BUG: Fixes incorrect number of found features in the feature Attribute Matrix

Author: imikejackson

src/Plugins/OrientationAnalysis/src/OrientationAnalysis/Filters/EBSDSegmentFeaturesFilter.cpp

@@ -64,7 +64,7 @@ Parameters EBSDSegmentFeaturesFilter::parameters() const
   params.insertSeparator(Parameters::Separator{"Input Parameter(s)"});
   params.insert(std::make_unique<Float32Parameter>(k_MisorientationTolerance_Key, "Misorientation Tolerance (Degrees)",
                                                    "Tolerance (in degrees) used to determine if neighboring Cells belong to the same Feature", 5.0f));
-  params.insert(std::make_unique<BoolParameter>(k_RandomizeFeatureIds_Key, "Randomize Feature IDs", "Specifies if feature IDs should be randomized during calculations", false));
+  params.insert(std::make_unique<BoolParameter>(k_RandomizeFeatureIds_Key, "Randomize Feature Ids", "Specifies if feature IDs should be randomized during calculations", false));
   params.insert(std::make_unique<ChoicesParameter>(k_NeighborScheme_Key, "Neighbor Scheme", "How many neighbors to use", segment_features::k_6NeighborIndex, segment_features::k_OperationChoices));
 
   params.insertSeparator(Parameters::Separator{"Optional Data Mask"});

src/Plugins/OrientationAnalysis/test/CAxisSegmentFeaturesTest.cpp

@@ -1,9 +1,14 @@
 #include <catch2/catch.hpp>
 
-#include "simplnx/UnitTest/UnitTestCommon.hpp"
-
 #include "OrientationAnalysis/Filters/CAxisSegmentFeaturesFilter.hpp"
 #include "OrientationAnalysis/OrientationAnalysis_test_dirs.hpp"
+#include "OrientationAnalysisTestUtils.hpp"
+
+#include "simplnx/Core/Application.hpp"
+#include "simplnx/Parameters/ArrayCreationParameter.hpp"
+#include "simplnx/Parameters/Dream3dImportParameter.hpp"
+#include "simplnx/Parameters/GeometrySelectionParameter.hpp"
+#include "simplnx/UnitTest/UnitTestCommon.hpp"
 
 #include <filesystem>
 
@@ -13,98 +18,120 @@ using namespace nx::core::Constants;
 
 namespace
 {
-const std::string k_ComputedFeatureIds = "NX_FeatureIds";
-const std::string k_ComputedCellFeatureData = "NX_CellFeatureData";
-} // namespace
+}
 
-TEST_CASE("OrientationAnalysis::CAxisSegmentFeaturesFilter: Valid Filter Execution", "[OrientationAnalysis][CAxisSegmentFeaturesFilter]")
+TEST_CASE("OrientationAnalysis::CAxisSegmentFeatures:No_Mask", "[OrientationAnalysis][CAxisSegmentFeatures]")
 {
   UnitTest::LoadPlugins();
-  const nx::core::UnitTest::TestFileSentinel testDataSentinel(nx::core::unit_test::k_CMakeExecutable, nx::core::unit_test::k_TestFilesDir, "caxis_data.tar.gz", "caxis_data");
 
+  const nx::core::UnitTest::TestFileSentinel testDataSentinel(nx::core::unit_test::k_CMakeExecutable, nx::core::unit_test::k_TestFilesDir, "segment_features_test_data.tar.gz",
+                                                              "segment_features_test_data");
   // Read Exemplar DREAM3D File Filter
-  auto exemplarFilePath = fs::path(fmt::format("{}/caxis_data/6_6_caxis_segment_features.dream3d", unit_test::k_TestFilesDir));
+  auto exemplarFilePath = fs::path(fmt::format("{}/segment_features_test_data/segment_features_test_data.dream3d", unit_test::k_TestFilesDir));
   DataStructure dataStructure = UnitTest::LoadDataStructure(exemplarFilePath);
 
-  // CAxis Segment Features Filter
+  // EBSD Segment Features/Semgent Features (Misorientation) Filter
   {
-    // Instantiate the filter, a DataStructure object and an Arguments Object
     CAxisSegmentFeaturesFilter filter;
     Arguments args;
 
