def Execute(self):
if self.Mesh1 == None:
self.PrintError('Error: No Mesh1.')
if self.Mesh2 == None:
self.PrintError('Error: No Mesh2.')
def addIds(mesh, offset):
if offset != 0:
cellids = mesh.GetCellData().GetScalars(
self.CellEntityIdsArrayName)
for i in range(cellids.GetNumberOfTuples()):
cellids.SetValue(i, cellids.GetValue(i) + offset)
addIds(self.Mesh1, self.CellEntityIdOffset1)
addIds(self.Mesh2, self.CellEntityIdOffset2)
if self.Mesh3 != None:
addIds(self.Mesh3, self.CellEntityIdOffset3)
merger = vtkvmtk.vtkvmtkAppendFilter()
merger.AddInput(self.Mesh1)
merger.AddInput(self.Mesh2)
if self.Mesh3 != None:
merger.AddInput(self.Mesh3)
merger.SetMergeDuplicatePoints(1)
merger.Update()
self.Mesh = merger.GetOutput()
def Execute(self):
if self.Mesh1 == None:
self.PrintError("Error: No Mesh1.")
if self.Mesh2 == None:
self.PrintError("Error: No Mesh2.")
def addIds(mesh, offset):
if offset != 0:
cellids = mesh.GetCellData().GetScalars(self.CellEntityIdsArrayName)
for i in range(cellids.GetNumberOfTuples()):
cellids.SetValue(i, cellids.GetValue(i) + offset)
addIds(self.Mesh1, self.CellEntityIdOffset1)
addIds(self.Mesh2, self.CellEntityIdOffset2)
if self.Mesh3 != None:
addIds(self.Mesh3, self.CellEntityIdOffset3)
merger = vtkvmtk.vtkvmtkAppendFilter()
merger.AddInput(self.Mesh1)
merger.AddInput(self.Mesh2)
if self.Mesh3 != None:
merger.AddInput(self.Mesh3)
merger.SetMergeDuplicatePoints(1)
merger.Update()
self.Mesh = merger.GetOutput()
def CreateSurfaceCells(self, inMesh):
#Remove the surface cells from the mesh
cellDimFilter = vtkvmtk.vtkvmtkCellDimensionFilter()
cellDimFilter.SetInputData(inMesh)
cellDimFilter.ThresholdByUpper(3)
cellDimFilter.Update()
volumetricMesh = cellDimFilter.GetOutput()
#Get new surface cells
geomFilter = vtk.vtkGeometryFilter()
geomFilter.SetInputConnection(cellDimFilter.GetOutputPort())
geomFilter.Update()
newSurfaceCells = geomFilter.GetOutput()
#If the celEntityIdArray exist, project the original entity ids
cellEntityIdsArray = newSurfaceCells.GetCellData().GetArray(
self.CellEntityIdsArrayName)
if (cellEntityIdsArray != None):
#Convert the surface cells to poly data
surfaceCellsToSurface = vmtkscripts.vmtkMeshToSurface()
surfaceCellsToSurface.Mesh = newSurfaceCells
surfaceCellsToSurface.Execute()
#Get the original surface cells
meshThreshold = vtk.vtkThreshold()
meshThreshold.SetInputData(self.Mesh)
meshThreshold.ThresholdByUpper(self.WallCellEntityId + 0.5)
meshThreshold.SetInputArrayToProcess(0, 0, 0, 1,
self.CellEntityIdsArrayName)
meshThreshold.Update()
meshToSurface = vmtkscripts.vmtkMeshToSurface()
meshToSurface.Mesh = meshThreshold.GetOutput()
meshToSurface.Execute()
#Project the entity ids form the old surface cells to the new surface cells
#TODO: This is hackish(need for a tolerance), find a beeter way
projector = vtkvmtk.vtkvmtkSurfaceProjectCellArray()
projector.SetInputData(surfaceCellsToSurface.Surface)
projector.SetReferenceSurface(meshToSurface.Surface)
projector.SetProjectedArrayName(self.CellEntityIdsArrayName)
projector.SetDefaultValue(self.WallCellEntityId)
projector.SetDistanceTolerance(self.Tolerance)
projector.Update()
#Convert the surface cells back to unstructured grid
surfaceToMesh = vmtkscripts.vmtkSurfaceToMesh()
