adopted to new hdf4/5 approach of NeXus.
This commit is contained in:
@@ -30,6 +30,10 @@
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#ifndef _PRUNDATAHANDLER_H_
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#define _PRUNDATAHANDLER_H_
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#include <any>
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#include <iostream>
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#include <string>
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#include <TString.h>
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#include "PMusr.h"
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@@ -432,6 +436,8 @@ class PRunDataHandler
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virtual Bool_t FileExistsCheck(const Bool_t fileName, const Int_t idx);
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virtual Bool_t FileExistsCheck(const TString fileName);
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virtual Bool_t ReadRootFile();
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template <typename T> Bool_t ReadNexusFileIdf1(T& nxs_file);
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template <typename T> Bool_t ReadNexusFileIdf2(T& nxs_file);
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virtual Bool_t ReadNexusFile();
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virtual Bool_t ReadWkmFile();
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virtual Bool_t ReadPsiBinFile();
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@@ -443,7 +449,7 @@ class PRunDataHandler
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virtual Bool_t WriteMusrRootFile(Int_t tag=A2M_MUSR_ROOT_DIR, TString fln="");
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virtual Bool_t WriteRootFile(TString fln="");
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virtual Bool_t WriteNexusFile(TString fln="");
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virtual Bool_t WriteNexusFile(TString format, TString fln="");
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virtual Bool_t WriteWkmFile(TString fln="");
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virtual Bool_t WritePsiBinFile(TString fln="");
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virtual Bool_t WriteMudFile(TString fln="");
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@@ -464,4 +470,417 @@ class PRunDataHandler
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virtual TString GetYear(Int_t month);
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};
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//--------------------------------------------------------------------------
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// ReadNexusFileIdf1 (private)
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//--------------------------------------------------------------------------
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/**
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* <p>Reads a NeXus file with IDF version 1 format.
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*
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* <p>Extracts run metadata (laboratory, beamline, instrument, run title,
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* run number, temperature, field, sample info, time resolution, start/stop
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* times) and histogram data from the NeXus file structure.
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*
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* @tparam T NeXus file handler type (std::unique_ptr<nxH4::PNeXus> and std::unique_ptr<nxH5::PNeXus>)
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* @param nxs_file reference to the NeXus file handler
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*
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* <b>return:</b>
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* - true at successful reading,
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* - otherwise false.
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*/
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template <typename T>
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Bool_t PRunDataHandler::ReadNexusFileIdf1(T& nxs_file)
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{
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PRawRunData runData;
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PRawRunDataSet dataSet;
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TString str;
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std::string sstr;
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Int_t ival;
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Double_t dval, factor;
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bool ok;
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// get header information
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// get/set laboratory
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sstr = "n/a";
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if (nxs_file->HasDataset("/run/lab"))
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sstr = nxs_file->template GetDataset<std::string>("/run/lab").GetData()[0];
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runData.SetLaboratory(sstr);
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// get/set beamline
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sstr = "n/a";
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if (nxs_file->HasDataset("/run/beamline"))
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sstr = nxs_file->template GetDataset<std::string>("/run/beamline").GetData()[0];
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runData.SetBeamline(sstr);
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// get/set instrument
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sstr = "n/a";
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if (nxs_file->HasDataset("/run/instrument/name"))
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sstr = nxs_file->template GetDataset<std::string>("/run/instrument/name").GetData()[0];
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runData.SetInstrument(sstr);
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// get/set run title
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str = "n/a";
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if (nxs_file->HasDataset("/run/title"))
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sstr = nxs_file->template GetDataset<std::string>("/run/title").GetData()[0];
