diff --git a/src/Plugins/ITKImageProcessing/tools/itk_filter_generator.py b/src/Plugins/ITKImageProcessing/tools/itk_filter_generator.py index 6b4bc31c3f..9de0253f78 100644 --- a/src/Plugins/ITKImageProcessing/tools/itk_filter_generator.py +++ b/src/Plugins/ITKImageProcessing/tools/itk_filter_generator.py @@ -718,7 +718,7 @@ def get_itk_filter_struct(filter_data: FilterData) -> str: auto createFilter() const {{ using FilterType = {filter_type}; - auto filter = FilterType::New();{setters_str} + auto nx_filter = FilterType::New();{setters_str} return filter; }} }};''' diff --git a/wrapping/python/examples/pipelines/ITKImageProcessing/02_Image_Segmentation.py b/wrapping/python/examples/pipelines/ITKImageProcessing/02_Image_Segmentation.py index 55a1c50ad9..d203a4b683 100644 --- a/wrapping/python/examples/pipelines/ITKImageProcessing/02_Image_Segmentation.py +++ b/wrapping/python/examples/pipelines/ITKImageProcessing/02_Image_Segmentation.py @@ -24,9 +24,9 @@ generated_file_list_value.padding_digits = 2 # Instantiate Filter -filter = cxitk.ITKImportImageStack() +nx_filter = cxitk.ITKImportImageStack() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, cell_data_name="Cell Data", image_data_array_path="ImageData", @@ -36,7 +36,7 @@ origin=[0.0, 0.0, 0.0], spacing=[1.0, 1.0, 1.0] ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 2 # Set Up Thresholds and Instantiate Filter @@ -50,9 +50,9 @@ dt = nx.DataType.boolean # This line specifies the DataType for the threshold # Instantiate Filter -filter = nx.MultiThresholdObjects() +nx_filter = nx.MultiThresholdObjects() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, array_thresholds=threshold_set, created_data_path="Mask", @@ -62,14 +62,14 @@ # custom_false_value: float = ..., # Not currently part of the code # custom_true_value: float = ..., # Not currently part of the code ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 3 # Instantiate Filter -filter = nx.ScalarSegmentFeaturesFilter() +nx_filter = nx.ScalarSegmentFeaturesFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, active_array_path="Active", cell_feature_group_path="CellFeatureData", @@ -81,13 +81,13 @@ scalar_tolerance=0, use_mask=True ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 4 # Instantiate Filter -filter = nx.CalculateFeatureSizesFilter() +nx_filter = nx.CalculateFeatureSizesFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, equivalent_diameters_path="EquivalentDiameters", feature_attribute_matrix=nx.DataPath("ImageDataContainer/CellFeatureData"), @@ -97,25 +97,25 @@ save_element_sizes=False, volumes_path="Volumes" ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 5 # Instantiate Filter -filter = nx.CopyFeatureArrayToElementArray() +nx_filter = nx.CopyFeatureArrayToElementArray() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, created_array_suffix="Created Array Suffix", feature_ids_path=nx.DataPath("ImageDataContainer/Cell Data/FeatureIds"), selected_feature_array_path=[nx.DataPath("ImageDataContainer/CellFeatureData/EquivalentDiameters")] ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 6 # Instantiate Filter -filter = nx.CreateDataArray() +nx_filter = nx.CreateDataArray() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, advanced_options=False, component_count=1, @@ -125,13 +125,13 @@ output_data_array=nx.DataPath("ImageDataContainer/Cell Data/Phases") # tuple_dimensions: List[List[float]] = ... # Not currently part of the code ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 7 # Instantiate Filter -filter = nx.ConditionalSetValue() +nx_filter = nx.ConditionalSetValue() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, conditional_array_path=nx.DataPath("ImageDataContainer/Cell Data/Mask"), invert_mask=False, @@ -140,54 +140,54 @@ use_conditional=True # remove_value: str = ..., # Not currently part of the code ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 8 # Instantiate Filter -filter = nx.FindFeaturePhasesFilter() +nx_filter = nx.FindFeaturePhasesFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, cell_features_attribute_matrix_path=nx.DataPath("ImageDataContainer/CellFeatureData"), cell_phases_array_path=nx.DataPath("ImageDataContainer/Cell Data/Phases"), feature_ids_path=nx.DataPath("ImageDataContainer/Cell Data/FeatureIds"), feature_phases_array_name="Phases" ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 9 # Instantiate Filter -filter = nx.FindFeatureCentroidsFilter() +nx_filter = nx.FindFeatureCentroidsFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, centroids_array_path="Centroids", feature_attribute_matrix=nx.DataPath("ImageDataContainer/CellFeatureData"), feature_ids_path=nx.DataPath("ImageDataContainer/Cell Data/FeatureIds"), selected_image_geometry=nx.DataPath("ImageDataContainer") ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 10 # Instantiate Filter -filter = nx.CreateAttributeMatrixFilter() +nx_filter = nx.CreateAttributeMatrixFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, data_object_path=nx.DataPath("Ensemble AttributeMatrix"), tuple_dimensions=[[3.0]] ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 11 # Instantiate Filter -filter = nx.WriteDREAM3DFilter() +nx_filter = nx.WriteDREAM3DFilter() # Execute Filter with Parameters output_file_path = nxtest.GetDataDirectory() + "/Output/ImagesStack/Images.dream3d" -result = filter.execute(data_structure=data_structure, +result = nx_filter.execute(data_structure=data_structure, export_file_path=output_file_path, write_xdmf_file=True) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # ***************************************************************************** # THIS SECTION IS ONLY HERE FOR CLEANING UP THE CI Machines diff --git a/wrapping/python/examples/pipelines/ITKImageProcessing/03_Porosity_Mesh_Export.py b/wrapping/python/examples/pipelines/ITKImageProcessing/03_Porosity_Mesh_Export.py index fc4f6d03f7..04156af101 100644 --- a/wrapping/python/examples/pipelines/ITKImageProcessing/03_Porosity_Mesh_Export.py +++ b/wrapping/python/examples/pipelines/ITKImageProcessing/03_Porosity_Mesh_Export.py @@ -11,7 +11,7 @@ # Filter 1 # Instantiate Filter -filter = cxitk.ITKImportImageStack() +nx_filter = cxitk.ITKImportImageStack() generated_file_list_value = nx.GeneratedFileListParameter.ValueType() generated_file_list_value.input_path = nxtest.GetDataDirectory() + "/Porosity_Image/" @@ -27,7 +27,7 @@ # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, cell_data_name="Cell Data", image_data_array_path="ImageData", @@ -37,7 +37,7 @@ origin=[0.0, 0.0, 0.0], spacing=[1.0, 1.0, 1.0] ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 2 # Set Up Thresholds and Instantiate Filter @@ -51,9 +51,9 @@ dt = nx.DataType.boolean # Instantiate Filter -filter = nx.MultiThresholdObjects() +nx_filter = nx.MultiThresholdObjects() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, array_thresholds=threshold_set, created_data_path="Mask", @@ -63,13 +63,13 @@ # custom_false_value: float = ..., # Not currently part of the code # custom_true_value: float = ..., # Not currently part of the code ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 3 # Instantiate Filter -filter = nx.ScalarSegmentFeaturesFilter() +nx_filter = nx.ScalarSegmentFeaturesFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, active_array_path="Active", cell_feature_group_path="CellFeatureData", @@ -81,13 +81,13 @@ scalar_tolerance=0, use_mask=True ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 4 # Instantiate Filter -filter = nx.QuickSurfaceMeshFilter() +nx_filter = nx.QuickSurfaceMeshFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, face_data_group_name="Face Data", face_feature_attribute_matrix_name="Face Feature Data", @@ -101,14 +101,14 @@ triangle_geometry_name=nx.DataPath("TriangleDataContainer"), vertex_data_group_name="Vertex Data" ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 5 # Instantiate Filter -filter = nx.LaplacianSmoothingFilter() +nx_filter = nx.LaplacianSmoothingFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, iteration_steps=15, lambda_value=0.2, @@ -122,13 +122,13 @@ triple_line_lambda=0.1, use_taubin_smoothing=True ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 6 # Instantiate Filter -filter = nx.SplitAttributeArrayFilter() +nx_filter = nx.SplitAttributeArrayFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, delete_original_array=True, multicomponent_array=nx.DataPath("TriangleDataContainer/Face Data/FaceLabels"), @@ -136,7 +136,7 @@ select_components_to_extract=False # components_to_extract: List[List[float]] = ..., # Not currently part of the code ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 7 @@ -151,9 +151,9 @@ dt = nx.DataType.boolean # This line specifies the DataType for the threshold # Instantiate Filter -filter = nx.MultiThresholdObjects() +nx_filter = nx.MultiThresholdObjects() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, array_thresholds=threshold_set, created_data_path="FaceLabels-0 Mask", @@ -163,7 +163,7 @@ # custom_false_value: float = ..., # Not currently part of the code # custom_true_value: float = ..., # Not currently part of the code ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 8 @@ -178,9 +178,9 @@ dt = nx.DataType.boolean # This line specifies the DataType for the threshold # Instantiate Filter -filter = nx.MultiThresholdObjects() +nx_filter = nx.MultiThresholdObjects() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, array_thresholds=threshold_set, created_data_path="FaceLabels-1 Mask", @@ -190,13 +190,13 @@ # custom_false_value: float = ..., # Not currently part of the code # custom_true_value: float = ..., # Not currently part of the code ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 9 # Instantiate Filter -filter = nx.ConditionalSetValue() +nx_filter = nx.ConditionalSetValue() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, conditional_array_path=nx.DataPath("TriangleDataContainer/Face Data/FaceLabels-0 Mask"), invert_mask=False, @@ -205,14 +205,14 @@ use_conditional=True # remove_value: str = ..., # Not currently part of the code ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 10 # Instantiate Filter -filter = nx.ConditionalSetValue() +nx_filter = nx.ConditionalSetValue() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, conditional_array_path=nx.DataPath("TriangleDataContainer/Face Data/FaceLabels-1 Mask"), invert_mask=False, @@ -221,13 +221,13 @@ use_conditional=True # remove_value: str = ..., # Not currently part of the code ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 11 # Instantiate Filter -filter = nx.CombineAttributeArraysFilter() +nx_filter = nx.CombineAttributeArraysFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, move_values=True, normalize_data=False, @@ -237,19 +237,19 @@ nx.DataPath("TriangleDataContainer/Face Data/FaceLabels-1") ] ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 12 # Instantiate Filter -filter = nx.WriteDREAM3DFilter() +nx_filter = nx.WriteDREAM3DFilter() # Execute Filter with Parameters output_file_path = nxtest.GetDataDirectory() + "/Output/Porosity_Analysis.dream3d" -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, export_file_path=output_file_path, write_xdmf_file=True ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # ***************************************************************************** # THIS SECTION IS ONLY HERE FOR CLEANING UP THE CI Machines diff --git a/wrapping/python/examples/pipelines/Incomplete/ImportBrukerNanoEspritData.py b/wrapping/python/examples/pipelines/Incomplete/ImportBrukerNanoEspritData.py index 8fd56ede00..84f5a9d83f 100644 --- a/wrapping/python/examples/pipelines/Incomplete/ImportBrukerNanoEspritData.py +++ b/wrapping/python/examples/pipelines/Incomplete/ImportBrukerNanoEspritData.py @@ -11,9 +11,9 @@ # Filter 1 # Instantiate Filter -filter = cxor.ReadH5OimDataFilter() +nx_filter = cxor.ReadH5OimDataFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, cell_attribute_matrix_name=("Cell Data"), cell_ensemble_attribute_matrix_name=("Cell Ensemble Data"), @@ -23,18 +23,18 @@ #selected_scan_names: ValueType = ..., z_spacing=1.0 ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 2 # Define output file path output_file_path = nxtest.GetDataDirectory() + "/Output/H5EspritData/H5EspritData.dream3d" # Instantiate Filter -filter = cx.WriteDREAM3DFilter() +nx_filter = cx.WriteDREAM3DFilter() # Execute WriteDREAM3DFilter with Parameters -result = filter.execute(data_structure=data_structure, +result = nx_filter.execute(data_structure=data_structure, export_file_path=output_file_path, write_xdmf_file=True ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) print("===> Pipeline Complete") \ No newline at end of file diff --git a/wrapping/python/examples/pipelines/Incomplete/ImportEdaxOIMData.py b/wrapping/python/examples/pipelines/Incomplete/ImportEdaxOIMData.py index 2327a69ad9..4b65311a17 100644 --- a/wrapping/python/examples/pipelines/Incomplete/ImportEdaxOIMData.py +++ b/wrapping/python/examples/pipelines/Incomplete/ImportEdaxOIMData.py @@ -11,9 +11,9 @@ # Filter 1 # Instantiate Filter -filter = cxor.ReadH5OimDataFilter() +nx_filter = cxor.ReadH5OimDataFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, cell_attribute_matrix_name=("Cell Data"), cell_ensemble_attribute_matrix_name=("Cell Ensemble Data"), @@ -22,24 +22,24 @@ read_pattern_data=False, z_spacing=1.0 ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 2 # Instantiate Filter -filter = cxor.RotateEulerRefFrameFilter() +nx_filter = cxor.RotateEulerRefFrameFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, euler_angles_array_path=cx.DataPath("ImageGeom/Cell Data/EulerAngles"), rotation_axis=[0.0, 0.0, 1.0, 90.0] ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 3 # Instantiate Filter -filter = cx.RotateSampleRefFrameFilter() +nx_filter = cx.RotateSampleRefFrameFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, remove_original_geometry=True, rotate_slice_by_slice=True, @@ -47,18 +47,18 @@ rotation_representation=("Axis Angle"), selected_image_geometry=cx.DataPath("ImageGeom") ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 4 # Define output file path output_file_path = nxtest.GetDataDirectory() + "/Output/EdaxOIMData/EdaxOIMData.dream3d" # Instantiate Filter -filter = cx.WriteDREAM3DFilter() +nx_filter = cx.WriteDREAM3DFilter() # Execute WriteDREAM3DFilter with Parameters -result = filter.execute(data_structure=data_structure, +result = nx_filter.execute(data_structure=data_structure, export_file_path=output_file_path, write_xdmf_file=True ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) print("===> Pipeline Complete") \ No newline at end of file diff --git a/wrapping/python/examples/pipelines/OrientationAnalysis/01_Small_IN100_Archive.py b/wrapping/python/examples/pipelines/OrientationAnalysis/01_Small_IN100_Archive.py index 36def1428b..cd49e152ac 100644 --- a/wrapping/python/examples/pipelines/OrientationAnalysis/01_Small_IN100_Archive.py +++ b/wrapping/python/examples/pipelines/OrientationAnalysis/01_Small_IN100_Archive.py @@ -24,9 +24,9 @@ generated_file_list_value.increment_index = 1 generated_file_list_value.padding_digits = 0 -filter = cxor.EbsdToH5EbsdFilter() +nx_filter = cxor.EbsdToH5EbsdFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, input_file_list_info=generated_file_list_value, output_file_path=nxtest.GetDataDirectory() + "/Output/Reconstruction/Small_IN100.h5ebsd", @@ -35,6 +35,6 @@ z_spacing=0.25 ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) print("===> Pipeline Complete") \ No newline at end of file diff --git a/wrapping/python/examples/pipelines/OrientationAnalysis/01_Small_IN100_Morphological_Statistics.py b/wrapping/python/examples/pipelines/OrientationAnalysis/01_Small_IN100_Morphological_Statistics.py index c36dc2598f..8c728e6907 100644 --- a/wrapping/python/examples/pipelines/OrientationAnalysis/01_Small_IN100_Morphological_Statistics.py +++ b/wrapping/python/examples/pipelines/OrientationAnalysis/01_Small_IN100_Morphological_Statistics.py @@ -16,45 +16,45 @@ import_data.data_paths = None # Instantiate Filter -filter = nx.ReadDREAM3DFilter() +nx_filter = nx.ReadDREAM3DFilter() # Execute Filter with Parameters -result = filter.execute(data_structure=data_structure, +result = nx_filter.execute(data_structure=data_structure, import_file_data=import_data ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 2 # Instantiate Filter -filter = nx.DeleteData() +nx_filter = nx.DeleteData() # Execute Filter With Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, removed_data_path=[nx.DataPath("DataContainer/CellFeatureData/EquivalentDiameters"), nx.DataPath("DataContainer/CellFeatureData/NumElements"), nx.DataPath("DataContainer/CellFeatureData/NumNeighbors"), nx.DataPath("DataContainer/CellFeatureData/NumNeighbors2")] ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 3 # Instantiate Filter -filter = nx.FindFeatureCentroidsFilter() +nx_filter = nx.FindFeatureCentroidsFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, centroids_array_path=("Centroids"), feature_attribute_matrix=nx.DataPath("DataContainer/CellFeatureData"), feature_ids_path=nx.DataPath("DataContainer/CellData/FeatureIds"), selected_image_geometry=nx.DataPath("DataContainer") ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 4 # Instantiate Filter -filter = nx.CalculateFeatureSizesFilter() +nx_filter = nx.CalculateFeatureSizesFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, equivalent_diameters_path=("EquivalentDiameters"), feature_attribute_matrix=nx.DataPath("DataContainer/CellFeatureData"), @@ -64,14 +64,14 @@ save_element_sizes=False, volumes_path=("Size Volumes") ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 5 # Instantiate Filter -filter = cxor.FindShapesFilter() +nx_filter = cxor.FindShapesFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, aspect_ratios_array_name=("AspectRatios"), axis_euler_angles_array_name=("AxisEulerAngles"), @@ -82,14 +82,14 @@ selected_image_geometry=nx.DataPath("DataContainer"), volumes_array_name=("Shape Volumes") ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 6 # Instantiate Filter -filter = nx.FindNeighbors() +nx_filter = nx.FindNeighbors() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, # Boundary cells parameter is not currently part of the code # boundary_cells: str = ..., @@ -104,15 +104,15 @@ # surface_features: str = ..., store_surface_features=False ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 7 # Instantiate Filter -filter = nx.FindNeighborhoodsFilter() +nx_filter = nx.FindNeighborhoodsFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, centroids_array_path=nx.DataPath("DataContainer/CellFeatureData/Centroids"), equivalent_diameters_array_path=nx.DataPath("DataContainer/CellFeatureData/EquivalentDiameters"), @@ -122,14 +122,14 @@ neighborhoods_array_name=("Neighborhoods"), selected_image_geometry_path=nx.DataPath("DataContainer") ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 8 # Instantiate Filter -filter = nx.FindEuclideanDistMapFilter() +nx_filter = nx.FindEuclideanDistMapFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, calc_manhattan_dist=True, do_boundaries=True, @@ -144,14 +144,14 @@ selected_image_geometry=nx.DataPath("DataContainer"), t_jdistances_array_name=("TJManhattanDistances") ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 9 # Instantiate Filter -filter = nx.FindSurfaceAreaToVolumeFilter() +nx_filter = nx.FindSurfaceAreaToVolumeFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, calculate_sphericity=True, feature_ids_path=nx.DataPath("DataContainer/CellData/FeatureIds"), @@ -160,21 +160,21 @@ sphericity_array_name=("Sphericity"), surface_area_volume_ratio_array_name=("SurfaceAreaVolumeRatio") ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 10 # Set Output File Path output_file_path = nxtest.GetDataDirectory() + "/Output/Statistics/SmallIN100_Morph.dream3d" # Instantiate Filter -filter = nx.WriteDREAM3DFilter() +nx_filter = nx.WriteDREAM3DFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, export_file_path=output_file_path, write_xdmf_file=True ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # ***************************************************************************** # THIS SECTION IS ONLY HERE FOR CLEANING UP THE CI Machines diff --git a/wrapping/python/examples/pipelines/OrientationAnalysis/01_Small_IN100_Quick_Mesh.py b/wrapping/python/examples/pipelines/OrientationAnalysis/01_Small_IN100_Quick_Mesh.py index 4a25dba412..72aa5b42a2 100644 --- a/wrapping/python/examples/pipelines/OrientationAnalysis/01_Small_IN100_Quick_Mesh.py +++ b/wrapping/python/examples/pipelines/OrientationAnalysis/01_Small_IN100_Quick_Mesh.py @@ -15,18 +15,18 @@ import_data.file_path = nxtest.GetDataDirectory() + "/Output/Statistics/SmallIN100_CrystalStats.dream3d" import_data.data_paths = None # Instantiate Filter -filter = nx.ReadDREAM3DFilter() +nx_filter = nx.ReadDREAM3DFilter() # Execute Filter with Parameters -result = filter.execute(data_structure=data_structure, +result = nx_filter.execute(data_structure=data_structure, import_file_data=import_data) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 2 # Instantiate Filter -filter = nx.CropImageGeometry() +nx_filter = nx.CropImageGeometry() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, cell_feature_attribute_matrix=nx.DataPath("DataContainer/CellFeatureData"), feature_ids=nx.DataPath("DataContainer/CellData/FeatureIds"), @@ -36,24 +36,24 @@ renumber_features=True, selected_image_geometry=nx.DataPath("DataContainer") ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 3 # Instantiate Filter -#filter = nx.MoveData() +#nx_filter = nx.MoveData() # Execute Filter with Parameters -#result = filter.execute( +#result = nx_filter.execute( # data_structure=data_structure, # data=[nx.DataPath("DataContainer/CellEnsembleData")], # new_parent=nx.DataPath("DataContainer") # ) -# nxtest.check_filter_result(filter, result) +# nxtest.check_filter_result(nx_filter, result) # Filter 4 # Instantiate Filter -filter = nx.QuickSurfaceMeshFilter() +nx_filter = nx.QuickSurfaceMeshFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, face_data_group_name=("FaceData"), face_feature_attribute_matrix_name=("Face Feature Data"), @@ -66,20 +66,20 @@ triangle_geometry_name=nx.DataPath("TriangleDataContainer"), vertex_data_group_name=("VertexData") ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 5 # Set Output File Path output_file_path = nxtest.GetDataDirectory() + "/Output/SurfaceMesh/SmallIN100_Mesh.dream3d" # Instantiate Filter -filter = nx.WriteDREAM3DFilter() +nx_filter = nx.WriteDREAM3DFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, export_file_path=output_file_path, write_xdmf_file=True ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # ***************************************************************************** diff --git a/wrapping/python/examples/pipelines/OrientationAnalysis/02_Small_IN100_Smooth_Mesh.py b/wrapping/python/examples/pipelines/OrientationAnalysis/02_Small_IN100_Smooth_Mesh.py index 4ed71d3d28..75184fb7f3 100644 --- a/wrapping/python/examples/pipelines/OrientationAnalysis/02_Small_IN100_Smooth_Mesh.py +++ b/wrapping/python/examples/pipelines/OrientationAnalysis/02_Small_IN100_Smooth_Mesh.py @@ -15,16 +15,16 @@ import_data.file_path = nxtest.GetDataDirectory() + "/Output/SurfaceMesh/SmallIN100_Mesh.dream3d" import_data.data_paths = None # Instantiate Filter -filter = nx.ReadDREAM3DFilter() +nx_filter = nx.ReadDREAM3DFilter() # Execute Filter with Parameters -result = filter.execute(data_structure=data_structure, import_file_data=import_data) -nxtest.check_filter_result(filter, result) +result = nx_filter.execute(data_structure=data_structure, import_file_data=import_data) +nxtest.check_filter_result(nx_filter, result) # Filter 2 # Instantiate Filter -filter = nx.LaplacianSmoothingFilter() +nx_filter = nx.LaplacianSmoothingFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, iteration_steps=100, lambda_value=0.25, @@ -38,18 +38,18 @@ triple_line_lambda=0.2, use_taubin_smoothing=True ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 3 # Instantiate Filter -filter = nx.WriteDREAM3DFilter() +nx_filter = nx.WriteDREAM3DFilter() # Set Output File Path output_file_path = nxtest.GetDataDirectory() + "/Output/SurfaceMesh/SmallIN100_Smoothed.dream3d" # Execute Filter with Parameters -result = filter.execute(data_structure=data_structure, +result = nx_filter.execute(data_structure=data_structure, export_file_path=output_file_path, write_xdmf_file=True) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # ***************************************************************************** # THIS SECTION IS ONLY HERE FOR CLEANING UP THE CI Machines diff --git a/wrapping/python/examples/pipelines/OrientationAnalysis/03_Small_IN100_Mesh_Statistics.py b/wrapping/python/examples/pipelines/OrientationAnalysis/03_Small_IN100_Mesh_Statistics.py index ee267936ff..62e874d95c 100644 --- a/wrapping/python/examples/pipelines/OrientationAnalysis/03_Small_IN100_Mesh_Statistics.py +++ b/wrapping/python/examples/pipelines/OrientationAnalysis/03_Small_IN100_Mesh_Statistics.py @@ -15,49 +15,49 @@ import_data.file_path = nxtest.GetDataDirectory() + "/Output/SurfaceMesh/SmallIN100_Smoothed.dream3d" import_data.data_paths = None # Instantiate Filter -filter = nx.ReadDREAM3DFilter() +nx_filter = nx.ReadDREAM3DFilter() # Execute Filter with Parameters -result = filter.execute(data_structure=data_structure, import_file_data=import_data) -nxtest.check_filter_result(filter, result) +result = nx_filter.execute(data_structure=data_structure, import_file_data=import_data) +nxtest.check_filter_result(nx_filter, result) # Filter 2 # Instantiate Filter -filter = nx.CalculateTriangleAreasFilter() +nx_filter = nx.CalculateTriangleAreasFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, triangle_areas_array_path="FaceAreas", triangle_geometry_data_path=nx.DataPath("TriangleDataContainer") ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 3 # Instantiate Filter -filter = nx.TriangleNormalFilter() +nx_filter = nx.TriangleNormalFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, surface_mesh_triangle_normals_array_path="FaceNormals", tri_geometry_data_path=nx.DataPath("TriangleDataContainer") ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 4 # Instantiate Filter -filter = nx.TriangleDihedralAngleFilter() +nx_filter = nx.TriangleDihedralAngleFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, surface_mesh_triangle_dihedral_angles_array_name="FaceDihedralAngles", tri_geometry_data_path=nx.DataPath("TriangleDataContainer") ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 5 # Instantiate Filter -filter = cxor.GenerateFaceIPFColoringFilter() +nx_filter = cxor.GenerateFaceIPFColoringFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, crystal_structures_array_path=nx.DataPath("DataContainer/CellEnsembleData/CrystalStructures"), feature_euler_angles_array_path=nx.DataPath("DataContainer/CellFeatureData/AvgEulerAngles"), @@ -66,13 +66,13 @@ surface_mesh_face_labels_array_path=nx.DataPath("TriangleDataContainer/FaceData/FaceLabels"), surface_mesh_face_normals_array_path=nx.DataPath("TriangleDataContainer/FaceData/FaceNormals") ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 6 # Instantiate Filter -filter = cxor.GenerateFaceMisorientationColoringFilter() +nx_filter = cxor.GenerateFaceMisorientationColoringFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, avg_quats_array_path=nx.DataPath("DataContainer/CellFeatureData/AvgQuats"), crystal_structures_array_path=nx.DataPath("DataContainer/CellEnsembleData/CrystalStructures"), @@ -80,13 +80,13 @@ surface_mesh_face_labels_array_path=nx.DataPath("TriangleDataContainer/FaceData/FaceLabels"), surface_mesh_face_misorientation_colors_array_name="FaceMisorientationColors" ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 7 # Instantiate Filter -filter = nx.SharedFeatureFaceFilter() +nx_filter = nx.SharedFeatureFaceFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, face_labels_array_path=nx.DataPath("TriangleDataContainer/FaceData/FaceLabels"), feature_face_ids_array_name="SharedFeatureFaceId", @@ -96,20 +96,20 @@ randomize_features=False, triangle_geometry_path=nx.DataPath("TriangleDataContainer") ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 8 # Instantiate Filter -filter = nx.WriteDREAM3DFilter() +nx_filter = nx.WriteDREAM3DFilter() # Execute Filter with Parameters output_file_path = nxtest.GetDataDirectory() + "/Output/SurfaceMesh/SmallIN100_MeshStats.dream3d" -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, export_file_path=output_file_path, write_xdmf_file=True ) # Check result for errors or warnings -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # ***************************************************************************** # THIS SECTION IS ONLY HERE FOR CLEANING UP THE CI Machines diff --git a/wrapping/python/examples/pipelines/OrientationAnalysis/04_Small_IN100_GBCD.py b/wrapping/python/examples/pipelines/OrientationAnalysis/04_Small_IN100_GBCD.py index 6a4c79dc7a..13bca5d555 100644 --- a/wrapping/python/examples/pipelines/OrientationAnalysis/04_Small_IN100_GBCD.py +++ b/wrapping/python/examples/pipelines/OrientationAnalysis/04_Small_IN100_GBCD.py @@ -15,16 +15,16 @@ import_data.file_path = nxtest.GetDataDirectory() + "/Output/SurfaceMesh/SmallIN100_MeshStats.dream3d" import_data.data_paths = None # Instantiate Filter -filter = nx.ReadDREAM3DFilter() +nx_filter = nx.ReadDREAM3DFilter() # Execute Filter with Parameters -result = filter.execute(data_structure=data_structure, import_file_data=import_data) -nxtest.check_filter_result(filter, result) +result = nx_filter.execute(data_structure=data_structure, import_file_data=import_data) +nxtest.check_filter_result(nx_filter, result) # Filter 2 # Instantiate Filter -filter = cxor.FindGBCDFilter() +nx_filter = cxor.FindGBCDFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, crystal_structures_array_path=nx.DataPath("DataContainer/CellEnsembleData/CrystalStructures"), face_ensemble_attribute_matrix_name="FaceEnsembleData", @@ -37,14 +37,14 @@ surface_mesh_face_normals_array_path=nx.DataPath("TriangleDataContainer/FaceData/FaceNormals"), triangle_geometry=nx.DataPath("TriangleDataContainer") ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 3 # Instantiate Filter -filter = cxor.GenerateGBCDPoleFigureFilter() +nx_filter = cxor.GenerateGBCDPoleFigureFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, cell_attribute_matrix_name="Cell Data", cell_intensity_array_name="MRD", @@ -55,13 +55,13 @@ output_image_dimension=100, phase_of_interest=1 ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 4 # Instantiate Filter -filter = cxor.GenerateGBCDPoleFigureFilter() +nx_filter = cxor.GenerateGBCDPoleFigureFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, cell_attribute_matrix_name="Cell Data", cell_intensity_array_name="MRD", @@ -72,13 +72,13 @@ output_image_dimension=100, phase_of_interest=1 ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 5 # Instantiate Filter -filter = cxor.GenerateGBCDPoleFigureFilter() +nx_filter = cxor.GenerateGBCDPoleFigureFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, cell_attribute_matrix_name="Cell Data", cell_intensity_array_name="MRD", @@ -89,13 +89,13 @@ output_image_dimension=100, phase_of_interest=1 ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 6 # Instantiate Filter -filter = cxor.WriteGBCDGMTFileFilter() +nx_filter = cxor.WriteGBCDGMTFileFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, crystal_structures_array_path=nx.DataPath("DataContainer/CellEnsembleData/CrystalStructures"), gbcd_array_path=nx.DataPath("TriangleDataContainer/FaceEnsembleData/GBCD"), @@ -103,13 +103,13 @@ output_file="Data/Output/SmallIN100GBCD/SmallIn100GMT_1.dat", phase_of_interest=1 ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 7 # Instantiate Filter -filter = cxor.WriteGBCDTriangleDataFilter() +nx_filter = cxor.WriteGBCDTriangleDataFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, feature_euler_angles_array_path=nx.DataPath("DataContainer/CellFeatureData/AvgEulerAngles"), output_file="Data/Output/SmallIN100GBCD/SmallIn100Triangles.ph", @@ -117,19 +117,19 @@ surface_mesh_face_labels_array_path=nx.DataPath("TriangleDataContainer/FaceData/FaceLabels"), surface_mesh_face_normals_array_path=nx.DataPath("TriangleDataContainer/FaceData/FaceNormals") ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 8 # Instantiate Filter -filter = nx.WriteDREAM3DFilter() +nx_filter = nx.WriteDREAM3DFilter() # Set Output File Path output_file_path = nxtest.GetDataDirectory() + "/Output/SurfaceMesh/SmallIN100_GBCD.dream3d" # Execute Filter with Parameters -result = filter.execute(data_structure=data_structure, +result = nx_filter.execute(data_structure=data_structure, export_file_path=output_file_path, write_xdmf_file=True ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # ***************************************************************************** # THIS SECTION IS ONLY HERE FOR CLEANING UP THE CI Machines diff --git a/wrapping/python/examples/pipelines/OrientationAnalysis/05_Small_IN100_Crystallographic_Statistics.py b/wrapping/python/examples/pipelines/OrientationAnalysis/05_Small_IN100_Crystallographic_Statistics.py index c25193920e..72bca2e73d 100644 --- a/wrapping/python/examples/pipelines/OrientationAnalysis/05_Small_IN100_Crystallographic_Statistics.py +++ b/wrapping/python/examples/pipelines/OrientationAnalysis/05_Small_IN100_Crystallographic_Statistics.py @@ -15,38 +15,38 @@ import_data.file_path = nxtest.GetDataDirectory() + "/Output/Statistics/SmallIN100_Morph.dream3d" import_data.data_paths = None # Instantiate Filter -filter = nx.ReadDREAM3DFilter() +nx_filter = nx.ReadDREAM3DFilter() # Execute Filter with Parameters -result = filter.execute(data_structure=data_structure, import_file_data=import_data) -nxtest.check_filter_result(filter, result) +result = nx_filter.execute(data_structure=data_structure, import_file_data=import_data) +nxtest.check_filter_result(nx_filter, result) # Filter 2 # Instantiate Filter -filter = nx.DeleteData() +nx_filter = nx.DeleteData() # Execute Filter With Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, removed_data_path=[nx.DataPath("DataContainer/CellFeatureData/AvgQuats"), nx.DataPath("DataContainer/CellFeatureData/AvgEulerAngles")] ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 3 # Instantiate and Execute Filter # Note: This filter might need additional parameters depending on the intended data removal. -filter = nx.DeleteData() -result = filter.execute( +nx_filter = nx.DeleteData() +result = nx_filter.execute( data_structure=data_structure # removed_data_path: List[DataPath] = ... # Not currently part of the code ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 4 # Instantiate Filter -filter = cxor.FindAvgOrientationsFilter() +nx_filter = cxor.FindAvgOrientationsFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, avg_euler_angles_array_path="AvgEulerAngles", avg_quats_array_path="AvgQuats", @@ -56,13 +56,13 @@ cell_quats_array_path=nx.DataPath("DataContainer/CellData/Quats"), crystal_structures_array_path=nx.DataPath("DataContainer/CellEnsembleData/CrystalStructures") ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 5 # Instantiate Filter -filter = cxor.FindMisorientationsFilter() +nx_filter = cxor.FindMisorientationsFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, avg_quats_array_path=nx.DataPath("DataContainer/CellFeatureData/AvgQuats"), crystal_structures_array_path=nx.DataPath("DataContainer/CellEnsembleData/CrystalStructures"), @@ -72,13 +72,13 @@ neighbor_list_array_path=nx.DataPath("DataContainer/CellFeatureData/NeighborhoodList") # avg_misorientations_array_name: str = ..., # Not currently part of the code ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 6 # Instantiate Filter -filter = cxor.FindSchmidsFilter() +nx_filter = cxor.FindSchmidsFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, avg_quats_array_path=nx.DataPath("DataContainer/CellFeatureData/AvgQuats"), crystal_structures_array_path=nx.DataPath("DataContainer/CellEnsembleData/CrystalStructures"), @@ -94,13 +94,13 @@ # slip_direction: List[float] = ..., # Not currently part of the code # slip_plane: List[float] = ..., # Not currently part of the code ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 7 # Instantiate Filter -filter = cxor.FindFeatureReferenceMisorientationsFilter() +nx_filter = cxor.FindFeatureReferenceMisorientationsFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, avg_quats_array_path=nx.DataPath("DataContainer/CellFeatureData/AvgQuats"), cell_phases_array_path=nx.DataPath("DataContainer/CellData/Phases"), @@ -113,13 +113,13 @@ # cell_feature_attribute_matrix_path=nx.DataPath("DataContainer/"), # Not currently part of the code # g_beuclidean_distances_array_path=nx.DataPath("DataContainer/"), # Not currently part of the code ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 8 # Instantiate Filter -filter = cxor.FindKernelAvgMisorientationsFilter() +nx_filter = cxor.FindKernelAvgMisorientationsFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, cell_phases_array_path=nx.DataPath("DataContainer/CellData/Phases"), crystal_structures_array_path=nx.DataPath("DataContainer/CellEnsembleData/CrystalStructures"), @@ -129,20 +129,20 @@ quats_array_path=nx.DataPath("DataContainer/CellData/Quats"), selected_image_geometry_path=nx.DataPath("DataContainer") ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 9 # Instantiate Filter -filter = nx.WriteDREAM3DFilter() +nx_filter = nx.WriteDREAM3DFilter() # Set Output File Path output_file_path = nxtest.GetDataDirectory() + "/Output/Statistics/SmallIN100_CrystalStats.dream3d" # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, export_file_path=output_file_path, write_xdmf_file=True ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # ***************************************************************************** # THIS SECTION IS ONLY HERE FOR CLEANING UP THE CI Machines diff --git a/wrapping/python/examples/pipelines/OrientationAnalysis/05_Small_IN100_GBCD_Metric.py b/wrapping/python/examples/pipelines/OrientationAnalysis/05_Small_IN100_GBCD_Metric.py index c4fb2b1809..cafeda240b 100644 --- a/wrapping/python/examples/pipelines/OrientationAnalysis/05_Small_IN100_GBCD_Metric.py +++ b/wrapping/python/examples/pipelines/OrientationAnalysis/05_Small_IN100_GBCD_Metric.py @@ -73,18 +73,18 @@ ] # Instantiate Filter -filter = nx.ReadDREAM3DFilter() +nx_filter = nx.ReadDREAM3DFilter() # Execute Filter with Parameters -result = filter.execute(data_structure=data_structure, +result = nx_filter.execute(data_structure=data_structure, import_file_data=import_data) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 2 # Instantiate Filter -filter = nx.SharedFeatureFaceFilter() +nx_filter = nx.SharedFeatureFaceFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, face_labels_array_path=nx.DataPath("TriangleDataContainer/FaceData/FaceLabels"), feature_face_ids_array_name="SharedFeatureFaceId", @@ -94,13 +94,13 @@ randomize_features=False, triangle_geometry_path=nx.DataPath("TriangleDataContainer") ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 3 # Instantiate Filter -filter = cxor.FindGBCDMetricBasedFilter() +nx_filter = cxor.FindGBCDMetricBasedFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, chosen_limit_dists=0, crystal_structures_array_path=nx.DataPath("DataContainer/CellEnsembleData/CrystalStructures"), @@ -120,20 +120,20 @@ surface_mesh_feature_face_labels_array_path=nx.DataPath("TriangleDataContainer/SharedFeatureFace/FaceLabels"), triangle_geometry_path=nx.DataPath("TriangleDataContainer") ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 4 # Instantiate Filter -filter = nx.WriteDREAM3DFilter() +nx_filter = nx.WriteDREAM3DFilter() # Set Output File Path output_file_path = nxtest.GetDataDirectory() + "/Output/SurfaceMesh/SmallIN100_GBCD_Metric.dream3d" # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, export_file_path=output_file_path, write_xdmf_file=True ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # ***************************************************************************** # THIS SECTION IS ONLY HERE FOR CLEANING UP THE CI Machines diff --git a/wrapping/python/examples/pipelines/OrientationAnalysis/08_Small_IN100_Full_Reconstruction.py b/wrapping/python/examples/pipelines/OrientationAnalysis/08_Small_IN100_Full_Reconstruction.py index c1aa767dcb..a151fb004c 100644 --- a/wrapping/python/examples/pipelines/OrientationAnalysis/08_Small_IN100_Full_Reconstruction.py +++ b/wrapping/python/examples/pipelines/OrientationAnalysis/08_Small_IN100_Full_Reconstruction.py @@ -20,16 +20,16 @@ filter_parameter.start_slice=6 filter_parameter.use_recommended_transform=True -filter = cxor.ReadH5EbsdFilter() +nx_filter = cxor.ReadH5EbsdFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, cell_attribute_matrix_name="CellData", cell_ensemble_attribute_matrix_name="CellEnsembleData", data_container_name=nx.DataPath("DataContainer"), read_h5_ebsd_parameter=filter_parameter ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 2 # Set Up Thresholds and Instantiate Filter @@ -48,21 +48,21 @@ dt = nx.DataType.boolean # Instantiate Filter -filter = nx.MultiThresholdObjects() +nx_filter = nx.MultiThresholdObjects() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, array_thresholds=threshold_set, created_data_path="Mask", created_mask_type=nx.DataType.boolean ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 3 # Instantiate Filter -filter = cxor.ConvertOrientations() +nx_filter = cxor.ConvertOrientations() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, input_orientation_array_path=nx.DataPath("DataContainer/CellData/EulerAngles"), input_type=0, @@ -70,13 +70,13 @@ output_type=2 ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 4 # Instantiate Filter -filter = cxor.AlignSectionsMisorientationFilter() +nx_filter = cxor.AlignSectionsMisorientationFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, cell_phases_array_path=nx.DataPath("DataContainer/CellData/Phases"), crystal_structures_array_path=nx.DataPath("DataContainer/CellEnsembleData/CrystalStructures"), @@ -88,25 +88,25 @@ write_alignment_shifts=False # alignment_shift_file_name: PathLike = ..., # Not currently part of the code ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 5 # Instantiate Filter -filter = nx.IdentifySample() +nx_filter = nx.IdentifySample() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, fill_holes=False, mask_array_path=nx.DataPath("DataContainer/CellData/Mask"), image_geometry=nx.DataPath("DataContainer") ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 6 # Instantiate Filter -filter = nx.AlignSectionsFeatureCentroidFilter() +nx_filter = nx.AlignSectionsFeatureCentroidFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, mask_array_path=nx.DataPath("DataContainer/CellData/Mask"), reference_slice=0, @@ -116,14 +116,14 @@ write_alignment_shifts=False # alignment_shift_file_name: PathLike = ..., # Not currently part of the code ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 7 # Instantiate Filter -filter = cxor.BadDataNeighborOrientationCheckFilter() +nx_filter = cxor.BadDataNeighborOrientationCheckFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, cell_phases_array_path=nx.DataPath("DataContainer/CellData/Phases"), crystal_structures_array_path=nx.DataPath("DataContainer/CellEnsembleData/CrystalStructures"), @@ -133,13 +133,13 @@ number_of_neighbors=4, quats_array_path=nx.DataPath("DataContainer/CellData/Quats") ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 8 # Instantiate Filter -filter = cxor.NeighborOrientationCorrelationFilter() +nx_filter = cxor.NeighborOrientationCorrelationFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, cell_phases_array_path=nx.DataPath("DataContainer/CellData/Phases"), correlation_array_path=nx.DataPath("DataContainer/CellData/Confidence Index"), @@ -151,13 +151,13 @@ quats_array_path=nx.DataPath("DataContainer/CellData/Quats") # ignored_data_array_paths: List[DataPath] = ..., # Not currently part of the code ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 9 # Instantiate Filter -filter = cxor.EBSDSegmentFeaturesFilter() +nx_filter = cxor.EBSDSegmentFeaturesFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, active_array_name="Active", cell_feature_attribute_matrix_name="CellFeatureData", @@ -171,27 +171,27 @@ randomize_features=True, use_mask=True ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 10 # Instantiate Filter -filter = nx.FindFeaturePhasesFilter() +nx_filter = nx.FindFeaturePhasesFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, cell_features_attribute_matrix_path=nx.DataPath("DataContainer/CellFeatureData"), cell_phases_array_path=nx.DataPath("DataContainer/CellData/Phases"), feature_ids_path=nx.DataPath("DataContainer/CellData/FeatureIds"), feature_phases_array_name="Phases" ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 11 # Instantiate Filter -filter = cxor.FindAvgOrientationsFilter() +nx_filter = cxor.FindAvgOrientationsFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, avg_euler_angles_array_path="AvgEulerAngles", avg_quats_array_path="AvgQuats", @@ -201,13 +201,13 @@ cell_quats_array_path=nx.DataPath("DataContainer/CellData/Quats"), crystal_structures_array_path=nx.DataPath("DataContainer/CellEnsembleData/CrystalStructures") ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 12 # Instantiate Filter -filter = nx.FindNeighbors() +nx_filter = nx.FindNeighbors() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, cell_feature_arrays=nx.DataPath("DataContainer/CellFeatureData"), feature_ids=nx.DataPath("DataContainer/CellData/FeatureIds"), @@ -220,14 +220,14 @@ # boundary_cells: str = ..., # Not currently part of the code # surface_features: str = ... # Not currently part of the code ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 13 # Instantiate Filter -filter = cxor.MergeTwinsFilter() +nx_filter = cxor.MergeTwinsFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, active_array_name="Active", angle_tolerance=2.0, @@ -243,13 +243,13 @@ use_non_contiguous_neighbors=False # non_contiguous_neighbor_list_array_path: DataPath = ..., # Not currently part of the code ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 14 # Instantiate Filter -filter = nx.CalculateFeatureSizesFilter() +nx_filter = nx.CalculateFeatureSizesFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, equivalent_diameters_path="EquivalentDiameters", feature_attribute_matrix=nx.DataPath("DataContainer/CellFeatureData"), @@ -259,13 +259,13 @@ save_element_sizes=False, volumes_path="Volumes" ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 15 # Instantiate Filter -filter = nx.RemoveMinimumSizeFeaturesFilter() +nx_filter = nx.RemoveMinimumSizeFeaturesFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, apply_single_phase=False, feature_ids_path=nx.DataPath("DataContainer/CellData/FeatureIds"), @@ -275,14 +275,14 @@ # feature_phases_path: DataPath = ..., # Not currently part of the code # phase_number: int = ... # Not currently part of the code ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 16 # Instantiate Filter -filter = nx.FindNeighbors() +nx_filter = nx.FindNeighbors() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, cell_feature_arrays=nx.DataPath("DataContainer/CellFeatureData"), feature_ids=nx.DataPath("DataContainer/CellData/FeatureIds"), @@ -295,13 +295,13 @@ # boundary_cells: str = ..., # Not currently part of the code # surface_features: str = ... # Not currently part of the code ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 17 # Instantiate Filter -filter = nx.MinNeighbors() +nx_filter = nx.MinNeighbors() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, apply_to_single_phase=False, cell_attribute_matrix=nx.DataPath("DataContainer/CellData"), @@ -313,13 +313,13 @@ # feature_phases: DataPath = ..., # Not currently part of the code # ignored_voxel_arrays: List[DataPath] = ... # Not currently part of the code ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 18 # Instantiate Filter -filter = nx.FillBadDataFilter() +nx_filter = nx.FillBadDataFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, feature_ids_path=nx.DataPath("DataContainer/CellData/FeatureIds"), min_allowed_defect_size=1000, @@ -328,14 +328,14 @@ # cell_phases_array_path: DataPath = ..., # Not currently part of the code # ignored_data_array_paths: List[DataPath] = ... # Not currently part of the code ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 19 # Instantiate Filter -filter = nx.ErodeDilateBadDataFilter() +nx_filter = nx.ErodeDilateBadDataFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, feature_ids_path=nx.DataPath("DataContainer/CellData/FeatureIds"), num_iterations=2, @@ -346,13 +346,13 @@ z_dir_on=True, ignored_data_array_paths=[] ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 20 # Instantiate Filter -filter = nx.ErodeDilateBadDataFilter() +nx_filter = nx.ErodeDilateBadDataFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, feature_ids_path=nx.DataPath("DataContainer/CellData/FeatureIds"), num_iterations=2, @@ -363,13 +363,13 @@ z_dir_on=True, ignored_data_array_paths=[] ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 21 # Instantiate Filter -filter = cxor.GenerateIPFColorsFilter() +nx_filter = cxor.GenerateIPFColorsFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, cell_euler_angles_array_path=nx.DataPath("DataContainer/CellData/EulerAngles"), cell_ipf_colors_array_name="IPFColors", @@ -379,21 +379,21 @@ reference_dir=[0.0, 0.0, 1.0], use_mask=True ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 22 # Instantiate Filter -filter = nx.WriteDREAM3DFilter() +nx_filter = nx.WriteDREAM3DFilter() # Set Output File Path output_file_path = nxtest.GetDataDirectory() + "/Output/Reconstruction/SmallIN100_Final.dream3d" # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, export_file_path=output_file_path, write_xdmf_file=True ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # ***************************************************************************** # THIS SECTION IS ONLY HERE FOR CLEANING UP THE CI Machines diff --git a/wrapping/python/examples/pipelines/OrientationAnalysis/APTR12_Analysis.py b/wrapping/python/examples/pipelines/OrientationAnalysis/APTR12_Analysis.py index 5cec329727..c69b6e07ec 100644 --- a/wrapping/python/examples/pipelines/OrientationAnalysis/APTR12_Analysis.py +++ b/wrapping/python/examples/pipelines/OrientationAnalysis/APTR12_Analysis.py @@ -11,9 +11,9 @@ # Filter 1 # Instantiate Filter -filter = cxor.ReadCtfDataFilter() +nx_filter = cxor.ReadCtfDataFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, cell_attribute_matrix_name="Cell Data", cell_ensemble_attribute_matrix_name="CellEnsembleData", @@ -22,13 +22,13 @@ edax_hexagonal_alignment=True, input_file=nxtest.GetDataDirectory() + "/T12-MAI-2010/fw-ar-IF1-aptr12-corr.ctf" ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 2 # Instantiate Filter -filter = nx.RotateSampleRefFrameFilter() +nx_filter = nx.RotateSampleRefFrameFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, created_image_geometry=nx.DataPath("fw-ar-IF1-aptr12-corr"), remove_original_geometry=True, @@ -38,11 +38,11 @@ rotation_representation=0, selected_image_geometry=nx.DataPath("fw-ar-IF1-aptr12-corr") ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 3 # Instantiate Filter -filter = nx.MultiThresholdObjects() +nx_filter = nx.MultiThresholdObjects() # Set Threshold Conditions threshold_1 = nx.ArrayThreshold() threshold_1.array_path = nx.DataPath("fw-ar-IF1-aptr12-corr/Cell Data/Error") @@ -54,32 +54,32 @@ threshold_set.thresholds = [threshold_1] # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, array_thresholds=threshold_set, created_data_path="ThresholdArray", created_mask_type=nx.DataType.boolean ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 4 # Instantiate Filter -filter = cxor.ConvertOrientations() +nx_filter = cxor.ConvertOrientations() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, input_orientation_array_path=nx.DataPath("fw-ar-IF1-aptr12-corr/Cell Data/EulerAngles"), input_type=0, output_orientation_array_name="Quats", output_type=2 ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 5 # Instantiate Filter -filter = nx.ReplaceElementAttributesWithNeighborValuesFilter() +nx_filter = nx.ReplaceElementAttributesWithNeighborValuesFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, comparison_data_path=nx.DataPath("fw-ar-IF1-aptr12-corr/Cell Data/Error"), loop=False, @@ -87,13 +87,13 @@ selected_comparison=0, selected_image_geometry=nx.DataPath("fw-ar-IF1-aptr12-corr") ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 6 # Instantiate Filter -filter = cxor.GenerateIPFColorsFilter() +nx_filter = cxor.GenerateIPFColorsFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, cell_euler_angles_array_path=nx.DataPath("fw-ar-IF1-aptr12-corr/Cell Data/EulerAngles"), cell_ipf_colors_array_name="IPF_001", @@ -102,13 +102,13 @@ reference_dir=[0.0, 0.0, 1.0], use_mask=False ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 7 # Instantiate Filter -filter = cxitk.ITKImageWriter() +nx_filter = cxitk.ITKImageWriter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, file_name=nxtest.GetDataDirectory() + "/Output/fw-ar-IF1-aptr12-corr/fw-ar-IF1-aptr12-corr_001.png", image_array_path=nx.DataPath("fw-ar-IF1-aptr12-corr/Cell Data/IPF_001"), @@ -116,13 +116,13 @@ index_offset=0, plane=0 ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 8 # Instantiate Filter -filter = cxor.GenerateIPFColorsFilter() +nx_filter = cxor.GenerateIPFColorsFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, cell_euler_angles_array_path=nx.DataPath("fw-ar-IF1-aptr12-corr/Cell Data/EulerAngles"), cell_ipf_colors_array_name="IPF_010", @@ -132,13 +132,13 @@ reference_dir=[0.0, 0.0, 1.0], use_mask=False ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 9 # Instantiate Filter -filter = cxitk.ITKImageWriter() +nx_filter = cxitk.ITKImageWriter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, file_name=nxtest.GetDataDirectory() + "/Output/fw-ar-IF1-aptr12-corr/fw-ar-IF1-aptr12-corr_010.png", image_array_path=nx.DataPath("fw-ar-IF1-aptr12-corr/Cell Data/IPF_010"), @@ -146,13 +146,13 @@ index_offset=0, plane=0 ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 10 # Instantiate Filter -filter = cxor.GenerateIPFColorsFilter() +nx_filter = cxor.GenerateIPFColorsFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, cell_euler_angles_array_path=nx.DataPath("fw-ar-IF1-aptr12-corr/Cell Data/EulerAngles"), cell_ipf_colors_array_name="IPF_100", @@ -161,13 +161,13 @@ reference_dir=[1.0, 0.0, 0.0], use_mask=False ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 11 # Instantiate Filter -filter = cxitk.ITKImageWriter() +nx_filter = cxitk.ITKImageWriter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, file_name=nxtest.GetDataDirectory() + "/Output/fw-ar-IF1-aptr12-corr/fw-ar-IF1-aptr12-corr_100.png", image_array_path=nx.DataPath("fw-ar-IF1-aptr12-corr/Cell Data/IPF_100"), @@ -175,13 +175,13 @@ index_offset=0, plane=0 ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 12 # Instantiate Filter -filter = cxor.EBSDSegmentFeaturesFilter() +nx_filter = cxor.EBSDSegmentFeaturesFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, active_array_name="Active", cell_feature_attribute_matrix_name="CellFeatureData", @@ -195,13 +195,13 @@ randomize_features=True, use_mask=True ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 13 # Instantiate Filter -filter = nx.FillBadDataFilter() +nx_filter = nx.FillBadDataFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, feature_ids_path=nx.DataPath("fw-ar-IF1-aptr12-corr/Cell Data/FeatureIds"), min_allowed_defect_size=10, @@ -209,13 +209,13 @@ store_as_new_phase=False # cell_phases_array_path and ignored_data_array_paths parameters are not used in this context ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 14 # Instantiate Filter -filter = nx.CalculateFeatureSizesFilter() +nx_filter = nx.CalculateFeatureSizesFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, equivalent_diameters_path="EquivalentDiameters", feature_attribute_matrix=nx.DataPath("fw-ar-IF1-aptr12-corr/CellFeatureData"), @@ -225,13 +225,13 @@ save_element_sizes=False, volumes_path="Volumes" ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 15 # Instantiate Filter -filter = nx.RemoveMinimumSizeFeaturesFilter() +nx_filter = nx.RemoveMinimumSizeFeaturesFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, apply_single_phase=False, feature_ids_path=nx.DataPath("fw-ar-IF1-aptr12-corr/Cell Data/FeatureIds"), @@ -240,13 +240,13 @@ num_cells_path=nx.DataPath("fw-ar-IF1-aptr12-corr/CellFeatureData/NumElements") # feature_phases_path and phase_number parameters are not used in this context ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 16 # Instantiate Filter -filter = cxor.FindAvgOrientationsFilter() +nx_filter = cxor.FindAvgOrientationsFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, avg_euler_angles_array_path="AvgEulerAngles", avg_quats_array_path="AvgQuats", @@ -256,13 +256,13 @@ cell_quats_array_path=nx.DataPath("fw-ar-IF1-aptr12-corr/Cell Data/Quats"), crystal_structures_array_path=nx.DataPath("fw-ar-IF1-aptr12-corr/CellEnsembleData/CrystalStructures") ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 17 # Instantiate Filter -filter = cxor.FindKernelAvgMisorientationsFilter() +nx_filter = cxor.FindKernelAvgMisorientationsFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, cell_phases_array_path=nx.DataPath("fw-ar-IF1-aptr12-corr/Cell Data/Phases"), crystal_structures_array_path=nx.DataPath("fw-ar-IF1-aptr12-corr/CellEnsembleData/CrystalStructures"), @@ -272,26 +272,26 @@ quats_array_path=nx.DataPath("fw-ar-IF1-aptr12-corr/Cell Data/Quats"), selected_image_geometry_path=nx.DataPath("fw-ar-IF1-aptr12-corr") ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 18 # Instantiate Filter -filter = nx.FindFeatureCentroidsFilter() +nx_filter = nx.FindFeatureCentroidsFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, centroids_array_path="Centroids", feature_attribute_matrix=nx.DataPath("fw-ar-IF1-aptr12-corr/CellFeatureData"), feature_ids_path=nx.DataPath("fw-ar-IF1-aptr12-corr/Cell Data/FeatureIds"), selected_image_geometry=nx.DataPath("fw-ar-IF1-aptr12-corr") ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 