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.')
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):
from vmtk import vmtkscripts
if self.Surface == None:
self.PrintError('Error: No input surface.')
wallEntityOffset = 1
if self.SkipCapping or not self.BoundaryLayerOnCaps:
self.PrintLog("Not capping surface")
surface = self.Surface
cellEntityIdsArray = vtk.vtkIntArray()
cellEntityIdsArray.SetName(self.CellEntityIdsArrayName)
cellEntityIdsArray.SetNumberOfTuples(surface.GetNumberOfCells())
cellEntityIdsArray.FillComponent(0,0.0)
surface.GetCellData().AddArray(cellEntityIdsArray)
else:
self.PrintLog("Capping surface")
capper = vmtkscripts.vmtkSurfaceCapper()
capper.Surface = self.Surface
capper.Interactive = 0
capper.Method = self.CappingMethod
capper.TriangleOutput = 0
capper.CellEntityIdOffset = wallEntityOffset
capper.Execute()
surface = capper.Surface
if self.SkipRemeshing:
remeshedSurface = surface
else:
self.PrintLog("Remeshing surface")
remeshing = vmtkscripts.vmtkSurfaceRemeshing()
remeshing.Surface = surface
remeshing.CellEntityIdsArrayName = self.CellEntityIdsArrayName
remeshing.TargetEdgeLength = self.TargetEdgeLength
remeshing.MaxEdgeLength = self.MaxEdgeLength
remeshing.MinEdgeLength = self.MinEdgeLength
remeshing.TargetEdgeLengthFactor = self.TargetEdgeLengthFactor
remeshing.TargetEdgeLengthArrayName = self.TargetEdgeLengthArrayName
remeshing.TriangleSplitFactor = self.TriangleSplitFactor
remeshing.ElementSizeMode = self.ElementSizeMode
if self.RemeshCapsOnly:
remeshing.ExcludeEntityIds = [wallEntityOffset]
remeshing.Execute()
remeshedSurface = remeshing.Surface
if self.BoundaryLayer:
projection = vmtkscripts.vmtkSurfaceProjection()
projection.Surface = remeshedSurface
projection.ReferenceSurface = surface
projection.Execute()
normals = vmtkscripts.vmtkSurfaceNormals()
normals.Surface = projection.Surface
normals.NormalsArrayName = 'Normals'
normals.Execute()
surfaceToMesh = vmtkscripts.vmtkSurfaceToMesh()
surfaceToMesh.Surface = normals.Surface
surfaceToMesh.Execute()
self.PrintLog("Generating boundary layer")
placeholderCellEntityId = 9999
boundaryLayer = vmtkscripts.vmtkBoundaryLayer()
boundaryLayer.Mesh = surfaceToMesh.Mesh
boundaryLayer.WarpVectorsArrayName = 'Normals'
boundaryLayer.NegateWarpVectors = True
boundaryLayer.ThicknessArrayName = self.TargetEdgeLengthArrayName
if self.ElementSizeMode == 'edgelength':
boundaryLayer.ConstantThickness = True
else:
boundaryLayer.ConstantThickness = False
boundaryLayer.IncludeSurfaceCells = 0
boundaryLayer.NumberOfSubLayers = self.NumberOfSubLayers
boundaryLayer.NumberOfSubsteps = self.NumberOfSubsteps
boundaryLayer.Relaxation = self.Relaxation
boundaryLayer.LocalCorrectionFactor = self.LocalCorrectionFactor
boundaryLayer.SubLayerRatio = self.SubLayerRatio
boundaryLayer.Thickness = self.BoundaryLayerThicknessFactor * self.TargetEdgeLength
boundaryLayer.ThicknessRatio = self.BoundaryLayerThicknessFactor * self.TargetEdgeLengthFactor
boundaryLayer.MaximumThickness = self.BoundaryLayerThicknessFactor * self.MaxEdgeLength
if not self.BoundaryLayerOnCaps:
boundaryLayer.SidewallCellEntityId = placeholderCellEntityId
boundaryLayer.InnerSurfaceCellEntityId = wallEntityOffset
boundaryLayer.Execute()
meshToSurface = vmtkscripts.vmtkMeshToSurface()
meshToSurface.Mesh = boundaryLayer.InnerSurfaceMesh
meshToSurface.Execute()
innerSurface = meshToSurface.Surface
if not self.BoundaryLayerOnCaps:
self.PrintLog("Capping inner surface")
capper = vmtkscripts.vmtkSurfaceCapper()
capper.Surface = innerSurface
capper.Interactive = 0
capper.Method = self.CappingMethod
capper.TriangleOutput = 1
capper.CellEntityIdOffset = wallEntityOffset
capper.Execute()
self.PrintLog("Remeshing endcaps")
remeshing = vmtkscripts.vmtkSurfaceRemeshing()
remeshing.Surface = capper.Surface
remeshing.CellEntityIdsArrayName = self.CellEntityIdsArrayName
remeshing.TargetEdgeLength = self.TargetEdgeLength * self.EndcapsEdgeLengthFactor
remeshing.MaxEdgeLength = self.MaxEdgeLength
remeshing.MinEdgeLength = self.MinEdgeLength
remeshing.TargetEdgeLengthFactor = self.TargetEdgeLengthFactor * self.EndcapsEdgeLengthFactor
remeshing.TargetEdgeLengthArrayName = self.TargetEdgeLengthArrayName
remeshing.TriangleSplitFactor = self.TriangleSplitFactor
remeshing.ElementSizeMode = self.ElementSizeMode
remeshing.ExcludeEntityIds = [wallEntityOffset]
remeshing.Execute()
innerSurface = remeshing.Surface
self.PrintLog("Computing sizing function")
