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merge dks to master

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suter_a
2016-08-25 08:40:40 +02:00
parent 8f20d2fd4c e32d0e912c
commit 6aea6473ab
43 changed files with 745 additions and 261 deletions
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7
src/classes/PMusrCanvas.cpp
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@ -1142,6 +1142,13 @@ void PMusrCanvas::HandleCmdKey(Int_t event, Int_t x, Int_t y, TObject *selected)
cout << "**INFO** averaging of a single data set doesn't make any sense, will ignore 'a' ..." << endl;
return;
}
} else if (x == 'c') {
Int_t state = fDataTheoryPad->GetCrosshair();
if (state == 0)
fDataTheoryPad->SetCrosshair(2);
else
fDataTheoryPad->SetCrosshair(0);
fMainCanvas->Update();
} else {
fMainCanvas->Update();
}

30
src/classes/PRunAsymmetryRRF.cpp
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@ -187,15 +187,7 @@ Double_t PRunAsymmetryRRF::CalcChiSquare(const std::vector<Double_t>& par)
// calculate chi square
Double_t time(1.0);
Int_t i, N(static_cast<Int_t>(fData.GetValue()->size()));
// In order not to have an IF in the next loop, determine the start and end bins for the fit range now
Int_t startTimeBin = static_cast<Int_t>(ceil((fFitStartTime - fData.GetDataTimeStart())/fData.GetDataTimeStep()));
if (startTimeBin < 0)
startTimeBin = 0;
Int_t endTimeBin = static_cast<Int_t>(floor((fFitEndTime - fData.GetDataTimeStart())/fData.GetDataTimeStep())) + 1;
if (endTimeBin > N)
endTimeBin = N;
Int_t i;
// Calculate the theory function once to ensure one function evaluation for the current set of parameters.
// This is needed for the LF and user functions where some non-thread-save calculations only need to be calculated once
@ -204,12 +196,12 @@ Double_t PRunAsymmetryRRF::CalcChiSquare(const std::vector<Double_t>& par)
asymFcnValue = fTheory->Func(time, par, fFuncValues);
#ifdef HAVE_GOMP
Int_t chunk = (endTimeBin - startTimeBin)/omp_get_num_procs();
Int_t chunk = (fEndTimeBin - fStartTimeBin)/omp_get_num_procs();
if (chunk < 10)
chunk = 10;
#pragma omp parallel for default(shared) private(i,time,diff,asymFcnValue,a,b,f) schedule(dynamic,chunk) reduction(+:chisq)
#endif
for (i=startTimeBin; i<endTimeBin; ++i) {
for (i=fStartTimeBin; i<fEndTimeBin; ++i) {
time = fData.GetDataTimeStart() + (Double_t)i*fData.GetDataTimeStep();
switch (fAlphaBetaTag) {
case 1: // alpha == 1, beta == 1
@ -387,15 +379,15 @@ void PRunAsymmetryRRF::SetFitRangeBin(const TString fitRange)
void PRunAsymmetryRRF::CalcNoOfFitBins()
{
// In order not having to loop over all bins and to stay consistent with the chisq method, calculate the start and end bins explicitly
Int_t startTimeBin = static_cast<Int_t>(ceil((fFitStartTime - fData.GetDataTimeStart())/fData.GetDataTimeStep()));
if (startTimeBin < 0)
startTimeBin = 0;
Int_t endTimeBin = static_cast<Int_t>(floor((fFitEndTime - fData.GetDataTimeStart())/fData.GetDataTimeStep())) + 1;
if (endTimeBin > static_cast<Int_t>(fData.GetValue()->size()))
endTimeBin = fData.GetValue()->size();
fStartTimeBin = static_cast<Int_t>(ceil((fFitStartTime - fData.GetDataTimeStart())/fData.GetDataTimeStep()));
if (fStartTimeBin < 0)
fStartTimeBin = 0;
fEndTimeBin = static_cast<Int_t>(floor((fFitEndTime - fData.GetDataTimeStart())/fData.GetDataTimeStep())) + 1;
if (fEndTimeBin > static_cast<Int_t>(fData.GetValue()->size()))
fEndTimeBin = fData.GetValue()->size();
if (endTimeBin > startTimeBin)
fNoOfFitBins = endTimeBin - startTimeBin;
if (fEndTimeBin > fStartTimeBin)
fNoOfFitBins = fEndTimeBin - fStartTimeBin;
else
fNoOfFitBins = 0;
}

