def vmtk_cap_polydata(surface,
boundary_ids=None,
displacement=0.0,
in_plane_displacement=0.0):
"""Wrapper for vmtkCapPolyData.
Close holes in a surface model.
Args:
in_plane_displacement (float): Displacement of boundary baricenters, at section plane relative to the radius
displacement (float): Displacement of boundary baricenters along boundary normals relative to the radius.
boundary_ids (ndarray): Set ids of the boundaries to cap.
surface (vtkPolyData): Surface to be capped.
Returns:
surface (vtkPolyData): Capped surface.
"""
surface_capper = vtkvmtk.vtkvmtkCapPolyData()
surface_capper.SetInputData(surface)
surface_capper.SetDisplacement(displacement)
surface_capper.SetInPlaneDisplacement(in_plane_displacement)
if boundary_ids is not None:
surface_capper.SetBoundaryIds(boundary_ids)
surface_capper.Update()
return surface_capper.GetOutput()
def Execute(self):
if self.Surface == None:
self.PrintError('Error: No input surface.')
if self.CheckNonManifold:
self.PrintLog('NonManifold check.')
nonManifoldChecker = vmtkNonManifoldSurfaceChecker()
nonManifoldChecker.Surface = self.Surface
nonManifoldChecker.PrintError = self.PrintError
nonManifoldChecker.Execute()
if (nonManifoldChecker.NumberOfNonManifoldEdges > 0):
self.PrintLog(nonManifoldChecker.Report)
return
if not self.vmtkRenderer and self.SeedSelectorName in [
'pickpoint', 'openprofiles'
]:
self.vmtkRenderer = vmtkrenderer.vmtkRenderer()
self.vmtkRenderer.Initialize()
self.OwnRenderer = 1
self.PrintLog('Cleaning surface.')
surfaceCleaner = vtk.vtkCleanPolyData()
surfaceCleaner.SetInputData(self.Surface)
surfaceCleaner.Update()
self.PrintLog('Triangulating surface.')
surfaceTriangulator = vtk.vtkTriangleFilter()
surfaceTriangulator.SetInputConnection(surfaceCleaner.GetOutputPort())
surfaceTriangulator.PassLinesOff()
surfaceTriangulator.PassVertsOff()
surfaceTriangulator.Update()
centerlineInputSurface = surfaceTriangulator.GetOutput()
capCenterIds = None
if self.SeedSelectorName in [
'openprofiles', 'carotidprofiles', 'pickpoint', 'profileidlist'
]:
self.PrintLog('Capping surface.')
surfaceCapper = vtkvmtk.vtkvmtkCapPolyData()
surfaceCapper.SetInputConnection(
surfaceTriangulator.GetOutputPort())
surfaceCapper.SetDisplacement(self.CapDisplacement)
surfaceCapper.SetInPlaneDisplacement(self.CapDisplacement)
surfaceCapper.Update()
centerlineInputSurface = surfaceCapper.GetOutput()
capCenterIds = surfaceCapper.GetCapCenterIds()
if self.SeedSelector:
pass
elif self.SeedSelectorName:
if self.SeedSelectorName == 'pickpoint':
self.SeedSelector = vmtkPickPointSeedSelector()
self.SeedSelector.vmtkRenderer = self.vmtkRenderer
self.SeedSelector.Script = self
elif self.SeedSelectorName == 'openprofiles':
self.SeedSelector = vmtkOpenProfilesSeedSelector()
self.SeedSelector.vmtkRenderer = self.vmtkRenderer
self.SeedSelector.Script = self
self.SeedSelector.SetSeedIds(surfaceCapper.GetCapCenterIds())
elif self.SeedSelectorName == 'carotidprofiles':
self.SeedSelector = vmtkCarotidProfilesSeedSelector()
self.SeedSelector.SetSeedIds(surfaceCapper.GetCapCenterIds())
elif self.SeedSelectorName == 'idlist':
self.SeedSelector = vmtkIdListSeedSelector()
self.SeedSelector.SourceIds = self.SourceIds
self.SeedSelector.TargetIds = self.TargetIds
elif self.SeedSelectorName == 'pointlist':
self.SeedSelector = vmtkPointListSeedSelector()
self.SeedSelector.SourcePoints = self.SourcePoints
self.SeedSelector.TargetPoints = self.TargetPoints
elif self.SeedSelectorName != 'profileidlist':
self.PrintError(
"SeedSelectorName unknown (available: pickpoint, openprofiles, carotidprofiles, profileidlist, idlist, pointlist)"
)
return
else:
self.PrintError(
'vmtkCenterlines error: either SeedSelector or SeedSelectorName must be specified'
)
return
if self.SeedSelector:
self.SeedSelector.SetSurface(centerlineInputSurface)
self.SeedSelector.InputInfo = self.InputInfo
self.SeedSelector.InputText = self.InputText
self.SeedSelector.OutputText = self.OutputText
self.SeedSelector.PrintError = self.PrintError
self.SeedSelector.PrintLog = self.PrintLog
self.SeedSelector.Execute()
inletSeedIds = self.SeedSelector.GetSourceSeedIds()
outletSeedIds = self.SeedSelector.GetTargetSeedIds()
else:
inletSeedIds = vtk.vtkIdList()
outletSeedIds = vtk.vtkIdList()
for id in self.SourceIds:
inletSeedIds.InsertNextId(id)
if self.TargetIds:
for id in self.TargetIds:
outletSeedIds.InsertNextId(id)
else:
for i in range(capCenterIds.GetNumberOfIds()):
if i not in self.SourceIds:
outletSeedIds.InsertNextId(i)
self.PrintLog('Computing centerlines.')