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runData.SetRunTitle(sstr);
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// get/set run number
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ival = -1;
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if (nxs_file->HasDataset("/run/number"))
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ival = nxs_file->template GetDataset<int>("/run/number").GetData()[0];
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runData.SetRunNumber(ival);
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// get/set temperature
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dval = PMUSR_UNDEFINED;
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sstr = "n/a";
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if (nxs_file->HasDataset("/run/sample/temperature")) {
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auto tmp_ds = nxs_file->template GetDataset<float>("/run/sample/temperature");
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dval = tmp_ds.GetData()[0];
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if (tmp_ds.HasAttribute("units"))
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sstr = std::any_cast<std::string>(tmp_ds.GetAttribute("units"));
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if (sstr == "Celcius")
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dval += 273.16;
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}
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runData.SetTemperature(0, dval, 0.0);
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// get/set field
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dval = PMUSR_UNDEFINED;
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sstr = "n/a";
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factor = 1.0;
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if (nxs_file->HasDataset("/run/sample/magnetic_field")) {
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auto mag_ds = nxs_file->template GetDataset<float>("/run/sample/magnetic_field");
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dval = mag_ds.GetData()[0];
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if (mag_ds.HasAttribute("units"))
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sstr = std::any_cast<std::string>(mag_ds.GetAttribute("units"));
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if (sstr == "Tesla")
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factor = 1.0e4;
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}
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runData.SetField(dval*factor);
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// get/set implantation energy
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runData.SetEnergy(PMUSR_UNDEFINED);
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// get/set moderator HV
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runData.SetTransport(PMUSR_UNDEFINED);
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// get/set RA HV's (LEM specific)
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for (UInt_t i=0; i<4; i++)
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runData.SetRingAnode(i, PMUSR_UNDEFINED);
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// get/set setup
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sstr = "n/a";
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if (nxs_file->HasDataset("/run/notes"))
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sstr = nxs_file->template GetDataset<std::string>("/run/notes").GetData()[0];
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runData.SetSetup(sstr);
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// get/set sample
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sstr = "n/a";
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if (nxs_file->HasDataset("/run/sample/name"))
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sstr = nxs_file->template GetDataset<std::string>("/run/sample/name").GetData()[0];
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runData.SetSample(sstr);
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// get/set orientation
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runData.SetOrientation("??");
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// get/set time resolution (ns)
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dval = PMUSR_UNDEFINED;
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sstr = "n/a";
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factor = 1.0;
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if (nxs_file->HasDataset("/run/histogram_data_1/resolution")) {
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auto res_ds = nxs_file->template GetDataset<int>("/run/histogram_data_1/resolution");
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dval = res_ds.GetData()[0];
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if (res_ds.HasAttribute("units"))
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sstr = std::any_cast<std::string>(res_ds.GetAttribute("units"));
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if ((sstr == "picoseconds") || (sstr == "pico.seconds"))
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factor = 1.0e-3; // ps -> ns
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}
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runData.SetTimeResolution(dval*factor);
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// get/set start/stop time
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sstr = "n/a";
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TString date{"n/a"}, time{"n/a"};
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if (nxs_file->HasDataset("/run/start_time"))
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sstr = nxs_file->template GetDataset<std::string>("/run/start_time").GetData()[0];
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str = sstr;
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SplitTimeDate(str, time, date, ok);
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if (ok) {
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runData.SetStartTime(time);
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runData.SetStartDate(date);
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}
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sstr = "n/a";
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date = "n/a";
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time = "n/a";
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if (nxs_file->HasDataset("/run/stop_time"))
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sstr = nxs_file->template GetDataset<std::string>("/run/stop_time").GetData()[0];
