def ExecuteGeodesic(self, origInVolumeNode, inVolumeNode,
numberOfIterations, propagationScaling,
curvatureScaling, advectionScaling,
calculateFeatureImage):
self._helper.debug("Starting execution of Geodesic..")
if not inVolumeNode or not origInVolumeNode:
slicer.Application.ErrorMessage(
"Not enough information!!! Aborting Geodesic..\n")
return
else:
cast = slicer.vtkImageCast()
cast.SetInput(origInVolumeNode.GetImageData())
cast.SetOutputScalarTypeToFloat()
cast.Update()
origImage = cast.GetOutput()
image = inVolumeNode.GetImageData()
levelSets = slicer.vtkvmtkGeodesicActiveContourLevelSetImageFilter(
)
if calculateFeatureImage == 1:
levelSets.SetFeatureImage(
self.BuildGradientBasedFeatureImage(origImage))
else:
levelSets.SetFeatureImage(origImage)
levelSets.SetDerivativeSigma(self.FeatureDerivativeSigma)
levelSets.SetAutoGenerateSpeedAdvection(1)
levelSets.SetPropagationScaling(propagationScaling)
levelSets.SetCurvatureScaling(curvatureScaling)
levelSets.SetAdvectionScaling(advectionScaling)
levelSets.SetInput(image)
levelSets.SetNumberOfIterations(numberOfIterations)
levelSets.SetIsoSurfaceValue(self.IsoSurfaceValue)
levelSets.SetMaximumRMSError(self.MaximumRMSError)
levelSets.SetInterpolateSurfaceLocation(1)
levelSets.SetUseImageSpacing(1)
levelSets.Update()
matrix = slicer.vtkMatrix4x4()
inVolumeNode.GetIJKToRASMatrix(matrix)
outVolumeData = slicer.vtkImageData()
outVolumeData.DeepCopy(levelSets.GetOutput())
outVolumeData.Update()
outVolumeNode = slicer.vtkMRMLScalarVolumeNode()
outVolumeNode.SetAndObserveImageData(outVolumeData)
outVolumeNode.SetIJKToRASMatrix(matrix)
outputContainer = SlicerVMTKLevelSetContainer(outVolumeNode, 0.0)
return outputContainer
def ExecuteGeodesic(self,origInVolumeNode,inVolumeNode,numberOfIterations,propagationScaling,curvatureScaling,advectionScaling,calculateFeatureImage):
self._helper.debug("Starting execution of Geodesic..")
if not inVolumeNode or not origInVolumeNode:
slicer.Application.ErrorMessage("Not enough information!!! Aborting Geodesic..\n")
return
else:
cast = slicer.vtkImageCast()
cast.SetInput(origInVolumeNode.GetImageData())
cast.SetOutputScalarTypeToFloat()
cast.Update()
origImage = cast.GetOutput()
image = inVolumeNode.GetImageData()
levelSets = slicer.vtkvmtkGeodesicActiveContourLevelSetImageFilter()
if calculateFeatureImage==1:
levelSets.SetFeatureImage(self.BuildGradientBasedFeatureImage(origImage))
else:
levelSets.SetFeatureImage(origImage)
levelSets.SetDerivativeSigma(self.FeatureDerivativeSigma)
levelSets.SetAutoGenerateSpeedAdvection(1)
levelSets.SetPropagationScaling(propagationScaling)
levelSets.SetCurvatureScaling(curvatureScaling)
levelSets.SetAdvectionScaling(advectionScaling)
levelSets.SetInput(image)
levelSets.SetNumberOfIterations(numberOfIterations)
levelSets.SetIsoSurfaceValue(self.IsoSurfaceValue)
levelSets.SetMaximumRMSError(self.MaximumRMSError)
levelSets.SetInterpolateSurfaceLocation(1)
levelSets.SetUseImageSpacing(1)
levelSets.Update()
matrix = slicer.vtkMatrix4x4()
inVolumeNode.GetIJKToRASMatrix(matrix)
outVolumeData = slicer.vtkImageData()
outVolumeData.DeepCopy(levelSets.GetOutput())
outVolumeData.Update()
outVolumeNode = slicer.vtkMRMLScalarVolumeNode()
outVolumeNode.SetAndObserveImageData(outVolumeData)
outVolumeNode.SetIJKToRASMatrix(matrix)
outputContainer = SlicerVMTKLevelSetContainer(outVolumeNode,0.0)
return outputContainer
def ExecuteGAC(self, origImage, segmentationImage, numberOfIterations,
propagationScaling, curvatureScaling, advectionScaling,
method):
self._parentClass.GetHelper().debug("Starting GAC..")
