Merge pull request #38406 from robertapplin/38332-move-nexus-reading-…

…code-to-nexus-library

Move `H5Util` file to Mantid::Nexus library

Framework/DataHandling/CMakeLists.txt

@@ -27,7 +27,6 @@ set(SRC_FILES
     src/GenerateGroupingPowder2.cpp
     src/GroupDetectors.cpp
     src/GroupDetectors2.cpp
-    src/H5Util.cpp
     src/ISISDataArchive.cpp
     src/ISISJournal.cpp
     src/ISISJournalGetExperimentRuns.cpp
@@ -251,7 +250,6 @@ set(INC_FILES
     inc/MantidDataHandling/GenerateGroupingPowder2.h
     inc/MantidDataHandling/GroupDetectors.h
     inc/MantidDataHandling/GroupDetectors2.h
-    inc/MantidDataHandling/H5Util.h
     inc/MantidDataHandling/ISISDataArchive.h
     inc/MantidDataHandling/ISISJournal.h
     inc/MantidDataHandling/ISISJournalGetExperimentRuns.h
@@ -475,7 +473,6 @@ set(TEST_FILES
     GenerateGroupingPowder2Test.h
     GroupDetectors2Test.h
     GroupDetectorsTest.h
-    H5UtilTest.h
     ISISDataArchiveTest.h
     ISISJournalGetExperimentRunsTest.h
     ISISJournalTest.h

Framework/DataHandling/inc/MantidDataHandling/LoadHelper.h

@@ -6,8 +6,10 @@
 // SPDX - License - Identifier: GPL - 3.0 +
 #pragma once
 
+#include "MantidAPI/MatrixWorkspace_fwd.h"
 #include "MantidAPI/Run.h"
 #include "MantidDataHandling/DllConfig.h"
+#include "MantidKernel/Quat.h"
 #include "MantidNexus/NexusClasses.h"
 
 namespace Mantid {

Framework/DataHandling/inc/MantidDataHandling/LoadISISNexus2.h

@@ -116,7 +116,8 @@ class MANTID_DATAHANDLING_DLL LoadISISNexus2 : public API::IFileLoader<Kernel::N
   void validateMultiPeriodLogs(const Mantid::API::MatrixWorkspace_sptr &);
 
   // build the list of spectra numbers to load and include in the spectra list
-  void buildSpectraInd2SpectraNumMap(bool range_supplied, bool hasSpectraList, DataBlockComposite &dataBlockComposite);
+  void buildSpectraInd2SpectraNumMap(bool range_supplied, bool hasSpectraList,
+                                     const DataBlockComposite &dataBlockComposite);
 
   /// Check if any of the spectra block ranges overlap
   void checkOverlappingSpectraRange();
@@ -171,8 +172,8 @@ class MANTID_DATAHANDLING_DLL LoadISISNexus2 : public API::IFileLoader<Kernel::N
   boost::scoped_ptr< ::NeXus::File> m_nexusFile;
   // clang-format on
 
-  bool findSpectraDetRangeInFile(NeXus::NXEntry &entry, std::vector<specnum_t> &spectrum_index, int64_t ndets,
-                                 int64_t n_vms_compat_spectra, std::map<specnum_t, std::string> &monitors,
+  bool findSpectraDetRangeInFile(const NeXus::NXEntry &entry, std::vector<specnum_t> &spectrum_index, int64_t ndets,
+                                 int64_t n_vms_compat_spectra, const std::map<specnum_t, std::string> &monitors,
                                  bool excludeMonitors, bool separateMonitors);
 
   /// Check if is the file is a multiple time regime file

Framework/DataHandling/inc/MantidDataHandling/LoadMLZ.h

@@ -42,14 +42,14 @@ class MANTID_DATAHANDLING_DLL LoadMLZ : public API::IFileLoader<Kernel::NexusDes
 
   std::vector<std::vector<int>> getMonitorInfo(NeXus::NXEntry &firstEntry);
 
