adopt HDF4 support for proper hierarchical writing of the data.

src/external/nexus/PNeXus.cpp

@@ -1971,48 +1971,105 @@ void nxH4::PNeXus::Dump()
 //=============================================================================
 int nxH4::PNeXus::WriteNexusFile(const std::string& filename, int idfVersion)
 {
-  // Create new HDF4 file
+  // Create new HDF4 file using SD interface (for datasets)
   int32 sd_id = SDstart(filename.c_str(), DFACC_CREATE);
   if (sd_id == FAIL) {
     std::cerr << "**ERROR** Failed to create HDF4 file: " << filename << std::endl;
     return 1;
   }
 
-  // Write file attributes
+  // Write file-level attributes (NeXus_version, HDF4_version, etc.)
   WriteFileAttributes(sd_id);
 
-  // Write datasets based on IDF version
+  if ((idfVersion != 1) && (idfVersion != 2)) {
-  if ((idfVersion == 1) || (idfVersion == 2)) {
-    // Write all datasets from data map
-    for (const auto& [path, data_any] : fDataMap) {
-      // Try to write as int dataset
-      try {
-        auto data = std::any_cast<PNXdata<int>>(data_any);
-        WriteIntDataset(sd_id, path, data);
-        continue;
-      } catch (...) {}
-
-      // Try to write as float dataset
-      try {
-        auto data = std::any_cast<PNXdata<float>>(data_any);
-        WriteFloatDataset(sd_id, path, data);
-        continue;
-      } catch (...) {}
-
-      // Try to write as string dataset
-      try {
-        auto data = std::any_cast<PNXdata<std::string>>(data_any);
-        WriteStringDataset(sd_id, path, data);
-        continue;
-      } catch (...) {}
-    }
-  } else {
     std::cerr << "**ERROR** Unsupported IDF version for writing: " << idfVersion << std::endl;
     SDend(sd_id);
     return 1;
   }
 
+  // Write all SDS datasets and collect their references keyed by path
+  std::map<std::string, int32> sdsRefMap;
+
+  for (const auto& [path, data_any] : fDataMap) {
+    int32 sds_ref = -1;
+
+    // Try to write as int dataset
+    try {
+      auto data = std::any_cast<PNXdata<int>>(data_any);
+      sds_ref = WriteIntDataset(sd_id, path, data);
+    } catch (...) {}
+
+    if (sds_ref == -1) {
+      // Try to write as float dataset
+      try {
+        auto data = std::any_cast<PNXdata<float>>(data_any);
+        sds_ref = WriteFloatDataset(sd_id, path, data);
+      } catch (...) {}
+    }
+
+    if (sds_ref == -1) {
+      // Try to write as string dataset
+      try {
+        auto data = std::any_cast<PNXdata<std::string>>(data_any);
+        sds_ref = WriteStringDataset(sd_id, path, data);
+      } catch (...) {}
+    }
+
+    if (sds_ref != -1) {
+      sdsRefMap[path] = sds_ref;
+    }
+  }
+
+  // Close SD interface before building Vgroup hierarchy
   SDend(sd_id);
+
+  // Now open the file with Hopen/Vstart to build the Vgroup hierarchy
+  int32 file_id = Hopen(filename.c_str(), DFACC_WRITE, 0);
+  if (file_id == FAIL) {
+    std::cerr << "**ERROR** Failed to reopen HDF4 file for Vgroup creation: " << filename << std::endl;
+    return 1;
+  }
+
+  if (Vstart(file_id) == FAIL) {
+    std::cerr << "**ERROR** Failed to initialize Vgroup interface" << std::endl;
+    Hclose(file_id);
+    return 1;
+  }
+
+  // Build Vgroup hierarchy and link SDS datasets into the correct groups
+  std::map<std::string, int32> vgroupCache; // path -> vgroup ref
+
+  for (const auto& [path, sds_ref] : sdsRefMap) {
+    // Extract parent path
+    size_t lastSlash = path.find_last_of('/');
+    if (lastSlash == std::string::npos || lastSlash == 0) {
+      // Dataset is at root level, no Vgroup needed
+      continue;
+    }
+    std::string parentPath = path.substr(0, lastSlash);
+
+    // Create the Vgroup hierarchy for the parent path
+    int32 parent_vg_ref = CreateVGroupHierarchy(file_id, parentPath, vgroupCache);
+    if (parent_vg_ref == -1) {
+      std::cerr << "**ERROR** Failed to create Vgroup hierarchy for: " << parentPath << std::endl;
+      continue;
+    }
+
+    // Attach to parent Vgroup and add the SDS dataset
+    int32 parent_vg_id = Vattach(file_id, parent_vg_ref, "w");
+    if (parent_vg_id != FAIL) {
+      Vaddtagref(parent_vg_id, DFTAG_NDG, sds_ref);
+      Vdetach(parent_vg_id);
+    }
+  }
+
+  // Detach all cached Vgroups (they were left attached for reuse)
+  // No — Vgroups were detached after creation in CreateVGroupHierarchy.
+  // We only re-attach briefly above to add tag/refs.
+
+  Vend(file_id);
+  Hclose(file_id);
+
   return 0;
 }
 
