more work on HDF5 IDF V2.
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@@ -4830,20 +4830,20 @@ Bool_t PRunDataHandler::WriteNexusFile(TString format, TString fln)
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return false;
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return false;
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}
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}
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// set NeXus version
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nxs->AddGroupAttribute("/", "NeXus_version", std::string("4.3.0"));
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// set HDF5 version
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nxs->AddGroupAttribute("/", "HDF_version", nxs->GetHdf5LibVersion());
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// set file name
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nxs->AddGroupAttribute("/", "file_name", std::string(fln.Data()));
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// set creation time
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std::string dt = nxs::getIso8601TimestampLocal();
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nxs->AddGroupAttribute("/", "file_time", dt);
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if (fAny2ManyInfo->idf == 1) { // IDF V1
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if (fAny2ManyInfo->idf == 1) { // IDF V1
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// set NeXus version
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nxs->AddGroupAttribute("/", "NeXus_version", std::string("4.3.0"));
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// set HDF5 version
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nxs->AddGroupAttribute("/", "HDF_version", nxs->GetHdf5LibVersion());
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// set file name
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nxs->AddGroupAttribute("/", "file_name", std::string(fln.Data()));
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// set creation time
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std::string dt = nxs::getIso8601TimestampLocal();
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nxs->AddGroupAttribute("/", "file_time", dt);
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// set IDF version
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// set IDF version
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nxs->AddDataset<int>("/run/IDF_version", {(int)fAny2ManyInfo->idf}, {1}, H5::PredType::NATIVE_INT32);
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nxs->AddDataset<int>("/run/IDF_version", {(int)fAny2ManyInfo->idf}, {1}, H5::PredType::NATIVE_INT32);
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@@ -5037,8 +5037,150 @@ Bool_t PRunDataHandler::WriteNexusFile(TString format, TString fln)
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res = (float)(fData[0].GetTimeResolution()*fAny2ManyInfo->rebin*1.0e3)/2.0;
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res = (float)(fData[0].GetTimeResolution()*fAny2ManyInfo->rebin*1.0e3)/2.0;
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nxs->AddDatasetAttribute<int>("/run/histogram_data_1/counts", "offset", res);
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nxs->AddDatasetAttribute<int>("/run/histogram_data_1/counts", "offset", res);
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} else { // IDF V2
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} else { // IDF V2
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nxs->AddGroupAttribute("/raw_data_1", "NX_class", std::string("NXentry"));
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// set IDF version
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// set IDF version
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nxs->AddDataset<int>("/raw_data_1/IDF_version", {(int)fAny2ManyInfo->idf}, {1}, H5::PredType::NATIVE_INT32);
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nxs->AddDataset<int>("/raw_data_1/IDF_version", {(int)fAny2ManyInfo->idf}, {1}, H5::PredType::NATIVE_INT32);
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// set beamline
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str = *fData[0].GetBeamline();
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nxs->AddDataset<std::string>("/raw_data_1/beamline", {str}, {1}, H5::StrType(H5::PredType::C_S1, H5T_VARIABLE));
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// set definition
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nxs->AddDataset<std::string>("/raw_data_1/definition", {std::string("muonTD")}, {1}, H5::StrType(H5::PredType::C_S1, H5T_VARIABLE));
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// set run_number
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nxs->AddDataset<int>("/raw_data_1/run_number", {fData[0].GetRunNumber()}, {1}, H5::PredType::NATIVE_INT32);
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// set title
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nxs->AddDataset<std::string>("/raw_data_1/title", {fData[0].GetRunTitle()->Data()}, {1}, H5::StrType(H5::PredType::C_S1, H5T_VARIABLE));
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// set start time
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str = std::string(fData[0].GetStartDate()->Data()) + std::string("T") + std::string(fData[0].GetStartTime()->Data());
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nxs->AddDataset<std::string>("/raw_data_1/start_time", {str}, {1}, H5::StrType(H5::PredType::C_S1, H5T_VARIABLE));
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nxs->AddDatasetAttribute<std::string>("/raw_data_1/start_time", "units", "ISO8601");
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// set end time
