Python/GeodesicActiceContourSegmentation.py

#=========================================================================
#
#  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
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#=========================================================================

from __future__ import print_function

import SimpleITK as sitk
import os
import sys

if len ( sys.argv ) < 8:
    print( "Usage:", sys.argv[0], " <inputImage> <outputImage> <sigma> <InitialDistance> <PropagationScaling> <seedX> <seedY> <?seedZ>" )
    sys.exit ( 1 )

inputImage = sys.argv[1]
outputImage = sys.argv[2]
sigma = float(sys.argv[3])
initialDistance = float(sys.argv[4])
propagationScaling = float(sys.argv[5])
seed = [float(sys.argv[6]), float(sys.argv[7]) ]

if len( sys.argv ) > 8:
    seed.append( float(sys.argv[8]) )


reader = sitk.ImageFileReader()
reader.SetFileName ( inputImage )
image = reader.Execute()

gradientMagnitude = sitk.GradientMagnitudeRecursiveGaussianImageFilter()
gradientMagnitude.SetSigma( sigma )

featureImage = sitk.BoundedReciprocal( gradientMagnitude.Execute( image ) )

seedImage = sitk.Image( image.GetSize()[0], image.GetSize()[1], sitk.sitkUInt8 )
seedImage.SetSpacing( image.GetSpacing() )
seedImage.SetOrigin( image.GetOrigin() )
seedImage.SetDirection( image.GetDirection() )
seedImage[ seedImage.TransformPhysicalPointToIndex(seed) ] = 1

distance = sitk.SignedMaurerDistanceMapImageFilter()
distance.InsideIsPositiveOff()
distance.UseImageSpacingOn()

initialImage = sitk.BinaryThreshold( distance.Execute( seedImage ), -1000, 10 )
initialImage = sitk.Cast( initialImage, featureImage.GetPixelID() ) * -1 + 0.5


geodesicActiveContour = sitk.GeodesicActiveContourLevelSetImageFilter()
geodesicActiveContour.SetPropagationScaling( propagationScaling )
geodesicActiveContour.SetCurvatureScaling( .5 )
geodesicActiveContour.SetAdvectionScaling( 1.0 )
geodesicActiveContour.SetMaximumRMSError( 0.01 )
geodesicActiveContour.SetNumberOfIterations( 1000 )

levelset = geodesicActiveContour.Execute( initialImage, featureImage )

print( "RMS Change: ", geodesicActiveContour.GetRMSChange() )
print( "Elapsed Iterations: ", geodesicActiveContour.GetElapsedIterations() )

contour = sitk.BinaryContour( sitk.BinaryThreshold( levelset, -1000, 0 ) )

if ( not "SITK_NOSHOW" in os.environ ):
    sitk.Show( sitk.LabelOverlay( image, contour ), "Levelset Countour" )