ITK  6.0.0
Insight Toolkit
SphinxExamples/src/Bridge/NumPy/ConvertNumPyArrayToitkImage/Code.py
1 #!/usr/bin/env python
2 
3 # Copyright NumFOCUS
4 #
5 # Licensed under the Apache License, Version 2.0 (the "License");
6 # you may not use this file except in compliance with the License.
7 # You may obtain a copy of the License at
8 #
9 # https://www.apache.org/licenses/LICENSE-2.0.txt
10 #
11 # Unless required by applicable law or agreed to in writing, software
12 # distributed under the License is distributed on an "AS IS" BASIS,
13 # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
14 # See the License for the specific language governing permissions and
15 # limitations under the License.
16 
17 import sys
18 import itk
19 import numpy as np
20 
21 if len(sys.argv) != 3:
22  print("Usage: " + sys.argv[0] + " <input_image> <output_image>")
23  sys.exit(1)
24 
25 # Parse comamnd line arguments
26 input_file_name = sys.argv[1]
27 output_file_name = sys.argv[2]
28 
29 # Read input image
30 PixelType = itk.ctype("unsigned char")
31 ImageType = itk.Image[itk.UC, 2]
32 itk_image = itk.imread(input_file_name, PixelType)
33 OriginalRegion = itk_image.GetLargestPossibleRegion()
34 OriginalSize = OriginalRegion.GetSize()
35 
36 print(f"The size of the ITK image data read from the input file = {OriginalSize}\n")
37 
38 # There are two ways to bridge the data structures.
39 # i) Give direct access to memory holding the data called "View" functions for displaying
40 # purpose. But you can't modify the data
41 np_view_array = itk.GetArrayViewFromImage(itk_image, ttype=ImageType)
42 print(f"The size of the NumPy array viewed from itk::Image = {np_view_array.shape}")
43 
44 # ii) Generate a copy of the data using using array_from_image function.
45 # You can then freely modify the data as it has no effect on the original ITK image.
46 
47 # Copy itk.Image pixel data to numpy array
48 np_array = itk.GetArrayFromImage(itk_image, ttype=ImageType)
49 print(f"The size of the NumPy array copied from itk::Image = {np_array.shape}")
50 
51 # Create an ITK image from the numpy array and then write it out
52 itk_np = itk.GetImageFromArray(np.ascontiguousarray(np_array))
53 
54 region = itk_np.GetLargestPossibleRegion()
55 size = region.GetSize()
56 print(f"ITK image data size after convesion from NumPy = {size}\n")
57 
58 itk.imwrite(itk_np, output_file_name)
59 
60 
61 # The order of the indexes is according to the type of object the data is stored in.
62 # A numpy array is indexed by [row , col ] for 2D data or [slice , row , col ] for 3D data.
63 # While ITK image data is indexed by (x , y ) for 2D or (x , y , z ) for 3D data.
64 # To demonstrate here, we create a 2D pixel array data
65 # and access a pixel with the same indices
66 
67 np_data = np.array([[1, 2, 3], [4, 5, 6], [7, 8, 9]], np.int32)
68 itk_np_view_data = itk.image_view_from_array(np_data)
69 
70 print(f"ITK image data pixel value at [2,1] = {itk_np_view_data.GetPixel([2,1])}")
71 print(f"NumPy array pixel value at [2,1] = {np_data[2,1]}")
itk::Image
Templated n-dimensional image class.
Definition: itkImage.h:88