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4
ChangeLog
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@ -4,6 +4,10 @@
changes since 0.13.0
===================================
NEW 2015-02-13 first implementation of a standalone Fourier transform/plotter:
musrFT. Initially it is meant to be used for HAL-9500,
i.e. Fourier transform WITHOUT lifetime correction.
A first simple minded lifetime correction is implemented as well.
NEW 2015-01-17 adding a branch for ROOT 6.x. This needs some minor adaptations due
to the new rootcint/rootclang and the stricter c++11.
NEW 2014-12-18 first implementation of a GLOBAL block which allows to shorten

65
README
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@ -1,33 +1,32 @@
# musrfit - muSR data analysis package #
### Contents ###
This is a data analysis package to analyze time differential muSR data.
Currently it allows the following things:
* setting up most commonly used fitting functions for muSR
* fitting data, including global fits
* showing the fit results and the residuals
* showing the Fourier transform of the data
* extracting easily the fitting parameters to be used in other programs (gnuplot, qtiplot/origin, ...)
* allows to generate fitting input files for follow-up runs
* allows to generate global fitting input files based on a single run template
* allows to implement more sophisticated user functions
(e.g. GL vortex lattice, Meissner screening including low-energy muon stopping profiles)
### Currently supported platforms: ###
* Linux
* Mac OS X
* Windows - not really, only for the very brave ones
### Documentation ####
For a more exhaustive user documentation see:
http://lmu.web.psi.ch/musrfit/user/MUSR/WebHome.html
### Contact ###
<andreas.suter@psi.ch>
# musrfit - muSR data analysis package #
### Contents ###
This is a data analysis package to analyze time differential muSR and beta-NMR data.
Currently it allows the following things:
* setting up most commonly used fitting functions for muSR and beta-NMR
* fitting data, including global fits
* showing the fit results and the residuals
* showing the Fourier transform of the data
* extracting easily the fitting parameters to be used in other programs (gnuplot, qtiplot/origin, ...)
* allows to generate fitting input files for follow-up runs
* allows to generate global fitting input files based on a single run template
* allows to implement more sophisticated user functions
(e.g. GL vortex lattice, Meissner screening including low-energy muon stopping profiles)
### Currently supported platforms: ###
* Linux
* Mac OS X
* Windows - not really, only for the very brave ones
### Documentation ####
For a more exhaustive user documentation see:
http://lmu.web.psi.ch/musrfit/user/MUSR/WebHome.html
### Contact ###
<andreas.suter@psi.ch>

3
src/Makefile.am
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@ -34,13 +34,14 @@ SUBDIRS += $(EDITORDIR)
EXTRA_DIST = $(EDITORDIR)/Makefile
endif
bin_PROGRAMS = musrfit musrview musrt0 msr2msr msr2data any2many
bin_PROGRAMS = musrfit musrview musrt0 musrFT msr2msr msr2data any2many
bin_PROGRAMS += write_musrRoot_runHeader musrRootValidation
bin_PROGRAMS += dump_header
musrfit_SOURCES = musrfit.cpp
musrview_SOURCES = musrview.cpp
musrt0_SOURCES = musrt0.cpp
musrFT_SOURCES = musrFT.cpp
msr2msr_SOURCES = msr2msr.cpp
msr2data_SOURCES = msr2data.cpp
any2many_SOURCES = any2many.cpp

7
src/classes/Makefile.am
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@ -4,6 +4,7 @@ h_sources = \
../include/PFitterFcn.h \
../include/PFitter.h \
../include/PFourier.h \
../include/PFourierCanvas.h \
../include/PFunctionGrammar.h \
../include/PFunction.h \
../include/PFunctionHandler.h \
@ -12,6 +13,7 @@ h_sources = \
../include/PMusrCanvas.h \
../include/PMusr.h \
../include/PMusrT0.h \
../include/PPrepFourier.h \
../include/PRunAsymmetry.h \
../include/PRunBase.h \
../include/PRunDataHandler.h \
@ -26,6 +28,7 @@ h_sources_userFcn = \
../include/PUserFcnBase.h
h_linkdef = \
../include/PFourierCanvasLinkDef.h \
../include/PMusrCanvasLinkDef.h \
../include/PMusrT0LinkDef.h \
../include/PStartupHandlerLinkDef.h
@ -34,6 +37,7 @@ h_linkdef_userFcn = \
../include/PUserFcnBaseLinkDef.h
dict_h_sources = \
PFourierCanvasDict.h \
PMusrCanvasDict.h \
PMusrT0Dict.h \
PStartupHandlerDict.h
@ -45,6 +49,7 @@ cpp_sources = \
PFitter.cpp \
PFitterFcn.cpp \
PFourier.cpp \
PFourierCanvas.cpp \
PFunction.cpp \
PFunctionHandler.cpp \
PMsr2Data.cpp \
@ -52,6 +57,7 @@ cpp_sources = \
PMusrCanvas.cpp \
PMusr.cpp \
PMusrT0.cpp \
PPrepFourier.cpp \
PRunAsymmetry.cpp \
PRunBase.cpp \
PRunDataHandler.cpp \
@ -66,6 +72,7 @@ cpp_sources_userFcn = \
PUserFcnBase.cpp
dict_cpp_sources = \
PFourierCanvasDict.cpp \
PMusrCanvasDict.cpp \
PMusrT0Dict.cpp \
PStartupHandlerDict.cpp