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str = sstr;
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SplitTimeDate(str, time, date, ok);
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if (ok) {
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runData.SetStopTime(time);
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runData.SetStopDate(date);
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}
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// get/set deadtime relevant parameters
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if (nxs_file->HasDataset("/run/instrument/detector/deadtimes")) {
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std::vector<float> dt;
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dt = nxs_file->template GetDataset<float>("/run/instrument/detector/deadtimes").GetData();
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runData.SetDeadTimeParam(dt);
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}
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if (nxs_file->HasDataset("/run/instrument/beam/frames_good")) {
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ival = nxs_file->template GetDataset<float>("/run/instrument/beam/frames_good").GetData()[0];
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runData.SetNumberOfGoodFrames(ival);
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}
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// data with its metadata
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if (nxs_file->HasDataset("/run/histogram_data_1/counts")) {
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int t0_bin{-1}, fgb{-1}, lgb{-1}, noOfHistos{-1}, histoLength{-1};
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auto count_ds = nxs_file->template GetDataset<int>("/run/histogram_data_1/counts");
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auto count = count_ds.GetData();
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// get all necessary attributes
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if (count_ds.HasAttribute("t0_bin"))
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t0_bin = std::any_cast<int>(count_ds.GetAttribute("t0_bin"));
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if (count_ds.HasAttribute("first_good_bin"))
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fgb = std::any_cast<int>(count_ds.GetAttribute("first_good_bin"));
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if (count_ds.HasAttribute("last_good_bin"))
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lgb = std::any_cast<int>(count_ds.GetAttribute("last_good_bin"));
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if (count_ds.HasAttribute("number"))
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noOfHistos = std::any_cast<int>(count_ds.GetAttribute("number"));
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if (count_ds.HasAttribute("length"))
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histoLength = std::any_cast<int>(count_ds.GetAttribute("length"));
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if (static_cast<int>(count.size()) != noOfHistos*histoLength) {
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std::cerr << std::endl << "**ERROR** PNeXus data size error! count.size()=" << count.size() << ", #histos=" << noOfHistos << ", length=" << histoLength << "." << std::endl;
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return false;
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}
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// fill dataSet
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PDoubleVector data;
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for (int i=0; i<noOfHistos; i++) {
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dataSet.Clear();
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dataSet.SetHistoNo(i+1); // i.e. histo numbers start with 1
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dataSet.SetTimeZeroBin(t0_bin);
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dataSet.SetFirstGoodBin(fgb);
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dataSet.SetLastGoodBin(lgb);
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for (int j=0; j<histoLength; j++)
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data.push_back(count[i*histoLength+j]);
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dataSet.SetData(data);
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runData.SetDataSet(dataSet);
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data.clear();
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}
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// keep run name from the msr-file
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runData.SetRunName(fRunName);
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// keep the information
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fData.push_back(runData);
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} else { // no data found
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std::cerr << std::endl << "**ERROR** PNeXus couldn't obtain data: '/run/histogram_data_1/counts' is missing." << std::endl;
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return false;
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}
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return true;
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}
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//--------------------------------------------------------------------------
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// ReadNexusFileIdf2 (private)
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//--------------------------------------------------------------------------
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template <typename T>
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Bool_t PRunDataHandler::ReadNexusFileIdf2(T& nxs_file)
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{
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PRawRunData runData;
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PRawRunDataSet dataSet;
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TString str;
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std::string sstr;
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Int_t ival;
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Double_t dval, factor;
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bool ok;
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// get header information
