ENH: AppendImageGeometry now has option to mirror across the chosen a…

…xis. (#1052)

Signed-off-by: Joey Kleingers <[email protected]>

src/Plugins/OrientationAnalysis/test/AlignSectionsMisorientationTest.cpp

@@ -42,7 +42,7 @@ TEST_CASE("OrientationAnalysis::AlignSectionsMisorientation Small IN100 Pipeline
   const nx::core::UnitTest::TestFileSentinel testDataSentinel(nx::core::unit_test::k_CMakeExecutable, nx::core::unit_test::k_TestFilesDir, "6_6_align_sections_misorientation.tar.gz",
                                                               "6_6_align_sections_misorientation.dream3d");
 
-  const nx::core::UnitTest::TestFileSentinel testDataSentinel1(nx::core::unit_test::k_CMakeExecutable, nx::core::unit_test::k_TestFilesDir, "Small_IN100_dream3d.tar.gz", "Small_IN100.dream3d");
+  const nx::core::UnitTest::TestFileSentinel testDataSentinel1(nx::core::unit_test::k_CMakeExecutable, nx::core::unit_test::k_TestFilesDir, "Small_IN100_dream3d_v2.tar.gz", "Small_IN100.dream3d");
 
   const std::string kDataInputArchive2 = "align_sections.tar.gz";
   const std::string kExpectedOutputTopLevel2 = "align_sections_misorientation.txt";

src/Plugins/OrientationAnalysis/test/BadDataNeighborOrientationCheckTest.cpp

@@ -38,7 +38,7 @@ TEST_CASE("OrientationAnalysis::BadDataNeighborOrientationCheckFilter: Small IN1
   const nx::core::UnitTest::TestFileSentinel testDataSentinel(nx::core::unit_test::k_CMakeExecutable, nx::core::unit_test::k_TestFilesDir, "bad_data_neighbor_orientation_check.tar.gz",
                                                               "bad_data_neighbor_orientation_check.dream3d");
 
-  const nx::core::UnitTest::TestFileSentinel testDataSentinel1(nx::core::unit_test::k_CMakeExecutable, nx::core::unit_test::k_TestFilesDir, "Small_IN100_dream3d.tar.gz", "Small_IN100.dream3d");
+  const nx::core::UnitTest::TestFileSentinel testDataSentinel1(nx::core::unit_test::k_CMakeExecutable, nx::core::unit_test::k_TestFilesDir, "Small_IN100_dream3d_v2.tar.gz", "Small_IN100.dream3d");
 
   Application::GetOrCreateInstance()->loadPlugins(unit_test::k_BuildDir.view(), true);
   auto* filterList = Application::Instance()->getFilterList();