72
src/classes/PRunSingleHistoRRF.cpp
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@ -58,7 +58,8 @@ using namespace std;
PRunSingleHistoRRF::PRunSingleHistoRRF() : PRunBase()
{
fNoOfFitBins = 0;
fBackground = 0;
fBackground = 0.0;
fBkgErr = 1.0;
fRRFPacking = -1;
// the 2 following variables are need in case fit range is given in bins, and since
@ -159,15 +160,7 @@ Double_t PRunSingleHistoRRF::CalcChiSquare(const std::vector<Double_t>& par)
// calculate chi square
Double_t time(1.0);
Int_t i, N(static_cast<Int_t>(fData.GetValue()->size()));
// In order not to have an IF in the next loop, determine the start and end bins for the fit range now
Int_t startTimeBin = static_cast<Int_t>(ceil((fFitStartTime - fData.GetDataTimeStart())/fData.GetDataTimeStep()));
if (startTimeBin < 0)
startTimeBin = 0;
Int_t endTimeBin = static_cast<Int_t>(floor((fFitEndTime - fData.GetDataTimeStart())/fData.GetDataTimeStep())) + 1;
if (endTimeBin > N)
endTimeBin = N;
Int_t i;
// Calculate the theory function once to ensure one function evaluation for the current set of parameters.
// This is needed for the LF and user functions where some non-thread-save calculations only need to be calculated once
@ -176,12 +169,12 @@ Double_t PRunSingleHistoRRF::CalcChiSquare(const std::vector<Double_t>& par)
time = fTheory->Func(time, par, fFuncValues);
#ifdef HAVE_GOMP
Int_t chunk = (endTimeBin - startTimeBin)/omp_get_num_procs();
Int_t chunk = (fEndTimeBin - fStartTimeBin)/omp_get_num_procs();
if (chunk < 10)
chunk = 10;
#pragma omp parallel for default(shared) private(i,time,diff) schedule(dynamic,chunk) reduction(+:chisq)
#endif
for (i=startTimeBin; i<endTimeBin; ++i) {
for (i=fStartTimeBin; i<fEndTimeBin; ++i) {
time = fData.GetDataTimeStart() + (Double_t)i*fData.GetDataTimeStep();
diff = fData.GetValue()->at(i) - fTheory->Func(time, par, fFuncValues);
chisq += diff*diff / (fData.GetError()->at(i)*fData.GetError()->at(i));
@ -215,15 +208,7 @@ Double_t PRunSingleHistoRRF::CalcChiSquareExpected(const std::vector<Double_t>&
// calculate chi square
Double_t time(1.0);
Int_t i, N(static_cast<Int_t>(fData.GetValue()->size()));
// In order not to have an IF in the next loop, determine the start and end bins for the fit range now
Int_t startTimeBin = static_cast<Int_t>(ceil((fFitStartTime - fData.GetDataTimeStart())/fData.GetDataTimeStep()));
if (startTimeBin < 0)
startTimeBin = 0;
Int_t endTimeBin = static_cast<Int_t>(floor((fFitEndTime - fData.GetDataTimeStart())/fData.GetDataTimeStep())) + 1;
if (endTimeBin > N)
endTimeBin = N;
Int_t i;
// Calculate the theory function once to ensure one function evaluation for the current set of parameters.
// This is needed for the LF and user functions where some non-thread-save calculations only need to be calculated once
@ -232,12 +217,12 @@ Double_t PRunSingleHistoRRF::CalcChiSquareExpected(const std::vector<Double_t>&
time = fTheory->Func(time, par, fFuncValues);
#ifdef HAVE_GOMP
Int_t chunk = (endTimeBin - startTimeBin)/omp_get_num_procs();
Int_t chunk = (fEndTimeBin - fStartTimeBin)/omp_get_num_procs();
if (chunk < 10)
chunk = 10;
#pragma omp parallel for default(shared) private(i,time,diff) schedule(dynamic,chunk) reduction(+:chisq)
#endif
for (i=startTimeBin; i < endTimeBin; ++i) {
for (i=fStartTimeBin; i < fEndTimeBin; ++i) {
time = fData.GetDataTimeStart() + (Double_t)i*fData.GetDataTimeStep();
theo = fTheory->Func(time, par, fFuncValues);
diff = fData.GetValue()->at(i) - theo;
@ -412,15 +397,15 @@ void PRunSingleHistoRRF::SetFitRangeBin(const TString fitRange)
void PRunSingleHistoRRF::CalcNoOfFitBins()
