ENH: Fix issues reading some 3rd party written .dream3d files

Some data arrays had their component dimensions attribute written incorrectly. Signed-off-by: Michael Jackson <[email protected]> (cherry picked from commit b74f717)
BlueQuartzSoftware · Oct 29, 2024 · 2a174de · 2a174de
1 parent a3821da
commit 2a174de
Show file tree

Hide file tree

Showing 3 changed files with 54 additions and 27 deletions.
diff --git a/cmake/CopyDataFile.cmake.in b/cmake/CopyDataFile.cmake.in
diff --git a/cmake/Utility.cmake b/cmake/Utility.cmake
@@ -145,35 +145,14 @@ function(download_test_data)
   file(APPEND "${FETCH_FILE_PATH}" "${FETCH_FILE_CONTENTS}")
   file(REMOVE "${fetch_data_file}") # Remove the temporary file
 
-  if(ARGS_COPY_DATA)
-    configure_file(${simplnx_SOURCE_DIR}/cmake/CopyDataFile.cmake.in
-                   ${fetch_data_file}
-                   @ONLY
-                   )
-    file(READ "${fetch_data_file}" FETCH_FILE_CONTENTS)
-    file(APPEND "${FETCH_FILE_PATH}" "${FETCH_FILE_CONTENTS}")
-    file(REMOVE "${fetch_data_file}")
-  endif()
-
   #-----
   # If we are installing the data files then we need to create a custom install
   # rule to ensure the archive contents are actually decompressed and available. Since
   # we are possibly making a copy into the binary directory, use that as the source
   # location of the data. Running the unit tests might remove the decompressed data
   # as a by product.
   if(ARGS_INSTALL)
-    # If we did NOT already copy the data, then do that now during the build
-    if(NOT ARGS_COPY_DATA)
-      configure_file(${simplnx_SOURCE_DIR}/cmake/CopyDataFile.cmake.in
-                    ${fetch_data_file}
-                    @ONLY
-                    )
-      file(READ "${fetch_data_file}" FETCH_FILE_CONTENTS)
-      file(APPEND "${FETCH_FILE_PATH}" "${FETCH_FILE_CONTENTS}")
-      file(REMOVE "${fetch_data_file}")
-    endif()
-
-    if(is_multi_config)
+     if(is_multi_config)
       set(CX_CONFIG_DIR "$<CONFIG>")
     else()
       set(CX_CONFIG_DIR ".")

diff --git a/src/simplnx/Utilities/Parsing/DREAM3D/Dream3dIO.cpp b/src/simplnx/Utilities/Parsing/DREAM3D/Dream3dIO.cpp
@@ -835,7 +835,7 @@ Result<> readLegacyDataArrayDims(const nx::core::HDF5::DatasetReader& dataArrayR
       return nx::core::MakeWarningVoidResult(Legacy::k_FailedReadingTupleDims_Code, ss);
     }
     tDims = tupleAttrib.readAsVector<usize>();
-    std::reverse(tDims.begin(), tDims.end()); // SIMPL writes the Tuple Dimensions in reverse order to this attribute
+    // std::reverse(tDims.begin(), tDims.end()); // SIMPL writes the Tuple Dimensions in reverse order to this attribute
   }
 
   return {};
@@ -868,7 +868,17 @@ Result<> readLegacyStringArray(DataStructure& dataStructure, const nx::core::HDF
   return {};
 }
 
-Result<IDataArray*> readLegacyDataArray(DataStructure& dataStructure, const nx::core::HDF5::DatasetReader& dataArrayReader, DataObject::IdType parentId, bool preflight = false)
+/**
+ * @brief
+ * @param dataStructure
+ * @param dataArrayReader
+ * @param parentId
+ * @param amTDims
+ * @param preflight
+ * @return
+ */
+Result<IDataArray*> readLegacyDataArray(DataStructure& dataStructure, const nx::core::HDF5::DatasetReader& dataArrayReader, DataObject::IdType parentId, std::vector<uint64>& amTDims,
+                                        bool preflight = false)
 {
   auto size = H5Dget_storage_size(dataArrayReader.getId());
   auto typeId = dataArrayReader.getTypeId();
@@ -883,6 +893,44 @@ Result<IDataArray*> readLegacyDataArray(DataStructure& dataStructure, const nx::
   }
 
   Result<IDataArray*> daResult;
+  // Let's do some sanity checking of the tuple dims and the comp dims
+  // This is here because some 3rd party apps are trying to write .dream3d
+  // files but are getting confused about the Tuple Dims and the component
+  // dims. This bit of code will try to fix the specific issue where the
+  // .dream3d file essentially had _all_ the dimensions shoved in the
+  // tuple dimensions.
+  if(!amTDims.empty()) // If the amTDims are empty we are just reading a Data Array without an Attribute Matrix so skip.
+  {
+    //
+    if(tDims.size() > amTDims.size() && cDims.size() == 1 && cDims[0] == 1)
+    {
+      daResult.warnings().push_back(
+          {-9543, fmt::format(".dream3d file Tuple and Component Dimensions are not correct. DataSet {} does not have correct component dimensions of they are missing.", dataArrayReader.getName())});
+      cDims.clear();
+      // Find the index of the first non-matching dimension value.
+      for(size_t idx = 0; idx < tDims.size(); idx++)
+      {
+        // If we are past the end of the AM Dimensions, then copy the value to the component dimensions
+        if(idx >= amTDims.size())
+        {
+          cDims.push_back(tDims[idx]);
+        }
+        else if(amTDims[idx] != tDims[idx]) // something went wrong here. Each vector should have the same exact values at the start of the vector
+        {
+          // This should not happen at all. If so, bail out now.
+          cDims.clear(); // just put things back the way they were and fail.
+          cDims.push_back(1ULL);
+          daResult.errors().push_back({-9545, fmt::format(".dream3d file Tuple and Component Dimensions are not correct. DataSet {} does not have correct component dimensions of they are missing. An "
+                                                          "attempt was made to correct this situation but ultimately failed.",
+                                                          dataArrayReader.getName())});
+
+          break; // The first parts of the dimensions should MATCH for this algorithm to work.
+        }
+      }
+      tDims.resize(amTDims.size());
+    }
+  }
+
   if(H5Tequal(typeId, H5T_NATIVE_FLOAT) > 0)
   {
     daResult = createLegacyDataArray<float32>(dataStructure, parentId, dataArrayReader, tDims, cDims, preflight);
@@ -1092,7 +1140,7 @@ Result<> readLegacyAttributeMatrix(DataStructure& dataStructure, const nx::core:
     }
     else
     {
-      Result<> result = ConvertResult(std::move(readLegacyDataArray(dataStructure, dataArraySet, attributeMatrix->getId(), preflight)));
+      Result<> result = ConvertResult(std::move(readLegacyDataArray(dataStructure, dataArraySet, attributeMatrix->getId(), tDims, preflight)));
       daResults.push_back(result);
     }
   }
@@ -1154,7 +1202,8 @@ void readGenericGeomDims(IGeometry* geom, const nx::core::HDF5::GroupReader& geo
 Result<IDataArray*> readLegacyGeomArray(DataStructure& dataStructure, IGeometry* geometry, const nx::core::HDF5::GroupReader& geomGroup, const std::string& arrayName, bool preflight)
 {
   auto dataArraySet = geomGroup.openDataset(arrayName);
-  return readLegacyDataArray(dataStructure, dataArraySet, geometry->getId(), preflight);
+  std::vector<uint64> tDims;
+  return readLegacyDataArray(dataStructure, dataArraySet, geometry->getId(), tDims, preflight);
 }
 
 template <typename T>