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more work towards NeXus exchange

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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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4
ChangeLog
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@ -6,6 +6,8 @@
changes since 0.9.0
===================================
NEW 2011-12-22 added nexus_dump. It is used to dump nexus files in an ascii
form. For instance it can be used to read header info.
NEW if the background is estimated form an interval rather than fitted, it will be added as a comment
to the background interval tag. (MUSR-192).
NEW forward/backward accept now not only c0 c1 c2 ... cn, but also c0-cn cm-cp, or c0 c1-cn cm cx-cy, etc. (MUSR-201, improvement whish).
@ -19,7 +21,7 @@ NEW the chi^2 calculation in single-histogram and asymmetry fits is parallelized
if musrfit is built using a compiler supporting OpenMP (e.g. GCC >= 4.2)
Using --disable-omp this feature can be disabled on the configure level.
NEW any2many: force the user to define the exact NeXus ouput format (HDF4,HDF5,XML)
FIXED 2011-12-15 some more work towards a proper NeXus muon data format support.
FIXED 2011-12-22 some more work towards a proper NeXus muon data format support.
FIXED proper phase correction for Re/Im Fourier transform (MUSR-206)
FIXED when release or restore is called (command block commands), the
corresponding parameter error is set to 2% of its parameter value (MUSR-188).

BIN
doc/examples/data/EMU00005989_v2.nxs Normal file
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doc/examples/data/emu00005989_v2.nxs
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2
doc/examples/test-asy-NeXus2.msr
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@ -20,7 +20,7 @@ FUNCTIONS
fun1 = gamma_mu * par4
###############################################################
RUN data/emu00005989_v2 EMU ISIS NEXUS (name beamline institute data-file-format)
RUN data/EMU00005989_v2 EMU ISIS NEXUS (name beamline institute data-file-format)
fittype 2 (asymmetry fit)
alpha 1
map 0 0 0 0 0 0 0 0 0 0

4
doc/examples/test-histo-NeXus2.msr
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@ -26,7 +26,7 @@ fun1 = par2 + map1
fun2 = gamma_mu * par3
###############################################################
RUN data/emu00005989_v2 XXXX ISIS NEXUS (name beamline institute data-file-format)
RUN data/EMU00005989_v2 XXXX ISIS NEXUS (name beamline institute data-file-format)
fittype 0 (single histogram fit)
norm 7
backgr.fit 8
@ -37,7 +37,7 @@ data 40 1500
fit 0.2 14
packing 1
RUN data/emu00005989_v2 XXXX ISIS NEXUS (name beamline institute data-file-format)
RUN data/EMU00005989_v2 XXXX ISIS NEXUS (name beamline institute data-file-format)
fittype 0 (single histogram fit)
norm 9
backgr.fit 10

28
src/Makefile.am
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@ -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
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@ -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");

495
src/classes/PRunDataHandler.cpp
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@ -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;
}
// 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
@ -1109,36 +1106,14 @@ 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
@ -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;
}
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;
}
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 (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].GetT0(i);
t0[i] = fData[0].GetT0Estimated(i);
else
*(t0+i) = fData[0].GetT0(0);
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;
}
//--------------------------------------------------------------------------

516
src/external/nexus/PNeXus.cpp vendored
View File

@ -32,6 +32,7 @@
#include<cstdio>
#include<cstring>
#include<ctime>
#include<cassert>
#include <iostream>
#include <sstream>
@ -835,6 +836,7 @@ PNeXusDetector2::PNeXusDetector2()
PNeXusDetector2::~PNeXusDetector2()
{
fSpectrumIndex.clear();
fRawTime.clear();
if (fT0) {
delete [] fT0;
@ -891,8 +893,13 @@ bool PNeXusDetector2::IsValid(bool strict)
return false;
}
if ((fT0 == 0) || (fHisto == 0)) {
cerr << ">> **ERROR** IDF2 NXdetector problem with t0/counts settings (data)." << endl;
if (fT0 == 0) {
cerr << ">> **ERROR** IDF2 NXdetector t0 settings pointer is null." << endl;
return false;
}
if (fHisto == 0) {
cerr << ">> **ERROR** IDF2 NXdetector counts settings pointer is null." << endl;
return false;
}
@ -917,14 +924,20 @@ int PNeXusDetector2::GetT0(int idxp, int idxs)
{
int result = -1;
if ((idxp < 0) || (idxs < 0)) { // assumption: there is only ONE t0 for all spectra
if ((idxp < 0) && (idxs < 0)) { // assumption: there is only ONE t0 for all spectra
if (fT0 != 0) {
result = *fT0;
}
} else { // assumption: t0's are represented as t0[np][ns]
} else if ((idxp < 0) && (idxs >= 0)) { // assumption: t0's are represented as t0[ns]
if (idxs < fNoOfSpectra) {
result = *(fT0+idxs);
}
} else if ((idxp >= 0) && (idxs >= 0)) { // assumption: t0's are represented as t0[np][ns]
if ((idxp < fNoOfPeriods) || (idxs < fNoOfSpectra)) {
result = *(fT0+idxp*fNoOfSpectra+idxs);
}
} else {
result = -1;
}
return result;
@ -959,10 +972,18 @@ int PNeXusDetector2::SetT0(int *t0)
fErrorMsg = ss.str();
result = 0;
break;
case 1:
case 1: // just one single t0
size = 1;
break;
case 2:
case 2: // t0[#histos]
if (fNoOfSpectra <= 0) {
fErrorMsg = "PNeXusDetector2::SetT0(int *t0): ask for t0 vector (ns), but ns <= 0!";
result = 0;
} else {
size = fNoOfSpectra;
}
break;
case 3: // t0[np][#histos]
if ((fNoOfPeriods <= 0) || (fNoOfSpectra <= 0)) {
fErrorMsg = "PNeXusDetector2::SetT0(int *t0): ask for t0 vector (np, ns), but either np or ns <= 0!";
result = 0;
@ -1013,14 +1034,20 @@ int PNeXusDetector2::GetFirstGoodBin(int idxp, int idxs)
{
int result = -1;
if ((idxp < 0) || (idxs < 0)) { // assumption: there is only ONE t0 for all spectra
if ((idxp < 0) && (idxs < 0)) { // assumption: there is only ONE t0 for all spectra
if (fFirstGoodBin != 0) {
result = *fFirstGoodBin;
}
} else { // assumption: fgb's are represented as fgb[np][ns]
} else if ((idxp < 0) && (idxs >= 0)) { // assumptions: fgb's are represented as fgb[ns]
if (idxs < fNoOfSpectra) {
result = *(fFirstGoodBin+idxs);
}
} else if ((idxp >= 0) && (idxs >= 0)) { // assumption: fgb's are represented as fgb[np][ns]
if ((idxp < fNoOfPeriods) || (idxs < fNoOfSpectra)) {
result = *(fFirstGoodBin+idxp*fNoOfSpectra+idxs);
}
} else {
result = -1;
}
return result;
@ -1055,10 +1082,18 @@ int PNeXusDetector2::SetFirstGoodBin(int *fgb)
fErrorMsg = ss.str();
result = 0;
break;
case 1:
case 1: // single fgb
size = 1;
break;
case 2:
case 2: // fgb[#histos]
if (fNoOfSpectra <= 0) {
fErrorMsg = "PNeXusDetector2::SetFirstGoodBin(int *fgb): ask for fgb vector (ns), but ns <= 0!";
result = 0;
} else {
size = fNoOfSpectra;
}
break;
case 3: // fgb[np][#histos]
if ((fNoOfPeriods <= 0) || (fNoOfSpectra <= 0)) {
fErrorMsg = "PNeXusDetector2::SetFirstGoodBin(int *fgb): ask for fgb vector (np, ns), but either np or ns <= 0!";
result = 0;
@ -1109,14 +1144,20 @@ int PNeXusDetector2::GetLastGoodBin(int idxp, int idxs)
{
int result = -1;
if ((idxp < 0) || (idxs < 0)) { // assumption: there is only ONE t0 for all spectra
if ((idxp < 0) && (idxs < 0)) { // assumption: there is only ONE t0 for all spectra
if (fLastGoodBin != 0) {
result = *fLastGoodBin;
}
} else { // assumption: lgb's are represented as lgb[np][ns]
} else if ((idxp < 0) && (idxs >= 0)) { // assumption: lgb's are represented as lgb[ns]
if (idxs < fNoOfSpectra) {
result = *(fLastGoodBin+idxs);
}
} else if ((idxp >= 0) && (idxs >= 0)) { // assumption: lgb's are represented as lgb[np][ns]
if ((idxp < fNoOfPeriods) || (idxs < fNoOfSpectra)) {
result = *(fLastGoodBin+idxp*fNoOfSpectra+idxs);
}
} else {
result = -1;
}
return result;
@ -1151,10 +1192,18 @@ int PNeXusDetector2::SetLastGoodBin(int *lgb)
fErrorMsg = ss.str();
result = 0;
break;
case 1:
case 1: // single lgb only
size = 1;
break;
case 2:
case 2: // lgb[#histos]
if (fNoOfSpectra <= 0) {
fErrorMsg = "PNeXusDetector2::SetLastGoodBin(int *lgb): ask for lgb vector (ns), but ns <= 0!";
result = 0;
} else {
size = fNoOfSpectra;
}
break;
case 3: // lgb[np][#histos]
if ((fNoOfPeriods <= 0) || (fNoOfSpectra <= 0)) {
fErrorMsg = "PNeXusDetector2::SetLastGoodBin(int *lgb): ask for lgb vector (np, ns), but either np or ns <= 0!";
result = 0;
@ -1343,6 +1392,20 @@ void PNeXusDetector2::SetTimeResolution(double val, string units)
fTimeResolution = val * 1.0e6;
}
//------------------------------------------------------------------------------------------
// SetRawTime (public)
//------------------------------------------------------------------------------------------
/**
* <p>sets the raw time (deep copy).