self.InputInfo('Computing centerlines...')
centerlineFilter = vtkvmtk.vtkvmtkPolyDataCenterlines()
centerlineFilter.SetInputData(centerlineInputSurface)
if self.SeedSelectorName in [
'openprofiles', 'carotidprofiles', 'profileidlist'
]:
centerlineFilter.SetCapCenterIds(capCenterIds)
centerlineFilter.SetSourceSeedIds(inletSeedIds)
centerlineFilter.SetTargetSeedIds(outletSeedIds)
centerlineFilter.SetRadiusArrayName(self.RadiusArrayName)
centerlineFilter.SetCostFunction(self.CostFunction)
centerlineFilter.SetFlipNormals(self.FlipNormals)
centerlineFilter.SetAppendEndPointsToCenterlines(self.AppendEndPoints)
centerlineFilter.SetSimplifyVoronoi(self.SimplifyVoronoi)
if self.DelaunayTessellation != None:
centerlineFilter.GenerateDelaunayTessellationOff()
centerlineFilter.SetDelaunayTessellation(self.DelaunayTessellation)
centerlineFilter.SetDelaunayTolerance(self.DelaunayTolerance)
if self.UseTetGen == 1:
self.PrintLog('Running TetGen.')
from vmtk import vmtkscripts
surfaceToMesh = vmtkscripts.vmtkSurfaceToMesh()
surfaceToMesh.Surface = centerlineInputSurface
surfaceToMesh.Execute()
tetgen = vmtkscripts.vmtkTetGen()
tetgen.Mesh = surfaceToMesh.Mesh
tetgen.PLC = 1
tetgen.NoMerge = 1
tetgen.Quality = 0
if self.TetGenDetectInter == 1:
tetgen.DetectInter = 1
tetgen.NoMerge = 0
tetgen.OutputSurfaceElements = 0
tetgen.Execute()
centerlineFilter.GenerateDelaunayTessellationOff()
centerlineFilter.SetDelaunayTessellation(tetgen.Mesh)
centerlineFilter.SetCenterlineResampling(self.Resampling)
centerlineFilter.SetResamplingStepLength(self.ResamplingStepLength)
centerlineFilter.Update()
self.Centerlines = centerlineFilter.GetOutput()
self.VoronoiDiagram = centerlineFilter.GetVoronoiDiagram()
self.DelaunayTessellation = centerlineFilter.GetDelaunayTessellation()
self.PoleIds = centerlineFilter.GetPoleIds()
self.EikonalSolutionArrayName = centerlineFilter.GetEikonalSolutionArrayName(
)
self.EdgeArrayName = centerlineFilter.GetEdgeArrayName()
self.EdgePCoordArrayName = centerlineFilter.GetEdgePCoordArrayName()
self.CostFunctionArrayName = centerlineFilter.GetCostFunctionArrayName(
)
if self.OwnRenderer:
self.vmtkRenderer.Deallocate()
def Execute(self):
if self.Surface == None:
self.PrintError('Error: No input surface.')
if self.CheckNonManifold:
self.PrintLog('NonManifold check.')
nonManifoldChecker = vmtkNonManifoldSurfaceChecker()
nonManifoldChecker.Surface = self.Surface
nonManifoldChecker.PrintError = self.PrintError
nonManifoldChecker.Execute()
if nonManifoldChecker.NumberOfNonManifoldEdges > 0:
self.PrintLog(nonManifoldChecker.Report)
return
self.PrintLog('Cleaning surface.')
surfaceCleaner = vtk.vtkCleanPolyData()
surfaceCleaner.SetInputData(self.Surface)
surfaceCleaner.Update()
self.PrintLog('Triangulating surface.')
