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adopted to the not quite standard ISIS NeXus files.

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This commit is contained in:
suter_a 2021-06-05 10:51:19 +02:00
parent effab214f9
commit baf26aac7f
1 changed files with 407 additions and 320 deletions
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727
src/external/nexus/PNeXus.cpp vendored
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@ -818,10 +818,10 @@ PNeXusDetector2::PNeXusDetector2()
fNoOfBins = -1; fNoOfBins = -1;
fT0Tag = -1; fT0Tag = -1;
fT0 = 0; fT0 = nullptr;
fFirstGoodBin = 0; fFirstGoodBin = nullptr;
fLastGoodBin = 0; fLastGoodBin = nullptr;
fHisto = 0; fHisto = nullptr;
} }
//------------------------------------------------------------------------------------------ //------------------------------------------------------------------------------------------
@ -837,19 +837,19 @@ PNeXusDetector2::~PNeXusDetector2()
if (fT0) { if (fT0) {
delete [] fT0; delete [] fT0;
fT0 = 0; fT0 = nullptr;
} }
if (fFirstGoodBin) { if (fFirstGoodBin) {
delete [] fFirstGoodBin; delete [] fFirstGoodBin;
fFirstGoodBin = 0; fFirstGoodBin = nullptr;
} }
if (fLastGoodBin) { if (fLastGoodBin) {
delete [] fLastGoodBin; delete [] fLastGoodBin;
fLastGoodBin = 0; fLastGoodBin = nullptr;
} }
if (fHisto) { if (fHisto) {
delete [] fHisto; delete [] fHisto;
fHisto = 0; fHisto = nullptr;
} }
} }
@ -919,10 +919,16 @@ bool PNeXusDetector2::IsValid(bool strict)
*/ */
int PNeXusDetector2::GetT0(int idxp, int idxs) int PNeXusDetector2::GetT0(int idxp, int idxs)
{ {
int result = -1; int result = -1;
if (fT0Tag == 1) { // there is only ONE t0 present
if (fT0 != nullptr)
result = *fT0;
return result;
}
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) { if (fT0 != nullptr) {
result = *fT0; result = *fT0;
} }
} else if ((idxp < 0) && (idxs >= 0)) { // assumption: t0's are represented as t0[ns] } else if ((idxp < 0) && (idxs >= 0)) { // assumption: t0's are represented as t0[ns]
@ -1031,17 +1037,24 @@ int PNeXusDetector2::GetFirstGoodBin(int idxp, int idxs)
{ {
int result = -1; int result = -1;
if (fT0Tag == 1) { // there is only ONE t0 present
if (fT0 != nullptr)
result = *fFirstGoodBin;
return result;
}
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) { if (fFirstGoodBin != nullptr) {
result = *fFirstGoodBin; result = *fFirstGoodBin;
} }
} else if ((idxp < 0) && (idxs >= 0)) { // assumptions: fgb's are represented as fgb[ns] } else if ((idxp < 0) && (idxs >= 0)) { // assumptions: fgb's are represented as fgb[ns]
if (idxs < fNoOfSpectra) { if ((idxs < fNoOfSpectra) && (fFirstGoodBin != nullptr)) {
result = *(fFirstGoodBin+idxs); result = *(fFirstGoodBin+idxs);
} }
} else if ((idxp >= 0) && (idxs >= 0)) { // assumption: fgb's are represented as fgb[np][ns] } else if ((idxp >= 0) && (idxs >= 0)) { // assumption: fgb's are represented as fgb[np][ns]
if ((idxp < fNoOfPeriods) || (idxs < fNoOfSpectra)) { if ((idxp < fNoOfPeriods) || (idxs < fNoOfSpectra)) {
result = *(fFirstGoodBin+idxp*fNoOfSpectra+idxs); if (fFirstGoodBin != nullptr)
result = *(fFirstGoodBin+idxp*fNoOfSpectra+idxs);
} }
} else { } else {
result = -1; result = -1;
@ -1141,17 +1154,24 @@ int PNeXusDetector2::GetLastGoodBin(int idxp, int idxs)
{ {
int result = -1; int result = -1;
if (fT0Tag == 1) { // there is only ONE t0 present
if (fT0 != nullptr)
result = *fLastGoodBin;
return result;
}
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) { if (fLastGoodBin != nullptr) {
result = *fLastGoodBin; result = *fLastGoodBin;
} }
} else if ((idxp < 0) && (idxs >= 0)) { // assumption: lgb's are represented as lgb[ns] } else if ((idxp < 0) && (idxs >= 0)) { // assumption: lgb's are represented as lgb[ns]
if (idxs < fNoOfSpectra) { if ((idxs < fNoOfSpectra) && (fLastGoodBin != nullptr)) {
result = *(fLastGoodBin+idxs); result = *(fLastGoodBin+idxs);
} }
} else if ((idxp >= 0) && (idxs >= 0)) { // assumption: lgb's are represented as lgb[np][ns] } else if ((idxp >= 0) && (idxs >= 0)) { // assumption: lgb's are represented as lgb[np][ns]
if ((idxp < fNoOfPeriods) || (idxs < fNoOfSpectra)) { if ((idxp < fNoOfPeriods) || (idxs < fNoOfSpectra)) {
result = *(fLastGoodBin+idxp*fNoOfSpectra+idxs); if (fLastGoodBin != nullptr)