*
* \param rawTime raw time vector.
*/
void PNeXusDetector2::SetRawTime(vector<double> &rawTime)
{
for (unsigned int i=0; i<rawTime.size(); i++)
fRawTime.push_back(rawTime[i]);
}
//------------------------------------------------------------------------------------------
// GetSpectrumIndex (public)
//------------------------------------------------------------------------------------------
@ -1517,13 +1580,7 @@ bool PNeXusSample2::IsValid(bool strict)
string msg("");
if (!fName.compare("n/a")) {
msg = "IDF2 NXsample 'name' not set.";
if (strict) {
cerr << ">> **ERROR** " << msg << endl;
return false;
} else {
cerr << ">> **WARNING** " << msg << endl;
}
cerr << ">> **WARNING** IDF2 NXsample 'name' not set." << msg << endl;
}
if (!fDescription.compare("n/a")) {
@ -1996,14 +2053,14 @@ int PNeXus::ReadFile(const char *fileName)
status = ReadFileIdf1();
if (status != NX_OK) {
fErrorCode = PNEXUS_VAILD_READ_IDF1_FILE;
fErrorMsg = ">> **ERROR** coudn't read IDF Version 1 file '" + fFileName + "'.";
fErrorMsg = ">> **ERROR** while reading IDF Version 1 file '" + fFileName + "'.";
}
break;
case 2:
status = ReadFileIdf2();
if (status != NX_OK) {
fErrorCode = PNEXUS_VAILD_READ_IDF2_FILE;
fErrorMsg = ">> **ERROR** coudn't read IDF Version 2 file '" + fFileName + "'.";
fErrorMsg = ">> **ERROR** while reading IDF Version 2 file '" + fFileName + "'.";
}
break;
default:
@ -2082,9 +2139,12 @@ void PNeXus::Dump()
cout << endl << "++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++";
cout << endl << "NXfile:";
cout << endl << " NeXus_version : " << fNeXusVersion;
cout << endl << " user: ...";
cout << endl << " file format ver: " << fFileFormatVersion;
cout << endl << " file name : " << fFileName;
cout << endl << " file time : " << fFileTime;
cout << endl << " user : " << fCreator;
cout << endl << "NXentry:";
cout << endl << " IDF version : " << fIdfVersion;
cout << endl << " idf version : " << fIdfVersion;
cout << endl << " program name : " << fNxEntry1->GetProgramName() << ", version: " << fNxEntry1->GetProgramVersion();
cout << endl << " run number : " << fNxEntry1->GetRunNumber();
cout << endl << " title : " << fNxEntry1->GetTitle();
@ -2197,6 +2257,8 @@ void PNeXus::Dump()
cout << "...";
}
}
cout << endl << "++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++";
cout << endl << "that's all!";
cout << endl << endl;
} else if (fIdfVersion == 2) {
cout << endl << "++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++";
@ -2207,8 +2269,9 @@ void PNeXus::Dump()
cout << endl << " file format version : " << fFileFormatVersion;
cout << endl << " creator : " << fCreator;
cout << endl << "NXentry:";
cout << endl << " IDF version : " << fIdfVersion;
cout << endl << " idf version : " << fIdfVersion;
cout << endl << " definition : " << fNxEntry2->GetDefinition();
if (!fNxEntry2->GetProgramName().empty())
cout << endl << " program name : " << fNxEntry2->GetProgramName() << ", version: " << fNxEntry2->GetProgramVersion();
cout << endl << " run_number : " << fNxEntry2->GetRunNumber();
cout << endl << " run_title : " << fNxEntry2->GetTitle();
@ -2221,17 +2284,17 @@ void PNeXus::Dump()
cout << endl << " name : " << fNxEntry2->GetSample()->GetName();
cout << endl << " description : " << fNxEntry2->GetSample()->GetDescription();
cout << endl << " mag.field state : " << fNxEntry2->GetSample()->GetMagneticFieldState();
dval = fNxEntry2->GetSample()->GetPhysPropValue("temperature", ok);
dval = fNxEntry2->GetSample()->GetPhysPropValue("temperature_1", ok);
if (ok)
cout << endl << " temperature : " << dval;
fNxEntry2->GetSample()->GetPhysPropUnit("temperature", str, ok);
fNxEntry2->GetSample()->GetPhysPropUnit("temperature_1", str, ok);
if (ok)
cout << " (" << str << ")";
cout << endl << " temp.environment : " << fNxEntry2->GetSample()->GetEnvironmentTemp();
dval = fNxEntry2->GetSample()->GetPhysPropValue("magnetic_field", ok);
dval = fNxEntry2->GetSample()->GetPhysPropValue("magnetic_field_1", ok);
if (ok)
cout << endl << " magnetic_field : " << dval;
fNxEntry2->GetSample()->GetPhysPropUnit("magnetic_field", str, ok);
fNxEntry2->GetSample()->GetPhysPropUnit("magnetic_field_1", str, ok);
if (ok)
cout << " (" << str << ")";
cout << endl << " mag. field env. : " << fNxEntry2->GetSample()->GetEnvironmentField();
@ -2249,11 +2312,16 @@ void PNeXus::Dump()
if (fNxEntry2->GetInstrument()->GetDetector()->IsT0Present()) {
if (fNxEntry2->GetInstrument()->GetDetector()->GetT0Tag() == 1) { // only one t0 for all histograms
cout << endl << " t0 : " << fNxEntry2->GetInstrument()->GetDetector()->GetT0();
} else if (fNxEntry2->GetInstrument()->GetDetector()->GetT0Tag() == 2) { // t0[ns]
cout << endl << " t0 (idx_s/t0) : ";
for (int i=0; i<fNxEntry2->GetInstrument()->GetDetector()->GetNoOfSpectra(); i++) {
cout << "(" << i+1 << "/" << fNxEntry2->GetInstrument()->GetDetector()->GetT0(-1, i) << "), ";
}
} else { // t0 vector of the form t0[np][ns]
cout << endl << " t0 (idx_p/idx_s/t0): ";
for (int i=0; i<fNxEntry2->GetInstrument()->GetDetector()->GetNoOfPeriods(); i++) {
for (int j=0; j<fNxEntry2->GetInstrument()->GetDetector()->GetNoOfSpectra(); j++) {
cout << "(" << i << "/" << j << "/" << fNxEntry2->GetInstrument()->GetDetector()->GetT0(i,j);
cout << "(" << i+1 << "/" << j+1 << "/" << fNxEntry2->GetInstrument()->GetDetector()->GetT0(i,j) << "), ";
}
}
}
@ -2261,27 +2329,37 @@ void PNeXus::Dump()
cout << endl << " t0 : n/a";
}
if (fNxEntry2->GetInstrument()->GetDetector()->IsFirstGoodBinPresent()) {
if (fNxEntry2->GetInstrument()->GetDetector()->GetT0Tag() == 1) { // only one t0/fgb/lgb for all histograms
if (fNxEntry2->GetInstrument()->GetDetector()->GetT0Tag() == 1) { // only one fgb for all histograms
cout << endl << " first good bin : " << fNxEntry2->GetInstrument()->GetDetector()->GetFirstGoodBin();
} else if (fNxEntry2->GetInstrument()->GetDetector()->GetT0Tag() == 2) { // fgb[ns]
cout << endl << " fgb (idx_s/fgb) : ";
for (int i=0; i<fNxEntry2->GetInstrument()->GetDetector()->GetNoOfSpectra(); i++) {
cout << "(" << i+1 << "/" << fNxEntry2->GetInstrument()->GetDetector()->GetFirstGoodBin(-1,i) << ") , ";
}
} else { // fgb vector of the form fgb[np][ns]
cout << endl << " fgb (idx_p/idx_s/fgb): ";
for (int i=0; i<fNxEntry2->GetInstrument()->GetDetector()->GetNoOfPeriods(); i++) {
for (int j=0; j<fNxEntry2->GetInstrument()->GetDetector()->GetNoOfSpectra(); j++) {
cout << "(" << i << "/" << j << "/" << fNxEntry2->GetInstrument()->GetDetector()->GetFirstGoodBin(i,j);
cout << "(" << i+1 << "/" << j+1 << "/" << fNxEntry2->GetInstrument()->GetDetector()->GetFirstGoodBin(i,j);
}
}
}
} else {
cout << endl << " first good bin : n/a";
}
if (fNxEntry2->GetInstrument()->GetDetector()->IsFirstGoodBinPresent()) {
if (fNxEntry2->GetInstrument()->GetDetector()->GetT0Tag() == 1) { // only one t0/fgb/lgb for all histograms
if (fNxEntry2->GetInstrument()->GetDetector()->IsLastGoodBinPresent()) {
