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more work towards NeXus exchange

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This commit is contained in:
suter_a
2011-12-22 10:27:01 +00:00
parent 60a11bffa5
commit 7e2ea62ac3
16 changed files with 871 additions and 486 deletions
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28
src/Makefile.am
View File

@ -17,12 +17,23 @@ SUBDIRS = external/TLemRunHeader \
external/mud \
$(PNEXUSDIRS) \
classes \
external \
$(EDITORDIR)
external
if BUILD_MUSRGUI
SUBDIRS += $(EDITORDIR)
EXTRA_DIST = $(EDITORDIR)/Makefile
endif
if BUILD_MUSREDIT
SUBDIRS += $(EDITORDIR)
EXTRA_DIST = $(EDITORDIR)/Makefile
endif
bin_PROGRAMS = musrfit musrview musrt0 musrparam msr2msr msr2data any2many
if PNEXUS_ENABLED
bin_PROGRAMS += nexus_dump
endif
musrfit_SOURCES = musrfit.cpp
musrview_SOURCES = musrview.cpp
musrt0_SOURCES = musrt0.cpp
@ -30,6 +41,9 @@ musrparam_SOURCES = musrparam.cpp
msr2msr_SOURCES = msr2msr.cpp
msr2data_SOURCES = msr2data.cpp
any2many_SOURCES = any2many.cpp
if PNEXUS_ENABLED
nexus_dump_SOURCES = nexus_dump.cpp
endif
xmldir = $(bindir)
xml_DATA = musrfit_startup.xml
@ -39,6 +53,10 @@ LIBADD = $(PMUSR_LIBS) $(LEM_LIBS) $(PSIBIN_LIBS) $(MUD_LIBS) $(PNEXUS_LIBS)
AM_CXXFLAGS = $(LOCAL_BIN_CXXFLAGS)
AM_LDFLAGS = $(LOCAL_BIN_LDFLAGS)
INCLUDES = $(PMUSR_CFLAGS) $(FFTW3_CFLAGS) $(GSL_CFLAGS) $(BOOST_CFLAGS) $(ROOT_CFLAGS)
if PNEXUS_ENABLED
INCLUDES += $(HDF5_CFLAGS) $(NEXUS_CFLAGS) $(PNEXUS_CXXFLAGS)
endif
LIBS = $(PMUSR_LIBS) $(USERFCN_LIBS) $(LEM_LIBS) $(PSIBIN_LIBS) $(MUD_LIBS) $(PNEXUS_LIBS) $(FFTW3_LIBS) $(GSL_LIBS) $(ROOT_LIBS)
install-xmlDATA: $(xml_DATA)
@ -72,12 +90,10 @@ uninstall-xmlDATA:
read REMOVE && \
if test "$$REMOVE" = "y" || test "$$REMOVE" = "Y"; then \
echo "$(RM) '$(DESTDIR)$(xmldir)/$(xml_DATA)'" && \
$(RM) "$(DESTDIR)$(xmldir)/$(xml_DATA)" && \
rmdir "$(DESTDIR)$(xmldir)"; \
$(RM) "$(DESTDIR)$(xmldir)/$(xml_DATA)"; \
fi; \
else \
echo "$(RM) '$(DESTDIR)$(xmldir)/$(xml_DATA)'" && \
$(RM) "$(DESTDIR)$(xmldir)/$(xml_DATA)" && \
rmdir "$(DESTDIR)$(xmldir)"; \
$(RM) "$(DESTDIR)$(xmldir)/$(xml_DATA)"; \
fi; \
fi

4
src/any2many.cpp
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@ -53,8 +53,8 @@ void any2many_syntax()
cout << endl << "usage: any2many [--help] : will show this help.";
cout << endl << " any2many --version : will show the svn version.";
cout << endl << " any2many -f <filenameList-input> | -r <runList-input>";
cout << endl << " -c <convert-options> [-p <output-path>]";
cout << endl << " [-y <year>] [-t <in-template> <out-template>] [-s]";
cout << endl << " -c <convert-options> [-p <output-path>] [-y <year>]";
cout << endl << " [-o <outputFileName> | -t <in-template> <out-template>] [-s]";
cout << endl << " [-rebin <n>] [-z <compressed>]";
cout << endl << " -f <filenameList-input> : where <filenameList-input> is space";
cout << endl << " separeted a list of file names (not starting with a '-'),";

2
src/classes/PMusr.cpp
View File

@ -224,6 +224,8 @@ PRawRunData::PRawRunData()
fLaboratory = TString("n/a");
fBeamline = TString("n/a");
fInstrument = TString("n/a");
fMuonSource = TString("n/a");
fMuonSpecies = TString("n/a");
fRunName = TString("n/a");
fRunNumber = -1;
fRunTitle = TString("n/a");

