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# GeodesicActiveContourImageFilter.py
# Translated by Charl P. Botha <http://cpbotha.net/> from the cxx original.
# Id
# NOTE: This example won't work if your ITK is older that 2004-02-26
# 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 InsightToolkit as itk
import sys
def main():
if len(sys.argv) < 10:
errMsg = "Missing parameters\n" \
"Usage: %s\n" % (sys.argv[0],) + \
" inputImage outputImage\n" \
" seedX seedY InitialDistance\n" \
" Sigma SigmoidAlpha SigmoidBeta\n" \
" PropagationScaling\n"
print >> sys.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.
reader = itk.itkImageFileReaderF2_New()
reader.SetFileName(sys.argv[1])
writer = itk.itkImageFileWriterUS2_New()
writer.SetFileName(sys.argv[2])
smoothing = itk.itkCurvatureAnisotropicDiffusionImageFilterF2F2_New()
gM = itk.itkGradientMagnitudeRecursiveGaussianImageFilterF2F2_New()
gradientMagnitude = gM
sigmoid = itk.itkSigmoidImageFilterF2F2_New()
sigmoid.SetOutputMinimum( 0.0 )
sigmoid.SetOutputMaximum( 1.0 )
fastMarching = itk.itkFastMarchingImageFilterF2F2_New()
gAC = itk.itkGeodesicActiveContourLevelSetImageFilterF2F2_New()
geodesicActiveContour = gAC
propagationScaling = float(sys.argv[9])
geodesicActiveContour.SetPropagationScaling( propagationScaling );
geodesicActiveContour.SetCurvatureScaling( 1.0 );
geodesicActiveContour.SetAdvectionScaling( 1.0 );
geodesicActiveContour.SetMaximumRMSError( 0.02 );
geodesicActiveContour.SetNumberOfIterations( 800 );
smoothing.SetInput( reader.GetOutput() );
gradientMagnitude.SetInput( smoothing.GetOutput() );
sigmoid.SetInput( gradientMagnitude.GetOutput() );
geodesicActiveContour.SetInput( fastMarching.GetOutput() );
geodesicActiveContour.SetFeatureImage( sigmoid.GetOutput() );
thresholder = itk.itkBinaryThresholdImageFilterF2US2_New()
thresholder.SetLowerThreshold( -1000.0 );
thresholder.SetUpperThreshold( 0.0 );
thresholder.SetOutsideValue( 0 );
thresholder.SetInsideValue( 65535 );
thresholder.SetInput( geodesicActiveContour.GetOutput() );
writer.SetInput( thresholder.GetOutput() );
smoothing.SetTimeStep( 0.125 );
smoothing.SetNumberOfIterations( 5 );
smoothing.SetConductanceParameter( 3.0 );
sigma = float(sys.argv[6])
gradientMagnitude.SetSigma(sigma);
alpha = float(sys.argv[7])
beta = float(sys.argv[8])
sigmoid.SetAlpha(alpha)
sigmoid.SetBeta(beta)
# same as image
seedPosition = itk.itkIndex2()
seedPosition.SetElement(0, int(sys.argv[3]))
seedPosition.SetElement(1, int(sys.argv[4]))
initialDistance = float(sys.argv[5])
seedValue = - initialDistance
node = itk.itkLevelSetNodeF2()
node.SetValue(seedValue)
node.SetIndex(seedPosition)
seeds = itk.itkNodeContainerF2_New()
seeds.Initialize()
seeds.InsertElement(0, node)
fastMarching.SetTrialPoints(seeds.GetPointer())
fastMarching.SetSpeedConstant(1.0)
caster1 = itk.itkRescaleIntensityImageFilterF2US2_New()
writer1 = itk.itkImageFileWriterUS2_New()
caster1.SetInput( smoothing.GetOutput() );
writer1.SetInput( caster1.GetOutput() );
writer1.SetFileName("GeodesicActiveContourImageFilterOutput1.png");
caster1.SetOutputMinimum( 0 );
caster1.SetOutputMaximum( 65535 );
writer1.Update();
caster2 = itk.itkRescaleIntensityImageFilterF2US2_New()
writer2 = itk.itkImageFileWriterUS2_New()
caster2.SetInput( gradientMagnitude.GetOutput() );
writer2.SetInput( caster2.GetOutput() );
writer2.SetFileName("GeodesicActiveContourImageFilterOutput2.png");
caster2.SetOutputMinimum( 0 );
caster2.SetOutputMaximum( 65535 );
writer2.Update();
caster3 = itk.itkRescaleIntensityImageFilterF2US2_New()
writer3 = itk.itkImageFileWriterUS2_New()
caster3.SetInput( sigmoid.GetOutput() );
writer3.SetInput( caster3.GetOutput() );
writer3.SetFileName("GeodesicActiveContourImageFilterOutput3.png");
caster3.SetOutputMinimum( 0 );
caster3.SetOutputMaximum( 65535 );
writer3.Update();
caster4 = itk.itkRescaleIntensityImageFilterF2US2_New()
writer4 = itk.itkImageFileWriterUS2_New()
caster4.SetInput( fastMarching.GetOutput() );
writer4.SetInput( caster4.GetOutput() );
writer4.SetFileName("GeodesicActiveContourImageFilterOutput4.png");
caster4.SetOutputMinimum( 0 );
caster4.SetOutputMaximum( 65535 );
fastMarching.SetOutputSize(
reader.GetOutput().GetBufferedRegion().GetSize())
writer.Update()
# Print out some useful information
print "\n"
print "Max. no. iterations: %d" % (gAC.GetNumberOfIterations())
print "Max. RMS error: %.3f" % (gAC.GetMaximumRMSError())
print "No. elapsed iterations: %d" % (gAC.GetElapsedIterations())
print "RMS change: %.3f" % (gAC.GetRMSChange())
writer4.Update()
mapWriter = itk.itkImageFileWriterF2_New()
mapWriter.SetInput(fastMarching.GetOutput())
mapWriter.SetFileName("GeodesicActiveContourImageFilterOutput4.mha")
mapWriter.Update()
speedWriter = itk.itkImageFileWriterF2_New()
speedWriter.SetInput( sigmoid.GetOutput() )
speedWriter.SetFileName("GeodesicActiveContourImageFilterOutput3.mha")
speedWriter.Update()
gradientWriter = itk.itkImageFileWriterF2_New()
gradientWriter.SetInput( gradientMagnitude.GetOutput() )
gradientWriter.SetFileName("GeodesicActiveContourImageFilterOutput2.mha")
gradientWriter.Update();
if __name__ == "__main__":
main()
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