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str = std::string(fData[0].GetStopDate()->Data()) + std::string("T") + std::string(fData[0].GetStopTime()->Data());
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nxs->AddDataset<std::string>("/raw_data_1/end_time", {str}, {1}, H5::StrType(H5::PredType::C_S1, H5T_VARIABLE));
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nxs->AddDatasetAttribute<std::string>("/raw_data_1/end_time", "units", "ISO8601");
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// set experiment_identifier
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str = "n/a";
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nxs->AddDataset<std::string>("/raw_data_1/experiment_identifier", {str}, {1}, H5::StrType(H5::PredType::C_S1, H5T_VARIABLE));
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// set instrument attribute
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nxs->AddGroupAttribute("/raw_data_1/instrument", "NX_class", std::string("NXinstrument"));
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// set instrument name
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str = *fData[0].GetInstrument();
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nxs->AddDataset<std::string>("/raw_data_1/instrument/name", {str}, {1}, H5::StrType(H5::PredType::C_S1, H5T_VARIABLE));
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// set instrument/source attribute
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nxs->AddGroupAttribute("/raw_data_1/instrument/source", "NX_class", std::string("NXsource"));
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// set instrument/source/name
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str = fData[0].GetLaboratory()->Data();
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nxs->AddDataset<std::string>("/raw_data_1/instrument/source/name", {str}, {1}, H5::StrType(H5::PredType::C_S1, H5T_VARIABLE));
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// set instrument/source/type
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TString tstr = *fData[0].GetInstrument();
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std::string type{"n/a"};
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if (tstr.Contains("LEM", TString::kIgnoreCase)) {
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type = "low energy muon source";
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} else if (tstr.Contains("GPS", TString::kIgnoreCase) || tstr.Contains("GPD", TString::kIgnoreCase) ||
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tstr.Contains("LTF", TString::kIgnoreCase) || tstr.Contains("FLAME", TString::kIgnoreCase) ||
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tstr.Contains("HAL-9500", TString::kIgnoreCase) || tstr.Contains("DOLLY", TString::kIgnoreCase) ||
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tstr.Contains("VMS", TString::kIgnoreCase)) {
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type = "quasi-continous muon source";
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} else if (tstr.Contains("EMU", TString::kIgnoreCase) || tstr.Contains("MUSR", TString::kIgnoreCase) ||
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tstr.Contains("HIFI", TString::kIgnoreCase)) {
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type = "pulsed muon source";
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}
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nxs->AddDataset<std::string>("/raw_data_1/instrument/source/type", {type}, {1}, H5::StrType(H5::PredType::C_S1, H5T_VARIABLE));
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// set instrument/source/probe
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str = "positive muons";
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nxs->AddDataset<std::string>("/raw_data_1/instrument/source/probe", {str}, {1}, H5::StrType(H5::PredType::C_S1, H5T_VARIABLE));
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// set instrument/detector info
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nxs->AddGroupAttribute("/raw_data_1/instrument/detector_1", "NX_class", std::string("NXdetector"));
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// set instrument/detector/spectrum_index
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int noHistos = fData[0].GetNoOfHistos();
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std::vector<int> spectrum_index(noHistos);
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for (unsigned int i=0; i<spectrum_index.size(); i++)
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spectrum_index[i] = i+1;
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nxs->AddDataset<int>("/raw_data_1/instrument/detector_1/spectrum_index", spectrum_index, {spectrum_index.size()}, H5::PredType::NATIVE_INT32);
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// set instrument/detector/raw_time (not useful for quasi-continuous sources)
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int ival=0;
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nxs->AddDataset<int>("/raw_data_1/instrument/detector_1/raw_time", {ival}, {1}, H5::PredType::NATIVE_INT32);
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nxs->AddDatasetAttribute<int>("/raw_data_1/instrument/detector_1/raw_time", "available", 0);
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// set instrument/detector/counts
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// set counts
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// feed histos
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PRawRunDataSet *dataSet = nullptr;
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PIntVector data;
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UInt_t size = 0;
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int noHisto, histoLength;
