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#!/usr/bin/env python
## Program: VMTK
## Module: $RCSfile: vmtkimagevesselenhancement.py,v $
## Language: Python
## Date: $Date: 2006/07/17 09:53:14 $
## Version: $Revision: 1.8 $
## Copyright (c) Luca Antiga, David Steinman. All rights reserved.
## See LICENCE file for details.
## This software is distributed WITHOUT ANY WARRANTY; without even
## the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
## PURPOSE. See the above copyright notices for more information.
import vtk
import sys
import pypes
import vtkvmtk
vmtkimagevesselenhancement = 'vmtkImageVesselEnhancement'
class vmtkImageVesselEnhancement(pypes.pypeScript):
def __init__(self):
pypes.pypeScript.__init__(self)
self.Image = None
self.Method = "frangi"
self.EnhancedImage = None
self.SigmaMin = 1.0
self.SigmaMax = 1.0
self.NumberOfSigmaSteps = 1
self.SigmaStepMethod = 'equispaced'
self.Alpha = 0.5
self.Beta = 0.5
self.Gamma = 5.0
self.Alpha1 = 0.5
self.Alpha2 = 2.0
self.C = 1E-6
self.TimeStep = 1E-2
self.Epsilon = 1E-2
self.WStrength = 25.0
self.Sensitivity = 5.0
self.NumberOfIterations = 0
self.NumberOfDiffusionSubIterations = 0
self.SetScriptName('vmtkimagevesselenhancement')
self.SetScriptDoc('compute a feature image for use in segmentation')
self.SetInputMembers([
['Image','i','vtkImageData',1,'','the input image','vmtkimagereader'],
['Method','method','str',1,'["frangi","sato","ved","vedm"]'],
['SigmaMin','sigmamin','float',1,'(0.0,)'],
['SigmaMax','sigmamax','float',1,'(0.0,)'],
['NumberOfSigmaSteps','sigmasteps','int',1,'(0,)'],
['SigmaStepMethod','stepmethod','str',1,'["equispaced","logarithmic"]'],
['Alpha1','alpha1','float',1,'(0.0,)','(sato)'],
['Alpha2','alpha2','float',1,'(0.0,)','(sato)'],
['Alpha','alpha','float',1,'(0.0,)','(frangi, ved, vedm)'],
['Beta','beta','float',1,'(0.0,)','(frangi, ved, vedm)'],
['Gamma','gamma','float',1,'(0.0,)','(frangi, ved, vedm)'],
['C','c','float',1,'(0.0,)','(ved)'],
['TimeStep','timestep','float',1,'(0.0,)','(ved, vedm)'],
['Epsilon','epsilon','float',1,'(0.0,)','(ved, vedm)'],
['WStrength','wstrength','float',1,'(0.0,)','(ved, vedm)'],
['Sensitivity','sensitivity','float',1,'(0.0,)','(ved, vedm)'],
['NumberOfIterations','iterations','int',1,'(0,)','(ved, vedm)'],
['NumberOfDiffusionSubIterations','subiterations','int',1,'(1,)','(ved, vedm)']
])
self.SetOutputMembers([
['Image','o','vtkImageData',1,'','the output image','vmtkimagewriter']
])
def ApplyFrangiVesselness(self):
vesselness = vtkvmtk.vtkvmtkVesselnessMeasureImageFilter()
vesselness.SetInput(self.Image)
vesselness.SetSigmaMin(self.SigmaMin)
vesselness.SetSigmaMax(self.SigmaMax)
vesselness.SetNumberOfSigmaSteps(self.NumberOfSigmaSteps)
vesselness.SetAlpha(self.Alpha)
vesselness.SetBeta(self.Beta)
vesselness.SetGamma(self.Gamma)
if self.SigmaStepMethod == 'equispaced':
vesselness.SetSigmaStepMethodToEquispaced()
elif self.SigmaStepMethod == 'logarithmic':
vesselness.SetSigmaStepMethodToLogarithmic()
vesselness.Update()
self.EnhancedImage = vtk.vtkImageData()
self.EnhancedImage.DeepCopy(vesselness.GetOutput())