src/Plugins/OrientationAnalysis/test/CMakeLists.txt

@@ -135,7 +135,7 @@ if(EXISTS "${DREAM3D_DATA_DIR}" AND SIMPLNX_DOWNLOAD_TEST_FILES)
   download_test_data(DREAM3D_DATA_DIR ${DREAM3D_DATA_DIR} ARCHIVE_NAME neighbor_orientation_correlation.tar.gz SHA512 122367452174ade2f24dde7a4610bddc4f147a223722d9b30c1df9eaa2cd2bf25e1c7957aba83f3f9de79b4eadd79339b848f9530d1ebf44c69244ea5442cf85)
   download_test_data(DREAM3D_DATA_DIR ${DREAM3D_DATA_DIR} ARCHIVE_NAME PoleFigure_Exemplars_v2.tar.gz SHA512 1c7169e01e66cff074bd58fc188ec69d26df10c4eb61feeb2b123cab945ea44c0419b5d76ab422fc6c585e0a4078bf796f785e7e6ccccc84cc1c518631afb589)
   download_test_data(DREAM3D_DATA_DIR ${DREAM3D_DATA_DIR} ARCHIVE_NAME Small_IN100_Ang_Files.tar.gz SHA512 79e9f6948d4e8e06187e11216a67596fa786ffd2700e51f594ad014090383eb8bcc003e14de2e88082aa9ae512cc4fc9cee22c80066fc54f38c3ebc75267eb5b)
-  download_test_data(DREAM3D_DATA_DIR ${DREAM3D_DATA_DIR} ARCHIVE_NAME Small_IN100_dream3d.tar.gz SHA512 6dd8a3412532bdc7481f7781c7087b4477c6a1efbe6b214f997dad30c53c59714a751be522f084b98065fe75100c74df901bb8af2f512ef47344d8f7941575cf)
+  download_test_data(DREAM3D_DATA_DIR ${DREAM3D_DATA_DIR} ARCHIVE_NAME Small_IN100_dream3d_v2.tar.gz SHA512 d2c6d537e3085f944ef3ce6b79553b65ead81f7f25fc4810af642e1d3dc86c465727e2bfb886b77e6da41e987e502c4263a35164aa8c07453853659d10f3de24)
   download_test_data(DREAM3D_DATA_DIR ${DREAM3D_DATA_DIR} ARCHIVE_NAME Small_IN100_h5ebsd.tar.gz SHA512 31e606285ea9e8235dcb5f608fd2b252a5ab1492abd975e5ec33a21d083aa9720fe16fb8f752742c140f40e963d692f1a46256b9d36e96b1b09796c1e4ea3db9)
   download_test_data(DREAM3D_DATA_DIR ${DREAM3D_DATA_DIR} ARCHIVE_NAME so3_cubic_high_ipf_001.tar.gz SHA512 dfe4598cd4406e8b83f244302dc4fe0d4367527835c5ddd6567fe8d8ab3484d5b10ba24a8bb31db269256ec0b5272daa4340eedb5a8b397755541b32dd616b85)
   download_test_data(DREAM3D_DATA_DIR ${DREAM3D_DATA_DIR} ARCHIVE_NAME write_stats_gen_odf_angle_file.tar.gz SHA512 be3f663aae1f78e5b789200421534ed9fe293187ec3514796ac8177128b34ded18bb9a98b8e838bb283f9818ac30dc4b19ec379bdd581b1a98eb36d967cdd319)

src/Plugins/OrientationAnalysis/test/EBSDSegmentFeaturesFilterTest.cpp

@@ -23,7 +23,7 @@ TEST_CASE("OrientationAnalysis::EBSDSegmentFeatures: Valid Execution", "[Orienta
   const nx::core::UnitTest::TestFileSentinel testDataSentinel(nx::core::unit_test::k_CMakeExecutable, nx::core::unit_test::k_TestFilesDir, "6_6_ebsd_segment_features.tar.gz",
                                                               "6_6_ebsd_segment_features.dream3d");
 
-  const nx::core::UnitTest::TestFileSentinel testDataSentinel1(nx::core::unit_test::k_CMakeExecutable, nx::core::unit_test::k_TestFilesDir, "Small_IN100_dream3d.tar.gz", "Small_IN100.dream3d");
+  const nx::core::UnitTest::TestFileSentinel testDataSentinel1(nx::core::unit_test::k_CMakeExecutable, nx::core::unit_test::k_TestFilesDir, "Small_IN100_dream3d_v2.tar.gz", "Small_IN100.dream3d");
 
   Application::GetOrCreateInstance()->loadPlugins(unit_test::k_BuildDir.view(), true);
   auto* filterList = Application::Instance()->getFilterList();

src/Plugins/OrientationAnalysis/test/NeighborOrientationCorrelationTest.cpp

@@ -40,7 +40,7 @@ TEST_CASE("OrientationAnalysis::NeighborOrientationCorrelationFilter: Small IN10
   const nx::core::UnitTest::TestFileSentinel testDataSentinel(nx::core::unit_test::k_CMakeExecutable, nx::core::unit_test::k_TestFilesDir, "neighbor_orientation_correlation.tar.gz",
                                                               "neighbor_orientation_correlation.dream3d");
 
-  const nx::core::UnitTest::TestFileSentinel testDataSentinel1(nx::core::unit_test::k_CMakeExecutable, nx::core::unit_test::k_TestFilesDir, "Small_IN100_dream3d.tar.gz", "Small_IN100.dream3d");
+  const nx::core::UnitTest::TestFileSentinel testDataSentinel1(nx::core::unit_test::k_CMakeExecutable, nx::core::unit_test::k_TestFilesDir, "Small_IN100_dream3d_v2.tar.gz", "Small_IN100.dream3d");
 