507
src/classes/PRunDataHandler.cpp
View File

@ -39,6 +39,7 @@
#include <iomanip>
#include <fstream>
#include <string>
#include <sstream>
using namespace std;
#include <TROOT.h>
@ -584,7 +585,7 @@ Bool_t PRunDataHandler::ReadWriteFilesList()
}
//--------------------------------------------------------------------------
// FileAlreadyRead
// FileAlreadyRead (private)
//--------------------------------------------------------------------------
/**
* <p> Checks if a file has been already read in order to prevent multiple
@ -608,7 +609,7 @@ Bool_t PRunDataHandler::FileAlreadyRead(TString runName)
}
//--------------------------------------------------------------------------
// TestFileName -- private
// TestFileName (private)
//--------------------------------------------------------------------------
/**
* <p> Tests if a file exists (with or without given extension).
@ -622,75 +623,91 @@ void PRunDataHandler::TestFileName(TString &runName, const TString &ext)
TString tmpStr(runName), tmpExt(ext);
// check first if the file exists with the default extension which is not given with the run name
runName += TString(".") + ext;
if (gSystem->AccessPathName(runName.Data()) != true) { // found
return;
}
// test if the file exists with only upper-case letters
runName.ToUpper();
if (gSystem->AccessPathName(runName.Data()) != true) { // found
return;
}
// test if the file exists with only lower-case letters
runName.ToLower();
if (gSystem->AccessPathName(runName.Data()) != true) { // found
tmpStr += TString(".") + ext;
if (gSystem->AccessPathName(tmpStr.Data()) != true) { // found
runName = tmpStr;
return;
}
// test if the file exists with the given run name but an only upper-case extension which is not included in the file name
runName = tmpStr;
tmpStr = runName;
tmpExt.ToUpper();
runName += TString(".") + tmpExt;
if (gSystem->AccessPathName(runName.Data()) != true) { // found
tmpStr += TString(".") + tmpExt;
if (gSystem->AccessPathName(tmpStr.Data()) != true) { // found
runName = tmpStr;
return;
}
// test if the file exists with the given run name but an only lower-case extension which is not included in the file name
tmpStr = runName;
tmpExt.ToLower();
runName = runName.Replace(static_cast<Ssiz_t>(runName.Length()-tmpExt.Length()), tmpExt.Length(), tmpExt);
if (gSystem->AccessPathName(runName.Data()) != true) { // found
tmpStr += TString(".") + tmpExt;
if (gSystem->AccessPathName(tmpStr.Data()) != true) { // found
runName = tmpStr;
return;
}
runName = tmpStr;
// test if the file exists with only upper-case letters
tmpStr = runName + TString(".") + tmpExt;
tmpStr.ToUpper();
if (gSystem->AccessPathName(tmpStr.Data()) != true) { // found
runName = tmpStr;
return;
}
// test if the file exists with only lower-case letters
tmpStr.ToLower();
if (gSystem->AccessPathName(tmpStr.Data()) != true) { // found
runName = tmpStr;
return;
}
tmpStr = runName;
// the extension is already part of the file name, therefore, do not append it
if (runName.EndsWith(ext.Data(), TString::kIgnoreCase)) {
if (gSystem->AccessPathName(runName.Data()) != true) { // found
if (tmpStr.EndsWith(ext.Data(), TString::kIgnoreCase)) {
if (gSystem->AccessPathName(tmpStr.Data()) != true) { // found
runName = tmpStr;
return;
}
// assume some extension is part of the given file name but the real data file ends with an lower-case extension
tmpExt.ToLower();
runName = runName.Replace(static_cast<Ssiz_t>(runName.Length()-tmpExt.Length()), tmpExt.Length(), tmpExt);
if (gSystem->AccessPathName(runName.Data()) != true) { // found
tmpStr = tmpStr.Replace(static_cast<Ssiz_t>(tmpStr.Length()-tmpExt.Length()), tmpExt.Length(), tmpExt);
if (gSystem->AccessPathName(tmpStr.Data()) != true) { // found
runName = tmpStr;
return;
}
// assume some extension is part of the given file name but the real data file ends with an upper-case extension
tmpExt.ToUpper();
runName = runName.Replace(static_cast<Ssiz_t>(runName.Length()-tmpExt.Length()), tmpExt.Length(), tmpExt);
if (gSystem->AccessPathName(runName.Data()) != true) { // found
tmpStr = runName;
tmpStr = tmpStr.Replace(static_cast<Ssiz_t>(tmpStr.Length()-tmpExt.Length()), tmpExt.Length(), tmpExt);
if (gSystem->AccessPathName(tmpStr.Data()) != true) { // found
runName = tmpStr;
return;
}
// test if the file exists with only lower-case letters and the extension already included in the file name
runName.ToLower();
if (gSystem->AccessPathName(runName.Data()) != true) { // found
tmpStr = runName;
tmpStr.ToLower();
if (gSystem->AccessPathName(tmpStr.Data()) != true) { // found
runName = tmpStr;
return;
}
// test if the file exists with only upper-case letters and the extension already included in the file name
runName.ToUpper();
if (gSystem->AccessPathName(runName.Data()) != true) { // found
tmpStr = runName;
tmpStr.ToUpper();
if (gSystem->AccessPathName(tmpStr.Data()) != true) { // found
runName = tmpStr;
return;
}
}
// if the file has not been found, set the run name to be empty
runName = "";
return;
}
@ -1043,6 +1060,8 @@ Bool_t PRunDataHandler::ReadRootFile(UInt_t tag)
runData.SetLaboratory("PSI");
runData.SetBeamline("muE4");
runData.SetInstrument("LEM");
runData.SetMuonSource("low energy muon source");
