ENH: Crop Image Geometry now crops by physical units by default. (#1196)

* ENH: Crop Image Geometry now crops by physical units by default. * Update unit tests --------- Signed-off-by: Michael Jackson <[email protected]>
BlueQuartzSoftware · Feb 11, 2025 · cfc842b · cfc842b
1 parent 397ca6f
commit cfc842b
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Showing 9 changed files with 25 additions and 7 deletions.
diff --git a/src/Plugins/SimplnxCore/src/SimplnxCore/Filters/Algorithms/RemoveFlaggedFeatures.cpp b/src/Plugins/SimplnxCore/src/SimplnxCore/Filters/Algorithms/RemoveFlaggedFeatures.cpp
@@ -211,6 +211,7 @@ class RunCropImageGeometryImpl
     args.insertOrAssign(CropImageGeometryFilter::k_RemoveOriginalGeometry_Key, std::make_any<bool>(false));
     args.insertOrAssign(CropImageGeometryFilter::k_SelectedImageGeometryPath_Key, std::make_any<DataPath>(m_ImageGeometryPath));
     args.insertOrAssign(CropImageGeometryFilter::k_RenumberFeatures_Key, std::make_any<bool>(false));
+    args.insertOrAssign(CropImageGeometryFilter::k_UsePhysicalBounds_Key, std::make_any<bool>(false));
 
     args.insertOrAssign(CropImageGeometryFilter::k_MinVoxel_Key, std::make_any<std::vector<uint64>>(m_MinVoxelVector));
     args.insertOrAssign(CropImageGeometryFilter::k_MaxVoxel_Key, std::make_any<std::vector<uint64>>(m_MaxVoxelVector));

diff --git a/src/Plugins/SimplnxCore/src/SimplnxCore/Filters/CropImageGeometryFilter.cpp b/src/Plugins/SimplnxCore/src/SimplnxCore/Filters/CropImageGeometryFilter.cpp
@@ -182,7 +182,7 @@ Parameters CropImageGeometryFilter::parameters() const
 
   params.insertSeparator(Parameters::Separator{"Input Parameter(s)"});
   params.insertLinkableParameter(
-      std::make_unique<BoolParameter>(k_UsePhysicalBounds_Key, "Use Physical Units For Bounds", "If true define physical coordinates for bounds, If false define voxel indices for bounds", false));
+      std::make_unique<BoolParameter>(k_UsePhysicalBounds_Key, "Use Physical Units For Bounds", "If true define physical coordinates for bounds, If false define voxel indices for bounds", true));
   params.insert(std::make_unique<BoolParameter>(k_CropXDim_Key, "Crop X Dimension", "Enable cropping in the X dimension.", true));
   params.insert(std::make_unique<BoolParameter>(k_CropYDim_Key, "Crop Y Dimension", "Enable cropping in the Y dimension.", true));
   params.insert(std::make_unique<BoolParameter>(k_CropZDim_Key, "Crop Z Dimension", "Enable cropping in the Z dimension.", true));

diff --git a/src/Plugins/SimplnxCore/test/AppendImageGeometryTest.cpp b/src/Plugins/SimplnxCore/test/AppendImageGeometryTest.cpp
@@ -49,6 +49,7 @@ void cropGeometry(DataStructure& dataStructure, const DataPath& selectedPath, co
   args.insert(CropImageGeometryFilter::k_RenumberFeatures_Key, std::make_any<bool>(false));
   args.insert(CropImageGeometryFilter::k_CellFeatureIdsArrayPath_Key, std::make_any<DataPath>(DataPath{}));
   args.insert(CropImageGeometryFilter::k_RemoveOriginalGeometry_Key, std::make_any<bool>(false));
+  args.insert(CropImageGeometryFilter::k_UsePhysicalBounds_Key, std::make_any<bool>(false));
 