   Application::GetOrCreateInstance()->loadPlugins(unit_test::k_BuildDir.view(), true);
   auto* filterList = Application::Instance()->getFilterList();

src/Plugins/OrientationAnalysis/test/ReadH5EbsdTest.cpp

@@ -18,7 +18,7 @@ const std::string k_MaterialName("MaterialName");
 
 TEST_CASE("OrientationAnalysis::ReadH5Ebsd: Valid filter execution", "[OrientationAnalysis][ReadH5Ebsd]")
 {
-  const nx::core::UnitTest::TestFileSentinel testDataSentinel1(nx::core::unit_test::k_CMakeExecutable, nx::core::unit_test::k_TestFilesDir, "Small_IN100_dream3d.tar.gz", "Small_IN100.dream3d");
+  const nx::core::UnitTest::TestFileSentinel testDataSentinel1(nx::core::unit_test::k_CMakeExecutable, nx::core::unit_test::k_TestFilesDir, "Small_IN100_dream3d_v2.tar.gz", "Small_IN100.dream3d");
 
   const nx::core::UnitTest::TestFileSentinel testDataSentinel(nx::core::unit_test::k_CMakeExecutable, nx::core::unit_test::k_TestFilesDir, "Small_IN100_h5ebsd.tar.gz", "Small_IN100.h5ebsd");
 

src/Plugins/SimplnxCore/docs/AppendImageGeometryFilter.md

@@ -9,17 +9,52 @@ Sampling (Memory/Management)
 This filter allows the user to append one or multiple image geometries to a given image geometry, in any direction (X,Y,Z). The input and
 destination **ImageGeometry** objects must have the same dimensions in the directions that are NOT chosen.  If the X direction is chosen, the geometries must match in Y & Z.  If the Y direction is chosen, the geometries must match in X & Z.  If the Z direction is chosen, the geometries must match in X & Y.  Optional checks for equal **Resolution** values can also be performed.
 
-For the X direction example, if the user has an already existing **Image Geometry** that is 100 voxels in the *Y* direction by 300 pixels in the
-*Z* direction and composed of 10 *X* slices, then if the user appends another three data sets in the X direction that are the same dimensions in Y & Z but contain
-20 *X* slices each, the resulting **Image Geometry** will have a total of 70 *X* slices.
+This filter also has an option to mirror the resulting geometry in the chosen direction.  If the X direction is chosen, it will mirror the positions of the YZ planes.  If the Y direction is chosen, it will mirror the positions of the XZ planes.  If the Z direction is chosen, it will mirror the positions of the XY planes.
 
-For the Y direction example, if the user has an already existing **Image Geometry** that is 400 voxels in the *X* direction by 200 pixels in the
-*Z* direction and composed of 50 *Y* slices, then if the user appends another two data sets in the Y direction that are the same dimensions in X & Z but contain
-40 *Y* slices each, the resulting **Image Geometry** will have a total of 130 *Y* slices.
+### X Direction Examples
 