@@ -2064,7 +2121,7 @@ void nxH4::PNeXus::WriteFileAttributes(int32 sd_id)
 //=============================================================================
 // nxH4::PNeXus::WriteIntDataset
 //=============================================================================
-void nxH4::PNeXus::WriteIntDataset(int32 sd_id, const std::string& path,
+int32 nxH4::PNeXus::WriteIntDataset(int32 sd_id, const std::string& path,
                              const PNXdata<int>& data)
 {
   // Extract dataset name from path
@@ -2101,13 +2158,18 @@ void nxH4::PNeXus::WriteIntDataset(int32 sd_id, const std::string& path,
   // Write attributes
   WriteDatasetAttributes(sds_id, data);
 
+  // Get the SDS reference for Vgroup linking
+  int32 sds_ref = SDidtoref(sds_id);
+
   SDendaccess(sds_id);
+
+  return sds_ref;
 }
 
 //=============================================================================
 // nxH4::PNeXus::WriteFloatDataset
 //=============================================================================
-void nxH4::PNeXus::WriteFloatDataset(int32 sd_id, const std::string& path,
+int32 nxH4::PNeXus::WriteFloatDataset(int32 sd_id, const std::string& path,
                                const PNXdata<float>& data)
 {
   // Extract dataset name from path
@@ -2144,13 +2206,18 @@ void nxH4::PNeXus::WriteFloatDataset(int32 sd_id, const std::string& path,
   // Write attributes
   WriteDatasetAttributes(sds_id, data);
 
+  // Get the SDS reference for Vgroup linking
+  int32 sds_ref = SDidtoref(sds_id);
+
   SDendaccess(sds_id);
+
+  return sds_ref;
 }
 
 //=============================================================================
 // nxH4::PNeXus::WriteStringDataset
 //=============================================================================
-void nxH4::PNeXus::WriteStringDataset(int32 sd_id, const std::string& path,
+int32 nxH4::PNeXus::WriteStringDataset(int32 sd_id, const std::string& path,
                                 const PNXdata<std::string>& data)
 {
   // Extract dataset name from path
@@ -2162,7 +2229,7 @@ void nxH4::PNeXus::WriteStringDataset(int32 sd_id, const std::string& path,
 
   const auto& string_data = data.GetData();
   if (string_data.empty()) {
-    return;
+    return -1;
   }
 
   std::string str = string_data[0];
@@ -2185,7 +2252,12 @@ void nxH4::PNeXus::WriteStringDataset(int32 sd_id, const std::string& path,
   // Write attributes
   WriteDatasetAttributes(sds_id, data);
 
+  // Get the SDS reference for Vgroup linking
+  int32 sds_ref = SDidtoref(sds_id);
+
   SDendaccess(sds_id);
+
+  return sds_ref;
 }
 
