def vmtksurfaceremeshing(surface, edgelength=1.0, iterations=10): remesher = vmtkscripts.vmtkSurfaceRemeshing() remesher.Surface = surface remesher.NumberOfIterations = iterations remesher.ElementSizeMode = 'edgelength' remesher.TargetEdgeLength = edgelength remesher.Execute() return remesher.Surface
def Add_extension(path_reader, path_writer, extension_ratio=10, target_edge_length=0.7, nb_iterations=5): myReader = vmtkscripts.vmtkSurfaceReader() myReader.InputFileName = path_reader myReader.Format = 'stl' myReader.Execute() myCenterline = vmtkscripts.vmtkCenterlines() myCenterline.Surface = myReader.Surface myCenterline.SeedSelectorName = 'openprofiles' myCenterline.Execute() myExtension = vmtkscripts.vmtkFlowExtensions() myExtension.Surface = myReader.Surface myExtension.Centerlines = myCenterline.Centerlines myExtension.AdaptiveExtensionLength = 1 myExtension.AdaptiveExtensionRadius = 1 myExtension.ExtensionMode = "boundarynormal" myExtension.ExtensionRatio = extension_ratio myExtension.Interactive = 0 myExtension.Execute() mySmoother = vmtkscripts.vmtkSurfaceSmoothing() mySmoother.Surface = myExtension.Surface mySmoother.PassBand = 0.3 mySmoother.NumberOfIterations = 5 mySmoother.Execute() myRemesh = vmtkscripts.vmtkSurfaceRemeshing() myRemesh.Surface = mySmoother.Surface myRemesh.ElementSizeMode = 'edgelength' myRemesh.TargetEdgeLength = target_edge_length myRemesh.NumberOfIterations = nb_iterations myRemesh.Execute() myWriter = vmtkscripts.vmtkSurfaceWriter() myWriter.Surface = myRemesh.Surface myWriter.OutputFileName = path_writer myWriter.Format = 'stl' myWriter.Execute()
def vmtksurfaceremeshing(surface, edgelength=1.0, iterations=10): """Remesh a surface using high quality triangles. Args: surface: Surface mesh. edgelength: Target length of triangle edges. iterations: Number of iterations to optimize the mesh quality. Returns: Remeshed surface. """ remesher = vmtkscripts.vmtkSurfaceRemeshing() remesher.Surface = surface remesher.NumberOfIterations = iterations remesher.ElementSizeMode = 'edgelength' remesher.TargetEdgeLength = edgelength remesher.Execute() return remesher.Surface
def Surface_Remesh(path_reader, path_writer, target_edge_length=0.7, nb_iterations=10): myReader = vmtkscripts.vmtkSurfaceReader() myReader.InputFileName = path_reader myReader.Format = 'stl' myReader.Execute() myRemesh = vmtkscripts.vmtkSurfaceRemeshing() myRemesh.Surface = myReader.Surface myRemesh.ElementSizeMode = 'edgelength' myRemesh.TargetEdgeLength = target_edge_length myRemesh.NumberOfIterations = nb_iterations myRemesh.Execute() myWriter = vmtkscripts.vmtkSurfaceWriter() myWriter.Surface = myRemesh.Surface myWriter.OutputFileName = path_writer myWriter.Format = 'stl' myWriter.Execute()
from vmtk import vmtkscripts import argparse parser = argparse.ArgumentParser() parser.add_argument("fname", help="Enter the path to the input surface file", type=str) args = parser.parse_args() fname = args.fname outputName = fname.split('.')[:-1] + ['.vtu'] outputName = ''.join(outputName) surfaceReader = vmtkscripts.vmtkSurfaceReader() surfaceReader.InputFileName = fname surfaceReader.Execute() surfaceRemeshing = vmtkscripts.vmtkSurfaceRemeshing() surfaceRemeshing.Surface = surfaceReader.Surface surfaceRemeshing.ElementSizeMode = 'edgelength' surfaceRemeshing.TargetEdgeLength = 5.0 surfaceRemeshing.Execute() meshGenerator = vmtkscripts.vmtkMeshGenerator() meshGenerator.Surface = surfaceRemeshing.Surface meshGenerator.TargetEdgeLength = 5.0 meshGenerator.Execute() meshViewer = vmtkscripts.vmtkMeshViewer() meshViewer.Mesh = meshGenerator.Mesh meshViewer.Execute() meshWriter = vmtkscripts.vmtkMeshWriter() meshWriter.Mesh = meshGenerator.Mesh
