more work on the NeXus write routines.

src/classes/PRunDataHandler.cpp

@@ -4807,7 +4807,7 @@ Bool_t PRunDataHandler::WriteRootFile(TString fln)
 Bool_t PRunDataHandler::WriteNexusFile(TString format, TString fln)
 {
 #ifdef PNEXUS_ENABLED
-
+  std::string str{""};
   Bool_t ok = false;
   fln = GenerateOutputFileName(fln, ".nxs", ok);
   if (!ok)
@@ -4837,8 +4837,89 @@ Bool_t PRunDataHandler::WriteNexusFile(TString format, TString fln)
         nxs->AddGroupAttribute("/", "HDF_version", nxs->GetHdf5LibVersion());
         // set file name
         nxs->AddGroupAttribute("/", "file_name", std::string(fln.Data()));
+        // set creation time
+        std::string dt = nxs::getIso8601TimestampLocal();
+        nxs->AddGroupAttribute("/", "file_time", dt);
         // set IDF version
         nxs->AddDataset<int>("/run/IDF_version", {(int)fAny2ManyInfo->idf}, {1}, H5::PredType::NATIVE_INT32);
+        // set program name
+        nxs->AddDataset<std::string>("/run/program_name", {"any2many"}, {1}, H5::StrType(H5::PredType::C_S1, H5T_VARIABLE));
+        str="n/a";
+    #ifdef HAVE_CONFIG_H
+        str = PACKAGE_VERSION;
+    #endif
+        nxs->AddDatasetAttribute<std::string>("/run/program_name", "version", str);
+        // set run number
+        nxs->AddDataset<int>("/run/number", {fData[0].GetRunNumber()}, {1}, H5::PredType::NATIVE_INT32);
+        // set title
+        nxs->AddDataset<std::string>("/run/title", {fData[0].GetRunTitle()->Data()}, {1}, H5::StrType(H5::PredType::C_S1, H5T_VARIABLE));
+        // set notes
+        nxs->AddDataset<std::string>("/run/notes", {std::string("n/a")}, {1}, H5::StrType(H5::PredType::C_S1, H5T_VARIABLE));
+        // set analysis
+        nxs->AddDataset<std::string>("/run/notes", {std::string("muonTD")}, {1}, H5::StrType(H5::PredType::C_S1, H5T_VARIABLE));
+        // set lab
+        str = *fData[0].GetLaboratory();
+        nxs->AddDataset<std::string>("/run/lab", {str}, {1}, H5::StrType(H5::PredType::C_S1, H5T_VARIABLE));
+        // set beamline
+        str = *fData[0].GetBeamline();
+        nxs->AddDataset<std::string>("/run/beamline", {str}, {1}, H5::StrType(H5::PredType::C_S1, H5T_VARIABLE));
+        // set start time
+        str = std::string(fData[0].GetStartDate()->Data()) + std::string("T") + std::string(fData[0].GetStartTime()->Data());
+        nxs->AddDataset<std::string>("/run/start_time", {str}, {1}, H5::StrType(H5::PredType::C_S1, H5T_VARIABLE));
+        // set stop time
+        str = std::string(fData[0].GetStopDate()->Data()) + std::string("T") + std::string(fData[0].GetStopTime()->Data());
+        nxs->AddDataset<std::string>("/run/stop_time", {str}, {1}, H5::StrType(H5::PredType::C_S1, H5T_VARIABLE));
+        // set switching state
+        nxs->AddDataset<int>("/run/switching_states", {1}, {1}, H5::PredType::NATIVE_INT32);
+        // set user name
+        nxs->AddDataset<std::string>("/run/user/name", {std::string("n/a")}, {1}, H5::StrType(H5::PredType::C_S1, H5T_VARIABLE));
+        // set user experiment_number
+        nxs->AddDataset<std::string>("/run/user/experiment_number", {std::string("n/a")}, {1}, H5::StrType(H5::PredType::C_S1, H5T_VARIABLE));
+        // set sample name
+        nxs->AddDataset<std::string>("/run/sample/name", {fData[0].GetSample()->Data()}, {1}, H5::StrType(H5::PredType::C_S1, H5T_VARIABLE));
+        // set sample temperature
+        nxs->AddDataset<float>("/run/sample/temperature", {(float)fData[0].GetTemperature(0)}, {1}, H5::PredType::NATIVE_FLOAT);