sizingFunction = vtkvmtk.vtkvmtkPolyDataSizingFunction()
sizingFunction.SetInputData(innerSurface)
sizingFunction.SetSizingFunctionArrayName(self.SizingFunctionArrayName)
sizingFunction.SetScaleFactor(self.VolumeElementScaleFactor)
sizingFunction.Update()
surfaceToMesh2 = vmtkscripts.vmtkSurfaceToMesh()
surfaceToMesh2.Surface = sizingFunction.GetOutput()
surfaceToMesh2.Execute()
self.PrintLog("Generating volume mesh")
tetgen = vmtkscripts.vmtkTetGen()
tetgen.Mesh = surfaceToMesh2.Mesh
tetgen.GenerateCaps = 0
tetgen.UseSizingFunction = 1
tetgen.SizingFunctionArrayName = self.SizingFunctionArrayName
tetgen.CellEntityIdsArrayName = self.CellEntityIdsArrayName
tetgen.Order = 1
tetgen.Quality = 1
tetgen.PLC = 1
tetgen.NoBoundarySplit = 1
tetgen.RemoveSliver = 1
tetgen.OutputSurfaceElements = 0
tetgen.OutputVolumeElements = 1
tetgen.Execute()
#w = vtk.vtkXMLUnstructuredGridWriter()
#w.SetInput(tetgen.Mesh)
#w.SetFileName('tet.vtu')
#w.Write()
if tetgen.Mesh.GetNumberOfCells() == 0 and surfaceToMesh.Mesh.GetNumberOfCells() > 0:
self.PrintLog('An error occurred during tetrahedralization. Will only output surface mesh and boundary layer.')
if not self.BoundaryLayerOnCaps:
surfaceToMesh.Mesh.GetCellData().GetArray(self.CellEntityIdsArrayName).FillComponent(0,wallEntityOffset)
self.PrintLog("Assembling final mesh")
appendFilter = vtkvmtk.vtkvmtkAppendFilter()
appendFilter.AddInputData(surfaceToMesh.Mesh)
appendFilter.AddInputData(boundaryLayer.Mesh)
appendFilter.AddInputData(tetgen.Mesh)
#appendFilter.AddInput(boundaryLayer.InnerSurfaceMesh)
if not self.BoundaryLayerOnCaps:
threshold = vtk.vtkThreshold()
threshold.SetInputData(surfaceToMesh2.Mesh)
threshold.ThresholdByUpper(1.5)
threshold.SetInputArrayToProcess(0,0,0,1,self.CellEntityIdsArrayName)
threshold.Update()
endcaps = threshold.GetOutput()
appendFilter.AddInputData(endcaps)
appendFilter.Update()
self.Mesh = appendFilter.GetOutput()
if not self.BoundaryLayerOnCaps:
cellEntityIdsArray = self.Mesh.GetCellData().GetArray(self.CellEntityIdsArrayName)
def VisitNeighbors(i, cellEntityId):
cellPointIds = vtk.vtkIdList()
self.Mesh.GetCellPoints(i,cellPointIds)
neighborPointIds = vtk.vtkIdList()
neighborPointIds.SetNumberOfIds(1)
pointNeighborCellIds = vtk.vtkIdList()
neighborCellIds = vtk.vtkIdList()
for j in range(cellPointIds.GetNumberOfIds()):
neighborPointIds.SetId(0,cellPointIds.GetId(j))
self.Mesh.GetCellNeighbors(i,neighborPointIds,pointNeighborCellIds)
for k in range(pointNeighborCellIds.GetNumberOfIds()):
neighborCellIds.InsertNextId(pointNeighborCellIds.GetId(k))
for j in range(neighborCellIds.GetNumberOfIds()):
cellId = neighborCellIds.GetId(j)
neighborCellEntityId = cellEntityIdsArray.GetTuple1(cellId)
neighborCellType = self.Mesh.GetCellType(cellId)
if neighborCellType not in [vtk.VTK_TRIANGLE, vtk.VTK_QUADRATIC_TRIANGLE, vtk.VTK_QUAD]:
continue
if neighborCellEntityId != placeholderCellEntityId:
continue
cellEntityIdsArray.SetTuple1(cellId,cellEntityId)
VisitNeighbors(cellId,cellEntityId)
for i in range(self.Mesh.GetNumberOfCells()):
cellEntityId = cellEntityIdsArray.GetTuple1(i)
cellType = self.Mesh.GetCellType(i)
if cellType not in [vtk.VTK_TRIANGLE, vtk.VTK_QUADRATIC_TRIANGLE, vtk.VTK_QUAD]:
continue
if cellEntityId in [0, 1, placeholderCellEntityId]:
continue
VisitNeighbors(i,cellEntityId)
else:
self.PrintLog("Computing sizing function")
sizingFunction = vtkvmtk.vtkvmtkPolyDataSizingFunction()
sizingFunction.SetInputData(remeshedSurface)
sizingFunction.SetSizingFunctionArrayName(self.SizingFunctionArrayName)
sizingFunction.SetScaleFactor(self.VolumeElementScaleFactor)
sizingFunction.Update()
self.PrintLog("Converting surface to mesh")
surfaceToMesh = vmtkscripts.vmtkSurfaceToMesh()
surfaceToMesh.Surface = sizingFunction.GetOutput()
surfaceToMesh.Execute()
self.PrintLog("Generating volume mesh")
tetgen = vmtkscripts.vmtkTetGen()
tetgen.Mesh = surfaceToMesh.Mesh
tetgen.GenerateCaps = 0
tetgen.UseSizingFunction = 1
tetgen.SizingFunctionArrayName = self.SizingFunctionArrayName
tetgen.CellEntityIdsArrayName = self.CellEntityIdsArrayName
tetgen.Order = 1
tetgen.Quality = 1
tetgen.PLC = 1
tetgen.NoBoundarySplit = 1
tetgen.RemoveSliver = 1
tetgen.OutputSurfaceElements = 1
tetgen.OutputVolumeElements = 1
tetgen.Execute()
self.Mesh = tetgen.Mesh
if self.Mesh.GetNumberOfCells() == 0 and surfaceToMesh.Mesh.GetNumberOfCells() > 0:
self.PrintLog('An error occurred during tetrahedralization. Will only output surface mesh.')