calculateFeatureImage = 1
cast = slicer.vtkImageCast()
cast.SetInput(origImage)
cast.SetOutputScalarTypeToFloat()
cast.Update()
if method == 'curves':
levelSets = slicer.vtkvmtkCurvesLevelSetImageFilter()
else:
levelSets = slicer.vtkvmtkGeodesicActiveContourLevelSetImageFilter(
)
if calculateFeatureImage == 1:
levelSets.SetFeatureImage(
self.BuildGradientBasedFeatureImage(origImage))
else:
levelSets.SetFeatureImage(origImage)
levelSets.SetDerivativeSigma(self._featureDerivativeSigma)
levelSets.SetAutoGenerateSpeedAdvection(1)
levelSets.SetPropagationScaling(propagationScaling)
levelSets.SetCurvatureScaling(curvatureScaling)
levelSets.SetAdvectionScaling(advectionScaling)
levelSets.SetInput(segmentationImage)
levelSets.SetNumberOfIterations(numberOfIterations)
levelSets.SetIsoSurfaceValue(self._isoSurfaceValue)
levelSets.SetMaximumRMSError(self._maximumRMSError)
levelSets.SetInterpolateSurfaceLocation(1)
levelSets.SetUseImageSpacing(1)
levelSets.Update()
outVolumeData = slicer.vtkImageData()
outVolumeData.DeepCopy(levelSets.GetOutput())
outVolumeData.Update()
self._parentClass.GetHelper().debug("End of GAC..")
return outVolumeData
def ExecuteGAC(self,origImage,segmentationImage,numberOfIterations,propagationScaling,curvatureScaling,advectionScaling,method):
self._parentClass.GetHelper().debug("Starting GAC..")
calculateFeatureImage = 1
cast = slicer.vtkImageCast()
cast.SetInput(origImage)
cast.SetOutputScalarTypeToFloat()
cast.Update()
if method=='curves':
levelSets = slicer.vtkvmtkCurvesLevelSetImageFilter()
else:
levelSets = slicer.vtkvmtkGeodesicActiveContourLevelSetImageFilter()
if calculateFeatureImage==1:
levelSets.SetFeatureImage(self.BuildGradientBasedFeatureImage(origImage))
else:
levelSets.SetFeatureImage(origImage)
levelSets.SetDerivativeSigma(self._featureDerivativeSigma)
levelSets.SetAutoGenerateSpeedAdvection(1)
levelSets.SetPropagationScaling(propagationScaling)
levelSets.SetCurvatureScaling(curvatureScaling)
levelSets.SetAdvectionScaling(advectionScaling)
levelSets.SetInput(segmentationImage)
levelSets.SetNumberOfIterations(numberOfIterations)
levelSets.SetIsoSurfaceValue(self._isoSurfaceValue)
levelSets.SetMaximumRMSError(self._maximumRMSError)
levelSets.SetInterpolateSurfaceLocation(1)
levelSets.SetUseImageSpacing(1)
levelSets.Update()
outVolumeData = slicer.vtkImageData()
outVolumeData.DeepCopy(levelSets.GetOutput())
outVolumeData.Update()
self._parentClass.GetHelper().debug("End of GAC..")
return outVolumeData