N4BiasFieldCorrection/N4BiasFieldCorrection.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 SimpleITK as sitk
import sys
import os

if len ( sys.argv ) < 2:
    print( "Usage: N4BiasFieldCorrection inputImage " + \
        "outputImage [shrinkFactor] [maskImage] [numberOfIterations] " +\
        "[numberOfFittingLevels]" )
    sys.exit ( 1 )


inputImage = sitk.ReadImage( sys.argv[1] )

if len ( sys.argv ) > 4:
    maskImage = sitk.ReadImage( sys.argv[4] )
else:
    maskImage = sitk.OtsuThreshold( inputImage, 0, 1, 200 )

if len ( sys.argv ) > 3:
    inputImage = sitk.Shrink( inputImage, [ int(sys.argv[3]) ] * inputImage.GetDimension() )
    maskImage = sitk.Shrink( maskImage, [ int(sys.argv[3]) ] * inputImage.GetDimension() )

inputImage = sitk.Cast( inputImage, sitk.sitkFloat32 )

corrector = sitk.N4BiasFieldCorrectionImageFilter();

numberFittingLevels = 4

if len ( sys.argv ) > 6:
    numberFittingLevels = int( sys.argv[6] )

if len ( sys.argv ) > 5:
    corrector.SetMaximumNumberOfIterations( [ int( sys.argv[5] ) ] *numberFittingLevels  )


output = corrector.Execute( inputImage, maskImage )

sitk.WriteImage( output, sys.argv[2] )


if ( not "SITK_NOSHOW" in os.environ ):
    sitk.Show( output, "N4 Corrected" )