self.Mesh = surfaceToMesh.Mesh
if self.Tetrahedralize:
tetrahedralize = vtkvmtk.vtkvmtkUnstructuredGridTetraFilter()
tetrahedralize.SetInputData(self.Mesh)
tetrahedralize.Update()
self.Mesh = tetrahedralize.GetOutput()
self.RemeshedSurface = remeshedSurface
def Execute(self):
from vmtk import vmtkscripts
if self.Surface == None:
self.PrintError('Error: No input surface.')
wallEntityOffset = 1
if self.SkipCapping or not self.BoundaryLayerOnCaps:
self.PrintLog("Not capping surface")
surface = self.Surface
cellEntityIdsArray = vtk.vtkIntArray()
cellEntityIdsArray.SetName(self.CellEntityIdsArrayName)
cellEntityIdsArray.SetNumberOfTuples(surface.GetNumberOfCells())
cellEntityIdsArray.FillComponent(0,0.0)
surface.GetCellData().AddArray(cellEntityIdsArray)
else:
self.PrintLog("Capping surface")
capper = vmtkscripts.vmtkSurfaceCapper()
capper.Surface = self.Surface
capper.Interactive = 0
capper.Method = self.CappingMethod
capper.TriangleOutput = 0
capper.CellEntityIdOffset = wallEntityOffset
capper.Execute()
surface = capper.Surface
if self.SkipRemeshing:
remeshedSurface = surface
else:
self.PrintLog("Remeshing surface")
remeshing = vmtkscripts.vmtkSurfaceRemeshing()
remeshing.Surface = surface
remeshing.CellEntityIdsArrayName = self.CellEntityIdsArrayName
remeshing.TargetEdgeLength = self.TargetEdgeLength
remeshing.MaxEdgeLength = self.MaxEdgeLength
remeshing.MinEdgeLength = self.MinEdgeLength
remeshing.TargetEdgeLengthFactor = self.TargetEdgeLengthFactor
remeshing.TargetEdgeLengthArrayName = self.TargetEdgeLengthArrayName
remeshing.TriangleSplitFactor = self.TriangleSplitFactor
remeshing.ElementSizeMode = self.ElementSizeMode
if self.RemeshCapsOnly:
remeshing.ExcludeEntityIds = [wallEntityOffset]
remeshing.Execute()
remeshedSurface = remeshing.Surface
if self.BoundaryLayer:
projection = vmtkscripts.vmtkSurfaceProjection()
projection.Surface = remeshedSurface
projection.ReferenceSurface = surface
projection.Execute()
normals = vmtkscripts.vmtkSurfaceNormals()
normals.Surface = projection.Surface
normals.NormalsArrayName = 'Normals'
normals.Execute()
surfaceToMesh = vmtkscripts.vmtkSurfaceToMesh()
surfaceToMesh.Surface = normals.Surface
surfaceToMesh.Execute()
self.PrintLog("Generating boundary layer fluid")
placeholderCellEntityId = 9999
boundaryLayer = vmtkscripts.vmtkBoundaryLayer()
boundaryLayer.Mesh = surfaceToMesh.Mesh
boundaryLayer.WarpVectorsArrayName = 'Normals'
boundaryLayer.NegateWarpVectors = True
boundaryLayer.ThicknessArrayName = self.TargetEdgeLengthArrayName
if self.ElementSizeMode == 'edgelength':
boundaryLayer.ConstantThickness = True
else:
boundaryLayer.ConstantThickness = False
boundaryLayer.IncludeSurfaceCells = 0
boundaryLayer.NumberOfSubLayers = self.NumberOfSubLayers
boundaryLayer.NumberOfSubsteps = self.NumberOfSubsteps
boundaryLayer.Relaxation = self.Relaxation
boundaryLayer.LocalCorrectionFactor = self.LocalCorrectionFactor
boundaryLayer.SubLayerRatio = self.SubLayerRatio
boundaryLayer.Thickness = self.BoundaryLayerThicknessFactor * self.TargetEdgeLength
boundaryLayer.ThicknessRatio = self.BoundaryLayerThicknessFactor * self.TargetEdgeLengthFactor
boundaryLayer.MaximumThickness = self.BoundaryLayerThicknessFactor * self.MaxEdgeLength
if not self.BoundaryLayerOnCaps:
boundaryLayer.SidewallCellEntityId = placeholderCellEntityId
boundaryLayer.InnerSurfaceCellEntityId = wallEntityOffset
boundaryLayer.VolumeCellEntityId = self.VolumeId_fluid
boundaryLayer.Execute()
self.PrintLog("Generating boundary layer solid")
boundaryLayer2 = vmtkscripts.vmtkBoundaryLayer()
boundaryLayer2.Mesh = surfaceToMesh.Mesh
boundaryLayer2.WarpVectorsArrayName = 'Normals'
boundaryLayer2.NegateWarpVectors = True
boundaryLayer2.ThicknessArrayName = self.TargetEdgeLengthArrayName