{
// In order not having to loop over all bins and to stay consistent with the chisq method, calculate the start and end bins explicitly
Int_t startTimeBin = static_cast<Int_t>(ceil((fFitStartTime - fData.GetDataTimeStart())/fData.GetDataTimeStep()));
if (startTimeBin < 0)
startTimeBin = 0;
Int_t endTimeBin = static_cast<Int_t>(floor((fFitEndTime - fData.GetDataTimeStart())/fData.GetDataTimeStep())) + 1;
if (endTimeBin > static_cast<Int_t>(fData.GetValue()->size()))
endTimeBin = fData.GetValue()->size();
fStartTimeBin = static_cast<Int_t>(ceil((fFitStartTime - fData.GetDataTimeStart())/fData.GetDataTimeStep()));
if (fStartTimeBin < 0)
fStartTimeBin = 0;
fEndTimeBin = static_cast<Int_t>(floor((fFitEndTime - fData.GetDataTimeStart())/fData.GetDataTimeStep())) + 1;
if (fEndTimeBin > static_cast<Int_t>(fData.GetValue()->size()))
fEndTimeBin = fData.GetValue()->size();
if (endTimeBin > startTimeBin)
fNoOfFitBins = endTimeBin - startTimeBin;
if (fEndTimeBin > fStartTimeBin)
fNoOfFitBins = fEndTimeBin - fStartTimeBin;
else
fNoOfFitBins = 0;
}
@ -608,6 +593,9 @@ Bool_t PRunSingleHistoRRF::PrepareFitData(PRawRunData* runData, const UInt_t his
if (!EstimateBkg(histoNo))
return false;
}
// subtract background from fForward
for (UInt_t i=0; i<fForward.size(); i++)
fForward[i] -= fBackground;
} else { // fixed background given
for (UInt_t i=0; i<fForward.size(); i++) {
fForward[i] -= fRunInfo->GetBkgFix(0);
@ -628,7 +616,7 @@ Bool_t PRunSingleHistoRRF::PrepareFitData(PRawRunData* runData, const UInt_t his
exp_t_tau = exp(time_tau);
fForward[i] *= exp_t_tau;
fM.push_back(fForward[i]); // i.e. M(t) = [N(t)-Nbkg] exp(+t/tau); needed to estimate N0 later on
fMerr.push_back(exp_t_tau*sqrt(rawNt[i]-fBackground));
fMerr.push_back(exp_t_tau*sqrt(rawNt[i]+fBkgErr*fBkgErr));
}
// calculate weights
@ -636,7 +624,7 @@ Bool_t PRunSingleHistoRRF::PrepareFitData(PRawRunData* runData, const UInt_t his
if (fMerr[i] > 0.0)
fW.push_back(1.0/(fMerr[i]*fMerr[i]));
else
fW.push_back(0.0);
fW.push_back(1.0);
}
// now fForward = exp(+t/tau) [N(t)-Nbkg] = M(t)
@ -1075,6 +1063,9 @@ Double_t PRunSingleHistoRRF::GetMainFrequency(PDoubleVector &data)
if (power->GetBinContent(i)>power->GetBinContent(i+1))
continue;
}
// ignore everything below 10 MHz
if (power->GetBinCenter(i) < 10.0)
continue;
// check for maximum
if (power->GetBinContent(i) > maxFreqVal) {
maxFreqVal = power->GetBinContent(i);
@ -1105,15 +1096,17 @@ Double_t PRunSingleHistoRRF::EstimateN0(Double_t &errN0, Double_t freqMax)
{
// endBin is estimated such that the number of full cycles (according to the maximum frequency of the data)
// is approximately the time fN0EstimateEndTime.
Int_t endBin = (Int_t)round(fN0EstimateEndTime / fTimeResolution * ceil(freqMax)/freqMax);
Int_t endBin = (Int_t)round(ceil(fN0EstimateEndTime*freqMax/TMath::TwoPi()) * (TMath::TwoPi()/freqMax) / fTimeResolution);
Double_t n0 = 0.0;
Double_t wN = 0.0;
for (Int_t i=0; i<endBin; i++) {
n0 += fW[i]*fM[i];
// n0 += fW[i]*fM[i];
n0 += fM[i];
wN += fW[i];
}
n0 /= wN;
// n0 /= wN;
n0 /= endBin;
errN0 = 0.0;
for (Int_t i=0; i<endBin; i++) {
@ -1201,7 +1194,12 @@ Bool_t PRunSingleHistoRRF::EstimateBkg(UInt_t histoNo)
fBackground = bkg; // keep background (per bin)
cout << endl << "info> fBackground=" << fBackground << endl;
bkg = 0.0;
for (UInt_t i=start; i<end; i++)
bkg += pow(fForward[i]-fBackground, 2.0);
fBkgErr = sqrt(bkg/(static_cast<Double_t>(end - start)));
cout << endl << "info> fBackground=" << fBackground << "(" << fBkgErr << ")" << endl;
fRunInfo->SetBkgEstimated(fBackground, 0);