 //=============================================================================
@@ -2238,6 +2310,126 @@ void nxH4::PNeXus::WriteDatasetAttributes(int32 sds_id, const PNXdata<T>& data)
   }
 }
 
+//=============================================================================
+// nxH4::PNeXus::WriteVGroupAttributes
+//=============================================================================
+void nxH4::PNeXus::WriteVGroupAttributes(int32 vgroup_id,
+                                          const std::map<std::string, std::any>& attributes)
+{
+  for (const auto& [attr_name, attr_value] : attributes) {
+    // Try string
+    try {
+      std::string str = std::any_cast<std::string>(attr_value);
+      Vsetattr(vgroup_id, attr_name.c_str(), DFNT_CHAR8,
+               static_cast<int32>(str.length()), str.c_str());
+      continue;
+    } catch (...) {}
+
+    // Try scalar int
+    try {
+      int32 value = std::any_cast<int>(attr_value);
+      Vsetattr(vgroup_id, attr_name.c_str(), DFNT_INT32, 1, &value);
+      continue;
+    } catch (...) {}
+
+    // Try scalar float
+    try {
+      float32 value = std::any_cast<float>(attr_value);
+      Vsetattr(vgroup_id, attr_name.c_str(), DFNT_FLOAT32, 1, &value);
+      continue;
+    } catch (...) {}
+
+    // Try vector<int>
+    try {
+      std::vector<int> int_vec = std::any_cast<std::vector<int>>(attr_value);
+      std::vector<int32> data32(int_vec.begin(), int_vec.end());
+      Vsetattr(vgroup_id, attr_name.c_str(), DFNT_INT32,
+               static_cast<int32>(data32.size()), data32.data());
+      continue;
+    } catch (...) {}
+
+    // Try vector<float>
+    try {
+      std::vector<float> float_vec = std::any_cast<std::vector<float>>(attr_value);
+      std::vector<float32> data32(float_vec.begin(), float_vec.end());
+      Vsetattr(vgroup_id, attr_name.c_str(), DFNT_FLOAT32,
+               static_cast<int32>(data32.size()), data32.data());
+      continue;
+    } catch (...) {}
+  }
+}
+
+//=============================================================================
+// nxH4::PNeXus::CreateVGroupHierarchy
+//=============================================================================
+int32 nxH4::PNeXus::CreateVGroupHierarchy(int32 file_id, const std::string& path,
+                                           std::map<std::string, int32>& vgroupCache)
+{
+  std::vector<std::string> components = splitPath(path);
+  if (components.empty()) {
+    return -1;
+  }
+
+  std::string currentPath;
+  int32 parent_vg_ref = -1;
+
+  for (const auto& component : components) {
+    if (component.empty()) continue;
+
+    currentPath += "/" + component;
+
+    // Check if this Vgroup was already created
+    auto it = vgroupCache.find(currentPath);
+    if (it != vgroupCache.end()) {
+      parent_vg_ref = it->second;
+      continue;
+    }
+
+    // Create a new Vgroup
+    int32 vg_id = Vattach(file_id, -1, "w");
+    if (vg_id == FAIL) {
+      std::cerr << "**ERROR** Failed to create Vgroup for: " << currentPath << std::endl;
+      return -1;
+    }
+
+    Vsetname(vg_id, component.c_str());
+
+    // Write group attributes if any exist for this path
+    auto attrIt = fGroupAttributes.find(currentPath);
+    if (attrIt != fGroupAttributes.end()) {
+      // Check for NX_class attribute and set it as Vgroup class
+      auto classIt = attrIt->second.find("NX_class");
+      if (classIt != attrIt->second.end()) {
+        try {
+          std::string nxClass = std::any_cast<std::string>(classIt->second);
+          Vsetclass(vg_id, nxClass.c_str());
+        } catch (...) {}
+      }
+      WriteVGroupAttributes(vg_id, attrIt->second);
+    }
+
+    // Get the reference of the newly created Vgroup
+    int32 vg_ref = VQueryref(vg_id);
+
+    // If there is a parent Vgroup, add this one as a child
+    if (parent_vg_ref != -1) {
+      int32 parent_vg_id = Vattach(file_id, parent_vg_ref, "w");
+      if (parent_vg_id != FAIL) {
+        Vinsert(parent_vg_id, vg_id);
+        Vdetach(parent_vg_id);
+      }
+    }
+
+    Vdetach(vg_id);
+
+    // Cache the reference for this path
+    vgroupCache[currentPath] = vg_ref;
+    parent_vg_ref = vg_ref;
+  }
+
+  return parent_vg_ref;
+}
+
 //=============================================================================
 // Group attribute methods - manage attributes associated with HDF4 groups
 //=============================================================================