-  void initWorkSpace(NeXus::NXEntry &entry);
+  void initWorkspace(const NeXus::NXEntry &entry);
   void initInstrumentSpecific();
   void loadRunDetails(NeXus::NXEntry &entry);
   void loadExperimentDetails(const NeXus::NXEntry &entry);
 
   NeXus::NXData loadNexusFileData(NeXus::NXEntry &entry);
   void maskDetectors(const NeXus::NXEntry &entry);
-  void loadDataIntoTheWorkSpace(NeXus::NXEntry &entry); //, int ElasticPeakPosition = -1);
+  void loadDataIntoTheWorkSpace(const NeXus::NXEntry &entry); //, int ElasticPeakPosition = -1);
 
   void runLoadInstrument();
 

Framework/DataHandling/inc/MantidDataHandling/LoadNexusProcessed.h

@@ -13,6 +13,7 @@
 #include "MantidAPI/ITableWorkspace_fwd.h"
 #include "MantidAPI/MatrixWorkspace_fwd.h"
 #include "MantidAPI/NexusFileLoader.h"
+#include "MantidAPI/Sample.h"
 #include "MantidDataHandling/DllConfig.h"
 #include "MantidHistogramData/BinEdges.h"
 #include "MantidKernel/cow_ptr.h"

Framework/DataHandling/inc/MantidDataHandling/LoadSINQFocus.h

@@ -46,7 +46,7 @@ class MANTID_DATAHANDLING_DLL LoadSINQFocus : public API::IFileLoader<Kernel::Ne
   void init() override;
   void exec() override;
   void setInstrumentName(const NeXus::NXEntry &entry);
-  void initWorkSpace(NeXus::NXEntry &);
+  void initWorkSpace(const NeXus::NXEntry &);
   void loadDataIntoTheWorkSpace(NeXus::NXEntry &);
   /// Calculate error for y
   static double calculateError(double in) { return sqrt(in); }

Framework/DataHandling/src/DataBlockComposite.cpp

@@ -6,8 +6,10 @@
 // SPDX - License - Identifier: GPL - 3.0 +
 #include "MantidDataHandling/DataBlockComposite.h"
 #include "MantidDataHandling/DataBlockGenerator.h"
+
 #include <algorithm>
 #include <cassert>
+#include <numeric>
 
 namespace {
 
@@ -380,7 +382,7 @@ void DataBlockComposite::removeSpectra(DataBlockComposite &toRemove) {
   // Now create the new intervals which don't include the removeInterval
   // values
   std::vector<SpectrumPair> newIntervals;
-  for (auto &originalInterval : originalIntervals) {
+  for (const auto &originalInterval : originalIntervals) {
     // Find all relevant remove intervals. In principal this could
     // be made more efficient.
     auto currentRemovalIntervals =

Framework/DataHandling/src/LoadDiffCal.cpp

@@ -11,7 +11,6 @@
 #include "MantidAPI/Progress.h"
 #include "MantidAPI/Run.h"
 #include "MantidAPI/TableRow.h"
-#include "MantidDataHandling/H5Util.h"
 #include "MantidDataHandling/LoadCalFile.h"
 #include "MantidDataObjects/GroupingWorkspace.h"
 #include "MantidDataObjects/MaskWorkspace.h"
@@ -21,6 +20,7 @@
 #include "MantidKernel/Exception.h"
 #include "MantidKernel/OptionalBool.h"
 #include "MantidKernel/Unit.h"
+#include "MantidNexus/H5Util.h"
 
 #include <H5Cpp.h>
 #include <cmath>
@@ -44,6 +44,7 @@ using Mantid::Kernel::PropertyWithValue;
 using Mantid::Kernel::Exception::FileError;
 
 using namespace H5;
+using namespace NeXus;
 
 namespace {
 enum class CalibFilenameExtensionEnum { H5, HD5, HDF, CAL, enum_count };

