION})
 
 #LP - This option name is confusing, but I wont change it now.

Doc/Doxyfile

@@ -38,7 +38,7 @@ PROJECT_NAME           = "MaCh3"
 # could be handy for archiving the generated documentation or if some version
 # control system is used.
 
-PROJECT_NUMBER         = 1.2.0
+PROJECT_NUMBER         = 1.2.1
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer a

Doc/MaCh3DockerFiles/Ubuntu22.04/Dockerfile

@@ -13,7 +13,9 @@ RUN apt update && apt upgrade -y
 
 RUN apt-get install -y nlohmann-json3-dev
 #MISC_SW
-RUN apt install -y --no-install-recommends vim less nano gdb csh tcsh ed quota python3 python3-dev python3-pip cvs procmail ca-certificates
+RUN apt install -y --no-install-recommends \
+    vim less nano gdb csh tcsh ed quota python3 python3-dev python3-pip \
+    cvs procmail ca-certificates cmake ninja-build
 
 # Declare the build argument
 ARG MACH3_VERSION

covariance/covarianceBase.cpp

@@ -1,17 +1,26 @@
 #include "covariance/covarianceBase.h"
 
 // ********************************************
-covarianceBase::covarianceBase(std::string name, std::string file) : inputFile(file), pca(false) {
+covarianceBase::covarianceBase(std::string name, std::string file, double threshold, int FirstPCA, int LastPCA) : inputFile(file), pca(false),
+eigen_threshold(threshold), FirstPCAdpar(FirstPCA), LastPCAdpar(LastPCA) {
 // ********************************************
   MACH3LOG_INFO("Constructing instance of covarianceBase");
+  if (threshold < 0 || threshold >= 1) {
+    MACH3LOG_INFO("NOTE: {} {}", name, file);
+    MACH3LOG_INFO("Principal component analysis but given the threshold for the principal components to be less than 0, or greater than (or equal to) 1. This will not work");
+    MACH3LOG_INFO("Please specify a number between 0 and 1");
+    MACH3LOG_INFO("You specified: ");
+    MACH3LOG_INFO("Am instead calling the usual non-PCA constructor...");
+    pca = false;
+  }
   init(name, file);
-  FirstPCAdpar = -999;
-  LastPCAdpar = -999;
+
+  // Call the innocent helper function
+  if (pca) ConstructPCA();
 }
 // ********************************************
 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 ");
   for(unsigned int i = 0; i < YAMLFile.size(); i++)
   {

covariance/covarianceBase.h

@@ -24,7 +24,7 @@ class covarianceBase {
   /// @brief "Usual" constructors from root file
   /// @param name Matrix name
   /// @param file Path to matrix root file
-  covarianceBase(std::string name, std::string file);
+  covarianceBase(std::string name, std::string file, double threshold = -1, int FirstPCAdpar = -999, int LastPCAdpar = -999);
 
   /// @brief Destructor
   virtual ~covarianceBase();

plotting/GetPostfitParamPlots.cpp

@@ -556,7 +556,7 @@ void MakeXsecRidgePlots()
     auto blockContents = paramBlock[2].as<std::vector<std::string>>();
 
     // the directory of histograms
-    TDirectoryFile *posteriorDir = man->input().getFile(0).file->Get<TDirectoryFile>("Post");
+    TDirectoryFile *posteriorDir = man->input().getFile(0).file->Get<TDirectoryFile>("Post_1d_hists");
 
     // get num of params in the block
     int nParams = static_cast<int>(blockContents.size());
@@ -579,12 +579,10 @@ void MakeXsecRidgePlots()
     // use this to set the limits and also to plot the x axis and grid
     TH1D *axisPlot = new TH1D("axis plot", "", 1, blockLimits[0], blockLimits[1]);
 
-    for(int parId = 0; parId < nParams; parId++){
+    for(int parId = 0; parId < nParams; parId++) {
       std::string paramName = blockContents[parId];
 
-      TCanvas *posteriorDistCanv = nullptr;
       TH1D *posteriorDist = nullptr;
-
       // get the list of objects in the directory
       TIter next(posteriorDir->GetListOfKeys());
       while (TKey* key = static_cast<TKey*>(next())) {
@@ -595,13 +593,12 @@ void MakeXsecRidgePlots()
         bool foundPar = (pos == str.length() - name.length());
 
         if(foundPar){
-          posteriorDistCanv = posteriorDir->Get<TCanvas>(key->GetName());
-          posteriorDist = static_cast<TH1D*>(posteriorDistCanv->GetPrimitive(key->GetName()));
+          posteriorDist = posteriorDir->Get<TH1D>(key->GetName());
         }
       }
 
       if(posteriorDist == nullptr){
-        MACH3LOG_WARN("Couldnt find parameter {} when making ridgeline plots", paramName);
+        MACH3LOG_WARN("Couldn't find parameter {} when making ridgeline plots", paramName);
         continue;
       }
 
@@ -758,6 +755,20 @@ void GetPostfitParamPlots()
     postFitHist_tmp->SetLineWidth(man->getOption<int>("plotLineWidth"));
     leg->AddEntry(postFitHist_tmp, man->getFileLabel(fileId).c_str(), "lpf");
   }
+  /// @todo this is temporary hack
+  for(unsigned int fileId = 0; fileId < man->getNFiles(); fileId++)
+  {
+    TH1D *Hist = static_cast<TH1D*>((man->input().getFile(fileId).file->Get( ("param_xsec_"+plotType).c_str()))->Clone());
+
+    Hist->SetMarkerColor(TColor::GetColorPalette(fileId));
+    Hist->SetLineColor(TColor::GetColorPalette(fileId));
+    Hist->SetMarkerStyle(7);
+    Hist->SetLineStyle(1+fileId);
+    Hist->SetLineWidth(man->getOption<int>("plotLineWidth"));
+
+    PostfitHistVec.push_back(Hist);
+  }
+
   canv->cd();
   canv->Clear();
   leg->Draw();