result = *(fLastGoodBin+idxp*fNoOfSpectra+idxs);
} }
} else { } else {
result = -1; result = -1;
@ -3398,6 +3418,14 @@ int PNeXus::ReadFileIdf2()
return NX_ERROR; return NX_ERROR;
} }
// beamline
if (SearchInGroup("beamline", "name", nxname, nxclass, dataType)) {
if (!ErrorHandler(NXopendata(fFileHandle, "beamline"), PNEXUS_OPEN_DATA_ERROR, "couldn't open 'beamline' data in NXentry!")) return NX_ERROR;
if (!ErrorHandler(GetStringData(str), PNEXUS_GET_DATA_ERROR, "couldn't read 'beamline' data in NXentry!")) return NX_ERROR;
if (!ErrorHandler(NXclosedata(fFileHandle), PNEXUS_CLOSE_DATA_ERROR, "couldn't close 'beamline' data in NXentry!")) return NX_ERROR;
fNxEntry2->GetInstrument()->GetBeamline()->SetName(str);
}
// definition // definition
if (!ErrorHandler(NXopendata(fFileHandle, "definition"), PNEXUS_OPEN_DATA_ERROR, "couldn't open 'definition' data in NXentry!")) return NX_ERROR; if (!ErrorHandler(NXopendata(fFileHandle, "definition"), PNEXUS_OPEN_DATA_ERROR, "couldn't open 'definition' data in NXentry!")) return NX_ERROR;
if (!ErrorHandler(GetStringData(str), PNEXUS_GET_DATA_ERROR, "couldn't read 'definition' data in NXentry!")) return NX_ERROR; if (!ErrorHandler(GetStringData(str), PNEXUS_GET_DATA_ERROR, "couldn't read 'definition' data in NXentry!")) return NX_ERROR;
@ -3576,26 +3604,37 @@ int PNeXus::ReadFileIdf2()
// close group NXsource // close group NXsource
NXclosegroup(fFileHandle); NXclosegroup(fFileHandle);
// open group NXbeamline // open group NXbeamline
if (!ErrorHandler(NXopengroup(fFileHandle, "beamline", "NXbeamline"), PNEXUS_GROUP_OPEN_ERROR, "couldn't open NeXus subgroup beamline in NXinstrument!")) return NX_ERROR; if (SearchInGroup("beamline", "name", nxname, nxclass, dataType)) {
if (!ErrorHandler(NXopengroup(fFileHandle, "beamline", "NXbeamline"), PNEXUS_GROUP_OPEN_ERROR, "couldn't open NeXus subgroup beamline in NXinstrument!")) return NX_ERROR;
// beamline name // beamline name
if (!ErrorHandler(NXopendata(fFileHandle, "beamline"), PNEXUS_OPEN_DATA_ERROR, "couldn't open 'beamline' data in NXbeamline!")) return NX_ERROR; if (!ErrorHandler(NXopendata(fFileHandle, "beamline"), PNEXUS_OPEN_DATA_ERROR, "couldn't open 'beamline' data in NXbeamline!")) return NX_ERROR;
if (!ErrorHandler(GetStringData(str), PNEXUS_GET_DATA_ERROR, "couldn't read 'beamline' data in NXbeamline!")) return NX_ERROR; if (!ErrorHandler(GetStringData(str), PNEXUS_GET_DATA_ERROR, "couldn't read 'beamline' data in NXbeamline!")) return NX_ERROR;
if (!ErrorHandler(NXclosedata(fFileHandle), PNEXUS_CLOSE_DATA_ERROR, "couldn't close 'beamline' data in NXbeamline!")) return NX_ERROR; if (!ErrorHandler(NXclosedata(fFileHandle), PNEXUS_CLOSE_DATA_ERROR, "couldn't close 'beamline' data in NXbeamline!")) return NX_ERROR;
fNxEntry2->GetInstrument()->GetBeamline()->SetName(str); fNxEntry2->GetInstrument()->GetBeamline()->SetName(str);
// close group NXbeamline // close group NXbeamline
NXclosegroup(fFileHandle); NXclosegroup(fFileHandle);
} else {
std::cerr << "**WARNING** in class NXinstrument the object NXbeamline with name 'beamline' is missing!" << std::endl;
std::cerr << " Complain at the facility where you got this data file from!" << std::endl;
}
// open group NXdetector // open group NXdetector in instrument (NXinstrument)
if (!ErrorHandler(NXopengroup(fFileHandle, "detector_1", "NXdetector"), PNEXUS_GROUP_OPEN_ERROR, "couldn't open NeXus subgroup detector_1 in NXinstrument!")) return NX_ERROR; if (!ErrorHandler(NXopengroup(fFileHandle, "detector_1", "NXdetector"), PNEXUS_GROUP_OPEN_ERROR, "couldn't open NeXus subgroup detector_1 in NXinstrument!")) return NX_ERROR;
// description // description
if (!ErrorHandler(NXopendata(fFileHandle, "description"), PNEXUS_OPEN_DATA_ERROR, "couldn't open 'description' data in NXdetector!")) return NX_ERROR; if (SearchInGroup("description", "name", nxname, nxclass, dataType)) {
if (!ErrorHandler(GetStringData(str), PNEXUS_GET_DATA_ERROR, "couldn't read 'description' data in NXdetector!")) return NX_ERROR; if (!ErrorHandler(NXopendata(fFileHandle, "description"), PNEXUS_OPEN_DATA_ERROR, "couldn't open 'description' data in NXdetector!")) return NX_ERROR;
