def Execute(self): if self.Surface == None: self.PrintError('Error: No input surface.') if self.CheckNonManifold: self.PrintLog('NonManifold check.') nonManifoldChecker = vmtkNonManifoldSurfaceChecker() nonManifoldChecker.Surface = self.Surface nonManifoldChecker.PrintError = self.PrintError nonManifoldChecker.Execute() if nonManifoldChecker.NumberOfNonManifoldEdges > 0: self.PrintLog(nonManifoldChecker.Report) return self.PrintLog('Cleaning surface.') surfaceCleaner = vtk.vtkCleanPolyData() surfaceCleaner.SetInput(self.Surface) surfaceCleaner.Update() self.PrintLog('Triangulating surface.') surfaceTriangulator = vtk.vtkTriangleFilter() surfaceTriangulator.SetInput(surfaceCleaner.GetOutput()) surfaceTriangulator.PassLinesOff() surfaceTriangulator.PassVertsOff() surfaceTriangulator.Update() surfaceCapper = vtkvmtk.vtkvmtkCapPolyData() surfaceCapper.SetInput(surfaceTriangulator.GetOutput()) surfaceCapper.SetDisplacement(self.CapDisplacement) surfaceCapper.SetInPlaneDisplacement(self.CapDisplacement) surfaceCapper.Update() capCenterIds = surfaceCapper.GetCapCenterIds() surfaceNormals = vtk.vtkPolyDataNormals() surfaceNormals.SetInput(surfaceCapper.GetOutput()) surfaceNormals.SplittingOff() surfaceNormals.AutoOrientNormalsOn() surfaceNormals.SetFlipNormals(self.FlipNormals) surfaceNormals.ComputePointNormalsOn() surfaceNormals.ConsistencyOn() surfaceNormals.Update() inputSurface = surfaceNormals.GetOutput() if self.UseTetGen: self.PrintLog('Running TetGen.') import vmtkscripts surfaceToMesh = vmtkscripts.vmtkSurfaceToMesh() surfaceToMesh.Surface = inputSurface surfaceToMesh.Execute() tetgen = vmtkscripts.vmtkTetGen() tetgen.Mesh = surfaceToMesh.Mesh tetgen.PLC = 1 tetgen.NoMerge = 1 tetgen.Quality = 0 if self.TetGenDetectInter: tetgen.DetectInter = 1 tetgen.NoMerge = 0 tetgen.OutputSurfaceElements = 0 tetgen.Execute() self.DelaunayTessellation = tetgen.Mesh else: delaunayTessellator = vtk.vtkDelaunay3D() delaunayTessellator.CreateDefaultLocator() delaunayTessellator.SetInput(surfaceNormals.GetOutput()) delaunayTessellator.SetTolerance(self.DelaunayTolerance) delaunayTessellator.Update() self.DelaunayTessellation = delaunayTessellator.GetOutput() normalsArray = surfaceNormals.GetOutput().GetPointData().GetNormals() self.DelaunayTessellation.GetPointData().AddArray(normalsArray) internalTetrahedraExtractor = vtkvmtk.vtkvmtkInternalTetrahedraExtractor() internalTetrahedraExtractor.SetInput(self.DelaunayTessellation) internalTetrahedraExtractor.SetOutwardNormalsArrayName(normalsArray.GetName()) if self.RemoveSubresolutionTetrahedra: internalTetrahedraExtractor.RemoveSubresolutionTetrahedraOn() internalTetrahedraExtractor.SetSubresolutionFactor(self.SubresolutionFactor) internalTetrahedraExtractor.SetSurface(inputSurface) if capCenterIds.GetNumberOfIds() > 0: internalTetrahedraExtractor.UseCapsOn() internalTetrahedraExtractor.SetCapCenterIds(capCenterIds) internalTetrahedraExtractor.Update() self.DelaunayTessellation = internalTetrahedraExtractor.GetOutput() voronoiDiagramFilter = vtkvmtk.vtkvmtkVoronoiDiagram3D() voronoiDiagramFilter.SetInput(self.DelaunayTessellation) voronoiDiagramFilter.SetRadiusArrayName(self.RadiusArrayName) voronoiDiagramFilter.Update() self.PoleIds = voronoiDiagramFilter.GetPoleIds() self.VoronoiDiagram = voronoiDiagramFilter.GetOutput() if self.SimplifyVoronoi: voronoiDiagramSimplifier = vtkvmtk.vtkvmtkSimplifyVoronoiDiagram() voronoiDiagramSimplifier.SetInput(voronoiDiagramFilter.GetOutput()) voronoiDiagramSimplifier.SetUnremovablePointIds(voronoiDiagramFilter.GetPoleIds()) voronoiDiagramSimplifier.Update() self.VoronoiDiagram = voronoiDiagramSimplifier.GetOutput() self.Mesh = self.DelaunayTessellation self.Surface = self.VoronoiDiagram
def Execute(self): if self.Surface == None: self.PrintError('Error: No input surface.') wallEntityOffset = 1 if self.SkipCapping or not self.BoundaryLayerOnCaps: self.PrintLog("Not capping surface") surface = self.Surface cellEntityIdsArray = vtk.vtkIntArray() cellEntityIdsArray.SetName(self.CellEntityIdsArrayName) cellEntityIdsArray.SetNumberOfTuples(surface.GetNumberOfCells()) cellEntityIdsArray.FillComponent(0,0.0) surface.GetCellData().AddArray(cellEntityIdsArray) else: self.PrintLog("Capping surface") capper = vmtkscripts.vmtkSurfaceCapper() capper.Surface = self.Surface capper.Interactive = 0 capper.Method = self.CappingMethod capper.TriangleOutput = 0 capper.CellEntityIdOffset = wallEntityOffset capper.Execute() surface = capper.Surface if self.SkipRemeshing: remeshedSurface = surface else: self.PrintLog("Remeshing surface") remeshing = vmtkscripts.vmtkSurfaceRemeshing() remeshing.Surface = surface remeshing.CellEntityIdsArrayName = self.CellEntityIdsArrayName remeshing.TargetEdgeLength = self.TargetEdgeLength remeshing.MaxEdgeLength = self.MaxEdgeLength remeshing.MinEdgeLength = self.MinEdgeLength