Framework/DataHandling/src/LoadILLDiffraction.cpp

@@ -11,7 +11,6 @@
 #include "MantidAPI/RegisterFileLoader.h"
 #include "MantidAPI/Run.h"
 #include "MantidAPI/WorkspaceFactory.h"
-#include "MantidDataHandling/H5Util.h"
 #include "MantidDataHandling/LoadHelper.h"
 #include "MantidDataObjects/ScanningWorkspaceBuilder.h"
 #include "MantidGeometry/Instrument/ComponentHelper.h"
@@ -22,6 +21,7 @@
 #include "MantidKernel/ListValidator.h"
 #include "MantidKernel/PropertyWithValue.h"
 #include "MantidKernel/TimeSeriesProperty.h"
+#include "MantidNexus/H5Util.h"
 
 #include <H5Cpp.h>
 #include <Poco/Path.h>

Framework/DataHandling/src/LoadISISNexus2.cpp

@@ -16,6 +16,7 @@
 #include "MantidAPI/Axis.h"
 #include "MantidAPI/FileProperty.h"
 #include "MantidAPI/RegisterFileLoader.h"
+#include "MantidAPI/Sample.h"
 #include "MantidAPI/WorkspaceFactory.h"
 #include "MantidGeometry/Instrument.h"
 #include "MantidGeometry/Instrument/Detector.h"
@@ -604,7 +605,7 @@ below have to be processed rather then spectra list
 intervals
 **/
 void LoadISISNexus2::buildSpectraInd2SpectraNumMap(bool range_supplied, bool hasSpectraList,
-                                                   DataBlockComposite &dataBlockComposite) {
+                                                   const DataBlockComposite &dataBlockComposite) {
 
   if (range_supplied || hasSpectraList || true) {
     auto generator = dataBlockComposite.getGenerator();
@@ -943,9 +944,10 @@ double LoadISISNexus2::dblSqrt(double in) { return sqrt(in); }
  *                               (contain different number of time channels)
  *
  */
-bool LoadISISNexus2::findSpectraDetRangeInFile(NXEntry &entry, std::vector<specnum_t> &spectrum_index, int64_t ndets,
-                                               int64_t n_vms_compat_spectra, std::map<specnum_t, std::string> &monitors,
-                                               bool excludeMonitors, bool separateMonitors) {
+bool LoadISISNexus2::findSpectraDetRangeInFile(const NXEntry &entry, std::vector<specnum_t> &spectrum_index,
+                                               int64_t ndets, int64_t n_vms_compat_spectra,
+                                               const std::map<specnum_t, std::string> &monitors, bool excludeMonitors,
+                                               bool separateMonitors) {
   size_t nmons = monitors.size();
 
   if (nmons > 0) {

Framework/DataHandling/src/LoadInstrumentFromNexus.cpp

@@ -9,6 +9,7 @@
 //----------------------------------------------------------------------
 #include "MantidDataHandling/LoadInstrumentFromNexus.h"
 #include "MantidAPI/FileProperty.h"
+#include "MantidAPI/MatrixWorkspace.h"
 #include "MantidGeometry/Instrument.h"
 #include "MantidGeometry/Instrument/CompAssembly.h"
 #include "MantidGeometry/Instrument/Component.h"

Framework/DataHandling/src/LoadMLZ.cpp

@@ -10,6 +10,7 @@
 #include "MantidAPI/MatrixWorkspace.h"
 #include "MantidAPI/Progress.h"
 #include "MantidAPI/RegisterFileLoader.h"
+#include "MantidAPI/Sample.h"
 #include "MantidAPI/SpectrumInfo.h"
 #include "MantidAPI/WorkspaceFactory.h"
 #include "MantidDataHandling/LoadHelper.h"
@@ -77,7 +78,7 @@ void LoadMLZ::exec() {
   loadInstrumentDetails(dataFirstEntry);
   loadTimeDetails(dataFirstEntry);
 
-  initWorkSpace(dataFirstEntry);
+  initWorkspace(dataFirstEntry);
 
