ENH: Fix multiple compiler warnings and other small issues

CMakeLists.txt

@@ -148,6 +148,7 @@ cmake_policy(SET CMP0054 NEW)
 if(CMAKE_VERSION VERSION_GREATER \"3.28.0\")
   cmake_policy(SET CMP0152 NEW)
 endif()
+set(CONFIG \${CMAKE_CONFIG})
 ")
 
 set(TEST_WORKING_DIR "${CMAKE_LIBRARY_OUTPUT_DIRECTORY}")

cmake/FetchDataFile.cmake.in

@@ -3,6 +3,7 @@
 # STARTING @ARGS_ARCHIVE_NAME@
 # Download, Decompress, and possibly copy data archive
 # message(STATUS "[DATA DOWNLOAD] @ARGS_ARCHIVE_NAME@")
+# message(STATUS "CMAKE_CONFIG: ${CMAKE_CONFIG}")
 # --------------------------------------------------------------------------------------------------
 string(TIMESTAMP time_stamp_start %s)
 file(DOWNLOAD @DATA_ARCHIVE_WEB_SITE@@ARGS_ARCHIVE_NAME@
@@ -29,7 +30,10 @@ endif()
 
 # --------------------------------------------------------------------------------------------------
 # Oddly, if the status comes back as "No Error", that actually means that something got downloaded
-# If the file was downloaded then we should also decompress it.
+# Assuming the last command was successfull, if the developer wanted the data copied to the
+# build folder.
+# ARGS_COPY_DATA=@ARGS_COPY_DATA@
+# DATA_DEST_DIR=@DATA_DEST_DIR@
 # --------------------------------------------------------------------------------------------------
 if(@ARGS_COPY_DATA@)
   get_filename_component(archive_base_name "@ARGS_ARCHIVE_NAME@" NAME)
@@ -40,5 +44,7 @@ if(@ARGS_COPY_DATA@)
     OUTPUT_VARIABLE output
     ERROR_VARIABLE error
   )
-  execute_process(COMMAND ${CMAKE_COMMAND} -E copy_directory_if_different "@ARGS_DREAM3D_DATA_DIR@/TestFiles/@ARCHIVE_BASE_NAME@" "@DATA_DEST_DIR@/@ARCHIVE_BASE_NAME@")
+  execute_process(COMMAND ${CMAKE_COMMAND} -E copy_directory_if_different 
+                    "@ARGS_DREAM3D_DATA_DIR@/TestFiles/@ARCHIVE_BASE_NAME@" 
+                    "@DATA_DEST_DIR@/@ARCHIVE_BASE_NAME@")
 endif()

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 ".")

src/Plugins/SimplnxCore/CMakeLists.txt

@@ -466,35 +466,35 @@ if(EXISTS "${DREAM3D_DATA_DIR}" AND SIMPLNX_DOWNLOAD_TEST_FILES)
     INSTALL
     COPY_DATA
   )
-  add_custom_target(Copy_${PLUGIN_NAME}_ASCIIData ALL
-    COMMAND ${CMAKE_COMMAND} -E tar xzf "${DREAM3D_DATA_DIR}/TestFiles/ASCIIData.tar.gz"
-    COMMAND ${CMAKE_COMMAND} -E copy_directory_if_different "${DREAM3D_DATA_DIR}/TestFiles/ASCIIData" "${CMAKE_LIBRARY_OUTPUT_DIRECTORY}/${CX_CONFIG_DIR}/Data/ASCIIData"
-    COMMAND ${CMAKE_COMMAND} -E rm -rf "${DREAM3D_DATA_DIR}/TestFiles/ASCIIData"
-    WORKING_DIRECTORY "${DREAM3D_DATA_DIR}/TestFiles"
-    COMMENT "Copying ${PLUGIN_NAME}/ASCIIData data into Binary Directory"
-    DEPENDS Fetch_Remote_Data_Files  # Make sure all remote files are downloaded before trying this
-    COMMAND_EXPAND_LISTS
-    VERBATIM
-  )
-  set_target_properties(Copy_${PLUGIN_NAME}_ASCIIData PROPERTIES FOLDER Plugins/${PLUGIN_NAME})
+  # add_custom_target(Copy_${PLUGIN_NAME}_ASCIIData ALL
+  #   COMMAND ${CMAKE_COMMAND} -E tar xzf "${DREAM3D_DATA_DIR}/TestFiles/ASCIIData.tar.gz"
+  #   COMMAND ${CMAKE_COMMAND} -E copy_directory_if_different "${DREAM3D_DATA_DIR}/TestFiles/ASCIIData" "${CMAKE_LIBRARY_OUTPUT_DIRECTORY}/${CX_CONFIG_DIR}/Data/ASCIIData"
+  #   COMMAND ${CMAKE_COMMAND} -E rm -rf "${DREAM3D_DATA_DIR}/TestFiles/ASCIIData"
+  #   WORKING_DIRECTORY "${DREAM3D_DATA_DIR}/TestFiles"
+  #   COMMENT "Copying ${PLUGIN_NAME}/ASCIIData data into Binary Directory"
+  #   DEPENDS Fetch_Remote_Data_Files  # Make sure all remote files are downloaded before trying this
+  #   COMMAND_EXPAND_LISTS
+  #   VERBATIM
+  # )
+  # set_target_properties(Copy_${PLUGIN_NAME}_ASCIIData PROPERTIES FOLDER Plugins/${PLUGIN_NAME})
 
