added the option to write the content of the MINUIT2.OUTPUT ascii file as yaml. This extends the previous commit from Ryan M.L. McFadden.
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@ -265,8 +265,8 @@ UInt_t PSectorChisq::GetNDF(UInt_t idx)
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* \param runListCollection pointer of the run list collection (pre-processed historgrams)
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* \param chisq_only flag: true=calculate chisq only (no fitting)
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*/
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PFitter::PFitter(PMsrHandler *runInfo, PRunListCollection *runListCollection, Bool_t chisq_only) :
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fChisqOnly(chisq_only), fRunInfo(runInfo), fRunListCollection(runListCollection)
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PFitter::PFitter(PMsrHandler *runInfo, PRunListCollection *runListCollection, Bool_t chisq_only, Bool_t yaml_out) :
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fChisqOnly(chisq_only), fYamlOut(yaml_out), fRunInfo(runInfo), fRunListCollection(runListCollection)
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{
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// initialize variables
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fIsScanOnly = true;
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@ -2475,120 +2475,121 @@ Bool_t PFitter::ExecuteSave(Bool_t firstSave)
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hcorr->Write("hcorr", TObject::kOverwrite, sizeof(hcorr));
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ff.Close();
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// write the fit results to an easy-to-read/parse yaml file
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// note: the block names follow those used by Python library iminuit
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// https://github.com/scikit-hep/iminuit
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if (fYamlOut) {
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// write the fit results to an easy-to-read/parse yaml file
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// note: the block names follow those used by Python library iminuit
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// https://github.com/scikit-hep/iminuit
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// dynamically name the yaml output file
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// https://stackoverflow.com/a/25389052
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std::string yaml_filename(fRunInfo->GetFileName().Data());
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const std::string msr_ext(".msr");
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yaml_filename.replace(yaml_filename.find(msr_ext), msr_ext.length(),
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".yaml");
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// dynamically name the yaml output file
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// https://stackoverflow.com/a/25389052
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std::string yaml_filename(fRunInfo->GetFileName().Data());
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const std::string msr_ext(".msr");
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yaml_filename.replace(yaml_filename.find(msr_ext), msr_ext.length(),
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".yaml");
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// define yaml's 2-space indentation
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const std::string yaml_indent(" ");
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// define yaml's 2-space indentation
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const std::string yaml_indent(" ");
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// open the yaml file for writing
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std::ofstream yaml_file(yaml_filename);
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// open the yaml file for writing
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std::ofstream yaml_file(yaml_filename);
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// number formatting of the output
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yaml_file << std::scientific << std::setprecision(16);
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// number formatting of the output
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yaml_file << std::scientific << std::setprecision(16);
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// write the parameter values
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yaml_file << "values:\n";
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for (unsigned int i = 0; i < fParams.size(); ++i) {
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yaml_file << yaml_indent << fParams[i].fName.Data() << ": "
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<< fParams[i].fValue << "\n";
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}
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// write the parabolic errors
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yaml_file << "errors:\n";
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for (unsigned int i = 0; i < fParams.size(); ++i) {
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yaml_file << yaml_indent << fParams[i].fName.Data() << ": "
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<< fMnUserParams.Error(i) << "\n";
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}
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// write the minos errors
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yaml_file << "mnerrors:\n";
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for (unsigned int i = 0; i < fParams.size(); ++i) {
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// use boost's implementation of a variant, which can be streamed by
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// default - see: https://stackoverflow.com/q/47168477
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boost::variant<double, std::string> positive_error, negative_error;
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if (fParams[i].fPosErrorPresent) {
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positive_error = fParams[i].fPosError;
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negative_error = fParams[i].fStep;
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} else {
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positive_error = "null";
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negative_error = "null";
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// write the parameter values
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yaml_file << "values:\n";
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for (unsigned int i = 0; i < fParams.size(); ++i) {
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yaml_file << yaml_indent << fParams[i].fName.Data() << ": "
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<< fParams[i].fValue << "\n";
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}
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yaml_file << yaml_indent << fParams[i].fName.Data() << ":\n";
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yaml_file << yaml_indent << yaml_indent
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<< "positive: " << positive_error << "\n";
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yaml_file << yaml_indent << yaml_indent
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<< "negative: " << negative_error << "\n";
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}
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// write the parameter limits
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yaml_file << "limits:\n";
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for (unsigned int i = 0; i < fParams.size(); ++i) {
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// use boost's implementation of a variant, which can be streamed by
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// default - see: https://stackoverflow.com/q/47168477
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boost::variant<double, std::string> upper_limit, lower_limit;
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if (fParams[i].fLowerBoundaryPresent) {
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lower_limit = fParams[i].fLowerBoundary;
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} else {
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lower_limit = "null";
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}
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if (fParams[i].fUpperBoundaryPresent) {
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upper_limit = fParams[i].fUpperBoundary;
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} else {
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upper_limit = "null";
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// write the parabolic errors
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yaml_file << "errors:\n";
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for (unsigned int i = 0; i < fParams.size(); ++i) {
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yaml_file << yaml_indent << fParams[i].fName.Data() << ": "
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<< fMnUserParams.Error(i) << "\n";
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}