     // Create default Parameters for the filter.
+    args.insertOrAssign(CAxisSegmentFeaturesFilter::k_MisorientationTolerance_Key, std::make_any<float32>(5.0F));
+
+    args.insertOrAssign(CAxisSegmentFeaturesFilter::k_UseMask_Key, std::make_any<bool>(false));
+    args.insertOrAssign(CAxisSegmentFeaturesFilter::k_MaskArrayPath_Key, std::make_any<DataPath>(k_MaskArrayPath));
+
     args.insertOrAssign(CAxisSegmentFeaturesFilter::k_SelectedImageGeometryPath_Key, std::make_any<DataPath>(k_DataContainerPath));
-    args.insertOrAssign(CAxisSegmentFeaturesFilter::k_MisorientationTolerance_Key, std::make_any<float32>(5.0f));
-    args.insertOrAssign(CAxisSegmentFeaturesFilter::k_UseMask_Key, std::make_any<bool>(true));
-    args.insertOrAssign(CAxisSegmentFeaturesFilter::k_RandomizeFeatureIds_Key, std::make_any<bool>(false));
     args.insertOrAssign(CAxisSegmentFeaturesFilter::k_QuatsArrayPath_Key, std::make_any<DataPath>(k_QuatsArrayPath));
     args.insertOrAssign(CAxisSegmentFeaturesFilter::k_CellPhasesArrayPath_Key, std::make_any<DataPath>(k_PhasesArrayPath));
-    args.insertOrAssign(CAxisSegmentFeaturesFilter::k_MaskArrayPath_Key, std::make_any<DataPath>(k_MaskArrayPath));
     args.insertOrAssign(CAxisSegmentFeaturesFilter::k_CrystalStructuresArrayPath_Key, std::make_any<DataPath>(k_CrystalStructuresArrayPath));
-    args.insertOrAssign(CAxisSegmentFeaturesFilter::k_FeatureIdsArrayName_Key, std::make_any<std::string>(k_ComputedFeatureIds));
-    args.insertOrAssign(CAxisSegmentFeaturesFilter::k_CellFeatureAttributeMatrixName_Key, std::make_any<std::string>(k_ComputedCellFeatureData));
+
+    args.insertOrAssign(CAxisSegmentFeaturesFilter::k_FeatureIdsArrayName_Key, std::make_any<std::string>(k_FeatureIds));
+    args.insertOrAssign(CAxisSegmentFeaturesFilter::k_CellFeatureAttributeMatrixName_Key, std::make_any<std::string>(k_Grain_Data));
     args.insertOrAssign(CAxisSegmentFeaturesFilter::k_ActiveArrayName_Key, std::make_any<std::string>(k_ActiveName));
+    args.insertOrAssign(CAxisSegmentFeaturesFilter::k_RandomizeFeatureIds_Key, std::make_any<bool>(false));
 
     // Preflight the filter and check result
     auto preflightResult = filter.preflight(dataStructure, args);
-    SIMPLNX_RESULT_REQUIRE_VALID(preflightResult.outputActions)
+    SIMPLNX_RESULT_REQUIRE_VALID(preflightResult.outputActions);
 
     // Execute the filter and check the result
     auto executeResult = filter.execute(dataStructure, args);
-    SIMPLNX_RESULT_REQUIRE_VALID(executeResult.result)
+    SIMPLNX_RESULT_REQUIRE_VALID(executeResult.result);
   }
+
   {
-    DataPath activeArrayDataPath = k_DataContainerPath.createChildPath(k_ComputedCellFeatureData).createChildPath(k_ActiveName);
+    DataPath activeArrayDataPath = k_DataContainerPath.createChildPath(k_Grain_Data).createChildPath(k_ActiveName);
     UInt8Array& actives = dataStructure.getDataRefAs<UInt8Array>(activeArrayDataPath);
     size_t numFeatures = actives.getNumberOfTuples();
-    REQUIRE(numFeatures == 31229);
+    REQUIRE(numFeatures == 51);
   }
-
   // Loop and compare each array from the 'Exemplar Data / CellData' to the 'Data Container / CellData' group
   {
-    const auto& generatedFeatureIds = dataStructure.getDataRefAs<Int32Array>(k_CellAttributeMatrix.createChildPath(k_ComputedFeatureIds));
-    const auto& exemplarFeatureIds = dataStructure.getDataRefAs<Int32Array>(k_FeatureIdsArrayPath);
-    UnitTest::CompareDataArrays<int32>(generatedFeatureIds, exemplarFeatureIds);
+    const auto& generatedDataArray = dataStructure.getDataRefAs<Int32Array>(k_FeatureIdsArrayPath);
+    const auto& exemplarDataArray = dataStructure.getDataRefAs<Int32Array>(k_CellAttributeMatrix.createChildPath("CAxis_FeatureIds"));
+
+    UnitTest::CompareDataArrays<int32>(generatedDataArray, exemplarDataArray);
   }
 
-  UnitTest::CheckArraysInheritTupleDims(dataStructure);
+  UnitTest::CheckArraysInheritTupleDims(dataStructure, SmallIn100::k_TupleCheckIgnoredPaths);
 }
 