if (!ErrorHandler(NXclosedata(fFileHandle), PNEXUS_CLOSE_DATA_ERROR, "couldn't close 'description' data in NXdetector!")) return NX_ERROR; if (!ErrorHandler(GetStringData(str), PNEXUS_GET_DATA_ERROR, "couldn't read 'description' data in NXdetector!")) return NX_ERROR;
fNxEntry2->GetInstrument()->GetDetector()->SetDescription(str); if (!ErrorHandler(NXclosedata(fFileHandle), PNEXUS_CLOSE_DATA_ERROR, "couldn't close 'description' data in NXdetector!")) return NX_ERROR;
fNxEntry2->GetInstrument()->GetDetector()->SetDescription(str);
} else {
std::cerr << "**WARNING** in class NXdetector to object NX_CHAR with name 'description' is missing!" << std::endl;
std::cerr << " Complain at the facility where you got this data file from!" << std::endl;
}
// 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 // 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
// 1st check if 'histogram_resolution' is found // 1st check if 'histogram_resolution' is found
@ -3607,10 +3646,10 @@ int PNeXus::ReadFileIdf2()
fNxEntry2->GetInstrument()->GetDetector()->SetTimeResolution((double)fval, str); fNxEntry2->GetInstrument()->GetDetector()->SetTimeResolution((double)fval, str);
} else if (SearchInGroup("resolution", "name", nxname, nxclass, dataType)) { // 2nd check if 'resolution' is found } 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(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(NXgetdata(fFileHandle, &ival), 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(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; 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); fNxEntry2->GetInstrument()->GetDetector()->SetTimeResolution((double)ival, str);
} else { // 3nd 'histogram_resolution' is not present, hence extract the time resolution from the 'raw_time' vector } 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; if (!ErrorHandler(NXopendata(fFileHandle, "raw_time"), PNEXUS_OPEN_DATA_ERROR, "couldn't open 'raw_time' data in NXdetector!")) return NX_ERROR;
std::vector<double> rawTime; std::vector<double> rawTime;
@ -3626,6 +3665,51 @@ int PNeXus::ReadFileIdf2()
// check the dimensions of 'counts' // check the dimensions of 'counts'
if (!ErrorHandler(NXgetinfo(fFileHandle, &rank, dims, &type), PNEXUS_GET_META_INFO_ERROR, "couldn't get 'counts' info in NXdetector!")) return NX_ERROR; if (!ErrorHandler(NXgetinfo(fFileHandle, &rank, dims, &type), PNEXUS_GET_META_INFO_ERROR, "couldn't get 'counts' info in NXdetector!")) return NX_ERROR;
// check if last_good_bin, first_good_bin, and t0_bins are defined as attributes
int attLen = 1, attType = NX_INT32;
if (SearchAttrInData("first_good_bin", attLen, attType)) {
char cstr[1204];
memset(cstr, '\0', sizeof(cstr));
strncpy(cstr, "first_good_bin", sizeof(cstr));
status = NXgetattr(fFileHandle, cstr, (void*)&ival, &attLen, &attType);
fNxEntry2->GetInstrument()->GetDetector()->SetT0Tag(1); // a single set for t0, fgb, lgb is likely given
int *i_data_ptr = new int;
*i_data_ptr = ival;
if (!fNxEntry2->GetInstrument()->GetDetector()->SetFirstGoodBin(i_data_ptr)) {
std::cerr << std::endl << ">> **ERROR** " << fNxEntry2->GetInstrument()->GetDetector()->GetErrorMsg() << std::endl;
return NX_ERROR;
}
}
if (SearchAttrInData("last_good_bin", attLen, attType)) {
char cstr[1204];
memset(cstr, '\0', sizeof(cstr));
strncpy(cstr, "last_good_bin", sizeof(cstr));
status = NXgetattr(fFileHandle, cstr, (void*)&ival, &attLen, &attType);
fNxEntry2->GetInstrument()->GetDetector()->SetT0Tag(1); // a single set for t0, fgb, lgb is likely given
int *i_data_ptr = new int;
*i_data_ptr = ival;
if (!fNxEntry2->GetInstrument()->GetDetector()->SetLastGoodBin(i_data_ptr)) {
std::cerr << std::endl << ">> **ERROR** " << fNxEntry2->GetInstrument()->GetDetector()->GetErrorMsg() << std::endl;
return NX_ERROR;
}
}
if (SearchAttrInData("t0_bin", attLen, attType)) {
char cstr[1204];
memset(cstr, '\0', sizeof(cstr));
strncpy(cstr, "t0_bin", sizeof(cstr));
status = NXgetattr(fFileHandle, cstr, (void*)&ival, &attLen, &attType);
fNxEntry2->GetInstrument()->GetDetector()->SetT0Tag(1); // a single set for t0, fgb, lgb is likely given
int *i_data_ptr = new int;
*i_data_ptr = ival;
if (!fNxEntry2->GetInstrument()->GetDetector()->SetT0(i_data_ptr)) {
