adopted to the not quite standard ISIS NeXus files.
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119
src/external/nexus/PNeXus.cpp
vendored
119
src/external/nexus/PNeXus.cpp
vendored
@ -818,10 +818,10 @@ PNeXusDetector2::PNeXusDetector2()
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fNoOfBins = -1;
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fT0Tag = -1;
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fT0 = 0;
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fFirstGoodBin = 0;
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fLastGoodBin = 0;
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fHisto = 0;
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fT0 = nullptr;
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fFirstGoodBin = nullptr;
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fLastGoodBin = nullptr;
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fHisto = nullptr;
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}
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//------------------------------------------------------------------------------------------
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@ -837,19 +837,19 @@ PNeXusDetector2::~PNeXusDetector2()
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if (fT0) {
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delete [] fT0;
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fT0 = 0;
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fT0 = nullptr;
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}
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if (fFirstGoodBin) {
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delete [] fFirstGoodBin;
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fFirstGoodBin = 0;
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fFirstGoodBin = nullptr;
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}
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if (fLastGoodBin) {
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delete [] fLastGoodBin;
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fLastGoodBin = 0;
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fLastGoodBin = nullptr;
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}
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if (fHisto) {
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delete [] fHisto;
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fHisto = 0;
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fHisto = nullptr;
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}
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}
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@ -921,8 +921,14 @@ int PNeXusDetector2::GetT0(int idxp, int idxs)
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{
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int result = -1;
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if (fT0Tag == 1) { // there is only ONE t0 present
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if (fT0 != nullptr)
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result = *fT0;
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return result;
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}
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if ((idxp < 0) && (idxs < 0)) { // assumption: there is only ONE t0 for all spectra
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if (fT0 != 0) {
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if (fT0 != nullptr) {
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result = *fT0;
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}
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} else if ((idxp < 0) && (idxs >= 0)) { // assumption: t0's are represented as t0[ns]
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@ -1031,16 +1037,23 @@ int PNeXusDetector2::GetFirstGoodBin(int idxp, int idxs)
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{
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int result = -1;
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if (fT0Tag == 1) { // there is only ONE t0 present
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if (fT0 != nullptr)
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result = *fFirstGoodBin;
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return result;
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}
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if ((idxp < 0) && (idxs < 0)) { // assumption: there is only ONE t0 for all spectra
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if (fFirstGoodBin != 0) {
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if (fFirstGoodBin != nullptr) {
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result = *fFirstGoodBin;
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}
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} else if ((idxp < 0) && (idxs >= 0)) { // assumptions: fgb's are represented as fgb[ns]
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if (idxs < fNoOfSpectra) {
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if ((idxs < fNoOfSpectra) && (fFirstGoodBin != nullptr)) {
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result = *(fFirstGoodBin+idxs);
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}
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} else if ((idxp >= 0) && (idxs >= 0)) { // assumption: fgb's are represented as fgb[np][ns]
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if ((idxp < fNoOfPeriods) || (idxs < fNoOfSpectra)) {
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if (fFirstGoodBin != nullptr)
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result = *(fFirstGoodBin+idxp*fNoOfSpectra+idxs);
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}
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} else {
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@ -1141,16 +1154,23 @@ int PNeXusDetector2::GetLastGoodBin(int idxp, int idxs)
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{
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int result = -1;
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if (fT0Tag == 1) { // there is only ONE t0 present
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if (fT0 != nullptr)
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result = *fLastGoodBin;
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return result;
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}
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if ((idxp < 0) && (idxs < 0)) { // assumption: there is only ONE t0 for all spectra
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if (fLastGoodBin != 0) {
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if (fLastGoodBin != nullptr) {
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result = *fLastGoodBin;
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}
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} else if ((idxp < 0) && (idxs >= 0)) { // assumption: lgb's are represented as lgb[ns]
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if (idxs < fNoOfSpectra) {