if self.ElementSizeMode == 'edgelength':
boundaryLayer2.ConstantThickness = True
else:
boundaryLayer2.ConstantThickness = False
boundaryLayer2.IncludeSurfaceCells = 1
boundaryLayer2.NumberOfSubLayers = self.NumberOfSubLayers
boundaryLayer2.NumberOfSubsteps = self.NumberOfSubsteps
boundaryLayer2.Relaxation = self.Relaxation
boundaryLayer2.LocalCorrectionFactor = self.LocalCorrectionFactor
boundaryLayer2.SubLayerRatio = self.SubLayerRatio
boundaryLayer2.Thickness = self.BoundaryLayerThicknessFactor * self.TargetEdgeLength
boundaryLayer2.ThicknessRatio = self.BoundaryLayerThicknessFactor * self.TargetEdgeLengthFactor
boundaryLayer2.MaximumThickness = self.BoundaryLayerThicknessFactor * self.MaxEdgeLength
if not self.BoundaryLayerOnCaps:
boundaryLayer2.SidewallCellEntityId = self.SolidSideWallId #placeholderCellEntityId
boundaryLayer2.InnerSurfaceCellEntityId = self.InterfaceId_fsi # wallEntityOffset
boundaryLayer2.OuterSurfaceCellEntityId = self.InterfaceId_outer # wallEntityOffset
boundaryLayer2.VolumeCellEntityId = self.VolumeId_solid
boundaryLayer2.Execute()
meshToSurface = vmtkscripts.vmtkMeshToSurface()
meshToSurface.Mesh = boundaryLayer.InnerSurfaceMesh
meshToSurface.Execute()
innerSurface = meshToSurface.Surface
if not self.BoundaryLayerOnCaps:
self.PrintLog("Capping inner surface")
capper = vmtkscripts.vmtkSurfaceCapper()
capper.Surface = innerSurface
capper.Interactive = 0
capper.Method = self.CappingMethod
capper.TriangleOutput = 1
capper.CellEntityIdOffset = wallEntityOffset
capper.Execute()
self.PrintLog("Remeshing endcaps")
remeshing = vmtkscripts.vmtkSurfaceRemeshing()
remeshing.Surface = capper.Surface
remeshing.CellEntityIdsArrayName = self.CellEntityIdsArrayName
remeshing.TargetEdgeLength = self.TargetEdgeLength * self.EndcapsEdgeLengthFactor
remeshing.MaxEdgeLength = self.MaxEdgeLength
remeshing.MinEdgeLength = self.MinEdgeLength
remeshing.TargetEdgeLengthFactor = self.TargetEdgeLengthFactor * self.EndcapsEdgeLengthFactor
remeshing.TargetEdgeLengthArrayName = self.TargetEdgeLengthArrayName
remeshing.TriangleSplitFactor = self.TriangleSplitFactor
remeshing.ElementSizeMode = self.ElementSizeMode
remeshing.ExcludeEntityIds = [wallEntityOffset] # [wallEntityOffset, InterfaceId] #[wallEntityOffset]
remeshing.Execute()
innerSurface = remeshing.Surface
self.PrintLog("Computing sizing function")
sizingFunction = vtkvmtk.vtkvmtkPolyDataSizingFunction()
sizingFunction.SetInputData(innerSurface)
sizingFunction.SetSizingFunctionArrayName(self.SizingFunctionArrayName)
sizingFunction.SetScaleFactor(self.VolumeElementScaleFactor)
sizingFunction.Update()
surfaceToMesh2 = vmtkscripts.vmtkSurfaceToMesh()
surfaceToMesh2.Surface = sizingFunction.GetOutput()
surfaceToMesh2.Execute()
self.PrintLog("Generating volume mesh")
tetgen = vmtkscripts.vmtkTetGen()
tetgen.Mesh = surfaceToMesh2.Mesh
tetgen.GenerateCaps = 0
tetgen.UseSizingFunction = 1
tetgen.SizingFunctionArrayName = self.SizingFunctionArrayName
tetgen.CellEntityIdsArrayName = self.CellEntityIdsArrayName
tetgen.Order = 1
tetgen.Quality = 1
tetgen.PLC = 1
tetgen.NoBoundarySplit = 1
tetgen.RemoveSliver = 1
tetgen.OutputSurfaceElements = 1
tetgen.OutputVolumeElements = 1
tetgen.RegionAttrib = 0
tetgen.Execute()
##### ADDING CELL IDs
#array = vtk.vtkDoubleArray()
#array.SetNumberOfTuples(tetgen.Mesh.GetNumberOfCells())
#array.SetNumberOfComponents(1)
#array.FillComponent(0, 1.0)
#array.SetName('RegionIDs')
#tetgen.Mesh.GetCellData().AddArray(array)
#array = vtk.vtkDoubleArray()
#array.SetNumberOfTuples(boundaryLayer.Mesh.GetNumberOfCells())
#array.SetNumberOfComponents(1)
#array.FillComponent(0, 1.0)
#array.SetName('RegionIDs')
#boundaryLayer.Mesh.GetCellData().AddArray(array)
#array = vtk.vtkDoubleArray()
#array.SetNumberOfTuples(boundaryLayer2.Mesh.GetNumberOfCells())