runData.SetMuonSpecies("positive muons");
// get run title
TObjString ostr = runHeader->GetRunTitle();
@ -1072,36 +1091,14 @@ Bool_t PRunDataHandler::ReadRootFile(UInt_t tag)
time_t idt = (time_t)runHeader->GetStartTime();
runData.SetStartDateTime(idt);
struct tm *dt = localtime(&idt);
TString stime("");
Int_t yy = dt->tm_year;
if (yy > 100)
yy -= 100;
if (yy < 10)
stime += "0";
stime += yy;
stime += "-";
stime += GetMonth(dt->tm_mon);
stime += "-";
if (dt->tm_mday < 10)
stime += "0";
stime += dt->tm_mday;
char str[128];
strftime(str, sizeof(str), "%F", dt);
TString stime(str);
runData.SetStartDate(stime);
// start time
if (dt->tm_hour == 0)
stime = "00";
else if (dt->tm_hour < 10)
stime = "0";
else
stime = "";
stime += dt->tm_hour;
stime += ":";
if (dt->tm_min < 10)
stime += "0";
stime += dt->tm_min;
stime += ":";
if (dt->tm_sec < 10)
stime += "0";
stime += dt->tm_sec;
memset(str, 0, sizeof(str));
strftime(str, sizeof(str), "%T", dt);
stime = str;
runData.SetStartTime(stime);
// get stop time/date
@ -1109,43 +1106,21 @@ Bool_t PRunDataHandler::ReadRootFile(UInt_t tag)
idt = (time_t)runHeader->GetStopTime();
runData.SetStopDateTime(idt);
dt = localtime(&idt);
stime = "";
yy = dt->tm_year;
if (yy > 100)
yy -= 100;
if (yy < 10)
stime += "0";
stime += yy;
stime += "-";
stime += GetMonth(dt->tm_mon);
stime += "-";
if (dt->tm_mday < 10)
stime += "0";
stime += dt->tm_mday;
memset(str, 0, sizeof(str));
strftime(str, sizeof(str), "%F", dt);
stime = str;
runData.SetStopDate(stime);
// stop time
if (dt->tm_hour == 0)
stime = "00";
else if (dt->tm_hour < 10)
stime = "0";
else
stime = "";
stime += dt->tm_hour;
stime += ":";
if (dt->tm_min < 10)
stime += "0";
stime += dt->tm_min;
stime += ":";
if (dt->tm_sec < 10)
stime += "0";
stime += dt->tm_sec;
memset(str, 0, sizeof(str));
strftime(str, sizeof(str), "%T", dt);
stime = str;
runData.SetStopTime(stime);
// get time resolution
runData.SetTimeResolution(runHeader->GetTimeResolution());
// get number of histogramms
Int_t noOfHistos = runHeader->GetNHist();
Int_t noOfHistos = runHeader->GetNHist();
// get t0's
Double_t *t0 = runHeader->GetTimeZero();
@ -1155,6 +1130,11 @@ Bool_t PRunDataHandler::ReadRootFile(UInt_t tag)
for (Int_t i=0; i<noOfHistos; i++) {
runData.AppendT0((Int_t)t0[i]);
}
if (tag == ROOT_ALL) { // since NPP and PPC the t0's needs to be doubled
for (Int_t i=0; i<noOfHistos; i++) {
runData.AppendT0((Int_t)t0[i]);
}
}
}
// read run summary to obtain ring anode HV values
@ -1513,6 +1493,26 @@ Bool_t PRunDataHandler::ReadNexusFile()
}
// get header information
// get/set laboratory
str = TString(nxs_file->GetEntryIdf2()->GetInstrument()->GetSource()->GetName());
runData.SetLaboratory(str);
// get/set beamline
str = TString(nxs_file->GetEntryIdf2()->GetInstrument()->GetName());
runData.SetBeamline(str);
// get/set instrument
str = TString(nxs_file->GetEntryIdf2()->GetInstrument()->GetName());
runData.SetInstrument(str);
// get/set muon source
str = TString(nxs_file->GetEntryIdf2()->GetInstrument()->GetSource()->GetType());
runData.SetMuonSource(str);
// get/set muon species
str = TString(nxs_file->GetEntryIdf2()->GetInstrument()->GetSource()->GetProbe());
runData.SetMuonSpecies(str);
// get/set run title
str = TString(nxs_file->GetEntryIdf2()->GetTitle());
runData.SetRunTitle(str);
@ -1588,7 +1588,7 @@ Bool_t PRunDataHandler::ReadNexusFile()
int *lgb = nxs_file->GetEntryIdf2()->GetInstrument()->GetDetector()->GetLastGoodBins();
PIntPair goodDataBin;
if (nxs_file->GetEntryIdf2()->GetInstrument()->GetDetector()->GetT0Tag() == 2) { // t0, fgb, lgb: [][]
if (nxs_file->GetEntryIdf2()->GetInstrument()->GetDetector()->GetT0Tag() == 3) { // t0, fgb, lgb: [][]
for (int i=0; i<nxs_file->GetEntryIdf2()->GetInstrument()->GetDetector()->GetNoOfPeriods(); i++) {
for (int j=0; j<nxs_file->GetEntryIdf2()->GetInstrument()->GetDetector()->GetNoOfSpectra(); j++) {
if (fgb && lgb) {
@ -1601,6 +1601,17 @@ Bool_t PRunDataHandler::ReadNexusFile()
}
}
}
} else if (nxs_file->GetEntryIdf2()->GetInstrument()->GetDetector()->GetT0Tag() == 2) { // t0, fgb, lgb: []
for (int i=0; i<nxs_file->GetEntryIdf2()->GetInstrument()->GetDetector()->GetNoOfSpectra(); i++) {
if (fgb && lgb) {
goodDataBin.first = *(fgb+i);
goodDataBin.second = *(lgb+i);
}
runData.AppendT0(*(t0+i));
if (fgb && lgb) {
runData.AppendGoodDataBin(goodDataBin);
}
}
} else { // t0, fgb, lgb: single numbers
if (fgb && lgb) {
goodDataBin.first = *fgb;
@ -2011,27 +2022,42 @@ Bool_t PRunDataHandler::ReadPsiBinFile()
// filter from the file name the instrument
TString instrument("n/a"), beamline("n/a");
TString muonSource("n/a"), muonSpecies("n/a");
if (fRunPathName.Contains("_gps_", TString::kIgnoreCase)) {
instrument = "GPS";
beamline = "piM3.2";
muonSource = "continuous surface muon source";
muonSpecies = "positive muons";
} else if (fRunPathName.Contains("_ltf_", TString::kIgnoreCase)) {
instrument = "LTF";
beamline = "piM3.3";
muonSource = "continuous surface muon source";
muonSpecies = "positive muons";
} else if (fRunPathName.Contains("_gpd_", TString::kIgnoreCase)) {
instrument = "GPD";
beamline = "muE1";
muonSource = "continuous decay channel muon source";
muonSpecies = "positive muons";
} else if (fRunPathName.Contains("_dolly_", TString::kIgnoreCase)) {