remeshing.TargetEdgeLengthFactor = self.TargetEdgeLengthFactor remeshing.TargetEdgeLengthArrayName = self.TargetEdgeLengthArrayName remeshing.TriangleSplitFactor = self.TriangleSplitFactor remeshing.ElementSizeMode = self.ElementSizeMode if self.RemeshCapsOnly: remeshing.ExcludeEntityIds = [wallEntityOffset] remeshing.Execute() remeshedSurface = remeshing.Surface if self.BoundaryLayer: projection = vmtkscripts.vmtkSurfaceProjection() projection.Surface = remeshedSurface projection.ReferenceSurface = surface projection.Execute() normals = vmtkscripts.vmtkSurfaceNormals() normals.Surface = projection.Surface normals.NormalsArrayName = 'Normals' normals.Execute() surfaceToMesh = vmtkscripts.vmtkSurfaceToMesh() surfaceToMesh.Surface = normals.Surface surfaceToMesh.Execute() self.PrintLog("Generating boundary layer") placeholderCellEntityId = 9999 boundaryLayer = vmtkscripts.vmtkBoundaryLayer() boundaryLayer.Mesh = surfaceToMesh.Mesh boundaryLayer.WarpVectorsArrayName = 'Normals' boundaryLayer.NegateWarpVectors = True boundaryLayer.ThicknessArrayName = self.TargetEdgeLengthArrayName if self.ElementSizeMode == 'edgelength': boundaryLayer.ConstantThickness = True else: boundaryLayer.ConstantThickness = False boundaryLayer.IncludeSurfaceCells = 0 boundaryLayer.NumberOfSubLayers = self.NumberOfSubLayers boundaryLayer.NumberOfSubsteps = self.NumberOfSubsteps boundaryLayer.Relaxation = self.Relaxation boundaryLayer.LocalCorrectionFactor = self.LocalCorrectionFactor boundaryLayer.SubLayerRatio = self.SubLayerRatio boundaryLayer.Thickness = self.BoundaryLayerThicknessFactor * self.TargetEdgeLength boundaryLayer.ThicknessRatio = self.BoundaryLayerThicknessFactor * self.TargetEdgeLengthFactor boundaryLayer.MaximumThickness = self.BoundaryLayerThicknessFactor * self.MaxEdgeLength if not self.BoundaryLayerOnCaps: boundaryLayer.SidewallCellEntityId = placeholderCellEntityId boundaryLayer.InnerSurfaceCellEntityId = wallEntityOffset boundaryLayer.Execute() meshToSurface = vmtkscripts.vmtkMeshToSurface() meshToSurface.Mesh = boundaryLayer.InnerSurfaceMesh meshToSurface.Execute() innerSurface = meshToSurface.Surface if not self.BoundaryLayerOnCaps: self.PrintLog("Capping inner surface") capper = vmtkscripts.vmtkSurfaceCapper() capper.Surface = innerSurface capper.Interactive = 0 capper.Method = self.CappingMethod capper.TriangleOutput = 1 capper.CellEntityIdOffset = wallEntityOffset capper.Execute() self.PrintLog("Remeshing endcaps") remeshing = vmtkscripts.vmtkSurfaceRemeshing() remeshing.Surface = capper.Surface remeshing.CellEntityIdsArrayName = self.CellEntityIdsArrayName remeshing.TargetEdgeLength = self.TargetEdgeLength * self.EndcapsEdgeLengthFactor remeshing.MaxEdgeLength = self.MaxEdgeLength remeshing.MinEdgeLength = self.MinEdgeLength remeshing.TargetEdgeLengthFactor = self.TargetEdgeLengthFactor * self.EndcapsEdgeLengthFactor remeshing.TargetEdgeLengthArrayName = self.TargetEdgeLengthArrayName remeshing.TriangleSplitFactor = self.TriangleSplitFactor remeshing.ElementSizeMode = self.ElementSizeMode remeshing.ExcludeEntityIds = [wallEntityOffset] remeshing.Execute() innerSurface = remeshing.Surface self.PrintLog("Computing sizing function") sizingFunction = vtkvmtk.vtkvmtkPolyDataSizingFunction() sizingFunction.SetInputData(innerSurface) sizingFunction.SetSizingFunctionArrayName(self.SizingFunctionArrayName) sizingFunction.SetScaleFactor(self.VolumeElementScaleFactor) sizingFunction.Update() surfaceToMesh2 = vmtkscripts.vmtkSurfaceToMesh() surfaceToMesh2.Surface = sizingFunction.GetOutput() surfaceToMesh2.Execute() self.PrintLog("Generating volume mesh") tetgen = vmtkscripts.vmtkTetGen() tetgen.Mesh = surfaceToMesh2.Mesh tetgen.GenerateCaps = 0 tetgen.UseSizingFunction = 1 tetgen.SizingFunctionArrayName = self.SizingFunctionArrayName tetgen.CellEntityIdsArrayName = self.CellEntityIdsArrayName tetgen.Order = 1 tetgen.Quality = 1 tetgen.PLC = 1 tetgen.NoBoundarySplit = 1 tetgen.RemoveSliver = 1 tetgen.OutputSurfaceElements = 0 tetgen.OutputVolumeElements = 1 tetgen.Execute() #w = vtk.vtkXMLUnstructuredGridWriter() #w.SetInput(tetgen.Mesh) #w.SetFileName('tet.vtu') #w.Write() if tetgen.Mesh.GetNumberOfCells() == 0 and surfaceToMesh.Mesh.GetNumberOfCells() > 0: self.PrintLog('An error occurred during tetrahedralization. Will only output surface mesh and boundary layer.') surfaceToMesh.Mesh.GetCellData().GetArray(self.CellEntityIdsArrayName).FillComponent(0,wallEntityOffset) self.PrintLog("Assembling final mesh") appendFilter = vtkvmtk.vtkvmtkAppendFilter() appendFilter.AddInputData(surfaceToMesh.Mesh) appendFilter.AddInputData(boundaryLayer.Mesh) appendFilter.AddInputData(tetgen.Mesh) #appendFilter.AddInput(boundaryLayer.InnerSurfaceMesh) if not self.BoundaryLayerOnCaps: threshold = vtk.vtkThreshold() threshold.SetInputData(surfaceToMesh2.Mesh) threshold.ThresholdByUpper(1.5) threshold.SetInputArrayToProcess(0,0,0,1,self.CellEntityIdsArrayName) threshold.Update() endcaps = threshold.GetOutput() appendFilter.AddInputData(endcaps) appendFilter.Update() self.Mesh = appendFilter.GetOutput() if not self.BoundaryLayerOnCaps: cellEntityIdsArray = self.Mesh.GetCellData().GetArray(self.CellEntityIdsArrayName) def VisitNeighbors(i, cellEntityId): cellPointIds = vtk.vtkIdList() self.Mesh.GetCellPoints(i,cellPointIds) neighborPointIds = vtk.vtkIdList() neighborPointIds.SetNumberOfIds(1) pointNeighborCellIds = vtk.vtkIdList() neighborCellIds = vtk.vtkIdList() for j in range(cellPointIds.GetNumberOfIds()): neighborPointIds.SetId(0,cellPointIds.GetId(j)) self.Mesh.GetCellNeighbors(i,neighborPointIds,pointNeighborCellIds) for k in range(pointNeighborCellIds.GetNumberOfIds()): neighborCellIds.InsertNextId(pointNeighborCellIds.GetId(k)) for j in range(neighborCellIds.GetNumberOfIds()): cellId = neighborCellIds.GetId(j) neighborCellEntityId = cellEntityIdsArray.GetTuple1(cellId) neighborCellType = self.Mesh.GetCellType(cellId) if neighborCellType not in [vtk.VTK_TRIANGLE, vtk.VTK_QUADRATIC_TRIANGLE, vtk.VTK_QUAD]: continue if neighborCellEntityId != placeholderCellEntityId: continue cellEntityIdsArray.SetTuple1(cellId,cellEntityId) VisitNeighbors(cellId,cellEntityId) for i in range(self.Mesh.GetNumberOfCells()): cellEntityId = cellEntityIdsArray.GetTuple1(i) cellType = self.Mesh.GetCellType(i) if cellType not in [vtk.VTK_TRIANGLE, vtk.VTK_QUADRATIC_TRIANGLE, vtk.VTK_QUAD]: continue if cellEntityId in [0, 1, placeholderCellEntityId]: continue VisitNeighbors(i,cellEntityId) else: self.PrintLog("Computing sizing function") sizingFunction = vtkvmtk.vtkvmtkPolyDataSizingFunction() sizingFunction.SetInputData(remeshedSurface) sizingFunction.SetSizingFunctionArrayName(self.SizingFunctionArrayName) sizingFunction.SetScaleFactor(self.VolumeElementScaleFactor) sizingFunction.Update() self.PrintLog("Converting surface to mesh") surfaceToMesh = vmtkscripts.vmtkSurfaceToMesh() surfaceToMesh.Surface = sizingFunction.GetOutput() surfaceToMesh.Execute() self.PrintLog("Generating volume mesh") tetgen = vmtkscripts.vmtkTetGen() tetgen.Mesh = surfaceToMesh.Mesh tetgen.GenerateCaps = 0 tetgen.UseSizingFunction = 1 tetgen.SizingFunctionArrayName = self.SizingFunctionArrayName tetgen.CellEntityIdsArrayName = self.CellEntityIdsArrayName tetgen.Order = 1 tetgen.Quality = 1 tetgen.PLC = 1 tetgen.NoBoundarySplit = 1 tetgen.RemoveSliver = 1 tetgen.OutputSurfaceElements = 1 tetgen.OutputVolumeElements = 1 tetgen.Execute() self.Mesh = tetgen.Mesh if self.Mesh.GetNumberOfCells() == 0 and surfaceToMesh.Mesh.GetNumberOfCells() > 0: self.PrintLog('An error occurred during tetrahedralization. Will only output surface mesh.') self.Mesh = surfaceToMesh.Mesh if self.Tetrahedralize: tetrahedralize = vtkvmtk.vtkvmtkUnstructuredGridTetraFilter() tetrahedralize.SetInputData(self.Mesh) tetrahedralize.Update() self.Mesh = tetrahedralize.GetOutput() self.RemeshedSurface = remeshedSurface
def Execute(self): if self.Surface == None: self.PrintError('Error: No input surface.') if self.CheckNonManifold: self.PrintLog('NonManifold check.') nonManifoldChecker = vmtkNonManifoldSurfaceChecker() nonManifoldChecker.Surface = self.Surface nonManifoldChecker.PrintError = self.PrintError nonManifoldChecker.Execute() if (nonManifoldChecker.NumberOfNonManifoldEdges > 0): self.PrintLog(nonManifoldChecker.Report) return if not self.vmtkRenderer and self.SeedSelectorName in ['pickpoint','openprofiles']: self.vmtkRenderer = vmtkrenderer.vmtkRenderer() self.vmtkRenderer.Initialize() self.OwnRenderer = 1 self.PrintLog('Cleaning surface.') surfaceCleaner = vtk.vtkCleanPolyData() surfaceCleaner.SetInput(self.Surface) surfaceCleaner.Update() self.PrintLog('Triangulating surface.') surfaceTriangulator = vtk.vtkTriangleFilter() surfaceTriangulator.SetInput(surfaceCleaner.GetOutput()) surfaceTriangulator.PassLinesOff() surfaceTriangulator.PassVertsOff() surfaceTriangulator.Update() centerlineInputSurface = surfaceTriangulator.GetOutput() capCenterIds = None if (self.SeedSelectorName == 'openprofiles') | (self.SeedSelectorName == 'carotidprofiles') | (self.SeedSelectorName == 'pickpoint'): self.PrintLog('Capping surface.') surfaceCapper = vtkvmtk.vtkvmtkCapPolyData() surfaceCapper.SetInput(surfaceTriangulator.GetOutput()) surfaceCapper.SetDisplacement(self.CapDisplacement) surfaceCapper.SetInPlaneDisplacement(self.CapDisplacement) surfaceCapper.Update() centerlineInputSurface = surfaceCapper.GetOutput() capCenterIds = surfaceCapper.GetCapCenterIds() if self.SeedSelector: pass elif self.SeedSelectorName: if self.SeedSelectorName == 'pickpoint': self.SeedSelector = vmtkPickPointSeedSelector() self.SeedSelector.vmtkRenderer = self.vmtkRenderer elif self.SeedSelectorName == 'openprofiles': self.SeedSelector = vmtkOpenProfilesSeedSelector() self.SeedSelector.vmtkRenderer = self.vmtkRenderer self.SeedSelector.SetSeedIds(surfaceCapper.GetCapCenterIds()) elif self.SeedSelectorName == 'carotidprofiles': self.SeedSelector = vmtkCarotidProfilesSeedSelector() self.SeedSelector.SetSeedIds(surfaceCapper.GetCapCenterIds()) elif (self.SeedSelectorName == 'idlist'): self.SeedSelector = vmtkIdListSeedSelector() self.SeedSelector.SourceIds = self.SourceIds self.SeedSelector.TargetIds = self.TargetIds elif (self.SeedSelectorName == 'pointlist'): self.SeedSelector = vmtkPointListSeedSelector() self.SeedSelector.SourcePoints = self.SourcePoints self.SeedSelector.TargetPoints = self.TargetPoints else: self.PrintError("SeedSelectorName unknown (available: pickpoint | openprofiles | carotidprofiles | idlist | pointlist)") return else: self.PrintError('vmtkCenterlines error: either SeedSelector or SeedSelectorName must be specified') return self.SeedSelector.SetSurface(centerlineInputSurface) self.SeedSelector.InputText = self.InputText self.SeedSelector.OutputText = self.OutputText self.SeedSelector.PrintError = self.PrintError self.SeedSelector.PrintLog = self.PrintLog self.SeedSelector.Execute() inletSeedIds = self.SeedSelector.GetSourceSeedIds() outletSeedIds = self.SeedSelector.GetTargetSeedIds() self.PrintLog('Computing centerlines.') centerlineFilter = vtkvmtk.vtkvmtkPolyDataCenterlines() centerlineFilter.SetInput(centerlineInputSurface) if (self.SeedSelectorName == 'openprofiles') | (self.SeedSelectorName == 'carotidprofiles'): centerlineFilter.SetCapCenterIds(capCenterIds) centerlineFilter.SetSourceSeedIds(inletSeedIds) centerlineFilter.SetTargetSeedIds(outletSeedIds) centerlineFilter.SetRadiusArrayName(self.RadiusArrayName) centerlineFilter.SetCostFunction(self.CostFunction) centerlineFilter.SetFlipNormals(self.FlipNormals) centerlineFilter.SetAppendEndPointsToCenterlines(self.AppendEndPoints) centerlineFilter.SetSimplifyVoronoi(self.SimplifyVoronoi) if self.DelaunayTessellation != None: centerlineFilter.GenerateDelaunayTessellationOff() centerlineFilter.SetDelaunayTessellation(self.DelaunayTessellation) if self.UseTetGen==1: self.PrintLog('Running TetGen.') import vmtkscripts surfaceToMesh = vmtkscripts.vmtkSurfaceToMesh() surfaceToMesh.Surface = centerlineInputSurface surfaceToMesh.Execute() tetgen = vmtkscripts.vmtkTetGen() tetgen.Mesh = surfaceToMesh.Mesh tetgen.PLC = 1 tetgen.NoMerge = 1 tetgen.Quality = 0 if self.TetGenDetectInter == 1: tetgen.DetectInter = 1 tetgen.NoMerge = 0 tetgen.OutputSurfaceElements = 0 tetgen.Execute() centerlineFilter.GenerateDelaunayTessellationOff() centerlineFilter.SetDelaunayTessellation(tetgen.Mesh) centerlineFilter.SetCenterlineResampling(self.Resampling) centerlineFilter.SetResamplingStepLength(self.ResamplingStepLength) centerlineFilter.Update() self.Centerlines = centerlineFilter.GetOutput() self.VoronoiDiagram = centerlineFilter.GetVoronoiDiagram() self.DelaunayTessellation = centerlineFilter.GetDelaunayTessellation() self.PoleIds = centerlineFilter.GetPoleIds() self.EikonalSolutionArrayName = centerlineFilter.GetEikonalSolutionArrayName() self.EdgeArrayName = centerlineFilter.GetEdgeArrayName() self.EdgePCoordArrayName = centerlineFilter.GetEdgePCoordArrayName() self.CostFunctionArrayName = centerlineFilter.GetCostFunctionArrayName() if self.OwnRenderer: self.vmtkRenderer.Deallocate()
def Execute(self): if self.Surface == None: self.PrintError('Error: No input surface.') 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): if self.Surface == None: self.PrintError('Error: No input surface.') wallEntityOffset = 1 if self.SkipCapping: self.PrintLog("Not capping surface") surface = self.Surface else: self.PrintLog("Capping surface") capper = vmtkscripts.vmtkSurfaceCapper() capper.Surface = self.Surface capper.Interactive = 0 capper.Method = self.CappingMethod capper.TriangleOutput = 0 capper.CellEntityIdOffset = 1 capper.CellEntityIdOffset = wallEntityOffset capper.Execute() surface = capper.Surface if self.SkipRemeshing: remeshedSurface = surface else: self.PrintLog("Remeshing surface") remeshing = vmtkscripts.vmtkSurfaceRemeshing() remeshing.Surface = surface remeshing.CellEntityIdsArrayName = self.CellEntityIdsArrayName remeshing.TargetEdgeLength = self.TargetEdgeLength remeshing.MaxEdgeLength = self.MaxEdgeLength remeshing.MinEdgeLength = self.MinEdgeLength remeshing.TargetEdgeLengthFactor = self.TargetEdgeLengthFactor remeshing.TargetEdgeLengthArrayName = self.TargetEdgeLengthArrayName remeshing.ElementSizeMode = self.ElementSizeMode if self.RemeshCapsOnly: remeshing.ExcludeEntityIds = [wallEntityOffset] remeshing.Execute() remeshedSurface = remeshing.Surface if self.BoundaryLayer: projection = vmtkscripts.vmtkSurfaceProjection() projection.Surface = remeshedSurface projection.ReferenceSurface = surface projection.Execute() normals = vmtkscripts.vmtkSurfaceNormals() normals.Surface = projection.Surface