def Execute(self):
if self.Surface == None:
self.PrintError('Error: No input surface.')
smoothingFilter = None
if self.Method is 'taubin':
smoothingFilter = vtk.vtkWindowedSincPolyDataFilter()
smoothingFilter.SetInput(self.Surface)
smoothingFilter.SetNumberOfIterations(self.NumberOfIterations)
smoothingFilter.SetPassBand(self.PassBand)
smoothingFilter.SetBoundarySmoothing(self.BoundarySmoothing)
## smoothingFilter.NormalizeCoordinatesOn()
smoothingFilter.Update()
elif self.Method is 'laplace':
smoothingFilter = vtk.vtkSmoothPolyDataFilter()
smoothingFilter.SetInput(self.Surface)
smoothingFilter.SetNumberOfIterations(self.NumberOfIterations)
smoothingFilter.SetRelaxationFactor(self.RelaxationFactor)
smoothingFilter.Update()
else:
self.PrintError('Error: smoothing method not supported.')
self.Surface = smoothingFilter.GetOutput()
normals = vmtkscripts.vmtkSurfaceNormals()
normals.Surface = self.Surface
normals.Execute()
self.Surface = normals.Surface
if self.Surface.GetSource():
self.Surface.GetSource().UnRegisterAllOutputs()
def Execute(self):
if self.Surface == None:
self.PrintError('Error: no Surface.')
triangleFilter = vtk.vtkTriangleFilter()
triangleFilter.SetInput(self.Surface)
triangleFilter.Update()
self.Surface = triangleFilter.GetOutput()
if self.Loop == None:
self.PrintError('Error: no Loop.')
select = vtk.vtkImplicitSelectionLoop()
select.SetLoop(self.Loop.GetPoints())
normal = [0.0,0.0,0.0]
centroid = [0.0,0.0,0.0]
vtk.vtkPolygon().ComputeNormal(self.Loop.GetPoints(),normal)
#compute centroid and check normals
p = [0.0,0.0,0.0]
for i in range (self.Loop.GetNumberOfPoints()):
p = self.Loop.GetPoint(i)
centroid[0] += p[0]
centroid[1] += p[1]
centroid[2] += p[2]
centroid[0] = centroid[0] / self.Loop.GetNumberOfPoints()
centroid[1] = centroid[1] / self.Loop.GetNumberOfPoints()
centroid[2] = centroid[2] / self.Loop.GetNumberOfPoints()
print "loop centroid", centroid
locator = vtk.vtkPointLocator()
locator.SetDataSet(self.Surface)
locator.AutomaticOn()
locator.BuildLocator()
idsurface = locator.FindClosestPoint(centroid)
if (self.Surface.GetPointData().GetNormals() == None):
normalsFilter = vmtkscripts.vmtkSurfaceNormals()
normalsFilter.Surface = self.Surface
normalsFilter.NormalsArrayName = 'Normals'
normalsFilter.Execute()
self.Surface = normalsFilter.Surface
normalsurface = [0.0,0.0,0.0]
self.Surface.GetPointData().GetNormals().GetTuple(idsurface,normalsurface)
print "loop normal: ", normal
print "surface normal inside the loop: ", normalsurface
check = vtk.vtkMath.Dot(normalsurface,normal)
if check < 0:
normal[0] = - normal[0]
normal[1] = - normal[1]
normal[2] = - normal[2]
#compute plane
proj = float(vtk.vtkMath.Dot(self.Loop.GetPoint(0),normal))
point = [0.0,0.0,0.0]
self.Loop.GetPoint(0,point)
for i in range (self.Loop.GetNumberOfPoints()):
tmp = vtk.vtkMath.Dot(self.Loop.GetPoint(i),normal)
if tmp < proj:
proj = tmp
self.Loop.GetPoint(i,point)
origin = [0.0,0.0,0.0]
origin[0] = point[0] #- normal[0]
origin[1] = point[1] #- normal[1]
origin[2] = point[2] #- normal[2]
plane=vtk.vtkPlane()
plane.SetNormal(normal[0],normal[1],normal[2])
plane.SetOrigin(origin[0],origin[1],origin[2])
#set bool
Bool = vtk.vtkImplicitBoolean()
Bool.SetOperationTypeToDifference()
Bool.AddFunction(select)
Bool.AddFunction(plane)
clipper=vtk.vtkClipPolyData()
clipper.SetInput(self.Surface)
clipper.SetClipFunction(Bool)
clipper.GenerateClippedOutputOn()
clipper.InsideOutOff()
clipper.Update()
self.Surface = clipper.GetOutput()
def Execute(self):
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.')