std::cerr << std::endl << ">> **ERROR** " << fNxEntry2->GetInstrument()->GetDetector()->GetErrorMsg() << std::endl;
return NX_ERROR;
}
}
// calculate the needed size // calculate the needed size
size = dims[0]; size = dims[0];
for (int i=1; i<rank; i++) for (int i=1; i<rank; i++)
@ -3713,320 +3797,323 @@ int PNeXus::ReadFileIdf2()
if (!ErrorHandler(NXclosedata(fFileHandle), PNEXUS_CLOSE_DATA_ERROR, "couldn't close 'spectrum_index' data in NXdetector!")) return NX_ERROR; if (!ErrorHandler(NXclosedata(fFileHandle), PNEXUS_CLOSE_DATA_ERROR, "couldn't close 'spectrum_index' data in NXdetector!")) return NX_ERROR;
// handle t0's // only handle t0, fgb, lgb, if they are not already set as an attribute of /raw_data_1/instrument/detector_1/counts
if (SearchInGroup("time_zero_bin", "name", nxname, nxclass, dataType)) { // check for 'time_zero_bin' if (fNxEntry2->GetInstrument()->GetDetector()->GetT0Tag() == -1) {
if (!ErrorHandler(NXopendata(fFileHandle, "time_zero_bin"), PNEXUS_OPEN_DATA_ERROR, "couldn't open 'time_zero_bin' data in NXdetector!")) return NX_ERROR; // handle t0's
if (SearchInGroup("time_zero_bin", "name", nxname, nxclass, dataType)) { // check for 'time_zero_bin'
if (!ErrorHandler(NXopendata(fFileHandle, "time_zero_bin"), PNEXUS_OPEN_DATA_ERROR, "couldn't open 'time_zero_bin' data in NXdetector!")) return NX_ERROR;
// check the dimensions of the 'time_zero_bin' vector // 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 (!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 == 1) && (dims[0] == 1)) { // single t0 entry if ((rank == 1) && (dims[0] == 1)) { // single t0 entry
fNxEntry2->GetInstrument()->GetDetector()->SetT0Tag(1); fNxEntry2->GetInstrument()->GetDetector()->SetT0Tag(1);
} else if ((rank == 1) && (dims[0] > 1)) { // t0 of the form t0[ns] } else if ((rank == 1) && (dims[0] > 1)) { // t0 of the form t0[ns]
fNxEntry2->GetInstrument()->GetDetector()->SetT0Tag(2); fNxEntry2->GetInstrument()->GetDetector()->SetT0Tag(2);
} else if (rank == 2) { // t0 of the form t0[np][ns] } else if (rank == 2) { // t0 of the form t0[np][ns]
fNxEntry2->GetInstrument()->GetDetector()->SetT0Tag(3); fNxEntry2->GetInstrument()->GetDetector()->SetT0Tag(3);
} else {
std::cerr << std::endl << ">> **ERROR** found 'time_zero_bin' info in NXdetector with rank=" << rank << ". Do not know how to handle." << std::endl;
return NX_ERROR;
}
// calculate the needed size
size = dims[0];
for (int i=1; i<rank; i++)
size *= dims[i];
noOfElements = size;
size *= GetDataSize(type);
// allocate locale memory to get the data
char *data_ptr = new char[size];
if (data_ptr == nullptr) {
return NX_ERROR;
}
// get the data
int *i_data_ptr = (int*) data_ptr;
int status = NXgetdata(fFileHandle, i_data_ptr);
if (status != NX_OK) {
return NX_ERROR;
}
if (!fNxEntry2->GetInstrument()->GetDetector()->SetT0(i_data_ptr)) {
std::cerr << std::endl << ">> **ERROR** " << fNxEntry2->GetInstrument()->GetDetector()->GetErrorMsg() << std::endl;
return NX_ERROR;
}
// clean up
if (data_ptr) {
delete [] data_ptr;
data_ptr = nullptr;
}
if (!ErrorHandler(NXclosedata(fFileHandle), PNEXUS_CLOSE_DATA_ERROR, "couldn't close 'time_zero_bin' data in NXdetector!")) return NX_ERROR;
} else if (SearchInGroup("time_zero", "name", nxname, nxclass, dataType)) { // check for 'time_zero'
if (!ErrorHandler(NXopendata(fFileHandle, "time_zero"), PNEXUS_OPEN_DATA_ERROR, "couldn't open 'time_zero' data in NXdetector!")) return NX_ERROR;
// 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 == 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 {
std::cerr << std::endl << ">> **ERROR** found 'time_zero' info in NXdetector with rank=" << rank << ". Do not know how to handle." << std::endl;
return NX_ERROR;
}
// calculate the needed size
size = dims[0];
for (int i=1; i<rank; i++)
size *= dims[i];
noOfElements = size;
size *= GetDataSize(type);
// allocate locale memory to get the data
char *data_ptr = new char[size];
if (data_ptr == nullptr) {
return NX_ERROR;
}
// get the data
float *f_data_ptr = (float*) data_ptr;
int status = NXgetdata(fFileHandle, f_data_ptr);
if (status != NX_OK) {
return NX_ERROR;
}
if (!ErrorHandler(GetStringAttr("units", str), PNEXUS_GET_ATTR_ERROR, "couldn't read 'time_zero' units in NXdetector!")) return NX_ERROR;
