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#=========================================================================
#
# 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 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" )
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