surfaceTriangulator = vtk.vtkTriangleFilter()
surfaceTriangulator.SetInputConnection(surfaceCleaner.GetOutputPort())
surfaceTriangulator.PassLinesOff()
surfaceTriangulator.PassVertsOff()
surfaceTriangulator.Update()
surfaceCapper = vtkvmtk.vtkvmtkCapPolyData()
surfaceCapper.SetInputConnection(surfaceTriangulator.GetOutputPort())
surfaceCapper.SetDisplacement(self.CapDisplacement)
surfaceCapper.SetInPlaneDisplacement(self.CapDisplacement)
surfaceCapper.Update()
capCenterIds = surfaceCapper.GetCapCenterIds()
surfaceNormals = vtk.vtkPolyDataNormals()
surfaceNormals.SetInputConnection(surfaceCapper.GetOutputPort())
surfaceNormals.SplittingOff()
surfaceNormals.AutoOrientNormalsOn()
surfaceNormals.SetFlipNormals(self.FlipNormals)
surfaceNormals.ComputePointNormalsOn()
surfaceNormals.ConsistencyOn()
surfaceNormals.Update()
inputSurface = surfaceNormals.GetOutput()
if self.UseTetGen:
self.PrintLog('Running TetGen.')
from vmtk import vmtkscripts
surfaceToMesh = vmtkscripts.vmtkSurfaceToMesh()
surfaceToMesh.Surface = inputSurface
surfaceToMesh.Execute()
tetgen = vmtkscripts.vmtkTetGen()
tetgen.Mesh = surfaceToMesh.Mesh
tetgen.PLC = 1
tetgen.NoMerge = 1
tetgen.Quality = 0
if self.TetGenDetectInter:
tetgen.DetectInter = 1
tetgen.NoMerge = 0
tetgen.OutputSurfaceElements = 0
tetgen.Execute()
self.DelaunayTessellation = tetgen.Mesh
else:
delaunayTessellator = vtk.vtkDelaunay3D()
delaunayTessellator.CreateDefaultLocator()
delaunayTessellator.SetInputConnection(surfaceNormals.GetOutputPort())
delaunayTessellator.SetTolerance(self.DelaunayTolerance)
delaunayTessellator.Update()
self.DelaunayTessellation = delaunayTessellator.GetOutput()
normalsArray = surfaceNormals.GetOutput().GetPointData().GetNormals()
self.DelaunayTessellation.GetPointData().AddArray(normalsArray)
internalTetrahedraExtractor = vtkvmtk.vtkvmtkInternalTetrahedraExtractor()
internalTetrahedraExtractor.SetInputData(self.DelaunayTessellation)
internalTetrahedraExtractor.SetOutwardNormalsArrayName(normalsArray.GetName())
if self.RemoveSubresolutionTetrahedra:
internalTetrahedraExtractor.RemoveSubresolutionTetrahedraOn()
internalTetrahedraExtractor.SetSubresolutionFactor(self.SubresolutionFactor)
internalTetrahedraExtractor.SetSurface(inputSurface)
if capCenterIds.GetNumberOfIds() > 0:
internalTetrahedraExtractor.UseCapsOn()
internalTetrahedraExtractor.SetCapCenterIds(capCenterIds)
internalTetrahedraExtractor.Update()
self.DelaunayTessellation = internalTetrahedraExtractor.GetOutput()
voronoiDiagramFilter = vtkvmtk.vtkvmtkVoronoiDiagram3D()
voronoiDiagramFilter.SetInputData(self.DelaunayTessellation)
voronoiDiagramFilter.SetRadiusArrayName(self.RadiusArrayName)
voronoiDiagramFilter.Update()
self.PoleIds = voronoiDiagramFilter.GetPoleIds()
self.VoronoiDiagram = voronoiDiagramFilter.GetOutput()
if self.SimplifyVoronoi:
voronoiDiagramSimplifier = vtkvmtk.vtkvmtkSimplifyVoronoiDiagram()
voronoiDiagramSimplifier.SetInputConnection(voronoiDiagramFilter.GetOutputPort())
voronoiDiagramSimplifier.SetUnremovablePointIds(voronoiDiagramFilter.GetPoleIds())
voronoiDiagramSimplifier.Update()
self.VoronoiDiagram = voronoiDiagramSimplifier.GetOutput()
self.Mesh = self.DelaunayTessellation
self.Surface = self.VoronoiDiagram
def Execute(self):
if self.Surface == None:
self.PrintError('Error: No input surface.')
