1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
|
'''=========================================================================
'
' Copyright Insight Software Consortium
'
' Licensed under the Apache License, Version 2.0 (the "License");
' you may not use this file except in compliance with the License.
' You may obtain a copy of the License at
'
' http://www.apache.org/licenses/LICENSE-2.0.txt
'
' Unless required by applicable law or agreed to in writing, software
' distributed under the License is distributed on an "AS IS" BASIS,
' WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
' See the License for the specific language governing permissions and
' limitations under the License.
'
'========================================================================='''
from __future__ import print_function
import SimpleITK as sitk
import sys
import os
#
# Check Command Line
#
if len( sys.argv ) < 7:
print( "Usage: NeighborhoodConnectedImageFilter inputImage outputImage lowerThreshold upperThreshold seedX seedY [seed2X seed2Y ... ]")
sys.exit( 1 )
#
# Read the image
#
reader = sitk.ImageFileReader()
reader.SetFileName( sys.argv[1] )
image = reader.Execute();
#
# Blur using CurvatureFlowImageFilter
#
blurFilter = sitk.CurvatureFlowImageFilter()
blurFilter.SetNumberOfIterations( 5 )
blurFilter.SetTimeStep( 0.125 )
image = blurFilter.Execute( image )
#
# Set up NeighborhoodConnectedImageFilter for segmentation
#
segmentationFilter = sitk.NeighborhoodConnectedImageFilter()
segmentationFilter.SetLower( float(sys.argv[3]) )
segmentationFilter.SetUpper( float(sys.argv[4]) )
segmentationFilter.SetReplaceValue( 255 )
radius = [2,2]
segmentationFilter.SetRadius( radius )
for i in range( 5, len(sys.argv)-1, 2 ):
seed = [int(sys.argv[i]), int(sys.argv[i+1])]
segmentationFilter.AddSeed( seed )
print( "Adding seed at: ", seed, " with intensity: ", image.GetPixel(*seed) )
# Run the segmentation filter
image = segmentationFilter.Execute( image )
#
# Write out the result
#
writer = sitk.ImageFileWriter()
writer.SetFileName( sys.argv[2] )
writer.Execute( image )
if ( not "SITK_NOSHOW" in os.environ ):
sitk.Show( image, "NeighborhoodConnectedThreshold" )
|
