Beispiel #1
0
    def CreateSurfaceCells(self, inMesh):
        #Remove the surface cells from the mesh
        cellDimFilter = vtkvmtkcontrib.vtkvmtkCellDimensionFilter()
        cellDimFilter.SetInput(inMesh)
        cellDimFilter.ThresholdByUpper(3)
        cellDimFilter.Update()
        volumetricMesh = cellDimFilter.GetOutput()

        #Get new surface cells
        geomFilter = vtk.vtkGeometryFilter()
        geomFilter.SetInput(cellDimFilter.GetOutput())
        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.SetInput(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 = vtkvmtkcontrib.vtkvmtkSurfaceProjectCellArray()
            projector.SetInput(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 = vtkvmtkcontrib.vtkvmtkCellDimensionFilter()
     cellDimFilter.SetInput(inMesh)
     cellDimFilter.ThresholdByUpper(3)
     cellDimFilter.Update()
     volumetricMesh = cellDimFilter.GetOutput()
     
     #Get new surface cells
     geomFilter = vtk.vtkGeometryFilter()
     geomFilter.SetInput(cellDimFilter.GetOutput())
     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.SetInput(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 = vtkvmtkcontrib.vtkvmtkSurfaceProjectCellArray()
         projector.SetInput(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()
Beispiel #3
0
    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
Beispiel #4
0
    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.'
                )

            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
Beispiel #5
0
    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
Beispiel #6
0
    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 = vmtkcontribscripts.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)
            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()

        if self.Mesh.GetSource():
            self.Mesh.GetSource().UnRegisterAllOutputs()
    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.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 = vmtkcontribscripts.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)
            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()

        if self.Mesh.GetSource():
            self.Mesh.GetSource().UnRegisterAllOutputs()