-TEST_CASE("OrientationAnalysis::CAxisSegmentFeaturesFilter: Invalid Filter Execution", "[OrientationAnalysis][CAxisSegmentFeaturesFilter]")
+TEST_CASE("OrientationAnalysis::CAxisSegmentFeatures:Mask", "[OrientationAnalysis][CAxisSegmentFeatures]")
 {
+  const DataPath k_EbsdMaskArrayPath = k_CellAttributeMatrix.createChildPath("Mask (Y Pos)");
+
   UnitTest::LoadPlugins();
-  const nx::core::UnitTest::TestFileSentinel testDataSentinel(nx::core::unit_test::k_CMakeExecutable, nx::core::unit_test::k_TestFilesDir, "caxis_data.tar.gz", "caxis_data");
 
+  const nx::core::UnitTest::TestFileSentinel testDataSentinel(nx::core::unit_test::k_CMakeExecutable, nx::core::unit_test::k_TestFilesDir, "segment_features_test_data.tar.gz",
+                                                              "segment_features_test_data");
   // Read Exemplar DREAM3D File Filter
-  auto exemplarFilePath = fs::path(fmt::format("{}/caxis_data/7_0_find_caxis_data.dream3d", unit_test::k_TestFilesDir));
+  auto exemplarFilePath = fs::path(fmt::format("{}/segment_features_test_data/segment_features_test_data.dream3d", unit_test::k_TestFilesDir));
   DataStructure dataStructure = UnitTest::LoadDataStructure(exemplarFilePath);
 
-  auto& crystalStructs = dataStructure.getDataRefAs<UInt32Array>(k_CrystalStructuresArrayPath);
-  crystalStructs[1] = 1;
-
-  // Instantiate the filter, a DataStructure object and an Arguments Object
-  CAxisSegmentFeaturesFilter filter;
-  Arguments args;
-
-  // Invalid crystal structure type : should fail in execute
-  args.insertOrAssign(CAxisSegmentFeaturesFilter::k_SelectedImageGeometryPath_Key, std::make_any<DataPath>(k_DataContainerPath));
-  args.insertOrAssign(CAxisSegmentFeaturesFilter::k_MisorientationTolerance_Key, std::make_any<float32>(5.0f));
-  args.insertOrAssign(CAxisSegmentFeaturesFilter::k_UseMask_Key, std::make_any<bool>(false));
-  args.insertOrAssign(CAxisSegmentFeaturesFilter::k_RandomizeFeatureIds_Key, std::make_any<bool>(false));
-  args.insertOrAssign(CAxisSegmentFeaturesFilter::k_QuatsArrayPath_Key, std::make_any<DataPath>(k_QuatsArrayPath));
-  args.insertOrAssign(CAxisSegmentFeaturesFilter::k_CellPhasesArrayPath_Key, std::make_any<DataPath>(k_PhasesArrayPath));
-  args.insertOrAssign(CAxisSegmentFeaturesFilter::k_CrystalStructuresArrayPath_Key, std::make_any<DataPath>(k_CrystalStructuresArrayPath));
-  args.insertOrAssign(CAxisSegmentFeaturesFilter::k_FeatureIdsArrayName_Key, std::make_any<std::string>(k_ComputedFeatureIds));
-  args.insertOrAssign(CAxisSegmentFeaturesFilter::k_CellFeatureAttributeMatrixName_Key, std::make_any<std::string>(k_ComputedCellFeatureData));
-  args.insertOrAssign(CAxisSegmentFeaturesFilter::k_ActiveArrayName_Key, std::make_any<std::string>(k_ActiveName));
-
-  // Preflight the filter and check result
-  auto preflightResult = filter.preflight(dataStructure, args);
-  SIMPLNX_RESULT_REQUIRE_VALID(preflightResult.outputActions)
-
-  // Execute the filter and check the result
-  auto executeResult = filter.execute(dataStructure, args);
-  SIMPLNX_RESULT_REQUIRE_INVALID(executeResult.result)
-
-  UnitTest::CheckArraysInheritTupleDims(dataStructure);
+  // EBSD Segment Features/Semgent Features (Misorientation) Filter
+  {
+    CAxisSegmentFeaturesFilter filter;
+    Arguments args;
+
+    // Create default Parameters for the filter.
+    args.insertOrAssign(CAxisSegmentFeaturesFilter::k_MisorientationTolerance_Key, std::make_any<float32>(5.0F));
+
+    args.insertOrAssign(CAxisSegmentFeaturesFilter::k_UseMask_Key, std::make_any<bool>(true));
+    args.insertOrAssign(CAxisSegmentFeaturesFilter::k_MaskArrayPath_Key, std::make_any<DataPath>(k_EbsdMaskArrayPath));
+
+    args.insertOrAssign(CAxisSegmentFeaturesFilter::k_SelectedImageGeometryPath_Key, std::make_any<DataPath>(k_DataContainerPath));
+    args.insertOrAssign(CAxisSegmentFeaturesFilter::k_QuatsArrayPath_Key, std::make_any<DataPath>(k_QuatsArrayPath));
+    args.insertOrAssign(CAxisSegmentFeaturesFilter::k_CellPhasesArrayPath_Key, std::make_any<DataPath>(k_PhasesArrayPath));
+    args.insertOrAssign(CAxisSegmentFeaturesFilter::k_CrystalStructuresArrayPath_Key, std::make_any<DataPath>(k_CrystalStructuresArrayPath));
+
+    args.insertOrAssign(CAxisSegmentFeaturesFilter::k_FeatureIdsArrayName_Key, std::make_any<std::string>(k_FeatureIds));
+    args.insertOrAssign(CAxisSegmentFeaturesFilter::k_CellFeatureAttributeMatrixName_Key, std::make_any<std::string>(k_Grain_Data));
+    args.insertOrAssign(CAxisSegmentFeaturesFilter::k_ActiveArrayName_Key, std::make_any<std::string>(k_ActiveName));
+    args.insertOrAssign(CAxisSegmentFeaturesFilter::k_RandomizeFeatureIds_Key, std::make_any<bool>(false));
+
+    // Preflight the filter and check result
+    auto preflightResult = filter.preflight(dataStructure, args);
+    SIMPLNX_RESULT_REQUIRE_VALID(preflightResult.outputActions);
+
+    // Execute the filter and check the result
+    auto executeResult = filter.execute(dataStructure, args);
+    SIMPLNX_RESULT_REQUIRE_VALID(executeResult.result);
+  }
+
+  {
+    DataPath activeArrayDataPath = k_DataContainerPath.createChildPath(k_Grain_Data).createChildPath(k_ActiveName);
+    UInt8Array& actives = dataStructure.getDataRefAs<UInt8Array>(activeArrayDataPath);
+    size_t numFeatures = actives.getNumberOfTuples();
+    REQUIRE(numFeatures == 36);
+  }
+  // Loop and compare each array from the 'Exemplar Data / CellData' to the 'Data Container / CellData' group
+  {
+    const auto& generatedDataArray = dataStructure.getDataRefAs<Int32Array>(k_FeatureIdsArrayPath);
+    const auto& exemplarDataArray = dataStructure.getDataRefAs<Int32Array>(k_CellAttributeMatrix.createChildPath("CAxis_FeatureIds_Mask"));
+
+    UnitTest::CompareDataArrays<int32>(generatedDataArray, exemplarDataArray);
+  }
+
+  UnitTest::CheckArraysInheritTupleDims(dataStructure, SmallIn100::k_TupleCheckIgnoredPaths);
 }

