Merge pull request #453 from InsightSoftwareConsortium/rebase/convolve-image-with-kernel-python

ENH: Add Python example for ConvolveImageWithKernel

Author: hjmjohnson

CMake/ITKSphinxExamplesMacros.cmake

@@ -100,6 +100,10 @@ endmacro()
 #
 #   [OPTIONS myListOfOptions]        // Options to pass to ImageCompareCommand.
 #
+#   [NO_PYTHON_COMPARISON]           // Skip the auto-added Python baseline comparison
+#                                    // when the Python output is not pixel-comparable
+#                                    // to the C++ baseline (e.g. a Matplotlib figure).
+#
 #   [DEPENDS myListOfDependencies]   // Other tests that the comparison test will
 #                                    // depend on. By default, the dependency is assumed
 #                                    // to be ${EXAMPLE_NAME}Test. For Python, the comparison
@@ -110,6 +114,7 @@ endmacro()
 function(compare_to_baseline)
   set(options
     PYTHON_ONLY
+    NO_PYTHON_COMPARISON
   )
 
   set(oneValueArgs
@@ -174,7 +179,7 @@ function(compare_to_baseline)
     )
   endif()
 
-  if(ITK_WRAP_PYTHON AND EXISTS "${CMAKE_CURRENT_SOURCE_DIR}/${LOCAL_COMPARISON_EXAMPLE_NAME}/Code.py")
+  if(ITK_WRAP_PYTHON AND NOT LOCAL_COMPARISON_NO_PYTHON_COMPARISON AND EXISTS "${CMAKE_CURRENT_SOURCE_DIR}/${LOCAL_COMPARISON_EXAMPLE_NAME}/Code.py")
     set(python_test_name ${test_name}Python)
     get_filename_component(test_image_we "${test_image}" NAME_WE)
     get_filename_component(test_image_dir "${test_image}" DIRECTORY)

src/Filtering/Convolution/CMakeLists.txt

@@ -16,6 +16,9 @@ compare_to_baseline(EXAMPLE_NAME NormalizedCorrelationUsingFFTWithMaskImages
 add_example(ConvolveImageWithKernel)
 compare_to_baseline(EXAMPLE_NAME ConvolveImageWithKernel
   BASELINE_PREFIX ConvolveImageWithKernel
+  # The Python example emits a raw convolved image, not the C++ QuickView
+  # screenshot, so the two are not pixel-comparable.
+  NO_PYTHON_COMPARISON
   )
 
 # TODO:  Fix building of ColorNormalizedCorrelation example

src/Filtering/Convolution/ConvolveImageWithKernel/CMakeLists.txt

@@ -46,7 +46,7 @@ install(TARGETS ${PROJECT_NAME}
   COMPONENT Runtime
   )
 
-install(FILES Code.cxx CMakeLists.txt
+install(FILES Code.cxx Code.py CMakeLists.txt
   DESTINATION share/ITKSphinxExamples/Code/Filtering/Convolution/ConvolveImageWithKernel/
   COMPONENT Code
   )
@@ -57,3 +57,10 @@ add_test(NAME ConvolveImageWithKernelTest
   COMMAND ${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/${PROJECT_NAME}
     Yinyang.png
     10)
+
+if(ITK_WRAP_PYTHON)
+  add_test(NAME ConvolveImageWithKernelTestPython
+  COMMAND ${Python3_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/Code.py
+  ${CMAKE_CURRENT_BINARY_DIR}/Yinyang.png
+  10)
+endif()

src/Filtering/Convolution/ConvolveImageWithKernel/Code.py

@@ -0,0 +1,47 @@
+import itk
+import numpy as np
+import argparse
+
+parser = argparse.ArgumentParser(description="Convolve Image With Kernel")
+parser.add_argument("input_image")
+parser.add_argument("width", type=int)
+args = parser.parse_args()
+
+PixelType = itk.F
+
+# Read Image in float data type
+inputImage = itk.imread(args.input_image, PixelType)
+
+width = 10
+if args.width:
+    width = args.width
+
+
+def CreateSmoothKernel(width):
+    return np.ones([width, width], "float32") / (width * width)
+
+
+kernel = CreateSmoothKernel(width)
+kernel_image = itk.image_from_array(kernel)
+
+# Convolve image with kernel.
+filteredImage = itk.convolution_image_filter(inputImage, kernel_image=kernel_image)
+
+# PNG requires an integer pixel type, so rescale the float result to 8-bit.
+rescaledImage = itk.rescale_intensity_image_filter(
+    filteredImage, output_minimum=0, output_maximum=255
+)
+outputImage = rescaledImage.astype(itk.UC)
+
+# Write the output Image
+itk.imwrite(outputImage, "ConvolveImageWithKernelPython.png")
+
+# Visualize the result using matplotlib
+import matplotlib.pyplot as plt
+
+plot_image = np.concatenate((inputImage, filteredImage), axis=1)
+plt.imshow(plot_image)
+plt.title("Visualize using Matplotlib, Kernel width = " + str(width))
+plt.show(block=False)
+plt.pause(3)
+plt.close()

src/Filtering/Convolution/ConvolveImageWithKernel/Documentation.rst

@@ -26,6 +26,11 @@ Results
 
   Output In VTK Window
 
+.. figure:: MatplotlibVisualizeConvolution.png
+  :scale: 70%
+
+  Output In Matplotlib
+
 Code
 ----
 

src/Filtering/Convolution/ConvolveImageWithKernel/MatplotlibVisualizeConvolution.png.cid

@@ -0,0 +1 @@
+bafkreiejmu6wjzs35rezwhe4htcehxslunbdju424td6zjy3giucxgczvu