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if (fAny2ManyInfo->rebin == 1) {
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noHisto = fData[0].GetNoOfHistos();
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for (UInt_t i=0; i<fData[0].GetNoOfHistos(); i++) {
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dataSet = fData[0].GetDataSet(i, false); // i.e. the false means, that i is the index and NOT the histo number
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if (dataSet == nullptr) { // something is really wrong
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std::cerr << std::endl << ">> PRunDataHandler::WriteNexusFile: **ERROR** Couldn't get data set (idx=" << i << ")";
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std::cerr << std::endl << ">> something is really wrong!" << std::endl;
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return false;
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}
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size = dataSet->GetData()->size();
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histoLength = size;
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for (UInt_t j=0; j<size; j++) {
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data.push_back((UInt_t)dataSet->GetData()->at(j));
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}
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}
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} else { // rebin > 1
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UInt_t dataRebin = 0;
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UInt_t dataCount = 0;
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noHisto = fData[0].GetNoOfHistos();
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for (UInt_t i=0; i<fData[0].GetNoOfHistos(); i++) {
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dataSet = fData[0].GetDataSet(i, false); // i.e. the false means, that i is the index and NOT the histo number
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if (dataSet == nullptr) { // something is really wrong
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std::cerr << std::endl << ">> PRunDataHandler::WriteNexusFile: **ERROR** Couldn't get data set (idx=" << i << ")";
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std::cerr << std::endl << ">> something is really wrong!" << std::endl;
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return false;
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}
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size = dataSet->GetData()->size();
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dataCount = 0;
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for (UInt_t j=0; j<size; j++) {
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if ((j > 0) && (j % fAny2ManyInfo->rebin == 0)) {
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dataCount++;
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data.push_back(dataRebin);
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dataRebin = 0;
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}
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dataRebin += static_cast<UInt_t>(dataSet->GetData()->at(j));
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}
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}
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size = dataCount;
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}
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nxs->AddDataset<int>("/raw_data_1/instrument/detector_1/counts", data, {(long unsigned int)noHisto, size}, H5::PredType::NATIVE_INT32);
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nxs->AddDatasetAttribute<int>("/raw_data_1/instrument/detector_1/counts", "axis", std::string("spectrum_index,time_bin"));
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nxs->AddDatasetAttribute<int>("/raw_data_1/instrument/detector_1/counts", "long_name", std::string("positon counts"));
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nxs->AddDatasetAttribute<int>("/raw_data_1/instrument/detector_1/counts", "signal", 1);
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// t0_bin attributes
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std::vector<int> t0_bin;
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for (unsigned int i=0; i<fData[0].GetNoOfHistos(); i++)
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t0_bin.push_back((int)(fData[0].GetT0Bin(i+1)/fAny2ManyInfo->rebin));
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std::cerr << std::endl;
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for (unsigned int i=0; i<fData[0].GetNoOfHistos(); i++)
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std::cerr << i << ": " << t0_bin[i] << ", ";
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std::cerr << std::endl;
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nxs->AddDatasetAttribute<int>("/raw_data_1/instrument/detector_1/counts", "t0_bin", {t0_bin});
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nxs->AddDatasetAttribute<int>("/raw_data_1/instrument/detector_1/counts", "units", std::string("counts"));
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// set raw_data_1/detector info
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nxs->AddGroupAttribute("/raw_data_1/detector_1", "NX_class", std::string("NXdata"));
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}
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}
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int result = nxs->WriteNexusFile(fln.Data(), fAny2ManyInfo->idf);
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int result = nxs->WriteNexusFile(fln.Data(), fAny2ManyInfo->idf);
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