+        nxs->AddDatasetAttribute<float>("/run/sample/temperature", "units", std::string("Kelvin"));
+        // set magnetic field
+        nxs->AddDataset<float>("/run/sample/magnetic_field", {(float)fData[0].GetField()}, {1}, H5::PredType::NATIVE_FLOAT);
+        nxs->AddDatasetAttribute<float>("/run/sample/magnetic_field", "units", std::string("Gauss"));
+        // set sample environment
+        nxs->AddDataset<std::string>("/run/sample/environment", {fData[0].GetSetup()->Data()}, {1}, H5::StrType(H5::PredType::C_S1, H5T_VARIABLE));
+        // set sample shape
+        nxs->AddDataset<std::string>("/run/sample/shape", {std::string("n/a")}, {1}, H5::StrType(H5::PredType::C_S1, H5T_VARIABLE));
+        // set magnetic field vector
+        nxs->AddDataset<float>("/run/sample/magnetic_field_vector", {1.0, 1.0, 1.0}, {3}, H5::PredType::NATIVE_FLOAT);
+        nxs->AddDatasetAttribute<float>("/run/sample/magnetic_field_vector", "coordinate_system", std::string("cartesian"));
+        nxs->AddDatasetAttribute<float>("/run/sample/magnetic_field_vector", "units", std::string("Gauss"));
+        nxs->AddDatasetAttribute<float>("/run/sample/magnetic_field_vector", "available", 0);
+        // set instrument name
+        str = *fData[0].GetInstrument();
+        nxs->AddDataset<std::string>("/run/instrument/name", {str}, {1}, H5::StrType(H5::PredType::C_S1, H5T_VARIABLE));
+        // set instrument number of detectors
+        nxs->AddDataset<int>("/run/instrument/detector/number", {(int)fData[0].GetNoOfHistos()}, {1}, H5::PredType::NATIVE_INT32);
+        // set instrument collimator
+        nxs->AddDataset<std::string>("/run/instrument/collimator/type", {std::string("n/a")}, {1}, H5::StrType(H5::PredType::C_S1, H5T_VARIABLE));
+        // set instrument beam total number of counts in Mev
+        // calculate the total number of counts
+        double total_counts = 0;
+        PRawRunDataSet *dataSet = nullptr;
+        for (unsigned int i=0; i<fData[0].GetNoOfHistos(); i++) {
+          dataSet = fData[0].GetDataSet(i, false); // i.e. the false means, that i is the index and NOT the histo number
+          if (dataSet == nullptr) { // something is really wrong
+            std::cerr << std::endl << ">> PRunDataHandler::WriteNexusFile: **ERROR** Couldn't get data set (idx=0" << i << ")";
+            std::cerr << std::endl << ">>   something is really wrong!" << std::endl;
+            return false;
+          }
+          for (unsigned int j=0; j<dataSet->GetData()->size(); j++)
+            total_counts += dataSet->GetData()->at(j);
+        }
+        float total_counts_mev = (float) total_counts / 1.0e6;
+        nxs->AddDataset<float>("/run/instrument/beam/total_counts", {total_counts_mev}, {1}, H5::PredType::NATIVE_FLOAT);
+        nxs->AddDatasetAttribute<float>("/run/instrument/beam/total_counts", "units", std::string("MEv"));
+        // set time resolution (use FLOAT instead of INT)
+        float res = (float)(fData[0].GetTimeResolution()*fAny2ManyInfo->rebin*1.0e3);
+        nxs->AddDataset<float>("/run/histogram_data_1/resolution", {res}, {1}, H5::PredType::NATIVE_FLOAT);
+        nxs->AddDatasetAttribute<float>("/run/histogram_data_1/resolution", "units", std::string("picoseconds"));
       } else { // IDF V2
         // set IDF version
         nxs->AddDataset<int>("/raw_data_1/IDF_version", {(int)fAny2ManyInfo->idf}, {1}, H5::PredType::NATIVE_INT32);
@@ -4860,63 +4941,6 @@ Bool_t PRunDataHandler::WriteNexusFile(TString format, TString fln)
   if (fAny2ManyInfo->idf == 1) {
     // fill necessary data structures
 