#array.SetNumberOfComponents(1)
#array.FillComponent(0, 2.0)
#array.SetName('RegionIDs')
#boundaryLayer2.Mesh.GetCellData().AddArray(array)
#####
# w1 = vtk.vtkXMLUnstructuredGridWriter()
# w1.SetInputData(boundaryLayer2.Mesh)
# w1.SetFileName('BoundaryLayer2.vtu')
# w1.Write()
#
# w2 = vtk.vtkXMLUnstructuredGridWriter()
# w2.SetInputData(tetgen.Mesh)
# w2.SetFileName('Tetgen.vtu')
# w2.Write()
#
# w3 = vtk.vtkXMLUnstructuredGridWriter()
# w3.SetInputData(boundaryLayer.Mesh)
# w3.SetFileName('BoundaryLayer.vtu')
# w3.Write()
#
# w4 = vtk.vtkXMLUnstructuredGridWriter()
# w4.SetInputData(boundaryLayer.InnerSurfaceMesh)
# w4.SetFileName('InnerLayer.vtu')
# w4.Write()
#from IPython import embed; embed()
self.PrintLog("Assembling fluid mesh")
appendFilter = vtkvmtk.vtkvmtkAppendFilter()
appendFilter.AddInputData(boundaryLayer.Mesh)
appendFilter.AddInputData(tetgen.Mesh)
appendFilter.Update()
self.Mesh = appendFilter.GetOutput()
if not self.BoundaryLayerOnCaps:
cellEntityIdsArray = self.Mesh.GetCellData().GetArray(self.CellEntityIdsArrayName)
def VisitNeighbors(i, cellEntityId):
cellPointIds = vtk.vtkIdList()
self.Mesh.GetCellPoints(i,cellPointIds)
neighborPointIds = vtk.vtkIdList()
neighborPointIds.SetNumberOfIds(1)
pointNeighborCellIds = vtk.vtkIdList()
neighborCellIds = vtk.vtkIdList()
for j in range(cellPointIds.GetNumberOfIds()):
neighborPointIds.SetId(0,cellPointIds.GetId(j))
self.Mesh.GetCellNeighbors(i,neighborPointIds,pointNeighborCellIds)
for k in range(pointNeighborCellIds.GetNumberOfIds()):
neighborCellIds.InsertNextId(pointNeighborCellIds.GetId(k))
for j in range(neighborCellIds.GetNumberOfIds()):
cellId = neighborCellIds.GetId(j)
neighborCellEntityId = cellEntityIdsArray.GetTuple1(cellId)
neighborCellType = self.Mesh.GetCellType(cellId)
if neighborCellType not in [vtk.VTK_TRIANGLE, vtk.VTK_QUADRATIC_TRIANGLE, vtk.VTK_QUAD]:
continue
if neighborCellEntityId != placeholderCellEntityId:
continue
cellEntityIdsArray.SetTuple1(cellId,cellEntityId)
VisitNeighbors(cellId,cellEntityId)
for i in range(self.Mesh.GetNumberOfCells()):
cellEntityId = cellEntityIdsArray.GetTuple1(i)
cellType = self.Mesh.GetCellType(i)
if cellType not in [vtk.VTK_TRIANGLE, vtk.VTK_QUADRATIC_TRIANGLE, vtk.VTK_QUAD]:
continue
if cellEntityId in [0, 1, placeholderCellEntityId]:
continue
VisitNeighbors(i,cellEntityId)
self.PrintLog("Assembling final FSI mesh")
appendFilter2 = vtkvmtk.vtkvmtkAppendFilter()
appendFilter2.AddInputData(appendFilter.GetOutput())
appendFilter2.AddInputData(boundaryLayer2.Mesh)
appendFilter2.Update()
self.Mesh = appendFilter2.GetOutput()
else:
self.PrintLog("Computing sizing function")
sizingFunction = vtkvmtk.vtkvmtkPolyDataSizingFunction()
sizingFunction.SetInputData(remeshedSurface)
sizingFunction.SetSizingFunctionArrayName(self.SizingFunctionArrayName)
sizingFunction.SetScaleFactor(self.VolumeElementScaleFactor)
sizingFunction.Update()
self.PrintLog("Converting surface to mesh")
surfaceToMesh = vmtkscripts.vmtkSurfaceToMesh()
surfaceToMesh.Surface = sizingFunction.GetOutput()
surfaceToMesh.Execute()
self.PrintLog("Generating volume mesh")
tetgen = vmtkscripts.vmtkTetGen()
tetgen.Mesh = surfaceToMesh.Mesh
tetgen.GenerateCaps = 0
tetgen.UseSizingFunction = 1
tetgen.SizingFunctionArrayName = self.SizingFunctionArrayName
tetgen.CellEntityIdsArrayName = self.CellEntityIdsArrayName
tetgen.Order = 1
tetgen.Quality = 1
tetgen.PLC = 1
tetgen.NoBoundarySplit = 1
tetgen.RemoveSliver = 1
tetgen.OutputSurfaceElements = 1
tetgen.OutputVolumeElements = 1
tetgen.Execute()
self.Mesh = tetgen.Mesh
if self.Mesh.GetNumberOfCells() == 0 and surfaceToMesh.Mesh.GetNumberOfCells() > 0:
self.PrintLog('An error occurred during tetrahedralization. Will only output surface mesh.')
