ENH: Add test and strengthen the documentation

Author: andinet

src/Bridge/CMakeLists.txt

@@ -2,4 +2,4 @@ if(ENABLE_QUICKVIEW)
 add_subdirectory_if_module_enabled(VtkGlue)
 endif()
 
-add_subdirectory(NumPy)
+add_subdirectory_if_module_enabled( NumPy )

src/Bridge/NumPy/ConvertNumPyArrayToitkImage/CMakeLists.txt

@@ -6,7 +6,10 @@ find_package( ITK REQUIRED )
 include( ${ITK_USE_FILE} )
 
 if(ITK_WRAP_PYTHON)
+  enable_testing()
   add_test(NAME  ConvertNumPyArrayToitkImageTestPython
     COMMAND ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/Code.py
+    Slice.png
+    SliceRevised.png
     )
 endif()

src/Bridge/NumPy/ConvertNumPyArrayToitkImage/Code.py

@@ -22,17 +22,50 @@
     print("Usage: " + sys.argv[0] + " <input_image> <output_image>")
     sys.exit(1)
 
-input_file_name =  sys.argv[1]
+# Parse comamnd line arguments
+input_file_name = sys.argv[1]
 output_file_name = sys.argv[2]
 
 # Read input image
-itk_image = itk.imread(input_file_name)
+PixelType = itk.ctype("unsigned char")
+ImageType = itk.Image[itk.UC, 2]
+itk_image = itk.imread(input_file_name, PixelType)
+OriginalRegion = itk_image.GetLargestPossibleRegion()
+OriginalSize = OriginalRegion.GetSize()
 
-# Copy itk.Imag pixel data to numpy array
-np_array = itk.array_from_image(itk_image)
+print(f"The size of the ITK image data read from the input file  = {OriginalSize}\n")
 
-# Convert the numpy array pixel data back to ITK
-itk_np_copy = itk.image_from_array(np_array)
+# There are two ways to bridge the data structures.
+# i) Give direct access to memory holding the data called "View" functions for displaying
+# purpose. But you can't modify the data
+np_view_array = itk.GetArrayViewFromImage(itk_image, ttype=ImageType)
+print(f"The size of the NumPy array viewed from itk::Image = {np_view_array.shape}")
 
-# Write out the numpy array as an ITK image
-itk.imwrite(itk_np_copy,output_file_name)
+# ii) Generate a copy of the data using using array_from_image function.
+#  You can then freely modify the data as it has no effect on the original ITK image.
+
+# Copy itk.Image pixel data to numpy array
+np_array = itk.GetArrayFromImage(itk_image, ttype=ImageType)
+print(f"The size of the NumPy array copied from itk::Image = {np_array.shape}")
+
+# Create an ITK image from the numpy array and then write it out
+itk_np = itk.GetImageFromArray(np.ascontiguousarray(np_array))
+
+region = itk_np.GetLargestPossibleRegion()
+size = region.GetSize()
+print(f"ITK image data size after convesion from NumPy = {size}\n")
+
+itk.imwrite(itk_np, output_file_name)
+
+
+# The order of the indexes is according to the type of object the data is stored in.
+# A numpy array is indexed by [row , col ] for 2D data or [slice , row , col ] for 3D data.
+# While ITK image data is indexed by (x , y ) for 2D or (x , y , z ) for 3D data.
+# To demonstrate here, we create a 2D pixel array data
+# and access a pixel with the same indices
+
+np_data = np.array([[1, 2, 3], [4, 5, 6], [7, 8, 9]], np.int32)
+itk_np_view_data = itk.image_view_from_array(np_data)
+
+print(f"ITK image data pixel value at [2,1] = {itk_np_view_data.GetPixel([2,1])}")
+print(f"NumPy array pixel value at [2,1] = {np_data[2,1]}")

src/Bridge/NumPy/ConvertNumPyArrayToitkImage/Documentation.rst

@@ -10,8 +10,11 @@ Interface ITK with NumPy Array
 Synopsis
 --------
 
-This example illustrates interfacing ITK Image data with NumPy array.
-
+This example illustrates interfacing ITK Image data with NumPy array. While doing this, there are two key issues to
+to keep in mind. One, the order of indexes is different between ITK image data class and NumPy array.
+Second, there are two ways to access ITK image data as a NumPy array. i) Get direct access to memory with the data called
+"View" functions (array_view_from_image and image_view_from_array), or ii) Copy the data (array_from_image and image_from_array).
+If the view functions are used, the data can't be modified.
 
 Results
 -------

src/Bridge/NumPy/ConvertNumPyArrayToitkImage/Slice.png.sha512

@@ -0,0 +1 @@
+59ac2cc1a14666a72b9c21c1abd1a45aeef567d2e4690b761df2b36904dbc37f52458b54e6a22b32186f13fe45a4c91da6e9e0c3bcfbe0e959c81b514fb97237

src/Bridge/NumPy/ConvertNumPyArrayToitkImage/SliceRevised.png.sha512

@@ -0,0 +1 @@
+64dd1f56f598fb9dfe8ebbf725a5fe1530ecabe1962661376e1228a3640c31316741d7c703f482adfaf9086762b44018f05a863b37bb19608735c7fd8ba57ca0