instrument = "DOLLY";
beamline = "piE1";
muonSource = "continuous surface muon source";
muonSpecies = "positive muons";
} else if (fRunPathName.Contains("_alc_", TString::kIgnoreCase)) {
instrument = "ALC";
beamline = "piE3";
muonSource = "continuous surface muon source";
muonSpecies = "positive muons";
} else if (fRunPathName.Contains("_hifi_", TString::kIgnoreCase)) {
instrument = "HIFI";
beamline = "piE3";
muonSource = "continuous surface muon source";
muonSpecies = "positive muons";
}
runData.SetInstrument(instrument);
runData.SetBeamline(beamline);
runData.SetMuonSource(muonSource);
runData.SetMuonSpecies(muonSpecies);
// keep run name
runData.SetRunName(fRunName);
@ -2091,7 +2117,13 @@ Bool_t PRunDataHandler::ReadPsiBinFile()
if (sDateTime.size() < 2) {
cerr << endl << ">> **WARNING** psi-bin file: couldn't obtain run start date/time" << endl;
}
runData.SetStartDate(sDateTime[0]);
string date("");
if (DateToISO8601(sDateTime[0], date)) {
runData.SetStartDate(date);
} else {
cerr << endl << ">> **WARNING** failed to convert start date: " << sDateTime[0] << " into ISO 8601 date." << endl;
runData.SetStartDate(sDateTime[0]);
}
runData.SetStartTime(sDateTime[1]);
sDateTime.clear();
@ -2099,7 +2131,13 @@ Bool_t PRunDataHandler::ReadPsiBinFile()
if (sDateTime.size() < 2) {
cerr << endl << ">> **WARNING** psi-bin file: couldn't obtain run stop date/time" << endl;
}
runData.SetStopDate(sDateTime[0]);
date = string("");
if (DateToISO8601(sDateTime[0], date)) {
runData.SetStopDate(date);
} else {
cerr << endl << ">> **WARNING** failed to convert stop date: " << sDateTime[0] << " into ISO 8601 date." << endl;
runData.SetStopDate(sDateTime[0]);
}
runData.SetStopTime(sDateTime[1]);
sDateTime.clear();
@ -2209,41 +2247,20 @@ Bool_t PRunDataHandler::ReadMudFile()
time_t tval;
struct tm *dt;
TString stime("");
Int_t yy = 0;
success = MUD_getTimeBegin( fh, (UINT32*)&tval );
if (success) {
runData.SetStartDateTime((const time_t)tval);
dt = localtime((const time_t*)&tval);
assert(dt);
yy = dt->tm_year;
if (yy > 100)
yy -= 100;
if (yy < 10)
stime += "0";
stime += yy;
stime += "-";
stime += GetMonth(dt->tm_mon);
stime += "-";
if (dt->tm_mday < 10)
stime += "0";
stime += dt->tm_mday;
// start date
strftime(str, sizeof(str), "%F", dt);
stime = str;
runData.SetStartDate(stime);
// start time
if (dt->tm_hour == 0)
stime = "00";
else if (dt->tm_hour < 10)
stime = "0";
else
stime = "";
stime += dt->tm_hour;
stime += ":";
if (dt->tm_min < 10)
stime += "0";
stime += dt->tm_min;
stime += ":";
if (dt->tm_sec < 10)
stime += "0";
stime += dt->tm_sec;
memset(str, 0, sizeof(str));
strftime(str, sizeof(str), "%T", dt);
stime = str;
runData.SetStartTime(stime);
}
@ -2253,36 +2270,15 @@ Bool_t PRunDataHandler::ReadMudFile()
runData.SetStopDateTime((const time_t)tval);
dt = localtime((const time_t*)&tval);
assert(dt);
stime = "";
yy = dt->tm_year;
if (yy > 100)
yy -= 100;
if (yy < 10)
stime += "0";
stime += yy;
stime += "-";
stime += GetMonth(dt->tm_mon);
stime += "-";
if (dt->tm_mday < 10)
stime += "0";
stime += dt->tm_mday;
// stop date
strftime(str, sizeof(str), "%F", dt);
stime = str;
runData.SetStopDate(stime);
// stop time
if (dt->tm_hour == 0)
stime = "00";
else if (dt->tm_hour < 10)
stime = "0";
else
stime = "";
stime += dt->tm_hour;
stime += ":";
if (dt->tm_min < 10)
stime += "0";
stime += dt->tm_min;
stime += ":";
if (dt->tm_sec < 10)
stime += "0";
stime += dt->tm_sec;
memset(str, 0, sizeof(str));
strftime(str, sizeof(str), "%T", dt);
stime = str;
runData.SetStopTime(stime);
}
@ -3687,8 +3683,6 @@ Bool_t PRunDataHandler::WriteNexusFile(TString fln)
{
#ifdef PNEXUS_ENABLED
int *t0=0, *fgb=0, *lgb=0, *histo=0;
// generate output file name
if (fln.Length() == 0) {
Bool_t ok = false;
@ -3725,7 +3719,7 @@ Bool_t PRunDataHandler::WriteNexusFile(TString fln)
tm = localtime(&now);
string str("");
char cstr[128];
sprintf(cstr, "%04d-%02d-%02d %02d:%02d:%02d", 1900+tm->tm_year, tm->tm_mon, tm->tm_mday, tm->tm_hour, tm->tm_hour, tm->tm_sec);
strftime(cstr, sizeof(cstr), "%FT%T", tm);
str = string(cstr);
nxs->SetFileTime(str);
@ -3739,9 +3733,9 @@ Bool_t PRunDataHandler::WriteNexusFile(TString fln)
nxs->GetEntryIdf1()->SetLaboratory(fData[0].GetLaboratory()->Data());
if (*fData[0].GetBeamline() != "n/a")
nxs->GetEntryIdf1()->SetBeamline(fData[0].GetBeamline()->Data());
str = string(fData[0].GetStartDate()->Data()) + string(" ") + string(fData[0].GetStartTime()->Data());
str = string(fData[0].GetStartDate()->Data()) + string("T") + string(fData[0].GetStartTime()->Data());
nxs->GetEntryIdf1()->SetStartTime(str);
str = string(fData[0].GetStopDate()->Data()) + string(" ") + string(fData[0].GetStopTime()->Data());
str = string(fData[0].GetStopDate()->Data()) + string("T") + string(fData[0].GetStopTime()->Data());
nxs->GetEntryIdf1()->SetStopTime(str);
nxs->GetEntryIdf1()->SetSwitchingState(1);
nxs->GetEntryIdf1()->GetUser()->SetName("n/a");
@ -3749,13 +3743,23 @@ Bool_t PRunDataHandler::WriteNexusFile(TString fln)
nxs->GetEntryIdf1()->GetSample()->SetName(fData[0].GetSample()->Data());
nxs->GetEntryIdf1()->GetSample()->SetPhysProp("temperature", fData[0].GetTemperature(0), "Kelvin");