self.Mesh = surfaceToMesh.Mesh
if self.Tetrahedralize:
tetrahedralize = vtkvmtk.vtkvmtkUnstructuredGridTetraFilter()
tetrahedralize.SetInputData(self.Mesh)
tetrahedralize.Update()
self.Mesh = tetrahedralize.GetOutput()
self.RemeshedSurface = remeshedSurface
def Execute(self):
from vmtk import vmtkscripts
if self.Surface == None:
self.PrintError('Error: No input surface.')
wallEntityOffset = 1
if self.SkipCapping or not self.BoundaryLayerOnCaps:
self.PrintLog("Not capping surface")
surface = self.Surface
cellEntityIdsArray = vtk.vtkIntArray()
cellEntityIdsArray.SetName(self.CellEntityIdsArrayName)
cellEntityIdsArray.SetNumberOfTuples(surface.GetNumberOfCells())
cellEntityIdsArray.FillComponent(0, 0.0)
surface.GetCellData().AddArray(cellEntityIdsArray)
else:
self.PrintLog("Capping surface")
capper = vmtkscripts.vmtkSurfaceCapper()
capper.Surface = self.Surface
capper.Interactive = 0
capper.Method = self.CappingMethod
capper.TriangleOutput = 0
capper.CellEntityIdOffset = self.Vessel_inlet_outlet
capper.Execute()
surface = capper.Surface
if self.SkipRemeshing:
remeshedSurface = surface
else:
self.PrintLog("Remeshing surface")
remeshing = vmtkscripts.vmtkSurfaceRemeshing()
remeshing.Surface = surface
remeshing.CellEntityIdsArrayName = self.CellEntityIdsArrayName
remeshing.TargetEdgeLength = self.TargetEdgeLength
remeshing.MaxEdgeLength = self.MaxEdgeLength
remeshing.MinEdgeLength = self.MinEdgeLength
remeshing.TargetEdgeLengthFactor = self.TargetEdgeLengthFactor
remeshing.TargetEdgeLengthArrayName = self.TargetEdgeLengthArrayName
remeshing.TriangleSplitFactor = self.TriangleSplitFactor
remeshing.ElementSizeMode = self.ElementSizeMode
if self.RemeshCapsOnly:
remeshing.ExcludeEntityIds = [self.Vessel_wall]
remeshing.Execute()
remeshedSurface = remeshing.Surface
if self.BoundaryLayer:
projection = vmtkscripts.vmtkSurfaceProjection()
projection.Surface = remeshedSurface
projection.ReferenceSurface = surface
projection.Execute()
normals = vmtkscripts.vmtkSurfaceNormals()
normals.Surface = projection.Surface
normals.NormalsArrayName = 'Normals'
normals.Execute()
surfaceToMesh = vmtkscripts.vmtkSurfaceToMesh()
surfaceToMesh.Surface = normals.Surface
surfaceToMesh.Execute()
self.PrintLog("Generating 1st boundary layer -- PVS")
placeholderCellEntityId = 9999
boundaryLayer = vmtkscripts.vmtkBoundaryLayer()
boundaryLayer.Mesh = surfaceToMesh.Mesh
boundaryLayer.WarpVectorsArrayName = 'Normals'
boundaryLayer.NegateWarpVectors = True
boundaryLayer.ThicknessArrayName = self.TargetEdgeLengthArrayName
if self.ElementSizeMode == 'edgelength':
boundaryLayer.ConstantThickness = True
else:
boundaryLayer.ConstantThickness = False
boundaryLayer.IncludeSurfaceCells = 0
boundaryLayer.NumberOfSubLayers = self.NumberOfSubLayers
boundaryLayer.NumberOfSubsteps = self.NumberOfSubsteps
boundaryLayer.Relaxation = self.Relaxation
boundaryLayer.LocalCorrectionFactor = self.LocalCorrectionFactor
boundaryLayer.SubLayerRatio = self.SubLayerRatio
boundaryLayer.Thickness = self.BoundaryLayerThicknessFactor * self.TargetEdgeLength
boundaryLayer.ThicknessRatio = self.BoundaryLayerThicknessFactor * self.TargetEdgeLengthFactor
boundaryLayer.MaximumThickness = self.BoundaryLayerThicknessFactor * self.MaxEdgeLength
if not self.BoundaryLayerOnCaps:
boundaryLayer.SidewallCellEntityId = placeholderCellEntityId
boundaryLayer.InnerSurfaceCellEntityId = self.Vessel_wall
boundaryLayer.VolumeCellEntityId = self.PVS
boundaryLayer.Execute()
# We need a second boundary layer to make sure we have the right OuterSurface
self.PrintLog("Generating 2nd boundary layer -- PVS")
placeholderCellEntityId2 = 99999
boundaryLayer2 = vmtkscripts.vmtkBoundaryLayer()
boundaryLayer2.Mesh = surfaceToMesh.Mesh
boundaryLayer2.WarpVectorsArrayName = 'Normals'
