LMU/musrfit
LMU/musrfit
5
0
Fork 0
Code Issues 6 Pull Requests Actions Packages Projects Releases 3 Activity

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.

Browse Source
This commit is contained in:
suter_a 2024-06-18 11:16:15 +02:00
parent 6bcb26f9d5
commit 64d3b6192b
25 changed files with 251 additions and 122 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

2
CMakeLists.txt
View File

@ -1,7 +1,7 @@
# - musrfit
cmake_minimum_required(VERSION 3.17)
project(musrfit VERSION 1.9.4 LANGUAGES C CXX)
project(musrfit VERSION 1.9.5 LANGUAGES C CXX)
#--- musrfit specific options -------------------------------------------------
option(nexus "build optional NeXus support. Needed for ISIS" OFF)

205
src/classes/PFitter.cpp
View File

@ -265,8 +265,8 @@ UInt_t PSectorChisq::GetNDF(UInt_t idx)
* \param runListCollection pointer of the run list collection (pre-processed historgrams)
* \param chisq_only flag: true=calculate chisq only (no fitting)
*/
PFitter::PFitter(PMsrHandler *runInfo, PRunListCollection *runListCollection, Bool_t chisq_only) :
fChisqOnly(chisq_only), fRunInfo(runInfo), fRunListCollection(runListCollection)
PFitter::PFitter(PMsrHandler *runInfo, PRunListCollection *runListCollection, Bool_t chisq_only, Bool_t yaml_out) :
fChisqOnly(chisq_only), fYamlOut(yaml_out), fRunInfo(runInfo), fRunListCollection(runListCollection)
{
// initialize variables
fIsScanOnly = true;
@ -2475,120 +2475,121 @@ Bool_t PFitter::ExecuteSave(Bool_t firstSave)
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
if (fYamlOut) {
// 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");
// 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(" ");
// define yaml's 2-space indentation
const std::string yaml_indent(" ");
// open the yaml file for writing
std::ofstream yaml_file(yaml_filename);
// open the yaml file for writing
std::ofstream yaml_file(yaml_filename);
// number formatting of the output
yaml_file << std::scientific << std::setprecision(16);
// 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";
// 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";
}
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";
// 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";
}
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 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";
}
// 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";
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 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";
// 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();
}
// close the yaml file
yaml_file.close();
}
parNo.clear(); // clean up
} else {

3
src/include/PFitter.h
View File

@ -111,7 +111,7 @@ class PSectorChisq
class PFitter
{
public:
PFitter(PMsrHandler *runInfo, PRunListCollection *runListCollection, Bool_t chisq_only = false);
PFitter(PMsrHandler *runInfo, PRunListCollection *runListCollection, Bool_t chisq_only = false, Bool_t yaml_out = false);
virtual ~PFitter();
Bool_t IsValid() { return fIsValid; }
@ -124,6 +124,7 @@ class PFitter
Bool_t fIsScanOnly; ///< flag. true: scan along some parameters (no fitting).
Bool_t fConverged; ///< flag. true: the fit has converged.
Bool_t fChisqOnly; ///< flag. true: calculate chi^2 only (no fitting).
Bool_t fYamlOut; ///< flag. true: generate yaml output file of the fit results (MINUIT2.OUTPUT -> yaml)
Bool_t fUseChi2; ///< flag. true: chi^2 fit. false: log-max-likelihood
UInt_t fPrintLevel; ///< tag, showing the level of messages whished. 0=minimum, 1=standard, 2=maximum

4
src/msr2data.cpp
View File

@ -127,6 +127,7 @@ void msr2data_syntax()
std::cout << std::endl << " -k, --keep-mn2-output : if fitting is used, pass the option --keep-mn2-output to musrfit";
std::cout << std::endl << " -t, --title-from-data-file : if fitting is used, pass the option --title-from-data-file to musrfit";
std::cout << std::endl << " -e, --estimateN0: estimate N0 for single histogram fits.";
std::cout << std::endl << " -y, --yaml: write fit results (MINUIT2.OUTPUT) into a yaml-file. Output <msr-file>.yaml";
std::cout << std::endl << " -p, --per-run-block-chisq: will per run block chisq to the msr-file.";
std::cout << std::endl;
std::cout << std::endl << " global : switch on the global-fit mode";
@ -187,6 +188,7 @@ std::string msr2data_validArguments(const std::vector<std::string> &arg)
|| (!iter->substr(0,3).compare("fit")) || (!iter->compare("-k")) || (!iter->compare("--keep-mn2-output")) \
|| (!iter->compare("-t")) || (!iter->compare("--title-from-data-file")) \
|| (!iter->compare("-e")) || (!iter->compare("--estimateN0")) \
|| (!iter->compare("-y") || (!iter->compare("--yaml"))) \
|| (!iter->compare("-p")) || (!iter->compare("--per-run-block-chisq")) \
|| (!iter->compare("data")) || (!iter->substr(0,4).compare("msr-")) || (!iter->compare("global")) \
|| (!iter->compare("global+")) || (!iter->compare("global+!")) || (!iter->compare("new")) \
@ -716,6 +718,8 @@ int main(int argc, char *argv[])
musrfitOptions.append("-t ");
if (!msr2data_useOption(arg, "-e") || !msr2data_useOption(arg, "--estimateN0"))
musrfitOptions.append("-e ");
if (!msr2data_useOption(arg, "-y") || !msr2data_useOption(arg, "--yaml"))
musrfitOptions.append("-y ");
if (!msr2data_useOption(arg, "-p") || !msr2data_useOption(arg, "--per-run-block-chisq"))
musrfitOptions.append("-p ");
}