# cleaner = vtk.vtkCleanPolyData()
# cleaner.SetInput(self.Surface)
# cleaner.Update()
#
# triangleFilter = vtk.vtkTriangleFilter()
# triangleFilter.SetInput(cleaner.GetOutput())
# triangleFilter.Update()
#
# self.Surface = triangleFilter.GetOutput()
boundaryIds = vtk.vtkIdList()
if self.Interactive:
if not self.vmtkRenderer:
from vmtk import vmtkrenderer
self.vmtkRenderer = vmtkrenderer.vmtkRenderer()
self.vmtkRenderer.Initialize()
self.OwnRenderer = 1
self.vmtkRenderer.RegisterScript(self)
boundaryExtractor = vtkvmtk.vtkvmtkPolyDataBoundaryExtractor()
boundaryExtractor.SetInputData(self.Surface)
boundaryExtractor.Update()
boundaries = boundaryExtractor.GetOutput()
numberOfBoundaries = boundaries.GetNumberOfCells()
seedPoints = vtk.vtkPoints()
for i in range(numberOfBoundaries):
barycenter = [0.0, 0.0, 0.0]
vtkvmtk.vtkvmtkBoundaryReferenceSystems.ComputeBoundaryBarycenter(boundaries.GetCell(i).GetPoints(),barycenter)
seedPoints.InsertNextPoint(barycenter)
seedPolyData = vtk.vtkPolyData()
seedPolyData.SetPoints(seedPoints)
labelsMapper = vtk.vtkLabeledDataMapper();
labelsMapper.SetInputData(seedPolyData)
labelsMapper.SetLabelModeToLabelIds()
labelsActor = vtk.vtkActor2D()
labelsActor.SetMapper(labelsMapper)
self.vmtkRenderer.Renderer.AddActor(labelsActor)
surfaceMapper = vtk.vtkPolyDataMapper()
surfaceMapper.SetInputData(self.Surface)
surfaceMapper.ScalarVisibilityOff()
surfaceActor = vtk.vtkActor()
surfaceActor.SetMapper(surfaceMapper)
surfaceActor.GetProperty().SetOpacity(0.25)
self.vmtkRenderer.Renderer.AddActor(surfaceActor)
#self.vmtkRenderer.Render()
#self.vmtkRenderer.Renderer.RemoveActor(labelsActor)
#self.vmtkRenderer.Renderer.RemoveActor(surfaceActor)
ok = False
while not ok:
labelString = self.InputText("Please input boundary ids: ",self.LabelValidator)
labels = [int(label) for label in labelString.split()]
ok = True
for label in labels:
if label not in list(range(numberOfBoundaries)):
ok = False
for label in labels:
boundaryIds.InsertNextId(label)
if self.Method == 'simple':
capper = vtkvmtk.vtkvmtkSimpleCapPolyData()
capper.SetInputData(self.Surface)
elif self.Method == 'centerpoint':
capper = vtkvmtk.vtkvmtkCapPolyData()
capper.SetInputData(self.Surface)
capper.SetDisplacement(0.0)
capper.SetInPlaneDisplacement(0.0)
elif self.Method == 'smooth':
triangle = vtk.vtkTriangleFilter()
triangle.SetInputData(self.Surface)
triangle.PassLinesOff()
triangle.PassVertsOff()
triangle.Update()
capper = vtkvmtk.vtkvmtkSmoothCapPolyData()
capper.SetInputConnection(triangle.GetOutputPort())
capper.SetConstraintFactor(self.ConstraintFactor)
capper.SetNumberOfRings(self.NumberOfRings)
elif self.Method == 'annular':
capper = vtkvmtk.vtkvmtkAnnularCapPolyData()
capper.SetInputData(self.Surface)
elif self.Method == 'concaveannular':
from vmtk import vtkvmtkcontrib
capper = vtkvmtkcontrib.vtkvmtkConcaveAnnularCapPolyData()
capper.SetInputData(self.Surface)
if self.Interactive:
capper.SetBoundaryIds(boundaryIds)
capper.SetCellEntityIdsArrayName(self.CellEntityIdsArrayName)
capper.SetCellEntityIdOffset(self.CellEntityIdOffset)
capper.Update()
self.Surface = capper.GetOutput()
if self.TriangleOutput == 1:
triangle = vtk.vtkTriangleFilter()
triangle.SetInputData(self.Surface)
triangle.PassLinesOff()
triangle.PassVertsOff()
triangle.Update()
self.Surface = triangle.GetOutput()
normals = vtk.vtkPolyDataNormals()
normals.SetInputData(self.Surface)
normals.AutoOrientNormalsOn()
normals.SplittingOff()
normals.ConsistencyOn()
normals.Update()
self.Surface = normals.GetOutput()
def Execute(self):
if self.Surface == None:
self.PrintError('Error: No input surface.')