surfaceToMesh.Surface = projector.GetOutput()
surfaceToMesh.Execute()
newSurfaceCells = surfaceToMesh.Mesh
#append the new surface cells to the volumetric elements
appendFilter = vtkvmtk.vtkvmtkAppendFilter()
appendFilter.AddInput(volumetricMesh)
appendFilter.AddInput(newSurfaceCells)
appendFilter.Update()
return appendFilter.GetOutput()
def CreateSurfaceCells(self,inMesh):
#Remove the surface cells from the mesh
cellDimFilter = vtkvmtk.vtkvmtkCellDimensionFilter()
cellDimFilter.SetInputData(inMesh)
cellDimFilter.ThresholdByUpper(3)
cellDimFilter.Update()
volumetricMesh = cellDimFilter.GetOutput()
#Get new surface cells
geomFilter = vtk.vtkGeometryFilter()
geomFilter.SetInputConnection(cellDimFilter.GetOutputPort())
geomFilter.Update()
newSurfaceCells = geomFilter.GetOutput()
#If the celEntityIdArray exist, project the original entity ids
cellEntityIdsArray = newSurfaceCells.GetCellData().GetArray(self.CellEntityIdsArrayName)
if (cellEntityIdsArray != None):
#Convert the surface cells to poly data
surfaceCellsToSurface = vmtkscripts.vmtkMeshToSurface()
surfaceCellsToSurface.Mesh = newSurfaceCells
surfaceCellsToSurface.Execute()
#Get the original surface cells
meshThreshold = vtk.vtkThreshold()
meshThreshold.SetInputData(self.Mesh)
meshThreshold.ThresholdByUpper(self.WallCellEntityId+0.5)
meshThreshold.SetInputArrayToProcess(0,0,0,1,self.CellEntityIdsArrayName)
meshThreshold.Update()
meshToSurface = vmtkscripts.vmtkMeshToSurface()
meshToSurface.Mesh = meshThreshold.GetOutput()
meshToSurface.Execute()
#Project the entity ids form the old surface cells to the new surface cells
#TODO: This is hackish(need for a tolerance), find a beeter way
projector = vtkvmtk.vtkvmtkSurfaceProjectCellArray()
projector.SetInputData(surfaceCellsToSurface.Surface)
projector.SetReferenceSurface(meshToSurface.Surface)
projector.SetProjectedArrayName(self.CellEntityIdsArrayName)
projector.SetDefaultValue(self.WallCellEntityId)
projector.SetDistanceTolerance(self.Tolerance)
projector.Update()
#Convert the surface cells back to unstructured grid
surfaceToMesh = vmtkscripts.vmtkSurfaceToMesh()
surfaceToMesh.Surface = projector.GetOutput()
surfaceToMesh.Execute()
newSurfaceCells = surfaceToMesh.Mesh
#append the new surface cells to the volumetric elements
appendFilter = vtkvmtk.vtkvmtkAppendFilter()
appendFilter.AddInput(volumetricMesh)
appendFilter.AddInput(newSurfaceCells)
appendFilter.Update()
return appendFilter.GetOutput()
def Execute(self):
data = [(getattr(self, 'Mesh%d'%i), getattr(self, 'CellEntityIdOffset%d'%i))
for i in range(1,self.max_meshes+1)]
n = sum(0 if d[0] is None else 1 for d in data)
if n < 2:
self.PrintError('Error: Need at least 2 meshes to merge.')
def addIds(mesh, offset):
if mesh is not None and offset != 0:
cellids = mesh.GetCellData().GetScalars(self.CellEntityIdsArrayName)
for i in range(cellids.GetNumberOfTuples()):
cellids.SetValue(i, cellids.GetValue(i) + offset)
merger = vtkvmtk.vtkvmtkAppendFilter()
for mesh, offsets in data:
addIds(mesh, offsets)
if mesh != None:
merger.AddInput(mesh)
merger.SetMergeDuplicatePoints(1)
merger.Update()
self.Mesh = merger.GetOutput()
def Execute(self):
if self.Mesh == None:
self.PrintError('Error: No input mesh.')