normals.NormalsArrayName = 'Normals' normals.Execute() surfaceToMesh = vmtkscripts.vmtkSurfaceToMesh() surfaceToMesh.Surface = normals.Surface surfaceToMesh.Execute() self.PrintLog("Generating boundary layer") boundaryLayer = vmtkscripts.vmtkBoundaryLayer() boundaryLayer.Mesh = surfaceToMesh.Mesh boundaryLayer.WarpVectorsArrayName = 'Normals' boundaryLayer.NegateWarpVectors = True boundaryLayer.ThicknessArrayName = self.TargetEdgeLengthArrayName if self.ElementSizeMode == 'edgelength': boundaryLayer.ConstantThickness = True else: boundaryLayer.ConstantThickness = False boundaryLayer.IncludeSurfaceCells = 0 boundaryLayer.NumberOfSubLayers = self.NumberOfSubLayers boundaryLayer.SubLayerRatio = 0.5 boundaryLayer.Thickness = self.BoundaryLayerThicknessFactor * self.TargetEdgeLength boundaryLayer.ThicknessRatio = self.BoundaryLayerThicknessFactor * self.TargetEdgeLengthFactor boundaryLayer.MaximumThickness = self.BoundaryLayerThicknessFactor * self.MaxEdgeLength boundaryLayer.Execute() cellEntityIdsArray = vtk.vtkIntArray() cellEntityIdsArray.SetName(self.CellEntityIdsArrayName) cellEntityIdsArray.SetNumberOfTuples( boundaryLayer.Mesh.GetNumberOfCells()) cellEntityIdsArray.FillComponent(0, 0.0) boundaryLayer.Mesh.GetCellData().AddArray(cellEntityIdsArray) innerCellEntityIdsArray = vtk.vtkIntArray() innerCellEntityIdsArray.SetName(self.CellEntityIdsArrayName) innerCellEntityIdsArray.SetNumberOfTuples( boundaryLayer.InnerSurfaceMesh.GetNumberOfCells()) innerCellEntityIdsArray.FillComponent(0, 0.0) boundaryLayer.InnerSurfaceMesh.GetCellData().AddArray( cellEntityIdsArray) meshToSurface = vmtkscripts.vmtkMeshToSurface() meshToSurface.Mesh = boundaryLayer.InnerSurfaceMesh meshToSurface.Execute() self.PrintLog("Computing sizing function") sizingFunction = vtkvmtk.vtkvmtkPolyDataSizingFunction() sizingFunction.SetInput(meshToSurface.Surface) sizingFunction.SetSizingFunctionArrayName( self.SizingFunctionArrayName) sizingFunction.SetScaleFactor(self.VolumeElementScaleFactor) sizingFunction.Update() surfaceToMesh2 = vmtkscripts.vmtkSurfaceToMesh() surfaceToMesh2.Surface = sizingFunction.GetOutput() surfaceToMesh2.Execute() self.PrintLog("Generating volume mesh") tetgen = vmtkscripts.vmtkTetGen() tetgen.Mesh = surfaceToMesh2.Mesh tetgen.GenerateCaps = 0 tetgen.UseSizingFunction = 1 tetgen.SizingFunctionArrayName = self.SizingFunctionArrayName tetgen.CellEntityIdsArrayName = self.CellEntityIdsArrayName tetgen.Order = 1 tetgen.Quality = 1 tetgen.PLC = 1 tetgen.NoBoundarySplit = 1 tetgen.RemoveSliver = 1 tetgen.OutputSurfaceElements = 0 tetgen.OutputVolumeElements = 1 tetgen.Execute() if tetgen.Mesh.GetNumberOfCells( ) == 0 and surfaceToMesh.Mesh.GetNumberOfCells() > 0: self.PrintLog( 'An error occurred during tetrahedralization. Will only output surface mesh and boundary layer.' ) appendFilter = vtkvmtk.vtkvmtkAppendFilter() appendFilter.AddInput(surfaceToMesh.Mesh) appendFilter.AddInput(boundaryLayer.Mesh) appendFilter.AddInput(tetgen.Mesh) appendFilter.Update() self.Mesh = appendFilter.GetOutput() else: self.PrintLog("Computing sizing function") sizingFunction = vtkvmtk.vtkvmtkPolyDataSizingFunction() sizingFunction.SetInput(remeshedSurface) sizingFunction.SetSizingFunctionArrayName( self.SizingFunctionArrayName) sizingFunction.SetScaleFactor(self.VolumeElementScaleFactor) sizingFunction.Update() self.PrintLog("Converting surface to mesh") surfaceToMesh = vmtkscripts.vmtkSurfaceToMesh() surfaceToMesh.Surface = sizingFunction.GetOutput() surfaceToMesh.Execute() self.PrintLog("Generating volume mesh") tetgen = vmtkscripts.vmtkTetGen() tetgen.Mesh = surfaceToMesh.Mesh tetgen.GenerateCaps = 0 tetgen.UseSizingFunction = 1 tetgen.SizingFunctionArrayName = self.SizingFunctionArrayName tetgen.CellEntityIdsArrayName = self.CellEntityIdsArrayName tetgen.Order = 1 tetgen.Quality = 1 tetgen.PLC = 1 tetgen.NoBoundarySplit = 1 tetgen.RemoveSliver = 1 tetgen.OutputSurfaceElements = 1 tetgen.OutputVolumeElements = 1 tetgen.Execute() self.Mesh = tetgen.Mesh if self.Mesh.GetNumberOfCells( ) == 0 and surfaceToMesh.Mesh.GetNumberOfCells() > 0: self.PrintLog( 'An error occurred during tetrahedralization. Will only output surface mesh.' ) self.Mesh = surfaceToMesh.Mesh if self.Tetrahedralize: tetrahedralize = vtk.vtkDataSetTriangleFilter() tetrahedralize.SetInput(self.Mesh) tetrahedralize.Update() self.Mesh = tetrahedralize.GetOutput() self.RemeshedSurface = remeshedSurface