19 # Instantiate Filter -filter = nx.FindEuclideanDistMapFilter() +nx_filter = nx.FindEuclideanDistMapFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, calc_manhattan_dist=True, do_boundaries=True, @@ -303,13 +303,13 @@ selected_image_geometry=nx.DataPath("fw-ar-IF1-aptr12-corr") # Parameters for nearest_neighbors_array_name, q_pdistances_array_name, and t_jdistances_array_name are not used ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 20 # Instantiate Filter -filter = cxor.FindFeatureReferenceMisorientationsFilter() +nx_filter = cxor.FindFeatureReferenceMisorientationsFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, avg_quats_array_path=nx.DataPath("fw-ar-IF1-aptr12-corr/CellFeatureData/AvgQuats"), cell_phases_array_path=nx.DataPath("fw-ar-IF1-aptr12-corr/Cell Data/Phases"), @@ -321,13 +321,13 @@ reference_orientation=0 # Parameters for cell_feature_attribute_matrix_path and g_beuclidean_distances_array_path are not used ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 21 # Instantiate Filter -filter = nx.WriteFeatureDataCSVFilter() +nx_filter = nx.WriteFeatureDataCSVFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, cell_feature_attribute_matrix_path=nx.DataPath("fw-ar-IF1-aptr12-corr/CellFeatureData"), delimiter_choice_int=2, @@ -335,13 +335,13 @@ write_neighborlist_data=False, write_num_features_line=True ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 22 # Instantiate Filter -filter = nx.CalculateArrayHistogramFilter() +nx_filter = nx.CalculateArrayHistogramFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, histogram_suffix=" Histogram", new_data_group=True, @@ -350,33 +350,33 @@ selected_array_paths=[nx.DataPath("fw-ar-IF1-aptr12-corr/CellFeatureData/EquivalentDiameters")], user_defined_range=False ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 23 # Instantiate Filter -filter = nx.WriteASCIIDataFilter() +nx_filter = nx.WriteASCIIDataFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, delimiter=2, output_path=nxtest.GetDataDirectory() + "/Output/fw-ar-IF1-aptr12-corr/EqDiamHistogram.csv", output_style=1, selected_data_array_paths=[nx.DataPath("fw-ar-IF1-aptr12-corr/Histograms/EquivalentDiameters Histogram")] ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 24 # Instantiate Filter -filter = nx.WriteDREAM3DFilter() +nx_filter = nx.WriteDREAM3DFilter() output_file_path = nxtest.GetDataDirectory() + "/Output/fw-ar-IF1-aptr12-corr/fw-ar-IF1-aptr12-corr.dream3d" # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, export_file_path=output_file_path, write_xdmf_file=True ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # ***************************************************************************** # THIS SECTION IS ONLY HERE FOR CLEANING UP THE CI Machines diff --git a/wrapping/python/examples/pipelines/OrientationAnalysis/AVTR12_Analysis.py b/wrapping/python/examples/pipelines/OrientationAnalysis/AVTR12_Analysis.py index 03bf346987..b0458d967a 100644 --- a/wrapping/python/examples/pipelines/OrientationAnalysis/AVTR12_Analysis.py +++ b/wrapping/python/examples/pipelines/OrientationAnalysis/AVTR12_Analysis.py @@ -11,9 +11,9 @@ # Filter 1 # Instantiate Filter -filter = cxor.ReadCtfDataFilter() +nx_filter = cxor.ReadCtfDataFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, cell_attribute_matrix_name="Cell Data", cell_ensemble_attribute_matrix_name="CellEnsembleData", @@ -22,13 +22,13 @@ edax_hexagonal_alignment=True, input_file=nxtest.GetDataDirectory() + "/T12-MAI-2010/fw-ar-IF1-avtr12-corr.ctf" ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 2 # Instantiate Filter -filter = nx.RotateSampleRefFrameFilter() +nx_filter = nx.RotateSampleRefFrameFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, created_image_geometry=nx.DataPath("fw-ar-IF1-avtr12-corr"), remove_original_geometry=True, @@ -38,11 +38,11 @@ rotation_representation=0, selected_image_geometry=nx.DataPath("fw-ar-IF1-avtr12-corr") ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 3 # Instantiate Filter -filter = nx.MultiThresholdObjects() +nx_filter = nx.MultiThresholdObjects() # Set Threshold Conditions threshold_1 = nx.ArrayThreshold() threshold_1.array_path = nx.DataPath("fw-ar-IF1-avtr12-corr/Cell Data/Error") @@ -54,32 +54,32 @@ threshold_set.thresholds = [threshold_1] # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, array_thresholds=threshold_set, created_data_path="ThresholdArray", created_mask_type=nx.DataType.boolean ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 4 # Instantiate Filter -filter = cxor.ConvertOrientations() +nx_filter = cxor.ConvertOrientations() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, input_orientation_array_path=nx.DataPath("fw-ar-IF1-avtr12-corr/Cell Data/EulerAngles"), input_type=0, output_orientation_array_name="Quats", output_type=2 ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 5 # Instantiate Filter -filter = nx.ReplaceElementAttributesWithNeighborValuesFilter() +nx_filter = nx.ReplaceElementAttributesWithNeighborValuesFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, comparison_data_path=nx.DataPath("fw-ar-IF1-avtr12-corr/Cell Data/Error"), loop=False, @@ -87,13 +87,13 @@ selected_comparison=0, selected_image_geometry=nx.DataPath("fw-ar-IF1-avtr12-corr") ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 6 # Instantiate Filter -filter = cxor.GenerateIPFColorsFilter() +nx_filter = cxor.GenerateIPFColorsFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, cell_euler_angles_array_path=nx.DataPath("fw-ar-IF1-avtr12-corr/Cell Data/EulerAngles"), cell_ipf_colors_array_name="IPF_001", @@ -102,13 +102,13 @@ reference_dir=[0.0, 0.0, 1.0], use_mask=False ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 7 # Instantiate Filter -filter = cxitk.ITKImageWriter() +nx_filter = cxitk.ITKImageWriter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, file_name=nxtest.GetDataDirectory() + "/Output/fw-ar-IF1-avtr12-corr/fw-ar-IF1-avtr12-corr_001.png", image_array_path=nx.DataPath("fw-ar-IF1-avtr12-corr/Cell Data/IPF_001"), @@ -116,13 +116,13 @@ index_offset=0, plane=0 ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 8 # Instantiate Filter -filter = cxor.GenerateIPFColorsFilter() +nx_filter = cxor.GenerateIPFColorsFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, cell_euler_angles_array_path=nx.DataPath("fw-ar-IF1-avtr12-corr/Cell Data/EulerAngles"), cell_ipf_colors_array_name="IPF_010", @@ -132,13 +132,13 @@ reference_dir=[0.0, 0.0, 1.0], use_mask=False ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 9 # Instantiate Filter -filter = cxitk.ITKImageWriter() +nx_filter = cxitk.ITKImageWriter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, file_name=nxtest.GetDataDirectory() + "/Output/fw-ar-IF1-avtr12-corr/fw-ar-IF1-avtr12-corr_010.png", image_array_path=nx.DataPath("fw-ar-IF1-avtr12-corr/Cell Data/IPF_010"), @@ -146,13 +146,13 @@ index_offset=0, plane=0 ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 10 # Instantiate Filter -filter = cxor.GenerateIPFColorsFilter() +nx_filter = cxor.GenerateIPFColorsFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, cell_euler_angles_array_path=nx.DataPath("fw-ar-IF1-avtr12-corr/Cell Data/EulerAngles"), cell_ipf_colors_array_name="IPF_100", @@ -161,13 +161,13 @@ reference_dir=[1.0, 0.0, 0.0], use_mask=False ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 11 # Instantiate Filter -filter = cxitk.ITKImageWriter() +nx_filter = cxitk.ITKImageWriter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, file_name=nxtest.GetDataDirectory() + "/Output/fw-ar-IF1-avtr12-corr/fw-ar-IF1-avtr12-corr_100.png", image_array_path=nx.DataPath("fw-ar-IF1-avtr12-corr/Cell Data/IPF_100"), @@ -175,13 +175,13 @@ index_offset=0, plane=0 ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 12 # Instantiate Filter -filter = cxor.EBSDSegmentFeaturesFilter() +nx_filter = cxor.EBSDSegmentFeaturesFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, active_array_name="Active", cell_feature_attribute_matrix_name="CellFeatureData", @@ -195,13 +195,13 @@ randomize_features=True, use_mask=True ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 13 # Instantiate Filter -filter = nx.FillBadDataFilter() +nx_filter = nx.FillBadDataFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, feature_ids_path=nx.DataPath("fw-ar-IF1-avtr12-corr/Cell Data/FeatureIds"), min_allowed_defect_size=10, @@ -209,13 +209,13 @@ store_as_new_phase=False # cell_phases_array_path and ignored_data_array_paths parameters are not used in this context ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 14 # Instantiate Filter -filter = nx.CalculateFeatureSizesFilter() +nx_filter = nx.CalculateFeatureSizesFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, equivalent_diameters_path="EquivalentDiameters", feature_attribute_matrix=nx.DataPath("fw-ar-IF1-avtr12-corr/CellFeatureData"), @@ -225,13 +225,13 @@ save_element_sizes=False, volumes_path="Volumes" ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 15 # Instantiate Filter -filter = nx.RemoveMinimumSizeFeaturesFilter() +nx_filter = nx.RemoveMinimumSizeFeaturesFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, apply_single_phase=False, feature_ids_path=nx.DataPath("fw-ar-IF1-avtr12-corr/Cell Data/FeatureIds"), @@ -240,13 +240,13 @@ num_cells_path=nx.DataPath("fw-ar-IF1-avtr12-corr/CellFeatureData/NumElements") # feature_phases_path and phase_number parameters are not used in this context ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 16 # Instantiate Filter -filter = cxor.FindAvgOrientationsFilter() +nx_filter = cxor.FindAvgOrientationsFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, avg_euler_angles_array_path="AvgEulerAngles", avg_quats_array_path="AvgQuats", @@ -256,13 +256,13 @@ cell_quats_array_path=nx.DataPath("fw-ar-IF1-avtr12-corr/Cell Data/Quats"), crystal_structures_array_path=nx.DataPath("fw-ar-IF1-avtr12-corr/CellEnsembleData/CrystalStructures") ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 17 # Instantiate Filter -filter = cxor.FindKernelAvgMisorientationsFilter() +nx_filter = cxor.FindKernelAvgMisorientationsFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, cell_phases_array_path=nx.DataPath("fw-ar-IF1-avtr12-corr/Cell Data/Phases"), crystal_structures_array_path=nx.DataPath("fw-ar-IF1-avtr12-corr/CellEnsembleData/CrystalStructures"), @@ -272,26 +272,26 @@ quats_array_path=nx.DataPath("fw-ar-IF1-avtr12-corr/Cell Data/Quats"), selected_image_geometry_path=nx.DataPath("fw-ar-IF1-avtr12-corr") ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 18 # Instantiate Filter -filter = nx.FindFeatureCentroidsFilter() +nx_filter = nx.FindFeatureCentroidsFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, centroids_array_path="Centroids", feature_attribute_matrix=nx.DataPath("fw-ar-IF1-avtr12-corr/CellFeatureData"), feature_ids_path=nx.DataPath("fw-ar-IF1-avtr12-corr/Cell Data/FeatureIds"), selected_image_geometry=nx.DataPath("fw-ar-IF1-avtr12-corr") ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 19 # Instantiate Filter -filter = nx.FindEuclideanDistMapFilter() +nx_filter = nx.FindEuclideanDistMapFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, calc_manhattan_dist=True, do_boundaries=True, @@ -303,13 +303,13 @@ selected_image_geometry=nx.DataPath("fw-ar-IF1-avtr12-corr") # Parameters for nearest_neighbors_array_name, q_pdistances_array_name, and t_jdistances_array_name are not used ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 20 # Instantiate Filter -filter = cxor.FindFeatureReferenceMisorientationsFilter() +nx_filter = cxor.FindFeatureReferenceMisorientationsFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, avg_quats_array_path=nx.DataPath("fw-ar-IF1-avtr12-corr/CellFeatureData/AvgQuats"), cell_phases_array_path=nx.DataPath("fw-ar-IF1-avtr12-corr/Cell Data/Phases"), @@ -321,13 +321,13 @@ reference_orientation=0 # Parameters for cell_feature_attribute_matrix_path and g_beuclidean_distances_array_path are not used ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 21 # Instantiate Filter -filter = nx.WriteFeatureDataCSVFilter() +nx_filter = nx.WriteFeatureDataCSVFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, cell_feature_attribute_matrix_path=nx.DataPath("fw-ar-IF1-avtr12-corr/CellFeatureData"), delimiter_choice_int=2, @@ -335,13 +335,13 @@ write_neighborlist_data=False, write_num_features_line=True ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 22 # Instantiate Filter -filter = nx.CalculateArrayHistogramFilter() +nx_filter = nx.CalculateArrayHistogramFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, histogram_suffix=" Histogram", new_data_group=True, @@ -350,32 +350,32 @@ selected_array_paths=[nx.DataPath("fw-ar-IF1-avtr12-corr/CellFeatureData/EquivalentDiameters")], user_defined_range=False ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 23 # Instantiate Filter -filter = nx.WriteASCIIDataFilter() +nx_filter = nx.WriteASCIIDataFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, delimiter=2, output_path=nxtest.GetDataDirectory() + "/Output/fw-ar-IF1-avtr12-corr/EqDiamHistogram.csv", output_style=1, selected_data_array_paths=[nx.DataPath("fw-ar-IF1-avtr12-corr/Histograms/EquivalentDiameters Histogram")] ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 24 # Instantiate Filter -filter = nx.WriteDREAM3DFilter() +nx_filter = nx.WriteDREAM3DFilter() output_file_path = nxtest.GetDataDirectory() + "/Output/fw-ar-IF1-avtr12-corr/fw-ar-IF1-avtr12-corr.dream3d" # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, export_file_path=output_file_path, write_xdmf_file=True ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # ***************************************************************************** # THIS SECTION IS ONLY HERE FOR CLEANING UP THE CI Machines diff --git a/wrapping/python/examples/pipelines/OrientationAnalysis/AlignSectionsMutualInformation.py b/wrapping/python/examples/pipelines/OrientationAnalysis/AlignSectionsMutualInformation.py index 626c30576f..f070119779 100644 --- a/wrapping/python/examples/pipelines/OrientationAnalysis/AlignSectionsMutualInformation.py +++ b/wrapping/python/examples/pipelines/OrientationAnalysis/AlignSectionsMutualInformation.py @@ -21,16 +21,16 @@ h5ebsdParameter.use_recommended_transform=True # Instantiate Filter -filter = cxor.ReadH5EbsdFilter() +nx_filter = cxor.ReadH5EbsdFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, cell_attribute_matrix_name="CellData", cell_ensemble_attribute_matrix_name="CellEnsembleData", data_container_name=nx.DataPath("DataContainer"), read_h5_ebsd_parameter=h5ebsdParameter ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 2 # Set Up Thresholds and Instantiate Filter @@ -49,34 +49,34 @@ dt = nx.DataType.boolean # Instantiate Filter -filter = nx.MultiThresholdObjects() +nx_filter = nx.MultiThresholdObjects() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, array_thresholds=threshold_set, created_data_path="Mask", created_mask_type=nx.DataType.boolean ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 3 # Instantiate Filter -filter = cxor.ConvertOrientations() +nx_filter = cxor.ConvertOrientations() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, input_orientation_array_path=nx.DataPath("DataContainer/CellData/EulerAngles"), input_type=0, output_orientation_array_name="Quats", output_type=2 ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 4 # Instantiate Filter -filter = cxor.AlignSectionsMutualInformationFilter() +nx_filter = cxor.AlignSectionsMutualInformationFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, alignment_shift_file_name=nxtest.GetDataDirectory() + "/Output/OrientationAnalysis/Alignment_By_Mutual_Information_Shifts.txt", cell_phases_array_path=nx.DataPath("DataContainer/CellData/Phases"), @@ -88,20 +88,20 @@ use_mask=True, write_alignment_shifts=True ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 5 # Instantiate Filter -filter = nx.WriteDREAM3DFilter() +nx_filter = nx.WriteDREAM3DFilter() # Set Output File Path output_file_path = nxtest.GetDataDirectory() + "/Output/AlignSectionsMutualInformation/SmallIN100_AlignSectionsMutualInformation.dream3d" # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, export_file_path=output_file_path, write_xdmf_file=True ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # ***************************************************************************** # THIS SECTION IS ONLY HERE FOR CLEANING UP THE CI Machines diff --git a/wrapping/python/examples/pipelines/OrientationAnalysis/AvizoWriters.py b/wrapping/python/examples/pipelines/OrientationAnalysis/AvizoWriters.py index a5c78687cc..b23bde19a5 100644 --- a/wrapping/python/examples/pipelines/OrientationAnalysis/AvizoWriters.py +++ b/wrapping/python/examples/pipelines/OrientationAnalysis/AvizoWriters.py @@ -11,43 +11,43 @@ # Filter 1 # Instantiate Filter -filter = nx.ReadDREAM3DFilter() +nx_filter = nx.ReadDREAM3DFilter() # Set import parameters import_data = nx.Dream3dImportParameter.ImportData() import_data.file_path = nxtest.GetDataDirectory() + "/Output/Reconstruction/SmallIN100_Final.dream3d" import_data.data_paths = None # Execute Filter with Parameters -result = filter.execute(data_structure=data_structure, import_file_data=import_data) -nxtest.check_filter_result(filter, result) +result = nx_filter.execute(data_structure=data_structure, import_file_data=import_data) +nxtest.check_filter_result(nx_filter, result) # Filter 2 # Instantiate Filter -filter = nx.WriteAvizoUniformCoordinateFilter() +nx_filter = nx.WriteAvizoUniformCoordinateFilter() output_file_path = nxtest.GetDataDirectory() + "/Output/AzizoWriter/SmallIN100_AvizoUniform.am" # Execute Filter with Parameters -result = filter.execute(data_structure=data_structure, +result = nx_filter.execute(data_structure=data_structure, feature_ids_array_path=nx.DataPath("DataContainer/CellData/FeatureIds"), geometry_path=nx.DataPath("DataContainer"), output_file=output_file_path, units="meters", write_binary_file=False ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 3 # Instantiate Filter -filter = nx.WriteAvizoUniformCoordinateFilter() +nx_filter = nx.WriteAvizoUniformCoordinateFilter() output_file_path = nxtest.GetDataDirectory() + "/Output/AzizoWriter/SmallIN100_AvizoRectilinear.am" # Execute Filter with Parameters -result = filter.execute(data_structure=data_structure, +result = nx_filter.execute(data_structure=data_structure, feature_ids_array_path=nx.DataPath("DataContainer/CellData/FeatureIds"), geometry_path=nx.DataPath("DataContainer"), output_file=output_file_path, units="meters", write_binary_file=False ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # ***************************************************************************** # THIS SECTION IS ONLY HERE FOR CLEANING UP THE CI Machines diff --git a/wrapping/python/examples/pipelines/OrientationAnalysis/CI_Histogram.py b/wrapping/python/examples/pipelines/OrientationAnalysis/CI_Histogram.py index ab9be5e62b..65884e6051 100644 --- a/wrapping/python/examples/pipelines/OrientationAnalysis/CI_Histogram.py +++ b/wrapping/python/examples/pipelines/OrientationAnalysis/CI_Histogram.py @@ -11,33 +11,33 @@ # Filter 1 # Instantiate Filter -filter = cxor.ReadAngDataFilter() +nx_filter = cxor.ReadAngDataFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, cell_attribute_matrix_name=("Cell Data"), cell_ensemble_attribute_matrix_name=("CellEnsembleData"), data_container_name=nx.DataPath("DataContainer"), input_file=nxtest.GetDataDirectory() + "/Small_IN100/Slice_1.ang", ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 2 # Instantiate Filter -filter = cxor.RotateEulerRefFrameFilter() +nx_filter = cxor.RotateEulerRefFrameFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, euler_angles_array_path=nx.DataPath("DataContainer/Cell Data/EulerAngles"), rotation_axis=[0.0, 0.0, 1.0, 90.0] ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 3 # Instantiate Filter -filter = nx.RotateSampleRefFrameFilter() +nx_filter = nx.RotateSampleRefFrameFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, created_image_geometry=nx.DataPath("beans"), remove_original_geometry=False, @@ -46,11 +46,11 @@ rotation_representation=0, selected_image_geometry=nx.DataPath("DataContainer") ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 4 # Instantiate Filter -filter = nx.MultiThresholdObjects() +nx_filter = nx.MultiThresholdObjects() # Set Threshold Conditions threshold_1 = nx.ArrayThreshold() threshold_1.array_path = nx.DataPath("DataContainer/Cell Data/Confidence Index") @@ -62,19 +62,19 @@ threshold_set.thresholds = [threshold_1] # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, array_thresholds=threshold_set, created_data_path="Mask", created_mask_type=nx.DataType.boolean ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 5 # Instantiate Filter -filter = nx.ConditionalSetValue() +nx_filter = nx.ConditionalSetValue() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, conditional_array_path=nx.DataPath("DataContainer/Cell Data/Mask"), invert_mask=False, @@ -82,13 +82,13 @@ selected_array_path=nx.DataPath("DataContainer/Cell Data/Confidence Index"), use_conditional=True ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 6 # Instantiate Filter -filter = nx.CalculateArrayHistogramFilter() +nx_filter = nx.CalculateArrayHistogramFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, #data_group_name=nx.DataPath("DataContainer/Statistics"), histogram_suffix=" Histogram", @@ -100,14 +100,14 @@ selected_array_paths=[nx.DataPath("DataContainer/Cell Data/Confidence Index")], user_defined_range=True ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 7 # Instantiate Filter -filter = nx.WriteASCIIDataFilter() +nx_filter = nx.WriteASCIIDataFilter() output_file_path = nxtest.GetDataDirectory() + "/Output/OrientationAnalysis/Test/CI_Histogram.csv" # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, #file_extension: str = ..., delimiter=2, @@ -118,7 +118,7 @@ output_style=1, selected_data_array_paths=[nx.DataPath("DataContainer/Statistics/Confidence Index Histogram")] ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # ***************************************************************************** # THIS SECTION IS ONLY HERE FOR CLEANING UP THE CI Machines diff --git a/wrapping/python/examples/pipelines/OrientationAnalysis/Edax_IPF_Colors.py b/wrapping/python/examples/pipelines/OrientationAnalysis/Edax_IPF_Colors.py index f0d5f4c62a..21534085bf 100644 --- a/wrapping/python/examples/pipelines/OrientationAnalysis/Edax_IPF_Colors.py +++ b/wrapping/python/examples/pipelines/OrientationAnalysis/Edax_IPF_Colors.py @@ -11,33 +11,33 @@ # Filter 1 # Instantiate Filter -filter = cxor.ReadAngDataFilter() +nx_filter = cxor.ReadAngDataFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, cell_attribute_matrix_name=("Cell Data"), cell_ensemble_attribute_matrix_name=("CellEnsembleData"), data_container_name=nx.DataPath("DataContainer"), input_file=nxtest.GetDataDirectory() + "/Small_IN100/Slice_1.ang" ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 2 # Instantiate Filter -filter = cxor.RotateEulerRefFrameFilter() +nx_filter = cxor.RotateEulerRefFrameFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, euler_angles_array_path=nx.DataPath("DataContainer/Cell Data/EulerAngles"), rotation_axis=[0.0, 0.0, 1.0, 90.0] ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 3 # Instantiate Filter -filter = nx.RotateSampleRefFrameFilter() +nx_filter = nx.RotateSampleRefFrameFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, remove_original_geometry=True, rotate_slice_by_slice=False, @@ -45,7 +45,7 @@ rotation_representation=0, selected_image_geometry=nx.DataPath("DataContainer") ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 4 @@ -60,22 +60,22 @@ threshold_set.thresholds = [threshold_1] # Instantiate Filter -filter = nx.MultiThresholdObjects() +nx_filter = nx.MultiThresholdObjects() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, array_thresholds=threshold_set, created_data_path="Mask", created_mask_type=nx.DataType.boolean ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 5 # Instantiate Filter -filter = cxor.GenerateIPFColorsFilter() +nx_filter = cxor.GenerateIPFColorsFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, cell_euler_angles_array_path=nx.DataPath("DataContainer/Cell Data/EulerAngles"), cell_ipf_colors_array_name=("IPFColors"), @@ -85,14 +85,14 @@ reference_dir=[0.0, 0.0, 1.0], use_mask=True ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 6 # Instantiate Filter -filter = cxitk.ITKImageWriter() +nx_filter = cxitk.ITKImageWriter() output_file_path = nxtest.GetDataDirectory() + "/Output/Edax_IPF_Colors/Small_IN100_Slice_1.png" # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, file_name=output_file_path, image_array_path=nx.DataPath("DataContainer/Cell Data/IPFColors"), @@ -100,7 +100,7 @@ index_offset=0, plane=0 ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # ***************************************************************************** # THIS SECTION IS ONLY HERE FOR CLEANING UP THE CI Machines diff --git a/wrapping/python/examples/pipelines/OrientationAnalysis/FindBiasedFeatures.py b/wrapping/python/examples/pipelines/OrientationAnalysis/FindBiasedFeatures.py index 8cbbe77a06..a18c7f29d4 100644 --- a/wrapping/python/examples/pipelines/OrientationAnalysis/FindBiasedFeatures.py +++ b/wrapping/python/examples/pipelines/OrientationAnalysis/FindBiasedFeatures.py @@ -15,18 +15,18 @@ import_data.file_path = nxtest.GetDataDirectory() + "/Output/Statistics/SmallIN100_CrystalStats.dream3d" import_data.data_paths = None # Instantiate Filter -filter = nx.ReadDREAM3DFilter() +nx_filter = nx.ReadDREAM3DFilter() # Execute Filter with Parameters -result = filter.execute(data_structure=data_structure, +result = nx_filter.execute(data_structure=data_structure, import_file_data=import_data ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 2 # Instantiate Filter -filter = nx.DeleteData() +nx_filter = nx.DeleteData() # Execute Filter With Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, removed_data_path=[nx.DataPath("DataContainer/CellFeatureData/Centroids"), nx.DataPath("DataContainer/CellFeatureData/EquivalentDiameters"), @@ -44,14 +44,14 @@ nx.DataPath("DataContainer/CellFeatureData/AvgQuats"), nx.DataPath("DataContainer/CellFeatureData/AvgEulerAngles")] ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 2 # Instantiate Filter -filter = nx.FindNeighbors() +nx_filter = nx.FindNeighbors() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, #boundary_cells: str = ..., cell_feature_arrays=nx.DataPath("DataContainer/CellFeatureData"), @@ -64,26 +64,26 @@ store_surface_features=False #surface_features: str = ... ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 3 # Instantiate Filter -filter = nx.FindFeatureCentroidsFilter() +nx_filter = nx.FindFeatureCentroidsFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, centroids_array_path="Centroids", feature_attribute_matrix=nx.DataPath("DataContainer/CellFeatureData"), feature_ids_path=nx.DataPath("DataContainer/CellData/FeatureIds"), selected_image_geometry=nx.DataPath("DataContainer") ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 4 # Instantiate Filter -filter = nx.FindSurfaceFeatures() +nx_filter = nx.FindSurfaceFeatures() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, feature_attribute_matrix_path=nx.DataPath("DataContainer/CellFeatureData"), feature_geometry_path=nx.DataPath("DataContainer"), @@ -91,13 +91,13 @@ mark_feature_0_neighbors=True, surface_features_array_path="SurfaceFeatures" ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 5 # Instantiate Filter -filter = nx.FindBiasedFeaturesFilter() +nx_filter = nx.FindBiasedFeaturesFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, biased_features_array_name="BiasedFeatures", calc_by_phase=True, @@ -106,18 +106,18 @@ phases_array_path=nx.DataPath("DataContainer/CellFeatureData/Phases"), surface_features_array_path=nx.DataPath("DataContainer/CellFeatureData/SurfaceFeatures") ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 6 # Output file path for Filter 4 output_file_path = nxtest.GetDataDirectory() + "/Output/FindBiasedFeatures/FindBiasedFeatures.dream3d" # Instantiate Filter -filter = nx.WriteDREAM3DFilter() +nx_filter = nx.WriteDREAM3DFilter() # Execute Filter with Parameters -result = filter.execute(data_structure=data_structure, +result = nx_filter.execute(data_structure=data_structure, export_file_path=output_file_path, write_xdmf_file=True) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # ***************************************************************************** # THIS SECTION IS ONLY HERE FOR CLEANING UP THE CI Machines diff --git a/wrapping/python/examples/pipelines/OrientationAnalysis/FindBoundaryCells.py b/wrapping/python/examples/pipelines/OrientationAnalysis/FindBoundaryCells.py index 50862c45dd..04a976878b 100644 --- a/wrapping/python/examples/pipelines/OrientationAnalysis/FindBoundaryCells.py +++ b/wrapping/python/examples/pipelines/OrientationAnalysis/FindBoundaryCells.py @@ -17,17 +17,17 @@ import_data.data_paths = None # Instantiate Filter -filter = nx.ReadDREAM3DFilter() +nx_filter = nx.ReadDREAM3DFilter() # Execute Filter with Parameters -result = filter.execute(data_structure=data_structure, +result = nx_filter.execute(data_structure=data_structure, import_file_data=import_data) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 2 # Instantiate Filter -filter = nx.FindBoundaryCellsFilter() +nx_filter = nx.FindBoundaryCellsFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, boundary_cells_array_name="BoundaryCells", feature_ids_array_path=nx.DataPath("DataContainer/CellData/FeatureIds"), @@ -35,19 +35,19 @@ image_geometry_path=nx.DataPath("DataContainer"), include_volume_boundary=True, ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 3 # Output file path for Filter 3 output_file_path = nxtest.GetDataDirectory() + "/Output/FindBoundaryCells/SmallIN100_BoundaryCells.dream3d" # Instantiate Filter -filter = nx.WriteDREAM3DFilter() +nx_filter = nx.WriteDREAM3DFilter() # Execute Filter with Parameters -result = filter.execute(data_structure=data_structure, +result = nx_filter.execute(data_structure=data_structure, export_file_path=output_file_path, write_xdmf_file=True ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # ***************************************************************************** # THIS SECTION IS ONLY HERE FOR CLEANING UP THE CI Machines diff --git a/wrapping/python/examples/pipelines/OrientationAnalysis/FindGBCD-GBPDMetricBased.py b/wrapping/python/examples/pipelines/OrientationAnalysis/FindGBCD-GBPDMetricBased.py index 1e1347bb9f..824fd6e042 100644 --- a/wrapping/python/examples/pipelines/OrientationAnalysis/FindGBCD-GBPDMetricBased.py +++ b/wrapping/python/examples/pipelines/OrientationAnalysis/FindGBCD-GBPDMetricBased.py @@ -15,17 +15,17 @@ import_data.file_path = nxtest.GetDataDirectory() + "/Output/SurfaceMesh/SmallIN100_MeshStats.dream3d" import_data.data_paths = None # Instantiate Filter -filter = nx.ReadDREAM3DFilter() +nx_filter = nx.ReadDREAM3DFilter() # Execute Filter with Parameters -result = filter.execute(data_structure=data_structure, +result = nx_filter.execute(data_structure=data_structure, import_file_data=import_data) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 2 # Instantiate Filter -filter = nx.SharedFeatureFaceFilter() +nx_filter = nx.SharedFeatureFaceFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, face_labels_array_path=nx.DataPath("TriangleDataContainer/FaceData/FaceLabels"), feature_face_ids_array_name=("FeatureFaceId"), @@ -35,14 +35,14 @@ randomize_features=False, triangle_geometry_path=nx.DataPath("TriangleDataContainer") ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 3 # Instantiate Filter -filter = cxor.FindGBCDMetricBasedFilter() +nx_filter = cxor.FindGBCDMetricBasedFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, chosen_limit_dists=2, crystal_structures_array_path=nx.DataPath("DataContainer/CellEnsembleData/CrystalStructures"), @@ -62,14 +62,14 @@ surface_mesh_feature_face_labels_array_path=nx.DataPath("TriangleDataContainer/FaceFeatureData/FaceLabels"), triangle_geometry_path=nx.DataPath("TriangleDataContainer") ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 4 # Instantiate Filter -filter = cxor.FindGBPDMetricBasedFilter() +nx_filter = cxor.FindGBPDMetricBasedFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, crystal_structures_array_path=nx.DataPath("DataContainer/CellEnsembleData/CrystalStructures"), dist_output_file=nxtest.GetDataDirectory() + "/Output/GBPDMetricBased/gbpd_distribution.dat", @@ -88,7 +88,7 @@ surface_mesh_feature_face_labels_array_path=nx.DataPath("TriangleDataContainer/FaceFeatureData/FaceLabels"), triangle_geometry_path=nx.DataPath("TriangleDataContainer") ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # ***************************************************************************** diff --git a/wrapping/python/examples/pipelines/OrientationAnalysis/FindLargestCrossSections.py b/wrapping/python/examples/pipelines/OrientationAnalysis/FindLargestCrossSections.py index 5bfd17c789..c84d8fcb3e 100644 --- a/wrapping/python/examples/pipelines/OrientationAnalysis/FindLargestCrossSections.py +++ b/wrapping/python/examples/pipelines/OrientationAnalysis/FindLargestCrossSections.py @@ -11,7 +11,7 @@ # Filter 1 # Instantiate Filter -filter = cxor.ReadH5EbsdFilter() +nx_filter = cxor.ReadH5EbsdFilter() h5ebsdParameter = cxor.ReadH5EbsdFileParameter.ValueType() h5ebsdParameter.euler_representation=0 @@ -22,14 +22,14 @@ h5ebsdParameter.use_recommended_transform=True # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, cell_attribute_matrix_name="CellData", cell_ensemble_attribute_matrix_name="CellEnsembleData", data_container_name=nx.DataPath("DataContainer"), read_h5_ebsd_parameter=h5ebsdParameter ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 2 # Instantiate Filter @@ -52,26 +52,26 @@ created_data_path = "Mask", created_mask_type = nx.DataType.boolean, ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 3 # Instantiate Filter -filter = cxor.ConvertOrientations() +nx_filter = cxor.ConvertOrientations() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, input_orientation_array_path=nx.DataPath("DataContainer/CellData/EulerAngles"), input_type=0, output_orientation_array_name="Quats", output_type=2 ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 4 # Instantiate Filter -filter = cxor.EBSDSegmentFeaturesFilter() +nx_filter = cxor.EBSDSegmentFeaturesFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, active_array_name="Active", cell_feature_attribute_matrix_name="CellFeatureData", @@ -85,13 +85,13 @@ randomize_features=True, use_mask=True ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 5 # Instantiate Filter -filter = nx.FindLargestCrossSectionsFilter() +nx_filter = nx.FindLargestCrossSectionsFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, cell_feature_attribute_matrix_path=nx.DataPath("DataContainer/CellFeatureData"), feature_ids_array_path=nx.DataPath("DataContainer/CellData/FeatureIds"), @@ -99,20 +99,20 @@ largest_cross_sections_array_path="LargestCrossSections", plane=0 ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 6 # Instantiate Filter -filter = nx.WriteDREAM3DFilter() +nx_filter = nx.WriteDREAM3DFilter() # Define output file path output_file_path = nxtest.GetDataDirectory() + "/Output/Examples/SmallIN100_LargestCrossSections.dream3d" # Execute WriteDREAM3DFilter with Parameters -result = filter.execute(data_structure=data_structure, +result = nx_filter.execute(data_structure=data_structure, export_file_path=output_file_path, write_xdmf_file=True ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # ***************************************************************************** # THIS SECTION IS ONLY HERE FOR CLEANING UP THE CI Machines diff --git a/wrapping/python/examples/pipelines/OrientationAnalysis/ReadAng.py b/wrapping/python/examples/pipelines/OrientationAnalysis/ReadAng.py index 16fe0e6daa..c6f3a205b4 100644 --- a/wrapping/python/examples/pipelines/OrientationAnalysis/ReadAng.py +++ b/wrapping/python/examples/pipelines/OrientationAnalysis/ReadAng.py @@ -11,33 +11,33 @@ # Filter 1 # Instantiate Filter -filter = cxor.ReadAngDataFilter() +nx_filter = cxor.ReadAngDataFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, cell_attribute_matrix_name=("Cell Data"), cell_ensemble_attribute_matrix_name=("Cell Ensemble Data"), data_container_name=nx.DataPath("DataContainer"), input_file=nxtest.GetDataDirectory() + "/Small_IN100/Slice_1.ang" ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 2 # Instantiate Filter -filter = cxor.RotateEulerRefFrameFilter() +nx_filter = cxor.RotateEulerRefFrameFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, euler_angles_array_path=nx.DataPath("DataContainer/Cell Data/EulerAngles"), rotation_axis=[0.0, 0.0, 1.0, 90.0] ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 3 # Instantiate Filter -filter = nx.RotateSampleRefFrameFilter() +nx_filter = nx.RotateSampleRefFrameFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, #created_image_geometry: DataPath = ..., remove_original_geometry=True, @@ -47,7 +47,7 @@ rotation_representation=0, selected_image_geometry=nx.DataPath("DataContainer") ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 4 # Define ArrayThreshold object @@ -61,19 +61,19 @@ threshold_set.thresholds = [threshold_1] # Instantiate Filter -filter = nx.MultiThresholdObjects() +nx_filter = nx.MultiThresholdObjects() # Execute Filter with Parameters -result = filter.execute(data_structure=data_structure, +result = nx_filter.execute(data_structure=data_structure, array_thresholds=threshold_set, created_data_path="Mask", created_mask_type=nx.DataType.boolean) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 5 # Instantiate Filter -filter = cxor.GenerateIPFColorsFilter() +nx_filter = cxor.GenerateIPFColorsFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, cell_euler_angles_array_path=nx.DataPath("DataContainer/Cell Data/EulerAngles"), cell_ipf_colors_array_name=("IPFColors"), @@ -82,6 +82,6 @@ reference_dir=[0.0, 0.0, 1.0], use_mask=False ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) print("===> Pipeline Complete") \ No newline at end of file diff --git a/wrapping/python/examples/pipelines/OrientationAnalysis/ReadCTF.py b/wrapping/python/examples/pipelines/OrientationAnalysis/ReadCTF.py index 6e5c6bbc60..fcfdf26b57 100644 --- a/wrapping/python/examples/pipelines/OrientationAnalysis/ReadCTF.py +++ b/wrapping/python/examples/pipelines/OrientationAnalysis/ReadCTF.py @@ -11,9 +11,9 @@ # Filter 1 # Instantiate Filter -filter = cxor.ReadCtfDataFilter() +nx_filter = cxor.ReadCtfDataFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, cell_attribute_matrix_name=("Cell Data"), cell_ensemble_attribute_matrix_name=("CellEnsembleData"), @@ -22,13 +22,13 @@ edax_hexagonal_alignment=False, input_file=nxtest.GetDataDirectory() + "/T12-MAI-2010/fw-ar-IF1-aptr12-corr.ctf" ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 2 # Instantiate Filter -filter = nx.RotateSampleRefFrameFilter() +nx_filter = nx.RotateSampleRefFrameFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, #created_image_geometry=nx.DataPath("DataContainer/"), remove_original_geometry=True, @@ -38,7 +38,7 @@ rotation_representation=0, selected_image_geometry=nx.DataPath("DataContainer") ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 3 # Define ArrayThreshold object @@ -52,19 +52,19 @@ threshold_set.thresholds = [threshold_1] # Instantiate Filter -filter = nx.MultiThresholdObjects() +nx_filter = nx.MultiThresholdObjects() # Execute Filter with Parameters -result = filter.execute(data_structure=data_structure, +result = nx_filter.execute(data_structure=data_structure, array_thresholds=threshold_set, created_data_path="Mask", created_mask_type=nx.DataType.boolean) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 4 # Instantiate Filter -filter = cxor.GenerateIPFColorsFilter() +nx_filter = cxor.GenerateIPFColorsFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, cell_euler_angles_array_path=nx.DataPath("DataContainer/Cell Data/EulerAngles"), cell_ipf_colors_array_name=("IPFColors"), @@ -74,6 +74,6 @@ reference_dir=[0.0, 0.0, 1.0], use_mask=True ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) print("===> Pipeline Complete") \ No newline at end of file diff --git a/wrapping/python/examples/pipelines/OrientationAnalysis/TxCopper_Exposed.py b/wrapping/python/examples/pipelines/OrientationAnalysis/TxCopper_Exposed.py index 3ec7527b41..22d03da7dd 100644 --- a/wrapping/python/examples/pipelines/OrientationAnalysis/TxCopper_Exposed.py +++ b/wrapping/python/examples/pipelines/OrientationAnalysis/TxCopper_Exposed.py @@ -11,9 +11,9 @@ # Filter 1 # Instantiate Filter -filter = cxor.ReadCtfDataFilter() +nx_filter = cxor.ReadCtfDataFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, cell_attribute_matrix_name=("EBSD Scan Data"), cell_ensemble_attribute_matrix_name=("Phase Data"), @@ -22,13 +22,13 @@ edax_hexagonal_alignment=True, input_file=nxtest.GetDataDirectory() + "/Textured_Copper/Cugrid_after 2nd_15kv_2kx_2.ctf" ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 2 # Instantiate Filter -filter = nx.RotateSampleRefFrameFilter() +nx_filter = nx.RotateSampleRefFrameFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, remove_original_geometry=True, rotate_slice_by_slice=False, @@ -37,13 +37,13 @@ rotation_representation=0, selected_image_geometry=nx.DataPath("Cugrid_after 2nd_15kv_2kx_2") ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 3 # Instantiate Filter -filter = nx.CropImageGeometry() +nx_filter = nx.CropImageGeometry() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, max_voxel=[460, 399, 0], min_voxel=[0, 0, 0], @@ -52,7 +52,7 @@ selected_image_geometry=nx.DataPath("Cugrid_after 2nd_15kv_2kx_2") # update_origin=True ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 4 # Instantiate Filter @@ -68,13 +68,13 @@ created_data_path="Mask", created_mask_type=nx.DataType.boolean) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 5 # Instantiate Filter -filter = cxor.GenerateIPFColorsFilter() +nx_filter = cxor.GenerateIPFColorsFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, cell_euler_angles_array_path=nx.DataPath("Cugrid_after 2nd_15kv_2kx_2/EBSD Scan Data/EulerAngles"), cell_ipf_colors_array_name=("IPF_Exposed_001"), @@ -84,13 +84,13 @@ reference_dir=[0.0, 0.0, 1.0], use_mask=True ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 6 # Instantiate Filter -filter = cxitk.ITKImageWriter() +nx_filter = cxitk.ITKImageWriter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, file_name=nxtest.GetDataDirectory() + "/Output/TexturedCopper/IPF_Exposed.png", image_array_path=nx.DataPath("Cugrid_after 2nd_15kv_2kx_2/EBSD Scan Data/IPF_Exposed_001"), @@ -98,13 +98,13 @@ index_offset=0, plane=0 ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 7 # Instantiate Filter -filter = cxor.WritePoleFigureFilter() +nx_filter = cxor.WritePoleFigureFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, cell_euler_angles_array_path=nx.DataPath("Cugrid_after 2nd_15kv_2kx_2/EBSD Scan Data/EulerAngles"), cell_phases_array_path=nx.DataPath("Cugrid_after 2nd_15kv_2kx_2/EBSD Scan Data/Phases"), @@ -124,7 +124,7 @@ use_mask=True, write_image_to_disk=True ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # ***************************************************************************** # THIS SECTION IS ONLY HERE FOR CLEANING UP THE CI Machines diff --git a/wrapping/python/examples/pipelines/OrientationAnalysis/TxCopper_Unexposed.py b/wrapping/python/examples/pipelines/OrientationAnalysis/TxCopper_Unexposed.py index 5c03f5b4c2..fd1491bc8a 100644 --- a/wrapping/python/examples/pipelines/OrientationAnalysis/TxCopper_Unexposed.py +++ b/wrapping/python/examples/pipelines/OrientationAnalysis/TxCopper_Unexposed.py @@ -11,9 +11,9 @@ # Filter 1 # Instantiate Filter -filter = cxor.ReadCtfDataFilter() +nx_filter = cxor.ReadCtfDataFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, cell_attribute_matrix_name=("EBSD Scan Data"), cell_ensemble_attribute_matrix_name=("Phase Data"), @@ -22,13 +22,13 @@ edax_hexagonal_alignment=True, input_file=nxtest.GetDataDirectory() + "/Textured_Copper/Cugrid_after 2nd_15kv_2kx_2.ctf" ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 2 # Instantiate Filter -filter = nx.RotateSampleRefFrameFilter() +nx_filter = nx.RotateSampleRefFrameFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, remove_original_geometry=True, rotate_slice_by_slice=False, @@ -37,13 +37,13 @@ rotation_representation=0, selected_image_geometry=nx.DataPath("Cugrid_after 2nd_15kv_2kx_2") ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 3 # Instantiate Filter -filter = nx.CropImageGeometry() +nx_filter = nx.CropImageGeometry() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, max_voxel=[549, 399, 0], min_voxel=[488, 0, 0], @@ -51,7 +51,7 @@ renumber_features=False, selected_image_geometry=nx.DataPath("Cugrid_after 2nd_15kv_2kx_2") ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 4 # Instantiate Filter @@ -67,13 +67,13 @@ created_data_path="Mask", created_mask_type=nx.DataType.boolean) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 5 # Instantiate Filter -filter = cxor.GenerateIPFColorsFilter() +nx_filter = cxor.GenerateIPFColorsFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, cell_euler_angles_array_path=nx.DataPath("Cugrid_after 2nd_15kv_2kx_2/EBSD Scan Data/EulerAngles"), cell_ipf_colors_array_name=("IPF_Unexposed_001"), @@ -83,13 +83,13 @@ reference_dir=[0.0, 0.0, 1.0], use_mask=True ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 6 # Instantiate Filter -filter = cxitk.ITKImageWriter() +nx_filter = cxitk.ITKImageWriter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, file_name=nxtest.GetDataDirectory() + "/Output/TexturedCopper/IPF_Unexposed.png", image_array_path=nx.DataPath("Cugrid_after 2nd_15kv_2kx_2/EBSD Scan Data/IPF_Unexposed_001"), @@ -97,13 +97,13 @@ index_offset=0, plane=0 ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 7 # Instantiate Filter -filter = cxor.WritePoleFigureFilter() +nx_filter = cxor.WritePoleFigureFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, cell_euler_angles_array_path=nx.DataPath("Cugrid_after 2nd_15kv_2kx_2/EBSD Scan Data/EulerAngles"), cell_phases_array_path=nx.DataPath("Cugrid_after 2nd_15kv_2kx_2/EBSD Scan Data/Phases"), @@ -123,7 +123,7 @@ use_mask=True, write_image_to_disk=True ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # ***************************************************************************** # THIS SECTION IS ONLY HERE FOR CLEANING UP THE CI Machines diff --git a/wrapping/python/examples/pipelines/OrientationAnalysis/VtkRectilinearGridWriter.py b/wrapping/python/examples/pipelines/OrientationAnalysis/VtkRectilinearGridWriter.py index 1d16cf8dc5..9fd710fa17 100644 --- a/wrapping/python/examples/pipelines/OrientationAnalysis/VtkRectilinearGridWriter.py +++ b/wrapping/python/examples/pipelines/OrientationAnalysis/VtkRectilinearGridWriter.py @@ -16,17 +16,17 @@ import_data.data_paths = None # Instantiate Filter -filter = nx.ReadDREAM3DFilter() +nx_filter = nx.ReadDREAM3DFilter() # Execute Filter with Parameters -result = filter.execute(data_structure=data_structure, +result = nx_filter.execute(data_structure=data_structure, import_file_data=import_data) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 2 # Instantiate Filter -filter = nx.DeleteData() +nx_filter = nx.DeleteData() # Execute Filter -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, removed_data_path=[nx.DataPath("DataContainer/CellEnsembleData/MaterialName"), nx.DataPath("MergeTwins SeedValue")] @@ -34,10 +34,10 @@ # Filter 3 # Instantiate Filter -filter = nx.WriteVtkRectilinearGridFilter() +nx_filter = nx.WriteVtkRectilinearGridFilter() output_file_path = nxtest.GetDataDirectory() + "/Output/Examples/SmallIN100_Final.vtk" # Execute Filter -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, image_geometry_path=nx.DataPath("DataContainer"), output_file=output_file_path, @@ -57,7 +57,7 @@ nx.DataPath("DataContainer/CellData/X Position"), nx.DataPath("DataContainer/CellData/Y Position")] ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # ***************************************************************************** diff --git a/wrapping/python/examples/pipelines/Simplnx/AppendImageGeometryZSlice.py b/wrapping/python/examples/pipelines/Simplnx/AppendImageGeometryZSlice.py index 39ec128a66..310ac132f1 100644 --- a/wrapping/python/examples/pipelines/Simplnx/AppendImageGeometryZSlice.py +++ b/wrapping/python/examples/pipelines/Simplnx/AppendImageGeometryZSlice.py @@ -11,9 +11,9 @@ # Filter 1 # Instantiate Filter -filter = nx.CreateImageGeometry() +nx_filter = nx.CreateImageGeometry() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, cell_data_name="Cell Data", dimensions=[60, 80, 100], @@ -21,13 +21,13 @@ origin=[100.0, 100.0, 0.0], spacing=[1.0, 1.0, 1.0] ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 2 # Instantiate Filter -filter = nx.ReadTextDataArrayFilter() +nx_filter = nx.ReadTextDataArrayFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, advanced_options=True, data_format="", @@ -39,13 +39,13 @@ output_data_array=nx.DataPath("Confidence Index"), scalar_type=nx.NumericType.float32 ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 3 # Instantiate Filter -filter = nx.ReadTextDataArrayFilter() +nx_filter = nx.ReadTextDataArrayFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, advanced_options=True, data_format="", @@ -57,14 +57,14 @@ output_data_array=nx.DataPath("[Image Geometry]/Cell Data/FeatureIds"), scalar_type=nx.NumericType.int32 ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 4 # Instantiate Filter -filter = nx.ReadTextDataArrayFilter() +nx_filter = nx.ReadTextDataArrayFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, advanced_options=True, data_format="", @@ -76,12 +76,12 @@ output_data_array=nx.DataPath("[Image Geometry]/Cell Data/Image Quality"), scalar_type=nx.NumericType.float32 ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 5 # Instantiate Filter -filter = nx.ReadTextDataArrayFilter() +nx_filter = nx.ReadTextDataArrayFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, advanced_options=True, data_format="", @@ -93,12 +93,12 @@ output_data_array=nx.DataPath("[Image Geometry]/Cell Data/IPFColors"), scalar_type=nx.NumericType.uint8 ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 6 # Instantiate Filter -filter = nx.CropImageGeometry() +nx_filter = nx.CropImageGeometry() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, created_image_geometry=nx.DataPath("CroppedBottomHalf"), max_voxel=[59, 79, 50], @@ -110,14 +110,14 @@ # cell_feature_attribute_matrix: DataPath = ..., # Not currently part of the code # feature_ids: DataPath = ..., # Not currently part of the code ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 7 # Instantiate Filter -filter = nx.CropImageGeometry() +nx_filter = nx.CropImageGeometry() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, created_image_geometry=nx.DataPath("CroppedTopHalf"), max_voxel=[59, 79, 99], @@ -129,13 +129,13 @@ # cell_feature_attribute_matrix: DataPath = ..., # Not currently part of the code # feature_ids: DataPath = ..., # Not currently part of the code ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 8 # Instantiate Filter -filter = nx.AppendImageGeometryZSliceFilter() +nx_filter = nx.AppendImageGeometryZSliceFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, check_resolution=True, destination_geometry=nx.DataPath("CroppedBottomHalf"), @@ -143,20 +143,20 @@ new_geometry=nx.DataPath("AppendedImageGeom"), save_as_new_geometry=True ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 9 # Instantiate Filter -filter = nx.WriteDREAM3DFilter() +nx_filter = nx.WriteDREAM3DFilter() # Set Output File Path output_file_path = nxtest.GetDataDirectory() + "/Output/Examples/AppendImageGeometryZSlice.dream3d" # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, export_file_path=output_file_path, write_xdmf_file=True ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # ***************************************************************************** # THIS SECTION IS ONLY HERE FOR CLEANING UP THE CI Machines diff --git a/wrapping/python/examples/pipelines/Simplnx/ApplyTransformation_Demo.py b/wrapping/python/examples/pipelines/Simplnx/ApplyTransformation_Demo.py index 3dc8cf9816..09be9f1025 100644 --- a/wrapping/python/examples/pipelines/Simplnx/ApplyTransformation_Demo.py +++ b/wrapping/python/examples/pipelines/Simplnx/ApplyTransformation_Demo.py @@ -11,29 +11,29 @@ # Filter 1 # Instantiate Filter -filter = nx.CreateDataGroup() +nx_filter = nx.CreateDataGroup() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, data_object_path=nx.DataPath("Group 1") ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 2 # Instantiate Filter -filter = nx.CreateDataGroup() +nx_filter = nx.CreateDataGroup() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, data_object_path=nx.DataPath("Group 1/Group 2") ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 3 # Instantiate Filter -filter = nx.CreateGeometryFilter() +nx_filter = nx.CreateGeometryFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, array_handling=0, cell_attribute_matrix_name="Cell Data", @@ -57,14 +57,14 @@ #y_bounds: DataPath = ..., (not used here) #z_bounds: DataPath = ... (not used here) ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 4 # Instantiate Filter -filter = nx.CreateDataArray() +nx_filter = nx.CreateDataArray() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, component_count=1, data_format="", @@ -73,13 +73,13 @@ output_data_array=nx.DataPath("Group 1/Group 2/[Geometry]/Cell Data/Data"), tuple_dimensions=[[2.0, 10.0, 10.0]] ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 5 # Instantiate Filter -filter = nx.ApplyTransformationToGeometryFilter() +nx_filter = nx.ApplyTransformationToGeometryFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, cell_attribute_matrix_path=nx.DataPath("Group 1/Group 2/[Geometry]/Cell Data"), interpolation_type=1, @@ -88,7 +88,7 @@ transformation_type=5, translate_geometry_to_global_origin=False ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) print("===> Pipeline Complete") \ No newline at end of file diff --git a/wrapping/python/examples/pipelines/Simplnx/ApplyTransformation_Image.py b/wrapping/python/examples/pipelines/Simplnx/ApplyTransformation_Image.py index eba0b8bcd4..55dfae5edd 100644 --- a/wrapping/python/examples/pipelines/Simplnx/ApplyTransformation_Image.py +++ b/wrapping/python/examples/pipelines/Simplnx/ApplyTransformation_Image.py @@ -11,35 +11,35 @@ # Filter 1 # Instantiate Filter -filter = cxor.ReadAngDataFilter() +nx_filter = cxor.ReadAngDataFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, cell_attribute_matrix_name="Cell Data", cell_ensemble_attribute_matrix_name="CellEnsembleData", data_container_name=nx.DataPath("Small IN100"), input_file=nxtest.GetDataDirectory() + "/Small_IN100/Slice_1.ang" ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 2 # Instantiate Filter -filter = cxor.ReadAngDataFilter() +nx_filter = cxor.ReadAngDataFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, cell_attribute_matrix_name="Cell Data", cell_ensemble_attribute_matrix_name="CellEnsembleData", data_container_name=nx.DataPath("Transform [Rotate]"), input_file=nxtest.GetDataDirectory() + "/Small_IN100/Slice_1.ang" ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 3 # Instantiate Filter -filter = nx.ApplyTransformationToGeometryFilter() +nx_filter = nx.ApplyTransformationToGeometryFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, cell_attribute_matrix_path=nx.DataPath("Transform [Rotate]/Cell Data"), interpolation_type=1, @@ -52,27 +52,27 @@ # scale: List[float] = ..., # Not used here # translation: List[float] = ... # Not used here ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 4 # Instantiate Filter -filter = cxor.ReadAngDataFilter() +nx_filter = cxor.ReadAngDataFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, cell_attribute_matrix_name="Cell Data", cell_ensemble_attribute_matrix_name="CellEnsembleData", data_container_name=nx.DataPath("Transform [Scale]"), input_file=nxtest.GetDataDirectory() + "/Small_IN100/Slice_1.ang" ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 5 # Instantiate Filter -filter = nx.ApplyTransformationToGeometryFilter() +nx_filter = nx.ApplyTransformationToGeometryFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, cell_attribute_matrix_path=nx.DataPath("Transform [Scale]/Cell Data"), interpolation_type=1, @@ -85,26 +85,26 @@ # rotation: List[float] = ..., # translation: List[float] = ... ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 6 # Instantiate Filter -filter = cxor.ReadAngDataFilter() +nx_filter = cxor.ReadAngDataFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, cell_attribute_matrix_name="Cell Data", cell_ensemble_attribute_matrix_name="CellEnsembleData", data_container_name=nx.DataPath("Transform [Translate]"), input_file=nxtest.GetDataDirectory() + "/Small_IN100/Slice_1.ang" ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 7 # Instantiate Filter -filter = nx.ApplyTransformationToGeometryFilter() +nx_filter = nx.ApplyTransformationToGeometryFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, cell_attribute_matrix_path=nx.DataPath("Transform [Translate]/Cell Data"), interpolation_type=1, @@ -117,26 +117,26 @@ # rotation: List[float] = ..., # Not used here # scale: List[float] = ... # Not used here ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 8 # Instantiate Filter -filter = cxor.ReadAngDataFilter() +nx_filter = cxor.ReadAngDataFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, cell_attribute_matrix_name="Cell Data", cell_ensemble_attribute_matrix_name="CellEnsembleData", data_container_name=nx.DataPath("Transform [Rotation-Interpolation]"), input_file=nxtest.GetDataDirectory() + "/Small_IN100/Slice_1.ang" ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 9 # Instantiate Filter -filter = nx.ApplyTransformationToGeometryFilter() +nx_filter = nx.ApplyTransformationToGeometryFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, cell_attribute_matrix_path=nx.DataPath("Transform [Rotation-Interpolation]/Cell Data"), interpolation_type=0, @@ -149,27 +149,27 @@ # scale: List[float] = ..., # translation: List[float] = ... ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 10 # Instantiate Filter -filter = cxor.ReadAngDataFilter() +nx_filter = cxor.ReadAngDataFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, cell_attribute_matrix_name="Cell Data", cell_ensemble_attribute_matrix_name="CellEnsembleData", data_container_name=nx.DataPath("Transform [Scale-Interpolation]"), input_file=nxtest.GetDataDirectory() + "/Small_IN100/Slice_1.ang" ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 11 # Instantiate Filter -filter = nx.ApplyTransformationToGeometryFilter() +nx_filter = nx.ApplyTransformationToGeometryFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, cell_attribute_matrix_path=nx.DataPath("Transform [Scale-Interpolation]/Cell Data"), interpolation_type=0, @@ -182,20 +182,20 @@ # rotation: List[float] = ..., # translation: List[float] = ... ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 12 # Instantiate Filter -filter = nx.WriteDREAM3DFilter() +nx_filter = nx.WriteDREAM3DFilter() # Set Output File Path output_file_path = nxtest.GetDataDirectory() + "/Output/Transformation/ApplyTransformation_Image.dream3d" # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, export_file_path=output_file_path, write_xdmf_file=True ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # ***************************************************************************** # THIS SECTION IS ONLY HERE FOR CLEANING UP THE CI Machines diff --git a/wrapping/python/examples/pipelines/Simplnx/ApplyTransformation_Node.py b/wrapping/python/examples/pipelines/Simplnx/ApplyTransformation_Node.py index 2affb8b484..603acb5a12 100644 --- a/wrapping/python/examples/pipelines/Simplnx/ApplyTransformation_Node.py +++ b/wrapping/python/examples/pipelines/Simplnx/ApplyTransformation_Node.py @@ -11,9 +11,9 @@ # Filter 1 # Instantiate Filter -filter = nx.ReadStlFileFilter() +nx_filter = nx.ReadStlFileFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, face_attribute_matrix="Face Data", face_normals_data_path="Face Normals", @@ -22,13 +22,13 @@ triangle_geometry_name=nx.DataPath("Blade"), vertex_attribute_matrix="Vertex Data" ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 2 # Instantiate Filter -filter = nx.ReadStlFileFilter() +nx_filter = nx.ReadStlFileFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, face_attribute_matrix="Face Data", face_normals_data_path="Face Normals", @@ -38,13 +38,13 @@ triangle_geometry_name=nx.DataPath("Blade [Rotation]"), vertex_attribute_matrix="Vertex Data" ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 3 # Instantiate Filter -filter = nx.ApplyTransformationToGeometryFilter() +nx_filter = nx.ApplyTransformationToGeometryFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, #cell_attribute_matrix_path: DataPath = ..., #computed_transformation_matrix: DataPath = ..., @@ -57,13 +57,13 @@ translate_geometry_to_global_origin=False #translation: List[float] = ... ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 4 # Instantiate Filter -filter = nx.ReadStlFileFilter() +nx_filter = nx.ReadStlFileFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, face_attribute_matrix="Face Data", face_normals_data_path="Face Normals", @@ -72,13 +72,13 @@ triangle_geometry_name=nx.DataPath("Blade [Translation]"), vertex_attribute_matrix="Vertex Data" ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 5 # Instantiate Filter -filter = nx.ApplyTransformationToGeometryFilter() +nx_filter = nx.ApplyTransformationToGeometryFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, interpolation_type=2, selected_image_geometry=nx.DataPath("Blade [Translation]"), @@ -86,13 +86,13 @@ translate_geometry_to_global_origin=False, translation=[10.0, 10.0, 10.0] ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 6 # Instantiate Filter -filter = nx.ReadStlFileFilter() +nx_filter = nx.ReadStlFileFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, face_attribute_matrix="Face Data", face_normals_data_path="Face Normals", @@ -101,13 +101,13 @@ triangle_geometry_name=nx.DataPath("Blade [Scale]"), vertex_attribute_matrix="Vertex Data" ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 7 # Instantiate Filter -filter = nx.ApplyTransformationToGeometryFilter() +nx_filter = nx.ApplyTransformationToGeometryFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, interpolation_type=2, scale=[0.5, 0.5, 1.0], @@ -115,20 +115,20 @@ transformation_type=5, translate_geometry_to_global_origin=False ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 8 # Instantiate Filter -filter = nx.WriteDREAM3DFilter() +nx_filter = nx.WriteDREAM3DFilter() # Set Output File Path output_file_path = nxtest.GetDataDirectory() + "/Output/ApplyTransformation_Node.dream3d" # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, export_file_path=output_file_path, write_xdmf_file=True ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # ***************************************************************************** # THIS SECTION IS ONLY HERE FOR CLEANING UP THE CI Machines diff --git a/wrapping/python/examples/pipelines/Simplnx/ArrayCalculatorExample.py b/wrapping/python/examples/pipelines/Simplnx/ArrayCalculatorExample.py index f8508b3c3c..cc84c86fe5 100644 --- a/wrapping/python/examples/pipelines/Simplnx/ArrayCalculatorExample.py +++ b/wrapping/python/examples/pipelines/Simplnx/ArrayCalculatorExample.py @@ -11,9 +11,9 @@ # Filter 1 # Instantiate Filter -filter = nx.CreateDataArray() +nx_filter = nx.CreateDataArray() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, advanced_options=True, component_count=1, @@ -23,14 +23,14 @@ output_data_array=nx.DataPath("TestArray"), tuple_dimensions=[[10.0]] ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 2 # Instantiate Filter -filter = nx.CreateDataArray() +nx_filter = nx.CreateDataArray() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, advanced_options=True, component_count=1, @@ -40,13 +40,13 @@ output_data_array=nx.DataPath("Confidence Index"), tuple_dimensions=[[10.0]] ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 3 # Instantiate Filter -filter = nx.CreateDataArray() +nx_filter = nx.CreateDataArray() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, advanced_options=True, component_count=3, @@ -56,72 +56,72 @@ output_data_array=nx.DataPath("EulerAngles"), tuple_dimensions=[[10.0]] ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 4 # Instantiate Filter -filter = nx.ArrayCalculatorFilter() +nx_filter = nx.ArrayCalculatorFilter() calc_param = nx.CalculatorParameter.ValueType(nx.DataPath(""), "TestArray+TestArray", nx.CalculatorParameter.AngleUnits.Radians) # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, calculated_array=nx.DataPath("Caclulated_TestArray"), calculator_parameter=calc_param, scalar_type=nx.NumericType.float32 ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 5 # Instantiate Filter -filter = nx.ArrayCalculatorFilter() +nx_filter = nx.ArrayCalculatorFilter() calc_param = nx.CalculatorParameter.ValueType(nx.DataPath(""), "Confidence Index*100", nx.CalculatorParameter.AngleUnits.Radians) # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, calculated_array=nx.DataPath("Caclulated_ConfidenceIndex"), calculator_parameter=calc_param, scalar_type=nx.NumericType.float64 ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 6 # Instantiate Filter -filter = nx.ArrayCalculatorFilter() +nx_filter = nx.ArrayCalculatorFilter() calc_param = nx.CalculatorParameter.ValueType(nx.DataPath(""), "EulerAngles/2", nx.CalculatorParameter.AngleUnits.Radians) # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, calculated_array=nx.DataPath("Caclulated_EulerAngles"), calculator_parameter=calc_param, scalar_type=nx.NumericType.float32 ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 7 # Instantiate Filter -filter = nx.ArrayCalculatorFilter() +nx_filter = nx.ArrayCalculatorFilter() calc_param = nx.CalculatorParameter.ValueType(nx.DataPath(""), "EulerAngles[0]+EulerAngles[1]", nx.CalculatorParameter.AngleUnits.Radians) # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, calculated_array=nx.DataPath("Caclulated_EulerAngles2"), calculator_parameter=calc_param, scalar_type=nx.NumericType.float32 ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 8 # Define output file path output_file_path = nxtest.GetDataDirectory() + "//Output/ArrayCalculatorExampleResults.dream3d" # Instantiate Filter -filter = nx.WriteDREAM3DFilter() +nx_filter = nx.WriteDREAM3DFilter() # Execute Filter with Parameters -result = filter.execute(data_structure=data_structure, +result = nx_filter.execute(data_structure=data_structure, export_file_path=output_file_path, write_xdmf_file=True) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # ***************************************************************************** # THIS SECTION IS ONLY HERE FOR CLEANING UP THE CI Machines diff --git a/wrapping/python/examples/pipelines/Simplnx/CombineSTLFiles.py b/wrapping/python/examples/pipelines/Simplnx/CombineSTLFiles.py index 5fa55b64d8..89caa5d922 100644 --- a/wrapping/python/examples/pipelines/Simplnx/CombineSTLFiles.py +++ b/wrapping/python/examples/pipelines/Simplnx/CombineSTLFiles.py @@ -11,9 +11,9 @@ # Filter 1 # Instantiate Filter -filter = nx.CombineStlFilesFilter() +nx_filter = nx.CombineStlFilesFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, face_attribute_matrix_name="Face Data", face_normals_array_name="Face Normals", @@ -21,17 +21,17 @@ triangle_data_container_name=nx.DataPath("TriangleGeometry"), vertex_attribute_matrix_name="Vertex Data" ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 2 # Instantiate Filter -filter = nx.WriteDREAM3DFilter() +nx_filter = nx.WriteDREAM3DFilter() # Execute Filter with Parameters output_file_path = nxtest.GetDataDirectory() + "/Output/CombinedStlFiles.dream3d" -result = filter.execute(data_structure=data_structure, +result = nx_filter.execute(data_structure=data_structure, export_file_path=output_file_path, write_xdmf_file=True) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # ***************************************************************************** # THIS SECTION IS ONLY HERE FOR CLEANING UP THE CI Machines diff --git a/wrapping/python/examples/pipelines/Simplnx/EnsembleInfoReader.py b/wrapping/python/examples/pipelines/Simplnx/EnsembleInfoReader.py index 2a5488259b..db93ae6269 100644 --- a/wrapping/python/examples/pipelines/Simplnx/EnsembleInfoReader.py +++ b/wrapping/python/examples/pipelines/Simplnx/EnsembleInfoReader.py @@ -11,9 +11,9 @@ # Filter 1 # Instantiate Filter -filter = nx.CreateImageGeometry() +nx_filter = nx.CreateImageGeometry() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, cell_data_name=("Cell Data"), dimensions=[100, 100, 2], @@ -21,13 +21,13 @@ origin=[0.0, 0.0, 0.0], spacing=[1.0, 1.0, 1.0] ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 2 # Instantiate Filter -filter = nx.ReadRawBinaryFilter() +nx_filter = nx.ReadRawBinaryFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, created_attribute_array_path=nx.DataPath("[Image Geometry]/Cell Data/Quats"), endian=0, @@ -37,27 +37,27 @@ skip_header_bytes=0, tuple_dimensions=[[2.0, 100.0, 100.0]] ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 3 # Instantiate Filter -filter = cxor.ConvertOrientations() +nx_filter = cxor.ConvertOrientations() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, input_orientation_array_path=nx.DataPath("[Image Geometry]/Cell Data/Quats"), input_type=2, output_orientation_array_name="Eulers", output_type=0 ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 4 # Instantiate Filter -filter = nx.CreateDataArray() +nx_filter = nx.CreateDataArray() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, advanced_options=True, component_count=1, @@ -67,13 +67,13 @@ output_data_array=nx.DataPath("[Image Geometry]/Cell Data/Phases"), tuple_dimensions=[[2.0, 100.0, 100.0]] ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 5 # Instantiate Filter -filter = cxor.ReadEnsembleInfoFilter() +nx_filter = cxor.ReadEnsembleInfoFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, cell_ensemble_attribute_matrix_name=("Cell Ensemble"), crystal_structures_array_name=("CrystalStructures"), @@ -81,14 +81,14 @@ input_file=nxtest.GetDataDirectory() + "/OrientationAnalysis/Ensemble.ini", phase_types_array_name=("PhaseTypes") ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 6 # Instantiate Filter -filter = cxor.GenerateIPFColorsFilter() +nx_filter = cxor.GenerateIPFColorsFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, cell_euler_angles_array_path=nx.DataPath("[Image Geometry]/Cell Data/Eulers"), cell_ipf_colors_array_name=("IPFColors"), @@ -98,20 +98,20 @@ reference_dir=[0.0, 0.0, 1.0], use_mask=False ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 7 # Instantiate Filter -filter = nx.WriteDREAM3DFilter() +nx_filter = nx.WriteDREAM3DFilter() # Set Output file path output_file_path = nxtest.GetDataDirectory() + "/Output/Examples/EnsembleInfoReaderExample.dream3d" # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, export_file_path=output_file_path, write_xdmf_file=True ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # ***************************************************************************** # THIS SECTION IS ONLY HERE FOR CLEANING UP THE CI Machines diff --git a/wrapping/python/examples/pipelines/Simplnx/Import_ASCII.py b/wrapping/python/examples/pipelines/Simplnx/Import_ASCII.py index 6a5c4412cd..8ae9c25ff1 100644 --- a/wrapping/python/examples/pipelines/Simplnx/Import_ASCII.py +++ b/wrapping/python/examples/pipelines/Simplnx/Import_ASCII.py @@ -11,9 +11,9 @@ # Filter 1 # Instantiate Filter -filter = nx.CreateGeometryFilter() +nx_filter = nx.CreateGeometryFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, array_handling=0, cell_attribute_matrix_name="Cell Data", @@ -37,7 +37,7 @@ #y_bounds: DataPath = ..., #z_bounds: DataPath = ... ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 2 @@ -54,22 +54,22 @@ read_csv_data.header_mode = nx.ReadCSVDataParameter.HeaderMode.Custom # Instantiate Filter -filter = nx.ReadCSVFileFilter() +nx_filter = nx.ReadCSVFileFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, created_data_group=nx.DataPath("Imported Data"), read_csv_data=read_csv_data, selected_data_group=nx.DataPath("[Image Geometry]/Cell Data"), use_existing_group=True, ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 3 # Instantiate Filter -filter = nx.CreateDataArray() +nx_filter = nx.CreateDataArray() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, advanced_options=False, component_count=1, @@ -79,13 +79,13 @@ output_data_array=nx.DataPath("[Image Geometry]/Cell Data/Phase") #tuple_dimensions=[] ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 4 # Instantiate Filter -filter = nx.CombineAttributeArraysFilter() +nx_filter = nx.CombineAttributeArraysFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, move_values=True, normalize_data=False, @@ -94,7 +94,7 @@ nx.DataPath("[Image Geometry]/Cell Data/phi2")], stacked_data_array_name="Eulers" ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 5 # Define ensemble info parameters @@ -104,9 +104,9 @@ ensemble_info_parameter.append(["Cubic-High m-3m", "Primary", "Phase 2"]) # Instantiate Filter -filter = cxor.CreateEnsembleInfoFilter() +nx_filter = cxor.CreateEnsembleInfoFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, cell_ensemble_attribute_matrix_name=nx.DataPath("[Image Geometry]/CellEnsembleData"), crystal_structures_array_name="CrystalStructures", @@ -114,13 +114,13 @@ phase_types_array_name="PhaseTypes", ensemble=ensemble_info_parameter ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 6 # Instantiate Filter -filter = cxor.GenerateIPFColorsFilter() +nx_filter = cxor.GenerateIPFColorsFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, cell_euler_angles_array_path=nx.DataPath("[Image Geometry]/Cell Data/Eulers"), cell_ipf_colors_array_name="IPFColors", @@ -130,17 +130,17 @@ reference_dir=[0.0, 0.0, 1.0], use_mask=False ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 7 # Instantiate Filter -filter = cxitk.ITKImageWriter() +nx_filter = cxitk.ITKImageWriter() # Output file path for Filter 7 output_file_path = nxtest.GetDataDirectory() + "/Output/Import_ASCII/IPF.png" # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, file_name=output_file_path, image_array_path=nx.DataPath("[Image Geometry]/Cell Data/IPFColors"), @@ -148,7 +148,7 @@ index_offset=0, plane=0 ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # ***************************************************************************** # THIS SECTION IS ONLY HERE FOR CLEANING UP THE CI Machines diff --git a/wrapping/python/examples/pipelines/Simplnx/Import_CSV_Data.py b/wrapping/python/examples/pipelines/Simplnx/Import_CSV_Data.py index 2b27023dd2..2149768bc6 100644 --- a/wrapping/python/examples/pipelines/Simplnx/Import_CSV_Data.py +++ b/wrapping/python/examples/pipelines/Simplnx/Import_CSV_Data.py @@ -11,9 +11,9 @@ # Filter 1 # Instantiate Filter -filter = nx.CreateImageGeometry() +nx_filter = nx.CreateImageGeometry() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, cell_data_name="Cell Data", dimensions=[60, 80, 100], @@ -21,13 +21,13 @@ origin=[100.0, 100.0, 0.0], spacing=[1.0, 1.0, 1.0] ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 2 # Instantiate Filter -filter = nx.ReadTextDataArrayFilter() +nx_filter = nx.ReadTextDataArrayFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, advanced_options=False, data_format="", @@ -39,13 +39,13 @@ output_data_array=nx.DataPath("[Image Geometry]/Cell Data/Confidence Index"), scalar_type=nx.NumericType.float32 ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 3 # Instantiate Filter -filter = nx.ReadTextDataArrayFilter() +nx_filter = nx.ReadTextDataArrayFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, advanced_options=False, data_format="", @@ -57,13 +57,13 @@ output_data_array=nx.DataPath("[Image Geometry]/Cell Data/FeatureIds"), scalar_type=nx.NumericType.int32 ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 4 # Instantiate Filter -filter = nx.ReadTextDataArrayFilter() +nx_filter = nx.ReadTextDataArrayFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, advanced_options=False, data_format="", @@ -75,13 +75,13 @@ output_data_array=nx.DataPath("[Image Geometry]/Cell Data/Image Quality"), scalar_type=nx.NumericType.float32 ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 5 # Instantiate Filter -filter = nx.ReadTextDataArrayFilter() +nx_filter = nx.ReadTextDataArrayFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, advanced_options=False, data_format="", @@ -93,6 +93,6 @@ output_data_array=nx.DataPath("[Image Geometry]/Cell Data/IPFColors"), scalar_type=nx.NumericType.uint8 ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) print("===> Pipeline Complete") \ No newline at end of file diff --git a/wrapping/python/examples/pipelines/Simplnx/Import_STL_Model.py b/wrapping/python/examples/pipelines/Simplnx/Import_STL_Model.py index ccd157b865..c73a5695c8 100644 --- a/wrapping/python/examples/pipelines/Simplnx/Import_STL_Model.py +++ b/wrapping/python/examples/pipelines/Simplnx/Import_STL_Model.py @@ -11,9 +11,9 @@ # Filter 1 # Instantiate Filter -filter = nx.ReadStlFileFilter() +nx_filter = nx.ReadStlFileFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, face_attribute_matrix="Face Data", face_normals_data_path="Face Normals", @@ -22,24 +22,24 @@ triangle_geometry_name=nx.DataPath("[Triangle