boundaryLayer2.NegateWarpVectors = True
boundaryLayer2.ThicknessArrayName = self.TargetEdgeLengthArrayName
if self.ElementSizeMode == 'edgelength':
boundaryLayer2.ConstantThickness = True
else:
boundaryLayer2.ConstantThickness = False
boundaryLayer2.IncludeSurfaceCells = 1
boundaryLayer2.NumberOfSubLayers = self.NumberOfSubLayers
boundaryLayer2.NumberOfSubsteps = self.NumberOfSubsteps
boundaryLayer2.Relaxation = self.Relaxation
boundaryLayer2.LocalCorrectionFactor = self.LocalCorrectionFactor
boundaryLayer2.SubLayerRatio = self.SubLayerRatio
boundaryLayer2.Thickness = self.BoundaryLayerThicknessFactor * self.TargetEdgeLength
boundaryLayer2.ThicknessRatio = self.BoundaryLayerThicknessFactor * self.TargetEdgeLengthFactor
boundaryLayer2.MaximumThickness = self.BoundaryLayerThicknessFactor * self.MaxEdgeLength
if not self.BoundaryLayerOnCaps:
boundaryLayer2.SidewallCellEntityId = placeholderCellEntityId2
boundaryLayer2.OuterSurfaceCellEntityId = self.PVS_wall
boundaryLayer2.VolumeCellEntityId = self.PVS
boundaryLayer2.Execute()
meshToSurface = vmtkscripts.vmtkMeshToSurface()
meshToSurface.Mesh = boundaryLayer.InnerSurfaceMesh
meshToSurface.Execute()
innerSurface = meshToSurface.Surface
if not self.BoundaryLayerOnCaps:
self.PrintLog("Capping inner surface")
capper = vmtkscripts.vmtkSurfaceCapper()
capper.Surface = innerSurface
capper.Interactive = 0
capper.Method = self.CappingMethod
capper.TriangleOutput = 1
capper.CellEntityIdOffset = self.Vessel_inlet_outlet
capper.Execute()
self.PrintLog("Remeshing endcaps")
remeshing = vmtkscripts.vmtkSurfaceRemeshing()
remeshing.Surface = capper.Surface
remeshing.CellEntityIdsArrayName = self.CellEntityIdsArrayName
remeshing.TargetEdgeLength = self.TargetEdgeLength * self.EndcapsEdgeLengthFactor
remeshing.MaxEdgeLength = self.MaxEdgeLength
remeshing.MinEdgeLength = self.MinEdgeLength
remeshing.TargetEdgeLengthFactor = self.TargetEdgeLengthFactor * self.EndcapsEdgeLengthFactor
remeshing.TargetEdgeLengthArrayName = self.TargetEdgeLengthArrayName
remeshing.TriangleSplitFactor = self.TriangleSplitFactor
remeshing.ElementSizeMode = self.ElementSizeMode
remeshing.ExcludeEntityIds = [self.Vessel_wall]
remeshing.Execute()
innerSurface = remeshing.Surface
self.PrintLog("Computing sizing function")
sizingFunction = vtkvmtk.vtkvmtkPolyDataSizingFunction()
sizingFunction.SetInputData(innerSurface)
sizingFunction.SetSizingFunctionArrayName(
self.SizingFunctionArrayName)
sizingFunction.SetScaleFactor(self.VolumeElementScaleFactor)
sizingFunction.Update()
surfaceToMesh2 = vmtkscripts.vmtkSurfaceToMesh()
surfaceToMesh2.Surface = sizingFunction.GetOutput()
surfaceToMesh2.Execute()
self.PrintLog("Generating volume mesh")
tetgen = vmtkscripts.vmtkTetGen()
tetgen.Mesh = surfaceToMesh2.Mesh
tetgen.GenerateCaps = 0
tetgen.UseSizingFunction = 1
tetgen.SizingFunctionArrayName = self.SizingFunctionArrayName
tetgen.CellEntityIdsArrayName = self.CellEntityIdsArrayName
tetgen.Order = 1
tetgen.Quality = 1
tetgen.PLC = 1
tetgen.NoBoundarySplit = 1
tetgen.RemoveSliver = 1
tetgen.OutputSurfaceElements = 1
tetgen.OutputVolumeElements = 1
tetgen.RegionAttrib = 1
tetgen.Execute()
# Define VisitNeighbors used to differenciate markers in Sidewall areas
def VisitNeighbors(i, cellEntityId, cellEntityIdsArray,
placeholderTag):
cellPointIds = vtk.vtkIdList()
self.Mesh.GetCellPoints(i, cellPointIds)
neighborPointIds = vtk.vtkIdList()
neighborPointIds.SetNumberOfIds(1)
pointNeighborCellIds = vtk.vtkIdList()
neighborCellIds = vtk.vtkIdList()
for j in range(cellPointIds.GetNumberOfIds()):
neighborPointIds.SetId(0, cellPointIds.GetId(j))
self.Mesh.GetCellNeighbors(i, neighborPointIds,
pointNeighborCellIds)
for k in range(pointNeighborCellIds.GetNumberOfIds()):