   download_test_data(DREAM3D_DATA_DIR ${DREAM3D_DATA_DIR}
     ARCHIVE_NAME STL_Models.tar.gz
     SHA512 6a17caa1c5b60740a18d30732b10139b5864e12abd5009ce482972f4070f86e1762a3bf2bbceb8f178187b4d70bedbde1516f32397c3d4424404557b320dde9d
     INSTALL
     COPY_DATA
   )
-  add_custom_target(Copy_${PLUGIN_NAME}_STL_Models ALL
-    COMMAND ${CMAKE_COMMAND} -E tar xzf "${DREAM3D_DATA_DIR}/TestFiles/STL_Models.tar.gz"
-    COMMAND ${CMAKE_COMMAND} -E copy_directory_if_different "${DREAM3D_DATA_DIR}/TestFiles/STL_Models" "${CMAKE_LIBRARY_OUTPUT_DIRECTORY}/${CX_CONFIG_DIR}/Data/STL_Models"
-    COMMAND ${CMAKE_COMMAND} -E rm -rf "${DREAM3D_DATA_DIR}/TestFiles/STL_Models"
-    WORKING_DIRECTORY "${DREAM3D_DATA_DIR}/TestFiles"
-    COMMENT "Copying ${PLUGIN_NAME}/STL_Models data into Binary Directory"
-    DEPENDS Fetch_Remote_Data_Files  # Make sure all remote files are downloaded before trying this
-    COMMAND_EXPAND_LISTS
-    VERBATIM
-  )
-  set_target_properties(Copy_${PLUGIN_NAME}_STL_Models PROPERTIES FOLDER Plugins/${PLUGIN_NAME})
+  # add_custom_target(Copy_${PLUGIN_NAME}_STL_Models ALL
+  #   COMMAND ${CMAKE_COMMAND} -E tar xzf "${DREAM3D_DATA_DIR}/TestFiles/STL_Models.tar.gz"
+  #   COMMAND ${CMAKE_COMMAND} -E copy_directory_if_different "${DREAM3D_DATA_DIR}/TestFiles/STL_Models" "${CMAKE_LIBRARY_OUTPUT_DIRECTORY}/${CX_CONFIG_DIR}/Data/STL_Models"
+  #   COMMAND ${CMAKE_COMMAND} -E rm -rf "${DREAM3D_DATA_DIR}/TestFiles/STL_Models"
+  #   WORKING_DIRECTORY "${DREAM3D_DATA_DIR}/TestFiles"
+  #   COMMENT "Copying ${PLUGIN_NAME}/STL_Models data into Binary Directory"
+  #   DEPENDS Fetch_Remote_Data_Files  # Make sure all remote files are downloaded before trying this
+  #   COMMAND_EXPAND_LISTS
+  #   VERBATIM
+  # )
+  # set_target_properties(Copy_${PLUGIN_NAME}_STL_Models PROPERTIES FOLDER Plugins/${PLUGIN_NAME})
 
 endif()
 

src/Plugins/SimplnxCore/src/SimplnxCore/Filters/Algorithms/CreateAMScanPaths.cpp

@@ -347,7 +347,7 @@ Result<> CreateAMScanPaths::operator()()
               char good = determineIntersectCoord(p1, p2, vert1, vert2, coord);
               if(good == 'i')
               {
-                intersectionCoords.insert(std::pair<float, usize>(coord, 0));
+                intersectionCoords.insert(std::pair<float, usize>(coord, 0ULL));
               }
               else if(good == 'c' || good == 'd')
               {

src/Plugins/SimplnxCore/src/SimplnxCore/Filters/CreateDataArrayAdvancedFilter.cpp

