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vmtkimagefeatures.py
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204 lines (163 loc) · 7.54 KB
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#!/usr/bin/env python
## Program: VMTK
## Module: $RCSfile: vmtkimagefeatures.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 LICENSE 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.
from __future__ import absolute_import #NEEDS TO STAY AS TOP LEVEL MODULE FOR Py2-3 COMPATIBILITY
import vtk
import sys
from vmtk import pypes
from vmtk import vtkvmtk
class vmtkImageFeatures(pypes.pypeScript):
def __init__(self):
pypes.pypeScript.__init__(self)
self.Image = None
self.FeatureImage = None
self.Dimensionality = 3
self.DerivativeSigma = 0.0
self.SigmoidRemapping = 0
self.FeatureImageType = 'gradient'
self.UpwindFactor = 1.0
self.FWHMRadius = [3, 3, 3]
self.FWHMBackgroundValue = 0.0
self.SetScriptName('vmtkimagefeatures')
self.SetScriptDoc('compute a feature image for use in segmentation')
self.SetInputMembers([
['Image','i','vtkImageData',1,'','the input image','vmtkimagereader'],
['FeatureImageType','featureimagetype','str',1,'["vtkgradient","gradient","upwind","fwhm"]'],
['Dimensionality','dimensionality','int',1,'(2,3,1)'],
['SigmoidRemapping','sigmoid','bool',1],
['DerivativeSigma','derivativesigma','float',1,'(0.0,)'],
['UpwindFactor','upwindfactor','float',1,'(0.0,1.0)'],
['FWHMRadius','fwhmradius','int',3,'(0,)'],
['FWHMBackgroundValue','fwhmbackgroundvalue','float',1]
])
self.SetOutputMembers([
['Image','o','vtkImageData',1,'','the output image','vmtkimagewriter']
])
def BuildVTKGradientBasedFeatureImage(self):
cast = vtk.vtkImageCast()
cast.SetInputData(self.Image)
cast.SetOutputScalarTypeToFloat()
cast.Update()
gradientMagnitude = vtk.vtkImageGradientMagnitude()
gradientMagnitude.SetInputConnection(cast.GetOutputPort())
gradientMagnitude.SetDimensionality(self.Dimensionality)
gradientMagnitude.Update()
imageAdd = vtk.vtkImageMathematics()
imageAdd.SetInputConnection(gradientMagnitude.GetOutputPort())
imageAdd.SetOperationToAddConstant()
imageAdd.SetConstantC(1.0)
imageAdd.Update()
imageInvert = vtk.vtkImageMathematics()
imageInvert.SetInputConnection(imageAdd.GetOutputPort())
imageInvert.SetOperationToInvert()
imageInvert.SetConstantC(1E20)
imageInvert.DivideByZeroToCOn()
imageInvert.Update()
self.FeatureImage = vtk.vtkImageData()
self.FeatureImage.DeepCopy(imageInvert.GetOutput())
def BuildFWHMBasedFeatureImage(self):
cast = vtk.vtkImageCast()
cast.SetInputData(self.Image)
cast.SetOutputScalarTypeToFloat()
cast.Update()
fwhmFeatureImageFilter = vtkvmtk.vtkvmtkFWHMFeatureImageFilter()
fwhmFeatureImageFilter.SetInputConnection(cast.GetOutputPort())
fwhmFeatureImageFilter.SetRadius(self.FWHMRadius)
fwhmFeatureImageFilter.SetBackgroundValue(self.FWHMBackgroundValue)
fwhmFeatureImageFilter.Update()
self.FeatureImage = vtk.vtkImageData()
self.FeatureImage.DeepCopy(fwhmFeatureImageFilter.GetOutput())
def BuildUpwindGradientBasedFeatureImage(self):
cast = vtk.vtkImageCast()
cast.SetInputData(self.Image)
cast.SetOutputScalarTypeToFloat()