if not self.CellEntityIdsArrayName:
self.PrintError('Error: No input CellEntityIdsArrayName.')
return
cellEntityIdsArray = self.Mesh.GetCellData().GetArray(self.CellEntityIdsArrayName)
#cut off the volumetric elements
wallThreshold = vtk.vtkThreshold()
wallThreshold.SetInputData(self.Mesh)
wallThreshold.ThresholdByUpper(self.SurfaceCellEntityId-0.5)
wallThreshold.SetInputArrayToProcess(0,0,0,1,self.CellEntityIdsArrayName)
wallThreshold.Update()
meshToSurface = vmtkscripts.vmtkMeshToSurface()
meshToSurface.Mesh = wallThreshold.GetOutput()
meshToSurface.Execute()
#Compute the normals for this surface, orientation should be right because the surface is closed
#TODO: Add option for cell normals in vmtksurfacenormals
normalsFilter = vtk.vtkPolyDataNormals()
normalsFilter.SetInputData(meshToSurface.Surface)
normalsFilter.SetAutoOrientNormals(1)
normalsFilter.SetFlipNormals(0)
normalsFilter.SetConsistency(1)
normalsFilter.SplittingOff()
normalsFilter.ComputePointNormalsOff()
normalsFilter.ComputeCellNormalsOn()
normalsFilter.Update()
surfaceToMesh = vmtkscripts.vmtkSurfaceToMesh()
surfaceToMesh.Surface = normalsFilter.GetOutput()
surfaceToMesh.Execute()
#Save the current normals
wallWithBoundariesMesh = surfaceToMesh.Mesh
savedNormals = vtk.vtkDoubleArray()
savedNormals.DeepCopy(wallWithBoundariesMesh.GetCellData().GetNormals())
savedNormals.SetName('SavedNormals')
wallWithBoundariesMesh.GetCellData().AddArray(savedNormals)
#cut off the boundaries and other surfaces
extrudeThresholdLower = vtk.vtkThreshold()
extrudeThresholdLower.SetInputData(wallWithBoundariesMesh)
extrudeThresholdLower.ThresholdByLower(self.ExtrudeCellEntityId+0.5)
extrudeThresholdLower.SetInputArrayToProcess(0,0,0,1,self.CellEntityIdsArrayName)
extrudeThresholdLower.Update()
extrudeThresholdUpper = vtk.vtkThreshold()
extrudeThresholdUpper.SetInputConnection(extrudeThresholdLower.GetOutputPort())
extrudeThresholdUpper.ThresholdByUpper(self.ExtrudeCellEntityId-0.5)
extrudeThresholdUpper.SetInputArrayToProcess(0,0,0,1,self.CellEntityIdsArrayName)
extrudeThresholdUpper.Update()
meshToSurface = vmtkscripts.vmtkMeshToSurface()
meshToSurface.Mesh = extrudeThresholdUpper.GetOutput()
meshToSurface.Execute()
#Compute cell normals without boundaries
normalsFilter = vtk.vtkPolyDataNormals()
normalsFilter.SetInputData(meshToSurface.Surface)
normalsFilter.SetAutoOrientNormals(1)
normalsFilter.SetFlipNormals(0)
normalsFilter.SetConsistency(1)
normalsFilter.SplittingOff()
normalsFilter.ComputePointNormalsOn()
normalsFilter.ComputeCellNormalsOn()
normalsFilter.Update()
wallWithoutBoundariesSurface = normalsFilter.GetOutput()
normals = wallWithoutBoundariesSurface.GetCellData().GetNormals()
savedNormals = wallWithoutBoundariesSurface.GetCellData().GetArray('SavedNormals')
math = vtk.vtkMath()
#If the normal are inverted, recompute the normals with flipping on
if normals.GetNumberOfTuples() > 0 and math.Dot(normals.GetTuple3(0),savedNormals.GetTuple3(0)) < 0:
normalsFilter = vtk.vtkPolyDataNormals()
normalsFilter.SetInputData(meshToSurface.Surface)
normalsFilter.SetAutoOrientNormals(1)
normalsFilter.SetFlipNormals(1)
normalsFilter.SetConsistency(1)
normalsFilter.SplittingOff()
normalsFilter.ComputePointNormalsOn()
