diff --git a/pipelines/Combo-EBSD-osc_r0c0.d3dpipeline b/pipelines/Combo-EBSD-osc_r0c0.d3dpipeline index 3a5d20213b..e2557ea2bb 100644 --- a/pipelines/Combo-EBSD-osc_r0c0.d3dpipeline +++ b/pipelines/Combo-EBSD-osc_r0c0.d3dpipeline @@ -113,13 +113,13 @@ "cell_ipf_colors_array_name": "IPFColors", "cell_phases_array_path": "DataContainer/CellData/Phases", "crystal_structures_array_path": "DataContainer/CellEnsembleData/CrystalStructures", - "good_voxels_array_path": "DataContainer/CellData/Mask", + "mask_array_path": "DataContainer/CellData/Mask", "reference_dir": [ 0.0, 0.0, 1.0 ], - "use_good_voxels": true + "use_mask": true }, "comments": "", "filter": { @@ -164,12 +164,12 @@ "cell_phases_array_path": "DataContainer/CellData/Phases", "crystal_structures_array_path": "DataContainer/CellEnsembleData/CrystalStructures", "feature_ids_array_name": "FeatureIds", - "good_voxels_array_path": "DataContainer/CellData/Mask", + "mask_array_path": "DataContainer/CellData/Mask", "image_geometry_path": "DataContainer", "misorientation_tolerance": 5.0, "quats_array_path": "DataContainer/CellData/Quats", "randomize_feature_ids": true, - "use_good_voxels": true + "use_mask": true }, "comments": "", "filter": { diff --git a/src/Plugins/ComplexCore/pipelines/FindLargestCrossSections.d3dpipeline b/src/Plugins/ComplexCore/pipelines/FindLargestCrossSections.d3dpipeline index 94f05c00d0..5b1b3a7d0b 100644 --- a/src/Plugins/ComplexCore/pipelines/FindLargestCrossSections.d3dpipeline +++ b/src/Plugins/ComplexCore/pipelines/FindLargestCrossSections.d3dpipeline @@ -88,12 +88,12 @@ "cell_phases_array_path": "DataContainer/CellData/Phases", "crystal_structures_array_path": "DataContainer/CellEnsembleData/CrystalStructures", "feature_ids_array_name": "FeatureIds", - "good_voxels_array_path": "DataContainer/CellData/Mask", + "mask_array_path": "DataContainer/CellData/Mask", "grid_geometry_path": "DataContainer", "misorientation_tolerance": 5.0, "quats_array_path": "DataContainer/CellData/Quats", "randomize_features": true, - "use_good_voxels": true + "use_mask": true }, "comments": "", "filter": { diff --git a/src/Plugins/ComplexCore/pipelines/Import_ASCII.d3dpipeline b/src/Plugins/ComplexCore/pipelines/Import_ASCII.d3dpipeline index c3e30aa95c..88b3737991 100644 --- a/src/Plugins/ComplexCore/pipelines/Import_ASCII.d3dpipeline +++ b/src/Plugins/ComplexCore/pipelines/Import_ASCII.d3dpipeline @@ -149,13 +149,13 @@ "cell_ipf_colors_array_name": "IPFColors", "cell_phases_array_path": "[Image Geometry]/CellData/Phase", "crystal_structures_array_path": "[Image Geometry]/CellEnsembleData/CrystalStructures", - "good_voxels_array_path": "", + "mask_array_path": "", "reference_dir": [ 0.0, 0.0, 1.0 ], - "use_good_voxels": false + "use_mask": false }, "comments": "", "filter": { diff --git a/src/Plugins/ComplexCore/pipelines/ReplaceElementAttributesWithNeighbor.d3dpipeline b/src/Plugins/ComplexCore/pipelines/ReplaceElementAttributesWithNeighbor.d3dpipeline index 6c809c20b8..91211431b9 100644 --- a/src/Plugins/ComplexCore/pipelines/ReplaceElementAttributesWithNeighbor.d3dpipeline +++ b/src/Plugins/ComplexCore/pipelines/ReplaceElementAttributesWithNeighbor.d3dpipeline @@ -175,13 +175,13 @@ "cell_ipf_colors_array_name": "IPFColors", "cell_phases_array_path": "DataContainer/Cell Data/Phases", "crystal_structures_array_path": "DataContainer/CellEnsembleData/CrystalStructures", - "good_voxels_array_path": "DataContainer/Cell Data/Mask", + "mask_array_path": "DataContainer/Cell Data/Mask", "reference_dir": [ 0.0, 0.0, 1.0 ], - "use_good_voxels": true + "use_mask": true }, "comments": "", "filter": { diff --git a/src/Plugins/ComplexCore/pipelines/VtkRectilinearGridWriter.d3dpipeline b/src/Plugins/ComplexCore/pipelines/VtkRectilinearGridWriter.d3dpipeline index bde9946d37..cdee76e5a7 100644 --- a/src/Plugins/ComplexCore/pipelines/VtkRectilinearGridWriter.d3dpipeline +++ b/src/Plugins/ComplexCore/pipelines/VtkRectilinearGridWriter.d3dpipeline @@ -128,11 +128,11 @@ "alignment_shift_file_name": "Data/Output/Alignment_By_Misorientation_Shifts.txt", "cell_phases_array_path": "DataContainer/CellData/Phases", "crystal_structures_array_path": "DataContainer/CellEnsembleData/CrystalStructures", - "good_voxels_array_path": "DataContainer/CellData/Mask", + "mask_array_path": "DataContainer/CellData/Mask", "misorientation_tolerance": 5.0, "quats_array_path": "DataContainer/CellData/Quats", "selected_image_geometry_path": "DataContainer", - "use_good_voxels": true, + "use_mask": true, "write_alignment_shifts": false }, "comments": "", @@ -145,7 +145,7 @@ { "args": { "fill_holes": false, - "good_voxels": "DataContainer/CellData/Mask", + "mask_array_path": "DataContainer/CellData/Mask", "image_geometry": "DataContainer" }, "comments": "", @@ -158,7 +158,7 @@ { "args": { "alignment_shift_file_name": "Data/Output/Alignment_By_Feature_Centroid_Shifts.txt", - "good_voxels_array_path": "DataContainer/CellData/Mask", + "mask_array_path": "DataContainer/CellData/Mask", "reference_slice": 0, "selected_cell_data_path": "DataContainer/CellData", "selected_image_geometry_path": "DataContainer", @@ -176,7 +176,7 @@ "args": { "cell_phases_array_path": "DataContainer/CellData/Phases", "crystal_structures_array_path": "DataContainer/CellEnsembleData/CrystalStructures", - "good_voxels_array_path": "DataContainer/CellData/Mask", + "mask_array_path": "DataContainer/CellData/Mask", "image_geometry_path": "DataContainer", "misorientation_tolerance": 5.0, "number_of_neighbors": 4, @@ -215,12 +215,12 @@ "cell_phases_array_path": "DataContainer/CellData/Phases", "crystal_structures_array_path": "DataContainer/CellEnsembleData/CrystalStructures", "feature_ids_array_name": "FeatureIds", - "good_voxels_array_path": "DataContainer/CellData/Mask", + "mask_array_path": "DataContainer/CellData/Mask", "grid_geometry_path": "DataContainer", "misorientation_tolerance": 5.0, "quats_array_path": "DataContainer/CellData/Quats", "randomize_features": true, - "use_good_voxels": true + "use_mask": true }, "comments": "", "filter": { @@ -434,13 +434,13 @@ "cell_ipf_colors_array_name": "IPFColors", "cell_phases_array_path": "DataContainer/CellData/Phases", "crystal_structures_array_path": "DataContainer/CellEnsembleData/CrystalStructures", - "good_voxels_array_path": "DataContainer/CellData/Mask", + "mask_array_path": "DataContainer/CellData/Mask", "reference_dir": [ 0.0, 0.0, 1.0 ], - "use_good_voxels": true + "use_mask": true }, "comments": "", "filter": { diff --git a/src/Plugins/ComplexCore/src/ComplexCore/Filters/Algorithms/AlignSectionsFeatureCentroid.cpp b/src/Plugins/ComplexCore/src/ComplexCore/Filters/Algorithms/AlignSectionsFeatureCentroid.cpp index c3fdd5c8d9..415cdf28e4 100644 --- a/src/Plugins/ComplexCore/src/ComplexCore/Filters/Algorithms/AlignSectionsFeatureCentroid.cpp +++ b/src/Plugins/ComplexCore/src/ComplexCore/Filters/Algorithms/AlignSectionsFeatureCentroid.cpp @@ -60,12 +60,12 @@ Result<> AlignSectionsFeatureCentroid::findShifts(std::vector& xShifts, std::unique_ptr maskCompare; try { - maskCompare = InstantiateMaskCompare(m_DataStructure, m_InputValues->GoodVoxelsArrayPath); + maskCompare = InstantiateMaskCompare(m_DataStructure, m_InputValues->MaskArrayPath); } catch(const std::out_of_range& exception) { // This really should NOT be happening as the path was verified during preflight BUT we may be calling this from // somewhere else that is NOT going through the normal complex::IFilter API of Preflight and Execute - std::string message = fmt::format("Mask Array DataPath does not exist or is not of the correct type (Bool | UInt8) {}", m_InputValues->GoodVoxelsArrayPath.toString()); + std::string message = fmt::format("Mask Array DataPath does not exist or is not of the correct type (Bool | UInt8) {}", m_InputValues->MaskArrayPath.toString()); return MakeErrorResult(-53900, message); } diff --git a/src/Plugins/ComplexCore/src/ComplexCore/Filters/Algorithms/AlignSectionsFeatureCentroid.hpp b/src/Plugins/ComplexCore/src/ComplexCore/Filters/Algorithms/AlignSectionsFeatureCentroid.hpp index 77bf66eb8b..94331788b1 100644 --- a/src/Plugins/ComplexCore/src/ComplexCore/Filters/Algorithms/AlignSectionsFeatureCentroid.hpp +++ b/src/Plugins/ComplexCore/src/ComplexCore/Filters/Algorithms/AlignSectionsFeatureCentroid.hpp @@ -17,7 +17,7 @@ struct COMPLEXCORE_EXPORT AlignSectionsFeatureCentroidInputValues FileSystemPathParameter::ValueType AlignmentShiftFileName; bool UseReferenceSlice; int32 ReferenceSlice; - DataPath GoodVoxelsArrayPath; + DataPath MaskArrayPath; DataPath inputImageGeometry; DataPath cellDataGroupPath; }; diff --git a/src/Plugins/ComplexCore/src/ComplexCore/Filters/Algorithms/FindArrayStatistics.hpp b/src/Plugins/ComplexCore/src/ComplexCore/Filters/Algorithms/FindArrayStatistics.hpp index c4574b5471..5339bb5523 100644 --- a/src/Plugins/ComplexCore/src/ComplexCore/Filters/Algorithms/FindArrayStatistics.hpp +++ b/src/Plugins/ComplexCore/src/ComplexCore/Filters/Algorithms/FindArrayStatistics.hpp @@ -30,6 +30,7 @@ struct COMPLEXCORE_EXPORT FindArrayStatisticsInputValues bool FindStdDeviation; bool FindSummation; bool UseMask; + ; bool ComputeByIndex; bool StandardizeData; bool FindNumUniqueValues; diff --git a/src/Plugins/ComplexCore/src/ComplexCore/Filters/Algorithms/GenerateColorTable.cpp b/src/Plugins/ComplexCore/src/ComplexCore/Filters/Algorithms/GenerateColorTable.cpp index dc65af4afd..0054a04387 100644 --- a/src/Plugins/ComplexCore/src/ComplexCore/Filters/Algorithms/GenerateColorTable.cpp +++ b/src/Plugins/ComplexCore/src/ComplexCore/Filters/Algorithms/GenerateColorTable.cpp @@ -216,9 +216,9 @@ struct GenerateColorArrayFunctor auto& colorArray = dataStructure.getDataRefAs(rgbArrayPath); complex::IDataArray* goodVoxelsArray = nullptr; - if(inputValues->UseGoodVoxels) + if(inputValues->UseMask) { - goodVoxelsArray = dataStructure.getDataAs(inputValues->GoodVoxelsArrayPath); + goodVoxelsArray = dataStructure.getDataAs(inputValues->MaskArrayPath); } ParallelDataAlgorithm dataAlg; diff --git a/src/Plugins/ComplexCore/src/ComplexCore/Filters/Algorithms/GenerateColorTable.hpp b/src/Plugins/ComplexCore/src/ComplexCore/Filters/Algorithms/GenerateColorTable.hpp index f363100c30..7d8948bc19 100644 --- a/src/Plugins/ComplexCore/src/ComplexCore/Filters/Algorithms/GenerateColorTable.hpp +++ b/src/Plugins/ComplexCore/src/ComplexCore/Filters/Algorithms/GenerateColorTable.hpp @@ -17,8 +17,8 @@ struct COMPLEXCORE_EXPORT GenerateColorTableInputValues nlohmann::json SelectedPreset; DataPath SelectedDataArrayPath; DataPath RgbArrayPath; - bool UseGoodVoxels; - DataPath GoodVoxelsArrayPath; + bool UseMask; + DataPath MaskArrayPath; std::vector InvalidColor; }; diff --git a/src/Plugins/ComplexCore/src/ComplexCore/Filters/Algorithms/GenerateVectorColors.cpp b/src/Plugins/ComplexCore/src/ComplexCore/Filters/Algorithms/GenerateVectorColors.cpp index 26ed43cbdc..2ded59ea8e 100644 --- a/src/Plugins/ComplexCore/src/ComplexCore/Filters/Algorithms/GenerateVectorColors.cpp +++ b/src/Plugins/ComplexCore/src/ComplexCore/Filters/Algorithms/GenerateVectorColors.cpp @@ -40,12 +40,12 @@ Result<> GenerateVectorColors::operator()() std::unique_ptr maskCompare; try { - maskCompare = InstantiateMaskCompare(m_DataStructure, m_InputValues->GoodVoxelsArrayPath); + maskCompare = InstantiateMaskCompare(m_DataStructure, m_InputValues->MaskArrayPath); } catch(const std::out_of_range& exception) { // This really should NOT be happening as the path was verified during preflight BUT we may be calling this from // somewhere else that is NOT going through the normal complex::IFilter API of Preflight and Execute - return MakeErrorResult(-54700, fmt::format("Mask Array DataPath does not exist or is not of the correct type (Bool | UInt8) {}", m_InputValues->GoodVoxelsArrayPath.toString())); + return MakeErrorResult(-54700, fmt::format("Mask Array DataPath does not exist or is not of the correct type (Bool | UInt8) {}", m_InputValues->MaskArrayPath.toString())); } auto& vectors = m_DataStructure.getDataRefAs(m_InputValues->VectorsArrayPath); diff --git a/src/Plugins/ComplexCore/src/ComplexCore/Filters/Algorithms/GenerateVectorColors.hpp b/src/Plugins/ComplexCore/src/ComplexCore/Filters/Algorithms/GenerateVectorColors.hpp index 0234379a92..58864cedef 100644 --- a/src/Plugins/ComplexCore/src/ComplexCore/Filters/Algorithms/GenerateVectorColors.hpp +++ b/src/Plugins/ComplexCore/src/ComplexCore/Filters/Algorithms/GenerateVectorColors.hpp @@ -13,9 +13,9 @@ namespace complex struct COMPLEXCORE_EXPORT GenerateVectorColorsInputValues { - bool UseGoodVoxels; + bool UseMask; DataPath VectorsArrayPath; - DataPath GoodVoxelsArrayPath; + DataPath MaskArrayPath; DataPath CellVectorColorsArrayPath; }; diff --git a/src/Plugins/ComplexCore/src/ComplexCore/Filters/Algorithms/RawBinaryReader.cpp b/src/Plugins/ComplexCore/src/ComplexCore/Filters/Algorithms/RawBinaryReader.cpp index d01a94373c..d83054a848 100644 --- a/src/Plugins/ComplexCore/src/ComplexCore/Filters/Algorithms/RawBinaryReader.cpp +++ b/src/Plugins/ComplexCore/src/ComplexCore/Filters/Algorithms/RawBinaryReader.cpp @@ -82,10 +82,6 @@ Result<> ReadBinaryFile(IDataArray& dataArrayPtr, const std::string& filename, u { return MakeErrorResult(k_RbrFileTooSmall, "The file size is smaller than the allocated size"); } - if(err > 0) - { - return MakeWarningVoidResult(k_RbrFileTooBig, "The file size is larger than the allocated size"); - } Result<> result = ImportFromBinaryFile(fs::path(filename), dataArray, skipHeaderBytes, k_DefaultBlocksize); if(result.invalid()) diff --git a/src/Plugins/ComplexCore/src/ComplexCore/Filters/AlignSectionsFeatureCentroidFilter.cpp b/src/Plugins/ComplexCore/src/ComplexCore/Filters/AlignSectionsFeatureCentroidFilter.cpp index 142ba80de0..6f0ecb6922 100644 --- a/src/Plugins/ComplexCore/src/ComplexCore/Filters/AlignSectionsFeatureCentroidFilter.cpp +++ b/src/Plugins/ComplexCore/src/ComplexCore/Filters/AlignSectionsFeatureCentroidFilter.cpp @@ -75,7 +75,7 @@ Parameters AlignSectionsFeatureCentroidFilter::parameters() const params.insert(std::make_unique(k_SelectedImageGeometry_Key, "Selected Image Geometry", "The target geometry on which to perform the alignment", DataPath({"Data Container"}), GeometrySelectionParameter::AllowedTypes{IGeometry::Type::Image})); params.insert(std::make_unique(k_SelectedCellDataGroup_Key, "Cell Data Attribute Matrix", "Cell Data Attribute Matrix", DataPath{})); - params.insert(std::make_unique(k_GoodVoxelsArrayPath_Key, "Mask", "Path to the DataArray Mask", DataPath({"Mask"}), + params.insert(std::make_unique(k_MaskArrayPath_Key, "Mask Array", "Path to the DataArray Mask", DataPath({"Mask"}), ArraySelectionParameter::AllowedTypes{DataType::boolean, DataType::uint8}, ArraySelectionParameter::AllowedComponentShapes{{1}})); params.insertSeparator(Parameters::Separator{"Optional File Output"}); @@ -101,7 +101,7 @@ IFilter::PreflightResult AlignSectionsFeatureCentroidFilter::preflightImpl(const auto pWriteAlignmentShifts = filterArgs.value(k_WriteAlignmentShifts_Key); auto pAlignmentShiftFileName = filterArgs.value(k_AlignmentShiftFileName_Key); auto pReferenceSliceValue = filterArgs.value(k_ReferenceSlice_Key); - auto pGoodVoxelsArrayPath = filterArgs.value(k_GoodVoxelsArrayPath_Key); + auto pGoodVoxelsArrayPath = filterArgs.value(k_MaskArrayPath_Key); auto inputImageGeometry = filterArgs.value(k_SelectedImageGeometry_Key); auto cellDataGroupPath = filterArgs.value(k_SelectedCellDataGroup_Key); @@ -151,7 +151,7 @@ Result<> AlignSectionsFeatureCentroidFilter::executeImpl(DataStructure& dataStru inputValues.AlignmentShiftFileName = filterArgs.value(k_AlignmentShiftFileName_Key); inputValues.UseReferenceSlice = filterArgs.value(k_UseReferenceSlice_Key); inputValues.ReferenceSlice = filterArgs.value(k_ReferenceSlice_Key); - inputValues.GoodVoxelsArrayPath = filterArgs.value(k_GoodVoxelsArrayPath_Key); + inputValues.MaskArrayPath = filterArgs.value(k_MaskArrayPath_Key); inputValues.inputImageGeometry = filterArgs.value(k_SelectedImageGeometry_Key); inputValues.cellDataGroupPath = filterArgs.value(k_SelectedCellDataGroup_Key); diff --git a/src/Plugins/ComplexCore/src/ComplexCore/Filters/AlignSectionsFeatureCentroidFilter.hpp b/src/Plugins/ComplexCore/src/ComplexCore/Filters/AlignSectionsFeatureCentroidFilter.hpp index 171ffcca51..e4867a1c18 100644 --- a/src/Plugins/ComplexCore/src/ComplexCore/Filters/AlignSectionsFeatureCentroidFilter.hpp +++ b/src/Plugins/ComplexCore/src/ComplexCore/Filters/AlignSectionsFeatureCentroidFilter.hpp @@ -29,7 +29,7 @@ class COMPLEXCORE_EXPORT AlignSectionsFeatureCentroidFilter : public IFilter static inline constexpr StringLiteral k_AlignmentShiftFileName_Key = "alignment_shift_file_name"; static inline constexpr StringLiteral k_UseReferenceSlice_Key = "use_reference_slice"; static inline constexpr StringLiteral k_ReferenceSlice_Key = "reference_slice"; - static inline constexpr StringLiteral k_GoodVoxelsArrayPath_Key = "good_voxels_array_path"; + static inline constexpr StringLiteral k_MaskArrayPath_Key = "mask_array_path"; static inline constexpr StringLiteral k_SelectedImageGeometry_Key = "selected_image_geometry_path"; static inline constexpr StringLiteral k_SelectedCellDataGroup_Key = "selected_cell_data_path"; diff --git a/src/Plugins/ComplexCore/src/ComplexCore/Filters/ExtractVertexGeometryFilter.cpp b/src/Plugins/ComplexCore/src/ComplexCore/Filters/ExtractVertexGeometryFilter.cpp index 7b2616e618..b61efd30f0 100644 --- a/src/Plugins/ComplexCore/src/ComplexCore/Filters/ExtractVertexGeometryFilter.cpp +++ b/src/Plugins/ComplexCore/src/ComplexCore/Filters/ExtractVertexGeometryFilter.cpp @@ -56,8 +56,8 @@ Parameters ExtractVertexGeometryFilter::parameters() const params.insert( std::make_unique(k_ArrayHandling_Key, "Array Handling", "Move or Copy input data arrays", 0, ChoicesParameter::Choices{"Move Attribute Arrays", "Copy Attribute Arrays"})); params.insertLinkableParameter(std::make_unique(k_UseMask_Key, "Use Mask", "Specifies whether or not to use a mask array", false)); - params.insert(std::make_unique(k_MaskArrayPath_Key, "Mask", "DataPath to the boolean mask array. Values that are true will mark that cell/point as usable.", DataPath{}, - ArraySelectionParameter::AllowedTypes{DataType::boolean}, ArraySelectionParameter::AllowedComponentShapes{{1}})); + params.insert(std::make_unique(k_MaskArrayPath_Key, "Mask Array", "DataPath to the boolean mask array. Values that are true will mark that cell/point as usable.", + DataPath{}, ArraySelectionParameter::AllowedTypes{DataType::boolean}, ArraySelectionParameter::AllowedComponentShapes{{1}})); params.insert(std::make_unique(k_InputGeometryPath_Key, "Input Geometry", "The input Image/RectilinearGrid Geometry to convert", DataPath{}, DataGroupSelectionParameter::AllowedTypes{BaseGroup::GroupType::ImageGeom, BaseGroup::GroupType::RectGridGeom})); params.insert(std::make_unique(k_IncludedDataArrayPaths_Key, "Included Attribute Arrays", "The arrays to copy/move to the vertex array", @@ -104,12 +104,12 @@ IFilter::PreflightResult ExtractVertexGeometryFilter::preflightImpl(const DataSt usize geomElementCount = dims[0] * dims[1] * dims[2]; if(pUseMaskValue) { - const BoolArray& maskArray = dataStructure.getDataRefAs(pMaskArrayPathValue); - if(maskArray.getNumberOfTuples() != geomElementCount) + const BoolArray* maskArray = dataStructure.getDataAs(pMaskArrayPathValue); + if(maskArray->getNumberOfTuples() != geomElementCount) { return {MakeErrorResult(-2003, fmt::format("{0}: The data array with path '{1}' has a tuple count of {2}, but this does not match the " "number of tuples required by geometry '{3}' ({4})", - humanName(), pMaskArrayPathValue.toString(), maskArray.getNumberOfTuples(), geometry.getName(), geomElementCount))}; + humanName(), pMaskArrayPathValue.toString(), maskArray->getNumberOfTuples(), geometry.getName(), geomElementCount))}; } } @@ -119,7 +119,7 @@ IFilter::PreflightResult ExtractVertexGeometryFilter::preflightImpl(const DataSt DataPath parentPath = dataPath.getParent(); if(parentPath.empty()) { - return {MakeErrorResult(-2004, fmt::format("{}: The data array with path '{}' has no parent. It must have an AttributeMatrix as a parent.", humanName(), dataPath.toString()))}; + return {MakeErrorResult(-2004, fmt::format("{}: The data array with path '{}' has no parent. It must have an AttributeMatrix as a parent.", humanName(), dataPath.toString()))}; } if(dataStructure.getDataAs(parentPath) == nullptr) { @@ -168,14 +168,8 @@ IFilter::PreflightResult ExtractVertexGeometryFilter::preflightImpl(const DataSt } } - PreflightResult preflightResult; - std::vector preflightUpdatedValues; - // Store the preflight updated value(s) into the preflightUpdatedValues vector using - // the appropriate methods. - // None found based on the filter parameters - // Return both the resultOutputActions and the preflightUpdatedValues via std::move() return {std::move(resultOutputActions), std::move(preflightUpdatedValues)}; } diff --git a/src/Plugins/ComplexCore/src/ComplexCore/Filters/FindArrayStatisticsFilter.cpp b/src/Plugins/ComplexCore/src/ComplexCore/Filters/FindArrayStatisticsFilter.cpp index 2cb8e51083..a7f8837612 100644 --- a/src/Plugins/ComplexCore/src/ComplexCore/Filters/FindArrayStatisticsFilter.cpp +++ b/src/Plugins/ComplexCore/src/ComplexCore/Filters/FindArrayStatisticsFilter.cpp @@ -209,8 +209,8 @@ Parameters FindArrayStatisticsFilter::parameters() const params.insertSeparator(Parameters::Separator{"Optional Data Mask"}); params.insertLinkableParameter(std::make_unique(k_UseMask_Key, "Use Mask", "Specifies whether or not to use a mask