nxs->GetEntryIdf1()->GetSample()->SetPhysProp("magnetic_field", fData[0].GetField(), "Gauss");
nxs->GetEntryIdf1()->GetSample()->SetEnvironment("n/a");
nxs->GetEntryIdf1()->GetSample()->SetEnvironment(fData[0].GetSetup()->Data());
nxs->GetEntryIdf1()->GetSample()->SetShape("n/a");
nxs->GetEntryIdf1()->GetSample()->SetMagneticFieldVectorAvailable(0);
if (*fData[0].GetInstrument() != "n/a")
nxs->GetEntryIdf1()->GetInstrument()->SetName(fData[0].GetInstrument()->Data());
nxs->GetEntryIdf1()->GetInstrument()->GetDetector()->SetNumber(fData[0].GetNoOfHistos());
nxs->GetEntryIdf1()->GetInstrument()->GetCollimator()->SetType("n/a");
// calculate the total number of counts
int total_counts = 0;
for (unsigned int i=0; i<fData[0].GetNoOfHistos(); i++) {
for (unsigned int j=0; j<fData[0].GetDataBin(i)->size(); j++)
total_counts += fData[0].GetDataBin(i)->at(j);
}
double total_counts_mev = (double) total_counts / 1.0e6;
nxs->GetEntryIdf1()->GetInstrument()->GetBeam()->SetTotalCounts(total_counts_mev);
nxs->GetEntryIdf1()->GetInstrument()->GetBeam()->SetUnits("Mev");
nxs->GetEntryIdf1()->GetData()->SetTimeResolution(fData[0].GetTimeResolution(), "ns");
// t0
@ -3792,60 +3796,149 @@ Bool_t PRunDataHandler::WriteNexusFile(TString fln)
tm = localtime(&now);
string str("");
char cstr[128];
sprintf(cstr, "%04d-%02d-%02d %02d:%02d:%02d", 1900+tm->tm_year, tm->tm_mon, tm->tm_mday, tm->tm_hour, tm->tm_hour, tm->tm_sec);
strftime(cstr, sizeof(cstr), "%FT%T", tm);
str = string(cstr);
nxs->SetFileTime(str);
nxs->SetCreator("PSI - any2many");
// NXroot info
nxs->SetCreator("PSI: any2many");
nxs->GetEntryIdf2()->SetDefinition("pulsedTD");
// NXentry info
nxs->GetEntryIdf2()->SetDefinition("muonTD");
nxs->GetEntryIdf2()->SetProgramName("any2many");
nxs->GetEntryIdf2()->SetProgramVersion("$Id$");
nxs->GetEntryIdf2()->SetRunNumber(fData[0].GetRunNumber());
nxs->GetEntryIdf2()->SetTitle(fData[0].GetRunTitle()->Data());
str = string(fData[0].GetStartDate()->Data()) + string(" ") + string(fData[0].GetStartTime()->Data());
str = string(fData[0].GetStartDate()->Data()) + string("T") + string(fData[0].GetStartTime()->Data());
nxs->GetEntryIdf2()->SetStartTime(str);
str = string(fData[0].GetStopDate()->Data()) + string(" ") + string(fData[0].GetStopTime()->Data());
str = string(fData[0].GetStopDate()->Data()) + string("T") + string(fData[0].GetStopTime()->Data());
nxs->GetEntryIdf2()->SetStopTime(str);
nxs->GetEntryIdf2()->SetExperimentIdentifier("n/a");
// NXuser info
nxs->GetEntryIdf2()->GetUser()->SetName("n/a");
// NXsample info
nxs->GetEntryIdf2()->GetSample()->SetName(fData[0].GetSample()->Data());
nxs->GetEntryIdf2()->GetSample()->SetDescription("n/a");
nxs->GetEntryIdf2()->GetSample()->SetPhysProp("temperature_1", fData[0].GetTemperature(0), "Kelvin");
nxs->GetEntryIdf2()->GetSample()->SetPhysProp("magnetic_field_1", fData[0].GetField(), "Gauss");
nxs->GetEntryIdf2()->GetSample()->SetEnvironmentTemp("n/a");
nxs->GetEntryIdf2()->GetSample()->SetEnvironmentTemp(fData[0].GetSetup()->Data());
nxs->GetEntryIdf2()->GetSample()->SetEnvironmentField("n/a");
// here would be the information for NXinstrument. Currently there are not enough information to feed this
// here would be the information for NXinstrument. Currently there are not much information to feed this
nxs->GetEntryIdf2()->GetInstrument()->SetName(fData[0].GetInstrument()->Data());
nxs->GetEntryIdf2()->GetInstrument()->GetDetector()->SetDescription("n/a");
nxs->GetEntryIdf2()->GetInstrument()->GetDetector()->SetNoOfPeriods(1); // currently red/green is not distinguished
// NXinstrument/NXsource
nxs->GetEntryIdf2()->GetInstrument()->GetSource()->SetName(fData[0].GetLaboratory()->Data());
nxs->GetEntryIdf2()->GetInstrument()->GetSource()->SetType(fData[0].GetMuonSource()->Data());
nxs->GetEntryIdf2()->GetInstrument()->GetSource()->SetProbe(fData[0].GetMuonSpecies()->Data());
// NXinstrument/NXbeamline
nxs->GetEntryIdf2()->GetInstrument()->GetBeamline()->SetName(fData[0].GetBeamline()->Data());
// NXinstrument/NXdetector
nxs->GetEntryIdf2()->GetInstrument()->GetDetector()->SetDescription(fData[0].GetInstrument()->Data()); // assume that this should be the instrument name
nxs->GetEntryIdf2()->GetInstrument()->GetDetector()->SetNoOfPeriods(0); // currently red/green is not distinguished
nxs->GetEntryIdf2()->GetInstrument()->GetDetector()->SetNoOfSpectra(fData[0].GetNoOfHistos());
nxs->GetEntryIdf2()->GetInstrument()->GetDetector()->SetNoOfBins(fData[0].GetDataBin(0)->size());
nxs->GetEntryIdf2()->GetInstrument()->GetDetector()->SetTimeResolution(fData[0].GetTimeResolution(), "ns");
histo = new int[fData[0].GetNoOfHistos()*fData[0].GetDataBin(0)->size()];
int *histo = new int[fData[0].GetNoOfHistos()*fData[0].GetDataBin(0)->size()];
for (int i=0; i<nxs->GetEntryIdf2()->GetInstrument()->GetDetector()->GetNoOfSpectra(); i++) {
for (unsigned int j=0; j<fData[0].GetDataBin(0)->size(); j++) {
*(histo+i*fData[0].GetDataBin(0)->size()+j) = (int) fData[0].GetDataBin(i)->at(j);
}
}
nxs->GetEntryIdf2()->GetInstrument()->GetDetector()->SetHistos(histo);
// clean up
if (histo) {
delete [] histo;
histo = 0;
}
// handle spectrum index
for (int i=0; i<nxs->GetEntryIdf2()->GetInstrument()->GetDetector()->GetNoOfSpectra(); i++)