normalsFilter.ComputeCellNormalsOn()
normalsFilter.Update()
wallWithoutBoundariesSurface = normalsFilter.GetOutput()
wallWithoutBoundariesSurface.GetPointData().GetNormals().SetName('Normals')
wallWithoutBoundariesSurface.GetCellData().RemoveArray('SavedNormals')
surfaceToMesh = vmtkscripts.vmtkSurfaceToMesh()
surfaceToMesh.Surface = wallWithoutBoundariesSurface
surfaceToMesh.Execute()
#Offset to apply to the array
wallOffset = 0
if self.IncludeSurfaceCells or self.IncludeOriginalSurfaceCells:
wallOffset += 1
if self.IncludeSurfaceCells or self.IncludeExtrudedSurfaceCells:
wallOffset+=1
boundaryLayer = vmtkscripts.vmtkBoundaryLayer2()
boundaryLayer.Mesh = surfaceToMesh.Mesh
boundaryLayer.WarpVectorsArrayName = 'Normals'
boundaryLayer.NegateWarpVectors = False
boundaryLayer.ThicknessArrayName = self.ThicknessArrayName
boundaryLayer.ConstantThickness = self.ConstantThickness
boundaryLayer.IncludeSurfaceCells = self.IncludeSurfaceCells
boundaryLayer.NumberOfSubLayers = self.NumberOfSubLayers
boundaryLayer.SubLayerRatio = self.SubLayerRatio
boundaryLayer.Thickness = self.Thickness
boundaryLayer.ThicknessRatio = self.Thickness
boundaryLayer.MaximumThickness = self.MaximumThickness
boundaryLayer.CellEntityIdsArrayName = self.CellEntityIdsArrayName
boundaryLayer.IncludeExtrudedOpenProfilesCells = self.IncludeExtrudedOpenProfilesCells
boundaryLayer.IncludeExtrudedSurfaceCells = self.IncludeExtrudedSurfaceCells
boundaryLayer.IncludeOriginalSurfaceCells = self.IncludeOriginalSurfaceCells
boundaryLayer.LayerEntityId = self.SurfaceCellEntityId
boundaryLayer.SurfaceEntityId = self.InletOutletCellEntityId + 1
if cellEntityIdsArray != None:
#Append the new surface ids
idRange = cellEntityIdsArray.GetRange()
boundaryLayer.OpenProfilesEntityId = idRange[1] + wallOffset + 2
boundaryLayer.Execute()
if cellEntityIdsArray != None:
#offset the previous cellentityids to make room for the new ones
arrayCalculator = vtk.vtkArrayCalculator()
arrayCalculator.SetInputData(self.Mesh)
if vtk.vtkVersion.GetVTKMajorVersion()>=9 or (vtk.vtkVersion.GetVTKMajorVersion()>=8 and vtk.vtkVersion.GetVTKMinorVersion()>=1):
arrayCalculator.SetAttributeTypeToCellData()
else:
arrayCalculator.SetAttributeModeToUseCellData()
arrayCalculator.AddScalarVariable("entityid",self.CellEntityIdsArrayName,0)
arrayCalculator.SetFunction("if( entityid > " + str(self.InletOutletCellEntityId-1) +", entityid + " + str(wallOffset) + ", entityid)")
arrayCalculator.SetResultArrayName('CalculatorResult')
arrayCalculator.Update()
#This need to be copied in order to be of the right type (int)
cellEntityIdsArray.DeepCopy(arrayCalculator.GetOutput().GetCellData().GetArray('CalculatorResult'))
arrayCalculator.SetFunction("if( entityid > " + str(self.SurfaceCellEntityId-1) +", entityid + 1, entityid)")
arrayCalculator.Update()
##This need to be copied in order to be of the right type (int)
cellEntityIdsArray.DeepCopy(arrayCalculator.GetOutput().GetCellData().GetArray('CalculatorResult'))
appendFilter = vtkvmtk.vtkvmtkAppendFilter()
appendFilter.AddInput(self.Mesh)
appendFilter.AddInput(boundaryLayer.Mesh)
appendFilter.Update()
self.Mesh = appendFilter.GetOutput()
def Execute(self):
if self.Mesh == None:
self.PrintError('Error: No input mesh.')
