Segmentation/WatershedSegmentation1.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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#==========================================================================*/

import InsightToolkit as itk
import sys

reader = itk.itkImageFileReaderF2_New()
reader.SetFileName( sys.argv[1] )

diffusion = itk.itkGradientAnisotropicDiffusionImageFilterF2F2_New()
diffusion.SetInput(reader.GetOutput())
diffusion.SetTimeStep(0.0625)
diffusion.SetConductanceParameter(9.0)
diffusion.SetNumberOfIterations(  5 );

gradient = itk.itkGradientMagnitudeImageFilterF2F2_New()
gradient.SetInput(diffusion.GetOutput())

watershed = itk.itkWatershedImageFilterF2_New()
watershed.SetInput(gradient.GetOutput())
watershed.SetThreshold(0.01)
watershed.SetLevel(0.2)

writer = itk.itkImageFileWriterUL2_New()
writer.SetFileName( sys.argv[2] )
writer.SetInput( watershed.GetOutput()  )
writer.Update()