def Execute(self): if self.Surface == None: self.PrintError('Error: No input surface.') self.PrintLog("Capping surface") capper = vmtkscripts.vmtkSurfaceCapper() capper.Surface = self.Surface capper.Interactive = 0 capper.Method = 'simple' capper.TriangleOutput = 0 capper.CellEntityIdOffset = 1 capper.Execute() self.PrintLog("Remeshing surface") remeshing = vmtkscripts.vmtkSurfaceRemeshing() remeshing.Surface = capper.Surface remeshing.CellEntityIdsArrayName = capper.CellEntityIdsArrayName remeshing.TargetEdgeLength = self.TargetEdgeLength remeshing.MaxEdgeLength = self.MaxEdgeLength remeshing.MinEdgeLength = self.MinEdgeLength remeshing.TargetEdgeLengthFactor = self.TargetEdgeLengthFactor remeshing.TargetEdgeLengthArrayName = self.TargetEdgeLengthArrayName remeshing.ElementSizeMode = self.ElementSizeMode remeshing.Execute() if self.BoundaryLayer: projection = vmtkscripts.vmtkSurfaceProjection() projection.Surface = remeshing.Surface projection.ReferenceSurface = capper.Surface projection.Execute() normals = vmtkscripts.vmtkSurfaceNormals() normals.Surface = projection.Surface normals.NormalsArrayName = 'Normals' normals.Execute() surfaceToMesh = vmtkscripts.vmtkSurfaceToMesh() surfaceToMesh.Surface = normals.Surface surfaceToMesh.Execute() self.PrintLog("Generating boundary layer") boundaryLayer = vmtkscripts.vmtkBoundaryLayer() boundaryLayer.Mesh = surfaceToMesh.Mesh boundaryLayer.WarpVectorsArrayName = 'Normals' boundaryLayer.NegateWarpVectors = True boundaryLayer.ThicknessArrayName = self.TargetEdgeLengthArrayName if self.ElementSizeMode == 'edgelength': boundaryLayer.ConstantThickness = True else: boundaryLayer.ConstantThickness = False boundaryLayer.IncludeSurfaceCells = 0 boundaryLayer.NumberOfSubLayers = self.NumberOfSubLayers boundaryLayer.SubLayerRatio = 0.5 boundaryLayer.Thickness = self.BoundaryLayerThicknessFactor * self.TargetEdgeLength boundaryLayer.ThicknessRatio = self.BoundaryLayerThicknessFactor * self.TargetEdgeLengthFactor boundaryLayer.MaximumThickness = self.BoundaryLayerThicknessFactor * self.MaxEdgeLength boundaryLayer.Execute() cellEntityIdsArray = vtk.vtkIntArray() cellEntityIdsArray.SetName(self.CellEntityIdsArrayName) cellEntityIdsArray.SetNumberOfTuples(boundaryLayer.Mesh.GetNumberOfCells()) cellEntityIdsArray.FillComponent(0,0.0) boundaryLayer.Mesh.GetCellData().AddArray(cellEntityIdsArray) innerCellEntityIdsArray = vtk.vtkIntArray() innerCellEntityIdsArray.SetName(self.CellEntityIdsArrayName) innerCellEntityIdsArray.SetNumberOfTuples(boundaryLayer.InnerSurfaceMesh.GetNumberOfCells()) innerCellEntityIdsArray.FillComponent(0,0.0) boundaryLayer.InnerSurfaceMesh.GetCellData().AddArray(cellEntityIdsArray) meshToSurface = vmtkscripts.vmtkMeshToSurface() meshToSurface.Mesh = boundaryLayer.InnerSurfaceMesh meshToSurface.Execute() self.PrintLog("Computing sizing function") sizingFunction = vtkvmtk.vtkvmtkPolyDataSizingFunction() sizingFunction.SetInput(meshToSurface.Surface) sizingFunction.SetSizingFunctionArrayName(self.SizingFunctionArrayName) sizingFunction.SetScaleFactor(self.VolumeElementScaleFactor) sizingFunction.Update() surfaceToMesh2 = vmtkscripts.vmtkSurfaceToMesh() surfaceToMesh2.Surface = sizingFunction.GetOutput() surfaceToMesh2.Execute() self.PrintLog("Generating volume mesh") tetgen = vmtkscripts.vmtkTetGen() tetgen.Mesh = surfaceToMesh2.Mesh tetgen.GenerateCaps = 0 tetgen.UseSizingFunction = 1 tetgen.SizingFunctionArrayName = self.SizingFunctionArrayName tetgen.CellEntityIdsArrayName = self.CellEntityIdsArrayName tetgen.Order = 1 tetgen.Quality = 1 tetgen.PLC = 1 tetgen.NoBoundarySplit = 1 tetgen.RemoveSliver = 1 tetgen.OutputSurfaceElements = 0 tetgen.OutputVolumeElements = 1 tetgen.Execute() if tetgen.Mesh.GetNumberOfCells() == 0 and surfaceToMesh.Mesh.GetNumberOfCells() > 0: self.PrintLog('An error occurred during tetrahedralization. Will only output surface mesh and boundary layer.') appendFilter = vtkvmtk.vtkvmtkAppendFilter() appendFilter.AddInput(surfaceToMesh.Mesh) appendFilter.AddInput(boundaryLayer.Mesh) appendFilter.AddInput(tetgen.Mesh) appendFilter.Update() self.Mesh = appendFilter.GetOutput() else: self.PrintLog("Computing sizing function") sizingFunction = vtkvmtk.vtkvmtkPolyDataSizingFunction() sizingFunction.SetInput(remeshing.Surface) sizingFunction.SetSizingFunctionArrayName(self.SizingFunctionArrayName) sizingFunction.SetScaleFactor(self.VolumeElementScaleFactor) sizingFunction.Update() self.PrintLog("Converting surface to mesh") surfaceToMesh = vmtkscripts.vmtkSurfaceToMesh() surfaceToMesh.Surface = sizingFunction.GetOutput() surfaceToMesh.Execute() self.PrintLog("Generating volume mesh") tetgen = vmtkscripts.vmtkTetGen() tetgen.Mesh = surfaceToMesh.Mesh tetgen.GenerateCaps = 0 tetgen.UseSizingFunction = 1 tetgen.SizingFunctionArrayName = self.SizingFunctionArrayName tetgen.CellEntityIdsArrayName = self.CellEntityIdsArrayName tetgen.Order = 1 tetgen.Quality = 1 tetgen.PLC = 1 tetgen.NoBoundarySplit = 1 tetgen.RemoveSliver = 1 tetgen.OutputSurfaceElements = 1 tetgen.OutputVolumeElements = 1 tetgen.Execute() self.Mesh = tetgen.Mesh if self.Mesh.GetNumberOfCells() == 0 and surfaceToMesh.Mesh.GetNumberOfCells() > 0: self.PrintLog('An error occurred during tetrahedralization. Will only output surface mesh.') self.Mesh = surfaceToMesh.Mesh if self.Tetrahedralize: tetrahedralize = vtk.vtkDataSetTriangleFilter() tetrahedralize.SetInput(self.Mesh) tetrahedralize.Update() self.Mesh = tetrahedralize.GetOutput()
