Merge branch 'root6' of https://bitbucket.org/muonspin/musrfit into root6

.gitignore

@@ -0,0 +1,2 @@
+# ignore all files generated from an in-repo build
+build/

src/classes/PFitter.cpp

@@ -39,9 +39,10 @@
 #include <iomanip>
 #include <fstream>
 #include <limits>
-
 #include <cmath>
 
+#include <boost/variant/variant.hpp>
+
 #include <sys/time.h>
 
 #include "Minuit2/FunctionMinimum.h"
@@ -2473,6 +2474,121 @@ Bool_t PFitter::ExecuteSave(Bool_t firstSave)
       ccorr->Write("ccorr", TObject::kOverwrite, sizeof(ccorr));
       hcorr->Write("hcorr", TObject::kOverwrite, sizeof(hcorr));
       ff.Close();
+
+      // write the fit results to an easy-to-read/parse yaml file
+      // note: the block names follow those used by Python library iminuit
+      // https://github.com/scikit-hep/iminuit
+
+      // dynamically name the yaml output file
+      // https://stackoverflow.com/a/25389052
+      std::string yaml_filename(fRunInfo->GetFileName().Data());
+      const std::string msr_ext(".msr");
+      yaml_filename.replace(yaml_filename.find(msr_ext), msr_ext.length(),
+                            ".yaml");
+
+      // define yaml's 2-space indentation
+      const std::string yaml_indent("  ");
+
+      // open the yaml file for writing
+      std::ofstream yaml_file(yaml_filename);
+
+      // number formatting of the output
+      yaml_file << std::scientific << std::setprecision(16);
+
+      // write the parameter values
+      yaml_file << "values:\n";
+      for (unsigned int i = 0; i < fParams.size(); ++i) {
+        yaml_file << yaml_indent << fParams[i].fName.Data() << ": "
+                  << fParams[i].fValue << "\n";
+      }
+
+      // write the parabolic errors
+      yaml_file << "errors:\n";
+      for (unsigned int i = 0; i < fParams.size(); ++i) {
+        yaml_file << yaml_indent << fParams[i].fName.Data() << ": "
+                  << fMnUserParams.Error(i) << "\n";
+      }
+
+      // write the minos errors
+      yaml_file << "mnerrors:\n";
+      for (unsigned int i = 0; i < fParams.size(); ++i) {
+        // use boost's implementation of a variant, which can be streamed by
+        // default - see: https://stackoverflow.com/q/47168477
+        boost::variant<double, std::string> positive_error, negative_error;
+        if (fParams[i].fPosErrorPresent) {
+          positive_error = fParams[i].fPosError;
+          negative_error = fParams[i].fStep;
+        } else {
+          positive_error = "null";
+          negative_error = "null";
+        }
+
+        yaml_file << yaml_indent << fParams[i].fName.Data() << ":\n";
+        yaml_file << yaml_indent << yaml_indent
+                  << "positive: " << positive_error << "\n";
+        yaml_file << yaml_indent << yaml_indent
+                  << "negative: " << negative_error << "\n";
+      }
+
+      // write the parameter limits
+      yaml_file << "limits:\n";
+      for (unsigned int i = 0; i < fParams.size(); ++i) {
+        // use boost's implementation of a variant, which can be streamed by
+        // default - see: https://stackoverflow.com/q/47168477
+        boost::variant<double, std::string> upper_limit, lower_limit;
+        if (fParams[i].fLowerBoundaryPresent) {
+          lower_limit = fParams[i].fLowerBoundary;
+        } else {
+          lower_limit = "null";
+        }
+        if (fParams[i].fUpperBoundaryPresent) {
+          upper_limit = fParams[i].fUpperBoundary;
+        } else {
+          upper_limit = "null";
+        }
+
+        yaml_file << yaml_indent << fParams[i].fName.Data() << ":\n";
+        yaml_file << yaml_indent << yaml_indent << "lower: " << lower_limit
+                  << "\n";
+        yaml_file << yaml_indent << yaml_indent << "upper: " << upper_limit
+                  << "\n";
+      }
+
+      // write if the parameter is fixed
+      yaml_file << "fixed:\n";
+      for (unsigned int i = 0; i < fParams.size(); ++i) {
+        std::string is_fixed = fParams[i].fStep == 0.0 ? "true" : "false";
+        yaml_file << yaml_indent << fParams[i].fName.Data() << ": " << is_fixed
+                  << "\n";
+      }
+
+      // write the covariance matrix (omitting fixed parameters)
+      yaml_file << "covariance:\n";
+      for (unsigned int i = 0; i < cov.Nrow(); ++i) {
+        yaml_file << yaml_indent << mnState.Name(parNo[i]) << ":\n";
+        for (unsigned int j = 0; j < cov.Nrow(); ++j) {
+          yaml_file << yaml_indent << yaml_indent << mnState.Name(parNo[j])
+                    << ": " << cov(i, j) << "\n";
+        }
+      }
+
+      // write the correlation matrix (omitting fixed parameters)
+      yaml_file << "correlation:\n";
+      for (unsigned int i = 0; i < cov.Nrow(); ++i) {
+        yaml_file << yaml_indent << mnState.Name(parNo[i]) << ":\n";
+        for (unsigned int j = 0; j < cov.Nrow(); ++j) {
+          double correlation =
+              i == j ? 1.0
+                     : cov(i, j) / (fMnUserParams.Error(parNo[i]) *
+                                    fMnUserParams.Error(parNo[j]));
+          yaml_file << yaml_indent << yaml_indent << mnState.Name(parNo[j])
+                    << ": " << correlation << "\n";
+        }
+      }
+
+      // close the yaml file
+      yaml_file.close();
+
     }
     parNo.clear(); // clean up
   } else {