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):
if self.Surface == None:
self.PrintError('Error: No input surface.')
wallEntityOffset = 1
if self.SkipCapping:
self.PrintLog("Not capping surface")
surface = self.Surface
else:
self.PrintLog("Capping surface")
capper = vmtkscripts.vmtkSurfaceCapper()
capper.Surface = self.Surface
capper.Interactive = 0
capper.Method = self.CappingMethod
capper.TriangleOutput = 0
capper.CellEntityIdOffset = 1
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.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")
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.SubLayerRatio = 0.5
boundaryLayer.Thickness = self.BoundaryLayerThicknessFactor * self.TargetEdgeLength
boundaryLayer.ThicknessRatio = self.BoundaryLayerThicknessFactor * self.TargetEdgeLengthFactor
boundaryLayer.MaximumThickness = self.BoundaryLayerThicknessFactor * self.MaxEdgeLength
boundaryLayer.Execute()
cellEntityIdsArray = vtk.vtkIntArray()
cellEntityIdsArray.SetName(self.CellEntityIdsArrayName)
cellEntityIdsArray.SetNumberOfTuples(
boundaryLayer.Mesh.GetNumberOfCells())
cellEntityIdsArray.FillComponent(0, 0.0)
boundaryLayer.Mesh.GetCellData().AddArray(cellEntityIdsArray)
innerCellEntityIdsArray = vtk.vtkIntArray()
innerCellEntityIdsArray.SetName(self.CellEntityIdsArrayName)
innerCellEntityIdsArray.SetNumberOfTuples(
boundaryLayer.InnerSurfaceMesh.GetNumberOfCells())
innerCellEntityIdsArray.FillComponent(0, 0.0)
boundaryLayer.InnerSurfaceMesh.GetCellData().AddArray(
cellEntityIdsArray)
meshToSurface = vmtkscripts.vmtkMeshToSurface()
meshToSurface.Mesh = boundaryLayer.InnerSurfaceMesh
meshToSurface.Execute()
self.PrintLog("Computing sizing function")
sizingFunction = vtkvmtk.vtkvmtkPolyDataSizingFunction()
sizingFunction.SetInput(meshToSurface.Surface)
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()
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.'
)
appendFilter = vtkvmtk.vtkvmtkAppendFilter()
appendFilter.AddInput(surfaceToMesh.Mesh)
appendFilter.AddInput(boundaryLayer.Mesh)
appendFilter.AddInput(tetgen.Mesh)
appendFilter.Update()
self.Mesh = appendFilter.GetOutput()
else:
self.PrintLog("Computing sizing function")
sizingFunction = vtkvmtk.vtkvmtkPolyDataSizingFunction()
sizingFunction.SetInput(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 = vtk.vtkDataSetTriangleFilter()
tetrahedralize.SetInput(self.Mesh)
tetrahedralize.Update()
self.Mesh = tetrahedralize.GetOutput()
self.RemeshedSurface = remeshedSurface
def Execute(self):
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.'
)
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):
if self.Surface == None:
self.PrintError('Error: No input surface.')
self.PrintLog("Capping surface")
capper = vmtkscripts.vmtkSurfaceCapper()
capper.Surface = self.Surface
capper.Interactive = 0
capper.Method = 'simple'
capper.TriangleOutput = 0
capper.CellEntityIdOffset = 1
capper.Execute()
self.PrintLog("Remeshing surface")
remeshing = vmtkscripts.vmtkSurfaceRemeshing()
remeshing.Surface = capper.Surface
remeshing.CellEntityIdsArrayName = capper.CellEntityIdsArrayName
remeshing.TargetEdgeLength = self.TargetEdgeLength
remeshing.MaxEdgeLength = self.MaxEdgeLength
remeshing.MinEdgeLength = self.MinEdgeLength
remeshing.TargetEdgeLengthFactor = self.TargetEdgeLengthFactor
remeshing.TargetEdgeLengthArrayName = self.TargetEdgeLengthArrayName
remeshing.ElementSizeMode = self.ElementSizeMode
remeshing.Execute()
if self.BoundaryLayer:
projection = vmtkscripts.vmtkSurfaceProjection()
projection.Surface = remeshing.Surface
projection.ReferenceSurface = capper.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")
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.SubLayerRatio = 0.5
boundaryLayer.Thickness = self.BoundaryLayerThicknessFactor * self.TargetEdgeLength
boundaryLayer.ThicknessRatio = self.BoundaryLayerThicknessFactor * self.TargetEdgeLengthFactor
boundaryLayer.MaximumThickness = self.BoundaryLayerThicknessFactor * self.MaxEdgeLength
boundaryLayer.Execute()
cellEntityIdsArray = vtk.vtkIntArray()
cellEntityIdsArray.SetName(self.CellEntityIdsArrayName)
cellEntityIdsArray.SetNumberOfTuples(boundaryLayer.Mesh.GetNumberOfCells())
cellEntityIdsArray.FillComponent(0,0.0)
boundaryLayer.Mesh.GetCellData().AddArray(cellEntityIdsArray)
innerCellEntityIdsArray = vtk.vtkIntArray()
innerCellEntityIdsArray.SetName(self.CellEntityIdsArrayName)
innerCellEntityIdsArray.SetNumberOfTuples(boundaryLayer.InnerSurfaceMesh.GetNumberOfCells())
innerCellEntityIdsArray.FillComponent(0,0.0)
boundaryLayer.InnerSurfaceMesh.GetCellData().AddArray(cellEntityIdsArray)
meshToSurface = vmtkscripts.vmtkMeshToSurface()
meshToSurface.Mesh = boundaryLayer.InnerSurfaceMesh
meshToSurface.Execute()
self.PrintLog("Computing sizing function")
sizingFunction = vtkvmtk.vtkvmtkPolyDataSizingFunction()
sizingFunction.SetInput(meshToSurface.Surface)
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()
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.')