array", false)); - params.insert(std::make_unique(k_MaskArrayPath_Key, "Mask", "DataPath to the boolean mask array. Values that are true will mark that cell/point as usable.", DataPath{}, - ArraySelectionParameter::AllowedTypes{DataType::boolean, DataType::uint8}, ArraySelectionParameter::AllowedComponentShapes{{1}})); + params.insert(std::make_unique(k_MaskArrayPath_Key, "Mask Array", "DataPath to the boolean mask array. Values that are true will mark that cell/point as usable.", + DataPath{}, ArraySelectionParameter::AllowedTypes{DataType::boolean, DataType::uint8}, ArraySelectionParameter::AllowedComponentShapes{{1}})); params.insertSeparator(Parameters::Separator{"Algorithm Options"}); params.insertLinkableParameter( diff --git a/src/Plugins/ComplexCore/src/ComplexCore/Filters/FindFeaturePhasesBinaryFilter.cpp b/src/Plugins/ComplexCore/src/ComplexCore/Filters/FindFeaturePhasesBinaryFilter.cpp index 2b05955d38..f52f08329d 100644 --- a/src/Plugins/ComplexCore/src/ComplexCore/Filters/FindFeaturePhasesBinaryFilter.cpp +++ b/src/Plugins/ComplexCore/src/ComplexCore/Filters/FindFeaturePhasesBinaryFilter.cpp @@ -51,7 +51,7 @@ Parameters FindFeaturePhasesBinaryFilter::parameters() const params.insertSeparator(Parameters::Separator{"Required Input Data Objects"}); params.insert(std::make_unique(k_FeatureIdsArrayPath_Key, "Feature Ids", "Data Array that specifies to which Feature each Element belongs", DataPath{}, ArraySelectionParameter::AllowedTypes{DataType::int32})); - params.insert(std::make_unique(k_GoodVoxelsArrayPath_Key, "Mask", "Data Array that specifies if the Cell is to be counted in the algorithm", DataPath{}, + params.insert(std::make_unique(k_MaskArrayPath_Key, "Mask Array", "Data Array that specifies if the Cell is to be counted in the algorithm", DataPath{}, ArraySelectionParameter::AllowedTypes{DataType::boolean, DataType::uint8}, ArraySelectionParameter::AllowedComponentShapes{{1}})); params.insert(std::make_unique(k_CellDataAMPath_Key, "Cell Data Attribute Matrix", "The Cell Data Attribute Matrix within the Image Geometry where the Binary Phases Array will be created", DataPath{})); @@ -100,12 +100,12 @@ Result<> FindFeaturePhasesBinaryFilter::executeImpl(DataStructure& dataStructure std::unique_ptr goodVoxelsMask; try { - goodVoxelsMask = InstantiateMaskCompare(dataStructure, filterArgs.value(k_GoodVoxelsArrayPath_Key)); + goodVoxelsMask = InstantiateMaskCompare(dataStructure, filterArgs.value(k_MaskArrayPath_Key)); } catch(const std::out_of_range& exception) { // This really should NOT be happening as the path was verified during preflight BUT we may be calling this from // somewhere else that is NOT going through the normal complex::IFilter API of Preflight and Execute - std::string message = fmt::format("Mask Array DataPath does not exist or is not of the correct type (Bool | UInt8) {}", filterArgs.value(k_GoodVoxelsArrayPath_Key).toString()); + std::string message = fmt::format("Mask Array DataPath does not exist or is not of the correct type (Bool | UInt8) {}", filterArgs.value(k_MaskArrayPath_Key).toString()); return MakeErrorResult(-53800, message); } diff --git a/src/Plugins/ComplexCore/src/ComplexCore/Filters/FindFeaturePhasesBinaryFilter.hpp b/src/Plugins/ComplexCore/src/ComplexCore/Filters/FindFeaturePhasesBinaryFilter.hpp index b9a25ed4ad..e03c50e8dd 100644 --- a/src/Plugins/ComplexCore/src/ComplexCore/Filters/FindFeaturePhasesBinaryFilter.hpp +++ b/src/Plugins/ComplexCore/src/ComplexCore/Filters/FindFeaturePhasesBinaryFilter.hpp @@ -25,7 +25,7 @@ class COMPLEXCORE_EXPORT FindFeaturePhasesBinaryFilter : public IFilter // Parameter Keys static inline constexpr StringLiteral k_FeatureIdsArrayPath_Key = "feature_ids_array_path"; - static inline constexpr StringLiteral k_GoodVoxelsArrayPath_Key = "good_voxels_array_path"; + static inline constexpr StringLiteral k_MaskArrayPath_Key = "mask_array_path"; static inline constexpr StringLiteral k_FeaturePhasesArrayName_Key = "feature_phases_array_name"; static inline constexpr StringLiteral k_CellDataAMPath_Key = "cell_data_attribute_matrix_path"; diff --git a/src/Plugins/ComplexCore/src/ComplexCore/Filters/GenerateColorTableFilter.cpp b/src/Plugins/ComplexCore/src/ComplexCore/Filters/GenerateColorTableFilter.cpp index f8a4e92d94..c02b6ec8f8 100644 --- a/src/Plugins/ComplexCore/src/ComplexCore/Filters/GenerateColorTableFilter.cpp +++ b/src/Plugins/ComplexCore/src/ComplexCore/Filters/GenerateColorTableFilter.cpp @@ -70,13 +70,13 @@ Parameters GenerateColorTableFilter::parameters() const complex::GetAllDataTypes(), ArraySelectionParameter::AllowedComponentShapes{{1}})); params.insertSeparator(Parameters::Separator{"Optional Data Mask"}); - params.insertLinkableParameter(std::make_unique(k_UseGoodVoxels_Key, "Use Mask Array", "Whether to assign a black color to 'bad' Elements", false)); - params.insert(std::make_unique(k_GoodVoxelsPath_Key, "Mask", "Path to the data array used to define Elements as good or bad.", DataPath(), + params.insertLinkableParameter(std::make_unique(k_UseMask_Key, "Use Mask Array", "Whether to assign a black color to 'bad' Elements", false)); + params.insert(std::make_unique(k_MaskArrayPath_Key, "Mask Array", "Path to the data array used to define Elements as good or bad.", DataPath(), ArraySelectionParameter::AllowedTypes{DataType::boolean, DataType::uint8}, ArraySelectionParameter::AllowedComponentShapes{{1}})); params.insert(std::make_unique(k_InvalidColorValue_Key, "Masked Voxel Color (RGB)", "The color to assign to voxels that have a mask value of FALSE", VectorUInt8Parameter::ValueType{0, 0, 0}, std::vector{"Red", "Green", "Blue"})); // Associate the Linkable Parameter(s) to the children parameters that they control - params.linkParameters(k_UseGoodVoxels_Key, k_GoodVoxelsPath_Key, true); + params.linkParameters(k_UseMask_Key, k_MaskArrayPath_Key, true); params.insertSeparator({"Created Data Objects"}); params.insert(std::make_unique( @@ -99,8 +99,8 @@ IFilter::PreflightResult GenerateColorTableFilter::preflightImpl(const DataStruc auto pSelectedDataArrayPathValue = filterArgs.value(k_SelectedDataArrayPath_Key); auto pRgbArrayPathValue = pSelectedDataArrayPathValue.getParent().createChildPath(filterArgs.value(k_RgbArrayPath_Key)); - auto pUseGoodVoxelsValue = filterArgs.value(k_UseGoodVoxels_Key); - auto pGoodVoxelsArrayPathValue = filterArgs.value(k_GoodVoxelsPath_Key); + auto pUseGoodVoxelsValue = filterArgs.value(k_UseMask_Key); + auto pGoodVoxelsArrayPathValue = filterArgs.value(k_MaskArrayPath_Key); complex::Result resultOutputActions; std::vector preflightUpdatedValues; @@ -116,7 +116,7 @@ IFilter::PreflightResult GenerateColorTableFilter::preflightImpl(const DataStruc DataPath goodVoxelsPath; if(pUseGoodVoxelsValue) { - goodVoxelsPath = filterArgs.value(k_GoodVoxelsPath_Key); + goodVoxelsPath = filterArgs.value(k_MaskArrayPath_Key); const complex::IDataArray* goodVoxelsArray = dataStructure.getDataAs(goodVoxelsPath); if(nullptr == goodVoxelsArray) @@ -150,8 +150,8 @@ Result<> GenerateColorTableFilter::executeImpl(DataStructure& dataStructure, con inputValues.SelectedPreset = filterArgs.value(k_SelectedPreset_Key); inputValues.SelectedDataArrayPath = filterArgs.value(k_SelectedDataArrayPath_Key); inputValues.RgbArrayPath = inputValues.SelectedDataArrayPath.getParent().createChildPath(filterArgs.value(k_RgbArrayPath_Key)); - inputValues.UseGoodVoxels = filterArgs.value(k_UseGoodVoxels_Key); - inputValues.GoodVoxelsArrayPath = filterArgs.value(k_GoodVoxelsPath_Key); + inputValues.UseMask = filterArgs.value(k_UseMask_Key); + inputValues.MaskArrayPath = filterArgs.value(k_MaskArrayPath_Key); inputValues.InvalidColor = filterArgs.value>(k_InvalidColorValue_Key); return GenerateColorTable(dataStructure, messageHandler, shouldCancel, &inputValues)(); diff --git a/src/Plugins/ComplexCore/src/ComplexCore/Filters/GenerateColorTableFilter.hpp b/src/Plugins/ComplexCore/src/ComplexCore/Filters/GenerateColorTableFilter.hpp index 9923ea64c2..c0323d11b9 100644 --- a/src/Plugins/ComplexCore/src/ComplexCore/Filters/GenerateColorTableFilter.hpp +++ b/src/Plugins/ComplexCore/src/ComplexCore/Filters/GenerateColorTableFilter.hpp @@ -29,8 +29,8 @@ class COMPLEXCORE_EXPORT GenerateColorTableFilter : public IFilter static inline constexpr StringLiteral k_SelectedPreset_Key = "selected_preset"; static inline constexpr StringLiteral k_SelectedDataArrayPath_Key = "selected_data_array_path"; static inline constexpr StringLiteral k_RgbArrayPath_Key = "output_rgb_array_name"; - static inline constexpr StringLiteral k_UseGoodVoxels_Key = "use_good_voxels"; - static inline constexpr StringLiteral k_GoodVoxelsPath_Key = "good_voxels_array_path"; + static inline constexpr StringLiteral k_UseMask_Key = "use_mask"; + static inline constexpr StringLiteral k_MaskArrayPath_Key = "mask_array_path"; static inline constexpr StringLiteral k_InvalidColorValue_Key = "invalid_color_value"; /** diff --git a/src/Plugins/ComplexCore/src/ComplexCore/Filters/GenerateVectorColorsFilter.cpp b/src/Plugins/ComplexCore/src/ComplexCore/Filters/GenerateVectorColorsFilter.cpp index ec8813a60f..8a36051d9f 100644 --- a/src/Plugins/ComplexCore/src/ComplexCore/Filters/GenerateVectorColorsFilter.cpp +++ b/src/Plugins/ComplexCore/src/ComplexCore/Filters/GenerateVectorColorsFilter.cpp @@ -56,8 +56,8 @@ Parameters GenerateVectorColorsFilter::parameters() const // Create the parameter descriptors that are needed for this filter params.insertSeparator(Parameters::Separator{"Optional Data Mask"}); params.insertLinkableParameter( - std::make_unique(k_UseGoodVoxels_Key, "Apply to Good Voxels Only (Bad Voxels Will Be Black)", "Whether or not to assign colors to bad voxels or leave them black", false)); - params.insert(std::make_unique(k_GoodVoxelsArrayPath_Key, "Mask", "Used to define Elements as good or bad ", DataPath{}, + std::make_unique(k_UseMask_Key, "Apply to Good Voxels Only (Bad Voxels Will Be Black)", "Whether or not to assign colors to bad voxels or leave them black", false)); + params.insert(std::make_unique(k_MaskArrayPath_Key, "Mask Array", "Used to define Elements as good or bad ", DataPath{}, ArraySelectionParameter::AllowedTypes{DataType::boolean, DataType::uint8}, ArraySelectionParameter::AllowedComponentShapes{{1}})); params.insertSeparator(Parameters::Separator{"Required Data Objects"}); @@ -68,7 +68,7 @@ Parameters GenerateVectorColorsFilter::parameters() const params.insert(std::make_unique(k_CellVectorColorsArrayName_Key, "Vector Colors", "RGB colors", "Vector Colors Array")); // Associate the Linkable Parameter(s) to the children parameters that they control - params.linkParameters(k_UseGoodVoxels_Key, k_GoodVoxelsArrayPath_Key, true); + params.linkParameters(k_UseMask_Key, k_MaskArrayPath_Key, true); return params; } @@ -83,9 +83,9 @@ IFilter::UniquePointer GenerateVectorColorsFilter::clone() const IFilter::PreflightResult GenerateVectorColorsFilter::preflightImpl(const DataStructure& dataStructure, const Arguments& filterArgs, const MessageHandler& messageHandler, const std::atomic_bool& shouldCancel) const { - auto pUseGoodVoxelsValue = filterArgs.value(k_UseGoodVoxels_Key); + auto pUseGoodVoxelsValue = filterArgs.value(k_UseMask_Key); auto pVectorsArrayPathValue = filterArgs.value(k_VectorsArrayPath_Key); - auto pGoodVoxelsArrayPathValue = filterArgs.value(k_GoodVoxelsArrayPath_Key); + auto pGoodVoxelsArrayPathValue = filterArgs.value(k_MaskArrayPath_Key); auto pCellVectorColorsArrayNameValue = filterArgs.value(k_CellVectorColorsArrayName_Key); PreflightResult preflightResult; @@ -114,16 +114,16 @@ Result<> GenerateVectorColorsFilter::executeImpl(DataStructure& dataStructure, c { GenerateVectorColorsInputValues inputValues; - inputValues.UseGoodVoxels = filterArgs.value(k_UseGoodVoxels_Key); + inputValues.UseMask = filterArgs.value(k_UseMask_Key); inputValues.VectorsArrayPath = filterArgs.value(k_VectorsArrayPath_Key); - if(!inputValues.UseGoodVoxels) + if(!inputValues.UseMask) { - inputValues.GoodVoxelsArrayPath = k_MaskArrayPath; + inputValues.MaskArrayPath = k_MaskArrayPath; dataStructure.getDataAs(k_MaskArrayPath)->fill(true); } else { - inputValues.GoodVoxelsArrayPath = filterArgs.value(k_GoodVoxelsArrayPath_Key); + inputValues.MaskArrayPath = filterArgs.value(k_MaskArrayPath_Key); } inputValues.CellVectorColorsArrayPath = inputValues.VectorsArrayPath.getParent().createChildPath(filterArgs.value(k_CellVectorColorsArrayName_Key)); diff --git a/src/Plugins/ComplexCore/src/ComplexCore/Filters/GenerateVectorColorsFilter.hpp b/src/Plugins/ComplexCore/src/ComplexCore/Filters/GenerateVectorColorsFilter.hpp index 03094c3aed..7e4c036a86 100644 --- a/src/Plugins/ComplexCore/src/ComplexCore/Filters/GenerateVectorColorsFilter.hpp +++ b/src/Plugins/ComplexCore/src/ComplexCore/Filters/GenerateVectorColorsFilter.hpp @@ -24,9 +24,9 @@ class COMPLEXCORE_EXPORT GenerateVectorColorsFilter : public IFilter GenerateVectorColorsFilter& operator=(GenerateVectorColorsFilter&&) noexcept = delete; // Parameter Keys - static inline constexpr StringLiteral k_UseGoodVoxels_Key = "use_good_voxels"; + static inline constexpr StringLiteral k_UseMask_Key = "use_mask"; static inline constexpr StringLiteral k_VectorsArrayPath_Key = "vectors_array_path"; - static inline constexpr StringLiteral k_GoodVoxelsArrayPath_Key = "good_voxels_array_path"; + static inline constexpr StringLiteral k_MaskArrayPath_Key = "mask_array_path"; static inline constexpr StringLiteral k_CellVectorColorsArrayName_Key = "cell_vector_colors_array_name"; /** diff --git a/src/Plugins/ComplexCore/src/ComplexCore/Filters/IdentifySample.cpp b/src/Plugins/ComplexCore/src/ComplexCore/Filters/IdentifySample.cpp index 578ec6729b..6090c9d621 100644 --- a/src/Plugins/ComplexCore/src/ComplexCore/Filters/IdentifySample.cpp +++ b/src/Plugins/ComplexCore/src/ComplexCore/Filters/IdentifySample.cpp @@ -264,7 +264,7 @@ Parameters IdentifySample::parameters() const params.insert(std::make_unique(k_FillHoles_Key, "Fill Holes in Largest Feature", "Whether to fill holes within sample after it is identified", true)); params.insert(std::make_unique(k_ImageGeom_Key, "Image Geometry", "DataPath to the target ImageGeom", DataPath(), GeometrySelectionParameter::AllowedTypes{IGeometry::Type::Image})); - params.insert(std::make_unique(k_GoodVoxels_Key, "Mask", "DataPath to the mask array defining what is sample and what is not", DataPath(), + params.insert(std::make_unique(k_MaskArrayPath_Key, "Mask Array", "DataPath to the mask array defining what is sample and what is not", DataPath(), ArraySelectionParameter::AllowedTypes{complex::DataType::boolean, complex::DataType::uint8}, ArraySelectionParameter::AllowedComponentShapes{{1}})); return params; @@ -280,7 +280,7 @@ IFilter::UniquePointer IdentifySample::clone() const IFilter::PreflightResult IdentifySample::preflightImpl(const DataStructure& data, const Arguments& args, const MessageHandler& messageHandler, const std::atomic_bool& shouldCancel) const { const auto imageGeomPath = args.value(k_ImageGeom_Key); - const auto goodVoxelsArrayPath = args.value(k_GoodVoxels_Key); + const auto goodVoxelsArrayPath = args.value(k_MaskArrayPath_Key); const auto& inputData = data.getDataRefAs(goodVoxelsArrayPath); const DataType arrayType = inputData.getDataType(); @@ -299,7 +299,7 @@ Result<> IdentifySample::executeImpl(DataStructure& data, const Arguments& args, { const auto fillHoles = args.value(k_FillHoles_Key); const auto imageGeomPath = args.value(k_ImageGeom_Key); - const auto goodVoxelsArrayPath = args.value(k_GoodVoxels_Key); + const auto goodVoxelsArrayPath = args.value(k_MaskArrayPath_Key); const auto& inputData = data.getDataRefAs(goodVoxelsArrayPath); const DataType arrayType = inputData.getDataType(); diff --git a/src/Plugins/ComplexCore/src/ComplexCore/Filters/IdentifySample.hpp b/src/Plugins/ComplexCore/src/ComplexCore/Filters/IdentifySample.hpp index f089d6b140..76fac1cf04 100644 --- a/src/Plugins/ComplexCore/src/ComplexCore/Filters/IdentifySample.hpp +++ b/src/Plugins/ComplexCore/src/ComplexCore/Filters/IdentifySample.hpp @@ -23,7 +23,7 @@ class COMPLEXCORE_EXPORT IdentifySample : public IFilter // Parameter Keys static inline constexpr StringLiteral k_FillHoles_Key = "fill_holes"; static inline constexpr StringLiteral k_ImageGeom_Key = "image_geometry"; - static inline constexpr StringLiteral k_GoodVoxels_Key = "good_voxels"; + static inline constexpr StringLiteral k_MaskArrayPath_Key = "mask_array_path"; /** * @brief diff --git a/src/Plugins/ComplexCore/src/ComplexCore/Filters/KMeansFilter.cpp b/src/Plugins/ComplexCore/src/ComplexCore/Filters/KMeansFilter.cpp index 0fae499098..9ac3a12283 100644 --- a/src/Plugins/ComplexCore/src/ComplexCore/Filters/KMeansFilter.cpp +++ b/src/Plugins/ComplexCore/src/ComplexCore/Filters/KMeansFilter.cpp @@ -71,8 +71,8 @@ Parameters KMeansFilter::parameters() const params.insertSeparator(Parameters::Separator{"Input Parameters"}); params.insertLinkableParameter(std::make_unique(k_UseMask_Key, "Use Mask", "Specifies whether or not to use a mask array", false)); - params.insert(std::make_unique(k_MaskArrayPath_Key, "Mask", "DataPath to the boolean mask array. Values that are true will mark that cell/point as usable.", DataPath{}, - ArraySelectionParameter::AllowedTypes{DataType::boolean})); + params.insert(std::make_unique(k_MaskArrayPath_Key, "Mask Array", "DataPath to the boolean mask array. Values that are true will mark that cell/point as usable.", + DataPath{}, ArraySelectionParameter::AllowedTypes{DataType::boolean})); params.insert(std::make_unique(k_InitClusters_Key, "Number of Clusters", "This will be the tuple size for Cluster Attribute Matrix and the values within", 0)); params.insert( diff --git a/src/Plugins/ComplexCore/src/ComplexCore/Filters/KMedoidsFilter.cpp b/src/Plugins/ComplexCore/src/ComplexCore/Filters/KMedoidsFilter.cpp index 09239e9717..9a9131d2ab 100644 --- a/src/Plugins/ComplexCore/src/ComplexCore/Filters/KMedoidsFilter.cpp +++ b/src/Plugins/ComplexCore/src/ComplexCore/Filters/KMedoidsFilter.cpp @@ -71,8 +71,8 @@ Parameters KMedoidsFilter::parameters() const params.insertSeparator(Parameters::Separator{"Input Parameters"}); params.insertLinkableParameter(std::make_unique(k_UseMask_Key, "Use Mask", "Specifies whether or not to use a mask array", false)); - params.insert(std::make_unique(k_MaskArrayPath_Key, "Mask", "DataPath to the boolean mask array. Values that are true will mark that cell/point as usable.", DataPath{}, - ArraySelectionParameter::AllowedTypes{DataType::boolean})); + params.insert(std::make_unique(k_MaskArrayPath_Key, "Mask Array", "DataPath to the boolean mask array. Values that are true will mark that cell/point as usable.", + DataPath{}, ArraySelectionParameter::AllowedTypes{DataType::boolean})); params.insert(std::make_unique(k_InitClusters_Key, "Number of Clusters", "This will be the tuple size for Cluster Attribute Matrix and the values within", 0)); params.insert( std::make_unique(k_DistanceMetric_Key, "Distance Metric", "Distance Metric type to be used for calculations", to_underlying(KUtilities::DistanceMetric::Euclidean), diff --git a/src/Plugins/ComplexCore/src/ComplexCore/Filters/PointSampleTriangleGeometryFilter.cpp b/src/Plugins/ComplexCore/src/ComplexCore/Filters/PointSampleTriangleGeometryFilter.cpp index 06d2b7afda..6fd7aa3118 100644 --- a/src/Plugins/ComplexCore/src/ComplexCore/Filters/PointSampleTriangleGeometryFilter.cpp +++ b/src/Plugins/ComplexCore/src/ComplexCore/Filters/PointSampleTriangleGeometryFilter.cpp @@ -69,8 +69,8 @@ Parameters PointSampleTriangleGeometryFilter::parameters() const params.insert(std::make_unique(k_TriangleAreasArrayPath_Key, "Face Areas", "The complete path to the array specifying the area of each Face", DataPath{}, ArraySelectionParameter::AllowedTypes{DataType::float64}, ArraySelectionParameter::AllowedComponentShapes{{1}})); - params.insert(std::make_unique(k_MaskArrayPath_Key, "Mask", "DataPath to the boolean mask array. Values that are true will mark that cell/point as usable.", DataPath{}, - ArraySelectionParameter::AllowedTypes{DataType::boolean}, ArraySelectionParameter::AllowedComponentShapes{{1}})); + params.insert(std::make_unique(k_MaskArrayPath_Key, "Mask Array", "DataPath to the boolean mask array. Values that are true will mark that cell/point as usable.", + DataPath{}, ArraySelectionParameter::AllowedTypes{DataType::boolean}, ArraySelectionParameter::AllowedComponentShapes{{1}})); params.insert(std::make_unique(k_SelectedDataArrayPaths_Key, "Face Attribute Arrays to Transfer", "The paths to the Face Attribute Arrays to transfer to the created Vertex Geometry where the mask is false, if Use Mask is checked", MultiArraySelectionParameter::ValueType{}, MultiArraySelectionParameter::AllowedTypes{IArray::ArrayType::DataArray}, diff --git a/src/Plugins/ComplexCore/src/ComplexCore/Filters/RawBinaryReaderFilter.cpp b/src/Plugins/ComplexCore/src/ComplexCore/Filters/RawBinaryReaderFilter.cpp index 148012f6e6..6c6e00c692 100644 --- a/src/Plugins/ComplexCore/src/ComplexCore/Filters/RawBinaryReaderFilter.cpp +++ b/src/Plugins/ComplexCore/src/ComplexCore/Filters/RawBinaryReaderFilter.cpp @@ -146,14 +146,6 @@ IFilter::PreflightResult RawBinaryReaderFilter::preflightImpl(const DataStructur std::to_string(pSkipHeaderBytesValue), pInputFileValue.string()))}; } - usize numTuples = totalElements / pNumberOfComponentsValue; - - size_t tupleCountFromTable = std::accumulate(tupleDims.begin(), tupleDims.end(), static_cast(1), std::multiplies()); - if(numTuples != tupleCountFromTable) - { - return {MakeErrorResult(k_RbrTupleDimsInconsistent, fmt::format("Total Tuples based on file '{}' does not match