   auto executeResult = filter.execute(dataStructure, args);
   SIMPLNX_RESULT_REQUIRE_VALID(executeResult.result)
@@ -294,6 +295,7 @@ TEST_CASE("SimplnxCore::AppendImageGeometryFilter: Invalid Filter Execution", "[
       cropArgs.insert(CropImageGeometryFilter::k_RenumberFeatures_Key, std::make_any<bool>(false));
       cropArgs.insert(CropImageGeometryFilter::k_CellFeatureIdsArrayPath_Key, std::make_any<DataPath>(DataPath{}));
       cropArgs.insert(CropImageGeometryFilter::k_RemoveOriginalGeometry_Key, std::make_any<bool>(false));
+      cropArgs.insert(CropImageGeometryFilter::k_UsePhysicalBounds_Key, std::make_any<bool>(false));
 
       auto cropResult = cropFilter.execute(dataStructure, cropArgs);
       SIMPLNX_RESULT_REQUIRE_VALID(cropResult.result)

diff --git a/src/Plugins/SimplnxCore/test/CropImageGeometryTest.cpp b/src/Plugins/SimplnxCore/test/CropImageGeometryTest.cpp
@@ -75,6 +75,7 @@ TEST_CASE("SimplnxCore::CropImageGeometryFilter(Instantiate)", "[SimplnxCore][Cr
   args.insert(CropImageGeometryFilter::k_RenumberFeatures_Key, std::make_any<bool>(k_RenumberFeatures));
   args.insert(CropImageGeometryFilter::k_CellFeatureIdsArrayPath_Key, std::make_any<DataPath>(k_FeatureIdsPath));
   args.insert(CropImageGeometryFilter::k_RemoveOriginalGeometry_Key, std::make_any<bool>(true));
+  args.insert(CropImageGeometryFilter::k_UsePhysicalBounds_Key, std::make_any<bool>(false));
 
   // Preflight the filter and check result
   auto preflightResult = filter.preflight(dataStructure, args);
@@ -109,6 +110,7 @@ TEST_CASE("SimplnxCore::CropImageGeometryFilter Invalid Params", "[SimplnxCore][
   args.insertOrAssign(CropImageGeometryFilter::k_RenumberFeatures_Key, std::make_any<bool>(k_RenumberFeatures));
   args.insertOrAssign(CropImageGeometryFilter::k_CellFeatureIdsArrayPath_Key, std::make_any<DataPath>(k_FeatureIdsPath));
   args.insertOrAssign(CropImageGeometryFilter::k_RemoveOriginalGeometry_Key, std::make_any<bool>(true));
+  args.insertOrAssign(CropImageGeometryFilter::k_UsePhysicalBounds_Key, std::make_any<bool>(false));
 
   // Preflight the filter and check result
   auto preflightResult = filter.preflight(dataStructure, args);
@@ -196,6 +198,7 @@ TEST_CASE("SimplnxCore::CropImageGeometryFilter(Execute_Filter)", "[SimplnxCore]
   args.insert(CropImageGeometryFilter::k_CellFeatureIdsArrayPath_Key, std::make_any<DataPath>(k_FeatureIdsPath));
   args.insert(CropImageGeometryFilter::k_FeatureAttributeMatrixPath_Key, std::make_any<DataPath>(k_CellFeatureAMPath));
   args.insert(CropImageGeometryFilter::k_RemoveOriginalGeometry_Key, std::make_any<bool>(false));
+  args.insertOrAssign(CropImageGeometryFilter::k_UsePhysicalBounds_Key, std::make_any<bool>(false));
 
