def marchingCubes( self, image, ijkToRasMatrix, threshold ):
transformIJKtoRAS = vtk.vtkTransform()
transformIJKtoRAS.SetMatrix( ijkToRasMatrix )
marchingCubes = vtk.vtkMarchingCubes()
marchingCubes.SetInput( image )
marchingCubes.SetValue( 0, threshold )
marchingCubes.ComputeScalarsOn()
marchingCubes.ComputeGradientsOn()
marchingCubes.ComputeNormalsOn()
marchingCubes.GetOutput().ReleaseDataFlagOn()
marchingCubes.Update()
if transformIJKtoRAS.GetMatrix().Determinant() < 0:
reverser = vtk.vtkReverseSense()
reverser.SetInput( marchingCubes.GetOutput() )
reverser.ReverseNormalsOn()
reverser.GetOutput().ReleaseDataFlagOn()
reverser.Update()
correctedOutput = reverser.GetOutput()
else:
correctedOutput = marchingCubes.GetOutput()
transformer = vtk.vtkTransformPolyDataFilter()
transformer.SetInput( correctedOutput )
transformer.SetTransform( transformIJKtoRAS )
transformer.GetOutput().ReleaseDataFlagOn()
transformer.Update()
normals = vtk.vtkPolyDataNormals()
normals.ComputePointNormalsOn()
normals.SetInput( transformer.GetOutput() )
normals.SetFeatureAngle( 60 )
normals.SetSplitting( 1 )
normals.GetOutput().ReleaseDataFlagOn()
normals.Update()
stripper = vtk.vtkStripper()
stripper.SetInput( normals.GetOutput() )
stripper.GetOutput().ReleaseDataFlagOff()
stripper.Update()
stripper.GetOutput().Update()
result = vtk.vtkPolyData()
result.DeepCopy( stripper.GetOutput() )
result.Update()
return result
def marchingCubes(self,image,ijkToRasMatrix,threshold):
transformIJKtoRAS = vtk.vtkTransform()
transformIJKtoRAS.SetMatrix(ijkToRasMatrix)
marchingCubes = vtk.vtkMarchingCubes()
marchingCubes.SetInput(image)
marchingCubes.SetValue(0,threshold)
marchingCubes.ComputeScalarsOn()
marchingCubes.ComputeGradientsOn()
marchingCubes.ComputeNormalsOn()
marchingCubes.GetOutput().ReleaseDataFlagOn()
marchingCubes.Update()
if transformIJKtoRAS.GetMatrix().Determinant() < 0:
reverser = vtk.vtkReverseSense()
reverser.SetInput(marchingCubes.GetOutput())
reverser.ReverseNormalsOn()
reverser.GetOutput().ReleaseDataFlagOn()
reverser.Update()
correctedOutput = reverser.GetOutput()
else:
correctedOutput = marchingCubes.GetOutput()
transformer = vtk.vtkTransformPolyDataFilter()
transformer.SetInput(correctedOutput)
transformer.SetTransform(transformIJKtoRAS)
transformer.GetOutput().ReleaseDataFlagOn()
transformer.Update()
normals = vtk.vtkPolyDataNormals()
normals.ComputePointNormalsOn()
normals.SetInput(transformer.GetOutput())
normals.SetFeatureAngle(60)
normals.SetSplitting(1)
normals.GetOutput().ReleaseDataFlagOn()
normals.Update()
stripper = vtk.vtkStripper()
stripper.SetInput(normals.GetOutput())
stripper.GetOutput().ReleaseDataFlagOff()
stripper.Update()
stripper.GetOutput().Update()
result = vtk.vtkPolyData()
result.DeepCopy(stripper.GetOutput())
result.Update()
return result
def GetBoundaryPoints( self, inPolyData ):
featureEdges = vtk.vtkFeatureEdges()
featureEdges.FeatureEdgesOff()
featureEdges.NonManifoldEdgesOff()
featureEdges.ManifoldEdgesOff()
featureEdges.BoundaryEdgesOn()
featureEdges.SetInputData( inPolyData )
featureEdges.Update()
stripper = vtk.vtkStripper()
stripper.SetInputData( featureEdges.GetOutput() )
stripper.Update()
cleaner = vtk.vtkCleanPolyData()
cleaner.SetInputData( stripper.GetOutput() )
cleaner.Update()
return cleaner.GetOutput().GetPoints()
def PolyDataToImageData(self, inputPolydata_Ras, referenceVolumeNode_Ras, inVal=100, outVal=0):
""" We take in an polydata and convert it to an new image data , withing the Reference Voulume node
the reference volume node is cleared with a threshold because originally the volume may contain
alot of noisy pixels
PARAM: inputPolydata_Ras: Polydata we are looking to conver vtkPolydata()
PARAM: refernceVolumeNode_Ras vtkMRMLScalarVolumeNode()
RETURN : vtkImageData
"""
""" Transform the polydata from ras to ijk using the referenceVolumeNode """
#inputPolydataTriangulated_Ijk=polyToImage.GetOutput()
transformPolydataFilter=vtk.vtkTransformPolyDataFilter()
rasToIjkMatrix=vtk.vtkMatrix4x4()
referenceVolumeNode_Ras.GetRASToIJKMatrix(rasToIjkMatrix)
rasToIjkTransform = vtk.vtkTransform()
rasToIjkTransform.SetMatrix(rasToIjkMatrix)