19
src/musredit_qt5/musredit/PAdmin.cpp
View File

@ -160,6 +160,8 @@ bool PAdminXMLParser::startElement()
fKeyWord = eDumpRoot;
} else if (qName == "estimate_n0") {
fKeyWord = eEstimateN0;
} else if (qName == "yaml_out") {
fKeyWord = eYamlOut;
} else if (qName == "chisq_per_run_block") {
fKeyWord = eChisqPreRunBlock;
} else if (qName == "path_file_name") {
@ -389,6 +391,14 @@ bool PAdminXMLParser::characters()
fAdmin->fMsr2DataParam.estimateN0 = flag;
fAdmin->setEstimateN0Flag(flag);
break;
case eYamlOut:
if (str == "y")
flag = true;
else
flag = false;
fAdmin->fMsr2DataParam.yamlOut = flag;
fAdmin->setYamlOutFlag(flag);
break;
case eChisqPreRunBlock:
if (str == "y")
flag = true;
@ -608,6 +618,7 @@ void PAdminXMLParser::dump()
std::cout << "debug> title_from_data_file : " << fAdmin->getTitleFromDataFileFlag() << std::endl;
std::cout << "debug> chisq_per_run_block : " << fAdmin->getChisqPerRunBlockFlag() << std::endl;
std::cout << "debug> estimate_n0 : " << fAdmin->getEstimateN0Flag() << std::endl;
std::cout << "debug> yaml_out : " << fAdmin->getYamlOutFlag() << std::endl;
std::cout << "debug> musrview_show_fourier : " << fAdmin->getMusrviewShowFourierFlag() << std::endl;
std::cout << "debug> musrview_show_avg : " << fAdmin->getMusrviewShowAvgFlag() << std::endl;
std::cout << "debug> enable_musrt0 : " << fAdmin->getEnableMusrT0Flag() << std::endl;
@ -746,6 +757,7 @@ PAdmin::PAdmin() : QObject()
fEnableMusrT0 = false;
fLifetimeCorrection = true;
fEstimateN0 = true;
fYamlOut = false;
fChisqPreRunBlock = false;
fEditWidth = 900;
@ -760,6 +772,7 @@ PAdmin::PAdmin() : QObject()
fMsr2DataParam.ignoreDataHeaderInfo = false;
fMsr2DataParam.keepMinuit2Output = false;
fMsr2DataParam.estimateN0 = fEstimateN0;
fMsr2DataParam.yamlOut = false;
fMsr2DataParam.writeColumnData = false;
fMsr2DataParam.recreateDbFile = false;
fMsr2DataParam.chainFit = true;
@ -991,6 +1004,12 @@ int PAdmin::savePrefs(QString pref_fln)
else
data[i] = " <estimate_n0>n</estimate_n0>";
}
if (data[i].contains("<yaml_out>") && data[i].contains("</yaml_out>")) {
if (fYamlOut)
data[i] = " <yaml_out>y</yaml_out>";
else
data[i] = " <yaml_out>n</yaml_out>";
}
if (data[i].contains("<musrview_show_fourier>") && data[i].contains("</musrview_show_fourier>")) {
if (fMusrviewShowFourier)
data[i] = " <musrview_show_fourier>y</musrview_show_fourier>";