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44
src/classes/PMsrHandler.cpp
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@ -269,7 +269,7 @@ Int_t PMsrHandler::ReadMsrFile()
}
// fill parameter-in-use vector
if (result == PMUSR_SUCCESS)
if ((result == PMUSR_SUCCESS) && !fFourierOnly)
FillParameterInUse(theory, functions, run);
// check that each run fulfills the minimum requirements
@ -278,7 +278,7 @@ Int_t PMsrHandler::ReadMsrFile()
result = PMUSR_MSR_SYNTAX_ERROR;
// check that parameter names are unique
if (result == PMUSR_SUCCESS) {
if ((result == PMUSR_SUCCESS) && !fFourierOnly) {
UInt_t parX, parY;
if (!CheckUniquenessOfParamNames(parX, parY)) {
cerr << endl << ">> PMsrHandler::ReadMsrFile: **SEVERE ERROR** parameter name " << fParam[parX].fName.Data() << " is identical for parameter no " << fParam[parX].fNo << " and " << fParam[parY].fNo << "!";
@ -290,7 +290,7 @@ Int_t PMsrHandler::ReadMsrFile()
// check that if maps are present in the theory- and/or function-block,
// that there are really present in the run block
if (result == PMUSR_SUCCESS)
if ((result == PMUSR_SUCCESS) && !fFourierOnly)
if (!CheckMaps())
result = PMUSR_MSR_SYNTAX_ERROR;
@ -2387,6 +2387,10 @@ Int_t PMsrHandler::ParameterInUse(UInt_t paramNo)
*/
Bool_t PMsrHandler::HandleFitParameterEntry(PMsrLines &lines)
{
// If msr-file is used for musrFT only, nothing needs to be done here.
if (fFourierOnly)
return true;
PMsrParamStructure param;
Bool_t error = false;
@ -2599,6 +2603,10 @@ Bool_t PMsrHandler::HandleFitParameterEntry(PMsrLines &lines)
*/
Bool_t PMsrHandler::HandleTheoryEntry(PMsrLines &lines)
{
// If msr-file is used for musrFT only, nothing needs to be done here.
if (fFourierOnly)
return true;
// store the theory lines
fTheory = lines;
@ -2619,6 +2627,10 @@ Bool_t PMsrHandler::HandleTheoryEntry(PMsrLines &lines)
*/
Bool_t PMsrHandler::HandleFunctionsEntry(PMsrLines &lines)
{
// If msr-file is used for musrFT only, nothing needs to be done here.
if (fFourierOnly)
return true;
// store the functions lines
fFunctions = lines;
@ -3157,11 +3169,13 @@ Bool_t PMsrHandler::HandleRunEntry(PMsrLines &lines)
}
}
// check map entries, i.e. if the map values are within parameter bounds
for (UInt_t i=0; i<param.GetMap()->size(); i++) {
if ((param.GetMap(i) < 0) || (param.GetMap(i) > (Int_t) fParam.size())) {
cerr << endl << ">> PMsrHandler::HandleRunEntry: **SEVERE ERROR** map value " << param.GetMap(i) << " in line " << iter->fLineNo << " is out of range!";
error = true;
break;
if (!fFourierOnly) {
for (UInt_t i=0; i<param.GetMap()->size(); i++) {
if ((param.GetMap(i) < 0) || (param.GetMap(i) > (Int_t) fParam.size())) {
cerr << endl << ">> PMsrHandler::HandleRunEntry: **SEVERE ERROR** map value " << param.GetMap(i) << " in line " << iter->fLineNo << " is out of range!";
error = true;
break;
}
}
}
}
@ -3515,9 +3529,13 @@ Bool_t PMsrHandler::FilterNumber(TString str, const Char_t *filter, Int_t offset
*/
Bool_t PMsrHandler::HandleCommandsEntry(PMsrLines &lines)
{
// If msr-file is used for musrFT only, nothing needs to be done here.
if (fFourierOnly)
return true;
PMsrLines::iterator iter;
if (lines.empty() && !fFourierOnly) {
if (lines.empty()) {
cerr << endl << ">> PMsrHandler::HandleCommandsEntry(): **WARNING**: There is no COMMAND block! Do you really want this?";
cerr << endl;
}
@ -4352,7 +4370,11 @@ Bool_t PMsrHandler::HandlePlotEntry(PMsrLines &lines)
*/
Bool_t PMsrHandler::HandleStatisticEntry(PMsrLines &lines)
{
if (lines.empty() && !fFourierOnly) {
// If msr-file is used for musrFT only, nothing needs to be done here.
if (fFourierOnly)
return true;
if (lines.empty()) {
cerr << endl << ">> PMsrHandler::HandleStatisticEntry: **WARNING** There is no STATISTIC block! Do you really want this?";
cerr << endl;
fStatistic.fValid = false;
@ -5042,7 +5064,7 @@ Bool_t PMsrHandler::CheckRunBlockIntegrity()
}
}
// check fit range
if (!fRuns[i].IsFitRangeInBin()) { // fit range given as times in usec (RUN block)
if (!fRuns[i].IsFitRangeInBin() && !fFourierOnly) { // fit range given as times in usec (RUN block)
if ((fRuns[i].GetFitRange(0) == PMUSR_UNDEFINED) || (fRuns[i].GetFitRange(1) == PMUSR_UNDEFINED)) { // check fit range in RUN block
if (!fGlobal.IsFitRangeInBin()) { // fit range given as times in usec (GLOBAL block)
if ((fGlobal.GetFitRange(0) == PMUSR_UNDEFINED) || (fGlobal.GetFitRange(1) == PMUSR_UNDEFINED)) { // check fit range in GLOBAL block

