first full version for HDF5 IDF V1 write.

src/classes/PRunDataHandler.cpp

@@ -4833,15 +4833,20 @@ Bool_t PRunDataHandler::WriteNexusFile(TString format, TString fln)
       if (fAny2ManyInfo->idf == 1) { // IDF V1
         // set NeXus version
         nxs->AddGroupAttribute("/", "NeXus_version", std::string("4.3.0"));
+
         // set HDF5 version
         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";
@@ -4849,56 +4854,77 @@ Bool_t PRunDataHandler::WriteNexusFile(TString format, TString fln)
         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;
@@ -4916,10 +4942,100 @@ Bool_t PRunDataHandler::WriteNexusFile(TString format, TString fln)
         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"));
+
+        // set time zero time to 0. see t0_bin attribute of counts!
+        nxs->AddDataset<int>("/run/histogram_data_1/time_zero", {0}, {1}, H5::PredType::NATIVE_INT32);
+        nxs->AddDatasetAttribute<int>("/run/histogram_data_1/time_zero", "units", std::string("microseconds"));
+        nxs->AddDatasetAttribute<int>("/run/histogram_data_1/time_zero", "available", 0);
+
+        // set raw_time
+        res = (float)(fData[0].GetTimeResolution()*fAny2ManyInfo->rebin*1.0e-3);
+        dataSet = fData[0].GetDataSet(0, false); // i.e. the false means, that i is the index and NOT the histo number
+        unsigned int length = (int)(dataSet->GetData()->size() / fAny2ManyInfo->rebin);
+        std::vector<float> time;
+        for (unsigned int i=0; i<length; i++)
+          time.push_back(((float)i+0.5)*res);
+        nxs->AddDataset<float>("/run/histogram_data_1/raw_time", time, {length}, H5::PredType::NATIVE_FLOAT);
+        nxs->AddDatasetAttribute<float>("/run/histogram_data_1/raw_time", "axis", 1);
+        nxs->AddDatasetAttribute<float>("/run/histogram_data_1/raw_time", "primary", 0);
+        nxs->AddDatasetAttribute<float>("/run/histogram_data_1/raw_time", "units", std::string("microseconds"));
+        nxs->AddDatasetAttribute<float>("/run/histogram_data_1/raw_time", "available", 0);
+
+        // set corrected_time
+        nxs->AddDataset<float>("/run/histogram_data_1/corrected_time", time, {length}, H5::PredType::NATIVE_FLOAT);
+        nxs->AddDatasetAttribute<float>("/run/histogram_data_1/corrected_time", "axis", 1);
+        nxs->AddDatasetAttribute<float>("/run/histogram_data_1/corrected_time", "units", std::string("microseconds"));
+        nxs->AddDatasetAttribute<float>("/run/histogram_data_1/corrected_time", "available", 0);
+
+        // set grouping
+        std::vector<int> grouping(fData[0].GetNoOfHistos(), 0);
+        nxs->AddDataset<int>("/run/histogram_data_1/grouping", grouping, {grouping.size()}, H5::PredType::NATIVE_INT32);
+        nxs->AddDatasetAttribute<int>("/run/histogram_data_1/grouping", "avaliabe", 0);
+
+        // set alpha
+        int ival=1;
+        nxs->AddDataset<int>("/run/histogram_data_1/alpha", {ival}, {1}, H5::PredType::NATIVE_INT32);
+        nxs->AddDatasetAttribute<int>("/run/histogram_data_1/alpha", "avaliabe", 0);
+
+        // set counts
+        // feed histos
+        PIntVector data;
+        UInt_t size = 0;
+        int noHisto, histoLength;
+        if (fAny2ManyInfo->rebin == 1) {
+          noHisto = fData[0].GetNoOfHistos();
+          for (UInt_t 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=" << i << ")";
+              std::cerr << std::endl << ">>   something is really wrong!" << std::endl;
+              return false;
+            }
+            size = dataSet->GetData()->size();
+            histoLength = size;
+            for (UInt_t j=0; j<size; j++) {
+              data.push_back((UInt_t)dataSet->GetData()->at(j));
+            }
+          }
+        } else { // rebin > 1
+          UInt_t dataRebin = 0;
+          UInt_t dataCount = 0;
+          noHisto = fData[0].GetNoOfHistos();
+          for (UInt_t 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=" << i << ")";
+              std::cerr << std::endl << ">>   something is really wrong!" << std::endl;
+              return false;
+            }
+            size = dataSet->GetData()->size();
+            dataCount = 0;
+            for (UInt_t j=0; j<size; j++) {
+              if ((j > 0) && (j % fAny2ManyInfo->rebin == 0)) {
+                dataCount++;
+                data.push_back(dataRebin);
+                dataRebin = 0;
+              }
+              dataRebin += static_cast<UInt_t>(dataSet->GetData()->at(j));
+            }
+          }
+          size = dataCount;
+        }
+        nxs->AddDataset<int>("/run/histogram_data_1/counts", data, {(long unsigned int)noHisto, size}, H5::PredType::NATIVE_INT32);
+        nxs->AddDatasetAttribute<int>("/run/histogram_data_1/counts", "units", std::string("counts"));
+        nxs->AddDatasetAttribute<int>("/run/histogram_data_1/counts", "signal", 1);
+        nxs->AddDatasetAttribute<int>("/run/histogram_data_1/counts", "number", noHisto);
+        nxs->AddDatasetAttribute<int>("/run/histogram_data_1/counts", "length", size);
+        nxs->AddDatasetAttribute<int>("/run/histogram_data_1/counts", "t0_bin", 0);
+        nxs->AddDatasetAttribute<int>("/run/histogram_data_1/counts", "first_good_bin", 0);
+        nxs->AddDatasetAttribute<int>("/run/histogram_data_1/counts", "last_good_bin", 0);
+        res = (float)(fData[0].GetTimeResolution()*fAny2ManyInfo->rebin*1.0e3)/2.0;
+        nxs->AddDatasetAttribute<int>("/run/histogram_data_1/counts", "offset", res);
       } else { // IDF V2
         // set IDF version
         nxs->AddDataset<int>("/raw_data_1/IDF_version", {(int)fAny2ManyInfo->idf}, {1}, H5::PredType::NATIVE_INT32);
@@ -4938,58 +5054,6 @@ Bool_t PRunDataHandler::WriteNexusFile(TString format, TString fln)
   return true;
 