if not self.CellEntityIdsArrayName:
self.PrintError('Error: No input CellEntityIdsArrayName.')
return
cellEntityIdsArray = self.Mesh.GetCellData().GetArray(self.CellEntityIdsArrayName)
#cut off the volumetric elements
wallThreshold = vtk.vtkThreshold()
wallThreshold.SetInputData(self.Mesh)
wallThreshold.ThresholdByUpper(self.SurfaceCellEntityId-0.5)
wallThreshold.SetInputArrayToProcess(0,0,0,1,self.CellEntityIdsArrayName)
wallThreshold.Update()
meshToSurface = vmtkscripts.vmtkMeshToSurface()
meshToSurface.Mesh = wallThreshold.GetOutput()
meshToSurface.Execute()
#Compute the normals for this surface, orientation should be right because the surface is closed
#TODO: Add option for cell normals in vmtksurfacenormals
normalsFilter = vtk.vtkPolyDataNormals()
normalsFilter.SetInputData(meshToSurface.Surface)
normalsFilter.SetAutoOrientNormals(1)
normalsFilter.SetFlipNormals(0)
normalsFilter.SetConsistency(1)
normalsFilter.SplittingOff()
normalsFilter.ComputePointNormalsOff()
normalsFilter.ComputeCellNormalsOn()
normalsFilter.Update()
surfaceToMesh = vmtkscripts.vmtkSurfaceToMesh()
surfaceToMesh.Surface = normalsFilter.GetOutput()
surfaceToMesh.Execute()
#Save the current normals
wallWithBoundariesMesh = surfaceToMesh.Mesh
savedNormals = vtk.vtkDoubleArray()
savedNormals.DeepCopy(wallWithBoundariesMesh.GetCellData().GetNormals())
savedNormals.SetName('SavedNormals')
wallWithBoundariesMesh.GetCellData().AddArray(savedNormals)
#cut off the boundaries and other surfaces
extrudeThresholdLower = vtk.vtkThreshold()
extrudeThresholdLower.SetInputData(wallWithBoundariesMesh)
extrudeThresholdLower.ThresholdByLower(self.ExtrudeCellEntityId+0.5)
extrudeThresholdLower.SetInputArrayToProcess(0,0,0,1,self.CellEntityIdsArrayName)
extrudeThresholdLower.Update()
extrudeThresholdUpper = vtk.vtkThreshold()
extrudeThresholdUpper.SetInputConnection(extrudeThresholdLower.GetOutputPort())
extrudeThresholdUpper.ThresholdByUpper(self.ExtrudeCellEntityId-0.5)
extrudeThresholdUpper.SetInputArrayToProcess(0,0,0,1,self.CellEntityIdsArrayName)
extrudeThresholdUpper.Update()
meshToSurface = vmtkscripts.vmtkMeshToSurface()
meshToSurface.Mesh = extrudeThresholdUpper.GetOutput()
meshToSurface.Execute()
#Compute cell normals without boundaries
normalsFilter = vtk.vtkPolyDataNormals()
normalsFilter.SetInputData(meshToSurface.Surface)
normalsFilter.SetAutoOrientNormals(1)
normalsFilter.SetFlipNormals(0)
normalsFilter.SetConsistency(1)
normalsFilter.SplittingOff()
normalsFilter.ComputePointNormalsOn()
normalsFilter.ComputeCellNormalsOn()
normalsFilter.Update()
wallWithoutBoundariesSurface = normalsFilter.GetOutput()
normals = wallWithoutBoundariesSurface.GetCellData().GetNormals()
savedNormals = wallWithoutBoundariesSurface.GetCellData().GetArray('SavedNormals')
math = vtk.vtkMath()
#If the normal are inverted, recompute the normals with flipping on
if normals.GetNumberOfTuples() > 0 and math.Dot(normals.GetTuple3(0),savedNormals.GetTuple3(0)) < 0:
normalsFilter = vtk.vtkPolyDataNormals()
normalsFilter.SetInputData(meshToSurface.Surface)
normalsFilter.SetAutoOrientNormals(1)
normalsFilter.SetFlipNormals(1)
normalsFilter.SetConsistency(1)
normalsFilter.SplittingOff()
normalsFilter.ComputePointNormalsOn()
