tidy: add new TH2Poly related fucniton and more authros

Doc/Doxyfile

@@ -741,7 +741,7 @@ WARN_LOGFILE           =
 # spaces.
 # Note: If this tag is empty the current directory is searched.
 
-INPUT                  = . Doc/mainpage.md manager splines samplePDF mcmc Diagnostics plotting plotting/plottingUtils Diagnostics/Diagnostics_utils covariance
+INPUT                  = . Doc/mainpage.md manager splines samplePDF mcmc Diagnostics plotting plotting/plottingUtils Diagnostics/Diagnostics_utils covariance python
 
 # This tag can be used to specify the character encoding of the source files
 # that doxygen parses. Internally doxygen uses the UTF-8 encoding. Doxygen uses

cmake/Templates/Doxyfile.in

@@ -741,7 +741,7 @@ WARN_LOGFILE           =
 # spaces.
 # Note: If this tag is empty the current directory is searched.
 
-INPUT                  = . Doc/mainpage.md manager splines samplePDF mcmc Diagnostics plotting plotting/plottingUtils Diagnostics/Diagnostics_utils covariance
+INPUT                  = . Doc/mainpage.md manager splines samplePDF mcmc Diagnostics plotting plotting/plottingUtils Diagnostics/Diagnostics_utils covariance python
 
 # This tag can be used to specify the character encoding of the source files
 # that doxygen parses. Internally doxygen uses the UTF-8 encoding. Doxygen uses

covariance/covarianceBase.h

@@ -12,6 +12,9 @@ constexpr static const double _LARGE_LOGL_ = 1234567890.0;
 
 /// @brief Base class responsible for handling of systematic error parameters. Capable of using PCA or using adaptive throw matrix
 /// @see For more details, visit the [Wiki](https://github.com/mach3-software/MaCh3/wiki/02.-Implementation-of-Systematic).
+/// @author Dan Barrow
+/// @author Ed Atkin
+/// @author Kamil Skwarczynski
 class covarianceBase {
  public:
   /// @brief ETA - constructor for a YAML file

covariance/covarianceOsc.h

@@ -4,6 +4,8 @@
 #include "covariance/covarianceBase.h"
 
 /// @brief Class responsible for handling of neutrino oscillation  parameters.
+/// @author Richard Calland
+/// @author Asher Kaboth
 class covarianceOsc : public covarianceBase
 {
  public:
@@ -29,10 +31,8 @@ class covarianceOsc : public covarianceBase
   void Print();
 
  protected:
-
     /// Do we flip DeltaM23 or not
     bool flipdelM;
-
     /// There is special treatment for delta CP, therefore store enum keeping track when to apply special treatment
     int kDeltaCP;
     /// There is special treatment for DeltaM23, therefore store enum keeping track when to apply special treatment

manager/MaCh3Logger.h

@@ -9,7 +9,8 @@
 #include <functional>
 #include <string>
 
-//KS: Based on this https://github.com/gabime/spdlog/blob/a2b4262090fd3f005c2315dcb5be2f0f1774a005/include/spdlog/spdlog.h#L284
+/// @file MaCh3Logger.h
+/// @brief KS: Based on this https://github.com/gabime/spdlog/blob/a2b4262090fd3f005c2315dcb5be2f0f1774a005/include/spdlog/spdlog.h#L284
 
 #define MACH3LOG_TRACE SPDLOG_TRACE
 #define MACH3LOG_DEBUG SPDLOG_DEBUG

manager/Monitor.h

@@ -22,6 +22,7 @@
 
 /// @file Monitor.h
 /// @brief System and monitoring utilities for printing system information and status updates.
+/// @author Kamil Skwarczynski
 
 namespace MaCh3Utils {
   /// @brief KS: Prints welcome message with MaCh3 logo

manager/YamlHelper.h

@@ -15,6 +15,7 @@
 
 /// @file YamlHelper.h
 /// @brief Utility functions for handling YAML nodes
+/// @author Kamil Skwarczynski
 
 // **********************
 /// @brief Get content of config file if node is not found take default value specified

python/pyMaCh3.cpp

@@ -1,6 +1,9 @@
 #include <pybind11/pybind11.h>
 #include <pybind11/stl.h>
 
+/// @file pyMaCh3.cpp
+/// @author Ewan Miller
+
 namespace py = pybind11;
 
 void initPlotting(py::module &); // <- defined in python/plotting.cpp
@@ -17,4 +20,4 @@ PYBIND11_MODULE( _pyMaCh3, m ) {
     initManager(m);
     initCovariance(m);
     initSplines(m);
-}
+}

python/splines.cpp

@@ -244,4 +244,4 @@ void initSplines(py::module &m){
         .doc() = "This 'monolith' deals with event by event weighting using splines."
 