@@ -192,7 +192,7 @@ IFilter::PreflightResult CreateDataArrayAdvancedFilter::preflightImpl(const Data
   usize numComponents = std::accumulate(compDims.begin(), compDims.end(), static_cast<usize>(1), std::multiplies<>());
   if(numComponents <= 0)
   {
-    std::string compDimsStr = std::accumulate(compDims.begin() + 1, compDims.end(), std::to_string(compDims[0]), [](const std::string& a, int b) { return a + " x " + std::to_string(b); });
+    std::string compDimsStr = std::accumulate(compDims.begin() + 1ULL, compDims.end(), std::to_string(compDims[0]), [](const std::string& a, int b) { return a + " x " + std::to_string(b); });
     return MakePreflightErrorResult(
         -78601,
         fmt::format("The chosen component dimensions ({}) results in 0 total components.  Please choose component dimensions that result in a positive number of total components.", compDimsStr));

src/Plugins/SimplnxCore/src/SimplnxCore/Filters/DBSCANFilter.cpp

@@ -76,7 +76,7 @@ Parameters DBSCANFilter::parameters() const
 
   params.insertSeparator(Parameters::Separator{"Input Parameter(s)"});
   params.insert(std::make_unique<BoolParameter>(k_UsePrecaching_Key, "Use Precaching", "If true the algorithm will be significantly faster, but it requires more memory", true));
-  params.insert(std::make_unique<Float32Parameter>(k_Epsilon_Key, "Epsilon", "The epsilon-neighborhood around each point is queried", 0.0001));
+  params.insert(std::make_unique<Float32Parameter>(k_Epsilon_Key, "Epsilon", "The epsilon-neighborhood around each point is queried", 0.0001f));
   params.insert(std::make_unique<Int32Parameter>(k_MinPoints_Key, "Minimum Points",
                                                  "The minimum number of points needed to form a 'dense region' (i.e., the minimum number of points needed to be called a cluster)", 2));
   params.insert(

src/Plugins/SimplnxCore/src/SimplnxCore/Filters/SliceTriangleGeometryFilter.cpp

@@ -64,7 +64,7 @@ Parameters SliceTriangleGeometryFilter::parameters() const
   params.insertLinkableParameter(std::make_unique<ChoicesParameter>(k_SliceRange_Key, "Slice Range", "Type of slice range to use, either Full Range or User Defined Range", 0,
                                                                     ChoicesParameter::Choices{"Full Range", "User Defined Range"}));
   params.insert(std::make_unique<Float32Parameter>(k_Zstart_Key, "Slicing Start", "The z axis start value", 0.0f));
-  params.insert(std::make_unique<Float32Parameter>(k_Zend_Key, "Slicing End", "The z axis stop value", 0.0));
+  params.insert(std::make_unique<Float32Parameter>(k_Zend_Key, "Slicing End", "The z axis stop value", 0.0f));
   params.insert(std::make_unique<Float32Parameter>(k_SliceResolution_Key, "Slice Spacing", "The spacing between slices", 1.0f));
 
   params.insertSeparator(Parameters::Separator{"Input Geometry"});

src/Plugins/SimplnxCore/test/DBSCANTest.cpp

@@ -46,7 +46,7 @@ TEST_CASE("SimplnxCore::DBSCAN: Valid Filter Execution (Precached, Iterative)",
     // Create default Parameters for the filter.
     args.insertOrAssign(DBSCANFilter::k_InitTypeIndex_Key, std::make_any<ChoicesParameter::ValueType>(to_underlying(AlgType::Iterative)));
     args.insertOrAssign(DBSCANFilter::k_UsePrecaching_Key, std::make_any<bool>(true));
-    args.insertOrAssign(DBSCANFilter::k_Epsilon_Key, std::make_any<float32>(0.01));
+    args.insertOrAssign(DBSCANFilter::k_Epsilon_Key, std::make_any<float32>(0.01f));
     args.insertOrAssign(DBSCANFilter::k_MinPoints_Key, std::make_any<int32>(50));
     args.insertOrAssign(DBSCANFilter::k_UseMask_Key, std::make_any<bool>(false));
     args.insertOrAssign(DBSCANFilter::k_SelectedArrayPath_Key, std::make_any<DataPath>(k_TargetArrayPath));