normalsFilter.ComputeCellNormalsOn()
normalsFilter.Update()
wallWithoutBoundariesSurface = normalsFilter.GetOutput()
wallWithoutBoundariesSurface.GetPointData().GetNormals().SetName('Normals')
wallWithoutBoundariesSurface.GetCellData().RemoveArray('SavedNormals')
surfaceToMesh = vmtkscripts.vmtkSurfaceToMesh()
surfaceToMesh.Surface = wallWithoutBoundariesSurface
surfaceToMesh.Execute()
#Offset to apply to the array
wallOffset = 0
if self.IncludeSurfaceCells or self.IncludeOriginalSurfaceCells:
wallOffset += 1
if self.IncludeSurfaceCells or self.IncludeExtrudedSurfaceCells:
wallOffset+=1
boundaryLayer = vmtkscripts.vmtkBoundaryLayer2()
boundaryLayer.Mesh = surfaceToMesh.Mesh
boundaryLayer.WarpVectorsArrayName = 'Normals'
boundaryLayer.NegateWarpVectors = False
boundaryLayer.ThicknessArrayName = self.ThicknessArrayName
boundaryLayer.ConstantThickness = self.ConstantThickness
boundaryLayer.IncludeSurfaceCells = self.IncludeSurfaceCells
boundaryLayer.NumberOfSubLayers = self.NumberOfSubLayers
boundaryLayer.SubLayerRatio = self.SubLayerRatio
boundaryLayer.Thickness = self.Thickness
boundaryLayer.ThicknessRatio = self.Thickness
boundaryLayer.MaximumThickness = self.MaximumThickness
boundaryLayer.CellEntityIdsArrayName = self.CellEntityIdsArrayName
boundaryLayer.IncludeExtrudedOpenProfilesCells = self.IncludeExtrudedOpenProfilesCells
boundaryLayer.IncludeExtrudedSurfaceCells = self.IncludeExtrudedSurfaceCells
boundaryLayer.IncludeOriginalSurfaceCells = self.IncludeOriginalSurfaceCells
boundaryLayer.LayerEntityId = self.SurfaceCellEntityId
boundaryLayer.SurfaceEntityId = self.InletOutletCellEntityId + 1
if cellEntityIdsArray != None:
#Append the new surface ids
idRange = cellEntityIdsArray.GetRange()
boundaryLayer.OpenProfilesEntityId = idRange[1] + wallOffset + 2
boundaryLayer.Execute()
if cellEntityIdsArray != None:
#offset the previous cellentityids to make room for the new ones
arrayCalculator = vtk.vtkArrayCalculator()
arrayCalculator.SetInputData(self.Mesh)
if vtk.vtkVersion.GetVTKMajorVersion()>=9 or (vtk.vtkVersion.GetVTKMajorVersion()>=8 and vtk.vtkVersion.GetVTKMinorVersion()>=1):
arrayCalculator.SetAttributeTypeToCellData()
else:
arrayCalculator.SetAttributeModeToUseCellData()
arrayCalculator.AddScalarVariable("entityid",self.CellEntityIdsArrayName,0)
arrayCalculator.SetFunction("if( entityid > " + str(self.InletOutletCellEntityId-1) +", entityid + " + str(wallOffset) + ", entityid)")
arrayCalculator.SetResultArrayName('CalculatorResult')
arrayCalculator.Update()
#This need to be copied in order to be of the right type (int)
cellEntityIdsArray.DeepCopy(arrayCalculator.GetOutput().GetCellData().GetArray('CalculatorResult'))
arrayCalculator.SetFunction("if( entityid > " + str(self.SurfaceCellEntityId-1) +", entityid + 1, entityid)")
arrayCalculator.Update()
##This need to be copied in order to be of the right type (int)
cellEntityIdsArray.DeepCopy(arrayCalculator.GetOutput().GetCellData().GetArray('CalculatorResult'))
appendFilter = vtkvmtk.vtkvmtkAppendFilter()
appendFilter.AddInput(self.Mesh)
appendFilter.AddInput(boundaryLayer.Mesh)
appendFilter.Update()
self.Mesh = appendFilter.GetOutput()
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