cast.Update()
gradientMagnitude = vtkvmtk.vtkvmtkUpwindGradientMagnitudeImageFilter()
gradientMagnitude.SetInputConnection(cast.GetOutputPort())
gradientMagnitude.SetUpwindFactor(self.UpwindFactor)
gradientMagnitude.Update()
featureImage = None
if self.SigmoidRemapping==1:
scalarRange = gradientMagnitude.GetOutput().GetPointData().GetScalars().GetRange()
inputMinimum = scalarRange[0]
inputMaximum = scalarRange[1]
alpha = - (inputMaximum - inputMinimum) / 6.0
beta = (inputMaximum + inputMinimum) / 2.0
sigmoid = vtkvmtk.vtkvmtkSigmoidImageFilter()
sigmoid.SetInputConnection(gradientMagnitude.GetOutputPort())
sigmoid.SetAlpha(alpha)
sigmoid.SetBeta(beta)
sigmoid.SetOutputMinimum(0.0)
sigmoid.SetOutputMaximum(1.0)
sigmoid.Update()
featureImage = sigmoid.GetOutput()
else:
boundedReciprocal = vtkvmtk.vtkvmtkBoundedReciprocalImageFilter()
boundedReciprocal.SetInputConnection(gradientMagnitude.GetOutputPort())
boundedReciprocal.Update()
featureImage = boundedReciprocal.GetOutput()
self.FeatureImage = vtk.vtkImageData()
self.FeatureImage.DeepCopy(featureImage)
def BuildGradientBasedFeatureImage(self):
cast = vtk.vtkImageCast()
cast.SetInputData(self.Image)
cast.SetOutputScalarTypeToFloat()
cast.Update()
if (self.DerivativeSigma > 0.0):
gradientMagnitude = vtkvmtk.vtkvmtkGradientMagnitudeRecursiveGaussianImageFilter()
gradientMagnitude.SetInputConnection(cast.GetOutputPort())
gradientMagnitude.SetSigma(self.DerivativeSigma)
gradientMagnitude.SetNormalizeAcrossScale(0)
gradientMagnitude.Update()
else:
gradientMagnitude = vtkvmtk.vtkvmtkGradientMagnitudeImageFilter()
gradientMagnitude.SetInputConnection(cast.GetOutputPort())
gradientMagnitude.Update()
featureImage = None
if self.SigmoidRemapping==1:
scalarRange = gradientMagnitude.GetOutput().GetPointData().GetScalars().GetRange()
inputMinimum = scalarRange[0]
inputMaximum = scalarRange[1]
alpha = - (inputMaximum - inputMinimum) / 6.0
beta = (inputMaximum + inputMinimum) / 2.0
sigmoid = vtkvmtk.vtkvmtkSigmoidImageFilter()
sigmoid.SetInputConnection(gradientMagnitude.GetOutputPort())
sigmoid.SetAlpha(alpha)
sigmoid.SetBeta(beta)
sigmoid.SetOutputMinimum(0.0)
sigmoid.SetOutputMaximum(1.0)
sigmoid.Update()
featureImage = sigmoid.GetOutput()
else:
boundedReciprocal = vtkvmtk.vtkvmtkBoundedReciprocalImageFilter()
boundedReciprocal.SetInputData(gradientMagnitude.GetOutput())
boundedReciprocal.Update()
featureImage = boundedReciprocal.GetOutput()
self.FeatureImage = vtk.vtkImageData()
self.FeatureImage.DeepCopy(featureImage)
def Execute(self):
if self.Image == None:
self.PrintError('Error: No input image.')
if self.FeatureImageType == 'vtkgradient':
self.BuildVTKGradientBasedFeatureImage()
elif self.FeatureImageType == 'gradient':
self.BuildGradientBasedFeatureImage()
elif self.FeatureImageType == 'upwind':
self.BuildUpwindGradientBasedFeatureImage()
elif self.FeatureImageType == 'fwhm':
self.BuildFWHMBasedFeatureImage()
else:
self.PrintError('Error: unsupported feature image type')
self.Image = self.FeatureImage
if __name__=='__main__':
main = pypes.pypeMain()
main.Arguments = sys.argv
main.Execute()