nxs->GetEntryIdf2()->GetInstrument()->GetDetector()->SetSpectrumIndex(i+1);
nxs->GetEntryIdf2()->GetInstrument()->GetDetector()->SetT0Tag(2);
int *t0 = new int[fData[0].GetT0Size()];
// handle histogram resolution
nxs->GetEntryIdf2()->GetInstrument()->GetDetector()->SetTimeResolution(fData[0].GetTimeResolution(), "ns");
// handle raw time
vector<double> raw_time;
for (unsigned int i=0; i<fData[0].GetDataBin(0)->size(); i++) {
raw_time.push_back((double)i * fData[0].GetTimeResolution() * 1.0e-3); // since time resolution is given in ns, the factor 1.0e-3 is needed to convert to us
}
nxs->GetEntryIdf2()->GetInstrument()->GetDetector()->SetRawTime(raw_time);
nxs->GetEntryIdf2()->GetInstrument()->GetDetector()->SetRawTimeUnit("micro.second");
nxs->GetEntryIdf2()->GetInstrument()->GetDetector()->SetRawTimeName("time");
raw_time.clear();
// handle t0
nxs->GetEntryIdf2()->GetInstrument()->GetDetector()->SetT0Tag(2); // i.e. t0[#histo] format
int *t0 = new int[fData[0].GetNoOfHistos()];
for (unsigned int i=0; i<fData[0].GetNoOfHistos(); i++) {
if (i<fData[0].GetT0Size())
*(t0+i) = fData[0].GetT0(i);
else
*(t0+i) = fData[0].GetT0(0);
if (fData[0].GetT0Size() == 0) { // NO t0's present, hence take the estimated ones
if (i == 0) { // place a warning in case NO t0's were present
cerr << endl << ">> **WARNING** NO t0's are present in the original file, will use the estimated once, no waranty this is correct!!" << endl;
}
if (i<fData[0].GetT0Size())
t0[i] = fData[0].GetT0Estimated(i);
else
t0[i] = fData[0].GetT0Estimated(0);
} else { // t0's are given
if (i<fData[0].GetT0Size())
t0[i] = fData[0].GetT0(i);
else
t0[i] = fData[0].GetT0(0);
}
}
nxs->GetEntryIdf2()->GetInstrument()->GetDetector()->SetT0(t0);
// first_good_bin - still missing
// last_good_bin - still missing
// handle first_good_bin
int *fgb = new int[fData[0].GetNoOfHistos()];
for (unsigned int i=0; i<fData[0].GetNoOfHistos(); i++) {
if (fData[0].GetGoodDataBinSize() == 0) { // first good bin NOT present, hence fgb = t0 + 10ns
fgb[i] = t0[i] + (int)(10.0/fData[0].GetTimeResolution()); // t0 + 10ns
} else { // first good bin present
if (i < fData[0].GetGoodDataBinSize())
fgb[i] = fData[0].GetGoodDataBin(i).first;
else
fgb[i] = fData[0].GetGoodDataBin(0).first;
}
}
nxs->GetEntryIdf2()->GetInstrument()->GetDetector()->SetFirstGoodBin(fgb);
// clean up
if (fgb) {
delete [] fgb;
fgb = 0;
}
// handle last_good_bin
int *lgb = new int[fData[0].GetNoOfHistos()];
for (unsigned int i=0; i<fData[0].GetNoOfHistos(); i++) {
if (fData[0].GetGoodDataBinSize() == 0) { // last good bin NOT present, hence lgb = length of histo - 1
lgb[i] = fData[0].GetDataBin(i)->size() - 1;
} else { // first good bin present
if (i < fData[0].GetGoodDataBinSize())
lgb[i] = fData[0].GetGoodDataBin(i).second;
else
lgb[i] = fData[0].GetGoodDataBin(0).second;
}
}
nxs->GetEntryIdf2()->GetInstrument()->GetDetector()->SetLastGoodBin(lgb);
// clean up
if (lgb) {
delete [] lgb;
lgb = 0;
}
// clean up
if (t0) {
delete [] t0;
t0 = 0;
}
} else {
// clean up
if (nxs != 0) {
@ -3877,23 +3970,6 @@ Bool_t PRunDataHandler::WriteNexusFile(TString fln)
// write file
nxs->WriteFile(fln, fileType, fAny2ManyInfo->idf);
// clean up
if (t0) {
delete [] t0;
t0 = 0;
}
if (fgb) {
delete [] fgb;
fgb = 0;
}
if (lgb) {
delete [] lgb;
lgb = 0;
}
if (histo) {
delete [] histo;
histo = 0;
}
if (nxs != 0) {
delete nxs;
nxs = 0;
@ -4915,49 +4991,32 @@ TString PRunDataHandler::FileNameFromTemplate(TString &fileNameTemplate, Int_t r
}
//--------------------------------------------------------------------------
// GetMonth (private)
// DateToISO8601 (private)
//--------------------------------------------------------------------------
/**
* <p>Spits out the month as MMM for a given numerical month 0..11
* <p>If possible converts a inDate, into a ISO8601 standard date.
*
* <b>return:</b>
* - constructed file name from template, run number, and year
* - empty string
* <p><b>return:</b> true if conversion was successfull otherwise false.
*
* \param template template string
* \param inDate input date which should be converted to an ISO 8601 date.
* \param iso8601Date on success the converted iso8601Date, otherwise an empty string
*/
TString PRunDataHandler::GetMonth(Int_t month)
bool PRunDataHandler::DateToISO8601(string inDate, string &iso8601Date)
{
TString mm("");
iso8601Date = string("");
if (month == 0)
mm = "JAN";
else if (month == 1)
mm = "FEB";
else if (month == 2)
mm = "MAR";
else if (month == 3)
mm = "APR";
else if (month == 4)
mm = "MAY";
else if (month == 5)
mm = "JUN";
else if (month == 6)
mm = "JUL";
else if (month == 7)
mm = "AUG";
else if (month == 8)
mm = "SEP";
else if (month == 9)
mm = "OCT";
else if (month == 10)
mm = "NOV";
else if (month == 11)
mm = "DEC";
else
mm = "???";
struct tm tm;
return mm;
// currently only dates like dd-mmm-yy are handled, where dd day of the month, mmm month as abbrivation, e.g. JAN, and yy as the year
if (!strptime(inDate.c_str(), "%d-%b-%y", &tm)) // failed
return false;
TString str("");
str.Form("%04d-%02d-%02d", 1900+tm.tm_year, tm.tm_mon, tm.tm_mday);
iso8601Date = str.Data();
return true;
}
//--------------------------------------------------------------------------