5
src/musredit_qt5/musredit/PAdmin.h
View File

@ -71,7 +71,7 @@ class PAdminXMLParser
private:
enum EAdminKeyWords {eEmpty, eTimeout, eKeepMinuit2Output, eDumpAscii, eDumpRoot,
eTitleFromDataFile, eChisqPreRunBlock, eEstimateN0,
eTitleFromDataFile, eChisqPreRunBlock, eEstimateN0, eYamlOut,
eMusrviewShowFourier, eMusrviewShowAvg, eMusrviewShowOneToOne, eEnableMusrT0,
eDarkThemeIconsMenu, eDarkThemeIconsToolbar, eEditW, eEditH,
eFontName, eFontSize, eExecPath, eDefaultSavePath,
@ -129,6 +129,7 @@ class PAdmin : public QObject
bool getDumpAsciiFlag() { return fDumpAscii; }
bool getDumpRootFlag() { return fDumpRoot; }
bool getEstimateN0Flag() { return fEstimateN0; }
bool getYamlOutFlag() { return fYamlOut; }
bool getChisqPerRunBlockFlag() { return fChisqPreRunBlock; }
bool getDarkThemeIconsMenuFlag() { return fDarkThemeIconsMenu; }
bool getDarkThemeIconsToolbarFlag() { return fDarkThemeIconsToolbar; }
@ -157,6 +158,7 @@ class PAdmin : public QObject
void setDumpAsciiFlag(const bool flag) { fDumpAscii = flag; }
void setDumpRootFlag(const bool flag) { fDumpRoot = flag; }
void setEstimateN0Flag(const bool flag) { fEstimateN0 = flag; }
void setYamlOutFlag(const bool flag) { fYamlOut = flag; }
void setChisqPerRunBlockFlag(const bool flag) { fChisqPreRunBlock = flag; }
void setDarkThemeIconsMenuFlag(const bool flag) { fDarkThemeIconsMenu = flag; }
void setDarkThemeIconsToolbarFlag(const bool flag) { fDarkThemeIconsToolbar = flag; }
@ -205,6 +207,7 @@ class PAdmin : public QObject
bool fTitleFromDataFile; ///< flag indicating if the title should be extracted from the data file (default: yes).
bool fChisqPreRunBlock; ///< flag indicating if musrfit shall write 'per run block' chisq to the msr-file (default: no).
bool fEstimateN0; ///< flag indicating if musrfit shall estimate N0 for single histogram fits (default: yes).
bool fYamlOut; ///< flag indicating if the MINUIT2.OUTPUT file should also be written as <msr-file>.yaml output. (default: no).
bool fEnableMusrT0; ///< flag indicating if musrT0 shall be enabled at startup from within musredit (default: yes).
bool fDarkThemeIconsMenu; ///< flag indicating if dark theme icons shall be used in the menu (default: no)
bool fDarkThemeIconsToolbar; ///< flag indicating if dark theme icons shall be used in the toolbar (default: no)

2
src/musredit_qt5/musredit/PMsr2DataDialog.cpp
View File

@ -84,6 +84,7 @@ PMsr2DataDialog::PMsr2DataDialog(PMsr2DataParam *msr2DataParam, const QString he
fIgnoreDataHeaderInfo_checkBox->setChecked(fMsr2DataParam->ignoreDataHeaderInfo);
fKeepMinuit2Output_checkBox->setChecked(fMsr2DataParam->keepMinuit2Output);
fEstimateN0_checkBox->setChecked(fMsr2DataParam->estimateN0);
fYamlOut_checkBox->setChecked(fMsr2DataParam->yamlOut);
fWriteColumnData_checkBox->setChecked(fMsr2DataParam->writeColumnData);
fRecreateDataFile_checkBox->setChecked(fMsr2DataParam->recreateDbFile);
fChainFit_checkBox->setChecked(fMsr2DataParam->chainFit);
@ -121,6 +122,7 @@ PMsr2DataParam* PMsr2DataDialog::getMsr2DataParam()
fMsr2DataParam->ignoreDataHeaderInfo = fIgnoreDataHeaderInfo_checkBox->isChecked();
fMsr2DataParam->keepMinuit2Output = fKeepMinuit2Output_checkBox->isChecked();
fMsr2DataParam->estimateN0 = fEstimateN0_checkBox->isChecked();
fMsr2DataParam->yamlOut = fYamlOut_checkBox->isChecked();
fMsr2DataParam->writeColumnData = fWriteColumnData_checkBox->isChecked();
fMsr2DataParam->recreateDbFile = fRecreateDataFile_checkBox->isChecked();
fMsr2DataParam->chainFit = fChainFit_checkBox->isChecked();

1
src/musredit_qt5/musredit/PPrefsDialog.cpp
View File

@ -76,6 +76,7 @@ PPrefsDialog::PPrefsDialog(PAdmin *admin) : fAdmin(admin)
fEnableMusrT0_checkBox->setChecked(fAdmin->getEnableMusrT0Flag());
fPerRunBlockChisq_checkBox->setChecked(fAdmin->getChisqPerRunBlockFlag());
fEstimateN0_checkBox->setChecked(fAdmin->getEstimateN0Flag());
fYamlOut_checkBox->setChecked(fAdmin->getYamlOutFlag());
fFourier_checkBox->setChecked(fAdmin->getMusrviewShowFourierFlag());
fAvg_checkBox->setChecked(fAdmin->getMusrviewShowAvgFlag());
fOneToOne_checkBox->setChecked(fAdmin->getMusrviewShowOneToOneFlag());