if (fNxEntry2->GetInstrument()->GetDetector()->GetT0Tag() == 1) { // only one lgb for all histograms
cout << endl << " last good bin : " << fNxEntry2->GetInstrument()->GetDetector()->GetLastGoodBin();
} else if (fNxEntry2->GetInstrument()->GetDetector()->GetT0Tag() == 2) { // lgb[ns]
cout << endl << " lgb (idx_s/lgb) : ";
for (int i=0; i<fNxEntry2->GetInstrument()->GetDetector()->GetNoOfSpectra(); i++) {
cout << "(" << i+1 << "/" << fNxEntry2->GetInstrument()->GetDetector()->GetLastGoodBin(-1,i) << "), ";
}
} else { // lgb vector of the form lgb[np][ns]
cout << endl << " lgb (idx_p/idx_s/lgb): ";
for (int i=0; i<fNxEntry2->GetInstrument()->GetDetector()->GetNoOfPeriods(); i++) {
for (int j=0; j<fNxEntry2->GetInstrument()->GetDetector()->GetNoOfSpectra(); j++) {
cout << "(" << i << "/" << j << "/" << fNxEntry2->GetInstrument()->GetDetector()->GetLastGoodBin(i,j);
cout << "(" << i+1 << "/" << j+1 << "/" << fNxEntry2->GetInstrument()->GetDetector()->GetLastGoodBin(i,j) << "), ";
}
}
}
@ -2332,6 +2410,7 @@ void PNeXus::Dump()
cout << "...";
}
}
cout << endl << "++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++";
cout << endl << "that's all!";
cout << endl << endl;
}
@ -2645,7 +2724,7 @@ NXstatus PNeXus::GetIntVectorData(vector<int> &data)
*/
int PNeXus::ReadFileIdf1()
{
cout << endl << ">> reading NeXus Version 1 file ..." << endl;
cout << endl << ">> reading NeXus IDF Version 1 file ..." << endl;
// create first the necessary NXentry object for IDF Version 1
fNxEntry1 = new PNeXusEntry1();
@ -2659,6 +2738,8 @@ int PNeXus::ReadFileIdf1()
char cstr[128];
int ival;
float fval;
int attlen, atttype;
NXname data_value, nxAttrName;
// open file
NXstatus status;
@ -2669,6 +2750,44 @@ int PNeXus::ReadFileIdf1()
return NX_ERROR;
}
// collect the NXroot attribute information
do {
status = NXgetnextattr(fFileHandle, nxAttrName, &attlen, &atttype);
if (status == NX_OK) {
if (!strcmp(nxAttrName, "HDF_version")) {
attlen = VGNAMELENMAX - 1;
atttype = NX_CHAR;
status = NXgetattr(fFileHandle, nxAttrName, data_value, &attlen, &atttype);
if (status == NX_OK) {
fFileFormatVersion = string(data_value);
}
} else if (!strcmp(nxAttrName, "HDF5_Version")) {
attlen = VGNAMELENMAX - 1;
atttype = NX_CHAR;
status = NXgetattr(fFileHandle, nxAttrName, data_value, &attlen, &atttype);
if (status == NX_OK) {
fFileFormatVersion = string("HDF5: ")+string(data_value);
}
} else if (!strcmp(nxAttrName, "XML_version")) {
attlen = VGNAMELENMAX - 1;
atttype = NX_CHAR;
status = NXgetattr(fFileHandle, nxAttrName, data_value, &attlen, &atttype);
if (status == NX_OK) {
fFileFormatVersion = string(data_value);
}
} else if (!strcmp(nxAttrName, "file_name")) {
if (!ErrorHandler(GetStringAttr("file_name", str), PNEXUS_GET_ATTR_ERROR, "couldn't read NXroot 'file_name' attribute!")) return NX_ERROR;
fFileName = str;
} else if (!strcmp(nxAttrName, "file_time")) {
if (!ErrorHandler(GetStringAttr("file_time", str), PNEXUS_GET_ATTR_ERROR, "couldn't read NXroot 'file_time' attribute!")) return NX_ERROR;
fFileTime = str;
} else if (!strcmp(nxAttrName, "user")) {
if (!ErrorHandler(GetStringAttr("user", str), PNEXUS_GET_ATTR_ERROR, "couldn't read NXroot 'user' attribute!")) return NX_ERROR;
fCreator = str;
}
}
} while (status == NX_OK);
// look for the first occurring NXentry
bool found = false;
NXname nxname, nxclass;
@ -2819,11 +2938,12 @@ int PNeXus::ReadFileIdf1()
if (!ErrorHandler(NXclosedata(fFileHandle), PNEXUS_CLOSE_DATA_ERROR, "couldn't close 'magnetic_field' data in sample group")) return NX_ERROR;
fNxEntry1->GetSample()->SetPhysProp("magnetic_field", (double)fval, str);
// read sample shape, e.g. powder, single crystal, etc.
if (!ErrorHandler(NXopendata(fFileHandle, "shape"), PNEXUS_OPEN_DATA_ERROR, "couldn't open 'shape' data in sample group!")) return NX_ERROR;
// read sample shape, e.g. powder, single crystal, etc (THIS IS AN OPTIONAL ENTRY)
if (NXopendata(fFileHandle, "shape") == NX_OK) {
if (!ErrorHandler(GetStringData(str), PNEXUS_GET_DATA_ERROR, "couldn't read 'shape' data in sample group!")) return NX_ERROR;
if (!ErrorHandler(NXclosedata(fFileHandle), PNEXUS_CLOSE_DATA_ERROR, "couldn't close 'shape' data in sample group")) return NX_ERROR;
fNxEntry1->GetSample()->SetShape(str);
}
// read magnetic field state, e.g. TF, LF, ZF
if (!ErrorHandler(NXopendata(fFileHandle, "magnetic_field_state"), PNEXUS_OPEN_DATA_ERROR, "couldn't open 'magnetic_field_state' data in sample group!")) return NX_ERROR;
@ -3182,7 +3302,7 @@ int PNeXus::ReadFileIdf1()
*/
int PNeXus::ReadFileIdf2()
{
cout << endl << ">> reading NeXus Version 2 file ..." << endl;
cout << endl << ">> reading NeXus IDF Version 2 file ..." << endl;
// create first the necessary NXentry object for IDF Version 1
fNxEntry2 = new PNeXusEntry2();
@ -3195,7 +3315,7 @@ int PNeXus::ReadFileIdf2()
string str;
int ival, attlen, atttype;
float fval;
NXname data_value;
NXname data_value, nxAttrName;
int rank, type, dims[32], size, noOfElements;
// open file
@ -3203,55 +3323,68 @@ int PNeXus::ReadFileIdf2()
status = NXopen(fFileName.c_str(), NXACC_READ, &fFileHandle);
if (status != NX_OK) {
fErrorCode = PNEXUS_FILE_OPEN_ERROR;
fErrorMsg = "PNeXus::ReadFile() **ERROR** Couldn't open file '"+fFileName+"' !";
fErrorMsg = "PNeXus::ReadFileIdf2() **ERROR** Couldn't open file '"+fFileName+"' !";
return NX_ERROR;
}
// collect the NXroot attribute information
do {
status = NXgetnextattr(fFileHandle, nxAttrName, &attlen, &atttype);
if (status == NX_OK) {
if (!strcmp(nxAttrName, "HDF_version")) {
attlen = VGNAMELENMAX - 1;
atttype = NX_CHAR;
status = NXgetattr(fFileHandle, nxAttrName, data_value, &attlen, &atttype);
if (status == NX_OK) {
fFileFormatVersion = string(data_value);
}
} else if (!strcmp(nxAttrName, "HDF5_Version")) {
attlen = VGNAMELENMAX - 1;
atttype = NX_CHAR;
status = NXgetattr(fFileHandle, nxAttrName, data_value, &attlen, &atttype);
if (status == NX_OK) {
fFileFormatVersion = string("HDF5: ")+string(data_value);
}
} else if (!strcmp(nxAttrName, "XML_version")) {
attlen = VGNAMELENMAX - 1;
atttype = NX_CHAR;
status = NXgetattr(fFileHandle, nxAttrName, data_value, &attlen, &atttype);
if (status == NX_OK) {
fFileFormatVersion = string(data_value);
}
} else if (!strcmp(nxAttrName, "file_name")) {
if (!ErrorHandler(GetStringAttr("file_name", str), PNEXUS_GET_ATTR_ERROR, "couldn't read NXroot 'file_name' attribute!")) return NX_ERROR;
fFileName = str;
} else if (!strcmp(nxAttrName, "file_time")) {
if (!ErrorHandler(GetStringAttr("file_time", str), PNEXUS_GET_ATTR_ERROR, "couldn't read NXroot 'file_time' attribute!")) return NX_ERROR;
fFileTime = str;
} else if (!strcmp(nxAttrName, "creator")) {
if (!ErrorHandler(GetStringAttr("creator", str), PNEXUS_GET_ATTR_ERROR, "couldn't read NXroot 'creator' attribute!")) return NX_ERROR;
fCreator = str;
}
}
} while (status == NX_OK);
attlen = VGNAMELENMAX - 1;