-For the Z direction example, if the user has an already existing **Image Geometry** that is 100 voxels in the *X* direction by 200 pixels in the
-*Y* direction and composed of 5 *Z* slices, then if the user appends one other data set in the Z direction that is the same dimensions in X & Y but contains
-10 *Z* slices, the resulting **Image Geometry** will have a total of 15 *Z* slices.
+#### Example 1
+If the user has an already existing **Image Geometry** that is 100 voxels in the *Y* direction by 300 pixels in the
+*Z* direction and composed of 10 *X* slices, then if the user appends another three data sets in the X direction that are the same dimensions in Y & Z but contain 20 *X* slices each, the resulting **Image Geometry** will have a total of 70 *X* slices.
+
+#### Example 2 (Visual Example)
+Here's the SmallIN100 dataset example sliced into three pieces in the X direction:
+
+![](Images/AppendImageGeometry/x_direction_pieces.png)
+
+And here is what the geometry looks like after appending the three pieces together in the X direction.  On the left is the regular result, on the right is the mirrored result:
+| ![](Images/AppendImageGeometry/x_complete.png) | ![](Images/AppendImageGeometry/x_mirrored.png) |
+|:----------------------:|:----------------------:|
+
+### Y Direction Examples
+
+#### Example 1
+If the user has an already existing **Image Geometry** that is 400 voxels in the *X* direction by 200 pixels in the
+*Z* direction and composed of 50 *Y* slices, then if the user appends another two data sets in the Y direction that are the same dimensions in X & Z but contain 40 *Y* slices each, the resulting **Image Geometry** will have a total of 130 *Y* slices.
+
+#### Example 2 (Visual Example)
+Here's the SmallIN100 dataset example sliced into three pieces in the Y direction:
+
+![](Images/AppendImageGeometry/y_direction_pieces.png)
+
+And here is what the geometry looks like after appending the three pieces together in the Y direction.  On the left is the regular result, on the right is the mirrored result:
+| ![](Images/AppendImageGeometry/y_complete.png) | ![](Images/AppendImageGeometry/y_mirrored.png) |
+|:----------------------:|:----------------------:|
+
+### Z Direction Examples
+
+#### Example 1
+If the user has an already existing **Image Geometry** that is 100 voxels in the *X* direction by 200 pixels in the
+*Y* direction and composed of 5 *Z* slices, then if the user appends one other data set in the Z direction that is the same dimensions in X & Y but contains 10 *Z* slices, the resulting **Image Geometry** will have a total of 15 *Z* slices.
+
+#### Example 2 (Visual Example)
+Here's the SmallIN100 dataset example sliced into three pieces in the Z direction:
+
+![](Images/AppendImageGeometry/z_direction_pieces.png)
+
+And here is what the geometry looks like after appending the three pieces together in the Z direction.  On the left is the regular result, on the right is the mirrored result:
+| ![](Images/AppendImageGeometry/z_complete.png) | ![](Images/AppendImageGeometry/z_mirrored.png) |
+|:----------------------:|:----------------------:|
 
 % Auto generated parameter table will be inserted here
 

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

@@ -115,14 +115,20 @@ Result<> AppendImageGeometry::operator()()
     if(m_InputValues->SaveAsNewGeometry)
     {
       m_MessageHandler(fmt::format("Combining data into array {}", newCellDataPath.createChildPath(name).toString()));
-      CopyFromArray::RunParallelCombine(*newDataArray, taskRunner, inputDataArrays, inputTupleShapes, m_InputValues->Direction);
+      auto newGeometry = m_DataStructure.getDataRefAs<ImageGeom>(m_InputValues->NewGeometryPath);
+      auto newDestGeomDimsVec = newGeometry.getDimensions().toContainer<std::vector<usize>>();
+      std::reverse(newDestGeomDimsVec.begin(), newDestGeomDimsVec.end());
+      CopyFromArray::RunParallelCombine(*newDataArray, taskRunner, inputDataArrays, inputTupleShapes, newDestGeomDimsVec, m_InputValues->Direction, m_InputValues->MirrorGeometry);
     }
     else
     {
       m_MessageHandler(fmt::format("Appending data into array {}", newCellDataPath.createChildPath(name).toString()));
-      auto destGeomDimsVec = destGeomDims.toContainer<std::vector<usize>>();
-      std::reverse(destGeomDimsVec.begin(), destGeomDimsVec.end());
-      CopyFromArray::RunParallelAppend(*destDataArray, taskRunner, inputDataArrays, inputTupleShapes, destGeomDimsVec, m_InputValues->Direction);
+      auto originalDestGeomDimsVec = destGeomDims.toContainer<std::vector<usize>>();
+      std::reverse(originalDestGeomDimsVec.begin(), originalDestGeomDimsVec.end());
+      auto newDestGeomDimsVec = destGeometry.getDimensions().toContainer<std::vector<usize>>();
+      std::reverse(newDestGeomDimsVec.begin(), newDestGeomDimsVec.end());
+      CopyFromArray::RunParallelAppend(*destDataArray, taskRunner, inputDataArrays, inputTupleShapes, originalDestGeomDimsVec, newDestGeomDimsVec, m_InputValues->Direction,
+                                       m_InputValues->MirrorGeometry);
     }
   }
   taskRunner.wait(); // This will spill over if the number of DataArrays to process does not divide evenly by the number of threads.