total tuples entered. '{}' ", numTuples, tupleCountFromTable))}; - } - // Create the CreateArray action and add it to the resultOutputActions object { auto action = std::make_unique(ConvertNumericTypeToDataType(pScalarTypeValue), tupleDims, std::vector{pNumberOfComponentsValue}, pCreatedAttributeArrayPathValue); @@ -161,6 +153,15 @@ IFilter::PreflightResult RawBinaryReaderFilter::preflightImpl(const DataStructur resultOutputActions.value().appendAction(std::move(action)); } + usize numTuples = totalElements / pNumberOfComponentsValue; + size_t tupleCountFromTable = std::accumulate(tupleDims.begin(), tupleDims.end(), static_cast(1), std::multiplies()); + if(numTuples != tupleCountFromTable) + { + const std::string warningMessage = fmt::format("Total Tuples based on file '{}' does not match total tuples entered. '{}'. Reading a subsection of the file.", numTuples, tupleCountFromTable); + + resultOutputActions.warnings().push_back({k_RbrTupleDimsInconsistent, warningMessage}); + } + return {std::move(resultOutputActions)}; } diff --git a/src/Plugins/ComplexCore/src/ComplexCore/Filters/ScalarSegmentFeaturesFilter.cpp b/src/Plugins/ComplexCore/src/ComplexCore/Filters/ScalarSegmentFeaturesFilter.cpp index f07d6f2270..69a4832ae6 100644 --- a/src/Plugins/ComplexCore/src/ComplexCore/Filters/ScalarSegmentFeaturesFilter.cpp +++ b/src/Plugins/ComplexCore/src/ComplexCore/Filters/ScalarSegmentFeaturesFilter.cpp @@ -67,10 +67,10 @@ Parameters ScalarSegmentFeaturesFilter::parameters() const params.insertSeparator(Parameters::Separator{"Segmentation Parameters"}); params.insert(std::make_unique>(k_ScalarToleranceKey, "Scalar Tolerance", "Tolerance for segmenting input Cell Data", 1)); params.insert(std::make_unique(k_RandomizeFeatures_Key, "Randomize Feature IDs", "Specifies if feature IDs should be randomized during calculations", false)); - params.insertLinkableParameter(std::make_unique(k_UseGoodVoxelsKey, "Use Mask Array", "Determines if a mask array is used for segmenting", false)); - params.insert(std::make_unique(k_GoodVoxelsPath_Key, "Mask", "Path to the DataArray Mask", DataPath(), ArraySelectionParameter::AllowedTypes{DataType::boolean}, + params.insertLinkableParameter(std::make_unique(k_UseMask_Key, "Use Mask Array", "Determines if a mask array is used for segmenting", false)); + params.insert(std::make_unique(k_MaskArrayPath_Key, "Mask Array", "Path to the DataArray Mask", DataPath(), ArraySelectionParameter::AllowedTypes{DataType::boolean}, ArraySelectionParameter::AllowedComponentShapes{{1}})); - params.linkParameters(k_UseGoodVoxelsKey, k_GoodVoxelsPath_Key, std::make_any(true)); + params.linkParameters(k_UseMask_Key, k_MaskArrayPath_Key, std::make_any(true)); params.insertSeparator(Parameters::Separator{"Required Input Cell Data"}); params.insert(std::make_unique(k_GridGeomPath_Key, "Grid Geometry", "DataPath to target Grid Geometry", DataPath{})); @@ -102,11 +102,11 @@ IFilter::PreflightResult ScalarSegmentFeaturesFilter::preflightImpl(const DataSt auto activeArrayName = args.value(k_ActiveArrayPathKey); DataPath featureIdsPath = inputDataPath.getParent().createChildPath(featureIdsName); - bool useGoodVoxels = args.value(k_UseGoodVoxelsKey); + bool useGoodVoxels = args.value(k_UseMask_Key); DataPath goodVoxelsPath; if(useGoodVoxels) { - goodVoxelsPath = args.value(k_GoodVoxelsPath_Key); + goodVoxelsPath = args.value(k_MaskArrayPath_Key); } auto gridGeomPath = args.value(k_GridGeomPath_Key); @@ -193,8 +193,8 @@ Result<> ScalarSegmentFeaturesFilter::executeImpl(DataStructure& data, const Arg inputValues.pScalarTolerance = args.value(k_ScalarToleranceKey); inputValues.pShouldRandomizeFeatureIds = args.value(k_RandomizeFeatures_Key); inputValues.pFeatureIdsPath = inputValues.pInputDataPath.getParent().createChildPath(args.value(k_FeatureIdsPathKey)); - inputValues.pUseGoodVoxels = args.value(k_UseGoodVoxelsKey); - inputValues.pGoodVoxelsPath = args.value(k_GoodVoxelsPath_Key); + inputValues.pUseGoodVoxels = args.value(k_UseMask_Key); + inputValues.pGoodVoxelsPath = args.value(k_MaskArrayPath_Key); inputValues.pGridGeomPath = args.value(k_GridGeomPath_Key); inputValues.pCellFeaturesPath = inputValues.pGridGeomPath.createChildPath(args.value(k_CellFeaturePathKey)); inputValues.pActiveArrayPath = inputValues.pCellFeaturesPath.createChildPath(args.value(k_ActiveArrayPathKey)); diff --git a/src/Plugins/ComplexCore/src/ComplexCore/Filters/ScalarSegmentFeaturesFilter.hpp b/src/Plugins/ComplexCore/src/ComplexCore/Filters/ScalarSegmentFeaturesFilter.hpp index 2bf48ce0ef..6c3b8b8d27 100644 --- a/src/Plugins/ComplexCore/src/ComplexCore/Filters/ScalarSegmentFeaturesFilter.hpp +++ b/src/Plugins/ComplexCore/src/ComplexCore/Filters/ScalarSegmentFeaturesFilter.hpp @@ -31,8 +31,8 @@ class COMPLEXCORE_EXPORT ScalarSegmentFeaturesFilter : public IFilter static inline constexpr StringLiteral k_GridGeomPath_Key = "grid_geometry_path"; static inline constexpr StringLiteral k_ScalarToleranceKey = "scalar_tolerance"; static inline constexpr StringLiteral k_InputArrayPathKey = "input_array_path"; - static inline constexpr StringLiteral k_UseGoodVoxelsKey = "use_mask"; - static inline constexpr StringLiteral k_GoodVoxelsPath_Key = "mask_path"; + static inline constexpr StringLiteral k_UseMask_Key = "use_mask"; + static inline constexpr StringLiteral k_MaskArrayPath_Key = "mask_path"; static inline constexpr StringLiteral k_FeatureIdsPathKey = "feature_ids_path"; static inline constexpr StringLiteral k_CellFeaturePathKey = "cell_feature_group_path"; static inline constexpr StringLiteral k_ActiveArrayPathKey = "active_array_path"; diff --git a/src/Plugins/ComplexCore/src/ComplexCore/Filters/SilhouetteFilter.cpp b/src/Plugins/ComplexCore/src/ComplexCore/Filters/SilhouetteFilter.cpp index 6c3faf1235..2d2f0a823e 100644 --- a/src/Plugins/ComplexCore/src/ComplexCore/Filters/SilhouetteFilter.cpp +++ b/src/Plugins/ComplexCore/src/ComplexCore/Filters/SilhouetteFilter.cpp @@ -61,8 +61,8 @@ Parameters SilhouetteFilter::parameters() const // Create the parameter descriptors that are needed for this filter params.insertSeparator(Parameters::Separator{"Optional Parameters"}); params.insertLinkableParameter(std::make_unique(k_UseMask_Key, "Use Mask", "Specifies whether or not to use a mask array", false)); - params.insert(std::make_unique(k_MaskArrayPath_Key, "Mask", "DataPath to the boolean mask array. Values that are true will mark that cell/point as usable.", DataPath{}, - ArraySelectionParameter::AllowedTypes{DataType::boolean})); + params.insert(std::make_unique(k_MaskArrayPath_Key, "Mask Array", "DataPath to the boolean mask array. Values that are true will mark that cell/point as usable.", + DataPath{}, ArraySelectionParameter::AllowedTypes{DataType::boolean})); params.insertSeparator(Parameters::Separator{"Input Parameters"}); params.insert( diff --git a/src/Plugins/ComplexCore/test/AlignSectionsFeatureCentroidTest.cpp b/src/Plugins/ComplexCore/test/AlignSectionsFeatureCentroidTest.cpp index 76dfd093e8..6cebdb7497 100644 --- a/src/Plugins/ComplexCore/test/AlignSectionsFeatureCentroidTest.cpp +++ b/src/Plugins/ComplexCore/test/AlignSectionsFeatureCentroidTest.cpp @@ -56,7 +56,7 @@ TEST_CASE("ComplexCore::AlignSectionsFeatureCentroidFilter", "[Reconstruction][A constexpr StringLiteral k_AlignmentShiftFileName_Key = "alignment_shift_file_name"; constexpr StringLiteral k_UseReferenceSlice_Key = "use_reference_slice"; constexpr StringLiteral k_ReferenceSlice_Key = "reference_slice"; - constexpr StringLiteral k_GoodVoxelsArrayPath_Key = "good_voxels_array_path"; + constexpr StringLiteral k_MaskArrayPath_Key = "mask_array_path"; constexpr StringLiteral k_SelectedImageGeometry_Key = "selected_image_geometry_path"; constexpr StringLiteral k_SelectedCellDataGroup_Key = "selected_cell_data_path"; @@ -66,7 +66,7 @@ TEST_CASE("ComplexCore::AlignSectionsFeatureCentroidFilter", "[Reconstruction][A args.insertOrAssign(k_AlignmentShiftFileName_Key, std::make_any(computedShiftsFile)); args.insertOrAssign(k_UseReferenceSlice_Key, std::make_any(true)); args.insertOrAssign(k_ReferenceSlice_Key, std::make_any(0)); - args.insertOrAssign(k_GoodVoxelsArrayPath_Key, std::make_any(k_MaskArrayPath)); + args.insertOrAssign(k_MaskArrayPath_Key, std::make_any(k_MaskArrayPath)); args.insertOrAssign(k_SelectedImageGeometry_Key, std::make_any(k_DataContainerPath)); args.insertOrAssign(k_SelectedCellDataGroup_Key, std::make_any(k_CellAttributeMatrix)); diff --git a/src/Plugins/ComplexCore/test/FindFeaturePhasesBinaryTest.cpp b/src/Plugins/ComplexCore/test/FindFeaturePhasesBinaryTest.cpp index c3dc1534a9..ad4674bd22 100644 --- a/src/Plugins/ComplexCore/test/FindFeaturePhasesBinaryTest.cpp +++ b/src/Plugins/ComplexCore/test/FindFeaturePhasesBinaryTest.cpp @@ -28,7 +28,7 @@ TEST_CASE("ComplexCore::FindFeaturePhasesBinaryFilter: Valid Filter Execution", // Create default Parameters for the filter. args.insertOrAssign(FindFeaturePhasesBinaryFilter::k_FeatureIdsArrayPath_Key, std::make_any(DataPath({Constants::k_SmallIN100, Constants::k_EbsdScanData, Constants::k_FeatureIds}))); - args.insertOrAssign(FindFeaturePhasesBinaryFilter::k_GoodVoxelsArrayPath_Key, std::make_any(DataPath({Constants::k_SmallIN100, Constants::k_EbsdScanData, Constants::k_Mask}))); + args.insertOrAssign(FindFeaturePhasesBinaryFilter::k_MaskArrayPath_Key, std::make_any(DataPath({Constants::k_SmallIN100, Constants::k_EbsdScanData, Constants::k_Mask}))); args.insertOrAssign(FindFeaturePhasesBinaryFilter::k_CellDataAMPath_Key, std::make_any(DataPath({Constants::k_SmallIN100, Constants::k_EbsdScanData}))); args.insertOrAssign(FindFeaturePhasesBinaryFilter::k_FeaturePhasesArrayName_Key, std::make_any(k_BinaryFeaturePhasesName)); diff --git a/src/Plugins/ComplexCore/test/GenerateVectorColorsTest.cpp b/src/Plugins/ComplexCore/test/GenerateVectorColorsTest.cpp index 1918846645..a8f5690f3c 100644 --- a/src/Plugins/ComplexCore/test/GenerateVectorColorsTest.cpp +++ b/src/Plugins/ComplexCore/test/GenerateVectorColorsTest.cpp @@ -24,7 +24,7 @@ TEST_CASE("ComplexCore::GenerateVectorColorsFilter: Valid Filter Execution", "[C Arguments args; // Create default Parameters for the filter. - args.insertOrAssign(GenerateVectorColorsFilter::k_UseGoodVoxels_Key, std::make_any(false)); + args.insertOrAssign(GenerateVectorColorsFilter::k_UseMask_Key, std::make_any(false)); args.insertOrAssign(GenerateVectorColorsFilter::k_VectorsArrayPath_Key, std::make_any(eulerAnglesPath)); args.insertOrAssign(GenerateVectorColorsFilter::k_CellVectorColorsArrayName_Key, std::make_any(k_VecColorsNX)); diff --git a/src/Plugins/ComplexCore/test/IdentifySampleTest.cpp b/src/Plugins/ComplexCore/test/IdentifySampleTest.cpp index 09d77b0aab..244f399dc8 100644 --- a/src/Plugins/ComplexCore/test/IdentifySampleTest.cpp +++ b/src/Plugins/ComplexCore/test/IdentifySampleTest.cpp @@ -17,7 +17,7 @@ TEST_CASE("ComplexCore::IdentifySample : Valid filter execution", "[ComplexCore] IdentifySample filter; Arguments args; args.insert(IdentifySample::k_ImageGeom_Key, std::make_any(Constants::k_DataContainerPath)); - args.insert(IdentifySample::k_GoodVoxels_Key, std::make_any(Constants::k_MaskArrayPath)); + args.insert(IdentifySample::k_MaskArrayPath_Key, std::make_any(Constants::k_MaskArrayPath)); std::string k_ExemplarDataContainerName; @@ -57,7 +57,7 @@ TEST_CASE("ComplexCore::IdentifySample : Invalid filter execution", "[ComplexCor Arguments args; args.insert(IdentifySample::k_FillHoles_Key, std::make_any(false)); args.insert(IdentifySample::k_ImageGeom_Key, std::make_any(Constants::k_DataContainerPath)); - args.insert(IdentifySample::k_GoodVoxels_Key, std::make_any(Constants::k_CellAttributeMatrix.createChildPath(k_InvalidMaskArrayName))); + args.insert(IdentifySample::k_MaskArrayPath_Key, std::make_any(Constants::k_CellAttributeMatrix.createChildPath(k_InvalidMaskArrayName))); // Preflight the filter and check result auto preflightResult = filter.preflight(dataStructure, args); diff --git a/src/Plugins/ComplexCore/test/ScalarSegmentFeaturesFilterTest.cpp b/src/Plugins/ComplexCore/test/ScalarSegmentFeaturesFilterTest.cpp index 0d9618128a..3e520ee0a0 100644 --- a/src/Plugins/ComplexCore/test/ScalarSegmentFeaturesFilterTest.cpp +++ b/src/Plugins/ComplexCore/test/ScalarSegmentFeaturesFilterTest.cpp @@ -41,8 +41,8 @@ TEST_CASE("ComplexCore::ScalarSegmentFeatures", "[Reconstruction][ScalarSegmentF // Create default Parameters for the filter. args.insertOrAssign(ScalarSegmentFeaturesFilter::k_GridGeomPath_Key, std::make_any(gridGeomDataPath)); // Turn off the use of a Mask Array - args.insertOrAssign(ScalarSegmentFeaturesFilter::k_UseGoodVoxelsKey, std::make_any(false)); - args.insertOrAssign(ScalarSegmentFeaturesFilter::k_GoodVoxelsPath_Key, std::make_any(DataPath{})); + args.insertOrAssign(ScalarSegmentFeaturesFilter::k_UseMask_Key, std::make_any(false)); + args.insertOrAssign(ScalarSegmentFeaturesFilter::k_MaskArrayPath_Key, std::make_any(DataPath{})); // Set the input array and the tolerance args.insertOrAssign(ScalarSegmentFeaturesFilter::k_InputArrayPathKey, std::make_any(inputDataArrayPath)); args.insertOrAssign(ScalarSegmentFeaturesFilter::k_ScalarToleranceKey, std::make_any(scalarTolerance)); diff --git a/src/Plugins/OrientationAnalysis/pipelines/AlignSectionsMutualInformation.d3dpipeline b/src/Plugins/OrientationAnalysis/pipelines/AlignSectionsMutualInformation.d3dpipeline index 8e620543ac..338e5c8b4c 100644 --- a/src/Plugins/OrientationAnalysis/pipelines/AlignSectionsMutualInformation.d3dpipeline +++ b/src/Plugins/OrientationAnalysis/pipelines/AlignSectionsMutualInformation.d3dpipeline @@ -86,11 +86,11 @@ "alignment_shift_file_name": "Data/Output/OrientationAnalysis/Alignment_By_Mutual_Information_Shifts.txt", "cell_phases_array_path": "DataContainer/CellData/Phases", "crystal_structures_array_path": "DataContainer/CellEnsembleData/CrystalStructures", - "good_voxels_array_path": "DataContainer/CellData/Mask", + "mask_array_path": "DataContainer/CellData/Mask", "misorientation_tolerance": 5.0, "quats_array_path": "DataContainer/CellData/Quats", "selected_image_geometry_path": "DataContainer", - "use_good_voxels": true, + "use_mask": true, "write_alignment_shifts": true }, "comments": "", diff --git a/src/Plugins/OrientationAnalysis/pipelines/EBSD Reconstruction/(08) Small IN100 Full Reconstruction.d3dpipeline b/src/Plugins/OrientationAnalysis/pipelines/EBSD Reconstruction/(08) Small IN100 Full Reconstruction.d3dpipeline index 61c8108a69..00555e0600 100644 --- a/src/Plugins/OrientationAnalysis/pipelines/EBSD Reconstruction/(08) Small IN100 Full Reconstruction.d3dpipeline +++ b/src/Plugins/OrientationAnalysis/pipelines/EBSD Reconstruction/(08) Small IN100 Full Reconstruction.d3dpipeline @@ -86,11 +86,11 @@ "alignment_shift_file_name": "Data/Output/Alignment_By_Misorientation_Shifts.txt", "cell_phases_array_path": "DataContainer/CellData/Phases", "crystal_structures_array_path": "DataContainer/CellEnsembleData/CrystalStructures", - "good_voxels_array_path": "DataContainer/CellData/Mask", + "mask_array_path": "DataContainer/CellData/Mask", "misorientation_tolerance": 5.0, "quats_array_path": "DataContainer/CellData/Quats", "selected_image_geometry_path": "DataContainer", - "use_good_voxels": true, + "use_mask": true, "write_alignment_shifts": false }, "comments": "", @@ -103,7 +103,7 @@ { "args": { "fill_holes": false, - "good_voxels": "DataContainer/CellData/Mask", + "mask_array_path": "DataContainer/CellData/Mask", "image_geometry": "DataContainer" }, "comments": "", @@ -116,7 +116,7 @@ { "args": { "alignment_shift_file_name": "Data/Output/Alignment_By_Feature_Centroid_Shifts.txt", - "good_voxels_array_path": "DataContainer/CellData/Mask", + "mask_array_path": "DataContainer/CellData/Mask", "reference_slice": 0, "selected_cell_data_path": "DataContainer/CellData", "selected_image_geometry_path": "DataContainer", @@ -134,7 +134,7 @@ "args": { "cell_phases_array_path": "DataContainer/CellData/Phases", "crystal_structures_array_path": "DataContainer/CellEnsembleData/CrystalStructures", - "good_voxels_array_path": "DataContainer/CellData/Mask", + "mask_array_path": "DataContainer/CellData/Mask", "image_geometry_path": "DataContainer", "misorientation_tolerance": 5.0, "number_of_neighbors": 4, @@ -173,12 +173,12 @@ "cell_phases_array_path": "DataContainer/CellData/Phases", "crystal_structures_array_path": "DataContainer/CellEnsembleData/CrystalStructures", "feature_ids_array_name": "FeatureIds", - "good_voxels_array_path": "DataContainer/CellData/Mask", + "mask_array_path": "DataContainer/CellData/Mask", "grid_geometry_path": "DataContainer", "misorientation_tolerance": 5.0, "quats_array_path": "DataContainer/CellData/Quats", "randomize_features": true, - "use_good_voxels": true + "use_mask": true }, "comments": "", "filter": { @@ -395,13 +395,13 @@ "cell_ipf_colors_array_name": "IPFColors", "cell_phases_array_path": "DataContainer/CellData/Phases", "crystal_structures_array_path": "DataContainer/CellEnsembleData/CrystalStructures", - "good_voxels_array_path": "DataContainer/CellData/Mask", + "mask_array_path": "DataContainer/CellData/Mask", "reference_dir": [ 0.0, 0.0, 1.0 ], - "use_good_voxels": true + "use_mask": true }, "comments": "", "filter": { diff --git a/src/Plugins/OrientationAnalysis/pipelines/EBSD Statistics/(05) Small IN100 Crystallographic Statistics.d3dpipeline b/src/Plugins/OrientationAnalysis/pipelines/EBSD Statistics/(05) Small IN100 Crystallographic Statistics.d3dpipeline index 173b8d39d3..81fe2cdfca 100644 --- a/src/Plugins/OrientationAnalysis/pipelines/EBSD Statistics/(05) Small IN100 Crystallographic Statistics.d3dpipeline +++ b/src/Plugins/OrientationAnalysis/pipelines/EBSD Statistics/(05) Small IN100 Crystallographic Statistics.d3dpipeline @@ -173,11 +173,11 @@ "alignment_shift_file_name": "Data/Output/Alignment_By_Misorientation_Shifts.txt", "cell_phases_array_path": "DataContainer/CellData/Phases", "crystal_structures_array_path": "DataContainer/CellEnsembleData/CrystalStructures", - "good_voxels_array_path": "DataContainer/CellData/Mask", + "mask_array_path": "DataContainer/CellData/Mask", "misorientation_tolerance": 5.0, "quats_array_path": "DataContainer/CellData/Quats", "selected_image_geometry_path": "DataContainer", - "use_good_voxels": true, + "use_mask": true, "write_alignment_shifts": false }, "comments": "", @@ -190,7 +190,7 @@ { "args": { "fill_holes": false, - "good_voxels": "DataContainer/CellData/Mask", + "mask_array_path": "DataContainer/CellData/Mask", "image_geometry": "DataContainer" }, "comments": "", @@ -203,7 +203,7 @@ { "args": { "alignment_shift_file_name": "Data/Output/Alignment_By_Feature_Centroid_Shifts.txt", - "good_voxels_array_path": "DataContainer/CellData/Mask", + "mask_array_path": "DataContainer/CellData/Mask", "reference_slice": 0, "selected_cell_data_path": "DataContainer/CellData", "selected_image_geometry_path": "DataContainer", @@ -221,7 +221,7 @@ "args": { "cell_phases_array_path": "DataContainer/CellData/Phases", "crystal_structures_array_path": "DataContainer/CellEnsembleData/CrystalStructures", - "good_voxels_array_path": "DataContainer/CellData/Mask", + "mask_array_path": "DataContainer/CellData/Mask", "image_geometry_path": "DataContainer", "misorientation_tolerance": 5.0, "number_of_neighbors": 4, @@ -260,12 +260,12 @@ "cell_phases_array_path": "DataContainer/CellData/Phases", "crystal_structures_array_path": "DataContainer/CellEnsembleData/CrystalStructures", "feature_ids_array_name": "FeatureIds", - "good_voxels_array_path": "DataContainer/CellData/Mask", + "mask_array_path": "DataContainer/CellData/Mask", "grid_geometry_path": "DataContainer", "misorientation_tolerance": 5.0, "quats_array_path": "DataContainer/CellData/Quats", "randomize_features": true, - "use_good_voxels": true + "use_mask": true }, "comments": "", "filter": { @@ -479,13 +479,13 @@ "cell_ipf_colors_array_name": "IPFColors", "cell_phases_array_path": "DataContainer/CellData/Phases", "crystal_structures_array_path": "DataContainer/CellEnsembleData/CrystalStructures", - "good_voxels_array_path": "DataContainer/CellData/Mask", + "mask_array_path": "DataContainer/CellData/Mask", "reference_dir": [ 0.0, 0.0, 1.0 ], - "use_good_voxels": true + "use_mask": true }, "comments": "", "filter": { diff --git a/src/Plugins/OrientationAnalysis/pipelines/Edax_IPF_Colors.d3dpipeline b/src/Plugins/OrientationAnalysis/pipelines/Edax_IPF_Colors.d3dpipeline index 08cd2272a0..505859a37d 100644 --- a/src/Plugins/OrientationAnalysis/pipelines/Edax_IPF_Colors.d3dpipeline +++ b/src/Plugins/OrientationAnalysis/pipelines/Edax_IPF_Colors.d3dpipeline @@ -104,13 +104,13 @@ "cell_ipf_colors_array_name": "IPFColors", "cell_phases_array_path": "DataContainer/Cell Data/Phases", "crystal_structures_array_path": "DataContainer/CellEnsembleData/CrystalStructures", - "good_voxels_array_path": "DataContainer/Cell Data/Mask", + "mask_array_path": "DataContainer/Cell Data/Mask", "reference_dir": [ 0.0, 0.0, 1.0 ], - "use_good_voxels": true + "use_mask": true }, "comments": "", "filter": { diff --git a/src/Plugins/OrientationAnalysis/pipelines/EnsembleInfoReader.d3dpipeline b/src/Plugins/OrientationAnalysis/pipelines/EnsembleInfoReader.d3dpipeline index 4e6b9ce9bb..52a4e0fdbf 100644 --- a/src/Plugins/OrientationAnalysis/pipelines/EnsembleInfoReader.d3dpipeline +++ b/src/Plugins/OrientationAnalysis/pipelines/EnsembleInfoReader.d3dpipeline @@ -109,13 +109,13 @@ "cell_ipf_colors_array_name": "IPFColors", "cell_phases_array_path": "[Image Geometry]/Cell Data/Phases", "crystal_structures_array_path": "[Image Geometry]/Cell