2033
src/classes/PMusrCanvas.cpp
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438
src/classes/PPrepFourier.cpp Normal file
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@ -0,0 +1,438 @@
/***************************************************************************
PPrepFourier.cpp
Author: Andreas Suter
e-mail: andreas.suter@psi.ch
***************************************************************************/
/***************************************************************************
* Copyright (C) 2007-2015 by Andreas Suter *
* andreas.suter@psi.ch *
* *
* This program is free software; you can redistribute it and/or modify *
* it under the terms of the GNU General Public License as published by *
* the Free Software Foundation; either version 2 of the License, or *
* (at your option) any later version. *
* *
* This program is distributed in the hope that it will be useful, *
* but WITHOUT ANY WARRANTY; without even the implied warranty of *
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the *
* GNU General Public License for more details. *
* *
* You should have received a copy of the GNU General Public License *
* along with this program; if not, write to the *
* Free Software Foundation, Inc., *
* 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. *
***************************************************************************/
#include "PPrepFourier.h"
//--------------------------------------------------------------------------
// Constructor
//--------------------------------------------------------------------------
/**
* <p>Constructor.
*/
PPrepFourier::PPrepFourier()
{
fBkgRange[0] = -1;
fBkgRange[1] = -1;
fPacking = 1;
}
//--------------------------------------------------------------------------
// Constructor
//--------------------------------------------------------------------------
/**
* <p>Constructor.
*/
PPrepFourier::PPrepFourier(const Int_t *bkgRange, const Int_t packing) :
fPacking(packing)
{
SetBkgRange(bkgRange);
}
//--------------------------------------------------------------------------
// Destructor
//--------------------------------------------------------------------------
/**
* <p>Destructor.
*/
PPrepFourier::~PPrepFourier()
{
fRawData.clear();
fData.clear();
}
//--------------------------------------------------------------------------
// SetBkgRange
//--------------------------------------------------------------------------
/**
* <p>set the background range.
*
* \param bkgRange array with background range
*/
void PPrepFourier::SetBkgRange(const Int_t *bkgRange)
{
int err=0;
if (bkgRange[0] >= -1) {
fBkgRange[0] = bkgRange[0];
} else {
err = 1;
}
if (bkgRange[1] >= -1) {
fBkgRange[1] = bkgRange[1];
} else {
if (err == 0)
err = 2;
else
err = 3;
}
TString errMsg("");
switch (err) {
case 1:
errMsg = TString::Format("start bkg range < 0 (given: %d), will ignore it.", bkgRange[0]);
break;
case 2:
errMsg = TString::Format("end bkg range < 0 (given: %d), will ignore it.", bkgRange[1]);
break;
case 3:
errMsg = TString::Format("start/end bkg range < 0 (given: %d/%d), will ignore it.", bkgRange[0], bkgRange[1]);
break;
default:
errMsg = TString("??");
break;
}
if (err != 0) {
cerr << endl << ">> PPrepFourier::SetBkgRange: **WARNING** " << errMsg << endl;
}
}
//--------------------------------------------------------------------------
// SetPacking
//--------------------------------------------------------------------------
/**
* <p>set the packing for the histograms.
*
* \param packing number to be used.
*/
void PPrepFourier::SetPacking(const Int_t packing)
{
if (packing > 0) {
fPacking = packing;
} else {
cerr << endl << ">> PPrepFourier::SetPacking: **WARNING** found packing=" << packing << " < 0, will ignore it." << endl;
}
}
//--------------------------------------------------------------------------
// AddData
//--------------------------------------------------------------------------
/**
* <p>add a data-set (time domain data + meta information) to the internal
* data vector.
*
* \param data set to be added
*/
void PPrepFourier::AddData(musrFT_data &data)
{
fRawData.push_back(data);
}
//--------------------------------------------------------------------------
// DoBkgCorrection
//--------------------------------------------------------------------------
/**
* <p>Correct the internal data sets according to a background interval given.
*/
void PPrepFourier::DoBkgCorrection()
{
// make sure fData are already present, and if not create the necessary data sets
if (fData.size() != fRawData.size()) {
InitData();
}
// if no bkg-range is given, nothing needs to be done
if ((fBkgRange[0] == -1) && (fBkgRange[1] == -1)) {
return;
}
// make sure that the bkg range is ok
for (unsigned int i=0; i<fRawData.size(); i++) {
if ((fBkgRange[0] >= fRawData[i].rawData.size()) || (fBkgRange[1] >= fRawData[i].rawData.size())) {
cerr << endl << "PPrepFourier::DoBkgCorrection() **ERROR** bkg-range out of data-range!";
return;
}
}
Double_t bkg=0.0;
for (unsigned int i=0; i<fRawData.size(); i++) {
// calculate the bkg for the given range
for (int j=fBkgRange[0]; j<=fBkgRange[1]; j++) {
bkg += fRawData[i].rawData[j];
}
bkg /= (fBkgRange[1]-fBkgRange[0]+1);
// correct data
for (unsigned int j=0; j<fData[i].size(); j++)
fData[i][j] -= bkg;
}
}
//--------------------------------------------------------------------------
// DoPacking
//--------------------------------------------------------------------------
/**
* <p>Rebin (pack) the internal data.
*/
void PPrepFourier::DoPacking()
{
// make sure fData are already present, and if not create the necessary data sets
if (fData.size() != fRawData.size()) {
InitData();
}
if (fPacking == 1) // nothing to be done
return;
PDoubleVector tmpData;
Double_t dval = 0.0;
for (unsigned int i=0; i<fData.size(); i++) {
tmpData.clear();
dval = 0.0;
for (unsigned int j=0; j<fData[i].size(); j++) {
if ((j % fPacking == 0) && (j != 0)) {
tmpData.push_back(dval);