if self.CheckNonManifold:
self.PrintLog('NonManifold check.')
nonManifoldChecker = vmtkNonManifoldSurfaceChecker()
nonManifoldChecker.Surface = self.Surface
nonManifoldChecker.PrintError = self.PrintError
nonManifoldChecker.Execute()
if nonManifoldChecker.NumberOfNonManifoldEdges > 0:
self.PrintLog(nonManifoldChecker.Report)
return
self.PrintLog('Cleaning surface.')
surfaceCleaner = vtk.vtkCleanPolyData()
surfaceCleaner.SetInputData(self.Surface)
surfaceCleaner.Update()
self.PrintLog('Triangulating surface.')
surfaceTriangulator = vtk.vtkTriangleFilter()
surfaceTriangulator.SetInputConnection(surfaceCleaner.GetOutputPort())
surfaceTriangulator.PassLinesOff()
surfaceTriangulator.PassVertsOff()
surfaceTriangulator.Update()
surfaceCapper = vtkvmtk.vtkvmtkCapPolyData()
surfaceCapper.SetInputConnection(surfaceTriangulator.GetOutputPort())
surfaceCapper.SetDisplacement(self.CapDisplacement)
surfaceCapper.SetInPlaneDisplacement(self.CapDisplacement)
surfaceCapper.Update()
capCenterIds = surfaceCapper.GetCapCenterIds()
surfaceNormals = vtk.vtkPolyDataNormals()
surfaceNormals.SetInputConnection(surfaceCapper.GetOutputPort())
surfaceNormals.SplittingOff()
surfaceNormals.AutoOrientNormalsOn()
surfaceNormals.SetFlipNormals(self.FlipNormals)
surfaceNormals.ComputePointNormalsOn()
surfaceNormals.ConsistencyOn()
surfaceNormals.Update()
inputSurface = surfaceNormals.GetOutput()
if self.UseTetGen:
self.PrintLog('Running TetGen.')
from vmtk import vmtkscripts
surfaceToMesh = vmtkscripts.vmtkSurfaceToMesh()
surfaceToMesh.Surface = inputSurface
surfaceToMesh.Execute()
tetgen = vmtkscripts.vmtkTetGen()
tetgen.Mesh = surfaceToMesh.Mesh
tetgen.PLC = 1
tetgen.NoMerge = 1
tetgen.Quality = 0
if self.TetGenDetectInter:
tetgen.DetectInter = 1
tetgen.NoMerge = 0
tetgen.OutputSurfaceElements = 0
tetgen.Execute()
self.DelaunayTessellation = tetgen.Mesh
else:
delaunayTessellator = vtk.vtkDelaunay3D()
delaunayTessellator.CreateDefaultLocator()
delaunayTessellator.SetInputConnection(surfaceNormals.GetOutputPort())
delaunayTessellator.SetTolerance(self.DelaunayTolerance)
delaunayTessellator.Update()
self.DelaunayTessellation = delaunayTessellator.GetOutput()
normalsArray = surfaceNormals.GetOutput().GetPointData().GetNormals()
self.DelaunayTessellation.GetPointData().AddArray(normalsArray)
internalTetrahedraExtractor = vtkvmtk.vtkvmtkInternalTetrahedraExtractor()
internalTetrahedraExtractor.SetInputData(self.DelaunayTessellation)
internalTetrahedraExtractor.SetOutwardNormalsArrayName(normalsArray.GetName())
if self.RemoveSubresolutionTetrahedra:
internalTetrahedraExtractor.RemoveSubresolutionTetrahedraOn()
internalTetrahedraExtractor.SetSubresolutionFactor(self.SubresolutionFactor)
internalTetrahedraExtractor.SetSurface(inputSurface)
if capCenterIds.GetNumberOfIds() > 0:
internalTetrahedraExtractor.UseCapsOn()
internalTetrahedraExtractor.SetCapCenterIds(capCenterIds)
internalTetrahedraExtractor.Update()
self.DelaunayTessellation = internalTetrahedraExtractor.GetOutput()
voronoiDiagramFilter = vtkvmtk.vtkvmtkVoronoiDiagram3D()
voronoiDiagramFilter.SetInputData(self.DelaunayTessellation)
voronoiDiagramFilter.SetRadiusArrayName(self.RadiusArrayName)
voronoiDiagramFilter.Update()
self.PoleIds = voronoiDiagramFilter.GetPoleIds()
self.VoronoiDiagram = voronoiDiagramFilter.GetOutput()
if self.SimplifyVoronoi:
voronoiDiagramSimplifier = vtkvmtk.vtkvmtkSimplifyVoronoiDiagram()
voronoiDiagramSimplifier.SetInputConnection(voronoiDiagramFilter.GetOutputPort())
voronoiDiagramSimplifier.SetUnremovablePointIds(voronoiDiagramFilter.GetPoleIds())
voronoiDiagramSimplifier.Update()
self.VoronoiDiagram = voronoiDiagramSimplifier.GetOutput()
self.Mesh = self.DelaunayTessellation
self.Surface = self.VoronoiDiagram
def Execute(self):
if self.Surface == None:
self.PrintError('Error: No input surface.')
