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# INPUTS: {BrainProtonDensitySlice.png}
# OUTPUTS: {ThresholdSegmentationLevelSetImageFilterWhiteMatter.png}
# 60 116 5 150 180
# INPUTS: {BrainProtonDensitySlice.png}
# OUTPUTS: {ThresholdSegmentationLevelSetImageFilterVentricle.png}
# 81 112 5 210 250
# INPUTS: {BrainProtonDensitySlice.png}
# OUTPUTS: {ThresholdSegmentationLevelSetImageFilterGrayMatter.png}
# 107 69 5 180 210
import itk
from sys import argv, stderr, exit
itk.auto_progress(2)
# itk.auto_progress(1)
if len(argv) < 8 :
print >> stderr, """Missing Parameters
Usage: ThresholdSegmentationLevelSetImageFilter.py inputImage outputImage seedX seedY InitialDistance LowerThreshold UpperThreshold [CurvatureScaling == 1.0]"""
exit(1)
InternalPixelType = itk.F
Dimension = 2
InternalImageType = itk.Image[ InternalPixelType, Dimension ]
OutputPixelType = itk.UC
OutputImageType = itk.Image[ OutputPixelType, Dimension ]
thresholder = itk.BinaryThresholdImageFilter[ InternalImageType, OutputImageType ].New()
thresholder.SetLowerThreshold( -1000.0 )
thresholder.SetUpperThreshold( 0.0 )
thresholder.SetOutsideValue( 0 )
thresholder.SetInsideValue( 255 )
ReaderType = itk.ImageFileReader[ InternalImageType ]
WriterType = itk.ImageFileWriter[ OutputImageType ]
reader = ReaderType.New()
writer = WriterType.New()
reader.SetFileName( argv[1] )
writer.SetFileName( argv[2] )
FastMarchingFilterType = itk.FastMarchingImageFilter[ InternalImageType, InternalImageType ]
fastMarching = FastMarchingFilterType.New()
ThresholdSegmentationLevelSetImageFilterType = itk.ThresholdSegmentationLevelSetImageFilter[ InternalImageType, InternalImageType, InternalPixelType ]
thresholdSegmentation = ThresholdSegmentationLevelSetImageFilterType.New()
thresholdSegmentation.SetPropagationScaling( 1.0 )
if len(argv) > 8 :
thresholdSegmentation.SetCurvatureScaling( float(argv[8]) )
else:
thresholdSegmentation.SetCurvatureScaling( 1.0 )
thresholdSegmentation.SetMaximumRMSError( 0.02 )
thresholdSegmentation.SetNumberOfIterations( 1200 )
thresholdSegmentation.SetUpperThreshold( float(argv[7]) )
thresholdSegmentation.SetLowerThreshold( float(argv[6]) )
thresholdSegmentation.SetIsoSurfaceValue(0.0)
thresholdSegmentation.SetInput( fastMarching.GetOutput() )
thresholdSegmentation.SetFeatureImage( reader.GetOutput() )
thresholder.SetInput( thresholdSegmentation.GetOutput() )
writer.SetInput( thresholder.GetOutput() )
NodeType = itk.LevelSetNode[InternalPixelType, Dimension]
NodeContainer = itk.VectorContainer[itk.UI, NodeType]
seeds = NodeContainer.New()
seedPosition = [int( argv[3] ), int( argv[4] )]
initialDistance = float( argv[5] )
node = NodeType()
seedValue = - initialDistance
node.SetValue( seedValue )
node.SetIndex( seedPosition )
seeds.Initialize()
seeds.InsertElement( 0, node )
fastMarching.SetTrialPoints( seeds )
fastMarching.SetSpeedConstant( 1.0 )
reader.Update()
fastMarching.SetOutputSize(
reader.GetOutput().GetBufferedRegion().GetSize() )
writer.Update()
itk.echo(thresholdSegmentation)
InternalWriterType = itk.ImageFileWriter[ InternalImageType ]
mapWriter = InternalWriterType.New()
mapWriter.SetInput( fastMarching.GetOutput() )
mapWriter.SetFileName("fastMarchingImage.mha")
mapWriter.Update()
speedWriter = InternalWriterType.New()
speedWriter.SetInput( thresholdSegmentation.GetSpeedImage() )
speedWriter.SetFileName("speedTermImage.mha")
speedWriter.Update()
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