dval = 0.0;
} else {
dval += fData[i][j];
}
}
// change the original data set with the packed one
fData[i].clear();
fData[i] = tmpData;
}
}
//--------------------------------------------------------------------------
// DoFiltering
//--------------------------------------------------------------------------
/**
* <p>Not implemented yet.
*/
void PPrepFourier::DoFiltering()
{
// make sure fData are already present, and if not create the necessary data sets
if (fData.size() != fRawData.size()) {
InitData();
}
}
//--------------------------------------------------------------------------
// DoLifeTimeCorrection
//--------------------------------------------------------------------------
/**
* <p>Try to do a muon life time correction. The idea is to estimate N0 without
* any theory. This will be OK for high fields (> couple kGauss) but not so good
* for low fields.
*
* \param fudge rescaling factor for the estimated N0. Should be around 1
*/
void PPrepFourier::DoLifeTimeCorrection(Double_t fudge)
{
// make sure fData are already present, and if not create the necessary data sets
if (fData.size() != fRawData.size()) {
InitData();
}
// calc exp(+t/tau)*N(t), where N(t) is already background corrected
Double_t scale;
for (unsigned int i=0; i<fData.size(); i++) {
scale = fRawData[i].timeResolution / PMUON_LIFETIME;
for (unsigned int j=0; j<fData[i].size(); j++) {
fData[i][j] *= exp(j*scale);
}
}
// calc N0
Double_t dval;
Double_t N0;
for (unsigned int i=0; i<fData.size(); i++) {
dval = 0.0;
for (unsigned int j=0; j<fData[i].size(); j++) {
dval += fData[i][j];
}
N0 = dval/fData[i].size();
N0 *= fudge;
for (unsigned int j=0; j<fData[i].size(); j++) {
fData[i][j] -= N0;
fData[i][j] /= N0;
}
}
}
//--------------------------------------------------------------------------
// GetInfo
//--------------------------------------------------------------------------
/**
* <p>Returns the meta information of a data set.
*
* \param idx index of the object
*/
TString PPrepFourier::GetInfo(const UInt_t idx)
{
TString info("");
if (idx < fRawData.size())
info = fRawData[idx].info;
return info;
}
//--------------------------------------------------------------------------
// GetData
//--------------------------------------------------------------------------
/**
* <p>Creates the requested TH1F objects and returns them. The ownership is with
* the caller.
*/
vector<TH1F*> PPrepFourier::GetData()
{
vector<TH1F*> data;
data.resize(fData.size());
// if not data are present, just return an empty vector
if (fData.size() == 0)
return data;
TString name("");
Double_t dt=0.0;
Double_t start=0.0;
Double_t end=0.0;
UInt_t size;
UInt_t startIdx;
UInt_t endIdx;
for (unsigned int i=0; i<fData.size(); i++) {
name = TString::Format("histo%2d", i);
dt = fRawData[i].timeResolution*fPacking;
start = fRawData[i].timeRange[0];
end = fRawData[i].timeRange[1];
// init size and start/end indices
size = fData[i].size();
startIdx = 1;
endIdx = size;
// time range given, hence calculate the proper size
if (start != -1.0) {
size = (UInt_t)((end-start)/dt);
if (start >= 0.0) {
startIdx = (UInt_t)(start/dt)+1;
endIdx = (UInt_t)(end/dt)+1;
} else {
cerr << endl << ">> PPrepFourier::GetData **WARNING** found start time < 0.0, will set it to 0.0" << endl;
endIdx = static_cast<UInt_t>(end/dt)+1;
}
}
if (start == -1.0) { // no time range given, hence start == 0.0 - dt/2
start = -dt/2.0;
} else { // time range given
start -= dt/2.0;
}
if (end == -1.0) { // no time range given, hence end == (fData[idx].size()-1)*dt + dt/2
end = (fData[i].size()-1)*dt+dt/2.0;
} else { // time range given
end += dt/2.0;
}
data[i] = new TH1F(name.Data(), fRawData[i].info.Data(), size, start, end);
for (unsigned int j=startIdx; j<endIdx; j++)
data[i]->SetBinContent(j-startIdx+1, fData[i][j]);
}
return data;
}
//--------------------------------------------------------------------------
// GetData
//--------------------------------------------------------------------------
/**
* <p>Creates the requested TH1F object and returns it. The ownership is with
* the caller.
*
* \param idx index of the requested histogram
*/
TH1F *PPrepFourier::GetData(const UInt_t idx)
{
if (fData.size() == 0) // no data present
return 0;
if (idx > fData.size()) // requested index out of range
return 0;
TString name = TString::Format("histo%2d", idx);
Double_t dt = fRawData[idx].timeResolution*fPacking;
Double_t start = fRawData[idx].timeRange[0];
Double_t end = fRawData[idx].timeRange[1];
UInt_t size = fData[idx].size();
UInt_t startIdx = 1;
UInt_t endIdx = size;
// time range given, hence calculate the proper size
if (start != -1.0) {
size = (UInt_t)((end-start)/dt);
if (start >= 0.0) {
startIdx = (UInt_t)(start/dt)+1;
endIdx = (UInt_t)(end/dt)+1;
} else {
cerr << endl << ">> PPrepFourier::GetData **WARNING** found start time < 0.0, will set it to 0.0" << endl;
endIdx = (UInt_t)(end/dt)+1;
}
}
if (start == -1.0) { // no time range given, hence start == 0.0 - dt/2
start = -dt/2.0;
} else { // time range given
start -= dt/2.0;
}
if (end == -1.0) { // no time range given, hence end == (fData[idx].size()-1)*dt + dt/2
end = (fData[idx].size()-1)*dt+dt/2.0;
} else { // time range given
end += dt/2.0;
}
TH1F *data = new TH1F(name.Data(), fRawData[idx].info.Data(), size, start, end);
for (unsigned int i=startIdx; i<endIdx; i++)
data->SetBinContent(i-startIdx+1, fData[idx][i]);
return data;
}
//--------------------------------------------------------------------------
// InitData
//--------------------------------------------------------------------------
/**
* <p>Copy raw-data to internal data from t0 to the size of raw-data.
*/
void PPrepFourier::InitData()
{
fData.resize(fRawData.size());
unsigned int t0;
for (unsigned int i=0; i<fRawData.size(); i++) {
if (fRawData[i].t0 >= 0)
t0 = fRawData[i].t0;
else
t0 = 0;
for (unsigned int j=t0; j<fRawData[i].rawData.size(); j++) {
fData[i].push_back(fRawData[i].rawData[j]);
}
}
}