   // Preflight the filter and check result
   auto preflightResult = filter.preflight(dataStructure, args);
@@ -278,6 +281,7 @@ TEST_CASE("SimplnxCore::CropImageGeometryFilter(Execute_Filter) - XY", "[Simplnx
   args.insert(CropImageGeometryFilter::k_FeatureAttributeMatrixPath_Key, std::make_any<DataPath>(k_CellFeatureAMPath));
   args.insert(CropImageGeometryFilter::k_RemoveOriginalGeometry_Key, std::make_any<bool>(false));
   args.insert(CropImageGeometryFilter::k_CropZDim_Key, std::make_any<bool>(false));
+  args.insert(CropImageGeometryFilter::k_UsePhysicalBounds_Key, std::make_any<bool>(false));
 
   // Preflight the filter and check result
   auto preflightResult = filter.preflight(dataStructure, args);
@@ -362,6 +366,7 @@ TEST_CASE("SimplnxCore::CropImageGeometryFilter(Execute_Filter) - XZ", "[Simplnx
   args.insert(CropImageGeometryFilter::k_FeatureAttributeMatrixPath_Key, std::make_any<DataPath>(k_CellFeatureAMPath));
   args.insert(CropImageGeometryFilter::k_RemoveOriginalGeometry_Key, std::make_any<bool>(false));
   args.insert(CropImageGeometryFilter::k_CropYDim_Key, std::make_any<bool>(false));
+  args.insert(CropImageGeometryFilter::k_UsePhysicalBounds_Key, std::make_any<bool>(false));
 
   // Preflight the filter and check result
   auto preflightResult = filter.preflight(dataStructure, args);
@@ -444,6 +449,7 @@ TEST_CASE("SimplnxCore::CropImageGeometryFilter(Execute_Filter) - YZ", "[Simplnx
   args.insert(CropImageGeometryFilter::k_FeatureAttributeMatrixPath_Key, std::make_any<DataPath>(k_CellFeatureAMPath));
   args.insert(CropImageGeometryFilter::k_RemoveOriginalGeometry_Key, std::make_any<bool>(false));
   args.insert(CropImageGeometryFilter::k_CropXDim_Key, std::make_any<bool>(false));
+  args.insert(CropImageGeometryFilter::k_UsePhysicalBounds_Key, std::make_any<bool>(false));
 
   // Preflight the filter and check result
   auto preflightResult = filter.preflight(dataStructure, args);
@@ -527,6 +533,7 @@ TEST_CASE("SimplnxCore::CropImageGeometryFilter(Execute_Filter) - X", "[SimplnxC
   args.insert(CropImageGeometryFilter::k_RemoveOriginalGeometry_Key, std::make_any<bool>(false));
   args.insert(CropImageGeometryFilter::k_CropYDim_Key, std::make_any<bool>(false));
   args.insert(CropImageGeometryFilter::k_CropZDim_Key, std::make_any<bool>(false));
+  args.insert(CropImageGeometryFilter::k_UsePhysicalBounds_Key, std::make_any<bool>(false));
 
   // Preflight the filter and check result
   auto preflightResult = filter.preflight(dataStructure, args);
@@ -610,6 +617,7 @@ TEST_CASE("SimplnxCore::CropImageGeometryFilter(Execute_Filter) - Y", "[SimplnxC
   args.insert(CropImageGeometryFilter::k_RemoveOriginalGeometry_Key, std::make_any<bool>(false));
   args.insert(CropImageGeometryFilter::k_CropXDim_Key, std::make_any<bool>(false));
   args.insert(CropImageGeometryFilter::k_CropZDim_Key, std::make_any<bool>(false));
+  args.insert(CropImageGeometryFilter::k_UsePhysicalBounds_Key, std::make_any<bool>(false));
 
   // Preflight the filter and check result
   auto preflightResult = filter.preflight(dataStructure, args);
@@ -693,6 +701,7 @@ TEST_CASE("SimplnxCore::CropImageGeometryFilter(Execute_Filter) - Z", "[SimplnxC
   args.insert(CropImageGeometryFilter::k_RemoveOriginalGeometry_Key, std::make_any<bool>(false));
   args.insert(CropImageGeometryFilter::k_CropXDim_Key, std::make_any<bool>(false));
   args.insert(CropImageGeometryFilter::k_CropYDim_Key, std::make_any<bool>(false));
+  args.insert(CropImageGeometryFilter::k_UsePhysicalBounds_Key, std::make_any<bool>(false));
 