src/Plugins/SimplnxCore/src/SimplnxCore/Filters/Algorithms/AppendImageGeometry.hpp

@@ -17,6 +17,7 @@ struct SIMPLNXCORE_EXPORT AppendImageGeometryInputValues
   DataPath DestinationGeometryPath;
   DataPath NewGeometryPath;
   bool CheckResolution;
+  bool MirrorGeometry;
   bool SaveAsNewGeometry;
   CopyFromArray::Direction Direction;
 };

src/Plugins/SimplnxCore/src/SimplnxCore/Filters/AppendImageGeometryFilter.cpp

@@ -62,13 +62,15 @@ Parameters AppendImageGeometryFilter::parameters() const
   params.insert(std::make_unique<GeometrySelectionParameter>(k_DestinationGeometry_Key, "Destination Image Geometry",
                                                              "The destination image geometry (cell data) that is the final location for the appended data.", DataPath{},
                                                              GeometrySelectionParameter::AllowedTypes{IGeometry::Type::Image}));
-  params.insert(std::make_unique<ChoicesParameter>(k_AppendDimension_Key, "Append Dimension", "The dimension that will be used to append the geometries.", to_underlying(CopyFromArray::Direction::Z),
+  params.insert(std::make_unique<ChoicesParameter>(k_Direction_Key, "Direction", "The direction that will be used to append the geometries.", to_underlying(CopyFromArray::Direction::Z),
                                                    std::vector<std::string>{"X", "Y", "Z"}));
+  params.insert(std::make_unique<BoolParameter>(k_MirrorGeometry_Key, "Mirror Geometry In Direction", "Mirrors the resulting geometry in the chosen direction.", false));
   params.insert(std::make_unique<BoolParameter>(k_CheckResolution_Key, "Check Spacing", "Checks to make sure the spacing for the input geometry and destination geometry match", false));
   params.insertLinkableParameter(std::make_unique<BoolParameter>(k_SaveAsNewGeometry_Key, "Save as new geometry",
                                                                  "Save the combined data as a new geometry instead of appending the input data to the destination geometry", false));
   params.insert(std::make_unique<DataGroupCreationParameter>(k_NewGeometry_Key, "New Image Geometry", "The path to the new geometry with the combined data from the input & destination geometry",
                                                              DataPath({"AppendedImageGeom"})));
+
   params.linkParameters(k_SaveAsNewGeometry_Key, k_NewGeometry_Key, true);
 
   return params;
@@ -86,7 +88,7 @@ IFilter::PreflightResult AppendImageGeometryFilter::preflightImpl(const DataStru
 {
   auto pInputGeometriesPathsValue = filterArgs.value<std::vector<DataPath>>(k_InputGeometries_Key);
   auto pDestinationGeometryPathValue = filterArgs.value<DataPath>(k_DestinationGeometry_Key);
-  auto pAppendDimension = static_cast<CopyFromArray::Direction>(filterArgs.value<ChoicesParameter::ValueType>(k_AppendDimension_Key));
+  auto pDirection = static_cast<CopyFromArray::Direction>(filterArgs.value<ChoicesParameter::ValueType>(k_Direction_Key));
   auto pCheckResolutionValue = filterArgs.value<bool>(k_CheckResolution_Key);
   auto pSaveAsNewGeometry = filterArgs.value<bool>(k_SaveAsNewGeometry_Key);
 