Ensemble/CrystalStructures", - "good_voxels_array_path": "", + "mask_array_path": "", "reference_dir": [ 0.0, 0.0, 1.0 ], - "use_good_voxels": false + "use_mask": false }, "comments": "", "filter": { diff --git a/src/Plugins/OrientationAnalysis/pipelines/FindGBCD-GBPDMetricBased.d3dpipeline b/src/Plugins/OrientationAnalysis/pipelines/FindGBCD-GBPDMetricBased.d3dpipeline index 21aae0488a..858ecf9f69 100644 --- a/src/Plugins/OrientationAnalysis/pipelines/FindGBCD-GBPDMetricBased.d3dpipeline +++ b/src/Plugins/OrientationAnalysis/pipelines/FindGBCD-GBPDMetricBased.d3dpipeline @@ -429,11 +429,11 @@ "alignment_shift_file_name": "Data/Output/Alignment_By_Misorientation_Shifts.txt", "cell_phases_array_path": "DataContainer/CellData/Phases", "crystal_structures_array_path": "DataContainer/CellEnsembleData/CrystalStructures", - "good_voxels_array_path": "DataContainer/CellData/Mask", + "mask_array_path": "DataContainer/CellData/Mask", "misorientation_tolerance": 5.0, "quats_array_path": "DataContainer/CellData/Quats", "selected_image_geometry_path": "DataContainer", - "use_good_voxels": true, + "use_mask": true, "write_alignment_shifts": false }, "comments": "", @@ -446,7 +446,7 @@ { "args": { "fill_holes": false, - "good_voxels": "DataContainer/CellData/Mask", + "mask_array_path": "DataContainer/CellData/Mask", "image_geometry": "DataContainer" }, "comments": "", @@ -459,7 +459,7 @@ { "args": { "alignment_shift_file_name": "Data/Output/Alignment_By_Feature_Centroid_Shifts.txt", - "good_voxels_array_path": "DataContainer/CellData/Mask", + "mask_array_path": "DataContainer/CellData/Mask", "reference_slice": 0, "selected_cell_data_path": "DataContainer/CellData", "selected_image_geometry_path": "DataContainer", @@ -477,7 +477,7 @@ "args": { "cell_phases_array_path": "DataContainer/CellData/Phases", "crystal_structures_array_path": "DataContainer/CellEnsembleData/CrystalStructures", - "good_voxels_array_path": "DataContainer/CellData/Mask", + "mask_array_path": "DataContainer/CellData/Mask", "image_geometry_path": "DataContainer", "misorientation_tolerance": 5.0, "number_of_neighbors": 4, @@ -516,12 +516,12 @@ "cell_phases_array_path": "DataContainer/CellData/Phases", "crystal_structures_array_path": "DataContainer/CellEnsembleData/CrystalStructures", "feature_ids_array_name": "FeatureIds", - "good_voxels_array_path": "DataContainer/CellData/Mask", + "mask_array_path": "DataContainer/CellData/Mask", "grid_geometry_path": "DataContainer", "misorientation_tolerance": 5.0, "quats_array_path": "DataContainer/CellData/Quats", "randomize_features": true, - "use_good_voxels": true + "use_mask": true }, "comments": "", "filter": { @@ -735,13 +735,13 @@ "cell_ipf_colors_array_name": "IPFColors", "cell_phases_array_path": "DataContainer/CellData/Phases", "crystal_structures_array_path": "DataContainer/CellEnsembleData/CrystalStructures", - "good_voxels_array_path": "DataContainer/CellData/Mask", + "mask_array_path": "DataContainer/CellData/Mask", "reference_dir": [ 0.0, 0.0, 1.0 ], - "use_good_voxels": true + "use_mask": true }, "comments": "", "filter": { diff --git a/src/Plugins/OrientationAnalysis/pipelines/ReadAng.d3dpipeline b/src/Plugins/OrientationAnalysis/pipelines/ReadAng.d3dpipeline index 2456008ab5..b7a961cc47 100644 --- a/src/Plugins/OrientationAnalysis/pipelines/ReadAng.d3dpipeline +++ b/src/Plugins/OrientationAnalysis/pipelines/ReadAng.d3dpipeline @@ -108,13 +108,13 @@ "cell_ipf_colors_array_name": "IPFColors", "cell_phases_array_path": "DataContainer/Cell Data/Phases", "crystal_structures_array_path": "DataContainer/Cell Ensemble Data/CrystalStructures", - "good_voxels_array_path": "", + "mask_array_path": "", "reference_dir": [ 0.0, 0.0, 1.0 ], - "use_good_voxels": false + "use_mask": false }, "comments": "", "filter": { diff --git a/src/Plugins/OrientationAnalysis/pipelines/ReadCTF.d3dpipeline b/src/Plugins/OrientationAnalysis/pipelines/ReadCTF.d3dpipeline index c0dd481341..d8cd20520d 100644 --- a/src/Plugins/OrientationAnalysis/pipelines/ReadCTF.d3dpipeline +++ b/src/Plugins/OrientationAnalysis/pipelines/ReadCTF.d3dpipeline @@ -102,13 +102,13 @@ "cell_ipf_colors_array_name": "IPFColors", "cell_phases_array_path": "DataContainer/Cell Data/Phases", "crystal_structures_array_path": "DataContainer/CellEnsembleData/CrystalStructures", - "good_voxels_array_path": "DataContainer/Cell Data/Mask", + "mask_array_path": "DataContainer/Cell Data/Mask", "reference_dir": [ 0.0, 0.0, 1.0 ], - "use_good_voxels": true + "use_mask": true }, "comments": "", "filter": { diff --git a/src/Plugins/OrientationAnalysis/pipelines/TxCopper_Exposed.d3dpipeline b/src/Plugins/OrientationAnalysis/pipelines/TxCopper_Exposed.d3dpipeline index c035467f9f..ff02254d93 100644 --- a/src/Plugins/OrientationAnalysis/pipelines/TxCopper_Exposed.d3dpipeline +++ b/src/Plugins/OrientationAnalysis/pipelines/TxCopper_Exposed.d3dpipeline @@ -116,13 +116,13 @@ "cell_ipf_colors_array_name": "IPF_Exposed_001", "cell_phases_array_path": "Cugrid_after 2nd_15kv_2kx_2/EBSD Scan Data/Phases", "crystal_structures_array_path": "Cugrid_after 2nd_15kv_2kx_2/Phase Data/CrystalStructures", - "good_voxels_array_path": "Cugrid_after 2nd_15kv_2kx_2/EBSD Scan Data/Mask", + "mask_array_path": "Cugrid_after 2nd_15kv_2kx_2/EBSD Scan Data/Mask", "reference_dir": [ 0.0, 0.0, 1.0 ], - "use_good_voxels": true + "use_mask": true }, "comments": "", "filter": { @@ -152,7 +152,7 @@ "cell_phases_array_path": "Cugrid_after 2nd_15kv_2kx_2/EBSD Scan Data/Phases", "crystal_structures_array_path": "Cugrid_after 2nd_15kv_2kx_2/Phase Data/CrystalStructures", "generation_algorithm": 0, - "good_voxels_array_path": "Cugrid_after 2nd_15kv_2kx_2/EBSD Scan Data/Mask", + "mask_array_path": "Cugrid_after 2nd_15kv_2kx_2/EBSD Scan Data/Mask", "image_geometry_path": "PoleFigure", "image_layout": 2, "image_prefix": "Cugrid_after 2nd_15kv_2kx_2_Exposed_", @@ -163,7 +163,7 @@ "output_path": "Data/Output/TexturedCopper", "save_as_image_geometry": true, "title": "Cugrid_after 2nd_15kv_2kx_2 Exposed", - "use_good_voxels": true, + "use_mask": true, "write_image_to_disk": true }, "comments": "", diff --git a/src/Plugins/OrientationAnalysis/pipelines/TxCopper_Unexposed.d3dpipeline b/src/Plugins/OrientationAnalysis/pipelines/TxCopper_Unexposed.d3dpipeline index 7adc57c9e1..23a7e8f16c 100644 --- a/src/Plugins/OrientationAnalysis/pipelines/TxCopper_Unexposed.d3dpipeline +++ b/src/Plugins/OrientationAnalysis/pipelines/TxCopper_Unexposed.d3dpipeline @@ -116,13 +116,13 @@ "cell_ipf_colors_array_name": "IPF_Unexposed_001", "cell_phases_array_path": "Cugrid_after 2nd_15kv_2kx_2/EBSD Scan Data/Phases", "crystal_structures_array_path": "Cugrid_after 2nd_15kv_2kx_2/Phase Data/CrystalStructures", - "good_voxels_array_path": "Cugrid_after 2nd_15kv_2kx_2/EBSD Scan Data/Mask", + "mask_array_path": "Cugrid_after 2nd_15kv_2kx_2/EBSD Scan Data/Mask", "reference_dir": [ 0.0, 0.0, 1.0 ], - "use_good_voxels": true + "use_mask": true }, "comments": "", "filter": { @@ -152,7 +152,7 @@ "cell_phases_array_path": "Cugrid_after 2nd_15kv_2kx_2/EBSD Scan Data/Phases", "crystal_structures_array_path": "Cugrid_after 2nd_15kv_2kx_2/Phase Data/CrystalStructures", "generation_algorithm": 0, - "good_voxels_array_path": "Cugrid_after 2nd_15kv_2kx_2/EBSD Scan Data/Mask", + "mask_array_path": "Cugrid_after 2nd_15kv_2kx_2/EBSD Scan Data/Mask", "image_geometry_path": "PoleFigure", "image_layout": 2, "image_prefix": "Cugrid_after 2nd_15kv_2kx_2_Unexposed_", @@ -163,7 +163,7 @@ "output_path": "Data/Output/TexturedCopper", "save_as_image_geometry": true, "title": "Cugrid_after 2nd_15kv_2kx_2 Unexposed", - "use_good_voxels": true, + "use_mask": true, "write_image_to_disk": true }, "comments": "", diff --git a/src/Plugins/OrientationAnalysis/pipelines/aptr12_Analysis.d3dpipeline b/src/Plugins/OrientationAnalysis/pipelines/aptr12_Analysis.d3dpipeline index e8979dd70d..6ef83799b0 100644 --- a/src/Plugins/OrientationAnalysis/pipelines/aptr12_Analysis.d3dpipeline +++ b/src/Plugins/OrientationAnalysis/pipelines/aptr12_Analysis.d3dpipeline @@ -127,13 +127,13 @@ "cell_ipf_colors_array_name": "IPF_001", "cell_phases_array_path": "fw-ar-IF1-aptr12-corr/Cell Data/Phases", "crystal_structures_array_path": "fw-ar-IF1-aptr12-corr/CellEnsembleData/CrystalStructures", - "good_voxels_array_path": "", + "mask_array_path": "", "reference_dir": [ 0.0, 0.0, 1.0 ], - "use_good_voxels": false + "use_mask": false }, "comments": "", "filter": { @@ -163,13 +163,13 @@ "cell_ipf_colors_array_name": "IPF_010", "cell_phases_array_path": "fw-ar-IF1-aptr12-corr/Cell Data/Phases", "crystal_structures_array_path": "fw-ar-IF1-aptr12-corr/CellEnsembleData/CrystalStructures", - "good_voxels_array_path": "", + "mask_array_path": "", "reference_dir": [ 0.0, 1.0, 0.0 ], - "use_good_voxels": false + "use_mask": false }, "comments": "", "filter": { @@ -199,13 +199,13 @@ "cell_ipf_colors_array_name": "IPF_100", "cell_phases_array_path": "fw-ar-IF1-aptr12-corr/Cell Data/Phases", "crystal_structures_array_path": "fw-ar-IF1-aptr12-corr/CellEnsembleData/CrystalStructures", - "good_voxels_array_path": "", + "mask_array_path": "", "reference_dir": [ 1.0, 0.0, 0.0 ], - "use_good_voxels": false + "use_mask": false }, "comments": "", "filter": { @@ -236,12 +236,12 @@ "cell_phases_array_path": "fw-ar-IF1-aptr12-corr/Cell Data/Phases", "crystal_structures_array_path": "fw-ar-IF1-aptr12-corr/CellEnsembleData/CrystalStructures", "feature_ids_array_name": "FeatureIds", - "good_voxels_array_path": "fw-ar-IF1-aptr12-corr/Cell Data/ThresholdArray", + "mask_array_path": "fw-ar-IF1-aptr12-corr/Cell Data/ThresholdArray", "grid_geometry_path": "fw-ar-IF1-aptr12-corr", "misorientation_tolerance": 5.0, "quats_array_path": "fw-ar-IF1-aptr12-corr/Cell Data/Quats", "randomize_features": true, - "use_good_voxels": true + "use_mask": true }, "comments": "", "filter": { diff --git a/src/Plugins/OrientationAnalysis/pipelines/avtr12_Analysis.d3dpipeline b/src/Plugins/OrientationAnalysis/pipelines/avtr12_Analysis.d3dpipeline index b5fa667cfa..1c0ec2c5ef 100644 --- a/src/Plugins/OrientationAnalysis/pipelines/avtr12_Analysis.d3dpipeline +++ b/src/Plugins/OrientationAnalysis/pipelines/avtr12_Analysis.d3dpipeline @@ -127,13 +127,13 @@ "cell_ipf_colors_array_name": "IPF_001", "cell_phases_array_path": "fw-ar-IF1-avtr12-corr/Cell Data/Phases", "crystal_structures_array_path": "fw-ar-IF1-avtr12-corr/CellEnsembleData/CrystalStructures", - "good_voxels_array_path": "", + "mask_array_path": "", "reference_dir": [ 0.0, 0.0, 1.0 ], - "use_good_voxels": false + "use_mask": false }, "comments": "", "filter": { @@ -163,13 +163,13 @@ "cell_ipf_colors_array_name": "IPF_010", "cell_phases_array_path": "fw-ar-IF1-avtr12-corr/Cell Data/Phases", "crystal_structures_array_path": "fw-ar-IF1-avtr12-corr/CellEnsembleData/CrystalStructures", - "good_voxels_array_path": "", + "mask_array_path": "", "reference_dir": [ 0.0, 1.0, 0.0 ], - "use_good_voxels": false + "use_mask": false }, "comments": "", "filter": { @@ -199,13 +199,13 @@ "cell_ipf_colors_array_name": "IPF_100", "cell_phases_array_path": "fw-ar-IF1-avtr12-corr/Cell Data/Phases", "crystal_structures_array_path": "fw-ar-IF1-avtr12-corr/CellEnsembleData/CrystalStructures", - "good_voxels_array_path": "", + "mask_array_path": "", "reference_dir": [ 1.0, 0.0, 0.0 ], - "use_good_voxels": false + "use_mask": false }, "comments": "", "filter": { @@ -236,12 +236,12 @@ "cell_phases_array_path": "fw-ar-IF1-avtr12-corr/Cell Data/Phases", "crystal_structures_array_path": "fw-ar-IF1-avtr12-corr/CellEnsembleData/CrystalStructures", "feature_ids_array_name": "FeatureIds", - "good_voxels_array_path": "fw-ar-IF1-avtr12-corr/Cell Data/ThresholdArray", + "mask_array_path": "fw-ar-IF1-avtr12-corr/Cell Data/ThresholdArray", "grid_geometry_path": "fw-ar-IF1-avtr12-corr", "misorientation_tolerance": 5.0, "quats_array_path": "fw-ar-IF1-avtr12-corr/Cell Data/Quats", "randomize_features": false, - "use_good_voxels": true + "use_mask": true }, "comments": "", "filter": { diff --git a/src/Plugins/OrientationAnalysis/src/OrientationAnalysis/Filters/Algorithms/AlignSectionsMutualInformation.cpp b/src/Plugins/OrientationAnalysis/src/OrientationAnalysis/Filters/Algorithms/AlignSectionsMutualInformation.cpp index a32310469d..b9e4250449 100644 --- a/src/Plugins/OrientationAnalysis/src/OrientationAnalysis/Filters/Algorithms/AlignSectionsMutualInformation.cpp +++ b/src/Plugins/OrientationAnalysis/src/OrientationAnalysis/Filters/Algorithms/AlignSectionsMutualInformation.cpp @@ -247,7 +247,7 @@ void AlignSectionsMutualInformation::formFeaturesSections(std::vector& mi auto orientationOps = LaueOps::GetAllOrientationOps(); Float32Array& quats = m_DataStructure.getDataRefAs(m_InputValues->QuatsArrayPath); - BoolArray* goodVoxelsPtr = m_DataStructure.getDataAs(m_InputValues->GoodVoxelsArrayPath); + BoolArray* goodVoxelsPtr = m_DataStructure.getDataAs(m_InputValues->MaskArrayPath); Int32Array& m_CellPhases = m_DataStructure.getDataRefAs(m_InputValues->CellPhasesArrayPath); UInt32Array& m_CrystalStructures = m_DataStructure.getDataRefAs(m_InputValues->CrystalStructuresArrayPath); @@ -276,7 +276,7 @@ void AlignSectionsMutualInformation::formFeaturesSections(std::vector& mi for(int64 point = currentStartPoint; point < endPoint; point++) { - if((!m_InputValues->UseGoodVoxels || (goodVoxelsPtr != nullptr && (*goodVoxelsPtr)[point])) && miFeatureIds[point] == 0 && m_CellPhases[point] > 0) + if((!m_InputValues->UseMask || (goodVoxelsPtr != nullptr && (*goodVoxelsPtr)[point])) && miFeatureIds[point] == 0 && m_CellPhases[point] > 0) { seed = point; currentStartPoint = point; diff --git a/src/Plugins/OrientationAnalysis/src/OrientationAnalysis/Filters/Algorithms/AlignSectionsMutualInformation.hpp b/src/Plugins/OrientationAnalysis/src/OrientationAnalysis/Filters/Algorithms/AlignSectionsMutualInformation.hpp index 2566065ca1..c1eb920b61 100644 --- a/src/Plugins/OrientationAnalysis/src/OrientationAnalysis/Filters/Algorithms/AlignSectionsMutualInformation.hpp +++ b/src/Plugins/OrientationAnalysis/src/OrientationAnalysis/Filters/Algorithms/AlignSectionsMutualInformation.hpp @@ -18,11 +18,11 @@ struct ORIENTATIONANALYSIS_EXPORT AlignSectionsMutualInformationInputValues bool WriteAlignmentShifts; FileSystemPathParameter::ValueType AlignmentShiftFileName; float32 MisorientationTolerance; - bool UseGoodVoxels; + bool UseMask; DataPath ImageGeometryPath; DataPath QuatsArrayPath; DataPath CellPhasesArrayPath; - DataPath GoodVoxelsArrayPath; + DataPath MaskArrayPath; DataPath CrystalStructuresArrayPath; }; diff --git a/src/Plugins/OrientationAnalysis/src/OrientationAnalysis/Filters/Algorithms/BadDataNeighborOrientationCheck.cpp b/src/Plugins/OrientationAnalysis/src/OrientationAnalysis/Filters/Algorithms/BadDataNeighborOrientationCheck.cpp index c033800ca1..6ade0a7ccb 100644 --- a/src/Plugins/OrientationAnalysis/src/OrientationAnalysis/Filters/Algorithms/BadDataNeighborOrientationCheck.cpp +++ b/src/Plugins/OrientationAnalysis/src/OrientationAnalysis/Filters/Algorithms/BadDataNeighborOrientationCheck.cpp @@ -45,12 +45,12 @@ Result<> BadDataNeighborOrientationCheck::operator()() std::unique_ptr maskCompare = nullptr; try { - maskCompare = InstantiateMaskCompare(m_DataStructure, m_InputValues->GoodVoxelsArrayPath); + maskCompare = InstantiateMaskCompare(m_DataStructure, m_InputValues->MaskArrayPath); } catch(const std::out_of_range& exception) { // This really should NOT be happening as the path was verified during preflight BUT we may be calling this from // somewhere else that is NOT going through the normal complex::IFilter API of Preflight and Execute - std::string message = fmt::format("Mask Array DataPath does not exist or is not of the correct type (Bool | UInt8) {}", m_InputValues->GoodVoxelsArrayPath.toString()); + std::string message = fmt::format("Mask Array DataPath does not exist or is not of the correct type (Bool | UInt8) {}", m_InputValues->MaskArrayPath.toString()); return MakeErrorResult(-54900, message); } diff --git a/src/Plugins/OrientationAnalysis/src/OrientationAnalysis/Filters/Algorithms/BadDataNeighborOrientationCheck.hpp b/src/Plugins/OrientationAnalysis/src/OrientationAnalysis/Filters/Algorithms/BadDataNeighborOrientationCheck.hpp index c643d76f82..0edf040a4e 100644 --- a/src/Plugins/OrientationAnalysis/src/OrientationAnalysis/Filters/Algorithms/BadDataNeighborOrientationCheck.hpp +++ b/src/Plugins/OrientationAnalysis/src/OrientationAnalysis/Filters/Algorithms/BadDataNeighborOrientationCheck.hpp @@ -13,7 +13,7 @@ inputValues.MisorientationTolerance = filterArgs.value(k_MisorientationTolerance_Key); inputValues.NumberOfNeighbors = filterArgs.value(k_NumberOfNeighbors_Key); inputValues.QuatsArrayPath = filterArgs.value(k_QuatsArrayPath_Key); - inputValues.GoodVoxelsArrayPath = filterArgs.value(k_GoodVoxelsArrayPath_Key); + inputValues.MaskArrayPath = filterArgs.value(k_MaskArrayPath_Key); inputValues.CellPhasesArrayPath = filterArgs.value(k_CellPhasesArrayPath_Key); inputValues.CrystalStructuresArrayPath = filterArgs.value(k_CrystalStructuresArrayPath_Key); @@ -29,7 +29,7 @@ struct ORIENTATIONANALYSIS_EXPORT BadDataNeighborOrientationCheckInputValues int32 NumberOfNeighbors; DataPath ImageGeomPath; DataPath QuatsArrayPath; - DataPath GoodVoxelsArrayPath; + DataPath MaskArrayPath; DataPath CellPhasesArrayPath; DataPath CrystalStructuresArrayPath; }; diff --git a/src/Plugins/OrientationAnalysis/src/OrientationAnalysis/Filters/Algorithms/CAxisSegmentFeatures.cpp b/src/Plugins/OrientationAnalysis/src/OrientationAnalysis/Filters/Algorithms/CAxisSegmentFeatures.cpp index 6322b1ae55..e49543cc5e 100644 --- a/src/Plugins/OrientationAnalysis/src/OrientationAnalysis/Filters/Algorithms/CAxisSegmentFeatures.cpp +++ b/src/Plugins/OrientationAnalysis/src/OrientationAnalysis/Filters/Algorithms/CAxisSegmentFeatures.cpp @@ -34,16 +34,16 @@ Result<> CAxisSegmentFeatures::operator()() auto* imageGeometry = m_DataStructure.getDataAs(m_InputValues->ImageGeometryPath); m_QuatsArray = m_DataStructure.getDataAs(m_InputValues->QuatsArrayPath); m_CellPhases = m_DataStructure.getDataAs(m_InputValues->CellPhasesArrayPath); - if(m_InputValues->UseGoodVoxels) + if(m_InputValues->UseMask) { try { - m_GoodVoxelsArray = InstantiateMaskCompare(m_DataStructure, m_InputValues->GoodVoxelsArrayPath); + m_GoodVoxelsArray = InstantiateMaskCompare(m_DataStructure, m_InputValues->MaskArrayPath); } catch(const std::out_of_range&) { // This really should NOT be happening as the path was verified during preflight BUT we may be calling this from // somewhere else that is NOT going through the normal complex::IFilter API of Preflight and Execute - return MakeErrorResult(-8362, fmt::format("Mask Array DataPath does not exist or is not of the correct type (Bool | UInt8) {}", m_InputValues->GoodVoxelsArrayPath.toString())); + return MakeErrorResult(-8362, fmt::format("Mask Array DataPath does not exist or is not of the correct type (Bool | UInt8) {}", m_InputValues->MaskArrayPath.toString())); } } const auto& crystalStructures = m_DataStructure.getDataRefAs(m_InputValues->CrystalStructuresArrayPath); @@ -100,7 +100,7 @@ int64 CAxisSegmentFeatures::getSeed(int32 gnum, int64 nextSeed) const { if(featureIds[randPoint] == 0) // If the GrainId of the voxel is ZERO then we can use this as a seed point { - if((!m_InputValues->UseGoodVoxels || m_GoodVoxelsArray->isTrue(randPoint)) && cellPhases[randPoint] > 0) + if((!m_InputValues->UseMask || m_GoodVoxelsArray->isTrue(randPoint)) && cellPhases[randPoint] > 0) { seed = static_cast(randPoint); } @@ -145,7 +145,7 @@ bool CAxisSegmentFeatures::determineGrouping(int64 referencepoint, int64 neighbo { neighborPointIsGood = m_GoodVoxelsArray->isTrue(neighborpoint); } - if(featureIds[neighborpoint] == 0 && (!m_InputValues->UseGoodVoxels || neighborPointIsGood)) + if(featureIds[neighborpoint] == 0 && (!m_InputValues->UseMask || neighborPointIsGood)) { const QuatF q1(currentQuat[referencepoint * 4], currentQuat[referencepoint * 4 + 1], currentQuat[referencepoint * 4 + 2], currentQuat[referencepoint * 4 + 3]); const QuatF q2(currentQuat[neighborpoint * 4 + 0], currentQuat[neighborpoint * 4 + 1], currentQuat[neighborpoint * 4 + 2], currentQuat[neighborpoint * 4 + 3]); diff --git a/src/Plugins/OrientationAnalysis/src/OrientationAnalysis/Filters/Algorithms/CAxisSegmentFeatures.hpp b/src/Plugins/OrientationAnalysis/src/OrientationAnalysis/Filters/Algorithms/CAxisSegmentFeatures.hpp index 9881be8446..f2d74bbe98 100644 --- a/src/Plugins/OrientationAnalysis/src/OrientationAnalysis/Filters/Algorithms/CAxisSegmentFeatures.hpp +++ b/src/Plugins/OrientationAnalysis/src/OrientationAnalysis/Filters/Algorithms/CAxisSegmentFeatures.hpp @@ -14,12 +14,12 @@ namespace complex struct ORIENTATIONANALYSIS_EXPORT CAxisSegmentFeaturesInputValues { float32 MisorientationTolerance; - bool UseGoodVoxels; + bool UseMask; bool RandomizeFeatureIds; DataPath ImageGeometryPath; DataPath QuatsArrayPath; DataPath CellPhasesArrayPath; - DataPath GoodVoxelsArrayPath; + DataPath MaskArrayPath; DataPath CrystalStructuresArrayPath; DataPath FeatureIdsArrayName; DataPath CellFeatureAttributeMatrixName; diff --git a/src/Plugins/OrientationAnalysis/src/OrientationAnalysis/Filters/Algorithms/WritePoleFigure.cpp b/src/Plugins/OrientationAnalysis/src/OrientationAnalysis/Filters/Algorithms/WritePoleFigure.cpp index 6833b91bd5..f6570c2322 100644 --- a/src/Plugins/OrientationAnalysis/src/OrientationAnalysis/Filters/Algorithms/WritePoleFigure.cpp +++ b/src/Plugins/OrientationAnalysis/src/OrientationAnalysis/Filters/Algorithms/WritePoleFigure.cpp @@ -343,16 +343,16 @@ Result<> WritePoleFigure::operator()() complex::StringArray& materialNames = m_DataStructure.getDataRefAs(m_InputValues->MaterialNameArrayPath); std::unique_ptr maskCompare = nullptr; - if(m_InputValues->UseGoodVoxels) + if(m_InputValues->UseMask) { try { - maskCompare = InstantiateMaskCompare(m_DataStructure, m_InputValues->GoodVoxelsArrayPath); + maskCompare = InstantiateMaskCompare(m_DataStructure, m_InputValues->MaskArrayPath); } catch(const std::out_of_range& exception) { // This really should NOT be happening as the path was verified during preflight BUT we may be calling this from // some other context that is NOT going through the normal complex::IFilter API of Preflight and Execute - return MakeErrorResult(-53900, fmt::format("Mask Array DataPath does not exist or is not of the correct type (Bool | UInt8) {}", m_InputValues->GoodVoxelsArrayPath.toString())); + return MakeErrorResult(-53900, fmt::format("Mask Array DataPath does not exist or is not of the correct type (Bool | UInt8) {}", m_InputValues->MaskArrayPath.toString())); } } @@ -388,7 +388,7 @@ Result<> WritePoleFigure::operator()() { if(phases[i] == phase) { - if(!m_InputValues->UseGoodVoxels || maskCompare->isTrue(i)) + if(!m_InputValues->UseMask || maskCompare->isTrue(i)) { count++; } @@ -405,7 +405,7 @@ Result<> WritePoleFigure::operator()() { if(phases[i] == phase) { - if(!m_InputValues->UseGoodVoxels || maskCompare->isTrue(i)) + if(!m_InputValues->UseMask || maskCompare->isTrue(i)) { subEulers[count * 3] = eulers[i * 3]; subEulers[count * 3 + 1] = eulers[i * 3 + 1]; diff --git a/src/Plugins/OrientationAnalysis/src/OrientationAnalysis/Filters/Algorithms/WritePoleFigure.hpp b/src/Plugins/OrientationAnalysis/src/OrientationAnalysis/Filters/Algorithms/WritePoleFigure.hpp index 1d536514a7..bb634c46d3 100644 --- a/src/Plugins/OrientationAnalysis/src/OrientationAnalysis/Filters/Algorithms/WritePoleFigure.hpp +++ b/src/Plugins/OrientationAnalysis/src/OrientationAnalysis/Filters/Algorithms/WritePoleFigure.hpp @@ -29,10 +29,10 @@ struct ORIENTATIONANALYSIS_EXPORT WritePoleFigureInputValues FileSystemPathParameter::ValueType OutputPath; StringParameter::ValueType ImagePrefix; int32 ImageSize; - bool UseGoodVoxels; + bool UseMask; DataPath CellEulerAnglesArrayPath; DataPath CellPhasesArrayPath; - DataPath GoodVoxelsArrayPath; + DataPath MaskArrayPath; DataPath CrystalStructuresArrayPath; DataPath MaterialNameArrayPath; diff --git a/src/Plugins/OrientationAnalysis/src/OrientationAnalysis/Filters/Algorithms/WriteStatsGenOdfAngleFile.cpp b/src/Plugins/OrientationAnalysis/src/OrientationAnalysis/Filters/Algorithms/WriteStatsGenOdfAngleFile.cpp index 1831a99420..7bb83e8ccf 100644 --- a/src/Plugins/OrientationAnalysis/src/OrientationAnalysis/Filters/Algorithms/WriteStatsGenOdfAngleFile.cpp +++ b/src/Plugins/OrientationAnalysis/src/OrientationAnalysis/Filters/Algorithms/WriteStatsGenOdfAngleFile.cpp @@ -48,9 +48,9 @@ Result<> WriteStatsGenOdfAngleFile::operator()() const auto& cellPhases = m_DataStructure.getDataRefAs(m_InputValues->CellPhasesArrayPath); BoolArray* maskPtr = nullptr; - if(m_InputValues->UseGoodVoxels) + if(m_InputValues->UseMask) { - maskPtr = m_DataStructure.getDataAs(m_InputValues->GoodVoxelsArrayPath); + maskPtr = m_DataStructure.getDataAs(m_InputValues->MaskArrayPath); } // Figure out how many unique phase values we have by looping over all the phase values @@ -107,7 +107,7 @@ int WriteStatsGenOdfAngleFile::determineOutputLineCount(const Int32Array& cellPh { if(cellPhases[i] == phase) { - if(!m_InputValues->UseGoodVoxels || (m_InputValues->UseGoodVoxels && (*mask)[i])) + if(!m_InputValues->UseMask || (m_InputValues->UseMask && (*mask)[i])) { lineCount++; } @@ -147,7 +147,7 @@ Result<> WriteStatsGenOdfAngleFile::writeOutputFile(std::ofstream& out, const In if(cellPhases[i] == phase) { - if(!m_InputValues->UseGoodVoxels || (m_InputValues->UseGoodVoxels && (*mask)[i])) + if(!m_InputValues->UseMask || (m_InputValues->UseMask && (*mask)[i])) { writeLine = true; } diff --git a/src/Plugins/OrientationAnalysis/src/OrientationAnalysis/Filters/Algorithms/WriteStatsGenOdfAngleFile.hpp b/src/Plugins/OrientationAnalysis/src/OrientationAnalysis/Filters/Algorithms/WriteStatsGenOdfAngleFile.hpp index 046aea2500..917d8a0e71 100644 --- a/src/Plugins/OrientationAnalysis/src/OrientationAnalysis/Filters/Algorithms/WriteStatsGenOdfAngleFile.hpp +++ b/src/Plugins/OrientationAnalysis/src/OrientationAnalysis/Filters/Algorithms/WriteStatsGenOdfAngleFile.hpp @@ -18,10 +18,10 @@ struct ORIENTATIONANALYSIS_EXPORT WriteStatsGenOdfAngleFileInputValues int32 Sigma; ChoicesParameter::ValueType Delimiter; bool ConvertToDegrees; - bool UseGoodVoxels; + bool UseMask; DataPath CellEulerAnglesArrayPath; DataPath CellPhasesArrayPath; - DataPath GoodVoxelsArrayPath; + DataPath MaskArrayPath; }; /** diff --git a/src/Plugins/OrientationAnalysis/src/OrientationAnalysis/Filters/AlignSectionsMisorientationFilter.cpp b/src/Plugins/OrientationAnalysis/src/OrientationAnalysis/Filters/AlignSectionsMisorientationFilter.cpp index 49fa025e2f..1efe235271 100644 --- a/src/Plugins/OrientationAnalysis/src/OrientationAnalysis/Filters/AlignSectionsMisorientationFilter.cpp +++ b/src/Plugins/OrientationAnalysis/src/OrientationAnalysis/Filters/AlignSectionsMisorientationFilter.cpp @@ -75,11 +75,11 @@ Parameters AlignSectionsMisorientationFilter::parameters() const 5.0f)); params.insertSeparator(Parameters::Separator{"Optional Data Mask"}); - params.insertLinkableParameter(std::make_unique(k_GoodVoxels_Key, "Use Mask Array", "Whether to remove some Cells from consideration in the alignment process", false)); - params.insert(std::make_unique(k_GoodVoxelsArrayPath_Key, "Mask", "Path to the DataArray Mask", DataPath({"Mask"}), + params.insertLinkableParameter(std::make_unique(k_UseMask_Key, "Use Mask Array", "Whether to remove some Cells from consideration in the alignment process", false)); + params.insert(std::make_unique(k_MaskArrayPath_Key, "Mask Array", "Path to the DataArray Mask", DataPath({"Mask"}), ArraySelectionParameter::AllowedTypes{DataType::boolean, DataType::uint8}, ArraySelectionParameter::AllowedComponentShapes{{1}})); // Associate the Linkable Parameter(s) to the children parameters that they control - params.linkParameters(k_GoodVoxels_Key, k_GoodVoxelsArrayPath_Key, true); + params.linkParameters(k_UseMask_Key, k_MaskArrayPath_Key, true); params.insertSeparator(Parameters::Separator{"Required Input Cell Data"}); params.insert(std::make_unique(k_SelectedImageGeometry_Key, "Selected Image Geometry", "The target geometry", DataPath({"Data Container"}), @@ -117,10 +117,10 @@ IFilter::PreflightResult AlignSectionsMisorientationFilter::preflightImpl(const auto pWriteAlignmentShifts = filterArgs.value(k_WriteAlignmentShifts_Key); auto pAlignmentShiftFileName = filterArgs.value(k_AlignmentShiftFileName_Key); auto pMisorientationTolerance = filterArgs.value(k_MisorientationTolerance_Key); - auto pUseGoodVoxels = filterArgs.value(k_GoodVoxels_Key); + auto pUseGoodVoxels = filterArgs.value(k_UseMask_Key); auto pQuatsArrayPath = filterArgs.value(k_QuatsArrayPath_Key); auto pCellPhasesArrayPath = filterArgs.value(k_CellPhasesArrayPath_Key); - auto pGoodVoxelsArrayPath = filterArgs.value(k_GoodVoxelsArrayPath_Key); + auto pGoodVoxelsArrayPath = filterArgs.value(k_MaskArrayPath_Key); auto pCrystalStructuresArrayPath = filterArgs.value(k_CrystalStructuresArrayPath_Key); auto inputImageGeometry = filterArgs.value(k_SelectedImageGeometry_Key); @@ -188,10 +188,10 @@ Result<> AlignSectionsMisorientationFilter::executeImpl(DataStructure& dataStruc inputValues.writeAlignmentShifts = filterArgs.value(k_WriteAlignmentShifts_Key); inputValues.alignmentShiftFileName = filterArgs.value(k_AlignmentShiftFileName_Key); inputValues.misorientationTolerance = filterArgs.value(k_MisorientationTolerance_Key); - inputValues.useGoodVoxels = filterArgs.value(k_GoodVoxels_Key); + inputValues.useGoodVoxels = filterArgs.value(k_UseMask_Key); inputValues.quatsArrayPath = filterArgs.value(k_QuatsArrayPath_Key); inputValues.cellPhasesArrayPath = filterArgs.value(k_CellPhasesArrayPath_Key); - inputValues.goodVoxelsArrayPath = filterArgs.value(k_GoodVoxelsArrayPath_Key); + inputValues.goodVoxelsArrayPath = filterArgs.value(k_MaskArrayPath_Key); inputValues.crystalStructuresArrayPath = filterArgs.value(k_CrystalStructuresArrayPath_Key); return AlignSectionsMisorientation(dataStructure, messageHandler, shouldCancel, &inputValues)(); diff --git a/src/Plugins/OrientationAnalysis/src/OrientationAnalysis/Filters/AlignSectionsMisorientationFilter.hpp b/src/Plugins/OrientationAnalysis/src/OrientationAnalysis/Filters/AlignSectionsMisorientationFilter.hpp index f1787f7df0..d95882fd33 100644 --- a/src/Plugins/OrientationAnalysis/src/OrientationAnalysis/Filters/AlignSectionsMisorientationFilter.hpp +++ b/src/Plugins/OrientationAnalysis/src/OrientationAnalysis/Filters/AlignSectionsMisorientationFilter.hpp @@ -29,8 +29,8 @@ class ORIENTATIONANALYSIS_EXPORT AlignSectionsMisorientationFilter : public IFil static inline constexpr StringLiteral k_MisorientationTolerance_Key = "misorientation_tolerance"; - static inline constexpr StringLiteral k_GoodVoxels_Key = "use_good_voxels"; - static inline constexpr StringLiteral k_GoodVoxelsArrayPath_Key = "good_voxels_array_path"; + static inline constexpr StringLiteral k_UseMask_Key = "use_mask"; + static inline constexpr StringLiteral k_MaskArrayPath_Key = "mask_array_path"; static inline constexpr StringLiteral k_QuatsArrayPath_Key = "quats_array_path"; static inline constexpr StringLiteral k_CellPhasesArrayPath_Key = "cell_phases_array_path"; diff --git a/src/Plugins/OrientationAnalysis/src/OrientationAnalysis/Filters/AlignSectionsMutualInformationFilter.cpp b/src/Plugins/OrientationAnalysis/src/OrientationAnalysis/Filters/AlignSectionsMutualInformationFilter.cpp index b2b8efd59c..bcbe7d62d6 100644 --- a/src/Plugins/OrientationAnalysis/src/OrientationAnalysis/Filters/AlignSectionsMutualInformationFilter.cpp +++ b/src/Plugins/OrientationAnalysis/src/OrientationAnalysis/Filters/AlignSectionsMutualInformationFilter.cpp @@ -61,10 +61,10 @@ Parameters AlignSectionsMutualInformationFilter::parameters() const 5.0f)); params.insertSeparator(Parameters::Separator{"Optional Data Mask"}); - params.insertLinkableParameter(std::make_unique(k_UseGoodVoxels_Key, "Use Mask Array", "Whether to remove some Cells from consideration in the alignment process.", true)); - params.insert(std::make_unique(k_GoodVoxelsArrayPath_Key, "Mask", "Specifies if the Cell is to be counted in the algorithm. Only required if Use Mask Array is checked.", + params.insertLinkableParameter(std::make_unique(k_UseMask_Key, "Use Mask Array", "Whether to remove some Cells from consideration in the alignment process.", true)); + params.insert(std::make_unique(k_MaskArrayPath_Key, "Mask Array", "Specifies if the Cell is to be counted in the algorithm. Only required if Use Mask Array is checked.", DataPath{}, ArraySelectionParameter::AllowedTypes{DataType::boolean}, ArraySelectionParameter::AllowedComponentShapes{{1}})); - params.linkParameters(k_UseGoodVoxels_Key, k_GoodVoxelsArrayPath_Key, true); + params.linkParameters(k_UseMask_Key, k_MaskArrayPath_Key, true); params.insertSeparator(Parameters::Separator{"Required Input Cell Data"}); params.insert(std::make_unique(k_SelectedImageGeometry_Key, "Selected Image Geometry", "The target geometry", DataPath({"Data Container"}), @@ -102,11 +102,11 @@ IFilter::PreflightResult AlignSectionsMutualInformationFilter::preflightImpl(con auto pWriteAlignmentShiftsValue = filterArgs.value(k_WriteAlignmentShifts_Key); auto pAlignmentShiftFileNameValue = filterArgs.value(k_AlignmentShiftFileName_Key); auto pMisorientationToleranceValue = filterArgs.value(k_MisorientationTolerance_Key); - auto pUseGoodVoxelsValue = filterArgs.value(k_UseGoodVoxels_Key); + auto pUseGoodVoxelsValue = filterArgs.value(k_UseMask_Key); auto imageGeometryPath = filterArgs.value(k_SelectedImageGeometry_Key); auto pQuatsArrayPathValue = filterArgs.value(k_QuatsArrayPath_Key); auto pCellPhasesArrayPathValue = filterArgs.value(k_CellPhasesArrayPath_Key); - auto pGoodVoxelsArrayPathValue = filterArgs.value(k_GoodVoxelsArrayPath_Key); + auto pGoodVoxelsArrayPathValue = filterArgs.value(k_MaskArrayPath_Key); auto pCrystalStructuresArrayPathValue = filterArgs.value(k_CrystalStructuresArrayPath_Key); PreflightResult preflightResult; @@ -148,11 +148,11 @@ Result<> AlignSectionsMutualInformationFilter::executeImpl(DataStructure& dataSt inputValues.WriteAlignmentShifts = filterArgs.value(k_WriteAlignmentShifts_Key); inputValues.AlignmentShiftFileName = filterArgs.value(k_AlignmentShiftFileName_Key); inputValues.MisorientationTolerance = filterArgs.value(k_MisorientationTolerance_Key); - inputValues.UseGoodVoxels = filterArgs.value(k_UseGoodVoxels_Key); + inputValues.UseMask = filterArgs.value(k_UseMask_Key); inputValues.ImageGeometryPath = filterArgs.value(k_SelectedImageGeometry_Key); inputValues.QuatsArrayPath = filterArgs.value(k_QuatsArrayPath_Key); inputValues.CellPhasesArrayPath = filterArgs.value(k_CellPhasesArrayPath_Key); - inputValues.GoodVoxelsArrayPath = filterArgs.value(k_GoodVoxelsArrayPath_Key); + inputValues.MaskArrayPath = filterArgs.value(k_MaskArrayPath_Key); inputValues.CrystalStructuresArrayPath = filterArgs.value(k_CrystalStructuresArrayPath_Key); return AlignSectionsMutualInformation(dataStructure, messageHandler, shouldCancel, &inputValues)(); diff --git a/src/Plugins/OrientationAnalysis/src/OrientationAnalysis/Filters/AlignSectionsMutualInformationFilter.hpp b/src/Plugins/OrientationAnalysis/src/OrientationAnalysis/Filters/AlignSectionsMutualInformationFilter.hpp index 229f0c2c7f..22a86b82c4 100644 --- a/src/Plugins/OrientationAnalysis/src/OrientationAnalysis/Filters/AlignSectionsMutualInformationFilter.hpp +++ b/src/Plugins/OrientationAnalysis/src/OrientationAnalysis/Filters/AlignSectionsMutualInformationFilter.hpp @@ -28,10 +28,10 @@ class ORIENTATIONANALYSIS_EXPORT AlignSectionsMutualInformationFilter : public I static inline constexpr StringLiteral k_WriteAlignmentShifts_Key = "write_alignment_shifts"; static inline constexpr StringLiteral k_AlignmentShiftFileName_Key = "alignment_shift_file_name"; static inline constexpr StringLiteral k_MisorientationTolerance_Key = "misorientation_tolerance"; - static inline constexpr StringLiteral k_UseGoodVoxels_Key = "use_good_voxels"; + static inline constexpr StringLiteral k_UseMask_Key = "use_mask"; static inline constexpr StringLiteral k_QuatsArrayPath_Key = "quats_array_path"; static inline constexpr StringLiteral k_CellPhasesArrayPath_Key = "cell_phases_array_path"; - static inline constexpr StringLiteral k_GoodVoxelsArrayPath_Key = "good_voxels_array_path"; + static inline constexpr StringLiteral k_MaskArrayPath_Key = "mask_array_path"; static inline constexpr StringLiteral k_CrystalStructuresArrayPath_Key = "crystal_structures_array_path"; static inline constexpr StringLiteral k_SelectedImageGeometry_Key = "selected_image_geometry_path"; diff --git a/src/Plugins/OrientationAnalysis/src/OrientationAnalysis/Filters/BadDataNeighborOrientationCheckFilter.cpp b/src/Plugins/OrientationAnalysis/src/OrientationAnalysis/Filters/BadDataNeighborOrientationCheckFilter.cpp index 58b4cf21f3..c0f61aa98f 100644 --- a/src/Plugins/OrientationAnalysis/src/OrientationAnalysis/Filters/BadDataNeighborOrientationCheckFilter.cpp +++ b/src/Plugins/OrientationAnalysis/src/OrientationAnalysis/Filters/BadDataNeighborOrientationCheckFilter.cpp @@ -67,7 +67,7 @@ Parameters BadDataNeighborOrientationCheckFilter::parameters() const params.insertSeparator(Parameters::Separator{"Cell Data"}); params.insert(std::make_unique(k_QuatsArrayPath_Key, "Quaternions", "Specifies the orientation of the Cell in quaternion representation", DataPath{}, ArraySelectionParameter::AllowedTypes{DataType::float32}, ArraySelectionParameter::AllowedComponentShapes{{4}})); - params.insert(std::make_unique(k_GoodVoxelsArrayPath_Key, "Mask", "Used to define Cells as good or bad", DataPath{}, + params.insert(std::make_unique(k_MaskArrayPath_Key, "Mask Array", "Used to define Cells as good or bad", DataPath{}, ArraySelectionParameter::AllowedTypes{DataType::boolean}, ArraySelectionParameter::AllowedComponentShapes{{1}})); params.insert(std::make_unique(k_CellPhasesArrayPath_Key, "Cell Phases", "Specifies to which Ensemble each Cell belongs", DataPath({"Phases"}), ArraySelectionParameter::AllowedTypes{DataType::int32}, ArraySelectionParameter::AllowedComponentShapes{{1}})); @@ -94,7 +94,7 @@ IFilter::PreflightResult BadDataNeighborOrientationCheckFilter::preflightImpl(co auto pNumberOfNeighborsValue = filterArgs.value(k_NumberOfNeighbors_Key); auto pImageGeomPathValue = filterArgs.value(k_ImageGeometryPath_Key); auto pQuatsArrayPathValue = filterArgs.value(k_QuatsArrayPath_Key); - auto pGoodVoxelsArrayPathValue = filterArgs.value(k_GoodVoxelsArrayPath_Key); + auto pGoodVoxelsArrayPathValue = filterArgs.value(k_MaskArrayPath_Key); auto pCellPhasesArrayPathValue = filterArgs.value(k_CellPhasesArrayPath_Key); auto pCrystalStructuresArrayPathValue = filterArgs.value(k_CrystalStructuresArrayPath_Key); @@ -206,7 +206,7 @@ Result<> BadDataNeighborOrientationCheckFilter::executeImpl(DataStructure& dataS inputValues.NumberOfNeighbors = filterArgs.value(k_NumberOfNeighbors_Key); inputValues.ImageGeomPath = filterArgs.value(k_ImageGeometryPath_Key); inputValues.QuatsArrayPath = filterArgs.value(k_QuatsArrayPath_Key); - inputValues.GoodVoxelsArrayPath = filterArgs.value(k_GoodVoxelsArrayPath_Key); + inputValues.MaskArrayPath = filterArgs.value(k_MaskArrayPath_Key); inputValues.CellPhasesArrayPath = filterArgs.value(k_CellPhasesArrayPath_Key); inputValues.CrystalStructuresArrayPath = filterArgs.value(k_CrystalStructuresArrayPath_Key); diff --git a/src/Plugins/OrientationAnalysis/src/OrientationAnalysis/Filters/BadDataNeighborOrientationCheckFilter.hpp b/src/Plugins/OrientationAnalysis/src/OrientationAnalysis/Filters/BadDataNeighborOrientationCheckFilter.hpp index b6fc03a6ca..e9bc06685e 100644 --- a/src/Plugins/OrientationAnalysis/src/OrientationAnalysis/Filters/BadDataNeighborOrientationCheckFilter.hpp +++ b/src/Plugins/OrientationAnalysis/src/OrientationAnalysis/Filters/BadDataNeighborOrientationCheckFilter.hpp @@ -28,7 +28,7 @@ class ORIENTATIONANALYSIS_EXPORT BadDataNeighborOrientationCheckFilter : public static inline constexpr StringLiteral k_NumberOfNeighbors_Key = "number_of_neighbors"; static inline constexpr StringLiteral k_ImageGeometryPath_Key = "image_geometry_path"; static inline constexpr StringLiteral k_QuatsArrayPath_Key = "quats_array_path"; - static inline constexpr StringLiteral k_GoodVoxelsArrayPath_Key = "good_voxels_array_path"; + static inline constexpr StringLiteral k_MaskArrayPath_Key = "mask_array_path"; static inline constexpr StringLiteral k_CellPhasesArrayPath_Key = "cell_phases_array_path"; static inline constexpr StringLiteral k_CrystalStructuresArrayPath_Key = "crystal_structures_array_path"; diff --git a/src/Plugins/OrientationAnalysis/src/OrientationAnalysis/Filters/CAxisSegmentFeaturesFilter.cpp b/src/Plugins/OrientationAnalysis/src/OrientationAnalysis/Filters/CAxisSegmentFeaturesFilter.cpp index 4715b673d0..310ba2f116 100644 --- a/src/Plugins/OrientationAnalysis/src/OrientationAnalysis/Filters/CAxisSegmentFeaturesFilter.cpp +++ b/src/Plugins/OrientationAnalysis/src/OrientationAnalysis/Filters/CAxisSegmentFeaturesFilter.cpp @@ -58,14 +58,14 @@ Parameters CAxisSegmentFeaturesFilter::parameters() const params.insert(std::make_unique(k_MisorientationTolerance_Key, "C-Axis Misorientation Tolerance (Degrees)", "Tolerance (in degrees) used to determine if neighboring Cells belong to the same Feature", 5.0f)); params.insertLinkableParameter( - std::make_unique(k_UseGoodVoxels_Key, "Use Mask Array", "Specifies whether to use a boolean array to exclude some Cells from the Feature identification process", true)); + std::make_unique(k_UseMask_Key, "Use Mask Array", "Specifies whether to use a boolean array to exclude some Cells from the Feature identification process", true)); params.insert(std::make_unique(k_RandomizeFeatureIds_Key, "Randomize Feature Ids", "Specifies whether to randomize the feature ids", true)); params.insertSeparator(Parameters::Separator{"Required Cell Data"}); params.insert(std::make_unique(k_QuatsArrayPath_Key, "Quaternions", "Specifies the orientation of the Cell in quaternion representation", DataPath{}, ArraySelectionParameter::AllowedTypes{DataType::float32}, ArraySelectionParameter::AllowedComponentShapes{{4}})); params.insert(std::make_unique(k_CellPhasesArrayPath_Key, "Phases", "Specifies to which Ensemble each Cell belongs", DataPath{}, ArraySelectionParameter::AllowedTypes{DataType::int32}, ArraySelectionParameter::AllowedComponentShapes{{1}})); - params.insert(std::make_unique(k_GoodVoxelsArrayPath_Key, "Mask", "Specifies if the Cell is to be counted in the algorithm. Only required if Use Mask Array is checked", + params.insert(std::make_unique(k_MaskArrayPath_Key, "Mask Array", "Specifies if the Cell is to be counted in the algorithm. Only required if Use Mask Array is checked", DataPath{}, ArraySelectionParameter::AllowedTypes{DataType::boolean}, ArraySelectionParameter::AllowedComponentShapes{{1}})); params.insertSeparator(Parameters::Separator{"Required Cell Ensemble Data"}); params.insert(std::make_unique(k_CrystalStructuresArrayPath_Key, "Crystal Structures", "Enumeration representing the crystal structure for each Ensemble", DataPath{}, @@ -78,7 +78,7 @@ Parameters CAxisSegmentFeaturesFilter::parameters() const k_ActiveArrayName_Key, "Active", "Specifies