src/external/nexus/PNeXus.h

@@ -944,42 +944,59 @@ private:
   void WriteDatasetAttributes(int32 sds_id, const PNXdata<T>& data);
 
   /**
-   * @brief Write attributes to a group
+   * @brief Write attributes to a Vgroup
-   * @param sd_id HDF4 SD interface ID
+   * @param vgroup_id HDF4 Vgroup ID to write attributes to
-   * @param groupPath Group path
    * @param attributes Map of attribute names to values
    */
-  void WriteGroupAttributes(int32 sd_id, const std::string& groupPath,
+  void WriteVGroupAttributes(int32 vgroup_id,
                               const std::map<std::string, std::any>& attributes);
 
   /**
-   * @brief Write an integer dataset with attributes
+   * @brief Create the Vgroup hierarchy for a given path
+   *
+   * Given a path like "/run/sample", creates Vgroups "run" and "sample"
+   * (nested), writing any associated group attributes from fGroupAttributes.
+   * Uses a cache to avoid creating duplicate Vgroups.
+   *
+   * @param file_id HDF4 file ID (from Hopen)
+   * @param path The group path to create (e.g., "/run/sample")
+   * @param vgroupCache Map of already-created group paths to their Vgroup references
+   * @return The Vgroup reference of the deepest group in the path
+   */
+  int32 CreateVGroupHierarchy(int32 file_id, const std::string& path,
+                               std::map<std::string, int32>& vgroupCache);
+
+  /**
+   * @brief Write an integer dataset with attributes and return its SDS reference
    * @param sd_id HDF4 SD interface ID
-   * @param path Dataset path
+   * @param path Dataset path (leaf name used for SDS name)
    * @param data PNXdata object containing data, dimensions, and attributes
+   * @return SDS reference number for linking into Vgroups
    * @throws std::runtime_error if writing fails
    */
-  void WriteIntDataset(int32 sd_id, const std::string& path,
+  int32 WriteIntDataset(int32 sd_id, const std::string& path,
                          const PNXdata<int>& data);
 
   /**
-   * @brief Write a float dataset with attributes
+   * @brief Write a float dataset with attributes and return its SDS reference
    * @param sd_id HDF4 SD interface ID
-   * @param path Dataset path
+   * @param path Dataset path (leaf name used for SDS name)
    * @param data PNXdata object containing data, dimensions, and attributes
+   * @return SDS reference number for linking into Vgroups
    * @throws std::runtime_error if writing fails
    */
-  void WriteFloatDataset(int32 sd_id, const std::string& path,
+  int32 WriteFloatDataset(int32 sd_id, const std::string& path,
                            const PNXdata<float>& data);
 
   /**
-   * @brief Write a string dataset with attributes
+   * @brief Write a string dataset with attributes and return its SDS reference
    * @param sd_id HDF4 SD interface ID
-   * @param path Dataset path
+   * @param path Dataset path (leaf name used for SDS name)
    * @param data PNXdata object containing data, dimensions, and attributes
+   * @return SDS reference number for linking into Vgroups, or -1 for empty strings
    * @throws std::runtime_error if writing fails
    */
-  void WriteStringDataset(int32 sd_id, const std::string& path,
+  int32 WriteStringDataset(int32 sd_id, const std::string& path,
                             const PNXdata<std::string>& data);
 
   /**