702
src/external/nexus/PNeXus.cpp vendored
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File diff suppressed because it is too large Load Diff

13
src/external/nexus/PNeXus.h vendored
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@ -386,6 +386,9 @@ class PNeXusDetector2 {
virtual string GetDescription() { return fDescription; }
virtual double GetTimeResolution(string units);
virtual vector<double> *GetRawTime() { return &fRawTime; }
virtual string GetRawTimeName() { return fRawTimeName; }
virtual string GetRawTimeUnit() { return fRawTimeUnit; }
virtual bool IsT0Present() { return (fT0 == 0) ? false : true; }
virtual int GetT0Tag() { return fT0Tag; }
virtual int GetT0(int idxp=-1, int idxs=-1);
@ -393,7 +396,7 @@ class PNeXusDetector2 {
virtual bool IsFirstGoodBinPresent() { return (fFirstGoodBin == 0) ? false : true; }
virtual int GetFirstGoodBin(int idxp=-1, int idxs=-1);
virtual int* GetFirstGoodBins() { return fFirstGoodBin; }
virtual bool IsLastGoodBinPresent() { return (fFirstGoodBin == 0) ? false : true; }
virtual bool IsLastGoodBinPresent() { return (fLastGoodBin == 0) ? false : true; }
virtual int GetLastGoodBin(int idxp=-1, int idxs=-1);
virtual int* GetLastGoodBins() { return fLastGoodBin; }
virtual int GetNoOfPeriods() { return fNoOfPeriods; }
@ -407,6 +410,9 @@ class PNeXusDetector2 {
virtual void SetDescription(string description) { fDescription = description; }
virtual void SetTimeResolution(double val, string units);
virtual void SetRawTime(vector<double> &rawTime);
virtual void SetRawTimeName(string rawTimeName) { fRawTimeName = rawTimeName; }
virtual void SetRawTimeUnit(string rawTimeUnit) { fRawTimeUnit = rawTimeUnit; }
virtual void SetT0Tag(int tag) { fT0Tag = tag; }
virtual int SetT0(int *t0);
virtual int SetFirstGoodBin(int *fgb);
@ -423,12 +429,15 @@ class PNeXusDetector2 {
string fDescription; ///< description of the detector
double fTimeResolution; ///< keeps the time resolution in (ps)
vector<int> fSpectrumIndex; ///< list of global spectra
vector<double> fRawTime; ///< keeps a raw time vector
string fRawTimeName; ///< name of the raw time vector
string fRawTimeUnit; ///< unit of the raw time vector
int fNoOfPeriods; ///< number of periods or -1 if not defined
int fNoOfSpectra; ///< number of spectra or -1 if not defined
int fNoOfBins; ///< number of bins of a spectrum or -1 if not defined
int fT0Tag; ///< tag for t0, fgb, lgb structure. -1==not present, 1==NX_INT, 2=NX_INT[np][ns]
int fT0Tag; ///< tag for t0, fgb, lgb structure. -1==not present, 1==NX_INT, 2==NX_INT[ns], 3==NX_INT[np][ns]
int *fT0;
int *fFirstGoodBin;
int *fLastGoodBin;