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if ((idxs < fNoOfSpectra) && (fLastGoodBin != nullptr)) {
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result = *(fLastGoodBin+idxs);
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}
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} else if ((idxp >= 0) && (idxs >= 0)) { // assumption: lgb's are represented as lgb[np][ns]
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if ((idxp < fNoOfPeriods) || (idxs < fNoOfSpectra)) {
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if (fLastGoodBin != nullptr)
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result = *(fLastGoodBin+idxp*fNoOfSpectra+idxs);
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}
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} else {
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@ -3398,6 +3418,14 @@ int PNeXus::ReadFileIdf2()
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return NX_ERROR;
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}
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// beamline
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if (SearchInGroup("beamline", "name", nxname, nxclass, dataType)) {
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if (!ErrorHandler(NXopendata(fFileHandle, "beamline"), PNEXUS_OPEN_DATA_ERROR, "couldn't open 'beamline' data in NXentry!")) return NX_ERROR;
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if (!ErrorHandler(GetStringData(str), PNEXUS_GET_DATA_ERROR, "couldn't read 'beamline' data in NXentry!")) return NX_ERROR;
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if (!ErrorHandler(NXclosedata(fFileHandle), PNEXUS_CLOSE_DATA_ERROR, "couldn't close 'beamline' data in NXentry!")) return NX_ERROR;
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fNxEntry2->GetInstrument()->GetBeamline()->SetName(str);
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}
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// definition
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if (!ErrorHandler(NXopendata(fFileHandle, "definition"), PNEXUS_OPEN_DATA_ERROR, "couldn't open 'definition' data in NXentry!")) return NX_ERROR;
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if (!ErrorHandler(GetStringData(str), PNEXUS_GET_DATA_ERROR, "couldn't read 'definition' data in NXentry!")) return NX_ERROR;
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@ -3576,7 +3604,9 @@ int PNeXus::ReadFileIdf2()
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// close group NXsource
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NXclosegroup(fFileHandle);
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// open group NXbeamline
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if (SearchInGroup("beamline", "name", nxname, nxclass, dataType)) {
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if (!ErrorHandler(NXopengroup(fFileHandle, "beamline", "NXbeamline"), PNEXUS_GROUP_OPEN_ERROR, "couldn't open NeXus subgroup beamline in NXinstrument!")) return NX_ERROR;
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// beamline name
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@ -3587,15 +3617,24 @@ int PNeXus::ReadFileIdf2()
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// close group NXbeamline
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NXclosegroup(fFileHandle);
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} else {
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std::cerr << "**WARNING** in class NXinstrument the object NXbeamline with name 'beamline' is missing!" << std::endl;
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std::cerr << " Complain at the facility where you got this data file from!" << std::endl;
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}
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// open group NXdetector
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// open group NXdetector in instrument (NXinstrument)
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if (!ErrorHandler(NXopengroup(fFileHandle, "detector_1", "NXdetector"), PNEXUS_GROUP_OPEN_ERROR, "couldn't open NeXus subgroup detector_1 in NXinstrument!")) return NX_ERROR;
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// description
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if (SearchInGroup("description", "name", nxname, nxclass, dataType)) {
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if (!ErrorHandler(NXopendata(fFileHandle, "description"), PNEXUS_OPEN_DATA_ERROR, "couldn't open 'description' data in NXdetector!")) return NX_ERROR;
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if (!ErrorHandler(GetStringData(str), PNEXUS_GET_DATA_ERROR, "couldn't read 'description' data in NXdetector!")) return NX_ERROR;
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if (!ErrorHandler(NXclosedata(fFileHandle), PNEXUS_CLOSE_DATA_ERROR, "couldn't close 'description' data in NXdetector!")) return NX_ERROR;
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fNxEntry2->GetInstrument()->GetDetector()->SetDescription(str);
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} else {
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std::cerr << "**WARNING** in class NXdetector to object NX_CHAR with name 'description' is missing!" << std::endl;
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std::cerr << " Complain at the facility where you got this data file from!" << std::endl;
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}
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// get the time resolution. This is a little bit complicated since it is either present as 'histogram_resolution' or needs to be extracted from the 'raw_time' vector
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// 1st check if 'histogram_resolution' is found
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@ -3607,10 +3646,10 @@ int PNeXus::ReadFileIdf2()
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fNxEntry2->GetInstrument()->GetDetector()->SetTimeResolution((double)fval, str);
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} else if (SearchInGroup("resolution", "name", nxname, nxclass, dataType)) { // 2nd check if 'resolution' is found
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if (!ErrorHandler(NXopendata(fFileHandle, "resolution"), PNEXUS_OPEN_DATA_ERROR, "couldn't open 'resolution' data in NXdetector!")) return NX_ERROR;
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if (!ErrorHandler(NXgetdata(fFileHandle, &fval), PNEXUS_GET_DATA_ERROR, "couldn't read 'resolution' data in NXdetector!")) return NX_ERROR;
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if (!ErrorHandler(NXgetdata(fFileHandle, &ival), PNEXUS_GET_DATA_ERROR, "couldn't read 'resolution' data in NXdetector!")) return NX_ERROR;
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if (!ErrorHandler(GetStringAttr("units", str), PNEXUS_GET_ATTR_ERROR, "couldn't read time resolution units in NXdetector!")) return NX_ERROR;