atttype = NX_CHAR;
str = string("HDF_version");
status = NXgetattr(fFileHandle, (char *)str.c_str(), data_value, &attlen, &atttype);
if (status == NX_OK) {
fFileFormatVersion = string(data_value);
}
if (!fFileFormatVersion.compare("n/a")) {
attlen = VGNAMELENMAX - 1;
atttype = NX_CHAR;
str = string("HDF5_version");
status = NXgetattr(fFileHandle, (char *)str.c_str(), data_value, &attlen, &atttype);
if (status == NX_OK) {
fFileFormatVersion = string(data_value);
}
}
if (!fFileFormatVersion.compare("n/a")) {
attlen = VGNAMELENMAX - 1;
atttype = NX_CHAR;
str = string("XML_version");
status = NXgetattr(fFileHandle, (char *)str.c_str(), data_value, &attlen, &atttype);
if (status == NX_OK) {
fFileFormatVersion = string(data_value);
}
}
// look for the first occurring NXentry
// look for the first occurring NXentry which name ends on "_1"
NXname nxname, nxclass;
int dataType;
// make sure any NXentry has been found
if (!SearchInGroup("NXentry", "class", nxname, nxclass, dataType)) {
bool found = false;
size_t pos;
do {
status = NXgetnextentry(fFileHandle, nxname, nxclass, &dataType);
if (!strcmp(nxclass, "NXentry")) {
str = nxname;
pos = str.find_last_of("_1");
if (pos != str.npos)
found = true;
}
} while (!found && (status == NX_OK));
if (!found) {
fErrorCode = PNEXUS_NXENTRY_NOT_FOUND;
fErrorMsg = ">> **ERROR** Couldn't find any NXentry!";
fErrorMsg = ">> **ERROR** Couldn't find any NXentry on NXroot level!";
return NX_ERROR;
}
// open the NXentry group to obtain the necessary stuff
status = NXopengroup(fFileHandle, nxname, "NXentry");
if (status != NX_OK) {
@ -3267,7 +3400,8 @@ int PNeXus::ReadFileIdf2()
fNxEntry2->SetDefinition(str);
// program_name and version
if (NXopendata(fFileHandle, "program_name") == NX_OK) {
if (SearchInGroup("program_name", "name", nxname, nxclass, dataType)) {
if (!ErrorHandler(NXopendata(fFileHandle, "program_name"), PNEXUS_OPEN_DATA_ERROR, "couldn't open 'program_name' data in NXentry!")) return NX_ERROR;
if (!ErrorHandler(GetStringData(str), PNEXUS_GET_DATA_ERROR, "couldn't read 'program_name' data in NXentry!")) return NX_ERROR;
fNxEntry2->SetProgramName(str);
if (!ErrorHandler(GetStringAttr("version", str), PNEXUS_GET_ATTR_ERROR, "couldn't read 'program_name' attribute in NXentry!")) return NX_ERROR;
@ -3312,11 +3446,7 @@ int PNeXus::ReadFileIdf2()
fNxEntry2->SetExperimentIdentifier(str);
// find entry for NXuser
if (!SearchInGroup("NXuser", "class", nxname, nxclass, dataType)) {
fErrorCode = PNEXUS_NXUSER_NOT_FOUND;
fErrorMsg = ">> **ERROR** Couldn't find any NXuser int NXentry!";
return NX_ERROR;
}
if (SearchInGroup("NXuser", "class", nxname, nxclass, dataType)) {
// open the NXuser
status = NXopengroup(fFileHandle, nxname, "NXuser");
if (status != NX_OK) {
@ -3333,7 +3463,10 @@ int PNeXus::ReadFileIdf2()
// close group NXuser
NXclosegroup(fFileHandle);
}
// find entry for NXsample
if (SearchInGroup("NXsample", "class", nxname, nxclass, dataType)) {
// open group NXsample
if (!ErrorHandler(NXopengroup(fFileHandle, "sample", "NXsample"), PNEXUS_GROUP_OPEN_ERROR, "couldn't open NeXus subgroup sample!")) return NX_ERROR;
@ -3344,14 +3477,16 @@ int PNeXus::ReadFileIdf2()
fNxEntry2->GetSample()->SetName(str);
// sample description
if (NXopendata(fFileHandle, "description") == NX_OK) {
if (SearchInGroup("description", "name", nxname, nxclass, dataType)) {
if (!ErrorHandler(NXopendata(fFileHandle, "description"), PNEXUS_OPEN_DATA_ERROR, "couldn't open 'description' data in NXsample!")) return NX_ERROR;
if (!ErrorHandler(GetStringData(str), PNEXUS_GET_DATA_ERROR, "couldn't read 'description' data in NXsample!")) return NX_ERROR;
if (!ErrorHandler(NXclosedata(fFileHandle), PNEXUS_CLOSE_DATA_ERROR, "couldn't close 'description' data in NXsample!")) return NX_ERROR;
fNxEntry2->GetSample()->SetDescription(str);
}
// temperature
if (NXopendata(fFileHandle, "temperature_1") == NX_OK) {
if (SearchInGroup("temperature_1", "name", nxname, nxclass, dataType)) {
if (!ErrorHandler(NXopendata(fFileHandle, "temperature_1"), PNEXUS_OPEN_DATA_ERROR, "couldn't open 'temperature_1' data in NXsample!")) return NX_ERROR;
if (!ErrorHandler(NXgetdata(fFileHandle, &fval), PNEXUS_GET_DATA_ERROR, "couldn't read 'temperature_1' data in NXsample!")) return NX_ERROR;
if (!ErrorHandler(GetStringAttr("units", str), PNEXUS_GET_ATTR_ERROR, "couldn't read temperature units in NXsample!")) return NX_ERROR;
if (!ErrorHandler(NXclosedata(fFileHandle), PNEXUS_CLOSE_DATA_ERROR, "couldn't close 'temperature_1' data in NXsample!")) return NX_ERROR;
@ -3359,8 +3494,9 @@ int PNeXus::ReadFileIdf2()
}
// temperature environment
if (NXopengroup(fFileHandle, "temperature_1_env", "NXenvironment") == NX_OK) {
// user name
if (SearchInGroup("temperature_1_env", "name", nxname, nxclass, dataType)) {
if (!ErrorHandler(NXopengroup(fFileHandle, "temperature_1_env", "NXenvironment"), PNEXUS_GROUP_OPEN_ERROR, "couldn't open NeXus subgroup NXenvironment!")) return NX_ERROR;
// temperature environment name
if (!ErrorHandler(NXopendata(fFileHandle, "name"), PNEXUS_OPEN_DATA_ERROR, "couldn't open 'name' data in NXenvironment!")) return NX_ERROR;
if (!ErrorHandler(GetStringData(str), PNEXUS_GET_DATA_ERROR, "couldn't read 'name' data in NXenvironment!")) return NX_ERROR;
if (!ErrorHandler(NXclosedata(fFileHandle), PNEXUS_CLOSE_DATA_ERROR, "couldn't close 'name' data in NXenvironment!")) return NX_ERROR;
@ -3370,7 +3506,8 @@ int PNeXus::ReadFileIdf2()
}
// magnetic_field
if (NXopendata(fFileHandle, "magnetic_field_1") == NX_OK) {
if (SearchInGroup("magnetic_field_1", "name", nxname, nxclass, dataType)) {
if (!ErrorHandler(NXopendata(fFileHandle, "magnetic_field_1"), PNEXUS_OPEN_DATA_ERROR, "couldn't open 'magnetic_field_1' data in NXsample!")) return NX_ERROR;
if (!ErrorHandler(NXgetdata(fFileHandle, &fval), PNEXUS_GET_DATA_ERROR, "couldn't read 'magnetic_field_1' data in NXsample!")) return NX_ERROR;
if (!ErrorHandler(GetStringAttr("units", str), PNEXUS_GET_ATTR_ERROR, "couldn't read magnetic field units in NXsample!")) return NX_ERROR;
if (!ErrorHandler(NXclosedata(fFileHandle), PNEXUS_CLOSE_DATA_ERROR, "couldn't close 'magnetic_field_1' data in NXsample!")) return NX_ERROR;
@ -3378,15 +3515,17 @@ int PNeXus::ReadFileIdf2()
}
// magnetic field state
if (NXopendata(fFileHandle, "magnetic_field_state") == NX_OK) {
if (SearchInGroup("magnetic_field_state", "name", nxname, nxclass, dataType)) {
if (!ErrorHandler(NXopendata(fFileHandle, "magnetic_field_state"), PNEXUS_OPEN_DATA_ERROR, "couldn't open 'magnetic_field_state' data in NXsample!")) return NX_ERROR;
if (!ErrorHandler(GetStringData(str), PNEXUS_GET_DATA_ERROR, "couldn't read 'magnetic_field_state' data in NXsample!")) return NX_ERROR;
if (!ErrorHandler(NXclosedata(fFileHandle), PNEXUS_CLOSE_DATA_ERROR, "couldn't close 'magnetic_field_state' data in NXsample!")) return NX_ERROR;
fNxEntry2->GetSample()->SetMagneticFieldState(str);