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yaml_file << yaml_indent << fParams[i].fName.Data() << ":\n";
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yaml_file << yaml_indent << yaml_indent << "lower: " << lower_limit
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<< "\n";
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yaml_file << yaml_indent << yaml_indent << "upper: " << upper_limit
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<< "\n";
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}
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// write the minos errors
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yaml_file << "mnerrors:\n";
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for (unsigned int i = 0; i < fParams.size(); ++i) {
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// use boost's implementation of a variant, which can be streamed by
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// default - see: https://stackoverflow.com/q/47168477
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boost::variant<double, std::string> positive_error, negative_error;
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if (fParams[i].fPosErrorPresent) {
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positive_error = fParams[i].fPosError;
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negative_error = fParams[i].fStep;
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} else {
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positive_error = "null";
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negative_error = "null";
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}
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// write if the parameter is fixed
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yaml_file << "fixed:\n";
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for (unsigned int i = 0; i < fParams.size(); ++i) {
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std::string is_fixed = fParams[i].fStep == 0.0 ? "true" : "false";
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yaml_file << yaml_indent << fParams[i].fName.Data() << ": " << is_fixed
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<< "\n";
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}
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// write the covariance matrix (omitting fixed parameters)
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yaml_file << "covariance:\n";
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for (unsigned int i = 0; i < cov.Nrow(); ++i) {
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yaml_file << yaml_indent << mnState.Name(parNo[i]) << ":\n";
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for (unsigned int j = 0; j < cov.Nrow(); ++j) {
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yaml_file << yaml_indent << yaml_indent << mnState.Name(parNo[j])
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<< ": " << cov(i, j) << "\n";
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yaml_file << yaml_indent << fParams[i].fName.Data() << ":\n";
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yaml_file << yaml_indent << yaml_indent
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<< "positive: " << positive_error << "\n";
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yaml_file << yaml_indent << yaml_indent
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<< "negative: " << negative_error << "\n";
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}
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}
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// write the correlation matrix (omitting fixed parameters)
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yaml_file << "correlation:\n";
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for (unsigned int i = 0; i < cov.Nrow(); ++i) {
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yaml_file << yaml_indent << mnState.Name(parNo[i]) << ":\n";
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for (unsigned int j = 0; j < cov.Nrow(); ++j) {
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double correlation =
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i == j ? 1.0
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: cov(i, j) / (fMnUserParams.Error(parNo[i]) *
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fMnUserParams.Error(parNo[j]));
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yaml_file << yaml_indent << yaml_indent << mnState.Name(parNo[j])
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<< ": " << correlation << "\n";
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// write the parameter limits
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yaml_file << "limits:\n";
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for (unsigned int i = 0; i < fParams.size(); ++i) {
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// use boost's implementation of a variant, which can be streamed by
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// default - see: https://stackoverflow.com/q/47168477
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boost::variant<double, std::string> upper_limit, lower_limit;
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if (fParams[i].fLowerBoundaryPresent) {
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lower_limit = fParams[i].fLowerBoundary;
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} else {
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lower_limit = "null";
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}
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if (fParams[i].fUpperBoundaryPresent) {
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upper_limit = fParams[i].fUpperBoundary;
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} else {
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upper_limit = "null";
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}
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yaml_file << yaml_indent << fParams[i].fName.Data() << ":\n";
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yaml_file << yaml_indent << yaml_indent << "lower: " << lower_limit
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<< "\n";
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yaml_file << yaml_indent << yaml_indent << "upper: " << upper_limit
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<< "\n";
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}
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// write if the parameter is fixed
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yaml_file << "fixed:\n";
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for (unsigned int i = 0; i < fParams.size(); ++i) {
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std::string is_fixed = fParams[i].fStep == 0.0 ? "true" : "false";
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yaml_file << yaml_indent << fParams[i].fName.Data() << ": " << is_fixed
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<< "\n";
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}
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// write the covariance matrix (omitting fixed parameters)
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yaml_file << "covariance:\n";
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for (unsigned int i = 0; i < cov.Nrow(); ++i) {
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yaml_file << yaml_indent << mnState.Name(parNo[i]) << ":\n";
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for (unsigned int j = 0; j < cov.Nrow(); ++j) {
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yaml_file << yaml_indent << yaml_indent << mnState.Name(parNo[j])
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<< ": " << cov(i, j) << "\n";
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}
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}
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// write the correlation matrix (omitting fixed parameters)
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yaml_file << "correlation:\n";
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for (unsigned int i = 0; i < cov.Nrow(); ++i) {
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yaml_file << yaml_indent << mnState.Name(parNo[i]) << ":\n";
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for (unsigned int j = 0; j < cov.Nrow(); ++j) {
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double correlation =
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i == j ? 1.0
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: cov(i, j) / (fMnUserParams.Error(parNo[i]) *
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fMnUserParams.Error(parNo[j]));
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yaml_file << yaml_indent << yaml_indent << mnState.Name(parNo[j])
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<< ": " << correlation << "\n";
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}
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}
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// close the yaml file
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yaml_file.close();
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}
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// close the yaml file
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yaml_file.close();
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}
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parNo.clear(); // clean up
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} else {
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