if self.CheckNonManifold:
self.PrintLog('NonManifold check.')
nonManifoldChecker = vmtkNonManifoldSurfaceChecker()
nonManifoldChecker.Surface = self.Surface
nonManifoldChecker.PrintError = self.PrintError
nonManifoldChecker.Execute()
if (nonManifoldChecker.NumberOfNonManifoldEdges > 0):
self.PrintLog(nonManifoldChecker.Report)
return
if not self.vmtkRenderer and self.SeedSelectorName in ['pickpoint','openprofiles']:
self.vmtkRenderer = vmtkrenderer.vmtkRenderer()
self.vmtkRenderer.Initialize()
self.OwnRenderer = 1
self.PrintLog('Cleaning surface.')
surfaceCleaner = vtk.vtkCleanPolyData()
surfaceCleaner.SetInputData(self.Surface)
surfaceCleaner.Update()
self.PrintLog('Triangulating surface.')
surfaceTriangulator = vtk.vtkTriangleFilter()
surfaceTriangulator.SetInputConnection(surfaceCleaner.GetOutputPort())
surfaceTriangulator.PassLinesOff()
surfaceTriangulator.PassVertsOff()
surfaceTriangulator.Update()
centerlineInputSurface = surfaceTriangulator.GetOutput()
capCenterIds = None
if self.SeedSelectorName in ['openprofiles', 'carotidprofiles', 'pickpoint', 'profileidlist']:
self.PrintLog('Capping surface.')
surfaceCapper = vtkvmtk.vtkvmtkCapPolyData()
surfaceCapper.SetInputConnection(surfaceTriangulator.GetOutputPort())
surfaceCapper.SetDisplacement(self.CapDisplacement)
surfaceCapper.SetInPlaneDisplacement(self.CapDisplacement)
surfaceCapper.Update()
centerlineInputSurface = surfaceCapper.GetOutput()
capCenterIds = surfaceCapper.GetCapCenterIds()
if self.SeedSelector:
pass
elif self.SeedSelectorName:
if self.SeedSelectorName == 'pickpoint':
self.SeedSelector = vmtkPickPointSeedSelector()
self.SeedSelector.vmtkRenderer = self.vmtkRenderer
self.SeedSelector.Script = self
elif self.SeedSelectorName == 'openprofiles':
self.SeedSelector = vmtkOpenProfilesSeedSelector()
self.SeedSelector.vmtkRenderer = self.vmtkRenderer
self.SeedSelector.Script = self
self.SeedSelector.SetSeedIds(surfaceCapper.GetCapCenterIds())
elif self.SeedSelectorName == 'carotidprofiles':
self.SeedSelector = vmtkCarotidProfilesSeedSelector()
self.SeedSelector.SetSeedIds(surfaceCapper.GetCapCenterIds())
elif self.SeedSelectorName == 'idlist':
self.SeedSelector = vmtkIdListSeedSelector()
self.SeedSelector.SourceIds = self.SourceIds
self.SeedSelector.TargetIds = self.TargetIds
elif self.SeedSelectorName == 'pointlist':
self.SeedSelector = vmtkPointListSeedSelector()
self.SeedSelector.SourcePoints = self.SourcePoints
self.SeedSelector.TargetPoints = self.TargetPoints
elif self.SeedSelectorName != 'profileidlist':
self.PrintError("SeedSelectorName unknown (available: pickpoint, openprofiles, carotidprofiles, profileidlist, idlist, pointlist)")
return
else:
self.PrintError('vmtkCenterlines error: either SeedSelector or SeedSelectorName must be specified')
return
if self.SeedSelector:
self.SeedSelector.SetSurface(centerlineInputSurface)
self.SeedSelector.InputInfo = self.InputInfo
self.SeedSelector.InputText = self.InputText
self.SeedSelector.OutputText = self.OutputText
self.SeedSelector.PrintError = self.PrintError
self.SeedSelector.PrintLog = self.PrintLog
self.SeedSelector.Execute()
inletSeedIds = self.SeedSelector.GetSourceSeedIds()
outletSeedIds = self.SeedSelector.GetTargetSeedIds()
else:
inletSeedIds = vtk.vtkIdList()
outletSeedIds = vtk.vtkIdList()
for id in self.SourceIds:
inletSeedIds.InsertNextId(id)
if self.TargetIds:
for id in self.TargetIds:
outletSeedIds.InsertNextId(id)
else:
for i in range(capCenterIds.GetNumberOfIds()):
if i not in self.SourceIds:
outletSeedIds.InsertNextId(i)
self.PrintLog('Computing centerlines.')