1
src/musredit_qt5/musredit/PPrefsDialog.h
View File

@ -54,6 +54,7 @@ class PPrefsDialog : public QDialog, private Ui::PPrefsDialog
bool getEnableMusrT0Flag() { return fEnableMusrT0_checkBox->isChecked(); }
bool getKeepRunPerBlockChisqFlag() { return fPerRunBlockChisq_checkBox->isChecked(); }
bool getEstimateN0Flag() { return fEstimateN0_checkBox->isChecked(); }
bool getYamlOutFlag() { return fYamlOut_checkBox->isChecked(); }
bool getDarkThemeIconsMenuFlag() { return fDarkThemeIconsMenu_checkBox->isChecked(); }
bool getDarkThemeIconsToolbarFlag() { return fDarkThemeIconsToolbar_checkBox->isChecked(); }
bool getOneToOneFlag() { return fOneToOne_checkBox->isChecked(); }

11
src/musredit_qt5/musredit/PTextEdit.cpp
View File

@ -2104,6 +2104,11 @@ void PTextEdit::musrFit()
cmd.append("--estimateN0");
}
// check yamlOut flag
if (fAdmin->getYamlOutFlag()) {
cmd.append("--yaml");
}
// check per-run-block-chisq flag
if (fAdmin->getChisqPerRunBlockFlag()) {
cmd.append("--per-run-block-chisq");
@ -2336,6 +2341,11 @@ void PTextEdit::musrMsr2Data()
cmd.append("-e");
}
// yaml out. Add flag only if a fit is done
if (fMsr2DataParam->yamlOut && (fMsr2DataParam->fitOnly || fMsr2DataParam->templateRunNo != -1)) {
cmd.append("-y");
}
// write per-run-block chisq. Add flag only if a fit is done
if (fMsr2DataParam->perRunBlockChisq && (fMsr2DataParam->fitOnly || fMsr2DataParam->templateRunNo != -1)) {
cmd.append("-p");
@ -2719,6 +2729,7 @@ void PTextEdit::musrPrefs()
fAdmin->setTimeout(dlg->getTimeout());
fAdmin->setChisqPerRunBlockFlag(dlg->getKeepRunPerBlockChisqFlag());
fAdmin->setEstimateN0Flag(dlg->getEstimateN0Flag());
fAdmin->setYamlOutFlag(dlg->getYamlOutFlag());
}
delete dlg;

9
src/musredit_qt5/musredit/forms/PMsr2DataDialog.ui
View File

@ -338,7 +338,7 @@
<x>6</x>
<y>20</y>
<width>560</width>
<height>131</height>
<height>135</height>
</rect>
</property>
<layout class="QHBoxLayout" name="horizontalLayout_9">
@ -456,6 +456,13 @@
</property>
</widget>
</item>
<item>
<widget class="QCheckBox" name="fYamlOut_checkBox">
<property name="text">
<string>yaml out</string>
</property>
</widget>
</item>
<item>
<layout class="QHBoxLayout" name="horizontalLayout_8">
<item>

27
src/musredit_qt5/musredit/forms/PPrefsDialog.ui
View File

@ -33,7 +33,7 @@
<item>
<widget class="QTabWidget" name="fTabWidget">
<property name="currentIndex">
<number>2</number>
<number>1</number>
</property>
<widget class="QWidget" name="fGeneral_tab">
<attribute name="title">
@ -152,9 +152,9 @@
<widget class="QCheckBox" name="fTitleFromData_checkBox">
<property name="geometry">
<rect>
<x>190</x>
<x>170</x>
<y>10</y>
<width>241</width>
<width>161</width>
<height>23</height>
</rect>
</property>
@ -165,9 +165,9 @@
<widget class="QCheckBox" name="fPerRunBlockChisq_checkBox">
<property name="geometry">
<rect>
<x>190</x>
<x>170</x>
<y>35</y>
<width>241</width>
<width>181</width>
<height>22</height>
</rect>
</property>
@ -178,9 +178,9 @@
<widget class="QCheckBox" name="fEstimateN0_checkBox">
<property name="geometry">
<rect>
<x>190</x>
<x>170</x>
<y>60</y>
<width>241</width>
<width>171</width>
<height>22</height>
</rect>
</property>
@ -188,6 +188,19 @@
<string>estimate N0</string>
</property>
</widget>
<widget class="QCheckBox" name="fYamlOut_checkBox">
<property name="geometry">
<rect>
<x>350</x>
<y>10</y>
<width>85</width>
<height>21</height>
</rect>
</property>
<property name="text">
<string>yaml out</string>
</property>
</widget>
</widget>
<widget class="QWidget" name="fMusrview_tab">
<attribute name="title">

1
src/musredit_qt5/musredit/musredit.h
View File

@ -56,6 +56,7 @@ struct PMsr2DataParam {
bool openFilesAfterFitting; ///< flag: true = open msr-file after fit in musredit. false = do not open msr-file after fit.
bool titleFromDataFile; ///< flag indicating if the title for the msr-file shall be extracted from the data-file ('-t' in msr2data)
bool estimateN0; ///< flag indicating if the N0 shall be estimated for single histogram fitting
bool yamlOut; ///< flag indicating if the MINUIT2.OUTPUT content should be written to <msr-file>.yaml
bool perRunBlockChisq; ///< flag indicating if per-run-block-chisq shall be dumped into the msr-file
bool createMsrFileOnly; ///< flag: true = just create the msr-files without any fitting ('msr-<template>' in msr2data)
bool fitOnly; ///< flag: true = just perform the fits wihtout generating any msr-files ('fit' in msr2data).

