Refs #24078: Re-introduced closing/opening of nexus file

Needed for instrument loading.
Also re-instated the findGroup() function in NexusGeometryParser as the refactored
version was disfunctional (segfaults)

Framework/DataHandling/src/LoadEventNexus.cpp

@@ -646,12 +646,19 @@ void LoadEventNexus::loadEvents(API::Progress *const prog,
   if (!m_ws->getInstrument() || !m_instrument_loaded_correctly) {
     // Load the instrument (if not loaded before)
     prog->report("Loading instrument");
+    // Note that closing an re-opening the file is needed here for loading
+    // instruments directly from the nexus file containing the event data.
+    // This may not be needed in the future if both LoadEventNexus and
+    // LoadInstrument are made to use the same Nexus/HDF5 library
+    m_file->close();
     m_instrument_loaded_correctly =
         loadInstrument(m_filename, m_ws, m_top_entry_name, this);
 
     if (!m_instrument_loaded_correctly)
       throw std::runtime_error(
           "Instrument was not initialized correctly! Loading cannot continue.");
+    // reopen file
+    safeOpenFile(m_filename);
   }
 
   // top level file information

Framework/NexusGeometry/src/NexusGeometryParser.cpp

@@ -154,8 +154,7 @@ std::string get1DStringDataset(const std::string &dataset, const Group &group) {
  *   size 1.
  */
 std::vector<Group> openSubGroups(const Group &parentGroup,
-                                 const H5std_string &CLASS_TYPE,
-                                 const bool firstEntryOnly = false) {
+                                 const H5std_string &CLASS_TYPE) {
   std::vector<Group> subGroups;
   // Iterate over children, and determine if a group
   for (hsize_t i = 0; i < parentGroup.getNumObjs(); ++i) {
@@ -178,8 +177,6 @@ std::vector<Group> openSubGroups(const Group &parentGroup,
           // If group of correct type, append to subGroup vector
           if (classType == CLASS_TYPE) {
             subGroups.push_back(childGroup);
-            if (firstEntryOnly)
-              return subGroups;
           }
         }
       }
@@ -188,11 +185,45 @@ std::vector<Group> openSubGroups(const Group &parentGroup,
   return subGroups;
 }
 
+/// Find a single group inside parent (returns first match)
+//  TODO: refactor most of this and openSubGroups() to avoid duplication
+Group findGroup(const Group &parentGroup, const H5std_string &CLASS_TYPE) {
+  Group childGroup;
+  // Iterate over children, and determine if a group
+  for (hsize_t i = 0; i < parentGroup.getNumObjs(); ++i) {
+    if (parentGroup.getObjTypeByIdx(i) == GROUP_TYPE) {
+      H5std_string childPath = parentGroup.getObjnameByIdx(i);
+      // Open the sub group
+      childGroup = parentGroup.openGroup(childPath);
+      // Iterate through attributes to find NX_class
+      for (uint32_t attribute_index = 0;
+           attribute_index < static_cast<uint32_t>(childGroup.getNumAttrs());
+           ++attribute_index) {
+        // Test attribute at current index for NX_class
+        Attribute attribute = childGroup.openAttribute(attribute_index);
+        if (attribute.getName() == NX_CLASS) {
+          // Get attribute data type
+          DataType dataType = attribute.getDataType();
+          // Get the NX_class type
+          H5std_string classType;
+          attribute.read(dataType, classType);
+          // If group of correct type, return the childGroup
+          if (classType == CLASS_TYPE) {
+            return childGroup;
+          }
+        }
+      }
+    }
+  }
+  // TODO: would maybe be better to return boost::optional?
+  return childGroup;
+}
+
 // Get the instrument name
 std::string instrumentName(const Group &root) {
-  std::vector<Group> instrumentGroup = openSubGroups(
-      openSubGroups(root, NX_ENTRY, true)[0], NX_INSTRUMENT, true);
-  return get1DStringDataset("name", instrumentGroup[0]);
+  Group entryGroup = findGroup(root, NX_ENTRY);
+  Group instrumentGroup = findGroup(entryGroup, NX_INSTRUMENT);
+  return get1DStringDataset("name", instrumentGroup);
 }
 
 // Open all detector groups into a vector
@@ -572,12 +603,11 @@ parseNexusShape(const Group &detectorGroup, bool &searchTubes) {
 void parseAndAddSource(const H5File &file, const Group &root,
                        InstrumentBuilder &builder) {
   H5std_string sourcePath = "source";
-  std::vector<Group> sourceGroup =
-      openSubGroups(openSubGroups(openSubGroups(root, NX_ENTRY, true)[0],
-                                  NX_INSTRUMENT, true)[0],
-                    sourcePath, true);
-  auto sourceName = get1DStringDataset("name", sourceGroup[0]);
-  auto sourceTransformations = getTransformations(file, sourceGroup[0]);
+  Group entryGroup = findGroup(root, NX_ENTRY);
+  Group instrumentGroup = findGroup(entryGroup, NX_INSTRUMENT);
+  Group sourceGroup = findGroup(instrumentGroup, sourcePath);
+  auto sourceName = get1DStringDataset("name", sourceGroup);
+  auto sourceTransformations = getTransformations(file, sourceGroup);
   auto defaultPos = Eigen::Vector3d(0.0, 0.0, 0.0);
   builder.addSource(sourceName, sourceTransformations * defaultPos);
 }
@@ -587,9 +617,9 @@ void parseAndAddSample(const H5File &file, const Group &root,
                        InstrumentBuilder &builder) {
   std::string sampleName = "sample";
   H5std_string samplePath = sampleName;
-  std::vector<Group> sampleGroup =
-      openSubGroups(openSubGroups(root, NX_ENTRY, true)[0], samplePath, true);
-  auto sampleTransforms = getTransformations(file, sampleGroup[0]);
+  Group entryGroup = findGroup(root, NX_ENTRY);
+  Group sampleGroup = findGroup(entryGroup, samplePath);
+  auto sampleTransforms = getTransformations(file, sampleGroup);
   Eigen::Vector3d samplePos = sampleTransforms * Eigen::Vector3d(0.0, 0.0, 0.0);
   builder.addSample(sampleName, samplePos);
 }