// Set T0's
// check that the necessary time resolution is present
if (fNxEntry2->GetInstrument()->GetDetector()->GetTimeResolution(str) == 0.0) {
std::cerr << std::endl << ">> **ERROR** trying to set T0's based on 'time_zero'. Need a valid time resolution to do so, but this is not given." << std::endl;
return NX_ERROR;
}
// set the t0's based on the t0 time stamp and the time resolution
int *pt0 = nullptr;
if (rank == 1) {
pt0 = new int;
*pt0 = (int)(*f_data_ptr / (float)fNxEntry2->GetInstrument()->GetDetector()->GetTimeResolution(str));
} else { // rank == 2
pt0 = new int[noOfElements];
for (int i=0; i<noOfElements; i++) {
*(pt0+i) = (int)(*(f_data_ptr+i) / (float)fNxEntry2->GetInstrument()->GetDetector()->GetTimeResolution(str));
}
}
if (!fNxEntry2->GetInstrument()->GetDetector()->SetT0(pt0)) {
std::cerr << std::endl << ">> **ERROR** " << fNxEntry2->GetInstrument()->GetDetector()->GetErrorMsg() << std::endl;
return NX_ERROR;
}
// clean up
if (data_ptr) {
delete [] data_ptr;
data_ptr = nullptr;
}
std::cerr << std::endl << ">> **WARNING** found only 'time_zero' will convert it to 'time_zero_bin' values" << std::endl;
if (!ErrorHandler(NXclosedata(fFileHandle), PNEXUS_CLOSE_DATA_ERROR, "couldn't close 'time_zero' data in NXdetector!")) return NX_ERROR;
} else { } else {
std::cerr << std::endl << ">> **ERROR** found 'time_zero_bin' info in NXdetector with rank=" << rank << ". Do not know how to handle." << std::endl; std::cerr << std::endl << ">> **WARNING** found neither 'time_zero_bin' nor 'time_zero' values ..." << std::endl;
return NX_ERROR;
} }
// calculate the needed size // handle first good bin
size = dims[0]; if (SearchInGroup("first_good_bin", "name", nxname, nxclass, dataType)) {
for (int i=1; i<rank; i++) if (!ErrorHandler(NXopendata(fFileHandle, "first_good_bin"), PNEXUS_OPEN_DATA_ERROR, "couldn't open 'first_good_bin' data in NXdetector!")) return NX_ERROR;
size *= dims[i];
noOfElements = size;
size *= GetDataSize(type);
// allocate locale memory to get the data // check the dimensions of the 'first_good_bin' vector
char *data_ptr = new char[size]; 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 (data_ptr == nullptr) {
return NX_ERROR;
}
// get the data // calculate the needed size
int *i_data_ptr = (int*) data_ptr; size = dims[0];
int status = NXgetdata(fFileHandle, i_data_ptr); for (int i=1; i<rank; i++)
if (status != NX_OK) { size *= dims[i];
return NX_ERROR; noOfElements = size;
} size *= GetDataSize(type);
if (!fNxEntry2->GetInstrument()->GetDetector()->SetT0(i_data_ptr)) { // allocate locale memory to get the data
std::cerr << std::endl << ">> **ERROR** " << fNxEntry2->GetInstrument()->GetDetector()->GetErrorMsg() << std::endl; char *data_ptr = new char[size];
return NX_ERROR; if (data_ptr == nullptr) {
} return NX_ERROR;
}
// clean up // get the data
if (data_ptr) { int *i_data_ptr = (int*) data_ptr;
delete [] data_ptr; int status = NXgetdata(fFileHandle, i_data_ptr);
data_ptr = nullptr; if (status != NX_OK) {
} return NX_ERROR;
}
if (!ErrorHandler(NXclosedata(fFileHandle), PNEXUS_CLOSE_DATA_ERROR, "couldn't close 'time_zero_bin' data in NXdetector!")) return NX_ERROR; if (!fNxEntry2->GetInstrument()->GetDetector()->SetFirstGoodBin(i_data_ptr)) {
} else if (SearchInGroup("time_zero", "name", nxname, nxclass, dataType)) { // check for 'time_zero' std::cerr << std::endl << ">> **ERROR** " << fNxEntry2->GetInstrument()->GetDetector()->GetErrorMsg() << std::endl;
if (!ErrorHandler(NXopendata(fFileHandle, "time_zero"), PNEXUS_OPEN_DATA_ERROR, "couldn't open 'time_zero' data in NXdetector!")) return NX_ERROR; return NX_ERROR;
// 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 == 1) && (dims[0] == 1)) { // single t0 entry if (data_ptr) {
fNxEntry2->GetInstrument()->GetDetector()->SetT0Tag(1); delete [] data_ptr;
} else if ((rank == 1) && (dims[0] > 1)) { // t0 of the form t0[ns] data_ptr = nullptr;
fNxEntry2->GetInstrument()->GetDetector()->SetT0Tag(2); }
} else if (rank == 2) { // t0 of the form t0[np][ns]
fNxEntry2->GetInstrument()->GetDetector()->SetT0Tag(3); if (!ErrorHandler(NXclosedata(fFileHandle), PNEXUS_CLOSE_DATA_ERROR, "couldn't close 'first_good_bin' data in NXdetector!")) return NX_ERROR;