1
src/musredit_qt5/musredit/musredit_startup.xml.in
View File

@ -14,6 +14,7 @@
<title_from_data_file>y</title_from_data_file>
<chisq_per_run_block>n</chisq_per_run_block>
<estimate_n0>y</estimate_n0>
<yaml_out>n</yaml_out>
<musrview_show_fourier>n</musrview_show_fourier>
<musrview_show_avg>n</musrview_show_avg>
<musrview_show_one_to_one>n</musrview_show_one_to_one>

18
src/musredit_qt6/musredit/PAdmin.cpp
View File

@ -166,6 +166,8 @@ bool PAdminXMLParser::startElement()
fKeyWord = eDumpRoot;
} else if (qName == "estimate_n0") {
fKeyWord = eEstimateN0;
} else if (qName == "yaml_out") {
fKeyWord = eYamlOut;
} else if (qName == "chisq_per_run_block") {
fKeyWord = eChisqPreRunBlock;
} else if (qName == "path_file_name") {
@ -396,6 +398,13 @@ bool PAdminXMLParser::characters()
fAdmin->fMsr2DataParam.estimateN0 = flag;
fAdmin->setEstimateN0Flag(flag);
break;
case eYamlOut:
if (str == "y")
flag = true;
else
flag = false;
fAdmin->fMsr2DataParam.yamlOut = flag;
fAdmin->setYamlOutFlag(flag);
case eChisqPreRunBlock:
if (str == "y")
flag = true;
@ -615,6 +624,7 @@ void PAdminXMLParser::dump()
std::cout << "debug> title_from_data_file : " << fAdmin->getTitleFromDataFileFlag() << std::endl;
std::cout << "debug> chisq_per_run_block : " << fAdmin->getChisqPerRunBlockFlag() << std::endl;
std::cout << "debug> estimate_n0 : " << fAdmin->getEstimateN0Flag() << std::endl;
std::cout << "debug> yaml_out : " << fAdmin->getYamlOutFlag() << std::endl;
std::cout << "debug> musrview_show_fourier : " << fAdmin->getMusrviewShowFourierFlag() << std::endl;
std::cout << "debug> musrview_show_avg : " << fAdmin->getMusrviewShowAvgFlag() << std::endl;
std::cout << "debug> enable_musrt0 : " << fAdmin->getEnableMusrT0Flag() << std::endl;
@ -753,6 +763,7 @@ PAdmin::PAdmin() : QObject()
fEnableMusrT0 = false;
fLifetimeCorrection = true;
fEstimateN0 = true;
fYamlOut = false;
fChisqPreRunBlock = false;
fMsr2DataParam.runList = QString("");
@ -764,6 +775,7 @@ PAdmin::PAdmin() : QObject()
fMsr2DataParam.ignoreDataHeaderInfo = false;
fMsr2DataParam.keepMinuit2Output = false;
fMsr2DataParam.estimateN0 = fEstimateN0;
fMsr2DataParam.yamlOut = false;
fMsr2DataParam.writeColumnData = false;
fMsr2DataParam.recreateDbFile = false;
fMsr2DataParam.chainFit = true;
@ -995,6 +1007,12 @@ int PAdmin::savePrefs(QString pref_fln)
else
data[i] = " <estimate_n0>n</estimate_n0>";
}
if (data[i].contains("<yaml_out>") && data[i].contains("</yaml_out>")) {
if (fYamlOut)
data[i] = " <yaml_out>y</yaml_out>";
else
data[i] = " <yaml_out>n</yaml_out>";
}
if (data[i].contains("<musrview_show_fourier>") && data[i].contains("</musrview_show_fourier>")) {
if (fMusrviewShowFourier)
data[i] = " <musrview_show_fourier>y</musrview_show_fourier>";