src/Plugins/OrientationAnalysis/test/CMakeLists.txt

@@ -153,6 +153,7 @@ if(EXISTS "${DREAM3D_DATA_DIR}" AND SIMPLNX_DOWNLOAD_TEST_FILES)
   download_test_data(DREAM3D_DATA_DIR ${DREAM3D_DATA_DIR} ARCHIVE_NAME 7_ComputeAvgOrientation.tar.gz SHA512 5ee425b9a45da4daab1d43a870b54d57ac8d8e300acda162fa7a974a22b9f5662a98e768cebac1844eb87fcb2bb01624ffaf117d3aacc722aa8701712cbf3c52)
   download_test_data(DREAM3D_DATA_DIR ${DREAM3D_DATA_DIR} ARCHIVE_NAME 7_read_oem_ebsd_h5_files.tar.gz SHA512 95fa4cc0fb6bce26bfd6d28c0205a9e0f6497ad876a7cc4381117e668836936b35683ed5ec757cadd124a6c6fec7b38fe11f72512105bbd677bcf4210892ac19)
   download_test_data(DREAM3D_DATA_DIR ${DREAM3D_DATA_DIR} ARCHIVE_NAME compute_feature_neighbor_caxis_misalignments.tar.gz SHA512 955cd35b7ae24579ef9c533df34e1118012a8e5e2a71f8613117c714fc220c5dfa78d91a2964b41752e70684b79d4aa790e488e9a7be4c9dcf7b642ee2897ceb)
+  download_test_data(DREAM3D_DATA_DIR ${DREAM3D_DATA_DIR} ARCHIVE_NAME segment_features_test_data.tar.gz SHA512 c2b9582062a1776063bacac181828479ca73802e83abc6da8b3e58213395f7003aaaadd24df801e8dad35af955c368a68050c666f8ccc88ddde85abb9b5bedd4)
 
 endif()