Merge pull request #416 from thewtex/binary-mask-python

ENH: Add Python version of ExtractIsoSurface

Author: thewtex

src/Core/Mesh/ExtractIsoSurface/CMakeLists.txt

@@ -13,16 +13,31 @@ install(TARGETS ${PROJECT_NAME}
   COMPONENT Runtime
   )
 
-install(FILES Code.cxx CMakeLists.txt
+install(FILES Code.cxx CMakeLists.txt Code.py
   DESTINATION share/ITKSphinxExamples/Code/Core/Mesh/ExtractIsoSurface
   COMPONENT Code
   )
 
+set(input_volume ${CMAKE_CURRENT_BINARY_DIR}/HeadMRVolume.mha)
+set(output_mesh ${CMAKE_CURRENT_BINARY_DIR}/Output.vtk)
+set(lower_threshold 64)
+set(upper_threshold 255)
+
 enable_testing()
 add_test(NAME ExtractIsoSurfaceTest
   COMMAND ${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/${PROJECT_NAME}
-    ${CMAKE_CURRENT_BINARY_DIR}/HeadMRVolume.mha
-    ${CMAKE_CURRENT_BINARY_DIR}/Output.vtk
-    64
-    255
+    ${input_volume}
+    ${output_mesh}
+    ${lower_threshold}
+    ${upper_threshold}
 )
+
+if(ITK_WRAP_PYTHON)
+  add_test(NAME ExtractIsoSurfaceTestPython
+    COMMAND ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/Code.py
+    ${input_volume}
+    OutputPython.vtk
+    ${lower_threshold}
+    ${upper_threshold}
+    )
+endif()

src/Core/Mesh/ExtractIsoSurface/Code.py

@@ -0,0 +1,44 @@
+#!/usr/bin/env python
+
+# ==========================================================================
+#
+#   Copyright Insight Software Consortium
+#
+#   Licensed under the Apache License, Version 2.0 (the "License")
+#   you may not use this file except in compliance with the License.
+#   You may obtain a copy of the License at
+#
+#          https://www.apache.org/licenses/LICENSE-2.0.txt
+#
+#   Unless required by applicable law or agreed to in writing, software
+#   distributed under the License is distributed on an "AS IS" BASIS,
+#   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+#   See the License for the specific language governing permissions and
+#   limitations under the License.
+#
+# ==========================================================================*/
+
+import itk
+import numpy as np
+import argparse
+
+parser = argparse.ArgumentParser(description="Extract an isosurface.")
+parser.add_argument("input_image")
+parser.add_argument("output_mesh")
+parser.add_argument("lower_threshold", type=int)
+parser.add_argument("upper_threshold", type=int)
+args = parser.parse_args()
+
+input_image = itk.imread(args.input_image)
+
+thresholded = itk.binary_threshold_image_filter(
+    input_image,
+    lower_threshold=args.lower_threshold,
+    upper_threshold=args.upper_threshold,
+    outside_value=0,
+    inside_value=255,
+)
+
+output_mesh = itk.binary_mask3_d_mesh_source(thresholded, object_value=255)
+
+itk.meshwrite(output_mesh, args.output_mesh)