7
src/include/PMusr.h
View File

@ -279,6 +279,8 @@ class PRawRunData {
virtual const TString* GetBeamline() { return &fBeamline; }
virtual const TString* GetInstrument() { return &fInstrument; }
virtual const TString* GetRunName() { return &fRunName; }
virtual const TString* GetMuonSource() { return &fMuonSource; }
virtual const TString* GetMuonSpecies() { return &fMuonSpecies; }
virtual const Int_t GetRunNumber() { return fRunNumber; }
virtual const TString* GetRunTitle() { return &fRunTitle; }
virtual const TString* GetSetup() { return &fSetup; }
@ -305,6 +307,7 @@ class PRawRunData {
virtual const UInt_t GetT0EstimatedSize() { return fT0Estimated.size(); }
virtual const Int_t GetT0Estimated(const UInt_t idx);
virtual const PIntPair GetBkgBin(const UInt_t idx);
virtual const UInt_t GetGoodDataBinSize() { return fGoodDataBin.size(); }
virtual const PIntPair GetGoodDataBin(const UInt_t idx);
virtual const UInt_t GetNoOfHistos() { return fDataBin.size(); }
virtual const PDoubleVector* GetDataBin(const UInt_t idx);
@ -313,6 +316,8 @@ class PRawRunData {
virtual void SetLaboratory(const TString &str) { fLaboratory = str; }
virtual void SetBeamline(const TString &str) { fBeamline = str; }
virtual void SetInstrument(const TString &str) { fInstrument = str; }
virtual void SetMuonSource(const TString &str) { fMuonSource = str; }
virtual void SetMuonSpecies(const TString &str) { fMuonSpecies = str; }
virtual void SetRunName(const TString &str) { fRunName = str; }
virtual void SetRunNumber(const Int_t &val) { fRunNumber = val; }
virtual void SetRunTitle(const TString str) { fRunTitle = str; }
@ -347,6 +352,8 @@ class PRawRunData {
TString fLaboratory; ///< keeps the name of the laboratory, e.g. PSI, ISIS, TRIUMF, JPARC
TString fBeamline; ///< keeps the name of the be beamline, e.g. muE4, piM3.1, ...
TString fInstrument; ///< keeps the name of the instrument, e.g. LEM, GPS, MUSR, EMU, ...
TString fMuonSource; ///< keeps the type of muon source, e.g. continous surface beam, pulsed beam, low energy muon beam
TString fMuonSpecies; ///< positive muon or negative muon
TString fRunName; ///< name of the run
Int_t fRunNumber; ///< run number
TString fRunTitle; ///< run title

2
src/include/PRunDataHandler.h
View File

@ -95,7 +95,7 @@ class PRunDataHandler
virtual TString GetFileName(const TString extension, Bool_t &ok);
virtual TString FileNameFromTemplate(TString &fileNameTemplate, Int_t run, TString &year, Bool_t &ok);
virtual TString GetMonth(Int_t month);
virtual bool DateToISO8601(string inDate, string &iso8601Date);
virtual void SplitTimeDate(TString timeDate, TString &time, TString &date, Bool_t &ok);
};

74
src/nexus_dump.cpp Normal file
View File

@ -0,0 +1,74 @@
/***************************************************************************
nexus_read_test.cpp
Author: Andreas Suter
e-mail: andreas.suter@psi.ch
$Id: nexus_read_test.cpp 4981 2011-08-23 17:22:29Z nemu $
***************************************************************************/
/***************************************************************************
* Copyright (C) 2007-2011 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 <cstdio>
#include <cstdlib>
#include <cstring>
#include <iostream>
#include <string>
#include <vector>
using namespace std;
#include "PNeXus.h"
//---------------------------------------------------------------------------------------
void nexus_read_test_syntax()
{
cout << endl << ">>---------------------------------------------------------------------------------------";
cout << endl << ">> usage: nexus_dump <nexus-in-filename>";
cout << endl << ">> This will try to read a nexus-files <nexus-in-filename> and send the relevant";
cout << endl << ">> information to the standard output.";
cout << endl << ">>---------------------------------------------------------------------------------------";
cout << endl << endl;
}
//---------------------------------------------------------------------------------------
int main(int argc, char *argv[])
{
if (argc !=2) {
nexus_read_test_syntax();
return -1;
}
PNeXus *nxs_file = new PNeXus(argv[1]);
if (nxs_file->IsValid(false)) {
nxs_file->Dump();
}
if (nxs_file)
delete nxs_file;
return 0;
}

6
src/tests/nexus/Makefile
View File

@ -6,12 +6,12 @@ NEXUS_CLASS_DIR = ../../external/nexus
CXX = g++
CXXFLAGS = -g -Wall -fPIC
INCLUDES = -I /usr/local/include -I $(NEXUS_CLASS_DIR)
INCLUDES = -I /opt/nexus/include -I $(NEXUS_CLASS_DIR)
LD = g++
LDFLAGS = -g
LIBS = -L /usr/local/lib -lNeXus
LIBS += -L /usr/lib -lhdf5
LIBS = -L /opt/nexus/lib -lNeXus
LIBS += -L /opt/hdf/lib -lhdf5
EXEC = nexus_read_test

2
src/tests/nexus/nexus_read_test.cpp
View File

@ -67,7 +67,7 @@ int main(int argc, char *argv[])
PNeXus *nxs_file = new PNeXus(argv[1]);
if (nxs_file->IsValid(true)) {
if (nxs_file->IsValid(false)) {
nxs_file->Dump();
if (argc == 5) {