 /* //as35
-  if (fAny2ManyInfo->idf == 1) {
-    // fill necessary data structures
-
-    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);
-      nxs->GetEntryIdf1()->GetData()->SetFirstGoodBin(static_cast<Int_t>(dataSet->GetFirstGoodBin()/fAny2ManyInfo->rebin), i);
-      nxs->GetEntryIdf1()->GetData()->SetLastGoodBin(static_cast<Int_t>(dataSet->GetLastGoodBin()/fAny2ManyInfo->rebin), i);
-    }
-
-    // feed histos
-    PUIntVector data;
-    UInt_t size = 0;
-    if (fAny2ManyInfo->rebin == 1) {
-      for (UInt_t 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=" << i << ")";
-          std::cerr << std::endl << ">>   something is really wrong!" << std::endl;
-          return false;
-        }
-        size = dataSet->GetData()->size();
-        for (UInt_t j=0; j<size; j++) {
-          data.push_back((UInt_t)dataSet->GetData()->at(j));
-        }
-        nxs->GetEntryIdf1()->GetData()->SetHisto(data, i);
-        data.clear();
-      }
-    } else { // rebin > 1
-      UInt_t dataRebin = 0;
-      UInt_t dataCount = 0;
-      for (UInt_t 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=" << i << ")";
-          std::cerr << std::endl << ">>   something is really wrong!" << std::endl;
-          return false;
-        }
-        size = dataSet->GetData()->size();
-        dataCount = 0;
-        for (UInt_t j=0; j<size; j++) {
-          if ((j > 0) && (j % fAny2ManyInfo->rebin == 0)) {
-            dataCount++;
-            data.push_back(dataRebin);
-            dataRebin = 0;
-          }
-          dataRebin += static_cast<UInt_t>(dataSet->GetData()->at(j));
-        }
-        nxs->GetEntryIdf1()->GetData()->SetHisto(data, i);
-        data.clear();
-      }
-    }
   } else if (fAny2ManyInfo->idf == 2) {
     // fill necessary data structures
     nxs->SetFileName(fln.Data());