5
src/musredit_qt6/musredit/PAdmin.h
View File

@ -71,7 +71,7 @@ class PAdminXMLParser
private:
enum EAdminKeyWords {eEmpty, eTimeout, eKeepMinuit2Output, eDumpAscii, eDumpRoot,
eTitleFromDataFile, eChisqPreRunBlock, eEstimateN0,
eTitleFromDataFile, eChisqPreRunBlock, eEstimateN0, eYamlOut,
eMusrviewShowFourier, eMusrviewShowAvg, eMusrviewShowOneToOne, eEnableMusrT0,
eDarkThemeIconsMenu, eDarkThemeIconsToolbar, eEditW, eEditH,
eFontName, eFontSize, eExecPath, eDefaultSavePath,
@ -125,6 +125,7 @@ class PAdmin : public QObject
bool getMusrviewShowAvgFlag() { return fMusrviewShowAvg; }
bool getMusrviewShowOneToOneFlag() { return fMusrviewShowOneToOne; }
bool getEnableMusrT0Flag() { return fEnableMusrT0; }
bool getYamlOutFlag() { return fYamlOut; }
bool getKeepMinuit2OutputFlag() { return fKeepMinuit2Output; }
bool getDumpAsciiFlag() { return fDumpAscii; }
bool getDumpRootFlag() { return fDumpRoot; }
@ -157,6 +158,7 @@ class PAdmin : public QObject
void setDumpAsciiFlag(const bool flag) { fDumpAscii = flag; }
void setDumpRootFlag(const bool flag) { fDumpRoot = flag; }
void setEstimateN0Flag(const bool flag) { fEstimateN0 = flag; }
void setYamlOutFlag(const bool flag) { fYamlOut = flag; }
void setChisqPerRunBlockFlag(const bool flag) { fChisqPreRunBlock = flag; }
void setDarkThemeIconsMenuFlag(const bool flag) { fDarkThemeIconsMenu = flag; }
void setDarkThemeIconsToolbarFlag(const bool flag) { fDarkThemeIconsToolbar = flag; }
@ -205,6 +207,7 @@ class PAdmin : public QObject
bool fTitleFromDataFile; ///< flag indicating if the title should be extracted from the data file (default: yes).
bool fChisqPreRunBlock; ///< flag indicating if musrfit shall write 'per run block' chisq to the msr-file (default: no).
bool fEstimateN0; ///< flag indicating if musrfit shall estimate N0 for single histogram fits (default: yes).
bool fYamlOut; ///< flag indicating if the MINUIT2.OUTPUT file should also be written as <msr-file>.yaml output. (default: no).
bool fEnableMusrT0; ///< flag indicating if musrT0 shall be enabled at startup from within musredit (default: yes).
bool fDarkThemeIconsMenu; ///< flag indicating if dark theme icons shall be used in the menu (default: no)
bool fDarkThemeIconsToolbar; ///< flag indicating if dark theme icons shall be used in the toolbar (default: no)

2
src/musredit_qt6/musredit/PMsr2DataDialog.cpp
View File

@ -84,6 +84,7 @@ PMsr2DataDialog::PMsr2DataDialog(PMsr2DataParam *msr2DataParam, const QString he
fIgnoreDataHeaderInfo_checkBox->setChecked(fMsr2DataParam->ignoreDataHeaderInfo);
fKeepMinuit2Output_checkBox->setChecked(fMsr2DataParam->keepMinuit2Output);
fEstimateN0_checkBox->setChecked(fMsr2DataParam->estimateN0);
fYamlOut_checkBox->setChecked(fMsr2DataParam->yamlOut);
fWriteColumnData_checkBox->setChecked(fMsr2DataParam->writeColumnData);
fRecreateDataFile_checkBox->setChecked(fMsr2DataParam->recreateDbFile);
fChainFit_checkBox->setChecked(fMsr2DataParam->chainFit);
@ -121,6 +122,7 @@ PMsr2DataParam* PMsr2DataDialog::getMsr2DataParam()
fMsr2DataParam->ignoreDataHeaderInfo = fIgnoreDataHeaderInfo_checkBox->isChecked();
fMsr2DataParam->keepMinuit2Output = fKeepMinuit2Output_checkBox->isChecked();
fMsr2DataParam->estimateN0 = fEstimateN0_checkBox->isChecked();
fMsr2DataParam->yamlOut = fYamlOut_checkBox->isChecked();
fMsr2DataParam->writeColumnData = fWriteColumnData_checkBox->isChecked();
fMsr2DataParam->recreateDbFile = fRecreateDataFile_checkBox->isChecked();
fMsr2DataParam->chainFit = fChainFit_checkBox->isChecked();

1
src/musredit_qt6/musredit/PPrefsDialog.cpp
View File

@ -76,6 +76,7 @@ PPrefsDialog::PPrefsDialog(PAdmin *admin) : fAdmin(admin)
fEnableMusrT0_checkBox->setChecked(fAdmin->getEnableMusrT0Flag());
fPerRunBlockChisq_checkBox->setChecked(fAdmin->getChisqPerRunBlockFlag());
fEstimateN0_checkBox->setChecked(fAdmin->getEstimateN0Flag());
fYamlOut_checkBox->setChecked(fAdmin->getYamlOutFlag());
fFourier_checkBox->setChecked(fAdmin->getMusrviewShowFourierFlag());
fAvg_checkBox->setChecked(fAdmin->getMusrviewShowAvgFlag());
fOneToOne_checkBox->setChecked(fAdmin->getMusrviewShowOneToOneFlag());