appendFilter = vtkvmtk.vtkvmtkAppendFilter()
appendFilter.AddInput(surfaceToMesh.Mesh)
appendFilter.AddInput(boundaryLayer.Mesh)
appendFilter.AddInput(tetgen.Mesh)
appendFilter.Update()
self.Mesh = appendFilter.GetOutput()
else:
self.PrintLog("Computing sizing function")
sizingFunction = vtkvmtk.vtkvmtkPolyDataSizingFunction()
sizingFunction.SetInput(remeshing.Surface)
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 = vtk.vtkDataSetTriangleFilter()
tetrahedralize.SetInput(self.Mesh)
tetrahedralize.Update()
self.Mesh = tetrahedralize.GetOutput()
def Execute(self):
if self.Surface == None:
self.PrintError('Error: no Surface.')
triangleFilter = vtk.vtkTriangleFilter()
triangleFilter.SetInputData(self.Surface)
triangleFilter.Update()
self.Surface = triangleFilter.GetOutput()
if self.Loop == None:
self.PrintError('Error: no Loop.')
select = vtk.vtkImplicitSelectionLoop()
select.SetLoop(self.Loop.GetPoints())
normal = [0.0, 0.0, 0.0]
centroid = [0.0, 0.0, 0.0]
vtk.vtkPolygon().ComputeNormal(self.Loop.GetPoints(), normal)
#compute centroid and check normals
p = [0.0, 0.0, 0.0]
for i in range(self.Loop.GetNumberOfPoints()):
p = self.Loop.GetPoint(i)
centroid[0] += p[0]
centroid[1] += p[1]
centroid[2] += p[2]
centroid[0] = centroid[0] / self.Loop.GetNumberOfPoints()
centroid[1] = centroid[1] / self.Loop.GetNumberOfPoints()
centroid[2] = centroid[2] / self.Loop.GetNumberOfPoints()
print "loop centroid", centroid
locator = vtk.vtkPointLocator()
locator.SetDataSet(self.Surface)
locator.AutomaticOn()
locator.BuildLocator()
idsurface = locator.FindClosestPoint(centroid)
if (self.Surface.GetPointData().GetNormals() == None):
normalsFilter = vmtkscripts.vmtkSurfaceNormals()
normalsFilter.Surface = self.Surface
normalsFilter.NormalsArrayName = 'Normals'
normalsFilter.Execute()
self.Surface = normalsFilter.Surface
normalsurface = [0.0, 0.0, 0.0]
self.Surface.GetPointData().GetNormals().GetTuple(
idsurface, normalsurface)
print "loop normal: ", normal
print "surface normal inside the loop: ", normalsurface
check = vtk.vtkMath.Dot(normalsurface, normal)
if check < 0:
normal[0] = -normal[0]
normal[1] = -normal[1]
normal[2] = -normal[2]
#compute plane
proj = float(vtk.vtkMath.Dot(self.Loop.GetPoint(0), normal))
point = [0.0, 0.0, 0.0]
self.Loop.GetPoint(0, point)
for i in range(self.Loop.GetNumberOfPoints()):
tmp = vtk.vtkMath.Dot(self.Loop.GetPoint(i), normal)
if tmp < proj:
proj = tmp
self.Loop.GetPoint(i, point)
origin = [0.0, 0.0, 0.0]
origin[0] = point[0] #- normal[0]
origin[1] = point[1] #- normal[1]
origin[2] = point[2] #- normal[2]
plane = vtk.vtkPlane()
plane.SetNormal(normal[0], normal[1], normal[2])
plane.SetOrigin(origin[0], origin[1], origin[2])
#set bool
Bool = vtk.vtkImplicitBoolean()
Bool.SetOperationTypeToDifference()
Bool.AddFunction(select)
Bool.AddFunction(plane)
clipper = vtk.vtkClipPolyData()
clipper.SetInputData(self.Surface)
clipper.SetClipFunction(Bool)
clipper.GenerateClippedOutputOn()
clipper.InsideOutOff()
clipper.Update()
self.Surface = clipper.GetOutput()