def Execute(self): if self.Surface == None: self.PrintError('Error: No input surface.') if self.CheckNonManifold: self.PrintLog('NonManifold check.') nonManifoldChecker = vmtkNonManifoldSurfaceChecker() nonManifoldChecker.Surface = self.Surface nonManifoldChecker.PrintError = self.PrintError nonManifoldChecker.Execute() if (nonManifoldChecker.NumberOfNonManifoldEdges > 0): self.PrintLog(nonManifoldChecker.Report) return if not self.vmtkRenderer and self.SeedSelectorName in [ 'pickpoint', 'openprofiles' ]: self.vmtkRenderer = vmtkrenderer.vmtkRenderer() self.vmtkRenderer.Initialize() self.OwnRenderer = 1 self.PrintLog('Cleaning surface.') surfaceCleaner = vtk.vtkCleanPolyData() surfaceCleaner.SetInput(self.Surface) surfaceCleaner.Update() self.PrintLog('Triangulating surface.') surfaceTriangulator = vtk.vtkTriangleFilter() surfaceTriangulator.SetInput(surfaceCleaner.GetOutput()) surfaceTriangulator.PassLinesOff() surfaceTriangulator.PassVertsOff() surfaceTriangulator.Update() centerlineInputSurface = surfaceTriangulator.GetOutput() capCenterIds = None if self.SeedSelectorName in [ 'openprofiles', 'carotidprofiles', 'pickpoint', 'profileidlist' ]: self.PrintLog('Capping surface.') surfaceCapper = vtkvmtk.vtkvmtkCapPolyData() surfaceCapper.SetInput(surfaceTriangulator.GetOutput()) surfaceCapper.SetDisplacement(self.CapDisplacement) surfaceCapper.SetInPlaneDisplacement(self.CapDisplacement) surfaceCapper.Update() centerlineInputSurface = surfaceCapper.GetOutput() capCenterIds = surfaceCapper.GetCapCenterIds() if self.SeedSelector: pass elif self.SeedSelectorName: if self.SeedSelectorName == 'pickpoint': self.SeedSelector = vmtkPickPointSeedSelector() self.SeedSelector.vmtkRenderer = self.vmtkRenderer self.SeedSelector.Script = self elif self.SeedSelectorName == 'openprofiles': self.SeedSelector = vmtkOpenProfilesSeedSelector() self.SeedSelector.vmtkRenderer = self.vmtkRenderer self.SeedSelector.Script = self self.SeedSelector.SetSeedIds(surfaceCapper.GetCapCenterIds()) elif self.SeedSelectorName == 'carotidprofiles': self.SeedSelector = vmtkCarotidProfilesSeedSelector() self.SeedSelector.SetSeedIds(surfaceCapper.GetCapCenterIds()) elif self.SeedSelectorName == 'idlist': self.SeedSelector = vmtkIdListSeedSelector() self.SeedSelector.SourceIds = self.SourceIds self.SeedSelector.TargetIds = self.TargetIds elif self.SeedSelectorName == 'pointlist': self.SeedSelector = vmtkPointListSeedSelector() self.SeedSelector.SourcePoints = self.SourcePoints self.SeedSelector.TargetPoints = self.TargetPoints elif self.SeedSelectorName != 'profileidlist': self.PrintError( "SeedSelectorName unknown (available: pickpoint, openprofiles, carotidprofiles, profileidlist, idlist, pointlist)" ) return else: self.PrintError( 'vmtkCenterlines error: either SeedSelector or SeedSelectorName must be specified' ) return if self.SeedSelector: self.SeedSelector.SetSurface(centerlineInputSurface) self.SeedSelector.InputInfo = self.InputInfo self.SeedSelector.InputText = self.InputText self.SeedSelector.OutputText = self.OutputText self.SeedSelector.PrintError = self.PrintError self.SeedSelector.PrintLog = self.PrintLog self.SeedSelector.Execute() inletSeedIds = self.SeedSelector.GetSourceSeedIds() outletSeedIds = self.SeedSelector.GetTargetSeedIds() else: inletSeedIds = vtk.vtkIdList() outletSeedIds = vtk.vtkIdList() for id in self.SourceIds: inletSeedIds.InsertNextId(id) if self.TargetIds: for id in self.TargetIds: outletSeedIds.InsertNextId(id) else: for i in range(capCenterIds.GetNumberOfIds()): if i not in self.SourceIds: outletSeedIds.InsertNextId(i) self.PrintLog('Computing centerlines.') self.InputInfo('Computing centerlines...') centerlineFilter = vtkvmtk.vtkvmtkPolyDataCenterlines() centerlineFilter.SetInput(centerlineInputSurface) if self.SeedSelectorName in [ 'openprofiles', 'carotidprofiles', 'profileidlist' ]: centerlineFilter.SetCapCenterIds(capCenterIds) centerlineFilter.SetSourceSeedIds(inletSeedIds) centerlineFilter.SetTargetSeedIds(outletSeedIds) centerlineFilter.SetRadiusArrayName(self.RadiusArrayName) centerlineFilter.SetCostFunction(self.CostFunction) centerlineFilter.SetFlipNormals(self.FlipNormals) centerlineFilter.SetAppendEndPointsToCenterlines(self.AppendEndPoints) centerlineFilter.SetSimplifyVoronoi(self.SimplifyVoronoi) if self.DelaunayTessellation != None: centerlineFilter.GenerateDelaunayTessellationOff() centerlineFilter.SetDelaunayTessellation(self.DelaunayTessellation) centerlineFilter.SetDelaunayTolerance(self.DelaunayTolerance) if self.UseTetGen == 1: self.PrintLog('Running TetGen.') import vmtkscripts surfaceToMesh = vmtkscripts.vmtkSurfaceToMesh() surfaceToMesh.Surface = centerlineInputSurface surfaceToMesh.Execute() tetgen = vmtkscripts.vmtkTetGen() tetgen.Mesh = surfaceToMesh.Mesh tetgen.PLC = 1 tetgen.NoMerge = 1 tetgen.Quality = 0 if self.TetGenDetectInter == 1: tetgen.DetectInter = 1 tetgen.NoMerge = 0 tetgen.OutputSurfaceElements = 0 tetgen.Execute() centerlineFilter.GenerateDelaunayTessellationOff() centerlineFilter.SetDelaunayTessellation(tetgen.Mesh) centerlineFilter.SetCenterlineResampling(self.Resampling) centerlineFilter.SetResamplingStepLength(self.ResamplingStepLength) centerlineFilter.Update() self.Centerlines = centerlineFilter.GetOutput() self.VoronoiDiagram = centerlineFilter.GetVoronoiDiagram() self.DelaunayTessellation = centerlineFilter.GetDelaunayTessellation() self.PoleIds = centerlineFilter.GetPoleIds() self.EikonalSolutionArrayName = centerlineFilter.GetEikonalSolutionArrayName( ) self.EdgeArrayName = centerlineFilter.GetEdgeArrayName() self.EdgePCoordArrayName = centerlineFilter.GetEdgePCoordArrayName() self.CostFunctionArrayName = centerlineFilter.GetCostFunctionArrayName( ) if self.OwnRenderer: self.vmtkRenderer.Deallocate()
def Execute(self): if self.Surface == None: self.PrintError('Error: No input surface.') if self.CheckNonManifold: self.PrintLog('NonManifold check.') nonManifoldChecker = vmtkNonManifoldSurfaceChecker() nonManifoldChecker.Surface = self.Surface nonManifoldChecker.PrintError = self.PrintError nonManifoldChecker.Execute() if nonManifoldChecker.NumberOfNonManifoldEdges > 0: self.PrintLog(nonManifoldChecker.Report) return self.PrintLog('Cleaning surface.') surfaceCleaner = vtk.vtkCleanPolyData() surfaceCleaner.SetInputData(self.Surface) surfaceCleaner.Update() self.PrintLog('Triangulating surface.') surfaceTriangulator = vtk.vtkTriangleFilter() surfaceTriangulator.SetInputConnection(surfaceCleaner.GetOutputPort()) surfaceTriangulator.PassLinesOff() surfaceTriangulator.PassVertsOff() surfaceTriangulator.Update() surfaceCapper = vtkvmtk.vtkvmtkCapPolyData() surfaceCapper.SetInputConnection(surfaceTriangulator.GetOutputPort()) surfaceCapper.SetDisplacement(self.CapDisplacement) surfaceCapper.SetInPlaneDisplacement(self.CapDisplacement) surfaceCapper.Update() capCenterIds = surfaceCapper.GetCapCenterIds() surfaceNormals = vtk.vtkPolyDataNormals() surfaceNormals.SetInputConnection(surfaceCapper.GetOutputPort()) surfaceNormals.SplittingOff() surfaceNormals.AutoOrientNormalsOn() surfaceNormals.SetFlipNormals(self.FlipNormals) surfaceNormals.ComputePointNormalsOn() surfaceNormals.ConsistencyOn() surfaceNormals.Update() inputSurface = surfaceNormals.GetOutput() if self.UseTetGen: self.PrintLog('Running TetGen.') import vmtkscripts surfaceToMesh = vmtkscripts.vmtkSurfaceToMesh() surfaceToMesh.Surface = inputSurface surfaceToMesh.Execute() tetgen = vmtkscripts.vmtkTetGen() tetgen.Mesh = surfaceToMesh.Mesh tetgen.PLC = 1 tetgen.NoMerge = 1 tetgen.Quality = 0 if self.TetGenDetectInter: tetgen.DetectInter = 1 tetgen.NoMerge = 0 tetgen.OutputSurfaceElements = 0 tetgen.Execute() self.DelaunayTessellation = tetgen.Mesh else: delaunayTessellator = vtk.vtkDelaunay3D() delaunayTessellator.CreateDefaultLocator() delaunayTessellator.SetInputConnection(surfaceNormals.GetOutputPort()) delaunayTessellator.SetTolerance(self.DelaunayTolerance) delaunayTessellator.Update() self.DelaunayTessellation = delaunayTessellator.GetOutput() normalsArray = surfaceNormals.GetOutput().GetPointData().GetNormals() self.DelaunayTessellation.GetPointData().AddArray(normalsArray) internalTetrahedraExtractor = vtkvmtk.vtkvmtkInternalTetrahedraExtractor() internalTetrahedraExtractor.SetInputData(self.DelaunayTessellation) internalTetrahedraExtractor.SetOutwardNormalsArrayName(normalsArray.GetName()) if self.RemoveSubresolutionTetrahedra: internalTetrahedraExtractor.RemoveSubresolutionTetrahedraOn() internalTetrahedraExtractor.SetSubresolutionFactor(self.SubresolutionFactor) internalTetrahedraExtractor.SetSurface(inputSurface) if capCenterIds.GetNumberOfIds() > 0: internalTetrahedraExtractor.UseCapsOn() internalTetrahedraExtractor.SetCapCenterIds(capCenterIds) internalTetrahedraExtractor.Update() self.DelaunayTessellation = internalTetrahedraExtractor.GetOutput() voronoiDiagramFilter = vtkvmtk.vtkvmtkVoronoiDiagram3D() voronoiDiagramFilter.SetInputData(self.DelaunayTessellation) voronoiDiagramFilter.SetRadiusArrayName(self.RadiusArrayName) voronoiDiagramFilter.Update() self.PoleIds = voronoiDiagramFilter.GetPoleIds() self.VoronoiDiagram = voronoiDiagramFilter.GetOutput() if self.SimplifyVoronoi: voronoiDiagramSimplifier = vtkvmtk.vtkvmtkSimplifyVoronoiDiagram() voronoiDiagramSimplifier.SetInputConnection(voronoiDiagramFilter.GetOutputPort()) voronoiDiagramSimplifier.SetUnremovablePointIds(voronoiDiagramFilter.GetPoleIds()) voronoiDiagramSimplifier.Update() self.VoronoiDiagram = voronoiDiagramSimplifier.GetOutput() self.Mesh = self.DelaunayTessellation self.Surface = self.VoronoiDiagram