21
src/classes/PRunDataHandler.cpp
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@ -218,6 +218,7 @@ PRunDataHandler::~PRunDataHandler()
//--------------------------------------------------------------------------
/**
* <p>Checks if runName is found, and if so return these data.
* runName is as given in the msr-file.
*
* <b>return:</b>
* - if data are found: pointer to the data.
@ -240,6 +241,26 @@ PRawRunData* PRunDataHandler::GetRunData(const TString &runName)
return &fData[i];
}
//--------------------------------------------------------------------------
// GetRunData
//--------------------------------------------------------------------------
/**
* <p>return data-set with index idx.
*
* <b>return:</b>
* - if data are found: pointer to the data.
* - otherwise the null pointer will be returned.
*
* \param idx index of the raw data set.
*/
PRawRunData* PRunDataHandler::GetRunData(const UInt_t idx)
{
if (idx >= fData.size())
return 0;
else
return &fData[idx];
}
//--------------------------------------------------------------------------
// ReadData
//--------------------------------------------------------------------------

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src/external/libBNMR/045674.msr vendored Normal file
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src/external/libBNMR/ExpRlx-MUD.msr vendored Normal file
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@ -0,0 +1,73 @@
# Run Numbers: 1111
###############################################################
FITPARAMETER
###############################################################
# No Name Value Err Min Max
1 Alphap 1.11662 0.00020 none
2 Asyp 0 0.00038 none
3 T 1e6 0 none
4 Rlx 0.969e6 0.020 none
5 Pos 1 0 none
6 Neg -1 0 none
###############################################################
THEORY
###############################################################
asymmetry fun1
userFcn libBNMR.so ExpRlx 3 4
###############################################################
FUNCTIONS
###############################################################
fun1 = map1 * map2
###############################################################
RUN 045674 BNMR TRIUMF MUD (name beamline institute data-file-format)
fittype 2 (asymmetry fit)
alpha 1
forward 3
backward 4
data 11 799 11 799
background 800 900 800 900 # estimated bkg: 416.9700 / 465.7600
t0 0.0 0.0
map 2 5 0 0 0 0 0 0 0 0
fit 5e5 8e6
packing 5
RUN 045674 BNMR TRIUMF MUD (name beamline institute data-file-format)
fittype 2 (asymmetry fit)
alpha 1
forward 5
backward 6
data 11 799 11 799
background 800 900 800 900 # estimated bkg: 430.9200 / 479.4500
t0 0.0 0.0
map 2 6 0 0 0 0 0 0 0 0
fit 5e5 8e6
packing 5
###############################################################
COMMANDS
MINIMIZE
HESSE
SAVE
###############################################################
PLOT 2 (asymmetry plot)
runs 1 2
use_fit_ranges
###############################################################
FOURIER
units MHz # units either 'Gauss', 'MHz', or 'Mc/s'
fourier_power 12
apodization STRONG # NONE, WEAK, MEDIUM, STRONG
plot POWER # REAL, IMAG, REAL_AND_IMAG, POWER, PHASE
phase 8
#range FRQMIN FRQMAX
###############################################################
STATISTIC --- 2014-11-14 16:37:41
chisq = 372.2, NDF = 295, chisq/NDF = 1.261744

6
src/include/PFourier.h
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@ -8,7 +8,7 @@
***************************************************************************/
/***************************************************************************
* Copyright (C) 2007-2014 by Andreas Suter *
* Copyright (C) 2007-2015 by Andreas Suter *
* andreas.suter@psi.ch *
* *
* This program is free software; you can redistribute it and/or modify *
@ -52,6 +52,8 @@ class PFourier
virtual void Transform(UInt_t apodizationTag = 0);
virtual const char* GetDataTitle() { return fData->GetTitle(); }
virtual const Int_t GetUnitTag() { return fUnitTag; }
virtual Double_t GetResolution() { return fResolution; }
virtual TH1F* GetRealFourier(const Double_t scale = 1.0);
virtual TH1F* GetImaginaryFourier(const Double_t scale = 1.0);
@ -68,7 +70,7 @@ class PFourier
Int_t fApodization; ///< 0=none, 1=weak, 2=medium, 3=strong
Double_t fTimeResolution; ///< time resolution of the data histogram
Double_t fTimeResolution; ///< time resolution of the data histogram in (us)
Double_t fStartTime; ///< start time of the data histogram
Double_t fEndTime; ///< end time of the data histogram
Bool_t fDCCorrected; ///< if true, removed DC offset from signal before Fourier transformation, otherwise not