def ApplySatoVesselness(self):
vesselness = vtkvmtk.vtkvmtkSatoVesselnessMeasureImageFilter()
vesselness.SetInput(self.Image)
vesselness.SetSigmaMin(self.SigmaMin)
vesselness.SetSigmaMax(self.SigmaMax)
vesselness.SetNumberOfSigmaSteps(self.NumberOfSigmaSteps)
vesselness.SetAlpha1(self.Alpha1)
vesselness.SetAlpha2(self.Alpha2)
if self.SigmaStepMethod == 'equispaced':
vesselness.SetSigmaStepMethodToEquispaced()
elif self.SigmaStepMethod == 'logarithmic':
vesselness.SetSigmaStepMethodToLogarithmic()
vesselness.Update()
self.EnhancedImage = vtk.vtkImageData()
self.EnhancedImage.DeepCopy(vesselness.GetOutput())
def ApplyVED(self):
vesselness = vtkvmtk.vtkvmtkVesselEnhancingDiffusionImageFilter()
vesselness.SetInput(self.Image)
vesselness.SetSigmaMin(self.SigmaMin)
vesselness.SetSigmaMax(self.SigmaMax)
vesselness.SetNumberOfSigmaSteps(self.NumberOfSigmaSteps)
vesselness.SetAlpha(self.Alpha)
vesselness.SetBeta(self.Beta)
vesselness.SetGamma(self.Gamma)
vesselness.SetC(self.C)
vesselness.SetTimeStep(self.TimeStep)
vesselness.SetEpsilon(self.Epsilon)
vesselness.SetWStrength(self.WStrength)
vesselness.SetSensitivity(self.Sensitivity)
vesselness.SetNumberOfIterations(self.NumberOfIterations)
vesselness.SetNumberOfDiffusionSubIterations(self.NumberOfDiffusionSubIterations)
if self.SigmaStepMethod == 'equispaced':
vesselness.SetSigmaStepMethodToEquispaced()
elif self.SigmaStepMethod == 'logarithmic':
vesselness.SetSigmaStepMethodToLogarithmic()
vesselness.Update()
self.EnhancedImage = vtk.vtkImageData()
self.EnhancedImage.DeepCopy(vesselness.GetOutput())
def ApplyVEDManniesing(self):
vesselness = vtkvmtk.vtkvmtkVesselEnhancingDiffusion3DImageFilter()
vesselness.SetInput(self.Image)
vesselness.SetSigmaMin(self.SigmaMin)
vesselness.SetSigmaMax(self.SigmaMax)
vesselness.SetNumberOfSigmaSteps(self.NumberOfSigmaSteps)
vesselness.SetAlpha(self.Alpha)
vesselness.SetBeta(self.Beta)
vesselness.SetGamma(self.Gamma)
vesselness.SetTimeStep(self.TimeStep)
vesselness.SetEpsilon(self.Epsilon)
vesselness.SetOmega(self.WStrength)
vesselness.SetSensitivity(self.Sensitivity)
vesselness.SetNumberOfIterations(self.NumberOfIterations)
vesselness.SetRecalculateVesselness(self.NumberOfDiffusionSubIterations)
if self.SigmaStepMethod == 'equispaced':
vesselness.SetSigmaStepMethodToEquispaced()
elif self.SigmaStepMethod == 'logarithmic':
vesselness.SetSigmaStepMethodToLogarithmic()
vesselness.Update()
self.EnhancedImage = vtk.vtkImageData()
self.EnhancedImage.DeepCopy(vesselness.GetOutput())
def Execute(self):
if self.Image == None:
self.PrintError('Error: No input image.')
if self.SigmaMax < self.SigmaMin:
self.SigmaMax = self.SigmaMin
if self.Method == 'frangi':
self.ApplyFrangiVesselness()
elif self.Method == 'sato':
self.ApplySatoVesselness()
elif self.Method == 'ved':
self.ApplyVED()
elif self.Method == 'vedm':
self.ApplyVEDManniesing()
else:
self.PrintError('Error: unsupported vessel enhancement method')
self.Image = self.EnhancedImage
if __name__=='__main__':
main = pypes.pypeMain()
main.Arguments = sys.argv
main.Execute()
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