}
// magnetic field environment
if (NXopengroup(fFileHandle, "magnetic_field_1_env", "NXenvironment") == NX_OK) {
// user name
if (SearchInGroup("magnetic_field_1_env", "name", nxname, nxclass, dataType)) {
if (!ErrorHandler(NXopengroup(fFileHandle, "magnetic_field_1_env", "NXenvironment"), PNEXUS_GROUP_OPEN_ERROR, "couldn't open NeXus subgroup NXenvironment!")) return NX_ERROR;
// magnetic field environment name
if (!ErrorHandler(NXopendata(fFileHandle, "name"), PNEXUS_OPEN_DATA_ERROR, "couldn't open 'name' data in NXenvironment!")) return NX_ERROR;
if (!ErrorHandler(GetStringData(str), PNEXUS_GET_DATA_ERROR, "couldn't read 'name' data in NXenvironment!")) return NX_ERROR;
if (!ErrorHandler(NXclosedata(fFileHandle), PNEXUS_CLOSE_DATA_ERROR, "couldn't close 'name' data in NXenvironment!")) return NX_ERROR;
@ -3397,6 +3536,7 @@ int PNeXus::ReadFileIdf2()
// close group NXsample
NXclosegroup(fFileHandle);
}
// open group NXinstrument
if (!ErrorHandler(NXopengroup(fFileHandle, "instrument", "NXinstrument"), PNEXUS_GROUP_OPEN_ERROR, "couldn't open NeXus subgroup instrument in NXentry!")) return NX_ERROR;
@ -3456,11 +3596,17 @@ int PNeXus::ReadFileIdf2()
// 1st check if 'histogram_resolution' is found
if (SearchInGroup("histogram_resolution", "name", nxname, nxclass, dataType)) {
if (!ErrorHandler(NXopendata(fFileHandle, "histogram_resolution"), PNEXUS_OPEN_DATA_ERROR, "couldn't open 'histogram_resolution' data in NXdetector!")) return NX_ERROR;
if (!ErrorHandler(NXgetdata(fFileHandle, &ival), PNEXUS_GET_DATA_ERROR, "couldn't read 'histogram_resolution' data in NXdetector!")) return NX_ERROR;
if (!ErrorHandler(GetStringAttr("units", str), PNEXUS_GET_ATTR_ERROR, "couldn't read magnetic field units in NXsample!")) return NX_ERROR;
if (!ErrorHandler(NXgetdata(fFileHandle, &fval), PNEXUS_GET_DATA_ERROR, "couldn't read 'histogram_resolution' data in NXdetector!")) return NX_ERROR;
if (!ErrorHandler(GetStringAttr("units", str), PNEXUS_GET_ATTR_ERROR, "couldn't read time resolution units in NXdetector!")) return NX_ERROR;
if (!ErrorHandler(NXclosedata(fFileHandle), PNEXUS_CLOSE_DATA_ERROR, "couldn't close 'histogram_resolution' data in NXdetector!")) return NX_ERROR;
fNxEntry2->GetInstrument()->GetDetector()->SetTimeResolution((double)ival, str);
} else { // 2nd 'histogram_resolution' is not present, hence extract the time resolution from the 'raw_time' vector
fNxEntry2->GetInstrument()->GetDetector()->SetTimeResolution((double)fval, str);
} else if (SearchInGroup("resolution", "name", nxname, nxclass, dataType)) { // 2nd check if 'resolution' is found
if (!ErrorHandler(NXopendata(fFileHandle, "resolution"), PNEXUS_OPEN_DATA_ERROR, "couldn't open 'resolution' data in NXdetector!")) return NX_ERROR;
if (!ErrorHandler(NXgetdata(fFileHandle, &fval), PNEXUS_GET_DATA_ERROR, "couldn't read 'resolution' data in NXdetector!")) return NX_ERROR;
if (!ErrorHandler(GetStringAttr("units", str), PNEXUS_GET_ATTR_ERROR, "couldn't read time resolution units in NXdetector!")) return NX_ERROR;
if (!ErrorHandler(NXclosedata(fFileHandle), PNEXUS_CLOSE_DATA_ERROR, "couldn't close 'resolution' data in NXdetector!")) return NX_ERROR;
fNxEntry2->GetInstrument()->GetDetector()->SetTimeResolution((double)fval, str);
} else { // 3nd 'histogram_resolution' is not present, hence extract the time resolution from the 'raw_time' vector
if (!ErrorHandler(NXopendata(fFileHandle, "raw_time"), PNEXUS_OPEN_DATA_ERROR, "couldn't open 'raw_time' data in NXdetector!")) return NX_ERROR;
vector<double> rawTime;
if (!ErrorHandler(GetDoubleVectorData(rawTime), PNEXUS_GET_DATA_ERROR, "couldn't get 'raw_time' data in NXdetector!")) return NX_ERROR;
@ -3569,8 +3715,12 @@ int PNeXus::ReadFileIdf2()
// check the dimensions of the 'time_zero_bin' vector
if (!ErrorHandler(NXgetinfo(fFileHandle, &rank, dims, &type), PNEXUS_GET_META_INFO_ERROR, "couldn't get 'time_zero_bin' info in NXdetector!")) return NX_ERROR;
if (rank <= 2) {
fNxEntry2->GetInstrument()->GetDetector()->SetT0Tag(rank);
if ((rank == 1) && (dims[0] == 1)) { // single t0 entry
fNxEntry2->GetInstrument()->GetDetector()->SetT0Tag(1);
} else if ((rank == 1) && (dims[0] > 1)) { // t0 of the form t0[ns]
fNxEntry2->GetInstrument()->GetDetector()->SetT0Tag(2);
} else if (rank == 2) { // t0 of the form t0[np][ns]
fNxEntry2->GetInstrument()->GetDetector()->SetT0Tag(3);
} else {
cerr << endl << ">> **ERROR** found 'time_zero_bin' info in NXdetector with rank=" << rank << ". Do not know how to handle." << endl;
return NX_ERROR;
@ -3613,8 +3763,12 @@ int PNeXus::ReadFileIdf2()
// check the dimensions of the 'time_zero' vector
if (!ErrorHandler(NXgetinfo(fFileHandle, &rank, dims, &type), PNEXUS_GET_META_INFO_ERROR, "couldn't get 'time_zero' info in NXdetector!")) return NX_ERROR;
if (rank <= 2) {
fNxEntry2->GetInstrument()->GetDetector()->SetT0Tag(rank);
if ((rank == 1) && (dims[0] == 1)) { // single t0 entry
fNxEntry2->GetInstrument()->GetDetector()->SetT0Tag(1);
} else if ((rank == 1) && (dims[0] > 1)) { // t0 of the form t0[ns]
fNxEntry2->GetInstrument()->GetDetector()->SetT0Tag(2);
} else if (rank == 2) { // t0 of the form t0[np][ns]
fNxEntry2->GetInstrument()->GetDetector()->SetT0Tag(3);
} else {
cerr << endl << ">> **ERROR** found 'time_zero' info in NXdetector with rank=" << rank << ". Do not know how to handle." << endl;
return NX_ERROR;
@ -3684,16 +3838,6 @@ int PNeXus::ReadFileIdf2()
// check the dimensions of the 'first_good_bin' vector
if (!ErrorHandler(NXgetinfo(fFileHandle, &rank, dims, &type), PNEXUS_GET_META_INFO_ERROR, "couldn't get 'first_good_bin' info in NXdetector!")) return NX_ERROR;
if (rank <= 2) {
if (rank != fNxEntry2->GetInstrument()->GetDetector()->GetT0Tag()) {
cerr << endl << ">> **ERROR** rank of 'first_good_bin' (" << rank << ") is different than t0 rank=" << rank << ". Do not know how to handle." << endl;
return NX_ERROR;
}
} else {
cerr << endl << ">> **ERROR** found 'first_good_bin' info in NXdetector with rank=" << rank << ". Do not know how to handle." << endl;
return NX_ERROR;
}
// calculate the needed size
size = dims[0];
for (int i=1; i<rank; i++)
@ -3731,16 +3875,6 @@ int PNeXus::ReadFileIdf2()
// check the dimensions of the 'first_good_time' vector
if (!ErrorHandler(NXgetinfo(fFileHandle, &rank, dims, &type), PNEXUS_GET_META_INFO_ERROR, "couldn't get 'first_good_time' info in NXdetector!")) return NX_ERROR;
if (rank <= 2) {
if (rank != fNxEntry2->GetInstrument()->GetDetector()->GetT0Tag()) {
cerr << endl << ">> **ERROR** rank of 'first_good_time' (" << rank << ") is different than t0 rank=" << rank << ". Do not know how to handle." << endl;
return NX_ERROR;
}
} else {
cerr << endl << ">> **ERROR** found 'first_good_time' info in NXdetector with rank=" << rank << ". Do not know how to handle." << endl;
return NX_ERROR;
}
// calculate the needed size
size = dims[0];
for (int i=1; i<rank; i++)