} else if (SearchInGroup("first_good_time", "name", nxname, nxclass, dataType)) {
if (!ErrorHandler(NXopendata(fFileHandle, "first_good_time"), PNEXUS_OPEN_DATA_ERROR, "couldn't open 'first_good_time' data in NXdetector!")) return NX_ERROR;
// 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;
// calculate the needed size
size = dims[0];
for (int i=1; i<rank; i++)
size *= dims[i];
noOfElements = size;
size *= GetDataSize(type);
// allocate locale memory to get the data
char *data_ptr = new char[size];
if (data_ptr == nullptr) {
return NX_ERROR;
}
// get the data
float *f_data_ptr = (float*) data_ptr;
int status = NXgetdata(fFileHandle, f_data_ptr);
if (status != NX_OK) {
return NX_ERROR;
}
// set the fgb's based on the fgb time stamp and the time resolution
int *p_fgb = nullptr;
if (rank == 1) {
p_fgb = new int;
*p_fgb = (int)(*f_data_ptr / (float)fNxEntry2->GetInstrument()->GetDetector()->GetTimeResolution(str));
} else { // rank == 2
p_fgb = new int[noOfElements];
for (int i=0; i<noOfElements; i++) {
*(p_fgb+i) = (int)(*(f_data_ptr+i) / (float)fNxEntry2->GetInstrument()->GetDetector()->GetTimeResolution(str));
}
}
if (!fNxEntry2->GetInstrument()->GetDetector()->SetFirstGoodBin(p_fgb)) {
std::cerr << std::endl << ">> **ERROR** " << fNxEntry2->GetInstrument()->GetDetector()->GetErrorMsg() << std::endl;
return NX_ERROR;
}
// clean up
if (p_fgb) {
delete [] p_fgb;
p_fgb = 0;
}
if (data_ptr) {
delete [] data_ptr;
data_ptr = nullptr;
}
if (!ErrorHandler(NXclosedata(fFileHandle), PNEXUS_CLOSE_DATA_ERROR, "couldn't close 'first_good_time' data in NXdetector!")) return NX_ERROR;
} else { } else {
std::cerr << std::endl << ">> **ERROR** found 'time_zero' info in NXdetector with rank=" << rank << ". Do not know how to handle." << std::endl; std::cerr << std::endl << ">> **WARNING** found neither 'first_good_bin' nor 'first_good_time' values ..." << std::endl;
return NX_ERROR;
} }
// calculate the needed size // handle last good bin
size = dims[0]; if (SearchInGroup("last_good_bin", "name", nxname, nxclass, dataType)) {
for (int i=1; i<rank; i++) if (!ErrorHandler(NXopendata(fFileHandle, "last_good_bin"), PNEXUS_OPEN_DATA_ERROR, "couldn't open 'last_good_bin' data in NXdetector!")) return NX_ERROR;
size *= dims[i];
noOfElements = size;
size *= GetDataSize(type);
// allocate locale memory to get the data // check the dimensions of the 'last_good_bin' vector
char *data_ptr = new char[size]; 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 (data_ptr == nullptr) {
return NX_ERROR;
}
// get the data // calculate the needed size
float *f_data_ptr = (float*) data_ptr; size = dims[0];
int status = NXgetdata(fFileHandle, f_data_ptr); for (int i=1; i<rank; i++)
if (status != NX_OK) { size *= dims[i];
return NX_ERROR; noOfElements = size;
} size *= GetDataSize(type);
if (!ErrorHandler(GetStringAttr("units", str), PNEXUS_GET_ATTR_ERROR, "couldn't read 'time_zero' units in NXdetector!")) return NX_ERROR; // allocate locale memory to get the data
char *data_ptr = new char[size];
// Set T0's if (data_ptr == nullptr) {
// check that the necessary time resolution is present return NX_ERROR;
if (fNxEntry2->GetInstrument()->GetDetector()->GetTimeResolution(str) == 0.0) {
std::cerr << std::endl << ">> **ERROR** trying to set T0's based on 'time_zero'. Need a valid time resolution to do so, but this is not given." << std::endl;
return NX_ERROR;
}
// set the t0's based on the t0 time stamp and the time resolution
int *pt0 = nullptr;
if (rank == 1) {
pt0 = new int;
*pt0 = (int)(*f_data_ptr / (float)fNxEntry2->GetInstrument()->GetDetector()->GetTimeResolution(str));
} else { // rank == 2
pt0 = new int[noOfElements];
for (int i=0; i<noOfElements; i++) {
*(pt0+i) = (int)(*(f_data_ptr+i) / (float)fNxEntry2->GetInstrument()->GetDetector()->GetTimeResolution(str));
} }
}
if (!fNxEntry2->GetInstrument()->GetDetector()->SetT0(pt0)) { // get the data
std::cerr << std::endl << ">> **ERROR** " << fNxEntry2->GetInstrument()->GetDetector()->GetErrorMsg() << std::endl; int *i_data_ptr = (int*) data_ptr;
return NX_ERROR; int status = NXgetdata(fFileHandle, i_data_ptr);
} if (status != NX_OK) {
return NX_ERROR;
// clean up
if (data_ptr) {
delete [] data_ptr;
data_ptr = nullptr;
}
