FastMarchingSegmentation/FastMarchingSegmentation.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.
#
# =========================================================================
 
 
import SimpleITK as sitk
import sys
 
if len(sys.argv) < 10:
    print(
        "Usage:",
        sys.argv[0],
        " <inputImage> <outputImage> <seedX> <seedY> <Sigma>",
        "<SigmoidAlpha> <SigmoidBeta> <TimeThreshold>",
    )
    sys.exit(1)
 
inputFilename = sys.argv[1]
outputFilename = sys.argv[2]
 
seedPosition = (int(sys.argv[3]), int(sys.argv[4]))
 
sigma = float(sys.argv[5])
alpha = float(sys.argv[6])
beta = float(sys.argv[7])
timeThreshold = float(sys.argv[8])
stoppingTime = float(sys.argv[9])
 
inputImage = sitk.ReadImage(inputFilename, sitk.sitkFloat32)
 
print(inputImage)
 
smoothing = sitk.CurvatureAnisotropicDiffusionImageFilter()
smoothing.SetTimeStep(0.125)
smoothing.SetNumberOfIterations(5)
smoothing.SetConductanceParameter(9.0)
smoothingOutput = smoothing.Execute(inputImage)
 
gradientMagnitude = sitk.GradientMagnitudeRecursiveGaussianImageFilter()
gradientMagnitude.SetSigma(sigma)
gradientMagnitudeOutput = gradientMagnitude.Execute(smoothingOutput)
 
sigmoid = sitk.SigmoidImageFilter()
sigmoid.SetOutputMinimum(0.0)
sigmoid.SetOutputMaximum(1.0)
sigmoid.SetAlpha(alpha)
sigmoid.SetBeta(beta)
sigmoid.DebugOn()
sigmoidOutput = sigmoid.Execute(gradientMagnitudeOutput)
 
fastMarching = sitk.FastMarchingImageFilter()
 
seedValue = 0
trialPoint = (seedPosition[0], seedPosition[1], seedValue)
 
fastMarching.AddTrialPoint(trialPoint)
 
fastMarching.SetStoppingValue(stoppingTime)
 
fastMarchingOutput = fastMarching.Execute(sigmoidOutput)
 
thresholder = sitk.BinaryThresholdImageFilter()
thresholder.SetLowerThreshold(0.0)
thresholder.SetUpperThreshold(timeThreshold)
thresholder.SetOutsideValue(0)
thresholder.SetInsideValue(255)
 
result = thresholder.Execute(fastMarchingOutput)
 
sitk.WriteImage(result, outputFilename)