@ -3800,16 +3934,6 @@ int PNeXus::ReadFileIdf2()
// check the dimensions of the 'last_good_bin' vector
if (!ErrorHandler(NXgetinfo(fFileHandle, &rank, dims, &type), PNEXUS_GET_META_INFO_ERROR, "couldn't get 'last_good_bin' info in NXdetector!")) return NX_ERROR;
if (rank <= 2) {
if (rank != fNxEntry2->GetInstrument()->GetDetector()->GetT0Tag()) {
cerr << endl << ">> **ERROR** rank of 'last_good_bin' (" << rank << ") is different than t0 rank=" << rank << ". Do not know how to handle." << endl;
return NX_ERROR;
}
} else {
cerr << endl << ">> **ERROR** found 'last_good_bin' info in NXdetector with rank=" << rank << ". Do not know how to handle." << endl;
return NX_ERROR;
}
// calculate the needed size
size = dims[0];
for (int i=1; i<rank; i++)
@ -3848,16 +3972,6 @@ int PNeXus::ReadFileIdf2()
// check the dimensions of the 'last_good_time' vector
if (!ErrorHandler(NXgetinfo(fFileHandle, &rank, dims, &type), PNEXUS_GET_META_INFO_ERROR, "couldn't get 'last_good_time' info in NXdetector!")) return NX_ERROR;
if (rank <= 2) {
if (rank != fNxEntry2->GetInstrument()->GetDetector()->GetT0Tag()) {
cerr << endl << ">> **ERROR** rank of 'last_good_time' (" << rank << ") is different than t0 rank=" << rank << ". Do not know how to handle." << endl;
return NX_ERROR;
}
} else {
cerr << endl << ">> **ERROR** found 'last_good_time' info in NXdetector with rank=" << rank << ". Do not know how to handle." << endl;
return NX_ERROR;
}
// calculate the needed size
size = dims[0];
for (int i=1; i<rank; i++)
@ -4206,13 +4320,15 @@ int PNeXus::WriteFileIdf1(const char* fileName, const NXaccess access)
if (!ErrorHandler(NXputattr(fFileHandle, "units", cstr, strlen(cstr), NX_CHAR), PNEXUS_PUT_ATTR_ERROR, "couldn't put attribute 'units' for 'NXsample/magnetic_field'")) return NX_ERROR;
NXclosedata(fFileHandle);
// write sample 'shape'
// write sample 'shape' only if populated with something different than 'n/a'
if (fNxEntry1->GetSample()->GetShape() != "n/a") {
size = fNxEntry1->GetSample()->GetShape().length();
if (!ErrorHandler(NXmakedata(fFileHandle, "shape", NX_CHAR, 1, &size), PNEXUS_MAKE_DATA_ERROR, "couldn't create data entry 'NXsample/shape'.")) return NX_ERROR;
if (!ErrorHandler(NXopendata(fFileHandle, "shape"), PNEXUS_OPEN_DATA_ERROR, "couldn't open data 'NXsample/shape' for writting.")) return NX_ERROR;
strncpy(cstr, fNxEntry1->GetSample()->GetShape().c_str(), sizeof(cstr));
if (!ErrorHandler(NXputdata(fFileHandle, cstr), PNEXUS_PUT_DATA_ERROR, "couldn't put data 'NXsample/shape'.")) return NX_ERROR;
NXclosedata(fFileHandle);
}
// write sample 'magnetic_field_state'
size = fNxEntry1->GetSample()->GetMagneticFieldState().length();
@ -4556,7 +4672,8 @@ int PNeXus::WriteFileIdf2(const char* fileName, const NXaccess access)
int size, idata;
float fdata;
double dval;
NXlink clink;
NXlink nxLink;
vector<NXlink> nxLinkVec;
memset(cstr, '\0', sizeof(cstr));
snprintf(cstr, sizeof(cstr), "couldn't open file '%s' for writing", fileName);
@ -4594,6 +4711,20 @@ int PNeXus::WriteFileIdf2(const char* fileName, const NXaccess access)
if (!ErrorHandler(NXputdata(fFileHandle, cstr), PNEXUS_PUT_DATA_ERROR, "couldn't put data 'definition' in NXentry.")) return NX_ERROR;
NXclosedata(fFileHandle);
// write 'program_name' if present
if (!fNxEntry2->GetProgramName().empty()) {
size = fNxEntry2->GetProgramName().length();
if (!ErrorHandler(NXmakedata(fFileHandle, "program_name", NX_CHAR, 1, &size), PNEXUS_MAKE_DATA_ERROR, "couldn't create data entry 'program_name' in NXentry.")) return NX_ERROR;
if (!ErrorHandler(NXopendata(fFileHandle, "program_name"), PNEXUS_OPEN_DATA_ERROR, "couldn't open data 'program_name' in NXentry for writting.")) return NX_ERROR;
memset(cstr, '\0', sizeof(cstr));
strncpy(cstr, fNxEntry2->GetProgramName().c_str(), sizeof(cstr));
if (!ErrorHandler(NXputdata(fFileHandle, cstr), PNEXUS_PUT_DATA_ERROR, "couldn't put data 'program_name' in NXentry.")) return NX_ERROR;
memset(cstr, '\0', sizeof(cstr));
strncpy(cstr, fNxEntry2->GetProgramVersion().c_str(), sizeof(cstr));
if (!ErrorHandler(NXputattr(fFileHandle, "version", cstr, strlen(cstr), NX_CHAR), PNEXUS_PUT_ATTR_ERROR, "couldn't put attribute 'version' for 'program_name' in NXentry.")) return NX_ERROR;
NXclosedata(fFileHandle);
}
// write run 'run_number'
size = 1;
if (!ErrorHandler(NXmakedata(fFileHandle, "run_number", NX_INT32, 1, &size), PNEXUS_MAKE_DATA_ERROR, "couldn't create data entry 'run_number' in NXentry.")) return NX_ERROR;
@ -4638,6 +4769,8 @@ int PNeXus::WriteFileIdf2(const char* fileName, const NXaccess access)
if (!ErrorHandler(NXputdata(fFileHandle, cstr), PNEXUS_PUT_DATA_ERROR, "couldn't put data 'experiment_identifier' in NXentry.")) return NX_ERROR;
NXclosedata(fFileHandle);
// user_1 (NXuser) will only be written if there is at least a user name present
if (fNxEntry2->GetUser()->GetName() != "n/a") {
// make group 'user_1'
if (!ErrorHandler(NXmakegroup(fFileHandle, "user_1", "NXuser"), PNEXUS_CREATE_GROUP_ERROR, "couldn't create group 'user_1' in NXentry.")) return NX_ERROR;
// open group 'user'
@ -4654,6 +4787,7 @@ int PNeXus::WriteFileIdf2(const char* fileName, const NXaccess access)
// close group 'user_1'
NXclosegroup(fFileHandle);
}
// make group 'sample'
if (!ErrorHandler(NXmakegroup(fFileHandle, "sample", "NXsample"), PNEXUS_CREATE_GROUP_ERROR, "couldn't create group 'sample' in NXentry.")) return NX_ERROR;
@ -4683,10 +4817,10 @@ int PNeXus::WriteFileIdf2(const char* fileName, const NXaccess access)
// check if temperature is present and if yes, write it into the file
ok=false;
dval = fNxEntry2->GetSample()->GetPhysPropValue("temperature", ok);
dval = fNxEntry2->GetSample()->GetPhysPropValue("temperature_1", ok);
if (ok) {
fdata = (float)dval;
fNxEntry2->GetSample()->GetPhysPropUnit("temperature", str, ok);
fNxEntry2->GetSample()->GetPhysPropUnit("temperature_1", str, ok);
}
if (ok) {
size = 1;
@ -4701,22 +4835,28 @@ int PNeXus::WriteFileIdf2(const char* fileName, const NXaccess access)
// check if temperature environment info is present
if (fNxEntry2->GetSample()->GetEnvironmentTemp().compare("n/a")) {
// make group 'temperature_1_env'
if (!ErrorHandler(NXmakegroup(fFileHandle, "temperature_1_env", "NXenvironment"), PNEXUS_CREATE_GROUP_ERROR, "couldn't create group 'temperature_1_env' in NXsample.")) return NX_ERROR;
// open group 'temperature_1_env'
if (!ErrorHandler(NXopengroup(fFileHandle, "temperature_1_env", "NXenvironment"), PNEXUS_GROUP_OPEN_ERROR, "couldn't open group 'NXenvironment' in NXsample for writting.")) return NX_ERROR;
// write sample 'temperature_1_env'
size = fNxEntry2->GetSample()->GetEnvironmentTemp().length();
if (!ErrorHandler(NXmakedata(fFileHandle, "temperature_1_env", NX_CHAR, 1, &size), PNEXUS_MAKE_DATA_ERROR, "couldn't create data entry 'temperature_1_env' in NXsample.")) return NX_ERROR;