src/simplnx/DataStructure/IO/HDF5/DataStructureWriter.hpp

@@ -25,7 +25,7 @@ class IDataIO;
  */
 class SIMPLNX_EXPORT DataStructureWriter
 {
-  friend class DataObject;
+  friend class nx::core::DataObject;
   friend SIMPLNX_EXPORT Result<> WriteObjectAttributes(DataStructureWriter&, ObjectWriter&, const DataObject*, bool);
   friend class HDF5::IDataIO;
 

src/simplnx/Utilities/ClusteringUtilities.hpp

@@ -7,7 +7,7 @@
 
 namespace nx::core::ClusterUtilities
 {
-enum SIMPLNX_EXPORT DistanceMetric
+enum DistanceMetric
 {
   Euclidean,
   SquaredEuclidean,

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 {};
@@ -868,10 +868,19 @@ 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();
 
   std::vector<usize> tDims;
   std::vector<usize> cDims;
@@ -883,6 +892,46 @@ 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
+        {
+          // The first parts of the dimensions should MATCH for this algorithm to work.
+          // 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 or they are missing. An "
+                                                          "attempt was made to correct this situation but ultimately failed.",
+                                                          dataArrayReader.getName())});
+          return daResult;
+        }
+      }
+      tDims.resize(amTDims.size());
+    }
+  }
+
+  auto typeId = dataArrayReader.getTypeId();
+
   if(H5Tequal(typeId, H5T_NATIVE_FLOAT) > 0)
   {
     daResult = createLegacyDataArray<float32>(dataStructure, parentId, dataArrayReader, tDims, cDims, preflight);
@@ -1092,7 +1141,7 @@ 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 +1203,8 @@ 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>

test/CMakeLists.txt

@@ -96,4 +96,5 @@ add_custom_target(Copy_simplnx_Test_Data ALL
     COMMENT "Copying ${simplnx_SOURCE_DIR}/test/Data data into Binary Directory"
     COMMAND_EXPAND_LISTS
     VERBATIM
-  )
+  )
+set_target_properties(Copy_simplnx_Test_Data PROPERTIES FOLDER ZZ_COPY_FILES)

wrapping/python/docs/CMakeLists.txt

@@ -40,6 +40,7 @@ target_sources(generate_sphinx_docs
   PRIVATE
     "${CMAKE_CURRENT_BINARY_DIR}/plugin_source_dirs.hpp"
 )
+set_target_properties(generate_sphinx_docs PROPERTIES FOLDER simplnx_Python__Documentation)
 
 set(SIMPLNX_SPHINX_DOCS_DIR "${simplnx_BINARY_DIR}/wrapping/python/docs")
 
@@ -53,6 +54,7 @@ add_custom_target(sphinx_copy_sources ALL
   COMMAND ${CMAKE_COMMAND} -E copy_directory "${CMAKE_CURRENT_SOURCE_DIR}/source" "${SIMPLNX_SPHINX_DOCS_DIR}/source"
   COMMENT "SIMPLNX Python Docs: Copying static doc files to build directory at ${SIMPLNX_SPHINX_DOCS_DIR}"
 )
+set_target_properties(sphinx_copy_sources PROPERTIES FOLDER simplnx_Python__Documentation)
 
 #------------------------------------------------------------------------------
 # Execute the sphinx rst plugin generation tool
@@ -62,6 +64,7 @@ add_custom_target(sphinx_generate_plugin_rst ALL
   COMMAND "$<TARGET_FILE:generate_sphinx_docs>"
   COMMENT "SIMPLNX Python Docs: Generated Plugin .rst docs file"
 )
+set_target_properties(sphinx_generate_plugin_rst PROPERTIES FOLDER simplnx_Python__Documentation)
 
 #------------------------------------------------------------------------------
 # Find the `sphinx-build` executable
@@ -103,3 +106,4 @@ else()
     WORKING_DIRECTORY "${SIMPLNX_SPHINX_DOCS_DIR}"
   )
 endif()
+set_target_properties(sphinx_docs_generation PROPERTIES FOLDER simplnx_Python__Documentation)