1
src/musredit_qt6/musredit/PPrefsDialog.h
View File

@ -54,6 +54,7 @@ class PPrefsDialog : public QDialog, private Ui::PPrefsDialog
bool getEnableMusrT0Flag() { return fEnableMusrT0_checkBox->isChecked(); }
bool getKeepRunPerBlockChisqFlag() { return fPerRunBlockChisq_checkBox->isChecked(); }
bool getEstimateN0Flag() { return fEstimateN0_checkBox->isChecked(); }
bool getYamlOutFlag() { return fYamlOut_checkBox->isChecked(); }
bool getDarkThemeIconsMenuFlag() { return fDarkThemeIconsMenu_checkBox->isChecked(); }
bool getDarkThemeIconsToolbarFlag() { return fDarkThemeIconsToolbar_checkBox->isChecked(); }
bool getOneToOneFlag() { return fOneToOne_checkBox->isChecked(); }

13
src/musredit_qt6/musredit/PTextEdit.cpp
View File

@ -2108,6 +2108,11 @@ void PTextEdit::musrFit()
cmd.append("--estimateN0");
}
// check yamlOut flag
if (fAdmin->getYamlOutFlag()) {
cmd.append("--yaml");
}
// check per-run-block-chisq flag
if (fAdmin->getChisqPerRunBlockFlag()) {
cmd.append("--per-run-block-chisq");
@ -2184,6 +2189,7 @@ void PTextEdit::musrMsr2Data()
fMsr2DataParam->keepMinuit2Output = fAdmin->getKeepMinuit2OutputFlag();
fMsr2DataParam->titleFromDataFile = fAdmin->getTitleFromDataFileFlag();
fMsr2DataParam->estimateN0 = fAdmin->getEstimateN0Flag();
fMsr2DataParam->yamlOut = fAdmin->getYamlOutFlag();
fMsr2DataParam->perRunBlockChisq = fAdmin->getChisqPerRunBlockFlag();
PMsr2DataDialog *dlg = new PMsr2DataDialog(fMsr2DataParam, fAdmin->getHelpUrl("msr2data"));
@ -2206,6 +2212,7 @@ void PTextEdit::musrMsr2Data()
fAdmin->setKeepMinuit2OutputFlag(fMsr2DataParam->keepMinuit2Output);
fAdmin->setTitleFromDataFileFlag(fMsr2DataParam->titleFromDataFile);
fAdmin->setEstimateN0Flag(fMsr2DataParam->estimateN0);
fAdmin->setYamlOutFlag(fMsr2DataParam->yamlOut);
fAdmin->setChisqPerRunBlockFlag(fMsr2DataParam->perRunBlockChisq);
// analyze parameters
@ -2336,6 +2343,11 @@ void PTextEdit::musrMsr2Data()
cmd.append("-e");
}
// yaml out. Add flag only if a fit is done
if (fMsr2DataParam->yamlOut && (fMsr2DataParam->fitOnly || fMsr2DataParam->templateRunNo != -1)) {
cmd.append("-y");
}
// write per-run-block chisq. Add flag only if a fit is done
if (fMsr2DataParam->perRunBlockChisq && (fMsr2DataParam->fitOnly || fMsr2DataParam->templateRunNo != -1)) {
cmd.append("-p");
@ -2713,6 +2725,7 @@ void PTextEdit::musrPrefs()
fAdmin->setTimeout(dlg->getTimeout());
fAdmin->setChisqPerRunBlockFlag(dlg->getKeepRunPerBlockChisqFlag());
fAdmin->setEstimateN0Flag(dlg->getEstimateN0Flag());
fAdmin->setYamlOutFlag(dlg->getYamlOutFlag());
}
delete dlg;

9
src/musredit_qt6/musredit/forms/PMsr2DataDialog.ui
View File

@ -338,7 +338,7 @@
<x>6</x>
<y>20</y>
<width>560</width>
<height>131</height>
<height>135</height>
</rect>
</property>
<layout class="QHBoxLayout" name="horizontalLayout_9">
@ -456,6 +456,13 @@
</property>
</widget>
</item>
<item>
<widget class="QCheckBox" name="fYamlOut_checkBox">
<property name="text">
<string>yaml out</string>
</property>
</widget>
</item>
<item>
<layout class="QHBoxLayout" name="horizontalLayout_8">
<item>