if (!ErrorHandler(NXopendata(fFileHandle, "temperature_1_env"), PNEXUS_OPEN_DATA_ERROR, "couldn't open data 'temperature_1_env' in NXsample for writting.")) return NX_ERROR;
if (!ErrorHandler(NXmakedata(fFileHandle, "name", NX_CHAR, 1, &size), PNEXUS_MAKE_DATA_ERROR, "couldn't create data entry 'name' in 'temperature_1_env' in NXsample.")) return NX_ERROR;
if (!ErrorHandler(NXopendata(fFileHandle, "name"), PNEXUS_OPEN_DATA_ERROR, "couldn't open data 'name' in 'temperature_1_env' in NXsample for writting.")) return NX_ERROR;
memset(cstr, '\0', sizeof(cstr));
strncpy(cstr, fNxEntry2->GetSample()->GetEnvironmentTemp().c_str(), sizeof(cstr));
if (!ErrorHandler(NXputdata(fFileHandle, cstr), PNEXUS_PUT_DATA_ERROR, "couldn't put data 'temperature_1_env' in NXsample.")) return NX_ERROR;
NXclosedata(fFileHandle);
// close group 'temperature_1_env'
NXclosegroup(fFileHandle);
}
// check if magnetic field is present and if yes, write it into the file
ok=false;
dval = fNxEntry2->GetSample()->GetPhysPropValue("magnetic_field", ok);
dval = fNxEntry2->GetSample()->GetPhysPropValue("magnetic_field_1", ok);
if (ok) {
fdata = (float)dval;
fNxEntry2->GetSample()->GetPhysPropUnit("magnetic_field", str, ok);
fNxEntry2->GetSample()->GetPhysPropUnit("magnetic_field_1", str, ok);
}
if (ok) {
size = 1;
@ -4731,6 +4871,10 @@ int PNeXus::WriteFileIdf2(const char* fileName, const NXaccess access)
// check if magnetic field environment info is present
if (fNxEntry2->GetSample()->GetEnvironmentField().compare("n/a")) {
// make group 'magnetic_field_1_env'
if (!ErrorHandler(NXmakegroup(fFileHandle, "magnetic_field_1_env", "NXenvironment"), PNEXUS_CREATE_GROUP_ERROR, "couldn't create group 'magnetic_field_1_env' in NXsample.")) return NX_ERROR;
// open group 'magnetic_field_1_env'
if (!ErrorHandler(NXopengroup(fFileHandle, "magnetic_field_1_env", "NXenvironment"), PNEXUS_GROUP_OPEN_ERROR, "couldn't open group 'NXenvironment' in NXsample for writting.")) return NX_ERROR;
// write sample 'magnetic_field_1_env'
size = fNxEntry2->GetSample()->GetEnvironmentField().length();
if (!ErrorHandler(NXmakedata(fFileHandle, "magnetic_field_1_env", NX_CHAR, 1, &size), PNEXUS_MAKE_DATA_ERROR, "couldn't create data entry 'magnetic_field_1_env' in NXsample.")) return NX_ERROR;
@ -4739,6 +4883,8 @@ int PNeXus::WriteFileIdf2(const char* fileName, const NXaccess access)
strncpy(cstr, fNxEntry2->GetSample()->GetEnvironmentField().c_str(), sizeof(cstr));
if (!ErrorHandler(NXputdata(fFileHandle, cstr), PNEXUS_PUT_DATA_ERROR, "couldn't put data 'magnetic_field_1_env' in NXsample.")) return NX_ERROR;
NXclosedata(fFileHandle);
// close group 'magnetic_field_1_env'
NXclosegroup(fFileHandle);
}
// check if magnetic field state info is present
@ -4811,13 +4957,13 @@ int PNeXus::WriteFileIdf2(const char* fileName, const NXaccess access)
// open group 'beamline'
if (!ErrorHandler(NXopengroup(fFileHandle, "beamline", "NXbeamline"), PNEXUS_GROUP_OPEN_ERROR, "couldn't open group 'beamline' in NXentry for NXinstrument.")) return NX_ERROR;
// write instrument 'name'
// write beamline 'beamline'
size = fNxEntry2->GetInstrument()->GetBeamline()->GetName().length();
if (!ErrorHandler(NXmakedata(fFileHandle, "name", NX_CHAR, 1, &size), PNEXUS_MAKE_DATA_ERROR, "couldn't create data entry 'name' in NXbeamline.")) return NX_ERROR;
if (!ErrorHandler(NXopendata(fFileHandle, "name"), PNEXUS_OPEN_DATA_ERROR, "couldn't open data 'name' in NXbeamline for writting.")) return NX_ERROR;
if (!ErrorHandler(NXmakedata(fFileHandle, "beamline", NX_CHAR, 1, &size), PNEXUS_MAKE_DATA_ERROR, "couldn't create data entry 'beamline' in NXbeamline.")) return NX_ERROR;
if (!ErrorHandler(NXopendata(fFileHandle, "beamline"), PNEXUS_OPEN_DATA_ERROR, "couldn't open data 'beamline' in NXbeamline for writting.")) return NX_ERROR;
memset(cstr, '\0', sizeof(cstr));
strncpy(cstr, fNxEntry2->GetInstrument()->GetBeamline()->GetName().c_str(), sizeof(cstr));
if (!ErrorHandler(NXputdata(fFileHandle, cstr), PNEXUS_PUT_DATA_ERROR, "couldn't put data 'name' in NXbeamline.")) return NX_ERROR;
if (!ErrorHandler(NXputdata(fFileHandle, cstr), PNEXUS_PUT_DATA_ERROR, "couldn't put data 'beamline' in NXbeamline.")) return NX_ERROR;
NXclosedata(fFileHandle);
// close group 'beamline'
@ -4883,17 +5029,59 @@ int PNeXus::WriteFileIdf2(const char* fileName, const NXaccess access)
}
if (!ErrorHandler(NXputattr(fFileHandle, "long_name", cstr, strlen(cstr), NX_CHAR), PNEXUS_PUT_ATTR_ERROR, "couldn't put attribute 'long_name' for 'counts' in NXdetector.")) return NX_ERROR;
// create link of 'counts' for NXdata
if (!ErrorHandler(NXgetdataID(fFileHandle, &clink), PNEXUS_LINKING_ERROR, "couldn't obtain link of 'counts' in NXdetector.")) return NX_ERROR;
if (!ErrorHandler(NXgetdataID(fFileHandle, &nxLink), PNEXUS_LINKING_ERROR, "couldn't obtain link of 'counts' in NXdetector.")) return NX_ERROR;
nxLinkVec.push_back(nxLink);
NXclosedata(fFileHandle);
// write time resolution
fdata = (float)fNxEntry2->GetInstrument()->GetDetector()->GetTimeResolution("ns");
size = 1;
if (!ErrorHandler(NXmakedata(fFileHandle, "histogram_resolution", NX_FLOAT32, 1, &size), PNEXUS_MAKE_DATA_ERROR, "couldn't create data entry 'histogram_resolution' in NXdetector.")) return NX_ERROR;
if (!ErrorHandler(NXopendata(fFileHandle, "histogram_resolution"), PNEXUS_OPEN_DATA_ERROR, "couldn't open data 'histogram_resolution' in NXdetector for writting.")) return NX_ERROR;
if (!ErrorHandler(NXputdata(fFileHandle, (void*)&fdata), PNEXUS_PUT_DATA_ERROR, "couldn't put data 'histogram_resolution' in NXdetector.")) return NX_ERROR;
memset(cstr, '\0', sizeof(cstr));
strncpy(cstr, "nano.second", sizeof(cstr));
if (!ErrorHandler(NXputattr(fFileHandle, "units", cstr, strlen(cstr), NX_CHAR), PNEXUS_PUT_ATTR_ERROR, "couldn't put attribute 'units' for 'histogram_resolution' in NXdetector.")) return NX_ERROR;
// create link of 'histogram_resolution' for NXdata
if (!ErrorHandler(NXgetdataID(fFileHandle, &nxLink), PNEXUS_LINKING_ERROR, "couldn't obtain link of 'histogram_resolution' in NXdetector.")) return NX_ERROR;
nxLinkVec.push_back(nxLink);
NXclosedata(fFileHandle);
// write detector_1 'raw_time'
size = (int)fNxEntry2->GetInstrument()->GetDetector()->GetRawTime()->size();
float *p_fdata = new float[size];
assert(p_fdata);
for (int i=0; i<size; i++)
p_fdata[i] = (float)fNxEntry2->GetInstrument()->GetDetector()->GetRawTime()->at(i);
if (!ErrorHandler(NXmakedata(fFileHandle, "raw_time", NX_FLOAT32, 1, &size), PNEXUS_MAKE_DATA_ERROR, "couldn't create data entry 'raw_time' in NXdetector.")) return NX_ERROR;
if (!ErrorHandler(NXopendata(fFileHandle, "raw_time"), PNEXUS_OPEN_DATA_ERROR, "couldn't open data 'raw_time' in NXdetector for writting.")) return NX_ERROR;
if (!ErrorHandler(NXputdata(fFileHandle, (void*)p_fdata), PNEXUS_PUT_DATA_ERROR, "couldn't put data 'raw_time' in NXdetector.")) return NX_ERROR;