     ; // End of binding for EventSplineMonolith
-}
+}

samplePDF/HistogramUtils.cpp

@@ -128,7 +128,6 @@ TH1D* PolyProjectionX(TObject* poly, std::string TempName, const std::vector<dou
 //WP: Helper function for projecting TH2Poly onto the Y axis
 TH1D* PolyProjectionY(TObject* poly, std::string TempName, const std::vector<double>& ybins, const bool computeErrors) {
 // **************************************************
-
   TH1D* hProjY = new TH1D((TempName+"_y").c_str(),(TempName+"_y").c_str(),int(ybins.size()-1),&ybins[0]);
   //KS: Temp Histogram to store error, use double as this is thread safe
   std::vector<double> hProjY_Error(hProjY->GetXaxis()->GetNbins() + 1, 0.0);
@@ -327,6 +326,29 @@ double PolyIntegralWidth(TH2Poly *Histogram) {
   return integral;
 }
 
+// *********************
+TH2Poly* MakePolyHist(const std::string& name, const std::vector<double>& BinArray_x, const std::vector<double>& BinArray_y) {
+// *********************
+  TH2Poly* poly = new TH2Poly();
+  poly->SetName(name.c_str());
+  poly->SetTitle(name.c_str());
+  double xmax, xmin, ymax, ymin;
+  for(unsigned int iy = 0; iy < BinArray_y.size()-1; iy++)
+  {
+    ymax = BinArray_y[iy+1];
+    ymin = BinArray_y[iy];
+    for(unsigned int ix = 0; ix < BinArray_x.size()-1; ix++)
+    {
+      xmax = BinArray_x[ix+1];
+      xmin = BinArray_x[ix];
+      double binofx[] = {xmin, xmax, xmax, xmin};
+      double binofy[] = {ymin, ymin, ymax, ymax};
+      poly->AddBin(4,binofx,binofy);
+    }
+  }
+  return poly;
+}
+
 // *********************
 //KS: Remove fitted TF1 from hist to make comparison easier
 void RemoveFitter(TH1D* hist, const std::string& name) {

samplePDF/HistogramUtils.h

@@ -8,6 +8,9 @@
 // MaCh3 inlcudes
 #include "samplePDF/Structs.h"
 
+/// @file HistogramUtils.h
+/// @author Will Parker
+
 /// @brief WP: Helper function for calculating unbinned Integral of TH2Poly i.e including overflow
 double OverflowIntegral(TH2Poly* poly);
 
@@ -32,6 +35,12 @@ TH2Poly* PolyScaleWidth(TH2Poly *Histogram, double scale);
 /// @brief WP: Helper to calc integral of th2poly analogous to th2d integra; with option "width"
 double PolyIntegralWidth(TH2Poly *Histogram);
 
+/// @brief WP: Helper function to create TH2Poly histogram with uniform binning
+/// @param name This will be tittle of output histogram
+/// @param BinArray_x Bin edges for X axis
+/// @param BinArray_y Bin edges for Y axis
+TH2Poly* MakePolyHist(const std::string& name, const std::vector<double>& BinArray_x, const std::vector<double>& BinArray_y);
+
 /// @brief KS: ROOT changes something with binning when moving from ROOT 5 to ROOT 6. If you open ROOT5 produced file with ROOT6 you will be missing 9 last bins
 /// @brief However if you use ROOT6 and have ROOT6 file exactly the same code will work. Something have changed with how TH2Poly bins are stored in TFile
 /// @param file ROOT file that we will make version checks

samplePDF/Structs.h

@@ -78,6 +78,15 @@ constexpr static const int Unity_Int = 1;
 #include "Constants/OscillatorConstants.h"
 #pragma GCC diagnostic pop
 
+
+/// @file Structs.h
+/// @author Asher Kaboth
+/// @author Clarence Wret
+/// @author Patrick Dunne
+/// @author Dan Barrow
+/// @author Ed Atkin
+/// @author Kamil Skwarczynski
+
 // *******************
 /// @brief Template to make vector out of an array of any length
 template< typename T, size_t N >

splines/SplineCommon.h

@@ -6,6 +6,8 @@
 /// @details This file includes macros and enums for defining spline coefficients.
 /// It is designed to be compatible with older CUDA versions, so be cautious
 /// when adding new features or including other headers.
+/// @author Clarence Wret
+/// @author Kamil Skwarczynski
 
 #ifndef _BAD_SPLINE_
 #define _BAD_SPLINE_ 123456789
@@ -25,7 +27,6 @@ enum SplineSegmentCoeffs
   kCoeffD = 3  ///< Coefficient D
 };
 
-
 // *******************
 /// @brief KS: Struct storing information for spline monolith
 /// @details This structure holds the X coefficients, other spline coefficients,

splines/SplineStructs.h

@@ -13,6 +13,8 @@
 
 /// @file SplineStructs.h
 /// @brief Contains structures and helper functions for handling spline representations of systematic parameters in the MaCh3.
+/// @author Clarence Wret
+/// @author Kamil Skwarczynski
 
 // *******************
 /// @brief CW: Add a struct to hold info about the splinified xsec parameters and help with FindSplineSegment