25
src/musredit_qt6/musredit/forms/PPrefsDialog.ui
View File

@ -33,7 +33,7 @@
<item>
<widget class="QTabWidget" name="fTabWidget">
<property name="currentIndex">
<number>2</number>
<number>1</number>
</property>
<widget class="QWidget" name="fGeneral_tab">
<attribute name="title">
@ -152,9 +152,9 @@
<widget class="QCheckBox" name="fTitleFromData_checkBox">
<property name="geometry">
<rect>
<x>190</x>
<x>170</x>
<y>10</y>
<width>241</width>
<width>171</width>
<height>23</height>
</rect>
</property>
@ -165,7 +165,7 @@
<widget class="QCheckBox" name="fPerRunBlockChisq_checkBox">
<property name="geometry">
<rect>
<x>190</x>
<x>170</x>
<y>35</y>
<width>241</width>
<height>22</height>
@ -178,9 +178,9 @@
<widget class="QCheckBox" name="fEstimateN0_checkBox">
<property name="geometry">
<rect>
<x>190</x>
<x>170</x>
<y>60</y>
<width>241</width>
<width>101</width>
<height>22</height>
</rect>
</property>
@ -188,6 +188,19 @@
<string>estimate N0</string>
</property>
</widget>
<widget class="QCheckBox" name="fYamlOut_checkBox">
<property name="geometry">
<rect>
<x>360</x>
<y>10</y>
<width>85</width>
<height>21</height>
</rect>
</property>
<property name="text">
<string>yaml out</string>
</property>
</widget>
</widget>
<widget class="QWidget" name="fMusrview_tab">
<attribute name="title">

1
src/musredit_qt6/musredit/musredit.h
View File

@ -56,6 +56,7 @@ struct PMsr2DataParam {
bool openFilesAfterFitting; ///< flag: true = open msr-file after fit in musredit. false = do not open msr-file after fit.
bool titleFromDataFile; ///< flag indicating if the title for the msr-file shall be extracted from the data-file ('-t' in msr2data)
bool estimateN0; ///< flag indicating if the N0 shall be estimated for single histogram fitting
bool yamlOut; ///< flag indicating if the MINUIT2.OUTPUT content should be written to <msr-file>.yaml
bool perRunBlockChisq; ///< flag indicating if per-run-block-chisq shall be dumped into the msr-file
bool createMsrFileOnly; ///< flag: true = just create the msr-files without any fitting ('msr-<template>' in msr2data)
bool fitOnly; ///< flag: true = just perform the fits wihtout generating any msr-files ('fit' in msr2data).

1
src/musredit_qt6/musredit/musredit_startup.xml.in
View File

@ -14,6 +14,7 @@
<title_from_data_file>y</title_from_data_file>
<chisq_per_run_block>n</chisq_per_run_block>
<estimate_n0>y</estimate_n0>
<yaml_out>n</yaml_out>
<musrview_show_fourier>n</musrview_show_fourier>
<musrview_show_avg>n</musrview_show_avg>
<musrview_show_one_to_one>n</musrview_show_one_to_one>

6
src/musrfit.cpp
View File

@ -127,6 +127,7 @@ void musrfit_syntax()
std::cout << std::endl << " (ii) if present under $HOME/.musrfit/";
std::cout << std::endl << " (iii) if present under $MUSRFITPATH/";
std::cout << std::endl << " (iv) if present under $ROOTSYS/";
std::cout << std::endl << " -y, --yaml: write fit results (MINUIT2.OUTPUT) into a yaml-file. Output <msr-file>.yaml";
std::cout << std::endl << " --dump <type> is writing a data file with the fit data and the theory";
std::cout << std::endl << " <type> can be 'ascii', 'root'";
std::cout << std::endl << " --timeout <timeout_tag>: overwrites to predefined timeout of " << timeout << " (sec).";
@ -446,6 +447,7 @@ int main(int argc, char *argv[])
int status;
bool keep_mn2_output = false;
bool chisq_only = false;
bool yaml_out = false;
bool title_from_data_file = false;
bool timeout_enabled = true;
bool reset_startup_file = false;
@ -532,6 +534,8 @@ int main(int argc, char *argv[])
startup_options.estimateN0 = true;
} else if (!strcmp(argv[i], "-p") || !strcmp(argv[i], "--per-run-block-chisq")) {
startup_options.writeExpectedChisq = true;
} else if (!strcmp(argv[i], "-y") || !strcmp(argv[i], "--yaml")) {
yaml_out = true;
} else if (!strcmp(argv[i], "-n") || !strcmp(argv[i], "--no-of-cores-avail")) {
#ifdef HAVE_GOMP
std::cout << std::endl;
@ -724,7 +728,7 @@ int main(int argc, char *argv[])
// do fitting
std::unique_ptr<PFitter> fitter;
if (success) {
fitter = std::make_unique<PFitter>(msrHandler.get(), runListCollection.get(), chisq_only);
fitter = std::make_unique<PFitter>(msrHandler.get(), runListCollection.get(), chisq_only, yaml_out);
if (fitter->IsValid()) {
fitter->DoFit();
if (!fitter->IsScanOnly())