if the Feature is still in the sample (true if the Feature is in the sample and false if it is not). At the end of the Filter, all Features will be Active", "Active")); // Associate the Linkable Parameter(s) to the children parameters that they control - params.linkParameters(k_UseGoodVoxels_Key, k_GoodVoxelsArrayPath_Key, true); + params.linkParameters(k_UseMask_Key, k_MaskArrayPath_Key, true); return params; } @@ -94,7 +94,7 @@ IFilter::PreflightResult CAxisSegmentFeaturesFilter::preflightImpl(const DataStr const std::atomic_bool& shouldCancel) const { auto pImageGeometryPath = filterArgs.value(k_ImageGeometryPath_Key); - auto pUseGoodVoxelsValue = filterArgs.value(k_UseGoodVoxels_Key); + auto pUseGoodVoxelsValue = filterArgs.value(k_UseMask_Key); auto pQuatsArrayPathValue = filterArgs.value(k_QuatsArrayPath_Key); auto pCellPhasesArrayPathValue = filterArgs.value(k_CellPhasesArrayPath_Key); auto pCrystalStructuresArrayPathValue = filterArgs.value(k_CrystalStructuresArrayPath_Key); @@ -113,7 +113,7 @@ IFilter::PreflightResult CAxisSegmentFeaturesFilter::preflightImpl(const DataStr std::vector dataPaths = {pQuatsArrayPathValue, pCellPhasesArrayPathValue}; if(pUseGoodVoxelsValue) { - dataPaths.push_back(filterArgs.value(k_GoodVoxelsArrayPath_Key)); + dataPaths.push_back(filterArgs.value(k_MaskArrayPath_Key)); } const auto& imageGeo = dataStructure.getDataRefAs(pImageGeometryPath); @@ -151,11 +151,11 @@ Result<> CAxisSegmentFeaturesFilter::executeImpl(DataStructure& dataStructure, c inputValues.ImageGeometryPath = filterArgs.value(k_ImageGeometryPath_Key); inputValues.MisorientationTolerance = filterArgs.value(k_MisorientationTolerance_Key) * Constants::k_PiOver180F; - inputValues.UseGoodVoxels = filterArgs.value(k_UseGoodVoxels_Key); + inputValues.UseMask = filterArgs.value(k_UseMask_Key); inputValues.RandomizeFeatureIds = filterArgs.value(k_RandomizeFeatureIds_Key); inputValues.QuatsArrayPath = filterArgs.value(k_QuatsArrayPath_Key); inputValues.CellPhasesArrayPath = filterArgs.value(k_CellPhasesArrayPath_Key); - inputValues.GoodVoxelsArrayPath = filterArgs.value(k_GoodVoxelsArrayPath_Key); + inputValues.MaskArrayPath = filterArgs.value(k_MaskArrayPath_Key); inputValues.CrystalStructuresArrayPath = filterArgs.value(k_CrystalStructuresArrayPath_Key); inputValues.FeatureIdsArrayName = inputValues.QuatsArrayPath.getParent().createChildPath(filterArgs.value(k_FeatureIdsArrayName_Key)); inputValues.CellFeatureAttributeMatrixName = inputValues.ImageGeometryPath.createChildPath(filterArgs.value(k_CellFeatureAttributeMatrixName_Key)); diff --git a/src/Plugins/OrientationAnalysis/src/OrientationAnalysis/Filters/CAxisSegmentFeaturesFilter.hpp b/src/Plugins/OrientationAnalysis/src/OrientationAnalysis/Filters/CAxisSegmentFeaturesFilter.hpp index 036a64695c..ede4be2b44 100644 --- a/src/Plugins/OrientationAnalysis/src/OrientationAnalysis/Filters/CAxisSegmentFeaturesFilter.hpp +++ b/src/Plugins/OrientationAnalysis/src/OrientationAnalysis/Filters/CAxisSegmentFeaturesFilter.hpp @@ -26,11 +26,11 @@ class ORIENTATIONANALYSIS_EXPORT CAxisSegmentFeaturesFilter : public IFilter // Parameter Keys static inline constexpr StringLiteral k_ImageGeometryPath_Key = "image_geometry_path"; static inline constexpr StringLiteral k_MisorientationTolerance_Key = "misorientation_tolerance"; - static inline constexpr StringLiteral k_UseGoodVoxels_Key = "use_good_voxels"; + static inline constexpr StringLiteral k_UseMask_Key = "use_mask"; static inline constexpr StringLiteral k_RandomizeFeatureIds_Key = "randomize_feature_ids"; static inline constexpr StringLiteral k_QuatsArrayPath_Key = "quats_array_path"; static inline constexpr StringLiteral k_CellPhasesArrayPath_Key = "cell_phases_array_path"; - static inline constexpr StringLiteral k_GoodVoxelsArrayPath_Key = "good_voxels_array_path"; + static inline constexpr StringLiteral k_MaskArrayPath_Key = "mask_array_path"; static inline constexpr StringLiteral k_CrystalStructuresArrayPath_Key = "crystal_structures_array_path"; static inline constexpr StringLiteral k_FeatureIdsArrayName_Key = "feature_ids_array_name"; static inline constexpr StringLiteral k_CellFeatureAttributeMatrixName_Key = "cell_feature_attribute_matrix_name"; diff --git a/src/Plugins/OrientationAnalysis/src/OrientationAnalysis/Filters/EBSDSegmentFeaturesFilter.cpp b/src/Plugins/OrientationAnalysis/src/OrientationAnalysis/Filters/EBSDSegmentFeaturesFilter.cpp index 570606f40c..dac2c332c6 100644 --- a/src/Plugins/OrientationAnalysis/src/OrientationAnalysis/Filters/EBSDSegmentFeaturesFilter.cpp +++ b/src/Plugins/OrientationAnalysis/src/OrientationAnalysis/Filters/EBSDSegmentFeaturesFilter.cpp @@ -65,11 +65,11 @@ Parameters EBSDSegmentFeaturesFilter::parameters() const "Tolerance (in degrees) used to determine if neighboring Cells belong to the same Feature", 5.0f)); params.insert(std::make_unique(k_RandomizeFeatures_Key, "Randomize Feature IDs", "Specifies if feature IDs should be randomized during calculations", false)); params.insertLinkableParameter( - std::make_unique(k_UseGoodVoxels_Key, "Use Mask Array", "Specifies whether to use a boolean array to exclude some Cells from the Feature identification process", false)); - params.insert(std::make_unique(k_GoodVoxelsPath_Key, "Mask", "Path to the data array that specifies if the Cell is to be counted in the algorithm", DataPath(), + std::make_unique(k_UseMask_Key, "Use Mask Array", "Specifies whether to use a boolean array to exclude some Cells from the Feature identification process", false)); + params.insert(std::make_unique(k_MaskArrayPath_Key, "Mask Array", "Path to the data array that specifies if the Cell is to be counted in the algorithm", DataPath(), ArraySelectionParameter::AllowedTypes{DataType::boolean, DataType::uint8}, ArraySelectionParameter::AllowedComponentShapes{{1}})); // Associate the Linkable Parameter(s) to the children parameters that they control - params.linkParameters(k_UseGoodVoxels_Key, k_GoodVoxelsPath_Key, true); + params.linkParameters(k_UseMask_Key, k_MaskArrayPath_Key, true); params.insertSeparator(Parameters::Separator{"Required Input Cell Data"}); params.insert(std::make_unique(k_GridGeomPath_Key, "Grid Geometry", "DataPath to target Grid Geometry", DataPath{}, @@ -151,11 +151,11 @@ IFilter::PreflightResult EBSDSegmentFeaturesFilter::preflightImpl(const DataStru dataPaths.push_back(pCellPhasesArrayPathValue); // Validate the GoodVoxels/Mask Array combination - bool useGoodVoxels = args.value(k_UseGoodVoxels_Key); + bool useGoodVoxels = args.value(k_UseMask_Key); DataPath goodVoxelsPath; if(useGoodVoxels) { - goodVoxelsPath = args.value(k_GoodVoxelsPath_Key); + goodVoxelsPath = args.value(k_MaskArrayPath_Key); const auto* goodVoxelsArray = dataStructure.getDataAs(goodVoxelsPath); if(nullptr == goodVoxelsArray) @@ -197,12 +197,12 @@ Result<> EBSDSegmentFeaturesFilter::executeImpl(DataStructure& dataStructure, co // Store the misorientation tolerance as radians inputValues.misorientationTolerance = filterArgs.value(k_MisorientationTolerance_Key) * static_cast(complex::numbers::pi / 180.0f); - inputValues.useGoodVoxels = filterArgs.value(k_UseGoodVoxels_Key); + inputValues.useGoodVoxels = filterArgs.value(k_UseMask_Key); inputValues.shouldRandomizeFeatureIds = filterArgs.value(k_RandomizeFeatures_Key); inputValues.gridGeomPath = filterArgs.value(k_GridGeomPath_Key); inputValues.quatsArrayPath = filterArgs.value(k_QuatsArrayPath_Key); inputValues.cellPhasesArrayPath = filterArgs.value(k_CellPhasesArrayPath_Key); - inputValues.goodVoxelsArrayPath = filterArgs.value(k_GoodVoxelsPath_Key); + inputValues.goodVoxelsArrayPath = filterArgs.value(k_MaskArrayPath_Key); inputValues.crystalStructuresArrayPath = filterArgs.value(k_CrystalStructuresArrayPath_Key); auto cellDataAMPath = dataStructure.getDataAs(inputValues.gridGeomPath)->getCellDataPath(); inputValues.featureIdsArrayPath = cellDataAMPath.createChildPath(filterArgs.value(k_FeatureIdsArrayName_Key)); diff --git a/src/Plugins/OrientationAnalysis/src/OrientationAnalysis/Filters/EBSDSegmentFeaturesFilter.hpp b/src/Plugins/OrientationAnalysis/src/OrientationAnalysis/Filters/EBSDSegmentFeaturesFilter.hpp index 2389763649..5d98cc802a 100644 --- a/src/Plugins/OrientationAnalysis/src/OrientationAnalysis/Filters/EBSDSegmentFeaturesFilter.hpp +++ b/src/Plugins/OrientationAnalysis/src/OrientationAnalysis/Filters/EBSDSegmentFeaturesFilter.hpp @@ -26,10 +26,10 @@ class ORIENTATIONANALYSIS_EXPORT EBSDSegmentFeaturesFilter : public IFilter // Parameter Keys static inline constexpr StringLiteral k_GridGeomPath_Key = "grid_geometry_path"; static inline constexpr StringLiteral k_MisorientationTolerance_Key = "misorientation_tolerance"; - static inline constexpr StringLiteral k_UseGoodVoxels_Key = "use_good_voxels"; + static inline constexpr StringLiteral k_UseMask_Key = "use_mask"; static inline constexpr StringLiteral k_QuatsArrayPath_Key = "quats_array_path"; static inline constexpr StringLiteral k_CellPhasesArrayPath_Key = "cell_phases_array_path"; - static inline constexpr StringLiteral k_GoodVoxelsPath_Key = "good_voxels_array_path"; + static inline constexpr StringLiteral k_MaskArrayPath_Key = "mask_array_path"; static inline constexpr StringLiteral k_CrystalStructuresArrayPath_Key = "crystal_structures_array_path"; static inline constexpr StringLiteral k_FeatureIdsArrayName_Key = "feature_ids_array_name"; static inline constexpr StringLiteral k_CellFeatureAttributeMatrixName_Key = "cell_feature_attribute_matrix_name"; diff --git a/src/Plugins/OrientationAnalysis/src/OrientationAnalysis/Filters/GenerateFZQuaternions.cpp b/src/Plugins/OrientationAnalysis/src/OrientationAnalysis/Filters/GenerateFZQuaternions.cpp index 3c8292649a..af958af029 100644 --- a/src/Plugins/OrientationAnalysis/src/OrientationAnalysis/Filters/GenerateFZQuaternions.cpp +++ b/src/Plugins/OrientationAnalysis/src/OrientationAnalysis/Filters/GenerateFZQuaternions.cpp @@ -154,8 +154,8 @@ Parameters GenerateFZQuaternions::parameters() const params.insert(std::make_unique(k_CellPhasesArrayPath_Key, "Input Phases", "The phases of the data. The data should be the indices into the Crystal Structures Data Array.", DataPath{}, ArraySelectionParameter::AllowedTypes{DataType::int32}, ArraySelectionParameter::AllowedComponentShapes{{1}})); params.insertLinkableParameter( - std::make_unique(k_UseGoodVoxels_Key, "Apply to Good Elements Only (Bad Elements Will Be Black)", "Whether to assign a black color to 'bad' Elements", false)); - params.insert(std::make_unique(k_GoodVoxelsArrayPath_Key, "Input Mask [Optional]", "Optional Mask array where valid data is TRUE or 1.", DataPath{}, + std::make_unique(k_UseMask_Key, "Apply to Good Elements Only (Bad Elements Will Be Black)", "Whether to assign a black color to 'bad' Elements", false)); + params.insert(std::make_unique(k_MaskArrayPath_Key, "Input Mask [Optional]", "Optional Mask array where valid data is TRUE or 1.", DataPath{}, ArraySelectionParameter::AllowedTypes{DataType::int8, DataType::uint8, DataType::boolean}, ArraySelectionParameter::AllowedComponentShapes{{1}})); params.insertSeparator(Parameters::Separator{"Ensemble Data"}); @@ -166,7 +166,7 @@ Parameters GenerateFZQuaternions::parameters() const params.insert(std::make_unique(k_FZQuatsArrayPath_Key, "Created FZ Quaternions", "The name of the array containing the Quaternion that represents an orientation within the fundamental zone for each Element", "")); // Associate the Linkable Parameter(s) to the children parameters that they control - params.linkParameters(k_UseGoodVoxels_Key, k_GoodVoxelsArrayPath_Key, true); + params.linkParameters(k_UseMask_Key, k_MaskArrayPath_Key, true); return params; } @@ -181,10 +181,10 @@ IFilter::PreflightResult GenerateFZQuaternions::preflightImpl(const DataStructur const std::atomic_bool& shouldCancel) const { - auto pUseGoodVoxelsValue = filterArgs.value(k_UseGoodVoxels_Key); + auto pUseGoodVoxelsValue = filterArgs.value(k_UseMask_Key); auto pQuatsArrayPathValue = filterArgs.value(k_QuatsArrayPath_Key); auto pCellPhasesArrayPathValue = filterArgs.value(k_CellPhasesArrayPath_Key); - auto pGoodVoxelsArrayPathValue = filterArgs.value(k_GoodVoxelsArrayPath_Key); + auto pGoodVoxelsArrayPathValue = filterArgs.value(k_MaskArrayPath_Key); auto pCrystalStructuresArrayPathValue = filterArgs.value(k_CrystalStructuresArrayPath_Key); auto pFZQuatsArrayPathValue = pQuatsArrayPathValue.getParent().createChildPath(filterArgs.value(k_FZQuatsArrayPath_Key)); @@ -248,10 +248,10 @@ IFilter::PreflightResult GenerateFZQuaternions::preflightImpl(const DataStructur Result<> GenerateFZQuaternions::executeImpl(DataStructure& dataStructure, const Arguments& filterArgs, const PipelineFilter* pipelineNode, const MessageHandler& messageHandler, const std::atomic_bool& shouldCancel) const { - auto pUseGoodVoxelsValue = filterArgs.value(k_UseGoodVoxels_Key); + auto pUseGoodVoxelsValue = filterArgs.value(k_UseMask_Key); auto pQuatsArrayPathValue = filterArgs.value(k_QuatsArrayPath_Key); auto pCellPhasesArrayPathValue = filterArgs.value(k_CellPhasesArrayPath_Key); - auto pGoodVoxelsArrayPathValue = filterArgs.value(k_GoodVoxelsArrayPath_Key); + auto pGoodVoxelsArrayPathValue = filterArgs.value(k_MaskArrayPath_Key); auto pCrystalStructuresArrayPathValue = filterArgs.value(k_CrystalStructuresArrayPath_Key); auto pFZQuatsArrayPathValue = pQuatsArrayPathValue.getParent().createChildPath(filterArgs.value(k_FZQuatsArrayPath_Key)); diff --git a/src/Plugins/OrientationAnalysis/src/OrientationAnalysis/Filters/GenerateFZQuaternions.hpp b/src/Plugins/OrientationAnalysis/src/OrientationAnalysis/Filters/GenerateFZQuaternions.hpp index a259cecace..a013f8c9bd 100644 --- a/src/Plugins/OrientationAnalysis/src/OrientationAnalysis/Filters/GenerateFZQuaternions.hpp +++ b/src/Plugins/OrientationAnalysis/src/OrientationAnalysis/Filters/GenerateFZQuaternions.hpp @@ -24,10 +24,10 @@ class ORIENTATIONANALYSIS_EXPORT GenerateFZQuaternions : public IFilter GenerateFZQuaternions& operator=(GenerateFZQuaternions&&) noexcept = delete; // Parameter Keys - static inline constexpr StringLiteral k_UseGoodVoxels_Key = "use_good_voxels"; + static inline constexpr StringLiteral k_UseMask_Key = "use_mask"; static inline constexpr StringLiteral k_QuatsArrayPath_Key = "quats_array_path"; static inline constexpr StringLiteral k_CellPhasesArrayPath_Key = "cell_phases_array_path"; - static inline constexpr StringLiteral k_GoodVoxelsArrayPath_Key = "good_voxels_array_path"; + static inline constexpr StringLiteral k_MaskArrayPath_Key = "mask_array_path"; static inline constexpr StringLiteral k_CrystalStructuresArrayPath_Key = "crystal_structures_array_path"; static inline constexpr StringLiteral k_FZQuatsArrayPath_Key = "f_zquats_array_path"; diff --git a/src/Plugins/OrientationAnalysis/src/OrientationAnalysis/Filters/GenerateIPFColorsFilter.cpp b/src/Plugins/OrientationAnalysis/src/OrientationAnalysis/Filters/GenerateIPFColorsFilter.cpp index 6e5658ca9b..25df971f87 100644 --- a/src/Plugins/OrientationAnalysis/src/OrientationAnalysis/Filters/GenerateIPFColorsFilter.cpp +++ b/src/Plugins/OrientationAnalysis/src/OrientationAnalysis/Filters/GenerateIPFColorsFilter.cpp @@ -65,11 +65,11 @@ Parameters GenerateIPFColorsFilter::parameters() const std::vector(3))); params.insertSeparator(Parameters::Separator{"Optional Data Mask"}); - params.insertLinkableParameter(std::make_unique(k_UseGoodVoxels_Key, "Use Mask Array", "Whether to assign a black color to 'bad' Elements", false)); - params.insert(std::make_unique(k_GoodVoxelsPath_Key, "Mask", "Path to the data array used to define Elements as good or bad.", DataPath(), + params.insertLinkableParameter(std::make_unique(k_UseMask_Key, "Use Mask Array", "Whether to assign a black color to 'bad' Elements", false)); + params.insert(std::make_unique(k_MaskArrayPath_Key, "Mask Array", "Path to the data array used to define Elements as good or bad.", DataPath(), ArraySelectionParameter::AllowedTypes{DataType::boolean, DataType::uint8}, ArraySelectionParameter::AllowedComponentShapes{{1}})); // Associate the Linkable Parameter(s) to the children parameters that they control - params.linkParameters(k_UseGoodVoxels_Key, k_GoodVoxelsPath_Key, true); + params.linkParameters(k_UseMask_Key, k_MaskArrayPath_Key, true); params.insertSeparator(Parameters::Separator{"Required Input Cell Data"}); params.insert(std::make_unique(k_CellEulerAnglesArrayPath_Key, "Euler Angles", "Three angles defining the orientation of the Element in Bunge convention (Z-X-Z)", @@ -100,10 +100,10 @@ IFilter::PreflightResult GenerateIPFColorsFilter::preflightImpl(const DataStruct { auto pReferenceDirValue = filterArgs.value(k_ReferenceDir_Key); - auto pUseGoodVoxelsValue = filterArgs.value(k_UseGoodVoxels_Key); + auto pUseGoodVoxelsValue = filterArgs.value(k_UseMask_Key); auto pCellEulerAnglesArrayPathValue = filterArgs.value(k_CellEulerAnglesArrayPath_Key); auto pCellPhasesArrayPathValue = filterArgs.value(k_CellPhasesArrayPath_Key); - auto pGoodVoxelsArrayPathValue = filterArgs.value(k_GoodVoxelsPath_Key); + auto pGoodVoxelsArrayPathValue = filterArgs.value(k_MaskArrayPath_Key); auto pCrystalStructuresArrayPathValue = filterArgs.value(k_CrystalStructuresArrayPath_Key); auto pCellIPFColorsArrayNameValue = pCellEulerAnglesArrayPathValue.getParent().createChildPath(filterArgs.value(k_CellIPFColorsArrayName_Key)); @@ -136,7 +136,7 @@ IFilter::PreflightResult GenerateIPFColorsFilter::preflightImpl(const DataStruct DataPath goodVoxelsPath; if(pUseGoodVoxelsValue) { - goodVoxelsPath = filterArgs.value(k_GoodVoxelsPath_Key); + goodVoxelsPath = filterArgs.value(k_MaskArrayPath_Key); const complex::IDataArray* goodVoxelsArray = dataStructure.getDataAs(goodVoxelsPath); if(nullptr == goodVoxelsArray) @@ -177,10 +177,10 @@ Result<> GenerateIPFColorsFilter::executeImpl(DataStructure& dataStructure, cons GenerateIPFColorsInputValues inputValues; inputValues.referenceDirection = filterArgs.value(k_ReferenceDir_Key); - inputValues.useGoodVoxels = filterArgs.value(k_UseGoodVoxels_Key); + inputValues.useGoodVoxels = filterArgs.value(k_UseMask_Key); inputValues.cellEulerAnglesArrayPath = filterArgs.value(k_CellEulerAnglesArrayPath_Key); inputValues.cellPhasesArrayPath = filterArgs.value(k_CellPhasesArrayPath_Key); - inputValues.goodVoxelsArrayPath = filterArgs.value(k_GoodVoxelsPath_Key); + inputValues.goodVoxelsArrayPath = filterArgs.value(k_MaskArrayPath_Key); inputValues.crystalStructuresArrayPath = filterArgs.value(k_CrystalStructuresArrayPath_Key); inputValues.cellIpfColorsArrayPath = inputValues.cellEulerAnglesArrayPath.getParent().createChildPath(filterArgs.value(k_CellIPFColorsArrayName_Key)); diff --git a/src/Plugins/OrientationAnalysis/src/OrientationAnalysis/Filters/GenerateIPFColorsFilter.hpp b/src/Plugins/OrientationAnalysis/src/OrientationAnalysis/Filters/GenerateIPFColorsFilter.hpp index d29f0a7be8..1ea8c41b12 100644 --- a/src/Plugins/OrientationAnalysis/src/OrientationAnalysis/Filters/GenerateIPFColorsFilter.hpp +++ b/src/Plugins/OrientationAnalysis/src/OrientationAnalysis/Filters/GenerateIPFColorsFilter.hpp @@ -25,10 +25,10 @@ class ORIENTATIONANALYSIS_EXPORT GenerateIPFColorsFilter : public IFilter // Parameter Keys static inline constexpr StringLiteral k_ReferenceDir_Key = "reference_dir"; - static inline constexpr StringLiteral k_UseGoodVoxels_Key = "use_good_voxels"; + static inline constexpr StringLiteral k_UseMask_Key = "use_mask"; static inline constexpr StringLiteral k_CellEulerAnglesArrayPath_Key = "cell_euler_angles_array_path"; static inline constexpr StringLiteral k_CellPhasesArrayPath_Key = "cell_phases_array_path"; - static inline constexpr StringLiteral k_GoodVoxelsPath_Key = "good_voxels_array_path"; + static inline constexpr StringLiteral k_MaskArrayPath_Key = "mask_array_path"; static inline constexpr StringLiteral k_CrystalStructuresArrayPath_Key = "crystal_structures_array_path"; static inline constexpr StringLiteral k_CellIPFColorsArrayName_Key = "cell_ipf_colors_array_name"; diff --git a/src/Plugins/OrientationAnalysis/src/OrientationAnalysis/Filters/WritePoleFigureFilter.cpp b/src/Plugins/OrientationAnalysis/src/OrientationAnalysis/Filters/WritePoleFigureFilter.cpp index 1263c2101d..f735755328 100644 --- a/src/Plugins/OrientationAnalysis/src/OrientationAnalysis/Filters/WritePoleFigureFilter.cpp +++ b/src/Plugins/OrientationAnalysis/src/OrientationAnalysis/Filters/WritePoleFigureFilter.cpp @@ -99,8 +99,8 @@ Parameters WritePoleFigureFilter::parameters() const params.insert(std::make_unique(k_CellPhasesArrayPath_Key, "Phases", "Specifies to which Ensemble each cell belongs", DataPath{}, ArraySelectionParameter::AllowedTypes{DataType::int32}, ArraySelectionParameter::AllowedComponentShapes{{1}})); params.insertSeparator(Parameters::Separator{"Optional Data Mask"}); - params.insertLinkableParameter(std::make_unique(k_UseGoodVoxels_Key, "Use Mask Array", "Should the algorithm use a mask array to remove non-indexed points", false)); - params.insert(std::make_unique(k_GoodVoxelsArrayPath_Key, "Mask", "DataPath to the input Mask DataArray", DataPath({"Mask"}), + params.insertLinkableParameter(std::make_unique(k_UseMask_Key, "Use Mask Array", "Should the algorithm use a mask array to remove non-indexed points", false)); + params.insert(std::make_unique(k_MaskArrayPath_Key, "Mask Array", "DataPath to the input Mask DataArray", DataPath({"Mask"}), ArraySelectionParameter::AllowedTypes{DataType::boolean, DataType::uint8}, ArraySelectionParameter::AllowedComponentShapes{{1}})); params.insertSeparator(Parameters::Separator{"Required Input Cell Ensemble