src/musrFT.cpp

@@ -1437,19 +1437,18 @@ Int_t main(Int_t argc, Char_t *argv[])
     musrFT_dumpData(startupParam.dumpFln, fourier, startupParam.fourierRange[0], startupParam.fourierRange[1]);
   } else { // do Canvas
 
-    // if Fourier graphical export is whished, switch to batch mode
+    // if Fourier graphical export is wished, switch to batch mode
     Bool_t batch = false;
-    int cc=0;
-    char **arg;
+    // create list of essential arguments to pass to the ROOT application
+    std::vector<char*> args;
+    args.push_back(argv[0]); // program name
     if (startupParam.graphicFormat.Length() != 0) {
       batch = true;
-      arg[cc] = (Char_t*)malloc(16*sizeof(Char_t));
-      strcpy(arg[cc], "-b");
-      cc++;
+      args.push_back((char*)"-b"); // batch mode flag
     }
-
+    int cc = args.size();
     // plot the Fourier transform
-    TApplication app("App", &cc, arg);
+    TApplication app("App", &cc, args.data());
 
     if (startupHandler) {
       fourierCanvas = std::unique_ptr<PFourierCanvas>(new PFourierCanvas(fourier, dataSetTag, startupParam.title.Data(),

src/musrview.cpp

@@ -37,6 +37,7 @@
 
 #include <iostream>
 #include <memory>
+#include <vector>
 
 #include <TApplication.h>
 #include <TSAXParser.h>
@@ -301,15 +302,15 @@ int main(int argc, char *argv[])
   }
 
   if (result == PMUSR_SUCCESS) {
-    // generate Root application needed for PMusrCanvas
-    int cc=0;
-    char **arg;
+    // create the ROOT application needed for PMusrCanvas
+    // and pass it only essential arguments
+    std::vector<char*> args;
+    args.push_back(argv[0]); // program name
     if (graphicsOutput || asciiOutput) {
-      arg[cc] = (char*)malloc(16*sizeof(char));
-      strcpy(arg[cc], "-b");
-      cc++;
+      args.push_back((char*)"-b"); // batch mode flag
     }
-    TApplication app("App", &cc, arg);
+    int cc = args.size();
+    TApplication app("App", &cc, args.data());
 
     std::vector<PMusrCanvas*> canvasVector;
     PMusrCanvas *musrCanvas;