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if (!ErrorHandler(NXclosedata(fFileHandle), PNEXUS_CLOSE_DATA_ERROR, "couldn't close 'resolution' data in NXdetector!")) return NX_ERROR;
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fNxEntry2->GetInstrument()->GetDetector()->SetTimeResolution((double)fval, str);
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fNxEntry2->GetInstrument()->GetDetector()->SetTimeResolution((double)ival, str);
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} else { // 3nd 'histogram_resolution' is not present, hence extract the time resolution from the 'raw_time' vector
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if (!ErrorHandler(NXopendata(fFileHandle, "raw_time"), PNEXUS_OPEN_DATA_ERROR, "couldn't open 'raw_time' data in NXdetector!")) return NX_ERROR;
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std::vector<double> rawTime;
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@ -3626,6 +3665,51 @@ int PNeXus::ReadFileIdf2()
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// check the dimensions of 'counts'
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if (!ErrorHandler(NXgetinfo(fFileHandle, &rank, dims, &type), PNEXUS_GET_META_INFO_ERROR, "couldn't get 'counts' info in NXdetector!")) return NX_ERROR;
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// check if last_good_bin, first_good_bin, and t0_bins are defined as attributes
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int attLen = 1, attType = NX_INT32;
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if (SearchAttrInData("first_good_bin", attLen, attType)) {
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char cstr[1204];
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memset(cstr, '\0', sizeof(cstr));
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strncpy(cstr, "first_good_bin", sizeof(cstr));
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status = NXgetattr(fFileHandle, cstr, (void*)&ival, &attLen, &attType);
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fNxEntry2->GetInstrument()->GetDetector()->SetT0Tag(1); // a single set for t0, fgb, lgb is likely given
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int *i_data_ptr = new int;
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*i_data_ptr = ival;
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if (!fNxEntry2->GetInstrument()->GetDetector()->SetFirstGoodBin(i_data_ptr)) {
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std::cerr << std::endl << ">> **ERROR** " << fNxEntry2->GetInstrument()->GetDetector()->GetErrorMsg() << std::endl;
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return NX_ERROR;
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}
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}
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if (SearchAttrInData("last_good_bin", attLen, attType)) {
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char cstr[1204];
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memset(cstr, '\0', sizeof(cstr));
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strncpy(cstr, "last_good_bin", sizeof(cstr));
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status = NXgetattr(fFileHandle, cstr, (void*)&ival, &attLen, &attType);
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fNxEntry2->GetInstrument()->GetDetector()->SetT0Tag(1); // a single set for t0, fgb, lgb is likely given
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int *i_data_ptr = new int;
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*i_data_ptr = ival;
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if (!fNxEntry2->GetInstrument()->GetDetector()->SetLastGoodBin(i_data_ptr)) {
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std::cerr << std::endl << ">> **ERROR** " << fNxEntry2->GetInstrument()->GetDetector()->GetErrorMsg() << std::endl;
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return NX_ERROR;
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}
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}
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if (SearchAttrInData("t0_bin", attLen, attType)) {
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char cstr[1204];
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memset(cstr, '\0', sizeof(cstr));
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strncpy(cstr, "t0_bin", sizeof(cstr));
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status = NXgetattr(fFileHandle, cstr, (void*)&ival, &attLen, &attType);
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fNxEntry2->GetInstrument()->GetDetector()->SetT0Tag(1); // a single set for t0, fgb, lgb is likely given
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int *i_data_ptr = new int;
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*i_data_ptr = ival;
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if (!fNxEntry2->GetInstrument()->GetDetector()->SetT0(i_data_ptr)) {
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std::cerr << std::endl << ">> **ERROR** " << fNxEntry2->GetInstrument()->GetDetector()->GetErrorMsg() << std::endl;
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return NX_ERROR;
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}
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}
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// calculate the needed size
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size = dims[0];
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for (int i=1; i<rank; i++)
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@ -3713,6 +3797,8 @@ int PNeXus::ReadFileIdf2()
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if (!ErrorHandler(NXclosedata(fFileHandle), PNEXUS_CLOSE_DATA_ERROR, "couldn't close 'spectrum_index' data in NXdetector!")) return NX_ERROR;
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// only handle t0, fgb, lgb, if they are not already set as an attribute of /raw_data_1/instrument/detector_1/counts
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if (fNxEntry2->GetInstrument()->GetDetector()->GetT0Tag() == -1) {
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// handle t0's
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if (SearchInGroup("time_zero_bin", "name", nxname, nxclass, dataType)) { // check for 'time_zero_bin'
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if (!ErrorHandler(NXopendata(fFileHandle, "time_zero_bin"), PNEXUS_OPEN_DATA_ERROR, "couldn't open 'time_zero_bin' data in NXdetector!")) return NX_ERROR;
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@ -4028,6 +4114,7 @@ int PNeXus::ReadFileIdf2()
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} else {
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std::cerr << std::endl << ">> **WARNING** found neither 'last_good_bin' nor 'last_good_time' values ..." << std::endl;
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}
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}
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// close group NXdetector
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NXclosegroup(fFileHandle);
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