Data"}); params.insert(std::make_unique(k_CrystalStructuresArrayPath_Key, "Crystal Structures", "Enumeration representing the crystal structure for each Ensemble", @@ -121,7 +121,7 @@ Parameters WritePoleFigureFilter::parameters() const params.insert(std::make_unique(k_ImageGeometryPath_Key, "Created Image Geometry", "The path to the created Image Geometry", DataPath({"PoleFigure"}))); // Associate the Linkable Parameter(s) to the children parameters that they control - params.linkParameters(k_UseGoodVoxels_Key, k_GoodVoxelsArrayPath_Key, true); + params.linkParameters(k_UseMask_Key, k_MaskArrayPath_Key, true); params.linkParameters(k_GenerationAlgorithm_Key, k_LambertSize_Key, std::make_any(0)); params.linkParameters(k_GenerationAlgorithm_Key, k_NumColors_Key, std::make_any(0)); @@ -151,7 +151,7 @@ IFilter::PreflightResult WritePoleFigureFilter::preflightImpl(const DataStructur auto pImageSizeValue = filterArgs.value(k_ImageSize_Key); auto pCellEulerAnglesArrayPathValue = filterArgs.value(k_CellEulerAnglesArrayPath_Key); auto pCellPhasesArrayPathValue = filterArgs.value(k_CellPhasesArrayPath_Key); - auto pGoodVoxelsArrayPathValue = filterArgs.value(k_GoodVoxelsArrayPath_Key); + auto pGoodVoxelsArrayPathValue = filterArgs.value(k_MaskArrayPath_Key); auto pCrystalStructuresArrayPathValue = filterArgs.value(k_CrystalStructuresArrayPath_Key); auto pMaterialNameArrayPathValue = filterArgs.value(k_MaterialNameArrayPath_Key); @@ -232,10 +232,10 @@ Result<> WritePoleFigureFilter::executeImpl(DataStructure& dataStructure, const inputValues.OutputPath = filterArgs.value(k_OutputPath_Key); inputValues.ImagePrefix = filterArgs.value(k_ImagePrefix_Key); inputValues.ImageSize = filterArgs.value(k_ImageSize_Key); - inputValues.UseGoodVoxels = filterArgs.value(k_UseGoodVoxels_Key); + inputValues.UseMask = filterArgs.value(k_UseMask_Key); inputValues.CellEulerAnglesArrayPath = filterArgs.value(k_CellEulerAnglesArrayPath_Key); inputValues.CellPhasesArrayPath = filterArgs.value(k_CellPhasesArrayPath_Key); - inputValues.GoodVoxelsArrayPath = filterArgs.value(k_GoodVoxelsArrayPath_Key); + inputValues.MaskArrayPath = filterArgs.value(k_MaskArrayPath_Key); inputValues.CrystalStructuresArrayPath = filterArgs.value(k_CrystalStructuresArrayPath_Key); inputValues.MaterialNameArrayPath = filterArgs.value(k_MaterialNameArrayPath_Key); inputValues.SaveAsImageGeometry = filterArgs.value(k_SaveAsImageGeometry_Key); diff --git a/src/Plugins/OrientationAnalysis/src/OrientationAnalysis/Filters/WritePoleFigureFilter.hpp b/src/Plugins/OrientationAnalysis/src/OrientationAnalysis/Filters/WritePoleFigureFilter.hpp index d54c877219..c9b91ba147 100644 --- a/src/Plugins/OrientationAnalysis/src/OrientationAnalysis/Filters/WritePoleFigureFilter.hpp +++ b/src/Plugins/OrientationAnalysis/src/OrientationAnalysis/Filters/WritePoleFigureFilter.hpp @@ -33,10 +33,10 @@ class ORIENTATIONANALYSIS_EXPORT WritePoleFigureFilter : public IFilter static inline constexpr StringLiteral k_OutputPath_Key = "output_path"; static inline constexpr StringLiteral k_ImagePrefix_Key = "image_prefix"; static inline constexpr StringLiteral k_ImageSize_Key = "image_size"; - static inline constexpr StringLiteral k_UseGoodVoxels_Key = "use_good_voxels"; + static inline constexpr StringLiteral k_UseMask_Key = "use_mask"; static inline constexpr StringLiteral k_CellEulerAnglesArrayPath_Key = "cell_euler_angles_array_path"; static inline constexpr StringLiteral k_CellPhasesArrayPath_Key = "cell_phases_array_path"; - static inline constexpr StringLiteral k_GoodVoxelsArrayPath_Key = "good_voxels_array_path"; + static inline constexpr StringLiteral k_MaskArrayPath_Key = "mask_array_path"; static inline constexpr StringLiteral k_CrystalStructuresArrayPath_Key = "crystal_structures_array_path"; static inline constexpr StringLiteral k_MaterialNameArrayPath_Key = "material_name_array_path"; static inline constexpr StringLiteral k_SaveAsImageGeometry_Key = "save_as_image_geometry"; diff --git a/src/Plugins/OrientationAnalysis/src/OrientationAnalysis/Filters/WriteStatsGenOdfAngleFileFilter.cpp b/src/Plugins/OrientationAnalysis/src/OrientationAnalysis/Filters/WriteStatsGenOdfAngleFileFilter.cpp index 1058fcc796..bec2a8a675 100644 --- a/src/Plugins/OrientationAnalysis/src/OrientationAnalysis/Filters/WriteStatsGenOdfAngleFileFilter.cpp +++ b/src/Plugins/OrientationAnalysis/src/OrientationAnalysis/Filters/WriteStatsGenOdfAngleFileFilter.cpp @@ -66,8 +66,8 @@ Parameters WriteStatsGenOdfAngleFileFilter::parameters() const params.insertSeparator(Parameters::Separator{"Optional Data Mask"}); params.insertLinkableParameter( - std::make_unique(k_UseGoodVoxels_Key, "Only Write Good Elements", "Whether to only write the Euler angles for those elements denoted as true in the supplied mask array", false)); - params.insert(std::make_unique(k_GoodVoxelsArrayPath_Key, "Mask", "Used to define Elements as good or bad. Only required if Only Write Good Elements is checked", DataPath{}, + std::make_unique(k_UseMask_Key, "Only Write Good Elements", "Whether to only write the Euler angles for those elements denoted as true in the supplied mask array", false)); + params.insert(std::make_unique(k_MaskArrayPath_Key, "Mask Array", "Used to define Elements as good or bad. Only required if Only Write Good Elements is checked", DataPath{}, ArraySelectionParameter::AllowedTypes{DataType::boolean}, ArraySelectionParameter::AllowedComponentShapes{{1}})); params.insertSeparator(Parameters::Separator{"Required Element Data"}); @@ -76,7 +76,7 @@ Parameters WriteStatsGenOdfAngleFileFilter::parameters() const params.insert(std::make_unique(k_CellPhasesArrayPath_Key, "Phases", "Specifies to which Ensemble each Element belongs", DataPath{}, ArraySelectionParameter::AllowedTypes{DataType::int32}, ArraySelectionParameter::AllowedComponentShapes{{1}})); // Associate the Linkable Parameter(s) to the children parameters that they control - params.linkParameters(k_UseGoodVoxels_Key, k_GoodVoxelsArrayPath_Key, true); + params.linkParameters(k_UseMask_Key, k_MaskArrayPath_Key, true); return params; } @@ -96,10 +96,10 @@ IFilter::PreflightResult WriteStatsGenOdfAngleFileFilter::preflightImpl(const Da auto pSigmaValue = filterArgs.value(k_Sigma_Key); auto pDelimiterValue = filterArgs.value(k_Delimiter_Key); auto pConvertToDegreesValue = filterArgs.value(k_ConvertToDegrees_Key); - auto pUseGoodVoxelsValue = filterArgs.value(k_UseGoodVoxels_Key); + auto pUseGoodVoxelsValue = filterArgs.value(k_UseMask_Key); auto pCellEulerAnglesArrayPathValue = filterArgs.value(k_CellEulerAnglesArrayPath_Key); auto pCellPhasesArrayPathValue = filterArgs.value(k_CellPhasesArrayPath_Key); - auto pGoodVoxelsArrayPathValue = filterArgs.value(k_GoodVoxelsArrayPath_Key); + auto pGoodVoxelsArrayPathValue = filterArgs.value(k_MaskArrayPath_Key); PreflightResult preflightResult; complex::Result resultOutputActions; @@ -140,10 +140,10 @@ Result<> WriteStatsGenOdfAngleFileFilter::executeImpl(DataStructure& dataStructu inputValues.Sigma = filterArgs.value(k_Sigma_Key); inputValues.Delimiter = filterArgs.value(k_Delimiter_Key); inputValues.ConvertToDegrees = filterArgs.value(k_ConvertToDegrees_Key); - inputValues.UseGoodVoxels = filterArgs.value(k_UseGoodVoxels_Key); + inputValues.UseMask = filterArgs.value(k_UseMask_Key); inputValues.CellEulerAnglesArrayPath = filterArgs.value(k_CellEulerAnglesArrayPath_Key); inputValues.CellPhasesArrayPath = filterArgs.value(k_CellPhasesArrayPath_Key); - inputValues.GoodVoxelsArrayPath = filterArgs.value(k_GoodVoxelsArrayPath_Key); + inputValues.MaskArrayPath = filterArgs.value(k_MaskArrayPath_Key); return WriteStatsGenOdfAngleFile(dataStructure, messageHandler, shouldCancel, &inputValues)(); } diff --git a/src/Plugins/OrientationAnalysis/src/OrientationAnalysis/Filters/WriteStatsGenOdfAngleFileFilter.hpp b/src/Plugins/OrientationAnalysis/src/OrientationAnalysis/Filters/WriteStatsGenOdfAngleFileFilter.hpp index 80c7aee78a..f71b58b008 100644 --- a/src/Plugins/OrientationAnalysis/src/OrientationAnalysis/Filters/WriteStatsGenOdfAngleFileFilter.hpp +++ b/src/Plugins/OrientationAnalysis/src/OrientationAnalysis/Filters/WriteStatsGenOdfAngleFileFilter.hpp @@ -29,10 +29,10 @@ class ORIENTATIONANALYSIS_EXPORT WriteStatsGenOdfAngleFileFilter : public IFilte static inline constexpr StringLiteral k_Sigma_Key = "sigma"; static inline constexpr StringLiteral k_Delimiter_Key = "delimiter"; static inline constexpr StringLiteral k_ConvertToDegrees_Key = "convert_to_degrees"; - static inline constexpr StringLiteral k_UseGoodVoxels_Key = "use_good_voxels"; + static inline constexpr StringLiteral k_UseMask_Key = "use_mask"; static inline constexpr StringLiteral k_CellEulerAnglesArrayPath_Key = "cell_euler_angles_array_path"; static inline constexpr StringLiteral k_CellPhasesArrayPath_Key = "cell_phases_array_path"; - static inline constexpr StringLiteral k_GoodVoxelsArrayPath_Key = "good_voxels_array_path"; + static inline constexpr StringLiteral k_MaskArrayPath_Key = "mask_array_path"; static inline constexpr uint64 k_CommaDelimiter = 0; static inline constexpr uint64 k_SemiColonDelimiter = 1; diff --git a/src/Plugins/OrientationAnalysis/test/AlignSectionsMisorientationTest.cpp b/src/Plugins/OrientationAnalysis/test/AlignSectionsMisorientationTest.cpp index 9f0d733c0a..e1921ab072 100644 --- a/src/Plugins/OrientationAnalysis/test/AlignSectionsMisorientationTest.cpp +++ b/src/Plugins/OrientationAnalysis/test/AlignSectionsMisorientationTest.cpp @@ -117,8 +117,8 @@ TEST_CASE("OrientationAnalysis::AlignSectionsMisorientation Small IN100 Pipeline args.insertOrAssign(AlignSectionsMisorientationFilter::k_MisorientationTolerance_Key, std::make_any(5.0F)); - args.insertOrAssign(AlignSectionsMisorientationFilter::k_GoodVoxels_Key, std::make_any(true)); - args.insertOrAssign(AlignSectionsMisorientationFilter::k_GoodVoxelsArrayPath_Key, std::make_any(k_MaskArrayPath)); + args.insertOrAssign(AlignSectionsMisorientationFilter::k_UseMask_Key, std::make_any(true)); + args.insertOrAssign(AlignSectionsMisorientationFilter::k_MaskArrayPath_Key, std::make_any(k_MaskArrayPath)); args.insertOrAssign(AlignSectionsMisorientationFilter::k_QuatsArrayPath_Key, std::make_any(k_QuatsArrayPath)); args.insertOrAssign(AlignSectionsMisorientationFilter::k_CellPhasesArrayPath_Key, std::make_any(k_PhasesArrayPath)); diff --git a/src/Plugins/OrientationAnalysis/test/AlignSectionsMutualInformationTest.cpp b/src/Plugins/OrientationAnalysis/test/AlignSectionsMutualInformationTest.cpp index c3a263df7c..463e570857 100644 --- a/src/Plugins/OrientationAnalysis/test/AlignSectionsMutualInformationTest.cpp +++ b/src/Plugins/OrientationAnalysis/test/AlignSectionsMutualInformationTest.cpp @@ -55,11 +55,11 @@ TEST_CASE("OrientationAnalysis::AlignSectionsMutualInformationFilter: Valid filt args.insertOrAssign(AlignSectionsMutualInformationFilter::k_WriteAlignmentShifts_Key, std::make_any(true)); args.insertOrAssign(AlignSectionsMutualInformationFilter::k_AlignmentShiftFileName_Key, std::make_any(computedShiftsFile)); args.insertOrAssign(AlignSectionsMutualInformationFilter::k_MisorientationTolerance_Key, std::make_any(5.0f)); - args.insertOrAssign(AlignSectionsMutualInformationFilter::k_UseGoodVoxels_Key, std::make_any(true)); + args.insertOrAssign(AlignSectionsMutualInformationFilter::k_UseMask_Key, std::make_any(true)); args.insertOrAssign(AlignSectionsMutualInformationFilter::k_SelectedImageGeometry_Key, std::make_any(Constants::k_DataContainerPath)); args.insertOrAssign(AlignSectionsMutualInformationFilter::k_QuatsArrayPath_Key, std::make_any(Constants::k_QuatsArrayPath)); args.insertOrAssign(AlignSectionsMutualInformationFilter::k_CellPhasesArrayPath_Key, std::make_any(Constants::k_PhasesArrayPath)); - args.insertOrAssign(AlignSectionsMutualInformationFilter::k_GoodVoxelsArrayPath_Key, std::make_any(Constants::k_MaskArrayPath)); + args.insertOrAssign(AlignSectionsMutualInformationFilter::k_MaskArrayPath_Key, std::make_any(Constants::k_MaskArrayPath)); args.insertOrAssign(AlignSectionsMutualInformationFilter::k_CrystalStructuresArrayPath_Key, std::make_any(Constants::k_CrystalStructuresArrayPath)); // Preflight the filter and check result @@ -165,17 +165,17 @@ TEST_CASE("OrientationAnalysis::AlignSectionsMutualInformationFilter: InValid fi args.insertOrAssign(AlignSectionsMutualInformationFilter::k_AlignmentShiftFileName_Key, std::make_any(fs::path(fmt::format("{}/AlignSectionsMutualInformation_2.txt", unit_test::k_BinaryDir)))); args.insertOrAssign(AlignSectionsMutualInformationFilter::k_MisorientationTolerance_Key, std::make_any(5.0f)); - args.insertOrAssign(AlignSectionsMutualInformationFilter::k_UseGoodVoxels_Key, std::make_any(true)); + args.insertOrAssign(AlignSectionsMutualInformationFilter::k_UseMask_Key, std::make_any(true)); args.insertOrAssign(AlignSectionsMutualInformationFilter::k_SelectedImageGeometry_Key, std::make_any(Constants::k_DataContainerPath)); args.insertOrAssign(AlignSectionsMutualInformationFilter::k_QuatsArrayPath_Key, std::make_any(Constants::k_QuatsArrayPath)); args.insertOrAssign(AlignSectionsMutualInformationFilter::k_CellPhasesArrayPath_Key, std::make_any(Constants::k_PhasesArrayPath)); - args.insertOrAssign(AlignSectionsMutualInformationFilter::k_GoodVoxelsArrayPath_Key, + args.insertOrAssign(AlignSectionsMutualInformationFilter::k_MaskArrayPath_Key, std::make_any(DataPath({Constants::k_DataContainer, Constants::k_CellFeatureData, Constants::k_ActiveName}))); args.insertOrAssign(AlignSectionsMutualInformationFilter::k_CrystalStructuresArrayPath_Key, std::make_any(Constants::k_CrystalStructuresArrayPath)); SECTION("Mismatching cell data tuples") { - args.insertOrAssign(AlignSectionsMutualInformationFilter::k_GoodVoxelsArrayPath_Key, + args.insertOrAssign(AlignSectionsMutualInformationFilter::k_MaskArrayPath_Key, std::make_any(DataPath({Constants::k_DataContainer, Constants::k_CellFeatureData, Constants::k_ActiveName}))); } diff --git a/src/Plugins/OrientationAnalysis/test/BadDataNeighborOrientationCheckTest.cpp b/src/Plugins/OrientationAnalysis/test/BadDataNeighborOrientationCheckTest.cpp index fd318fde74..da48d8394e 100644 --- a/src/Plugins/OrientationAnalysis/test/BadDataNeighborOrientationCheckTest.cpp +++ b/src/Plugins/OrientationAnalysis/test/BadDataNeighborOrientationCheckTest.cpp @@ -77,7 +77,7 @@ TEST_CASE("OrientationAnalysis::BadDataNeighborOrientationCheckFilter: Small IN1 args.insertOrAssign(BadDataNeighborOrientationCheckFilter::k_NumberOfNeighbors_Key, std::make_any(4)); args.insertOrAssign(BadDataNeighborOrientationCheckFilter::k_ImageGeometryPath_Key, std::make_any(k_DataContainerPath)); args.insertOrAssign(BadDataNeighborOrientationCheckFilter::k_QuatsArrayPath_Key, std::make_any(k_QuatsArrayPath)); - args.insertOrAssign(BadDataNeighborOrientationCheckFilter::k_GoodVoxelsArrayPath_Key, std::make_any(k_MaskArrayPath)); + args.insertOrAssign(BadDataNeighborOrientationCheckFilter::k_MaskArrayPath_Key, std::make_any(k_MaskArrayPath)); args.insertOrAssign(BadDataNeighborOrientationCheckFilter::k_CellPhasesArrayPath_Key, std::make_any(k_PhasesArrayPath)); args.insertOrAssign(BadDataNeighborOrientationCheckFilter::k_CrystalStructuresArrayPath_Key, std::make_any(k_CrystalStructuresArrayPath)); diff --git a/src/Plugins/OrientationAnalysis/test/CAxisSegmentFeaturesTest.cpp b/src/Plugins/OrientationAnalysis/test/CAxisSegmentFeaturesTest.cpp index d05b7f5b4a..fa682bceba 100644 --- a/src/Plugins/OrientationAnalysis/test/CAxisSegmentFeaturesTest.cpp +++ b/src/Plugins/OrientationAnalysis/test/CAxisSegmentFeaturesTest.cpp @@ -35,11 +35,11 @@ TEST_CASE("OrientationAnalysis::CAxisSegmentFeaturesFilter: Valid Filter Executi // Create default Parameters for the filter. args.insertOrAssign(CAxisSegmentFeaturesFilter::k_ImageGeometryPath_Key, std::make_any(k_DataContainerPath)); args.insertOrAssign(CAxisSegmentFeaturesFilter::k_MisorientationTolerance_Key, std::make_any(5.0f)); - args.insertOrAssign(CAxisSegmentFeaturesFilter::k_UseGoodVoxels_Key, std::make_any(true)); + args.insertOrAssign(CAxisSegmentFeaturesFilter::k_UseMask_Key, std::make_any(true)); args.insertOrAssign(CAxisSegmentFeaturesFilter::k_RandomizeFeatureIds_Key, std::make_any(false)); args.insertOrAssign(CAxisSegmentFeaturesFilter::k_QuatsArrayPath_Key, std::make_any(k_QuatsArrayPath)); args.insertOrAssign(CAxisSegmentFeaturesFilter::k_CellPhasesArrayPath_Key, std::make_any(k_PhasesArrayPath)); - args.insertOrAssign(CAxisSegmentFeaturesFilter::k_GoodVoxelsArrayPath_Key, std::make_any(k_MaskArrayPath)); + args.insertOrAssign(CAxisSegmentFeaturesFilter::k_MaskArrayPath_Key, std::make_any(k_MaskArrayPath)); args.insertOrAssign(CAxisSegmentFeaturesFilter::k_CrystalStructuresArrayPath_Key, std::make_any(k_CrystalStructuresArrayPath)); args.insertOrAssign(CAxisSegmentFeaturesFilter::k_FeatureIdsArrayName_Key, std::make_any(k_ComputedFeatureIds)); args.insertOrAssign(CAxisSegmentFeaturesFilter::k_CellFeatureAttributeMatrixName_Key, std::make_any(k_ComputedCellFeatureData)); @@ -84,7 +84,7 @@ TEST_CASE("OrientationAnalysis::CAxisSegmentFeaturesFilter: Invalid Filter Execu // Invalid crystal structure type : should fail in execute args.insertOrAssign(CAxisSegmentFeaturesFilter::k_ImageGeometryPath_Key, std::make_any(k_DataContainerPath)); args.insertOrAssign(CAxisSegmentFeaturesFilter::k_MisorientationTolerance_Key, std::make_any(5.0f)); - args.insertOrAssign(CAxisSegmentFeaturesFilter::k_UseGoodVoxels_Key, std::make_any(false)); + args.insertOrAssign(CAxisSegmentFeaturesFilter::k_UseMask_Key, std::make_any(false)); args.insertOrAssign(CAxisSegmentFeaturesFilter::k_RandomizeFeatureIds_Key, std::make_any(false)); args.insertOrAssign(CAxisSegmentFeaturesFilter::k_QuatsArrayPath_Key, std::make_any(k_QuatsArrayPath)); args.insertOrAssign(CAxisSegmentFeaturesFilter::k_CellPhasesArrayPath_Key, std::make_any(k_PhasesArrayPath)); diff --git a/src/Plugins/OrientationAnalysis/test/EBSDSegmentFeaturesFilterTest.cpp b/src/Plugins/OrientationAnalysis/test/EBSDSegmentFeaturesFilterTest.cpp index 35b8222b78..e6cbe0c976 100644 --- a/src/Plugins/OrientationAnalysis/test/EBSDSegmentFeaturesFilterTest.cpp +++ b/src/Plugins/OrientationAnalysis/test/EBSDSegmentFeaturesFilterTest.cpp @@ -63,11 +63,11 @@ TEST_CASE("OrientationAnalysis::EBSDSegmentFeatures: Valid Execution", "[Orienta // Create default Parameters for the filter. args.insertOrAssign(EBSDSegmentFeaturesFilter::k_MisorientationTolerance_Key, std::make_any(5.0F)); - args.insertOrAssign(EBSDSegmentFeaturesFilter::k_UseGoodVoxels_Key, std::make_any(true)); + args.insertOrAssign(EBSDSegmentFeaturesFilter::k_UseMask_Key, std::make_any(true)); args.insertOrAssign(EBSDSegmentFeaturesFilter::k_GridGeomPath_Key, std::make_any(k_DataContainerPath)); args.insertOrAssign(EBSDSegmentFeaturesFilter::k_QuatsArrayPath_Key, std::make_any(k_QuatsArrayPath)); args.insertOrAssign(EBSDSegmentFeaturesFilter::k_CellPhasesArrayPath_Key, std::make_any(k_PhasesArrayPath)); - args.insertOrAssign(EBSDSegmentFeaturesFilter::k_GoodVoxelsPath_Key, std::make_any(k_MaskArrayPath)); + args.insertOrAssign(EBSDSegmentFeaturesFilter::k_MaskArrayPath_Key, std::make_any(k_MaskArrayPath)); args.insertOrAssign(EBSDSegmentFeaturesFilter::k_CrystalStructuresArrayPath_Key, std::make_any(k_CrystalStructuresArrayPath)); args.insertOrAssign(EBSDSegmentFeaturesFilter::k_FeatureIdsArrayName_Key, std::make_any(k_FeatureIds)); args.insertOrAssign(EBSDSegmentFeaturesFilter::k_CellFeatureAttributeMatrixName_Key, std::make_any(k_Grain_Data)); diff --git a/src/Plugins/OrientationAnalysis/test/GenerateFZQuaternionsTest.cpp b/src/Plugins/OrientationAnalysis/test/GenerateFZQuaternionsTest.cpp index 0b6d320836..a55615106f 100644 --- a/src/Plugins/OrientationAnalysis/test/GenerateFZQuaternionsTest.cpp +++ b/src/Plugins/OrientationAnalysis/test/GenerateFZQuaternionsTest.cpp @@ -76,8 +76,8 @@ TEST_CASE("OrientationAnalysis::GenerateFZQuaternions", "[OrientationAnalysis][G args.insertOrAssign(GenerateFZQuaternions::k_CellPhasesArrayPath_Key, std::make_any(scanDataPath.createChildPath(k_Phases))); args.insertOrAssign(GenerateFZQuaternions::k_CrystalStructuresArrayPath_Key, std::make_any(DataPath({k_SmallIN100, k_PhaseData, k_LaueClass}))); - args.insertOrAssign(GenerateFZQuaternions::k_UseGoodVoxels_Key, std::make_any(false)); - args.insertOrAssign(GenerateFZQuaternions::k_GoodVoxelsArrayPath_Key, std::make_any(DataPath{})); + args.insertOrAssign(GenerateFZQuaternions::k_UseMask_Key, std::make_any(false)); + args.insertOrAssign(GenerateFZQuaternions::k_MaskArrayPath_Key, std::make_any(DataPath{})); // Preflight the filter and check result auto preflightResult = filter.preflight(dataStructure, args); diff --git a/src/Plugins/OrientationAnalysis/test/GenerateIPFColorsTest.cpp b/src/Plugins/OrientationAnalysis/test/GenerateIPFColorsTest.cpp index 9da8857390..7ab2571a71 100644 --- a/src/Plugins/OrientationAnalysis/test/GenerateIPFColorsTest.cpp +++ b/src/Plugins/OrientationAnalysis/test/GenerateIPFColorsTest.cpp @@ -71,10 +71,10 @@ TEST_CASE("OrientationAnalysis::GenerateIPFColors", "[OrientationAnalysis][Gener // Create default Parameters for the filter. args.insertOrAssign(GenerateIPFColorsFilter::k_ReferenceDir_Key, std::make_any({0.0F, 0.0F, 