std::cerr << std::endl << ">> **WARNING** found only 'time_zero' will convert it to 'time_zero_bin' values" << std::endl;
if (!ErrorHandler(NXclosedata(fFileHandle), PNEXUS_CLOSE_DATA_ERROR, "couldn't close 'time_zero' data in NXdetector!")) return NX_ERROR;
} else {
std::cerr << std::endl << ">> **WARNING** found neither 'time_zero_bin' nor 'time_zero' values ..." << std::endl;
}
// handle first good bin
if (SearchInGroup("first_good_bin", "name", nxname, nxclass, dataType)) {
if (!ErrorHandler(NXopendata(fFileHandle, "first_good_bin"), PNEXUS_OPEN_DATA_ERROR, "couldn't open 'first_good_bin' data in NXdetector!")) return NX_ERROR;
// 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;
// calculate the needed size
size = dims[0];
for (int i=1; i<rank; i++)
size *= dims[i];
noOfElements = size;
size *= GetDataSize(type);
// allocate locale memory to get the data
char *data_ptr = new char[size];
if (data_ptr == nullptr) {
return NX_ERROR;
}
// get the data
int *i_data_ptr = (int*) data_ptr;
int status = NXgetdata(fFileHandle, i_data_ptr);
if (status != NX_OK) {
return NX_ERROR;
}
if (!fNxEntry2->GetInstrument()->GetDetector()->SetFirstGoodBin(i_data_ptr)) {
std::cerr << std::endl << ">> **ERROR** " << fNxEntry2->GetInstrument()->GetDetector()->GetErrorMsg() << std::endl;
return NX_ERROR;
}
if (data_ptr) {
delete [] data_ptr;
data_ptr = nullptr;
}
if (!ErrorHandler(NXclosedata(fFileHandle), PNEXUS_CLOSE_DATA_ERROR, "couldn't close 'first_good_bin' data in NXdetector!")) return NX_ERROR;
} else if (SearchInGroup("first_good_time", "name", nxname, nxclass, dataType)) {
if (!ErrorHandler(NXopendata(fFileHandle, "first_good_time"), PNEXUS_OPEN_DATA_ERROR, "couldn't open 'first_good_time' data in NXdetector!")) return NX_ERROR;
// 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;
// calculate the needed size
size = dims[0];
for (int i=1; i<rank; i++)
size *= dims[i];
noOfElements = size;
size *= GetDataSize(type);
// allocate locale memory to get the data
char *data_ptr = new char[size];
if (data_ptr == nullptr) {
return NX_ERROR;
}
// get the data
float *f_data_ptr = (float*) data_ptr;
int status = NXgetdata(fFileHandle, f_data_ptr);
if (status != NX_OK) {
return NX_ERROR;
}
// set the fgb's based on the fgb time stamp and the time resolution
int *p_fgb = nullptr;
if (rank == 1) {
p_fgb = new int;
*p_fgb = (int)(*f_data_ptr / (float)fNxEntry2->GetInstrument()->GetDetector()->GetTimeResolution(str));
} else { // rank == 2
p_fgb = new int[noOfElements];
for (int i=0; i<noOfElements; i++) {
*(p_fgb+i) = (int)(*(f_data_ptr+i) / (float)fNxEntry2->GetInstrument()->GetDetector()->GetTimeResolution(str));
} }
}
if (!fNxEntry2->GetInstrument()->GetDetector()->SetFirstGoodBin(p_fgb)) { if (!fNxEntry2->GetInstrument()->GetDetector()->SetLastGoodBin(i_data_ptr)) {
std::cerr << std::endl << ">> **ERROR** " << fNxEntry2->GetInstrument()->GetDetector()->GetErrorMsg() << std::endl; std::cerr << std::endl << ">> **ERROR** " << fNxEntry2->GetInstrument()->GetDetector()->GetErrorMsg() << std::endl;
return NX_ERROR; return NX_ERROR;
}
// clean up
if (p_fgb) {
delete [] p_fgb;
p_fgb = 0;
}
if (data_ptr) {
delete [] data_ptr;
data_ptr = nullptr;
}
if (!ErrorHandler(NXclosedata(fFileHandle), PNEXUS_CLOSE_DATA_ERROR, "couldn't close 'first_good_time' data in NXdetector!")) return NX_ERROR;
} else {
std::cerr << std::endl << ">> **WARNING** found neither 'first_good_bin' nor 'first_good_time' values ..." << std::endl;
}
// handle last good bin
if (SearchInGroup("last_good_bin", "name", nxname, nxclass, dataType)) {
if (!ErrorHandler(NXopendata(fFileHandle, "last_good_bin"), PNEXUS_OPEN_DATA_ERROR, "couldn't open 'last_good_bin' data in NXdetector!")) return NX_ERROR;
// 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;
// calculate the needed size
size = dims[0];
for (int i=1; i<rank; i++)
size *= dims[i];
noOfElements = size;
size *= GetDataSize(type);
// allocate locale memory to get the data
char *data_ptr = new char[size];
if (data_ptr == nullptr) {
return NX_ERROR;
}
// get the data
int *i_data_ptr = (int*) data_ptr;
int status = NXgetdata(fFileHandle, i_data_ptr);
if (status != NX_OK) {
return NX_ERROR;
}
if (!fNxEntry2->GetInstrument()->GetDetector()->SetLastGoodBin(i_data_ptr)) {
