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# GeodesicActiveContourImageFilter.py
# Translated by Charl P. Botha <http://cpbotha.net/> from the cxx original.
# Id
# example runs:
# ------------
# 1. Left ventricle:
# python GeodesicActiveContourImageFilter.py \
# ../Data/BrainProtonDensitySlice.png lventricle.png \
# 81 114 5 1 -0.5 3 2
#
# 2. White matter:
# python GeodesicActiveContourImageFilter.py \
# ../Data/BrainProtonDensitySlice.png wmatter.png \
# 56 92 5 1 -0.3 2 10
#
# See the ITK Software Guide, section 9.3.3 "Geodesic Active Contours
# Segmentation" as well as the CXX example for more comments.
import itk
from sys import argv, stderr
itk.auto_progress(2)
def main():
if len(argv) < 10:
errMsg = "Missing parameters\n" \
"Usage: %s\n" % (argv[0],) + \
" inputImage outputImage\n" \
" seedX seedY InitialDistance\n" \
" Sigma SigmoidAlpha SigmoidBeta\n" \
" PropagationScaling\n"
print >> stderr, errMsg
return
# We're going to build the following pipelines:
# 1. reader -> smoothing -> gradientMagnitude -> sigmoid -> FI
# 2. fastMarching -> geodesicActiveContour(FI) -> thresholder -> writer
# The output of pipeline 1 is a feature image that is used by the
# geodesicActiveContour object. Also see figure 9.18 in the ITK
# Software Guide.
# we wan't to know what is happening
# itk.auto_progress(True)
InternalPixelType = itk.F
Dimension = 2
InternalImageType = itk.Image[InternalPixelType, Dimension]
OutputPixelType = itk.UC
OutputImageType = itk.Image[OutputPixelType, Dimension]
reader = itk.ImageFileReader[InternalImageType].New(FileName=argv[1])
# needed to give the size to the fastmarching filter
reader.Update()
smoothing = itk.CurvatureAnisotropicDiffusionImageFilter[InternalImageType, InternalImageType].New(reader,
TimeStep=0.125,
NumberOfIterations=5,
ConductanceParameter=9.0)
gradientMagnitude = itk.GradientMagnitudeRecursiveGaussianImageFilter[InternalImageType, InternalImageType].New(smoothing,
Sigma=float(argv[6]))
sigmoid = itk.SigmoidImageFilter[InternalImageType, InternalImageType].New(gradientMagnitude,
OutputMinimum=0.0,
OutputMaximum=1.1,
Alpha=float(argv[7]),
Beta=float(argv[8]))
seedPosition = itk.Index[2]()
seedPosition.SetElement(0, int(argv[3]))
seedPosition.SetElement(1, int(argv[4]))
node = itk.LevelSetNode[InternalPixelType, Dimension]()
node.SetValue(-float(argv[5]))
node.SetIndex(seedPosition)
seeds = itk.VectorContainer[itk.UI, itk.LevelSetNode[InternalPixelType, Dimension]].New()
seeds.Initialize()
seeds.InsertElement(0, node)
fastMarching = itk.FastMarchingImageFilter[InternalImageType, InternalImageType].New(sigmoid,
TrialPoints=seeds,
SpeedConstant=1.0,
OutputSize=reader.GetOutput().GetBufferedRegion().GetSize() )
geodesicActiveContour = itk.GeodesicActiveContourLevelSetImageFilter[InternalImageType, InternalImageType, InternalPixelType].New(fastMarching, sigmoid,
PropagationScaling=float(argv[9]),
CurvatureScaling=1.0,
AdvectionScaling=1.0,
MaximumRMSError=0.02,
NumberOfIterations=800
)
thresholder = itk.BinaryThresholdImageFilter[InternalImageType, OutputImageType].New(geodesicActiveContour,
LowerThreshold=-1000,
UpperThreshold=0,
OutsideValue=0,
InsideValue=255)
writer = itk.ImageFileWriter[OutputImageType].New(thresholder, FileName=argv[2])
def rescaleAndWrite(filter, fileName):
caster = itk.RescaleIntensityImageFilter[InternalImageType, OutputImageType].New(filter,
OutputMinimum=0,
OutputMaximum=255)
itk.write(caster, fileName)
rescaleAndWrite(smoothing, "GeodesicActiveContourImageFilterOutput1.png")
rescaleAndWrite(gradientMagnitude, "GeodesicActiveContourImageFilterOutput2.png")
rescaleAndWrite(sigmoid, "GeodesicActiveContourImageFilterOutput3.png")
rescaleAndWrite(fastMarching, "GeodesicActiveContourImageFilterOutput4.png")
writer.Update()
print
print "Max. no. iterations: %d" % (geodesicActiveContour.GetNumberOfIterations())
print "Max. RMS error: %.3f" % (geodesicActiveContour.GetMaximumRMSError())
print
print "No. elapsed iterations: %d" % (geodesicActiveContour.GetElapsedIterations())
print "RMS change: %.3f" % (geodesicActiveContour.GetRMSChange())
itk.write(fastMarching, "GeodesicActiveContourImageFilterOutput4.mha")
itk.write(sigmoid, "GeodesicActiveContourImageFilterOutput3.mha")
itk.write(gradientMagnitude, "GeodesicActiveContourImageFilterOutput2.mha")
if __name__ == "__main__":
main()
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