1.0F})); - args.insertOrAssign(GenerateIPFColorsFilter::k_UseGoodVoxels_Key, std::make_any(true)); + args.insertOrAssign(GenerateIPFColorsFilter::k_UseMask_Key, std::make_any(true)); args.insertOrAssign(GenerateIPFColorsFilter::k_CellEulerAnglesArrayPath_Key, std::make_any(cellEulerAnglesPath)); args.insertOrAssign(GenerateIPFColorsFilter::k_CellPhasesArrayPath_Key, std::make_any(cellPhasesArrayPath)); - args.insertOrAssign(GenerateIPFColorsFilter::k_GoodVoxelsPath_Key, std::make_any(goodVoxelsPath)); + args.insertOrAssign(GenerateIPFColorsFilter::k_MaskArrayPath_Key, std::make_any(goodVoxelsPath)); args.insertOrAssign(GenerateIPFColorsFilter::k_CrystalStructuresArrayPath_Key, std::make_any(crystalStructuresArrayPath)); args.insertOrAssign(GenerateIPFColorsFilter::k_CellIPFColorsArrayName_Key, std::make_any(Constants::k_OutputIPFColors)); diff --git a/src/Plugins/OrientationAnalysis/test/MergeTwinsTest.cpp b/src/Plugins/OrientationAnalysis/test/MergeTwinsTest.cpp index 7afad45d33..bd81064a49 100644 --- a/src/Plugins/OrientationAnalysis/test/MergeTwinsTest.cpp +++ b/src/Plugins/OrientationAnalysis/test/MergeTwinsTest.cpp @@ -88,8 +88,8 @@ TEST_CASE("Reconstruction::MergeTwinsFilter: Valid Execution", "[Reconstruction] args.insertOrAssign(EBSDSegmentFeaturesFilter::k_MisorientationTolerance_Key, std::make_any(5.0f)); args.insertOrAssign(EBSDSegmentFeaturesFilter::k_RandomizeFeatures_Key, std::make_any(false)); - args.insertOrAssign(EBSDSegmentFeaturesFilter::k_UseGoodVoxels_Key, std::make_any(true)); - args.insertOrAssign(EBSDSegmentFeaturesFilter::k_GoodVoxelsPath_Key, std::make_any(k_MaskArrayPath)); + args.insertOrAssign(EBSDSegmentFeaturesFilter::k_UseMask_Key, std::make_any(true)); + args.insertOrAssign(EBSDSegmentFeaturesFilter::k_MaskArrayPath_Key, std::make_any(k_MaskArrayPath)); args.insertOrAssign(EBSDSegmentFeaturesFilter::k_GridGeomPath_Key, std::make_any(k_DataContainerPath)); args.insertOrAssign(EBSDSegmentFeaturesFilter::k_QuatsArrayPath_Key, std::make_any(k_QuatsArrayPath)); args.insertOrAssign(EBSDSegmentFeaturesFilter::k_CellPhasesArrayPath_Key, std::make_any(k_PhasesArrayPath)); diff --git a/src/Plugins/OrientationAnalysis/test/OrientationAnalysisTestUtils.hpp b/src/Plugins/OrientationAnalysis/test/OrientationAnalysisTestUtils.hpp index 53dcb42839..dcfd650322 100644 --- a/src/Plugins/OrientationAnalysis/test/OrientationAnalysisTestUtils.hpp +++ b/src/Plugins/OrientationAnalysis/test/OrientationAnalysisTestUtils.hpp @@ -136,10 +136,10 @@ inline void ExecuteEbsdSegmentFeatures(DataStructure& dataStructure, const Filte // Parameter Keys constexpr StringLiteral k_GridGeomPath_Key = "grid_geometry_path"; constexpr StringLiteral k_MisorientationTolerance_Key = "misorientation_tolerance"; - constexpr StringLiteral k_UseGoodVoxels_Key = "use_good_voxels"; + constexpr StringLiteral k_UseMask_Key = "use_mask"; constexpr StringLiteral k_QuatsArrayPath_Key = "quats_array_path"; constexpr StringLiteral k_CellPhasesArrayPath_Key = "cell_phases_array_path"; - constexpr StringLiteral k_GoodVoxelsPath_Key = "good_voxels_array_path"; + constexpr StringLiteral k_MaskArrayPath_Key = "mask_array_path"; constexpr StringLiteral k_CrystalStructuresArrayPath_Key = "crystal_structures_array_path"; constexpr StringLiteral k_FeatureIdsArrayName_Key = "feature_ids_array_name"; constexpr StringLiteral k_CellFeatureAttributeMatrixName_Key = "cell_feature_attribute_matrix_name"; @@ -150,11 +150,11 @@ inline void ExecuteEbsdSegmentFeatures(DataStructure& dataStructure, const Filte // Create default Parameters for the filter. args.insertOrAssign(k_MisorientationTolerance_Key, std::make_any(5.0F)); - args.insertOrAssign(k_UseGoodVoxels_Key, std::make_any(true)); + args.insertOrAssign(k_UseMask_Key, std::make_any(true)); args.insertOrAssign(k_GridGeomPath_Key, std::make_any(Constants::k_DataContainerPath)); args.insertOrAssign(k_QuatsArrayPath_Key, std::make_any(Constants::k_QuatsArrayPath)); args.insertOrAssign(k_CellPhasesArrayPath_Key, std::make_any(Constants::k_PhasesArrayPath)); - args.insertOrAssign(k_GoodVoxelsPath_Key, std::make_any(Constants::k_MaskArrayPath)); + args.insertOrAssign(k_MaskArrayPath_Key, std::make_any(Constants::k_MaskArrayPath)); args.insertOrAssign(k_CrystalStructuresArrayPath_Key, std::make_any(Constants::k_CrystalStructuresArrayPath)); args.insertOrAssign(k_FeatureIdsArrayName_Key, std::make_any(Constants::k_FeatureIds)); args.insertOrAssign(k_CellFeatureAttributeMatrixName_Key, std::make_any(Constants::k_Grain_Data)); @@ -183,8 +183,8 @@ inline void ExecuteAlignSectionsMisorientation(DataStructure& dataStructure, con constexpr StringLiteral k_MisorientationTolerance_Key = "misorientation_tolerance"; - constexpr StringLiteral k_GoodVoxels_Key = "use_good_voxels"; - constexpr StringLiteral k_GoodVoxelsArrayPath_Key = "good_voxels_array_path"; + constexpr StringLiteral k_UseMask_Key = "use_mask"; + constexpr StringLiteral k_MaskArrayPath_Key = "mask_array_path"; constexpr StringLiteral k_QuatsArrayPath_Key = "quats_array_path"; constexpr StringLiteral k_CellPhasesArrayPath_Key = "cell_phases_array_path"; @@ -200,8 +200,8 @@ inline void ExecuteAlignSectionsMisorientation(DataStructure& dataStructure, con args.insertOrAssign(k_MisorientationTolerance_Key, std::make_any(5.0F)); - args.insertOrAssign(k_GoodVoxels_Key, std::make_any(true)); - args.insertOrAssign(k_GoodVoxelsArrayPath_Key, std::make_any(Constants::k_MaskArrayPath)); + args.insertOrAssign(k_UseMask_Key, std::make_any(true)); + args.insertOrAssign(k_MaskArrayPath_Key, std::make_any(Constants::k_MaskArrayPath)); args.insertOrAssign(k_QuatsArrayPath_Key, std::make_any(Constants::k_QuatsArrayPath)); args.insertOrAssign(k_CellPhasesArrayPath_Key, std::make_any(Constants::k_PhasesArrayPath)); @@ -231,7 +231,7 @@ inline void ExecuteAlignSectionsFeatureCentroid(DataStructure& dataStructure, co constexpr StringLiteral k_AlignmentShiftFileName_Key = "alignment_shift_file_name"; constexpr StringLiteral k_UseReferenceSlice_Key = "use_reference_slice"; constexpr StringLiteral k_ReferenceSlice_Key = "reference_slice"; - constexpr StringLiteral k_GoodVoxelsArrayPath_Key = "good_voxels_array_path"; + constexpr StringLiteral k_MaskArrayPath_Key = "mask_array_path"; constexpr StringLiteral k_SelectedImageGeometry_Key = "selected_image_geometry_path"; constexpr StringLiteral k_SelectedCellDataGroup_Key = "selected_cell_data_path"; @@ -241,7 +241,7 @@ inline void ExecuteAlignSectionsFeatureCentroid(DataStructure& dataStructure, co args.insertOrAssign(k_AlignmentShiftFileName_Key, std::make_any(shiftsFile)); args.insertOrAssign(k_UseReferenceSlice_Key, std::make_any(true)); args.insertOrAssign(k_ReferenceSlice_Key, std::make_any(0)); - args.insertOrAssign(k_GoodVoxelsArrayPath_Key, std::make_any(Constants::k_MaskArrayPath)); + args.insertOrAssign(k_MaskArrayPath_Key, std::make_any(Constants::k_MaskArrayPath)); args.insertOrAssign(k_SelectedImageGeometry_Key, std::make_any(Constants::k_DataContainerPath)); args.insertOrAssign(k_SelectedCellDataGroup_Key, std::make_any(Constants::k_CellAttributeMatrix)); @@ -266,7 +266,7 @@ inline void ExecuteBadDataNeighborOrientationCheck(DataStructure& dataStructure, constexpr StringLiteral k_NumberOfNeighbors_Key = "number_of_neighbors"; constexpr StringLiteral k_ImageGeometryPath_Key = "image_geometry_path"; constexpr StringLiteral k_QuatsArrayPath_Key = "quats_array_path"; - constexpr StringLiteral k_GoodVoxelsArrayPath_Key = "good_voxels_array_path"; + constexpr StringLiteral k_MaskArrayPath_Key = "mask_array_path"; constexpr StringLiteral k_CellPhasesArrayPath_Key = "cell_phases_array_path"; constexpr StringLiteral k_CrystalStructuresArrayPath_Key = "crystal_structures_array_path"; @@ -276,7 +276,7 @@ inline void ExecuteBadDataNeighborOrientationCheck(DataStructure& dataStructure, args.insertOrAssign(k_NumberOfNeighbors_Key, std::make_any(4)); args.insertOrAssign(k_ImageGeometryPath_Key, std::make_any(Constants::k_DataContainerPath)); args.insertOrAssign(k_QuatsArrayPath_Key, std::make_any(Constants::k_QuatsArrayPath)); - args.insertOrAssign(k_GoodVoxelsArrayPath_Key, std::make_any(Constants::k_MaskArrayPath)); + args.insertOrAssign(k_MaskArrayPath_Key, std::make_any(Constants::k_MaskArrayPath)); args.insertOrAssign(k_CellPhasesArrayPath_Key, std::make_any(Constants::k_PhasesArrayPath)); args.insertOrAssign(k_CrystalStructuresArrayPath_Key, std::make_any(Constants::k_CrystalStructuresArrayPath)); diff --git a/src/Plugins/OrientationAnalysis/test/WritePoleFigureTest.cpp b/src/Plugins/OrientationAnalysis/test/WritePoleFigureTest.cpp index 40b611bf9c..d4d3cdefc5 100644 --- a/src/Plugins/OrientationAnalysis/test/WritePoleFigureTest.cpp +++ b/src/Plugins/OrientationAnalysis/test/WritePoleFigureTest.cpp @@ -46,7 +46,7 @@ TEST_CASE("OrientationAnalysis::WritePoleFigureFilter-1", "[OrientationAnalysis] args.insertOrAssign(WritePoleFigureFilter::k_ImageSize_Key, std::make_any(1024)); args.insertOrAssign(WritePoleFigureFilter::k_SaveAsImageGeometry_Key, std::make_any(true)); args.insertOrAssign(WritePoleFigureFilter::k_WriteImageToDisk, std::make_any(true)); - args.insertOrAssign(WritePoleFigureFilter::k_UseGoodVoxels_Key, std::make_any(false)); + args.insertOrAssign(WritePoleFigureFilter::k_UseMask_Key, std::make_any(false)); args.insertOrAssign(WritePoleFigureFilter::k_ImageGeometryPath_Key, std::make_any(DataPath({"fw-ar-IF1-aptr12-corr Discrete Pole Figure [CALCULATED]"}))); DataPath calculatedImageData({"fw-ar-IF1-aptr12-corr Discrete Pole Figure [CALCULATED]", "CellData", fmt::format("{}Phase_{}", k_ImagePrefix, 1)}); @@ -54,7 +54,7 @@ TEST_CASE("OrientationAnalysis::WritePoleFigureFilter-1", "[OrientationAnalysis] args.insertOrAssign(WritePoleFigureFilter::k_CellEulerAnglesArrayPath_Key, std::make_any(DataPath({"fw-ar-IF1-aptr12-corr", "Cell Data", "EulerAngles"}))); args.insertOrAssign(WritePoleFigureFilter::k_CellPhasesArrayPath_Key, std::make_any(DataPath({"fw-ar-IF1-aptr12-corr", "Cell Data", "Phases"}))); - args.insertOrAssign(WritePoleFigureFilter::k_GoodVoxelsArrayPath_Key, std::make_any(DataPath({"fw-ar-IF1-aptr12-corr", "Cell Data", "ThresholdArray"}))); + args.insertOrAssign(WritePoleFigureFilter::k_MaskArrayPath_Key, std::make_any(DataPath({"fw-ar-IF1-aptr12-corr", "Cell Data", "ThresholdArray"}))); args.insertOrAssign(WritePoleFigureFilter::k_CrystalStructuresArrayPath_Key, std::make_any(DataPath({"fw-ar-IF1-aptr12-corr", "CellEnsembleData", "CrystalStructures"}))); args.insertOrAssign(WritePoleFigureFilter::k_MaterialNameArrayPath_Key, std::make_any(DataPath({"fw-ar-IF1-aptr12-corr", "CellEnsembleData", "MaterialName"}))); @@ -95,7 +95,7 @@ TEST_CASE("OrientationAnalysis::WritePoleFigureFilter-2", "[OrientationAnalysis] args.insertOrAssign(WritePoleFigureFilter::k_ImageSize_Key, std::make_any(1024)); args.insertOrAssign(WritePoleFigureFilter::k_SaveAsImageGeometry_Key, std::make_any(true)); args.insertOrAssign(WritePoleFigureFilter::k_WriteImageToDisk, std::make_any(true)); - args.insertOrAssign(WritePoleFigureFilter::k_UseGoodVoxels_Key, std::make_any(true)); + args.insertOrAssign(WritePoleFigureFilter::k_UseMask_Key, std::make_any(true)); args.insertOrAssign(WritePoleFigureFilter::k_ImageGeometryPath_Key, std::make_any(DataPath({"fw-ar-IF1-aptr12-corr Discrete Pole Figure Masked [CALCULATED]"}))); DataPath calculatedImageData({"fw-ar-IF1-aptr12-corr Discrete Pole Figure Masked [CALCULATED]", "CellData", fmt::format("{}Phase_{}", k_ImagePrefix, 1)}); @@ -103,7 +103,7 @@ TEST_CASE("OrientationAnalysis::WritePoleFigureFilter-2", "[OrientationAnalysis] args.insertOrAssign(WritePoleFigureFilter::k_CellEulerAnglesArrayPath_Key, std::make_any(DataPath({"fw-ar-IF1-aptr12-corr", "Cell Data", "EulerAngles"}))); args.insertOrAssign(WritePoleFigureFilter::k_CellPhasesArrayPath_Key, std::make_any(DataPath({"fw-ar-IF1-aptr12-corr", "Cell Data", "Phases"}))); - args.insertOrAssign(WritePoleFigureFilter::k_GoodVoxelsArrayPath_Key, std::make_any(DataPath({"fw-ar-IF1-aptr12-corr", "Cell Data", "ThresholdArray"}))); + args.insertOrAssign(WritePoleFigureFilter::k_MaskArrayPath_Key, std::make_any(DataPath({"fw-ar-IF1-aptr12-corr", "Cell Data", "ThresholdArray"}))); args.insertOrAssign(WritePoleFigureFilter::k_CrystalStructuresArrayPath_Key, std::make_any(DataPath({"fw-ar-IF1-aptr12-corr", "CellEnsembleData", "CrystalStructures"}))); args.insertOrAssign(WritePoleFigureFilter::k_MaterialNameArrayPath_Key, std::make_any(DataPath({"fw-ar-IF1-aptr12-corr", "CellEnsembleData", "MaterialName"}))); @@ -145,7 +145,7 @@ TEST_CASE("OrientationAnalysis::WritePoleFigureFilter-3", "[OrientationAnalysis] args.insertOrAssign(WritePoleFigureFilter::k_ImageSize_Key, std::make_any(1024)); args.insertOrAssign(WritePoleFigureFilter::k_SaveAsImageGeometry_Key, std::make_any(true)); args.insertOrAssign(WritePoleFigureFilter::k_WriteImageToDisk, std::make_any(true)); - args.insertOrAssign(WritePoleFigureFilter::k_UseGoodVoxels_Key, std::make_any(true)); + args.insertOrAssign(WritePoleFigureFilter::k_UseMask_Key, std::make_any(true)); args.insertOrAssign(WritePoleFigureFilter::k_ImageGeometryPath_Key, std::make_any(DataPath({"fw-ar-IF1-aptr12-corr Discrete Pole Figure Masked Color [CALCULATED]"}))); DataPath calculatedImageData({"fw-ar-IF1-aptr12-corr Discrete Pole Figure Masked Color [CALCULATED]", "CellData", fmt::format("{}Phase_{}", k_ImagePrefix, 1)}); @@ -153,7 +153,7 @@ TEST_CASE("OrientationAnalysis::WritePoleFigureFilter-3", "[OrientationAnalysis] args.insertOrAssign(WritePoleFigureFilter::k_CellEulerAnglesArrayPath_Key, std::make_any(DataPath({"fw-ar-IF1-aptr12-corr", "Cell Data", "EulerAngles"}))); args.insertOrAssign(WritePoleFigureFilter::k_CellPhasesArrayPath_Key, std::make_any(DataPath({"fw-ar-IF1-aptr12-corr", "Cell Data", "Phases"}))); - args.insertOrAssign(WritePoleFigureFilter::k_GoodVoxelsArrayPath_Key, std::make_any(DataPath({"fw-ar-IF1-aptr12-corr", "Cell Data", "ThresholdArray"}))); + args.insertOrAssign(WritePoleFigureFilter::k_MaskArrayPath_Key, std::make_any(DataPath({"fw-ar-IF1-aptr12-corr", "Cell Data", "ThresholdArray"}))); args.insertOrAssign(WritePoleFigureFilter::k_CrystalStructuresArrayPath_Key, std::make_any(DataPath({"fw-ar-IF1-aptr12-corr", "CellEnsembleData", "CrystalStructures"}))); args.insertOrAssign(WritePoleFigureFilter::k_MaterialNameArrayPath_Key, std::make_any(DataPath({"fw-ar-IF1-aptr12-corr", "CellEnsembleData", "MaterialName"}))); diff --git a/src/Plugins/OrientationAnalysis/test/WriteStatsGenOdfAngleFileTest.cpp b/src/Plugins/OrientationAnalysis/test/WriteStatsGenOdfAngleFileTest.cpp index 523f2a249f..0e0140a626 100644 --- a/src/Plugins/OrientationAnalysis/test/WriteStatsGenOdfAngleFileTest.cpp +++ b/src/Plugins/OrientationAnalysis/test/WriteStatsGenOdfAngleFileTest.cpp @@ -37,10 +37,10 @@ TEST_CASE("OrientationAnalysis::WriteStatsGenOdfAngleFileFilter: Valid Filter Ex args.insertOrAssign(WriteStatsGenOdfAngleFileFilter::k_Sigma_Key, std::make_any(1)); args.insertOrAssign(WriteStatsGenOdfAngleFileFilter::k_Delimiter_Key, std::make_any(WriteStatsGenOdfAngleFileFilter::k_SpaceDelimiter)); args.insertOrAssign(WriteStatsGenOdfAngleFileFilter::k_ConvertToDegrees_Key, std::make_any(true)); - args.insertOrAssign(WriteStatsGenOdfAngleFileFilter::k_UseGoodVoxels_Key, std::make_any(true)); + args.insertOrAssign(WriteStatsGenOdfAngleFileFilter::k_UseMask_Key, std::make_any(true)); args.insertOrAssign(WriteStatsGenOdfAngleFileFilter::k_CellEulerAnglesArrayPath_Key, std::make_any(Constants::k_EulersArrayPath)); args.insertOrAssign(WriteStatsGenOdfAngleFileFilter::k_CellPhasesArrayPath_Key, std::make_any(Constants::k_PhasesArrayPath)); - args.insertOrAssign(WriteStatsGenOdfAngleFileFilter::k_GoodVoxelsArrayPath_Key, std::make_any(Constants::k_MaskArrayPath)); + args.insertOrAssign(WriteStatsGenOdfAngleFileFilter::k_MaskArrayPath_Key, std::make_any(Constants::k_MaskArrayPath)); auto preflightResult = filter.preflight(dataStructure, args); COMPLEX_RESULT_REQUIRE_VALID(preflightResult.outputActions) auto executeResult = filter.execute(dataStructure, args); @@ -49,7 +49,7 @@ TEST_CASE("OrientationAnalysis::WriteStatsGenOdfAngleFileFilter: Valid Filter Ex args.insertOrAssign(WriteStatsGenOdfAngleFileFilter::k_OutputFile_Key, std::make_any(fs::path(fmt::format("{}/StatsGenODF_RadiansNoMask.txt", unit_test::k_BinaryTestOutputDir)))); args.insertOrAssign(WriteStatsGenOdfAngleFileFilter::k_ConvertToDegrees_Key, std::make_any(false)); - args.insertOrAssign(WriteStatsGenOdfAngleFileFilter::k_UseGoodVoxels_Key, std::make_any(false)); + args.insertOrAssign(WriteStatsGenOdfAngleFileFilter::k_UseMask_Key, std::make_any(false)); preflightResult = filter.preflight(dataStructure, args); COMPLEX_RESULT_REQUIRE_VALID(preflightResult.outputActions) executeResult = filter.execute(dataStructure, args); @@ -82,9 +82,9 @@ TEST_CASE("OrientationAnalysis::WriteStatsGenOdfAngleFileFilter: InValid Filter args.insertOrAssign(WriteStatsGenOdfAngleFileFilter::k_Sigma_Key, std::make_any(1)); args.insertOrAssign(WriteStatsGenOdfAngleFileFilter::k_Delimiter_Key, std::make_any(WriteStatsGenOdfAngleFileFilter::k_SpaceDelimiter)); args.insertOrAssign(WriteStatsGenOdfAngleFileFilter::k_ConvertToDegrees_Key, std::make_any(true)); - args.insertOrAssign(WriteStatsGenOdfAngleFileFilter::k_UseGoodVoxels_Key, std::make_any(true)); + args.insertOrAssign(WriteStatsGenOdfAngleFileFilter::k_UseMask_Key, std::make_any(true)); args.insertOrAssign(WriteStatsGenOdfAngleFileFilter::k_CellEulerAnglesArrayPath_Key, std::make_any(Constants::k_EulersArrayPath)); - args.insertOrAssign(WriteStatsGenOdfAngleFileFilter::k_GoodVoxelsArrayPath_Key, std::make_any(Constants::k_MaskArrayPath)); + args.insertOrAssign(WriteStatsGenOdfAngleFileFilter::k_MaskArrayPath_Key, std::make_any(Constants::k_MaskArrayPath)); SECTION("default weight < 1") { diff --git a/test/UnitTestCommon/include/complex/UnitTest/UnitTestCommon.hpp b/test/UnitTestCommon/include/complex/UnitTest/UnitTestCommon.hpp index 7863574264..f4a1c24f23 100644 --- a/test/UnitTestCommon/include/complex/UnitTest/UnitTestCommon.hpp +++ b/test/UnitTestCommon/include/complex/UnitTest/UnitTestCommon.hpp @@ -1258,12 +1258,12 @@ inline void ExecuteIdentifySample(DataStructure& dataStructure, const FilterList // Parameter Keys constexpr StringLiteral k_FillHoles_Key = "fill_holes"; constexpr StringLiteral k_ImageGeom_Key = "image_geometry"; - constexpr StringLiteral k_GoodVoxels_Key = "good_voxels"; + constexpr StringLiteral k_MaskArrayPath_Key = "mask_array_path"; Arguments args; args.insertOrAssign(k_FillHoles_Key, std::make_any(false)); args.insertOrAssign(k_ImageGeom_Key, std::make_any(Constants::k_DataContainerPath)); - args.insertOrAssign(k_GoodVoxels_Key, std::make_any(Constants::k_MaskArrayPath)); + args.insertOrAssign(k_MaskArrayPath_Key, std::make_any(Constants::k_MaskArrayPath)); // Preflight the filter and check result auto preflightResult = filter->preflight(dataStructure, args); diff --git a/wrapping/python/examples/basic_ebsd_ipf.ipynb b/wrapping/python/examples/basic_ebsd_ipf.ipynb index baa3d9fa37..80ad84f542 100644 --- a/wrapping/python/examples/basic_ebsd_ipf.ipynb +++ b/wrapping/python/examples/basic_ebsd_ipf.ipynb @@ -170,9 +170,9 @@ " cell_ipf_colors_array_name='IPFColors',\n", " cell_phases_array_path=cx.DataPath(['Small IN100', 'Scan Data', 'Phases']),\n", " crystal_structures_array_path=cx.DataPath(['Small IN100', 'Phase Data', 'CrystalStructures']),\n", - " good_voxels_array_path=cx.DataPath(['Small IN100', 'Scan Data', 'Mask']),\n", + " mask_array_path=cx.DataPath(['Small IN100', 'Scan Data', 'Mask']),\n", " reference_dir=[0, 0, 1],\n", - " use_good_voxels=True,\n", + " use_mask=True,\n", ")\n", "print(f'Warnings: {result.warnings}')\n", "if not result:\n", @@ -253,7 +253,7 @@ " cell_phases_array_path=cx.DataPath(['Small IN100', 'Scan Data', 'Phases']),\n", " crystal_structures_array_path=cx.DataPath(['Small IN100', 'Phase Data', 'CrystalStructures']),\n", " generation_algorithm=1, # Discrete = 1\n", - " good_voxels_array_path=cx.DataPath(['Small IN100', 'Scan Data', 'Mask']),\n", + " mask_array_path=cx.DataPath(['Small IN100', 'Scan Data', 'Mask']),\n", " image_geometry_path=cx.DataPath(['Small IN100 Pole Figure']),\n", " image_layout=0, # O = Horizontal Layout\n", " image_prefix=prefix,\n", @@ -264,7 +264,7 @@ " output_path='/tmp/small_in100_pole_figure',\n", " save_as_image_geometry=True,\n", " title='Small IN100 Slice 1',\n", - " use_good_voxels=True,\n", + " use_mask=True,\n", " write_image_to_disk=True,\n", ")\n", "print(f'Warnings: {result.warnings}')\n", diff --git a/wrapping/python/examples/basic_ebsd_ipf.py b/wrapping/python/examples/basic_ebsd_ipf.py index f01d751f79..56f0c95bb1 100644 --- a/wrapping/python/examples/basic_ebsd_ipf.py +++ b/wrapping/python/examples/basic_ebsd_ipf.py @@ -90,9 +90,9 @@ cell_ipf_colors_array_name="IPFColors", cell_phases_array_path=cx.DataPath(["Small IN100", "Scan Data", "Phases"]), crystal_structures_array_path=cx.DataPath(["Small IN100", "Phase Data", "CrystalStructures"]), - good_voxels_array_path=cx.DataPath(["Small IN100", "Scan Data", "Mask"]), + mask_array_path=cx.DataPath(["Small IN100", "Scan Data", "Mask"]), reference_dir=[0,0,1], - use_good_voxels=True + use_mask=True ) if len(result.errors) != 0: print('Errors: {}', result.errors) @@ -157,7 +157,7 @@ cell_phases_array_path=cx.DataPath(["Small IN100", "Scan Data", "Phases"]), crystal_structures_array_path=cx.DataPath(["Small IN100", "Phase Data", "CrystalStructures"]), generation_algorithm=1, # Discrete = 1 - good_voxels_array_path=cx.DataPath(["Small IN100", "Scan Data", "Mask"]), + mask_array_path=cx.DataPath(["Small IN100", "Scan Data", "Mask"]), image_geometry_path=cx.DataPath(["Small IN100 Pole Figure"]), image_layout=0, # O = Horizontal Layout image_prefix=prefix, @@ -168,7 +168,7 @@ output_path="small_in100_pole_figure", save_as_image_geometry=True, title="Small IN100 Slice 1", - use_good_voxels=True, + use_mask=True, write_image_to_disk=True) if len(result.errors) != 0: print('Errors: {}', result.errors)