SimpleITK  
Python/NeighborhoodConnectedImageFilter.py
1 """=========================================================================
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
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13  ' WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
14  ' See the License for the specific language governing permissions and
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17  '========================================================================="""
18 
19 import os
20 import sys
21 
22 import SimpleITK as sitk
23 
24 #
25 # Check Command Line
26 #
27 if len(sys.argv) < 7:
28  print(
29  "Usage:",
30  sys.argv[1],
31  "inputImage outputImage lowerThreshold",
32  "upperThreshold seedX seedY [seed2X seed2Y ... ]",
33  )
34  sys.exit(1)
35 
36 #
37 # Read the image
38 #
39 reader = sitk.ImageFileReader()
40 reader.SetFileName(sys.argv[1])
41 image = reader.Execute()
42 
43 #
44 # Blur using CurvatureFlowImageFilter
45 #
46 blurFilter = sitk.CurvatureFlowImageFilter()
47 blurFilter.SetNumberOfIterations(5)
48 blurFilter.SetTimeStep(0.125)
49 image = blurFilter.Execute(image)
50 
51 #
52 # Set up NeighborhoodConnectedImageFilter for segmentation
53 #
54 segmentationFilter = sitk.NeighborhoodConnectedImageFilter()
55 segmentationFilter.SetLower(float(sys.argv[3]))
56 segmentationFilter.SetUpper(float(sys.argv[4]))
57 segmentationFilter.SetReplaceValue(255)
58 
59 radius = [2, 2]
60 segmentationFilter.SetRadius(radius)
61 
62 for i in range(5, len(sys.argv) - 1, 2):
63  seed = [int(sys.argv[i]), int(sys.argv[i + 1])]
64  segmentationFilter.AddSeed(seed)
65  print("Adding seed at: ", seed, " with intensity: ", image.GetPixel(*seed))
66 
67 # Run the segmentation filter
68 image = segmentationFilter.Execute(image)
69 
70 #
71 # Write out the result
72 #
73 writer = sitk.ImageFileWriter()
74 writer.SetFileName(sys.argv[2])
75 writer.Execute(image)
76 
77 if "SITK_NOSHOW" not in os.environ:
78  sitk.Show(image, "NeighborhoodConnectedThreshold")
itk::simple::NeighborhoodConnectedImageFilter
Label pixels that are connected to a seed and lie within a neighborhood.
Definition: sitkNeighborhoodConnectedImageFilter.h:41
itk::simple::Show
void SITKIO_EXPORT Show(const Image &image, const std::string &title="", const bool debugOn=ProcessObject::GetGlobalDefaultDebug())
itk::simple::ImageFileReader
Read an image file and return a SimpleITK Image.
Definition: sitkImageFileReader.h:74
itk::simple::CurvatureFlowImageFilter
Denoise an image using curvature driven flow.
Definition: sitkCurvatureFlowImageFilter.h:71
itk::simple::ImageFileWriter
Write out a SimpleITK image to the specified file location.
Definition: sitkImageFileWriter.h:51