Geometry]"), vertex_attribute_matrix="Vertex Data" ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 2 # Instantiate Filter -filter = nx.CalculateTriangleAreasFilter() +nx_filter = nx.CalculateTriangleAreasFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, triangle_areas_array_path="Areas", triangle_geometry_data_path=nx.DataPath("[Triangle Geometry]") ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 3 # Instantiate Filter -filter = nx.CreateDataArray() +nx_filter = nx.CreateDataArray() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, advanced_options=True, component_count=1, @@ -49,6 +49,6 @@ output_data_array=nx.DataPath("Node Type"), tuple_dimensions=[[1.0]] ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) print("===> Pipeline Complete") \ No newline at end of file diff --git a/wrapping/python/examples/pipelines/Simplnx/ReplaceElementAttributesWithNeighbor.py b/wrapping/python/examples/pipelines/Simplnx/ReplaceElementAttributesWithNeighbor.py index d61df5d77d..bf8d20db78 100644 --- a/wrapping/python/examples/pipelines/Simplnx/ReplaceElementAttributesWithNeighbor.py +++ b/wrapping/python/examples/pipelines/Simplnx/ReplaceElementAttributesWithNeighbor.py @@ -11,16 +11,16 @@ # Filter 1 # Instantiate Filter -filter = cxor.ReadAngDataFilter() +nx_filter = cxor.ReadAngDataFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, cell_attribute_matrix_name=("Cell Data"), cell_ensemble_attribute_matrix_name=("CellEnsembleData"), data_container_name=nx.DataPath("DataContainer"), input_file=nxtest.GetDataDirectory() + "/Small_IN100/Slice_1.ang" ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 2 # Instantiate ArrayThreshold objects @@ -40,22 +40,22 @@ dt = nx.DataType.boolean # Instantiate Filter -filter = nx.MultiThresholdObjects() +nx_filter = nx.MultiThresholdObjects() # Execute filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, array_thresholds=threshold_set, created_data_path="Mask", created_mask_type=nx.DataType.boolean ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 3 # Instantiate Filter -filter = nx.RotateSampleRefFrameFilter() +nx_filter = nx.RotateSampleRefFrameFilter() # Execute Filter -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, remove_original_geometry=True, rotate_slice_by_slice=False, @@ -63,25 +63,25 @@ rotation_representation=0, selected_image_geometry=nx.DataPath("DataContainer") ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 4 # Instantiate Filter -filter = cxor.RotateEulerRefFrameFilter() +nx_filter = cxor.RotateEulerRefFrameFilter() # Execute Filter -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, euler_angles_array_path=nx.DataPath("DataContainer/Cell Data/EulerAngles"), rotation_axis=[0.0, 0.0, 1.0, 90.0] ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 5 # Instantiate Filter -filter = nx.SetImageGeomOriginScalingFilter() +nx_filter = nx.SetImageGeomOriginScalingFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, change_origin=True, change_resolution=True, @@ -89,13 +89,13 @@ origin=[0.0, 0.0, 0.0], spacing=[1.0, 1.0, 1.0] ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 6 # Instantiate Filter -filter = nx.CropImageGeometry() +nx_filter = nx.CropImageGeometry() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, #cell_feature_attribute_matrix: DataPath = ..., #created_image_geometry: DataPath = ..., @@ -107,13 +107,13 @@ selected_image_geometry=nx.DataPath("DataContainer") # update_origin=False ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 7 # Instantiate Filter -filter = cxor.GenerateIPFColorsFilter() +nx_filter = cxor.GenerateIPFColorsFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, cell_euler_angles_array_path=nx.DataPath("DataContainer/Cell Data/EulerAngles"), cell_ipf_colors_array_name=("IPFColors"), @@ -123,13 +123,13 @@ reference_dir=[0.0, 0.0, 1.0], use_mask=True ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 8 # Instantiate Filter -filter = nx.ReplaceElementAttributesWithNeighborValuesFilter() +nx_filter = nx.ReplaceElementAttributesWithNeighborValuesFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, comparison_data_path=nx.DataPath("DataContainer/Cell Data/Confidence Index"), loop=True, @@ -137,19 +137,19 @@ selected_comparison=0, selected_image_geometry=nx.DataPath("DataContainer") ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 9 output_file_path = nxtest.GetDataDirectory() + "/Output/Examples/ReplaceElementAttributesWithNeighbor.dream3d" # Instantiate Filter -filter = nx.WriteDREAM3DFilter() +nx_filter = nx.WriteDREAM3DFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, export_file_path=output_file_path, write_xdmf_file=True ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # ***************************************************************************** # THIS SECTION IS ONLY HERE FOR CLEANING UP THE CI Machines diff --git a/wrapping/python/examples/pipelines/Simplnx/ResamplePorosityImage.py b/wrapping/python/examples/pipelines/Simplnx/ResamplePorosityImage.py index 1be6b90759..858b414fe5 100644 --- a/wrapping/python/examples/pipelines/Simplnx/ResamplePorosityImage.py +++ b/wrapping/python/examples/pipelines/Simplnx/ResamplePorosityImage.py @@ -24,9 +24,9 @@ generated_file_list_value.padding_digits = 2 # Instantiate Filter -filter = cxitk.ITKImportImageStack() +nx_filter = cxitk.ITKImportImageStack() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, cell_data_name="Cell Data", image_data_array_path="ImageData", @@ -36,14 +36,14 @@ origin=[0.0, 0.0, 0.0], spacing=[1.0, 1.0, 1.0] ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 2 # Instantiate Filter -filter = nx.ResampleImageGeomFilter() +nx_filter = nx.ResampleImageGeomFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, #cell_feature_attribute_matrix_path: DataPath = ..., #exact_dimensions: List[int] = ..., @@ -56,14 +56,14 @@ selected_image_geometry=nx.DataPath("Porosity_Image"), spacing=[2.0, 2.0, 2.0] ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 3 # Instantiate Filter -filter = nx.ResampleImageGeomFilter() +nx_filter = nx.ResampleImageGeomFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, #cell_feature_attribute_matrix_path: DataPath = ..., #exact_dimensions: List[int] = ..., @@ -77,14 +77,14 @@ #spacing: List[float] = ... ) # Error/Result Handling for Filter -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 4 # Instantiate Filter -filter = nx.ResampleImageGeomFilter() +nx_filter = nx.ResampleImageGeomFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, #cell_feature_attribute_matrix_path: DataPath = ..., exact_dimensions=[262, 195, 82], @@ -98,7 +98,7 @@ #spacing: List[float] = ... ) # Error/Result Handling for Filter -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 5 @@ -108,7 +108,7 @@ result = nx.WriteDREAM3DFilter.execute(data_structure=data_structure, export_file_path=output_file_path, write_xdmf_file=True) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # ***************************************************************************** # THIS SECTION IS ONLY HERE FOR CLEANING UP THE CI Machines diff --git a/wrapping/python/examples/pipelines/Simplnx/ResampleRectGridToImageGeom.py b/wrapping/python/examples/pipelines/Simplnx/ResampleRectGridToImageGeom.py index 4145e5a4e6..f23aed1f8e 100644 --- a/wrapping/python/examples/pipelines/Simplnx/ResampleRectGridToImageGeom.py +++ b/wrapping/python/examples/pipelines/Simplnx/ResampleRectGridToImageGeom.py @@ -25,23 +25,23 @@ read_csv_data.header_mode = nx.ReadCSVDataParameter.HeaderMode.Custom # Instantiate Filter -filter = nx.ReadCSVFileFilter() +nx_filter = nx.ReadCSVFileFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, created_data_group=nx.DataPath("Bounds"), read_csv_data=read_csv_data, # selected_data_group: DataPath = ..., use_existing_group=False, ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 2 # Instantiate Filter -filter = nx.CreateGeometryFilter() +nx_filter = nx.CreateGeometryFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, array_handling=1, cell_attribute_matrix_name="CellData", @@ -65,14 +65,14 @@ y_bounds=nx.DataPath("Bounds/y"), z_bounds=nx.DataPath("Bounds/z") ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 3 # Instantiate Filter -filter = nx.ReadTextDataArrayFilter() +nx_filter = nx.ReadTextDataArrayFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, advanced_options=False, data_format="", @@ -84,13 +84,13 @@ output_data_array=nx.DataPath("RectGridGeometry/CellData/ConfidenceIndex"), scalar_type=nx.NumericType.float32 ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 4 # Instantiate Filter -filter = nx.ReadTextDataArrayFilter() +nx_filter = nx.ReadTextDataArrayFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, advanced_options=False, data_format="", @@ -102,14 +102,14 @@ output_data_array=nx.DataPath("RectGridGeometry/CellData/ImageQuality"), scalar_type=nx.NumericType.float32 ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 5 # Instantiate Filter -filter = nx.ReadTextDataArrayFilter() +nx_filter = nx.ReadTextDataArrayFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, advanced_options=False, data_format="", @@ -121,13 +121,13 @@ output_data_array=nx.DataPath("RectGridGeometry/CellData/SEM Signal"), scalar_type=nx.NumericType.float32 ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 6 # Instantiate Filter -filter = nx.ReadTextDataArrayFilter() +nx_filter = nx.ReadTextDataArrayFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, advanced_options=False, data_format="", @@ -139,14 +139,14 @@ output_data_array=nx.DataPath("RectGridGeometry/CellData/Fit"), scalar_type=nx.NumericType.float32 ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 7 # Instantiate Filter -filter = nx.ReadTextDataArrayFilter() +nx_filter = nx.ReadTextDataArrayFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, advanced_options=False, data_format="", @@ -158,13 +158,13 @@ output_data_array=nx.DataPath("RectGridGeometry/CellData/EulerAngles"), scalar_type=nx.NumericType.float32 ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 8 # Instantiate Filter -filter = nx.ReadTextDataArrayFilter() +nx_filter = nx.ReadTextDataArrayFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, advanced_options=False, data_format="", @@ -176,14 +176,14 @@ output_data_array=nx.DataPath("RectGridGeometry/CellData/Phases"), scalar_type=nx.NumericType.int32 ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 9 # Instantiate Filter -filter = nx.ResampleRectGridToImageGeomFilter() +nx_filter = nx.ResampleRectGridToImageGeomFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, dimensions=[20, 20, 20], image_geom_cell_attribute_matrix="CellData", @@ -196,18 +196,18 @@ nx.DataPath("RectGridGeometry/CellData/Phases"), nx.DataPath("RectGridGeometry/CellData/SEM Signal")] ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Instantiate Filter -filter = nx.WriteDREAM3DFilter() +nx_filter = nx.WriteDREAM3DFilter() # Execute Filter with Parameters output_file_path = nxtest.GetDataDirectory() + "/Examples/ResampleRectGridToImageGeom.dream3d" -result = filter.execute(data_structure=data_structure, +result = nx_filter.execute(data_structure=data_structure, export_file_path=output_file_path, write_xdmf_file=True) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # ***************************************************************************** # THIS SECTION IS ONLY HERE FOR CLEANING UP THE CI Machines diff --git a/wrapping/python/examples/pipelines/Simplnx/SurfaceNets_Demo.py b/wrapping/python/examples/pipelines/Simplnx/SurfaceNets_Demo.py index 53e22ef2b7..9a36a91e80 100644 --- a/wrapping/python/examples/pipelines/Simplnx/SurfaceNets_Demo.py +++ b/wrapping/python/examples/pipelines/Simplnx/SurfaceNets_Demo.py @@ -24,9 +24,9 @@ generated_file_list_value.padding_digits = 2 # Instantiate Filter -filter = cxitk.ITKImportImageStack() +nx_filter = cxitk.ITKImportImageStack() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, cell_data_name="Optical Data", image_data_array_path="Image Data", @@ -36,7 +36,7 @@ origin=[0.0, 0.0, 0.0], spacing=[1.0, 1.0, 1.0] ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 2 # Instantiate ArrayThreshold objects @@ -50,21 +50,21 @@ dt = nx.DataType.boolean # Instantiate Filter -filter = nx.MultiThresholdObjects() +nx_filter = nx.MultiThresholdObjects() # Execute filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, array_thresholds=threshold_set, created_data_path="Mask", created_mask_type=nx.DataType.boolean ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 3 # Instantiate Filter -filter = nx.ScalarSegmentFeaturesFilter() +nx_filter = nx.ScalarSegmentFeaturesFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, active_array_path="Active", cell_feature_group_path="Pore Data", @@ -76,13 +76,13 @@ scalar_tolerance=0, use_mask=False ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 4 # Instantiate Filter -filter = nx.SurfaceNetsFilter() +nx_filter = nx.SurfaceNetsFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, apply_smoothing=True, face_data_group_name="Face Data", @@ -98,7 +98,7 @@ triangle_geometry_name=nx.DataPath("TriangleDataContainer"), vertex_data_group_name="Vertex Data" ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 5 output_file_path = nxtest.GetDataDirectory() + "/Output/SurfaceMesh/SurfaceNets_Demo.dream3d" @@ -106,7 +106,7 @@ export_file_path=output_file_path, write_xdmf_file=True) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # ***************************************************************************** # THIS SECTION IS ONLY HERE FOR CLEANING UP THE CI Machines diff --git a/wrapping/python/examples/pipelines/Simplnx/Triangle_Face_Data_Demo.py b/wrapping/python/examples/pipelines/Simplnx/Triangle_Face_Data_Demo.py index b2ab3ae963..1d96f5bf37 100644 --- a/wrapping/python/examples/pipelines/Simplnx/Triangle_Face_Data_Demo.py +++ b/wrapping/python/examples/pipelines/Simplnx/Triangle_Face_Data_Demo.py @@ -11,9 +11,9 @@ # Filter 1 # Instantiate Filter -filter = nx.ReadStlFileFilter() +nx_filter = nx.ReadStlFileFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, face_attribute_matrix="Face Data", face_normals_data_path="Face Normals", @@ -23,50 +23,50 @@ triangle_geometry_name=nx.DataPath("[Triangle Geometry]"), vertex_attribute_matrix="Vertex Data" ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 2 # Instantiate Filter -filter = nx.CalculateTriangleAreasFilter() +nx_filter = nx.CalculateTriangleAreasFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, triangle_areas_array_path="Face Areas", triangle_geometry_data_path=nx.DataPath("[Triangle Geometry]") ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 3 # Instantiate Filter -filter = nx.TriangleNormalFilter() +nx_filter = nx.TriangleNormalFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, surface_mesh_triangle_normals_array_path="Face Normals (Calculated)", tri_geometry_data_path=nx.DataPath("[Triangle Geometry]") ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 4 # Instantiate Filter -filter = nx.TriangleDihedralAngleFilter() +nx_filter = nx.TriangleDihedralAngleFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, surface_mesh_triangle_dihedral_angles_array_name="Dihedral Angles", tri_geometry_data_path=nx.DataPath("[Triangle Geometry]") ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) # Filter 5 # Instantiate Filter -filter = nx.TriangleCentroidFilter() +nx_filter = nx.TriangleCentroidFilter() # Execute Filter with Parameters -result = filter.execute( +result = nx_filter.execute( data_structure=data_structure, centroids_array_name="Centroids", triangle_geometry_path=nx.DataPath("[Triangle Geometry]") ) -nxtest.check_filter_result(filter, result) +nxtest.check_filter_result(nx_filter, result) print("===> Pipeline Complete") \ No newline at end of file diff --git a/wrapping/python/examples/scripts/basic_arrays.py b/wrapping/python/examples/scripts/basic_arrays.py index 54bba9096f..0c2076da00 100644 --- a/wrapping/python/examples/scripts/basic_arrays.py +++ b/wrapping/python/examples/scripts/basic_arrays.py @@ -71,7 +71,7 @@ output_array_path = nx.DataPath(["Group", "1D Array"]) array_type = nx.NumericType.float32 tuple_dims = [[10]] -create_array_filter = nx.CreateDataArray() +create_array_nx_filter = nx.CreateDataArray() result = create_array_filter.execute(data_structure=data_structure, component_count=1, data_format="", @@ -94,7 +94,7 @@ # Example, and Image where 5 wide x 2 High output_array_path = nx.DataPath(["2D Array"]) tuple_dims = [[2,5]] -create_array_filter = nx.CreateDataArray() +create_array_nx_filter = nx.CreateDataArray() result = create_array_filter.execute(data_structure=data_structure, component_count=1, data_format="", @@ -123,7 +123,7 @@ # Example, and Image where 5 wide x 2 High output_array_path = nx.DataPath(["3D Array"]) tuple_dims = [[3, 2, 5]] -create_array_filter = nx.CreateDataArray() +create_array_nx_filter = nx.CreateDataArray() result = create_array_filter.execute(data_structure=data_structure, component_count=1, data_format="", diff --git a/wrapping/python/examples/scripts/geometry_examples.py b/wrapping/python/examples/scripts/geometry_examples.py index 32a4b9e03e..fb5e38ba92 100644 --- a/wrapping/python/examples/scripts/geometry_examples.py +++ b/wrapping/python/examples/scripts/geometry_examples.py @@ -82,7 +82,7 @@ # AttributeMatrix that we generated in the last filter. output_array_path = nx.DataPath("Image Geometry/Cell Data/Float Cell Data") array_type = nx.NumericType.float32 -create_array_filter = nx.CreateDataArray() +create_array_nx_filter = nx.CreateDataArray() result = create_array_filter.execute(data_structure=data_structure, component_count=1, data_format="", initialization_value="10", numeric_type=array_type, output_data_array=output_array_path) @@ -104,7 +104,7 @@ output_array_path = nx.DataPath("RectGridCoords/X Coords") array_type = nx.NumericType.float32 tuple_dims = [[10]] -create_array_filter = nx.CreateDataArray() +create_array_nx_filter = nx.CreateDataArray() result = create_array_filter.execute(data_structure=data_structure, component_count=1, data_format="", @@ -122,7 +122,7 @@ output_array_path = nx.DataPath("RectGridCoords/Y Coords") array_type = nx.NumericType.float32 tuple_dims = [[10]] -create_array_filter = nx.CreateDataArray() +create_array_nx_filter = nx.CreateDataArray() result = create_array_filter.execute(data_structure=data_structure, component_count=1, data_format="", @@ -140,7 +140,7 @@ output_array_path = nx.DataPath("RectGridCoords/Z Coords") array_type = nx.NumericType.float32 tuple_dims = [[10]] -create_array_filter = nx.CreateDataArray() +create_array_nx_filter = nx.CreateDataArray() result = create_array_filter.execute(data_structure=data_structure, component_count=1, data_format="", diff --git a/wrapping/python/examples/scripts/output_file.py b/wrapping/python/examples/scripts/output_file.py index 4d900dcb34..adbc67d26d 100644 --- a/wrapping/python/examples/scripts/output_file.py +++ b/wrapping/python/examples/scripts/output_file.py @@ -58,7 +58,7 @@ output_array_path = nx.DataPath(["3D Array"]) array_type = nx.NumericType.float32 tuple_dims = [[3, 2,5]] -create_array_filter = nx.CreateDataArray() +create_array_nx_filter = nx.CreateDataArray() result = create_array_filter.execute(data_structure=data_structure, component_count=1, data_format="", initialization_value="10", numeric_type=array_type, output_data_array=output_array_path, tuple_dimensions=tuple_dims) nxtest.check_filter_result(nx.CreateDataArray, result)