161
src/include/PFourierCanvas.h Normal file
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@ -0,0 +1,161 @@
/***************************************************************************
* Copyright (C) 2007-2015 by Andreas Suter *
* andreas.suter@psi.ch *
* *
* This program is free software; you can redistribute it and/or modify *
* it under the terms of the GNU General Public License as published by *
* the Free Software Foundation; either version 2 of the License, or *
* (at your option) any later version. *
* *
* This program is distributed in the hope that it will be useful, *
* but WITHOUT ANY WARRANTY; without even the implied warranty of *
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the *
* GNU General Public License for more details. *
* *
* You should have received a copy of the GNU General Public License *
* along with this program; if not, write to the *
* Free Software Foundation, Inc., *
* 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. *
***************************************************************************/
#ifndef _PFOURIERCANVAS_H_
#define _PFOURIERCANVAS_H_
#include <TObject.h>
#include <TQObject.h>
#include <TTimer.h>
#include <TStyle.h>
#include <TRootCanvas.h>
#include <TGMenu.h>
#include <TCanvas.h>
#include <TPaveText.h>
#include <TLegend.h>
#include <TPad.h>
#include <TH1F.h>
#include <TLatex.h>
#include "PMusr.h"
#include "PFourier.h"
// Canvas menu id's
#define P_MENU_ID_FOURIER 10001
#define P_MENU_ID_AVERAGE 10002
#define P_MENU_ID_SAVE_DATA 10003
#define P_MENU_ID_FOURIER_REAL 100
#define P_MENU_ID_FOURIER_IMAG 101
#define P_MENU_ID_FOURIER_REAL_AND_IMAG 102
#define P_MENU_ID_FOURIER_PWR 103
#define P_MENU_ID_FOURIER_PHASE 104
#define P_MENU_ID_FOURIER_PHASE_PLUS 105
#define P_MENU_ID_FOURIER_PHASE_MINUS 106
#define P_MENU_ID_SAVE_ASCII 200
//------------------------------------------------------------------------
/**
* <p>Structure holding all necessary Fourier histograms.
*/
typedef struct {
TH1F *dataFourierRe; ///< real part of the Fourier transform of the data histogram
TH1F *dataFourierIm; ///< imaginary part of the Fourier transform of the data histogram
TH1F *dataFourierPwr; ///< power spectrum of the Fourier transform of the data histogram
TH1F *dataFourierPhase; ///< phase spectrum of the Fourier transform of the data histogram
} PFourierCanvasDataSet;
//------------------------------------------------------------------------
/**
* <p>typedef to make to code more readable: list of histogram data sets.
*/
typedef vector<PFourierCanvasDataSet> PFourierCanvasDataList;
//--------------------------------------------------------------------------
/**
* <p>
*/
class PFourierCanvas : public TObject, public TQObject
{
public:
PFourierCanvas();
PFourierCanvas(vector<PFourier*> &fourier, const Char_t* title, const Bool_t showAverage,
const Int_t fourierPlotOpt, Double_t fourierXrange[2], Double_t phase,
Int_t wtopx, Int_t wtopy, Int_t ww, Int_t wh, const Bool_t batch);
PFourierCanvas(vector<PFourier*> &fourier, const Char_t* title, const Bool_t showAverage,
const Int_t fourierPlotOpt, Double_t fourierXrange[2], Double_t phase,
Int_t wtopx, Int_t wtopy, Int_t ww, Int_t wh,
const PIntVector markerList, const PIntVector colorList, const Bool_t batch);
virtual ~PFourierCanvas();
virtual void Done(Int_t status=0); // *SIGNAL*
virtual void HandleCmdKey(Int_t event, Int_t x, Int_t y, TObject *selected); // SLOT
virtual void HandleMenuPopup(Int_t id); // SLOT
virtual void LastCanvasClosed(); // SLOT
virtual void UpdateFourierPad();
virtual void UpdateInfoPad();
virtual Bool_t IsValid() { return fValid; }
virtual void SetTimeout(Int_t ival);
virtual void SaveGraphicsAndQuit(const Char_t *fileName);
virtual void SaveDataAscii();
private:
Int_t fTimeout; ///< timeout after which the Done signal should be emited. If timeout <= 0, no timeout is taking place
Bool_t fBatchMode; ///< musrview in ROOT batch mode
Bool_t fValid; ///< if true, everything looks OK
Bool_t fAveragedView; ///< tag showing that the averaged view or normal view should be presented.
Int_t fCurrentPlotView; ///< tag showing what the current plot view is: real, imag, power, phase, ...
Double_t fInitialXRange[2]; ///< keeps the initial x-range
Double_t fInitialYRange[2]; ///< keeps the initial y-range
TString fTitle;
TString fXaxisTitle;
vector<PFourier*> fFourier; ///< keeps all the Fourier data, ownership is with the caller
PFourierCanvasDataList fFourierHistos; ///< keeps all the Fourier histos
PFourierCanvasDataSet fFourierAverage; ///< keeps the average of the Fourier histos
Double_t fCurrentFourierPhase; ///< keeps the current Fourier phase (real/imag)
TLatex *fCurrentFourierPhaseText; ///< used in Re/Im Fourier to show the current phase in the pad
TStyle *fStyle; ///< A collection of all graphics attributes
TTimer *fTimeoutTimer; ///< timeout timer in order to terminate if no action is taking place for too long
PIntVector fMarkerList; ///< list of markers
PIntVector fColorList; ///< list of colors
// canvas menu related variables
TRootCanvas *fImp; ///< ROOT native GUI version of main window with menubar and drawing area
TGMenuBar *fBar; ///< menu bar
TGPopupMenu *fPopupMain; ///< popup menu MusrFT in the main menu bar
TGPopupMenu *fPopupSave; ///< popup menu of the MusrFT/Save Data sub menu
TGPopupMenu *fPopupFourier; ///< popup menu of the MusrFT/Fourier sub menu
// canvas related variables
TCanvas *fMainCanvas; ///< main canvas
TPaveText *fTitlePad; ///< title pad used to display a title
TPad *fFourierPad; ///< fourier pad used to display the fourier
TLegend *fInfoPad; ///< info pad used to display a legend of the data plotted
virtual void CreateXaxisTitle();
virtual void CreateStyle();
virtual void InitFourierDataSets();
virtual void InitFourierCanvas(const Char_t* title, Int_t wtopx, Int_t wtopy, Int_t ww, Int_t wh);
virtual void CleanupAverage();
virtual void HandleAverage();
virtual void PlotFourier();
virtual void PlotFourierPhaseValue();
virtual void PlotAverage();
virtual void IncrementFourierPhase();
virtual void DecrementFourierPhase();
virtual Double_t GetMaximum(TH1F* histo, Double_t xmin=-1.0, Double_t xmax=-1.0);
virtual Double_t GetMinimum(TH1F* histo, Double_t xmin=-1.0, Double_t xmax=-1.0);
virtual Double_t GetInterpolatedValue(TH1F* histo, Double_t xVal);
ClassDef(PFourierCanvas, 1)
};
#endif // _PFOURIERCANVAS_H_