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// get/set laboratory
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sstr = "n/a";
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if (nxs_file->HasDataset("/raw_data_1/instrument/source/name"))
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sstr = nxs_file->template GetDataset<std::string>("/raw_data_1/instrument/source/name").GetData()[0];
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runData.SetLaboratory(sstr);
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// get/set beamline
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sstr = "n/a";
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if (nxs_file->HasDataset("/raw_data_1/instrument/name"))
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sstr = nxs_file->template GetDataset<std::string>("/raw_data_1/instrument/name").GetData()[0];
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runData.SetBeamline(sstr);
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runData.SetBeamline(sstr);
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// get/set muon source
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sstr = "n/a";
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if (nxs_file->HasDataset("/raw_data_1/instrument/source/type"))
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sstr = nxs_file->template GetDataset<std::string>("/raw_data_1/instrument/source/type").GetData()[0];
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runData.SetMuonSource(sstr);
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// get/set muon species
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sstr = "n/a";
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if (nxs_file->HasDataset("/raw_data_1/instrument/source/probe"))
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sstr = nxs_file->template GetDataset<std::string>("/raw_data_1/instrument/source/probe").GetData()[0];
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runData.SetMuonSpecies(sstr);
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// get/set run title
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sstr = "n/a";
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if (nxs_file->HasDataset("/raw_data_1/title"))
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sstr = nxs_file->template GetDataset<std::string>("/raw_data_1/title").GetData()[0];
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runData.SetRunTitle(sstr);
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// get/set run number
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ival = -1;
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if (nxs_file->HasDataset("/raw_data_1/run_number"))
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ival = nxs_file->template GetDataset<int>("/raw_data_1/run_number").GetData()[0];
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runData.SetRunNumber(ival);
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// get/set temperature
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dval = PMUSR_UNDEFINED;
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sstr = "n/a";
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if (nxs_file->HasDataset("/raw_data_1/sample/temperature")) {
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auto tmp_ds = nxs_file->template GetDataset<float>("/raw_data_1/sample/temperature");
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dval = tmp_ds.GetData()[0];
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if (tmp_ds.HasAttribute("units"))
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sstr = std::any_cast<std::string>(tmp_ds.GetAttribute("units"));
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if (sstr == "Celcius")
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dval += 273.16;
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}
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runData.SetTemperature(0, dval, 0.0);
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// get/set field
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dval = PMUSR_UNDEFINED;
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sstr = "n/a";
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factor = 1.0;
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if (nxs_file->HasDataset("/raw_data_1/sample/magnetic_field")) {
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auto mag_ds = nxs_file->template GetDataset<float>("/raw_data_1/sample/magnetic_field");
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dval = mag_ds.GetData()[0];
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if (mag_ds.HasAttribute("units"))
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sstr = std::any_cast<std::string>(mag_ds.GetAttribute("units"));
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if (sstr == "Tesla")
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factor = 1.0e4;
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}
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runData.SetField(dval*factor);
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// get/set implantation energy
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runData.SetEnergy(PMUSR_UNDEFINED);
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// get/set implantation energy
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runData.SetEnergy(PMUSR_UNDEFINED);
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// get/set moderator HV
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runData.SetTransport(PMUSR_UNDEFINED);
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// get/set RA HV's (LEM specific)
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for (UInt_t i=0; i<4; i++)
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runData.SetRingAnode(i, PMUSR_UNDEFINED);
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// get/set setup
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sstr = "n/a";
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runData.SetSetup(str);
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// get/set sample
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sstr = "n/a";
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if (nxs_file->HasDataset("/raw_data_1/sample/name"))
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sstr = nxs_file->template GetDataset<std::string>("/raw_data_1/sample/name").GetData()[0];
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runData.SetSample(sstr);
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// get/set orientation
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runData.SetOrientation("n/a");