transformPolydataFilter.SetTransform(rasToIjkTransform)
transformPolydataFilter.SetInputData(inputPolydata_Ras)
transformPolydataFilter.Update()
inputPolydata_Ijk=transformPolydataFilter.GetOutput()
normalsFunction=vtk.vtkPolyDataNormals()
normalsFunction.SetInputData(inputPolydata_Ijk)
normalsFunction.ConsistencyOn()
trigFilter=vtk.vtkTriangleFilter()
trigFilter.SetInputConnection(normalsFunction.GetOutputPort())
stripper=vtk.vtkStripper()
stripper.SetInputConnection(trigFilter.GetOutputPort())
stripper.Update()
inputPolydataTriangulated_Ijk=stripper.GetOutput()
# Clone reference image and clear it
referenceImage_Ijk = referenceVolumeNode_Ras.GetImageData()
# Fill image with outVal (there is no volume Fill filter in VTK, therefore we need to use threshold filter)
thresh = vtk.vtkImageThreshold()
thresh.ReplaceInOn()
thresh.ReplaceOutOn()
thresh.SetInValue(outVal)
thresh.SetOutValue(outVal)
#thresh.SetOutputScalarType (vtk.VTK_UNSIGNED_CHAR)
thresh.SetInputData(referenceImage_Ijk)
thresh.Update()
whiteImage_Ijk = thresh.GetOutput()
# Convert polydata to stencil
polyToImage = vtk.vtkPolyDataToImageStencil()
polyToImage.SetInputData(inputPolydataTriangulated_Ijk)
polyToImage.SetOutputSpacing(whiteImage_Ijk.GetSpacing())
polyToImage.SetOutputOrigin(whiteImage_Ijk.GetOrigin())
polyToImage.SetOutputWholeExtent(whiteImage_Ijk.GetExtent())
polyToImage.Update()
imageStencil_Ijk=polyToImage.GetOutput()
# Convert stencil to image
imgstenc = vtk.vtkImageStencil()
imgstenc.SetInputData(whiteImage_Ijk)
imgstenc.SetStencilData(imageStencil_Ijk)
imgstenc.ReverseStencilOn()
imgstenc.SetBackgroundValue(inVal)
imgstenc.Update()
return imgstenc.GetOutput()
def PolyDataToImageData(self,
inputPolydata_Ras,
referenceVolumeNode_Ras,
inVal=100,
outVal=0):
""" We take in an polydata and convert it to an new image data , withing the Reference Voulume node
the reference volume node is cleared with a threshold because originally the volume may contain
alot of noisy pixels
PARAM: inputPolydata_Ras: Polydata we are looking to conver vtkPolydata()
PARAM: refernceVolumeNode_Ras vtkMRMLScalarVolumeNode()
RETURN : vtkImageData
"""
""" Transform the polydata from ras to ijk using the referenceVolumeNode """
#inputPolydataTriangulated_Ijk=polyToImage.GetOutput()
transformPolydataFilter = vtk.vtkTransformPolyDataFilter()
rasToIjkMatrix = vtk.vtkMatrix4x4()
referenceVolumeNode_Ras.GetRASToIJKMatrix(rasToIjkMatrix)
rasToIjkTransform = vtk.vtkTransform()
rasToIjkTransform.SetMatrix(rasToIjkMatrix)
transformPolydataFilter.SetTransform(rasToIjkTransform)
transformPolydataFilter.SetInputData(inputPolydata_Ras)
transformPolydataFilter.Update()
inputPolydata_Ijk = transformPolydataFilter.GetOutput()
normalsFunction = vtk.vtkPolyDataNormals()
normalsFunction.SetInputData(inputPolydata_Ijk)
normalsFunction.ConsistencyOn()
trigFilter = vtk.vtkTriangleFilter()
trigFilter.SetInputConnection(normalsFunction.GetOutputPort())
stripper = vtk.vtkStripper()
stripper.SetInputConnection(trigFilter.GetOutputPort())
stripper.Update()
inputPolydataTriangulated_Ijk = stripper.GetOutput()
# Clone reference image and clear it
referenceImage_Ijk = referenceVolumeNode_Ras.GetImageData()
# Fill image with outVal (there is no volume Fill filter in VTK, therefore we need to use threshold filter)
thresh = vtk.vtkImageThreshold()
thresh.ReplaceInOn()
thresh.ReplaceOutOn()
thresh.SetInValue(outVal)
thresh.SetOutValue(outVal)
#thresh.SetOutputScalarType (vtk.VTK_UNSIGNED_CHAR)
thresh.SetInputData(referenceImage_Ijk)
thresh.Update()
whiteImage_Ijk = thresh.GetOutput()
# Convert polydata to stencil
polyToImage = vtk.vtkPolyDataToImageStencil()
polyToImage.SetInputData(inputPolydataTriangulated_Ijk)
polyToImage.SetOutputSpacing(whiteImage_Ijk.GetSpacing())
polyToImage.SetOutputOrigin(whiteImage_Ijk.GetOrigin())
polyToImage.SetOutputWholeExtent(whiteImage_Ijk.GetExtent())
polyToImage.Update()
imageStencil_Ijk = polyToImage.GetOutput()
# Convert stencil to image
imgstenc = vtk.vtkImageStencil()
imgstenc.SetInputData(whiteImage_Ijk)
imgstenc.SetStencilData(imageStencil_Ijk)
imgstenc.ReverseStencilOn()
imgstenc.SetBackgroundValue(inVal)
imgstenc.Update()
return imgstenc.GetOutput()