self.InputInfo('Computing centerlines...')
centerlineFilter = vtkvmtk.vtkvmtkPolyDataCenterlines()
centerlineFilter.SetInputData(centerlineInputSurface)
if self.SeedSelectorName in ['openprofiles','carotidprofiles','profileidlist']:
centerlineFilter.SetCapCenterIds(capCenterIds)
centerlineFilter.SetSourceSeedIds(inletSeedIds)
centerlineFilter.SetTargetSeedIds(outletSeedIds)
centerlineFilter.SetRadiusArrayName(self.RadiusArrayName)
centerlineFilter.SetCostFunction(self.CostFunction)
centerlineFilter.SetFlipNormals(self.FlipNormals)
centerlineFilter.SetAppendEndPointsToCenterlines(self.AppendEndPoints)
centerlineFilter.SetSimplifyVoronoi(self.SimplifyVoronoi)
if self.DelaunayTessellation != None:
centerlineFilter.GenerateDelaunayTessellationOff()
centerlineFilter.SetDelaunayTessellation(self.DelaunayTessellation)
centerlineFilter.SetDelaunayTolerance(self.DelaunayTolerance)
if self.UseTetGen==1:
self.PrintLog('Running TetGen.')
from vmtk import vmtkscripts
surfaceToMesh = vmtkscripts.vmtkSurfaceToMesh()
surfaceToMesh.Surface = centerlineInputSurface
surfaceToMesh.Execute()
tetgen = vmtkscripts.vmtkTetGen()
tetgen.Mesh = surfaceToMesh.Mesh
tetgen.PLC = 1
tetgen.NoMerge = 1
tetgen.Quality = 0
if self.TetGenDetectInter == 1:
tetgen.DetectInter = 1
tetgen.NoMerge = 0
tetgen.OutputSurfaceElements = 0
tetgen.Execute()
centerlineFilter.GenerateDelaunayTessellationOff()
centerlineFilter.SetDelaunayTessellation(tetgen.Mesh)
centerlineFilter.SetCenterlineResampling(self.Resampling)
centerlineFilter.SetResamplingStepLength(self.ResamplingStepLength)
centerlineFilter.Update()
self.Centerlines = centerlineFilter.GetOutput()
self.VoronoiDiagram = centerlineFilter.GetVoronoiDiagram()
self.DelaunayTessellation = centerlineFilter.GetDelaunayTessellation()
self.PoleIds = centerlineFilter.GetPoleIds()
self.EikonalSolutionArrayName = centerlineFilter.GetEikonalSolutionArrayName()
self.EdgeArrayName = centerlineFilter.GetEdgeArrayName()
self.EdgePCoordArrayName = centerlineFilter.GetEdgePCoordArrayName()
self.CostFunctionArrayName = centerlineFilter.GetCostFunctionArrayName()
if self.OwnRenderer:
self.vmtkRenderer.Deallocate()
def Execute(self):
if self.Surface == None:
self.PrintError('Error: No input surface.')