39
src/include/PFourierCanvasLinkDef.h Normal file
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@ -0,0 +1,39 @@
/***************************************************************************
PMusrCanvasLinkDef.h
Author: Andreas Suter
e-mail: andreas.suter@psi.ch
***************************************************************************/
/***************************************************************************
* Copyright (C) 2007-2015 by Andreas Suter *
* andreas.suter@psi.ch *
* *
* This program is free software; you can redistribute it and/or modify *
* it under the terms of the GNU General Public License as published by *
* the Free Software Foundation; either version 2 of the License, or *
* (at your option) any later version. *
* *
* This program is distributed in the hope that it will be useful, *
* but WITHOUT ANY WARRANTY; without even the implied warranty of *
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the *
* GNU General Public License for more details. *
* *
* You should have received a copy of the GNU General Public License *
* along with this program; if not, write to the *
* Free Software Foundation, Inc., *
* 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. *
***************************************************************************/
#ifdef __CINT__
#pragma link off all globals;
#pragma link off all classes;
#pragma link off all functions;
#pragma link C++ class PFourierCanvas+;
#endif

5
src/include/PMusr.h
View File

@ -8,7 +8,7 @@
***************************************************************************/
/***************************************************************************
* Copyright (C) 2007-2014 by Andreas Suter *
* Copyright (C) 2007-2015 by Andreas Suter *
* andreas.suter@psi.ch *
* *
* This program is free software; you can redistribute it and/or modify *
@ -44,6 +44,7 @@ using namespace std;
#define PMUSR_TOKENIZE_ERROR -5
#define PMUSR_MSR_LOG_FILE_WRITE_ERROR -6
#define PMUSR_MSR_FILE_WRITE_ERROR -7
#define PMUSR_DATA_FILE_READ_ERROR -8
#define PRUN_SINGLE_HISTO 0
#define PRUN_ASYMMETRY 2
@ -703,7 +704,7 @@ typedef vector<PMsrRunBlock> PMsrRunList;
*/
typedef struct {
Bool_t fFourierBlockPresent; ///< flag indicating if a Fourier block is present in the msr-file
Int_t fUnits; ///< flag used to indicate the units. 0=field units (G); 1=frequency units (MHz); 2=Mc/s
Int_t fUnits; ///< flag used to indicate the units. 1=field units (G); 2=field units (T); 3=frequency units (MHz); 4=Mc/s
Bool_t fDCCorrected; ///< if set true, the dc offset of the signal/theory will be removed before the FFT is made.
Int_t fFourierPower; ///< i.e. zero padding up to 2^fFourierPower, default = 0 which means NO zero padding
Int_t fApodization; ///< tag indicating the kind of apodization wished, 0=no appodization (default), 1=weak, 2=medium, 3=strong (for details see the docu)

7
src/include/PMusrCanvas.h
View File

@ -229,6 +229,7 @@ class PMusrCanvas : public TObject, public TQObject
virtual void LastCanvasClosed(); // SLOT
virtual void SaveGraphicsAndQuit(Char_t *fileName, Char_t *graphicsFormat);
virtual void SaveDataAscii();
private:
Int_t fTimeout; ///< timeout after which the Done signal should be emited. If timeout <= 0, no timeout is taking place
@ -277,9 +278,7 @@ class PMusrCanvas : public TObject, public TQObject
PRunListCollection *fRunList; ///< data handler
#endif // __MAKECINT__
enum EAlignTag {eTime, eTheoTime, eFreq, eTheoFreq};
PMusrCanvasDataSet fDataAvg; ///< set of all averaged data to be plotted (asymmetry/single histogram)
PIntVector fAlignmentOffset; ///< holds the vector with the time/freq alignment offsets
PMusrCanvasDataList fData; ///< list of all histogram data to be plotted (asymmetry/single histogram)
PMusrCanvasNonMusrDataList fNonMusrData; ///< list of all error graphs to be plotted (non-muSR)
@ -329,12 +328,10 @@ class PMusrCanvas : public TObject, public TQObject
virtual void IncrementFourierPhase();
virtual void DecrementFourierPhase();
virtual void SaveDataAscii();
virtual Bool_t IsScaleN0AndBkg();
virtual UInt_t GetNeededAccuracy(PMsrParamStructure param);
virtual Bool_t CalcAlignment(const EAlignTag tag);
virtual Double_t GetInterpolatedValue(TH1F* histo, Double_t xVal);
ClassDef(PMusrCanvas, 1)
};

