def prepareModel(self, polydata):
if polydata == None:
return -1
# skip nonmanifold
surfaceCleaner = slicer.vtkCleanPolyData()
surfaceCleaner.SetInput(polydata)
surfaceCleaner.Update()
surfaceTriangulator = slicer.vtkTriangleFilter()
surfaceTriangulator.SetInput(surfaceCleaner.GetOutput())
surfaceTriangulator.PassLinesOff()
surfaceTriangulator.PassVertsOff()
surfaceTriangulator.Update()
# new steps for preparation to avoid problems because of slim models (f.e. at stenosis)
subdiv = slicer.vtkLinearSubdivisionFilter()
subdiv.SetInput(surfaceTriangulator.GetOutput())
subdiv.SetNumberOfSubdivisions(1)
subdiv.Update()
smooth = slicer.vtkWindowedSincPolyDataFilter()
smooth.SetInput(subdiv.GetOutput())
smooth.SetNumberOfIterations(20)
smooth.SetPassBand(0.1)
smooth.SetBoundarySmoothing(1)
smooth.NormalizeCoordinatesOn()
smooth.Update()
normals = slicer.vtkPolyDataNormals()
normals.SetInput(smooth.GetOutput())
normals.SetAutoOrientNormals(1)
normals.SetFlipNormals(0)
normals.SetConsistency(1)
normals.SplittingOff()
normals.Update()
surfaceCapper = slicer.vtkvmtkCapPolyData()
surfaceCapper.SetInput(normals.GetOutput())
surfaceCapper.SetDisplacement(self._capDisplacement)
surfaceCapper.SetInPlaneDisplacement(self._capDisplacement)
surfaceCapper.Update()
polyDataNew = slicer.vtkPolyData()
polyDataNew.DeepCopy(surfaceCapper.GetOutput())
polyDataNew.Update()
return polyDataNew
def prepareModel(self,polydata):
if polydata == None:
return -1
# skip nonmanifold
surfaceCleaner = slicer.vtkCleanPolyData()
surfaceCleaner.SetInput(polydata)
surfaceCleaner.Update()
surfaceTriangulator = slicer.vtkTriangleFilter()
surfaceTriangulator.SetInput(surfaceCleaner.GetOutput())
surfaceTriangulator.PassLinesOff()
surfaceTriangulator.PassVertsOff()
surfaceTriangulator.Update()
# new steps for preparation to avoid problems because of slim models (f.e. at stenosis)
subdiv = slicer.vtkLinearSubdivisionFilter()
subdiv.SetInput(surfaceTriangulator.GetOutput())
subdiv.SetNumberOfSubdivisions(1)
subdiv.Update()
smooth = slicer.vtkWindowedSincPolyDataFilter()
smooth.SetInput(subdiv.GetOutput())
smooth.SetNumberOfIterations(20)
smooth.SetPassBand(0.1)
smooth.SetBoundarySmoothing(1)
smooth.NormalizeCoordinatesOn()
smooth.Update()
normals = slicer.vtkPolyDataNormals()
normals.SetInput(smooth.GetOutput())
normals.SetAutoOrientNormals(1)
normals.SetFlipNormals(0)
normals.SetConsistency(1)
normals.SplittingOff()
normals.Update()
surfaceCapper = slicer.vtkvmtkCapPolyData()
surfaceCapper.SetInput(normals.GetOutput())
surfaceCapper.SetDisplacement(self._capDisplacement)
surfaceCapper.SetInPlaneDisplacement(self._capDisplacement)
surfaceCapper.Update()
polyDataNew = slicer.vtkPolyData()
polyDataNew.DeepCopy(surfaceCapper.GetOutput())
polyDataNew.Update()
return polyDataNew
def extractNetwork(self,polydata,seed):
surfaceTriangulator = slicer.vtkTriangleFilter()
surfaceTriangulator.SetInput(polydata)
surfaceTriangulator.PassLinesOff()
surfaceTriangulator.PassVertsOff()
surfaceTriangulator.Update()
# new steps for preparation to avoid problems because of slim models (f.e. at stenosis)
subdiv = slicer.vtkLinearSubdivisionFilter()
subdiv.SetInput(surfaceTriangulator.GetOutput())
subdiv.SetNumberOfSubdivisions(1)
subdiv.Update()
# now close the surface
surfaceCapper = slicer.vtkvmtkCapPolyData()
surfaceCapper.SetInput(subdiv.GetOutput())
surfaceCapper.SetDisplacement(0.0)
surfaceCapper.SetInPlaneDisplacement(0.0)
surfaceCapper.Update()
# re-open it where the seed is placed
someradius = 1.0
surface=surfaceCapper.GetOutput()
pointLocator = slicer.vtkPointLocator()
pointLocator.SetDataSet(surface)
pointLocator.BuildLocator()
id=pointLocator.FindClosestPoint(int(seed[0]),int(seed[1]),int(seed[2]))
seed = surface.GetPoint(id)
sphere = slicer.vtkSphere()
sphere.SetCenter(seed[0],seed[1],seed[2])
sphere.SetRadius(someradius)
clip = slicer.vtkClipPolyData()
clip.SetInput(surface)
clip.SetClipFunction(sphere)
clip.Update()
opensurface = clip.GetOutput()
networkExtraction = slicer.vtkvmtkPolyDataNetworkExtraction()
networkExtraction.SetInput(opensurface)
networkExtraction.SetAdvancementRatio(self._advancementRatio)
networkExtraction.SetRadiusArrayName(self._radiusArrayName)
networkExtraction.SetTopologyArrayName(self._topologyArrayName)
networkExtraction.SetMarksArrayName(self._marksArrayName)
networkExtraction.Update()
self._parentClass._helper.debug(self._topologyArrayName)
network=networkExtraction.GetOutput()
arrayNames = []
celldata = network.GetCellData()
for i in range(celldata.GetNumberOfArrays()):
array = celldata.GetArray(i)
arrayName = array.GetName()
if arrayName == None:
continue
if (arrayName[-1]=='_'):
continue
arrayNames.append(arrayName)
numberOfPoints = network.GetNumberOfPoints()
for i in range(numberOfPoints):
point = network.GetPoint(numberOfPoints - i - 1)
line = str(point[0]) + ' ' + str(point[1]) + ' ' + str(point[2])
for arrayName in arrayNames:
array = celldata.GetArray(arrayName)
for j in range(array.GetNumberOfComponents()):
line = line + ' ' + arrayName + ": " + str(array.GetComponent(numberOfPoints - i,j))
self._parentClass._helper.debug(line)
polyDataNew = slicer.vtkPolyData()
polyDataNew.DeepCopy(network)
polyDataNew.Update()
return polyDataNew