SimpleITK  1.3.0.dev466
Python/ConnectedThresholdImageFilter.py
1 '''=========================================================================
2 '
3 ' Copyright Insight Software Consortium
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 ' http://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 '========================================================================='''
18 
19 from __future__ import print_function
20 
21 import SimpleITK as sitk
22 import sys
23 import os
24 
25 #
26 # Check Command Line
27 #
28 if len( sys.argv ) < 7:
29  print("Usage: ConnectedThresholdImageFilter inputImage outputImage lowerThreshold upperThreshold seedX seedY [seed2X seed2Y ... ]");
30  sys.exit( 1 )
31 
32 
33 #
34 # Read the image
35 #
36 reader = sitk.ImageFileReader()
37 reader.SetFileName( sys.argv[1] )
38 image = reader.Execute();
39 
40 #
41 # Blur using CurvatureFlowImageFilter
42 #
43 blurFilter = sitk.CurvatureFlowImageFilter()
44 blurFilter.SetNumberOfIterations( 5 )
45 blurFilter.SetTimeStep( 0.125 )
46 image = blurFilter.Execute( image )
47 
48 #
49 # Set up ConnectedThresholdImageFilter for segmentation
50 #
51 segmentationFilter = sitk.ConnectedThresholdImageFilter()
52 segmentationFilter.SetLower( float(sys.argv[3]) )
53 segmentationFilter.SetUpper( float(sys.argv[4]) )
54 segmentationFilter.SetReplaceValue( 255 )
55 
56 for i in range( 5, len(sys.argv)-1, 2 ):
57  seed = [ int(sys.argv[i]), int(sys.argv[i+1]) ]
58  segmentationFilter.AddSeed( seed )
59  print( "Adding seed at: ", seed, " with intensity: ", image.GetPixel(*seed) )
60 
61 # Run the segmentation filter
62 image = segmentationFilter.Execute( image )
63 image[seed] = 255
64 
65 #
66 # Write out the result
67 #
68 writer = sitk.ImageFileWriter()
69 writer.SetFileName( sys.argv[2] )
70 writer.Execute( image )
71 
72 
73 if ( not "SITK_NOSHOW" in os.environ ):
74  sitk.Show( image, "ConntectedThreshold" )
75