88
src/include/PPrepFourier.h Normal file
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@ -0,0 +1,88 @@
/***************************************************************************
PPrepFourier.h
Author: Andreas Suter
e-mail: andreas.suter@psi.ch
***************************************************************************/
/***************************************************************************
* Copyright (C) 2007-2015 by Andreas Suter *
* andreas.suter@psi.ch *
* *
* This program is free software; you can redistribute it and/or modify *
* it under the terms of the GNU General Public License as published by *
* the Free Software Foundation; either version 2 of the License, or *
* (at your option) any later version. *
* *
* This program is distributed in the hope that it will be useful, *
* but WITHOUT ANY WARRANTY; without even the implied warranty of *
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the *
* GNU General Public License for more details. *
* *
* You should have received a copy of the GNU General Public License *
* along with this program; if not, write to the *
* Free Software Foundation, Inc., *
* 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. *
***************************************************************************/
#ifndef _PPREPFOURIER_H_
#define _PPREPFOURIER_H_
#include <iostream>
#include <vector>
using namespace std;
#include "TH1F.h"
#include "PMusr.h"
//----------------------------------------------------------------------------
/**
* <p>Data structure holding raw time domain uSR data together with some
* necessary meta information.
*/
typedef struct {
TString info; ///< keeps all the meta information
double timeResolution; ///< time resolution in (usec)
int t0; ///< keep the t0 bin
Double_t timeRange[2]; ///< time range to be used, given in (usec).
PDoubleVector rawData; ///< a single time domain data vector
} musrFT_data;
//----------------------------------------------------------------------------
/**
* <p>Little helper class to prepare time-domain data for Fourier transform, without
* theory, etc.
*/
class PPrepFourier {
public:
PPrepFourier();
PPrepFourier(const Int_t *bkgRange, const Int_t packing);
virtual ~PPrepFourier();
void SetBkgRange(const Int_t *bkgRange);
void SetPacking(const Int_t packing);
void AddData(musrFT_data &data);
void DoBkgCorrection();
void DoPacking();
void DoFiltering();
void DoLifeTimeCorrection(Double_t fudge);
TString GetInfo(const UInt_t idx);
UInt_t GetNoOfData() { return fRawData.size(); }
vector<TH1F*> GetData();
TH1F *GetData(const UInt_t idx);
private:
vector<musrFT_data> fRawData;
vector<PDoubleVector>fData;
Int_t fBkgRange[2];
Int_t fPacking;
void InitData();
};
#endif // _PPREPFOURIER_H_

3
src/include/PRunDataHandler.h
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@ -8,7 +8,7 @@
***************************************************************************/
/***************************************************************************
* Copyright (C) 2007-2014 by Andreas Suter *
* Copyright (C) 2007-2015 by Andreas Suter *
* andreas.suter@psi.ch *
* *
* This program is free software; you can redistribute it and/or modify *
@ -60,6 +60,7 @@ class PRunDataHandler
virtual Bool_t IsAllDataAvailable() const { return fAllDataAvailable; }
virtual PRawRunData* GetRunData(const TString &runName);
virtual PRawRunData* GetRunData(const UInt_t idx=0);
virtual TString GetRunPathName() {return fRunPathName; }
private:

1428
src/musrFT.cpp Normal file
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File diff suppressed because it is too large Load Diff

18
src/musrview.cpp
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@ -67,6 +67,8 @@ void musrview_syntax()
cout << endl << " eps, pdf, gif, jpg, png, svg, xpm, root";
cout << endl << " example: musrview 3310.msr --png, will produce a files 3310_X.png";
cout << endl << " where 'X' stands for the plot number (starting form 0)";
cout << endl << " --ascii: ";
cout << endl << " will produce an ascii dump of the data and fit as plotted.";
cout << endl << " --timeout <timeout>: <timeout> given in seconds after which musrview terminates.";
cout << endl << " If <timeout> <= 0, no timeout will take place. Default <timeout> is 0.";
cout << endl;
@ -100,6 +102,7 @@ int main(int argc, char *argv[])
bool success = true;
char fileName[128];
bool graphicsOutput = false;
bool asciiOutput = false;
char graphicsExtension[128];
int timeout = 0;
@ -135,6 +138,8 @@ int main(int argc, char *argv[])
graphicsOutput = true;
strcpy(graphicsExtension, argv[i]+2);
} else if (!strcmp(argv[i], "--ascii")) {
asciiOutput = true;
} else if (!strcmp(argv[i], "--timeout")) {
if (i+1 < argc) {
TString str(argv[i+1]);
@ -280,7 +285,7 @@ int main(int argc, char *argv[])
if (success) {
// generate Root application needed for PMusrCanvas
if (graphicsOutput) {
if (graphicsOutput || asciiOutput) {
argv[argc] = (char*)malloc(16*sizeof(char));
strcpy(argv[argc], "-b");
argc++;
@ -299,10 +304,10 @@ int main(int argc, char *argv[])
startupHandler->GetFourierDefaults(),
startupHandler->GetMarkerList(),
startupHandler->GetColorList(),
graphicsOutput);
graphicsOutput||asciiOutput);
else
musrCanvas = new PMusrCanvas(i, msrHandler->GetMsrTitle()->Data(),
10+i*100, 10+i*100, 800, 600, graphicsOutput);
10+i*100, 10+i*100, 800, 600, graphicsOutput||asciiOutput);
if (!musrCanvas->IsValid()) {
cerr << endl << ">> musrview **SEVERE ERROR** Couldn't invoke all necessary objects, will quit.";
@ -334,6 +339,12 @@ int main(int argc, char *argv[])
musrCanvas->SaveGraphicsAndQuit(fileName, graphicsExtension);
}
if (asciiOutput) {
// save data in batch mode
musrCanvas->SaveDataAscii();
musrCanvas->Done(0);
}
// keep musrCanvas objects
canvasVector.push_back(musrCanvas);
}
@ -349,7 +360,6 @@ int main(int argc, char *argv[])
sprintf(canvasName, "fMainCanvas%d", i);
if (gROOT->GetListOfCanvases()->FindObject(canvasName) != 0) {
canvasVector[i]->~PMusrCanvas();
} else {
}
}
canvasVector.empty();