Python/BoarderSegmentation.py

#!/usr/bin/env python
#=========================================================================
#
#  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 sys
import SimpleITK as sitk
import os

# verify that we have the correct number of arguments
if ( len( sys.argv ) != 5 ):
    sys.stderr.write( "Usage: prog inputFile outputFile replaceValue upperThreshold\n" )
    exit( 1 )
    
# copy the arguments in to variables
inputFileName = sys.argv[1]
outputFileName = sys.argv[2]
replaceValue = int( sys.argv[3] )
upperThreshold = float( sys.argv[4] )

# Read the file into an sitkImage
image = sitk.ReadImage( inputFileName )

# Threshold the value [0,2), results in values inside the range 1, 0 otherwise
boundary = sitk.BinaryThreshold( image, 0, upperThreshold, 1, 0 )

boundary = sitk.BinaryMorphologicalClosing( boundary, 1 )

# Remove any label pixel not connected to the boarder
boundary = sitk.BinaryGrindPeak( boundary )



boundary = sitk.Cast( boundary, image.GetPixelID() )

# Multiply, the input image by not the boarder.
# This will multiply the image by 0 or 1, where 0 is the
# boarder. Making the board 0
image = image * ~boundary

# add the replace value to the pixel on the board
image = image + ( boundary * replaceValue )


if ( not "SITK_NOSHOW" in os.environ ):
    sitk.Show( image, "Boarder Segmentation" )