-    // set file creating time
-    time_t now;
-    struct tm *tm;
-    time(&now);
-    tm = localtime(&now);
-    std::string str("");
-    char cstr[128];
-    strftime(cstr, sizeof(cstr), "%FT%T", tm);
-    str = std::string(cstr);
-    nxs->SetFileTime(str);
-
-    nxs->GetEntryIdf1()->SetProgramName("any2many");
-    nxs->GetEntryIdf1()->SetProgramVersion("$Id$");
-    nxs->GetEntryIdf1()->SetRunNumber(fData[0].GetRunNumber());
-    nxs->GetEntryIdf1()->SetTitle(fData[0].GetRunTitle()->Data());
-    nxs->GetEntryIdf1()->SetNotes("n/a");
-    nxs->GetEntryIdf1()->SetAnalysis("muonTD");
-    if (*fData[0].GetLaboratory() != "n/a")
-      nxs->GetEntryIdf1()->SetLaboratory(fData[0].GetLaboratory()->Data());
-    if (*fData[0].GetBeamline() != "n/a")
-      nxs->GetEntryIdf1()->SetBeamline(fData[0].GetBeamline()->Data());
-    str = std::string(fData[0].GetStartDate()->Data()) + std::string("T") + std::string(fData[0].GetStartTime()->Data());
-    nxs->GetEntryIdf1()->SetStartTime(str);
-    str = std::string(fData[0].GetStopDate()->Data()) + std::string("T") + std::string(fData[0].GetStopTime()->Data());
-    nxs->GetEntryIdf1()->SetStopTime(str);
-    nxs->GetEntryIdf1()->SetSwitchingState(1);
-    nxs->GetEntryIdf1()->GetUser()->SetName("n/a");
-    nxs->GetEntryIdf1()->GetUser()->SetExperimentNumber("n/a");
-    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(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
-    double total_counts = 0;
-    PRawRunDataSet *dataSet = nullptr;
-    for (unsigned int i=0; i<fData[0].GetNoOfHistos(); i++) {
-      dataSet = fData[0].GetDataSet(i, false); // i.e. the false means, that i is the index and NOT the histo number
-      if (dataSet == nullptr) { // something is really wrong
-        std::cerr << std::endl << ">> PRunDataHandler::WriteNexusFile: **ERROR** Couldn't get data set (idx=0" << i << ")";
-        std::cerr << std::endl << ">>   something is really wrong!" << std::endl;
-        return false;
-      }
-      for (unsigned int j=0; j<dataSet->GetData()->size(); j++)
-        total_counts += dataSet->GetData()->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()*fAny2ManyInfo->rebin, "ns");
-
     for (unsigned int i=0; i<fData[0].GetNoOfHistos(); i++) {
       dataSet = fData[0].GetDataSet(i, false); // i.e. the false means, that i is the index and NOT the histo number
       nxs->GetEntryIdf1()->GetData()->SetT0(static_cast<Int_t>(dataSet->GetTimeZeroBin()/fAny2ManyInfo->rebin), i);

src/include/PRunDataHandler.h

@@ -436,9 +436,9 @@ class PRunDataHandler
     virtual Bool_t FileExistsCheck(const Bool_t fileName, const Int_t idx);
     virtual Bool_t FileExistsCheck(const TString fileName);
     virtual Bool_t ReadRootFile();
-    virtual Bool_t ReadNexusFile();
     template <typename T> Bool_t ReadNexusFileIdf1(T& nxs_file);
     template <typename T> Bool_t ReadNexusFileIdf2(T& nxs_file);
+    virtual Bool_t ReadNexusFile();
     virtual Bool_t ReadWkmFile();
     virtual Bool_t ReadPsiBinFile();
     virtual Bool_t ReadMudFile();