std::cerr << std::endl << ">> **ERROR** " << fNxEntry2->GetInstrument()->GetDetector()->GetErrorMsg() << std::endl;
return NX_ERROR;
}
// clean up
if (data_ptr) {
delete [] data_ptr;
data_ptr = nullptr;
}
if (!ErrorHandler(NXclosedata(fFileHandle), PNEXUS_CLOSE_DATA_ERROR, "couldn't close 'last_good_bin' data in NXdetector!")) return NX_ERROR;
} else if (SearchInGroup("last_good_time", "name", nxname, nxclass, dataType)) {
if (!ErrorHandler(NXopendata(fFileHandle, "last_good_time"), PNEXUS_OPEN_DATA_ERROR, "couldn't open 'last_good_time' data in NXdetector!")) return NX_ERROR;
// 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;
// calculate the needed size
size = dims[0];
for (int i=1; i<rank; i++)
size *= dims[i];
noOfElements = size;
size *= GetDataSize(type);
// allocate locale memory to get the data
char *data_ptr = new char[size];
if (data_ptr == nullptr) {
return NX_ERROR;
}
// get the data
float *f_data_ptr = (float*) data_ptr;
int status = NXgetdata(fFileHandle, f_data_ptr);
if (status != NX_OK) {
return NX_ERROR;
}
// set the lgb's based on the lgb time stamp and the time resolution
int *p_lgb = nullptr;
if (rank == 1) {
p_lgb = new int;
*p_lgb = (int)(*f_data_ptr / (float)fNxEntry2->GetInstrument()->GetDetector()->GetTimeResolution(str));
} else { // rank == 2
p_lgb = new int[noOfElements];
for (int i=0; i<noOfElements; i++) {
*(p_lgb+i) = (int)(*(f_data_ptr+i) / (float)fNxEntry2->GetInstrument()->GetDetector()->GetTimeResolution(str));
} }
}
if (fNxEntry2->GetInstrument()->GetDetector()->SetFirstGoodBin(p_lgb)) { // clean up
std::cerr << std::endl << ">> **ERROR** " << fNxEntry2->GetInstrument()->GetDetector()->GetErrorMsg() << std::endl; if (data_ptr) {
return NX_ERROR; delete [] data_ptr;
} data_ptr = nullptr;
}
// clean up if (!ErrorHandler(NXclosedata(fFileHandle), PNEXUS_CLOSE_DATA_ERROR, "couldn't close 'last_good_bin' data in NXdetector!")) return NX_ERROR;
if (p_lgb) { } else if (SearchInGroup("last_good_time", "name", nxname, nxclass, dataType)) {
delete [] p_lgb; if (!ErrorHandler(NXopendata(fFileHandle, "last_good_time"), PNEXUS_OPEN_DATA_ERROR, "couldn't open 'last_good_time' data in NXdetector!")) return NX_ERROR;
p_lgb = 0;
}
if (data_ptr) {
delete [] data_ptr;
data_ptr = nullptr;
}
if (!ErrorHandler(NXclosedata(fFileHandle), PNEXUS_CLOSE_DATA_ERROR, "couldn't close 'last_good_time' data in NXdetector!")) return NX_ERROR; // check the dimensions of the 'last_good_time' vector
} else { if (!ErrorHandler(NXgetinfo(fFileHandle, &rank, dims, &type), PNEXUS_GET_META_INFO_ERROR, "couldn't get 'last_good_time' info in NXdetector!")) return NX_ERROR;
std::cerr << std::endl << ">> **WARNING** found neither 'last_good_bin' nor 'last_good_time' values ..." << std::endl;
// calculate the needed size
size = dims[0];
for (int i=1; i<rank; i++)
size *= dims[i];
noOfElements = size;
size *= GetDataSize(type);
// allocate locale memory to get the data
char *data_ptr = new char[size];
if (data_ptr == nullptr) {
return NX_ERROR;
}
// get the data
float *f_data_ptr = (float*) data_ptr;
int status = NXgetdata(fFileHandle, f_data_ptr);
if (status != NX_OK) {
return NX_ERROR;
}
// set the lgb's based on the lgb time stamp and the time resolution
int *p_lgb = nullptr;
if (rank == 1) {
p_lgb = new int;
*p_lgb = (int)(*f_data_ptr / (float)fNxEntry2->GetInstrument()->GetDetector()->GetTimeResolution(str));
} else { // rank == 2
p_lgb = new int[noOfElements];
for (int i=0; i<noOfElements; i++) {
*(p_lgb+i) = (int)(*(f_data_ptr+i) / (float)fNxEntry2->GetInstrument()->GetDetector()->GetTimeResolution(str));
}
}
if (fNxEntry2->GetInstrument()->GetDetector()->SetFirstGoodBin(p_lgb)) {
std::cerr << std::endl << ">> **ERROR** " << fNxEntry2->GetInstrument()->GetDetector()->GetErrorMsg() << std::endl;
return NX_ERROR;
}
// clean up
if (p_lgb) {
delete [] p_lgb;
p_lgb = 0;
}
if (data_ptr) {
delete [] data_ptr;
data_ptr = nullptr;
}
if (!ErrorHandler(NXclosedata(fFileHandle), PNEXUS_CLOSE_DATA_ERROR, "couldn't close 'last_good_time' data in NXdetector!")) return NX_ERROR;
} else {
std::cerr << std::endl << ">> **WARNING** found neither 'last_good_bin' nor 'last_good_time' values ..." << std::endl;
}
} }
// close group NXdetector // close group NXdetector