strncpy(cstr, fNxEntry2->GetInstrument()->GetDetector()->GetRawTimeUnit().c_str(), sizeof(cstr));
if (!ErrorHandler(NXputattr(fFileHandle, "units", cstr, strlen(cstr), NX_CHAR), PNEXUS_PUT_ATTR_ERROR, "couldn't put attribute 'units' for 'raw_time' in NXdetector.")) return NX_ERROR;
strncpy(cstr, fNxEntry2->GetInstrument()->GetDetector()->GetRawTimeName().c_str(), sizeof(cstr));
if (!ErrorHandler(NXputattr(fFileHandle, "long_name", cstr, strlen(cstr), NX_CHAR), PNEXUS_PUT_ATTR_ERROR, "couldn't put attribute 'long_name' for 'raw_time' in NXdetector.")) return NX_ERROR;
// create link of 'raw_time' for NXdata
if (!ErrorHandler(NXgetdataID(fFileHandle, &nxLink), PNEXUS_LINKING_ERROR, "couldn't obtain link of 'raw_time' in NXdetector.")) return NX_ERROR;
nxLinkVec.push_back(nxLink);
NXclosedata(fFileHandle);
// clean up
if (p_fdata) {
delete [] p_fdata;
p_fdata = 0;
}
// write detector_1 'spectrum_index'
size = fNxEntry2->GetInstrument()->GetDetector()->GetSpectrumIndexSize();
int *p_idata = new int[size];
assert(p_idata);
for (int i=0; i<size; i++)
*(p_idata+i) = fNxEntry2->GetInstrument()->GetDetector()->GetSpectrumIndex(i);
if (!ErrorHandler(NXmakedata(fFileHandle, "spectrum_index", NX_INT32, 1, &size), PNEXUS_MAKE_DATA_ERROR, "couldn't create data entry 'spectrum_index' in NXdetector.")) return NX_ERROR;
if (!ErrorHandler(NXopendata(fFileHandle, "spectrum_index"), PNEXUS_OPEN_DATA_ERROR, "couldn't open data 'spectrum_index' in NXdetector for writting.")) return NX_ERROR;
if (!ErrorHandler(NXputdata(fFileHandle, (void*)p_idata), PNEXUS_PUT_DATA_ERROR, "couldn't put data 'spectrum_index' in NXdetector.")) return NX_ERROR;
// create link of 'spectrum_index' for NXdata
if (!ErrorHandler(NXgetdataID(fFileHandle, &nxLink), PNEXUS_LINKING_ERROR, "couldn't obtain link of 'spectrum_index' in NXdetector.")) return NX_ERROR;
nxLinkVec.push_back(nxLink);
NXclosedata(fFileHandle);
if (p_idata) {
delete [] p_idata;
@ -4910,6 +5098,13 @@ int PNeXus::WriteFileIdf2(const char* fileName, const NXaccess access)
if (!ErrorHandler(NXputdata(fFileHandle, (void*)&idata), PNEXUS_PUT_DATA_ERROR, "couldn't put data 'time_zero_bin' in NXdetector.")) return NX_ERROR;
NXclosedata(fFileHandle);
} else if (fNxEntry2->GetInstrument()->GetDetector()->GetT0Tag() == 2) {
int dims[1];
dims[0] = fNxEntry2->GetInstrument()->GetDetector()->GetNoOfSpectra();
if (!ErrorHandler(NXmakedata(fFileHandle, "time_zero_bin", NX_INT32, 1, dims), PNEXUS_MAKE_DATA_ERROR, "couldn't create data entry 'time_zero_bin' in NXdetector.")) return NX_ERROR;
if (!ErrorHandler(NXopendata(fFileHandle, "time_zero_bin"), PNEXUS_OPEN_DATA_ERROR, "couldn't open data 'time_zero_bin' in NXdetector for writting.")) return NX_ERROR;
if (!ErrorHandler(NXputdata(fFileHandle, (void*)fNxEntry2->GetInstrument()->GetDetector()->GetT0s()), PNEXUS_PUT_DATA_ERROR, "couldn't put data 'time_zero_bin' in NXdetector.")) return NX_ERROR;
NXclosedata(fFileHandle);
} else if (fNxEntry2->GetInstrument()->GetDetector()->GetT0Tag() == 3) {
int dims[2];
dims[0] = fNxEntry2->GetInstrument()->GetDetector()->GetNoOfPeriods();
dims[1] = fNxEntry2->GetInstrument()->GetDetector()->GetNoOfSpectra();
@ -4932,6 +5127,13 @@ int PNeXus::WriteFileIdf2(const char* fileName, const NXaccess access)
if (!ErrorHandler(NXputdata(fFileHandle, (void*)&idata), PNEXUS_PUT_DATA_ERROR, "couldn't put data 'first_good_bin' in NXdetector.")) return NX_ERROR;
NXclosedata(fFileHandle);
} else if (fNxEntry2->GetInstrument()->GetDetector()->GetT0Tag() == 2) {
int dims[1];
dims[0] = fNxEntry2->GetInstrument()->GetDetector()->GetNoOfSpectra();
if (!ErrorHandler(NXmakedata(fFileHandle, "first_good_bin", NX_INT32, 1, dims), PNEXUS_MAKE_DATA_ERROR, "couldn't create data entry 'first_good_bin' in NXdetector.")) return NX_ERROR;
if (!ErrorHandler(NXopendata(fFileHandle, "first_good_bin"), PNEXUS_OPEN_DATA_ERROR, "couldn't open data 'first_good_bin' in NXdetector for writting.")) return NX_ERROR;
if (!ErrorHandler(NXputdata(fFileHandle, (void*)fNxEntry2->GetInstrument()->GetDetector()->GetFirstGoodBins()), PNEXUS_PUT_DATA_ERROR, "couldn't put data 'first_good_bin' in NXdetector.")) return NX_ERROR;
NXclosedata(fFileHandle);
} else if (fNxEntry2->GetInstrument()->GetDetector()->GetT0Tag() == 3) {
int dims[2];
dims[0] = fNxEntry2->GetInstrument()->GetDetector()->GetNoOfPeriods();
dims[1] = fNxEntry2->GetInstrument()->GetDetector()->GetNoOfSpectra();
@ -4954,6 +5156,13 @@ int PNeXus::WriteFileIdf2(const char* fileName, const NXaccess access)
if (!ErrorHandler(NXputdata(fFileHandle, (void*)&idata), PNEXUS_PUT_DATA_ERROR, "couldn't put data 'last_good_bin' in NXdetector.")) return NX_ERROR;
NXclosedata(fFileHandle);
} else if (fNxEntry2->GetInstrument()->GetDetector()->GetT0Tag() == 2) {
int dims[1];
dims[0] = fNxEntry2->GetInstrument()->GetDetector()->GetNoOfSpectra();
if (!ErrorHandler(NXmakedata(fFileHandle, "last_good_bin", NX_INT32, 1, dims), PNEXUS_MAKE_DATA_ERROR, "couldn't create data entry 'last_good_bin' in NXdetector.")) return NX_ERROR;
if (!ErrorHandler(NXopendata(fFileHandle, "last_good_bin"), PNEXUS_OPEN_DATA_ERROR, "couldn't open data 'last_good_bin' in NXdetector for writting.")) return NX_ERROR;
if (!ErrorHandler(NXputdata(fFileHandle, (void*)fNxEntry2->GetInstrument()->GetDetector()->GetLastGoodBins()), PNEXUS_PUT_DATA_ERROR, "couldn't put data 'last_good_bin' in NXdetector.")) return NX_ERROR;
NXclosedata(fFileHandle);
} else if (fNxEntry2->GetInstrument()->GetDetector()->GetT0Tag() == 3) {
int dims[2];
dims[0] = fNxEntry2->GetInstrument()->GetDetector()->GetNoOfPeriods();
dims[1] = fNxEntry2->GetInstrument()->GetDetector()->GetNoOfSpectra();
@ -4977,7 +5186,10 @@ int PNeXus::WriteFileIdf2(const char* fileName, const NXaccess access)
// open group 'detector_1' NXdata
if (!ErrorHandler(NXopengroup(fFileHandle, "detector_1", "NXdata"), PNEXUS_GROUP_OPEN_ERROR, "couldn't open group 'detector_1' in NXroot.")) return NX_ERROR;
if (!ErrorHandler(NXmakelink(fFileHandle, &clink), PNEXUS_LINKING_ERROR, "couldn't create link to 'counts' in NXdetector.")) return NX_ERROR;
for (unsigned int i=0; i<nxLinkVec.size(); i++) {
str = string("couldn't create link to ") + string(nxLinkVec[i].targetPath);
if (!ErrorHandler(NXmakelink(fFileHandle, &nxLinkVec[i]), PNEXUS_LINKING_ERROR, str.c_str())) return NX_ERROR;
}
// close group 'detector_1' NXdata
NXclosegroup(fFileHandle);
@ -4987,6 +5199,9 @@ int PNeXus::WriteFileIdf2(const char* fileName, const NXaccess access)
NXclose(&fFileHandle);
// clean up
nxLinkVec.clear();
return NX_OK;
}
@ -5092,6 +5307,7 @@ bool PNeXus::SearchInGroup(string str, string tag, NXname &nxname, NXname &nxcla
bool found = false;
int status;
NXinitgroupdir(fFileHandle);
do {
status = NXgetnextentry(fFileHandle, nxname, nxclass, &dataType);
if (!tag.compare("name")) {

13
src/external/nexus/PNeXus.h vendored
View File

@ -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) {