@@ -100,15 +102,15 @@ IFilter::PreflightResult AppendImageGeometryFilter::preflightImpl(const DataStru
   {
     const auto& inputGeometry = dataStructure.getDataRefAs<ImageGeom>(pInputGeometryPathValue);
     SizeVec3 inputGeomDims = inputGeometry.getDimensions();
-    if((pAppendDimension == CopyFromArray::Direction::Y || pAppendDimension == CopyFromArray::Direction::Z) && destGeomDims[0] != inputGeomDims[0])
+    if((pDirection == CopyFromArray::Direction::Y || pDirection == CopyFromArray::Direction::Z) && destGeomDims[0] != inputGeomDims[0])
     {
       return MakePreflightErrorResult(-8200, fmt::format("Input X Dim ({}) not equal to Destination X Dim ({})", inputGeomDims[0], destGeomDims[0]));
     }
-    if((pAppendDimension == CopyFromArray::Direction::X || pAppendDimension == CopyFromArray::Direction::Z) && destGeomDims[1] != inputGeomDims[1])
+    if((pDirection == CopyFromArray::Direction::X || pDirection == CopyFromArray::Direction::Z) && destGeomDims[1] != inputGeomDims[1])
     {
       return MakePreflightErrorResult(-8201, fmt::format("Input Y Dim ({}) not equal to Destination Y Dim ({})", inputGeomDims[1], destGeomDims[1]));
     }
-    if((pAppendDimension == CopyFromArray::Direction::X || pAppendDimension == CopyFromArray::Direction::Y) && destGeomDims[2] != inputGeomDims[2])
+    if((pDirection == CopyFromArray::Direction::X || pDirection == CopyFromArray::Direction::Y) && destGeomDims[2] != inputGeomDims[2])
     {
       return MakePreflightErrorResult(-8201, fmt::format("Input Z Dim ({}) not equal to Destination Z Dim ({})", inputGeomDims[2], destGeomDims[2]));
     }
@@ -138,7 +140,7 @@ IFilter::PreflightResult AppendImageGeometryFilter::preflightImpl(const DataStru
       return MakePreflightErrorResult(-8310, fmt::format("Input units ({}) not equal to Destination units ({})", IGeometry::LengthUnitToString(inputUnits), IGeometry::LengthUnitToString(destUnits)));
     }
 
-    switch(pAppendDimension)
+    switch(pDirection)
     {
     case CopyFromArray::Direction::X:
       newDims[0] += inputGeomDims[0];
@@ -307,8 +309,9 @@ Result<> AppendImageGeometryFilter::executeImpl(DataStructure& dataStructure, co
 
   inputValues.InputGeometriesPaths = filterArgs.value<std::vector<DataPath>>(k_InputGeometries_Key);
   inputValues.DestinationGeometryPath = filterArgs.value<DataPath>(k_DestinationGeometry_Key);
-  inputValues.Direction = static_cast<CopyFromArray::Direction>(filterArgs.value<ChoicesParameter::ValueType>(k_AppendDimension_Key));
+  inputValues.Direction = static_cast<CopyFromArray::Direction>(filterArgs.value<ChoicesParameter::ValueType>(k_Direction_Key));
   inputValues.CheckResolution = filterArgs.value<bool>(k_CheckResolution_Key);
+  inputValues.MirrorGeometry = filterArgs.value<bool>(k_MirrorGeometry_Key);
   inputValues.SaveAsNewGeometry = filterArgs.value<bool>(k_SaveAsNewGeometry_Key);
   inputValues.NewGeometryPath = filterArgs.value<DataPath>(k_NewGeometry_Key);
 

src/Plugins/SimplnxCore/src/SimplnxCore/Filters/AppendImageGeometryFilter.hpp

@@ -26,7 +26,8 @@ class SIMPLNXCORE_EXPORT AppendImageGeometryFilter : public IFilter
   // Parameter Keys
   static inline constexpr StringLiteral k_InputGeometries_Key = "input_image_geometries_paths";
   static inline constexpr StringLiteral k_DestinationGeometry_Key = "destination_image_geometry_path";
-  static inline constexpr StringLiteral k_AppendDimension_Key = "append_dimension_index";
+  static inline constexpr StringLiteral k_Direction_Key = "direction_index";
+  static inline constexpr StringLiteral k_MirrorGeometry_Key = "mirror_geometry";
   static inline constexpr StringLiteral k_CheckResolution_Key = "check_resolution";
   static inline constexpr StringLiteral k_SaveAsNewGeometry_Key = "save_as_new_geometry";
   static inline constexpr StringLiteral k_NewGeometry_Key = "output_image_geometry_path";