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// get/set time resolution (ns)
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dval = PMUSR_UNDEFINED;
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sstr = "n/a";
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factor = 1.0;
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if (nxs_file->HasDataset("/raw_data_1/instrument/detector_1/resolution")) {
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auto res_ds = nxs_file->template GetDataset<int>("/raw_data_1/instrument/detector_1/resolution");
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dval = res_ds.GetData()[0];
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if (res_ds.HasAttribute("units"))
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sstr = std::any_cast<std::string>(res_ds.GetAttribute("units"));
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if ((sstr == "picoseconds") || (sstr == "pico.seconds"))
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factor = 1.0e-3; // ps -> ns
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}
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runData.SetTimeResolution(dval*factor);
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// get/set start/stop time
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sstr = "n/a";
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TString date{"n/a"}, time{"n/a"};
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if (nxs_file->HasDataset("/raw_data_1/start_time"))
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sstr = nxs_file->template GetDataset<std::string>("/raw_data_1/start_time").GetData()[0];
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str = sstr;
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SplitTimeDate(str, time, date, ok);
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if (ok) {
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runData.SetStartTime(time);
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runData.SetStartDate(date);
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}
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sstr = "n/a";
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date = "n/a";
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time = "n/a";
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if (nxs_file->HasDataset("/raw_data_1/end_time"))
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sstr = nxs_file->template GetDataset<std::string>("/raw_data_1/end_time").GetData()[0];
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str = sstr;
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SplitTimeDate(str, time, date, ok);
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if (ok) {
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runData.SetStopTime(time);
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runData.SetStopDate(date);
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}
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// get/set deadtime relevant parameters
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if (nxs_file->HasDataset("/raw_data_1/instrument/detector_1/dead_time")) {
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std::vector<float> dt;
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dt = nxs_file->template GetDataset<float>("/raw_data_1/instrument/detector_1/dead_time").GetData();
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runData.SetDeadTimeParam(dt);
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}
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if (nxs_file->HasDataset("/raw_data_1/good_frames")) {
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ival = nxs_file->template GetDataset<int>("/raw_data_1/good_frames").GetData()[0];
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runData.SetNumberOfGoodFrames(ival);
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}
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// data with its metadata
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if (nxs_file->HasDataset("/raw_data_1/instrument/detector_1/counts")) {
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int t0_bin{-1}, fgb{-1}, lgb{-1}, noOfHistos{-1}, histoLength{-1};
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auto count_ds = nxs_file->template GetDataset<int>("/raw_data_1/instrument/detector_1/counts");
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auto count = count_ds.GetData();
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auto dims = count_ds.GetDimensions();
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if (dims.size() < 3) {
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std::cerr << std::endl << "**ERROR** PNeXus data dimension error! dims.size()=" << dims.size() << ", expecting == 3." << std::endl;
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return false;
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}
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noOfHistos = dims[1];
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histoLength = dims[2];
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// get all necessary attributes
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if (count_ds.HasAttribute("t0_bin"))
|
||||
t0_bin = std::any_cast<int>(count_ds.GetAttribute("t0_bin"));
|
||||
if (count_ds.HasAttribute("first_good_bin"))
|
||||
fgb = std::any_cast<int>(count_ds.GetAttribute("first_good_bin"));
|
||||
if (count_ds.HasAttribute("last_good_bin"))
|
||||
lgb = std::any_cast<int>(count_ds.GetAttribute("last_good_bin"));
|
||||
if (static_cast<int>(count.size()) != noOfHistos*histoLength) {
|
||||
std::cerr << std::endl << "**ERROR** PNeXus data size error! count.size()=" << count.size() << ", #histos=" << noOfHistos << ", length=" << histoLength << "." << std::endl;
|
||||
return false;
|
||||
}
|
||||
|
||||
// fill dataSet
|
||||
PDoubleVector data;
|
||||
for (int i=0; i<noOfHistos; i++) {
|
||||
dataSet.Clear();
|
||||
dataSet.SetHistoNo(i+1); // i.e. histo numbers start with 1
|
||||
dataSet.SetTimeZeroBin(t0_bin);
|
||||
dataSet.SetFirstGoodBin(fgb);
|
||||
dataSet.SetLastGoodBin(lgb);
|
||||
for (int j=0; j<histoLength; j++)
|
||||
data.push_back(count[i*histoLength+j]);
|
||||
dataSet.SetData(data);
|
||||
runData.SetDataSet(dataSet);
|
||||
data.clear();
|
||||
}
|
||||
|
||||
// keep run name from the msr-file
|
||||
runData.SetRunName(fRunName);
|
||||
|
||||
// keep the information
|
||||
fData.push_back(runData);
|
||||
}
|
||||
|
||||
return true;
|
||||
}
|
||||
|
||||
#endif // _PRUNDATAHANDLER_H_
|
||||
|
||||
Reference in New Issue
Block a user