46
src/classes/PStartupHandler.cpp
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@ -97,7 +97,6 @@ PStartupHandler::PStartupHandler()
Char_t *home=0;
Char_t musrpath[128];
Char_t startup_path_name[128];
Bool_t found = false;
strncpy(musrpath, "", sizeof(musrpath));
@ -106,32 +105,39 @@ PStartupHandler::PStartupHandler()
if (StartupFileExists(startup_path_name)) {
fStartupFileFound = true;
fStartupFilePath = TString(startup_path_name);
} else { // startup file is not found in the current directory
}
if (!fStartupFileFound) { // startup file not found in the current directory
// check if the startup file is found under $HOME/.musrfit
home = getenv("HOME");
if (home != 0) {
sprintf(musrpath, "%s/.musrfit", home);
found = true;
}
pmusrpath = getenv("MUSRFITPATH");
if (!found) {
// check if the MUSRFITPATH system variable is set
if (pmusrpath != 0) {
if (strcmp(pmusrpath, "")) { // MUSRFITPATH variable set but empty
found = true;
}
sprintf(startup_path_name, "%s/.musrfit/musrfit_startup.xml", home);
if (StartupFileExists(startup_path_name)) {
fStartupFilePath = TString(startup_path_name);
fStartupFileFound = true;
}
}
if (!found) { // MUSRFITPATH not set or empty, will try default one
home = getenv("ROOTSYS");
}
if (!fStartupFileFound) { // startup file not found in $HOME/.musrfit
// check if the MUSRFITPATH system variable is set
pmusrpath = getenv("MUSRFITPATH");
if (pmusrpath != 0) {
sprintf(startup_path_name, "%s/musrfit_startup.xml", pmusrpath);
if (StartupFileExists(startup_path_name)) {
fStartupFilePath = TString(startup_path_name);
fStartupFileFound = true;
}
}
}
if (!fStartupFileFound) { // MUSRFITPATH not set or empty, will try $ROOTSYS/bin
home = getenv("ROOTSYS");
if (home != 0) {
sprintf(musrpath, "%s/bin", home);
cerr << endl << "**WARNING** MUSRFITPATH environment variable not set will try " << musrpath << endl;
}
sprintf(startup_path_name, "%s/musrfit_startup.xml", musrpath);
fStartupFilePath = TString(startup_path_name);
if (StartupFileExists(startup_path_name)) {
fStartupFileFound = true;
sprintf(startup_path_name, "%s/musrfit_startup.xml", musrpath);
if (StartupFileExists(startup_path_name)) {
fStartupFilePath = TString(startup_path_name);
fStartupFileFound = true;
}
}
}
}