neighborCellIds.InsertNextId(
pointNeighborCellIds.GetId(k))
for j in range(neighborCellIds.GetNumberOfIds()):
cellId = neighborCellIds.GetId(j)
neighborCellEntityId = cellEntityIdsArray.GetTuple1(cellId)
neighborCellType = self.Mesh.GetCellType(cellId)
if neighborCellType not in [
vtk.VTK_TRIANGLE, vtk.VTK_QUADRATIC_TRIANGLE,
vtk.VTK_QUAD
]:
continue
if neighborCellEntityId != placeholderTag:
continue
cellEntityIdsArray.SetTuple1(cellId, cellEntityId)
VisitNeighbors(cellId, cellEntityId, cellEntityIdsArray,
placeholderTag)
self.PrintLog("Assembling PVS mesh - 1st layer")
appendFilter = vtkvmtk.vtkvmtkAppendFilter()
appendFilter.AddInputData(boundaryLayer.Mesh)
appendFilter.AddInputData(tetgen.Mesh)
appendFilter.Update()
self.Mesh = appendFilter.GetOutput()
# Use placeholderCellEntityId - inlet/outlet for the PVS-1
if not self.BoundaryLayerOnCaps:
cellEntityIdsArray = self.Mesh.GetCellData().GetArray(
self.CellEntityIdsArrayName)
for i in range(self.Mesh.GetNumberOfCells()):
cellEntityId = cellEntityIdsArray.GetTuple1(i)
cellType = self.Mesh.GetCellType(i)
if cellType not in [
vtk.VTK_TRIANGLE, vtk.VTK_QUADRATIC_TRIANGLE,
vtk.VTK_QUAD
]:
continue
if cellEntityId in [
0, 1, placeholderCellEntityId, self.Vessel_wall
]:
continue
VisitNeighbors(
i, cellEntityId + self.PVS_inlet_outlet -
self.Vessel_inlet_outlet, cellEntityIdsArray,
placeholderCellEntityId)
appendFilter.Update()
self.Mesh = appendFilter.GetOutput()
self.PrintLog("Assembling PVS mesh - 2nd layer")
appendFilter2 = vtkvmtk.vtkvmtkAppendFilter()
appendFilter2.AddInputData(appendFilter.GetOutput())
appendFilter2.AddInputData(boundaryLayer2.Mesh)
appendFilter2.Update()
self.Mesh = appendFilter2.GetOutput()
# Use placeholderCellEntityId2 - inlet/outlet for the PVS-2
if not self.BoundaryLayerOnCaps:
cellEntityIdsArray = self.Mesh.GetCellData().GetArray(
self.CellEntityIdsArrayName)
for i in range(self.Mesh.GetNumberOfCells()):
cellEntityId = cellEntityIdsArray.GetTuple1(i)
cellType = self.Mesh.GetCellType(i)
if cellType not in [
vtk.VTK_TRIANGLE, vtk.VTK_QUADRATIC_TRIANGLE,
vtk.VTK_QUAD
]:
continue
if cellEntityId in [
0, 1, placeholderCellEntityId2, self.Vessel_wall
]:
continue
VisitNeighbors(i, cellEntityId, cellEntityIdsArray,
placeholderCellEntityId2)
self.PrintLog("Assembling final mesh")
appendFilter2.Update()
self.Mesh = appendFilter2.GetOutput()
else:
self.PrintLog("Computing sizing function")
sizingFunction = vtkvmtk.vtkvmtkPolyDataSizingFunction()
sizingFunction.SetInputData(remeshedSurface)
sizingFunction.SetSizingFunctionArrayName(
self.SizingFunctionArrayName)
sizingFunction.SetScaleFactor(self.VolumeElementScaleFactor)
sizingFunction.Update()
self.PrintLog("Converting surface to mesh")
surfaceToMesh = vmtkscripts.vmtkSurfaceToMesh()
surfaceToMesh.Surface = sizingFunction.GetOutput()
surfaceToMesh.Execute()
self.PrintLog("Generating volume mesh")
tetgen = vmtkscripts.vmtkTetGen()
tetgen.Mesh = surfaceToMesh.Mesh
tetgen.GenerateCaps = 0
tetgen.UseSizingFunction = 1
tetgen.SizingFunctionArrayName = self.SizingFunctionArrayName
tetgen.CellEntityIdsArrayName = self.CellEntityIdsArrayName
tetgen.Order = 1
tetgen.Quality = 1
tetgen.PLC = 1
tetgen.NoBoundarySplit = 1
tetgen.RemoveSliver = 1
tetgen.OutputSurfaceElements = 1
tetgen.OutputVolumeElements = 1
tetgen.Execute()
self.Mesh = tetgen.Mesh
if self.Mesh.GetNumberOfCells(
) == 0 and surfaceToMesh.Mesh.GetNumberOfCells() > 0:
self.PrintLog(
'An error occurred during tetrahedralization. Will only output surface mesh.'
)
self.Mesh = surfaceToMesh.Mesh
if self.Tetrahedralize:
tetrahedralize = vtkvmtk.vtkvmtkUnstructuredGridTetraFilter()
tetrahedralize.SetInputData(self.Mesh)
tetrahedralize.Update()
self.Mesh = tetrahedralize.GetOutput()
self.RemeshedSurface = remeshedSurface