   // load the instrument from the IDF
   runLoadInstrument();
@@ -169,7 +170,7 @@ void LoadMLZ::loadInstrumentDetails(const NeXus::NXEntry &firstEntry) {
  * @param entry :: The Nexus entry
  *
  */
-void LoadMLZ::initWorkSpace(NeXus::NXEntry &entry) //, const std::vector<std::vector<int> >&monitors)
+void LoadMLZ::initWorkspace(const NeXus::NXEntry &entry) //, const std::vector<std::vector<int> >&monitors)
 {
   // read in the data
   NXData dataGroup = entry.openNXData("data");
@@ -352,7 +353,7 @@ void LoadMLZ::loadExperimentDetails(const NXEntry &entry) {
  *
  * @param entry :: The Nexus entry
  */
-void LoadMLZ::loadDataIntoTheWorkSpace(NeXus::NXEntry &entry) {
+void LoadMLZ::loadDataIntoTheWorkSpace(const NeXus::NXEntry &entry) {
   // read in the data
   NXData dataGroup = entry.openNXData("data");
   NXInt data = dataGroup.openIntData();

Framework/DataHandling/src/LoadMcStas.cpp

@@ -13,14 +13,14 @@
 #include "MantidAPI/RegisterFileLoader.h"
 #include "MantidAPI/WorkspaceFactory.h"
 #include "MantidAPI/WorkspaceGroup.h"
-#include "MantidDataHandling/H5Util.h"
 #include "MantidDataHandling/LoadEventNexus.h"
 #include "MantidGeometry/Instrument.h"
 #include "MantidGeometry/Instrument/InstrumentDefinitionParser.h"
 #include "MantidKernel/RegexStrings.h"
 #include "MantidKernel/Strings.h"
 #include "MantidKernel/Unit.h"
 #include "MantidKernel/UnitFactory.h"
+#include "MantidNexus/H5Util.h"
 
 #include <H5Cpp.h>
 #include <boost/algorithm/string.hpp>
@@ -29,6 +29,7 @@ namespace Mantid::DataHandling {
 using namespace Kernel;
 using namespace API;
 using namespace DataObjects;
+using namespace NeXus;
 
 // Register the algorithm into the AlgorithmFactory
 DECLARE_NEXUS_HDF5_FILELOADER_ALGORITHM(LoadMcStas)

Framework/DataHandling/src/LoadMuonNexus2.cpp

@@ -5,11 +5,13 @@
 //   Institut Laue - Langevin & CSNS, Institute of High Energy Physics, CAS
 // SPDX - License - Identifier: GPL - 3.0 +
 #include "MantidDataHandling/LoadMuonNexus2.h"
+
 #include "MantidAPI/Axis.h"
 #include "MantidAPI/FileProperty.h"
 #include "MantidAPI/Progress.h"
 #include "MantidAPI/RegisterFileLoader.h"
 #include "MantidAPI/Run.h"
+#include "MantidAPI/Sample.h"
 #include "MantidAPI/WorkspaceFactory.h"
 #include "MantidAPI/WorkspaceGroup.h"
 #include "MantidDataHandling/LoadMuonNexus1.h"
@@ -24,6 +26,7 @@
 #include "MantidKernel/UnitFactory.h"
 #include "MantidKernel/UnitLabelTypes.h"
 #include "MantidNexus/NexusClasses.h"
+
 #include <Poco/Path.h>
 #include <memory>
 // clang-format off
@@ -145,7 +148,7 @@ void LoadMuonNexus2::doExec() {
 
   std::string detectorName;
   // Only the first NXdata found
-  for (auto &group : entry.groups()) {
+  for (const auto &group : entry.groups()) {
     std::string className = group.nxclass;
     if (className == "NXdata") {
       detectorName = group.nxname;
@@ -483,7 +486,7 @@ std::map<int, std::set<int>> LoadMuonNexus2::loadDetectorMapping(const Mantid::N
   NXEntry entry = root.openEntry(m_entry_name);
   const std::string detectorName = [&entry]() {
     // Only the first NXdata found
-    for (auto &group : entry.groups()) {
+    for (const auto &group : entry.groups()) {
       std::string className = group.nxclass;
       if (className == "NXdata") {
         return group.nxname;