N4BiasFieldCorrection/N4BiasFieldCorrection.py

#!/usr/bin/env python
# =========================================================================
#
#  Copyright NumFOCUS
#
#  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], sitk.sitkUint8)
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 ("SITK_NOSHOW" not in os.environ):
    sitk.Show(output, "N4 Corrected")