# cleaner = vtk.vtkCleanPolyData()
# cleaner.SetInput(self.Surface)
# cleaner.Update()
#
# triangleFilter = vtk.vtkTriangleFilter()
# triangleFilter.SetInput(cleaner.GetOutput())
# triangleFilter.Update()
#
# self.Surface = triangleFilter.GetOutput()
boundaryIds = vtk.vtkIdList()
if self.Interactive:
if not self.vmtkRenderer:
from vmtk import vmtkrenderer
self.vmtkRenderer = vmtkrenderer.vmtkRenderer()
self.vmtkRenderer.Initialize()
self.OwnRenderer = 1
self.vmtkRenderer.RegisterScript(self)
boundaryExtractor = vtkvmtk.vtkvmtkPolyDataBoundaryExtractor()
boundaryExtractor.SetInputData(self.Surface)
boundaryExtractor.Update()
boundaries = boundaryExtractor.GetOutput()
numberOfBoundaries = boundaries.GetNumberOfCells()
seedPoints = vtk.vtkPoints()
for i in range(numberOfBoundaries):
barycenter = [0.0, 0.0, 0.0]
vtkvmtk.vtkvmtkBoundaryReferenceSystems.ComputeBoundaryBarycenter(boundaries.GetCell(i).GetPoints(),barycenter)
seedPoints.InsertNextPoint(barycenter)
seedPolyData = vtk.vtkPolyData()
seedPolyData.SetPoints(seedPoints)
labelsMapper = vtk.vtkLabeledDataMapper();
labelsMapper.SetInputData(seedPolyData)
labelsMapper.SetLabelModeToLabelIds()
labelsActor = vtk.vtkActor2D()
labelsActor.SetMapper(labelsMapper)
self.vmtkRenderer.Renderer.AddActor(labelsActor)
surfaceMapper = vtk.vtkPolyDataMapper()
surfaceMapper.SetInputData(self.Surface)
surfaceMapper.ScalarVisibilityOff()
surfaceActor = vtk.vtkActor()
surfaceActor.SetMapper(surfaceMapper)
surfaceActor.GetProperty().SetOpacity(0.25)
self.vmtkRenderer.Renderer.AddActor(surfaceActor)
#self.vmtkRenderer.Render()
#self.vmtkRenderer.Renderer.RemoveActor(labelsActor)
#self.vmtkRenderer.Renderer.RemoveActor(surfaceActor)
ok = False
while not ok:
labelString = self.InputText("Please input boundary ids: ",self.LabelValidator)
labels = [int(label) for label in labelString.split()]
ok = True
for label in labels:
if label not in list(range(numberOfBoundaries)):
ok = False
for label in labels:
boundaryIds.InsertNextId(label)
if self.Method == 'simple':
capper = vtkvmtk.vtkvmtkSimpleCapPolyData()
capper.SetInputData(self.Surface)
elif self.Method == 'centerpoint':
capper = vtkvmtk.vtkvmtkCapPolyData()
capper.SetInputData(self.Surface)
capper.SetDisplacement(0.0)
capper.SetInPlaneDisplacement(0.0)
elif self.Method == 'smooth':
triangle = vtk.vtkTriangleFilter()
triangle.SetInputData(self.Surface)
triangle.PassLinesOff()
triangle.PassVertsOff()
triangle.Update()
capper = vtkvmtk.vtkvmtkSmoothCapPolyData()
capper.SetInputConnection(triangle.GetOutputPort())
capper.SetConstraintFactor(self.ConstraintFactor)
capper.SetNumberOfRings(self.NumberOfRings)
elif self.Method == 'annular':
capper = vtkvmtk.vtkvmtkAnnularCapPolyData()
capper.SetInputData(self.Surface)
elif self.Method == 'concaveannular':
from vmtk import vtkvmtkcontrib
capper = vtkvmtkcontrib.vtkvmtkConcaveAnnularCapPolyData()
capper.SetInputData(self.Surface)
if self.Interactive:
capper.SetBoundaryIds(boundaryIds)
capper.SetCellEntityIdsArrayName(self.CellEntityIdsArrayName)
capper.SetCellEntityIdOffset(self.CellEntityIdOffset)
capper.Update()
self.Surface = capper.GetOutput()
if self.TriangleOutput == 1:
triangle = vtk.vtkTriangleFilter()
triangle.SetInputData(self.Surface)
triangle.PassLinesOff()
triangle.PassVertsOff()
triangle.Update()
self.Surface = triangle.GetOutput()
normals = vtk.vtkPolyDataNormals()
normals.SetInputData(self.Surface)
normals.AutoOrientNormalsOn()
normals.SplittingOff()
normals.ConsistencyOn()
normals.Update()
self.Surface = normals.GetOutput()
# show(surface)
surface = surface._polydata
surfaceCleaner = vtk.vtkCleanPolyData()
surfaceCleaner.SetInputData(surface)
surfaceCleaner.Update()
surfaceTriangulator = vtk.vtkTriangleFilter()
surfaceTriangulator.SetInputConnection(surfaceCleaner.GetOutputPort())
surfaceTriangulator.PassLinesOff()
surfaceTriangulator.PassVertsOff()
surfaceTriangulator.Update()
centerlineInputSurface = surfaceTriangulator.GetOutput()
surfaceCapper = vtkvmtk.vtkvmtkCapPolyData()
surfaceCapper.SetInputConnection(surfaceTriangulator.GetOutputPort())
surfaceCapper.SetDisplacement(0.0)
surfaceCapper.SetInPlaneDisplacement(0.0)
surfaceCapper.Update()
centerlineInputSurface = surfaceCapper.GetOutput()
capCenterIds = surfaceCapper.GetCapCenterIds()
pointLocator = vtk.vtkPointLocator()
pointLocator.SetDataSet(centerlineInputSurface)
pointLocator.BuildLocator()
sourceId = vtk.vtkIdList()
idsource = pointLocator.FindClosestPoint(source)
sourceId.InsertNextId(idsource)