6
src/include/PRunAsymmetryRRF.h
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@ -52,6 +52,9 @@ class PRunAsymmetryRRF : public PRunBase
virtual void SetFitRangeBin(const TString fitRange);
virtual Int_t GetStartTimeBin() { return fStartTimeBin; }
virtual Int_t GetEndTimeBin() { return fEndTimeBin; }
protected:
virtual void CalcNoOfFitBins();
virtual Bool_t PrepareData();
@ -70,6 +73,9 @@ class PRunAsymmetryRRF : public PRunBase
Int_t fGoodBins[4]; ///< keep first/last good bins. 0=fgb, 1=lgb (forward); 2=fgb, 3=lgb (backward)
Int_t fStartTimeBin; ///< bin at which the fit starts
Int_t fEndTimeBin; ///< bin at which the fit ends
Bool_t SubtractFixBkg();
Bool_t SubtractEstimatedBkg();

7
src/include/PRunSingleHistoRRF.h
View File

@ -51,6 +51,9 @@ class PRunSingleHistoRRF : public PRunBase
virtual void SetFitRangeBin(const TString fitRange);
virtual Int_t GetStartTimeBin() { return fStartTimeBin; }
virtual Int_t GetEndTimeBin() { return fEndTimeBin; }
protected:
virtual void CalcNoOfFitBins();
virtual Bool_t PrepareData();
@ -62,10 +65,14 @@ class PRunSingleHistoRRF : public PRunBase
UInt_t fNoOfFitBins; ///< number of bins to be fitted
Double_t fBackground; ///< needed if background range is given (units: 1/bin)
Double_t fBkgErr; ///< estimate error on the estimated background
Int_t fRRFPacking; ///< RRF packing for this particular run. Given in the GLOBAL-block.
Int_t fGoodBins[2]; ///< keep first/last good bins. 0=fgb, 1=lgb
Int_t fStartTimeBin; ///< bin at which the fit starts
Int_t fEndTimeBin; ///< bin at which the fit ends
PDoubleVector fForward; ///< forward histo data
PDoubleVector fM; ///< vector holding M(t) = [N(t)-N_bkg] exp(+t/tau). Needed to estimate N0.
PDoubleVector fMerr; ///< vector holding the error of M(t): M_err = exp(+t/tau) sqrt(N(t)).

6
src/musredit/musredit.pro
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@ -57,6 +57,12 @@ QMAKE_CC = $${CC}
QMAKE_CXX = $${CXX}
QMAKE_LINK = $${CXX}
# set proper permission for Mac OSX
macx {
QMAKE_INSTALL_FILE = install -m 6755 -p -o $$(USER) -g staff
QMAKE_INSTALL_PROGRAM = install -m 6755 -p -o root -g admin
}
# install path for the XML configuration file
unix:xml.path = $$(HOME)/.musrfit/musredit
macx:xml.path = $$(HOME)/.musrfit/musredit

6
src/musredit_qt5/musredit.pro
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@ -57,6 +57,12 @@ QMAKE_CC = $${CC}
QMAKE_CXX = $${CXX}
QMAKE_LINK = $${CXX}
# set proper permission for Mac OSX
macx {
QMAKE_INSTALL_FILE = install -m 6755 -p -o $$(USER) -g staff
QMAKE_INSTALL_PROGRAM = install -m 6755 -p -o root -g admin
}
# install path for the XML configuration file
unix:xml.path = $$(HOME)/.musrfit/musredit
macx:xml.path = $$(HOME)/.musrfit/musredit

9
src/musrfit.cpp
View File

@ -697,10 +697,15 @@ int main(int argc, char *argv[])
}
}
}
startupHandler->SetStartupOptions(startup_options);
if (startupHandler)
startupHandler->SetStartupOptions(startup_options);
// read msr-file
PMsrHandler *msrHandler = new PMsrHandler(filename, startupHandler->GetStartupOptions());
PMsrHandler *msrHandler = 0;
if (startupHandler)
msrHandler = new PMsrHandler(filename, startupHandler->GetStartupOptions());
else
msrHandler = new PMsrHandler(filename);
status = msrHandler->ReadMsrFile();
if (status != PMUSR_SUCCESS) {
switch (status) {