   // Preflight the filter and check result
   auto preflightResult = filter.preflight(dataStructure, args);

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
@@ -34,7 +34,8 @@
     min_voxel=[41, 41, 0],
     remove_original_geometry=True,
     renumber_features=True,
-    input_image_geometry_path=nx.DataPath("DataContainer")
+    input_image_geometry_path=nx.DataPath("DataContainer"),
+    use_physical_bounds=False
 )
 nxtest.check_filter_result(nx_filter, result)
 

diff --git a/wrapping/python/examples/pipelines/OrientationAnalysis/TxCopper_Exposed.py b/wrapping/python/examples/pipelines/OrientationAnalysis/TxCopper_Exposed.py
@@ -49,7 +49,8 @@
     min_voxel=[0, 0, 0],
     remove_original_geometry=True,
     renumber_features=False,
-    input_image_geometry_path=nx.DataPath("Cugrid_after 2nd_15kv_2kx_2")
+    input_image_geometry_path=nx.DataPath("Cugrid_after 2nd_15kv_2kx_2"),
+    use_physical_bounds=False
    # update_origin=True
 )
 nxtest.check_filter_result(nx_filter, result)

diff --git a/wrapping/python/examples/pipelines/OrientationAnalysis/TxCopper_Unexposed.py b/wrapping/python/examples/pipelines/OrientationAnalysis/TxCopper_Unexposed.py
@@ -49,7 +49,8 @@
     min_voxel=[488, 0, 0],
     remove_original_geometry=True,
     renumber_features=False,
-    input_image_geometry_path=nx.DataPath("Cugrid_after 2nd_15kv_2kx_2")
+    input_image_geometry_path=nx.DataPath("Cugrid_after 2nd_15kv_2kx_2"),
+    use_physical_bounds=False
 )
 nxtest.check_filter_result(nx_filter, result)
 

diff --git a/wrapping/python/examples/pipelines/Simplnx/AppendImageGeometry.py b/wrapping/python/examples/pipelines/Simplnx/AppendImageGeometry.py
@@ -105,7 +105,8 @@
     min_voxel=[0, 0, 0],
     remove_original_geometry=False,
     renumber_features=False,
-    input_image_geometry_path=nx.DataPath("[Image Geometry]")
+    input_image_geometry_path=nx.DataPath("[Image Geometry]"),
+    use_physical_bounds=False
     #update_origin=False
     # cell_feature_attribute_matrix: DataPath = ...,  # Not currently part of the code
     # feature_ids: DataPath = ...,  # Not currently part of the code
@@ -124,7 +125,8 @@
     min_voxel=[0, 0, 51],
     remove_original_geometry=False,
     renumber_features=False,
-    input_image_geometry_path=nx.DataPath("[Image Geometry]")
+    input_image_geometry_path=nx.DataPath("[Image Geometry]"),
+    use_physical_bounds=False
     # update_origin=True
     # cell_feature_attribute_matrix: DataPath = ...,  # Not currently part of the code
     # feature_ids: DataPath = ...,  # Not currently part of the code

diff --git a/wrapping/python/examples/pipelines/Simplnx/ReplaceElementAttributesWithNeighbor.py b/wrapping/python/examples/pipelines/Simplnx/ReplaceElementAttributesWithNeighbor.py
@@ -104,7 +104,8 @@
     min_voxel=[25, 25, 0],
     remove_original_geometry=True,
     renumber_features=False,
-    input_image_geometry_path=nx.DataPath("DataContainer")
+    input_image_geometry_path=nx.DataPath("DataContainer"),
+    use_physical_bounds=False
    # update_origin=False
 )
 nxtest.check_filter_result(nx_filter, result)