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#!/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" )
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