def vmtksurfaceremeshingarea(surface, iterations=10): remesher = vmtkscripts.vmtkSurfaceRemeshing() remesher.Surface = surface remesher.NumberOfIterations = iterations remesher.Execute() return remesher.Surface
def Execute(self): from vmtk import vmtkscripts if self.Surface == None: self.PrintError('Error: No input surface.') wallEntityOffset = 1 if self.SkipCapping or not self.BoundaryLayerOnCaps: self.PrintLog("Not capping surface") surface = self.Surface cellEntityIdsArray = vtk.vtkIntArray() cellEntityIdsArray.SetName(self.CellEntityIdsArrayName) cellEntityIdsArray.SetNumberOfTuples(surface.GetNumberOfCells()) cellEntityIdsArray.FillComponent(0,0.0) surface.GetCellData().AddArray(cellEntityIdsArray) else: self.PrintLog("Capping surface") capper = vmtkscripts.vmtkSurfaceCapper() capper.Surface = self.Surface capper.Interactive = 0 capper.Method = self.CappingMethod capper.TriangleOutput = 0 capper.CellEntityIdOffset = wallEntityOffset capper.Execute() surface = capper.Surface if self.SkipRemeshing: remeshedSurface = surface else: self.PrintLog("Remeshing surface") remeshing = vmtkscripts.vmtkSurfaceRemeshing() remeshing.Surface = surface remeshing.CellEntityIdsArrayName = self.CellEntityIdsArrayName remeshing.TargetEdgeLength = self.TargetEdgeLength remeshing.MaxEdgeLength = self.MaxEdgeLength remeshing.MinEdgeLength = self.MinEdgeLength remeshing.TargetEdgeLengthFactor = self.TargetEdgeLengthFactor remeshing.TargetEdgeLengthArrayName = self.TargetEdgeLengthArrayName remeshing.TriangleSplitFactor = self.TriangleSplitFactor remeshing.ElementSizeMode = self.ElementSizeMode if self.RemeshCapsOnly: remeshing.ExcludeEntityIds = [wallEntityOffset] remeshing.Execute() remeshedSurface = remeshing.Surface if self.BoundaryLayer: projection = vmtkscripts.vmtkSurfaceProjection() projection.Surface = remeshedSurface projection.ReferenceSurface = surface projection.Execute() normals = vmtkscripts.vmtkSurfaceNormals() normals.Surface = projection.Surface normals.NormalsArrayName = 'Normals' normals.Execute() surfaceToMesh = vmtkscripts.vmtkSurfaceToMesh() surfaceToMesh.Surface = normals.Surface surfaceToMesh.Execute() self.PrintLog("Generating boundary layer") placeholderCellEntityId = 9999 boundaryLayer = vmtkscripts.vmtkBoundaryLayer() boundaryLayer.Mesh = surfaceToMesh.Mesh boundaryLayer.WarpVectorsArrayName = 'Normals' boundaryLayer.NegateWarpVectors = True boundaryLayer.ThicknessArrayName = self.TargetEdgeLengthArrayName if self.ElementSizeMode == 'edgelength': boundaryLayer.ConstantThickness = True else: boundaryLayer.ConstantThickness = False boundaryLayer.IncludeSurfaceCells = 0 boundaryLayer.NumberOfSubLayers = self.NumberOfSubLayers boundaryLayer.NumberOfSubsteps = self.NumberOfSubsteps boundaryLayer.Relaxation = self.Relaxation boundaryLayer.LocalCorrectionFactor = self.LocalCorrectionFactor boundaryLayer.SubLayerRatio = self.SubLayerRatio boundaryLayer.Thickness = self.BoundaryLayerThicknessFactor * self.TargetEdgeLength boundaryLayer.ThicknessRatio = self.BoundaryLayerThicknessFactor * self.TargetEdgeLengthFactor boundaryLayer.MaximumThickness = self.BoundaryLayerThicknessFactor * self.MaxEdgeLength if not self.BoundaryLayerOnCaps: boundaryLayer.SidewallCellEntityId = placeholderCellEntityId boundaryLayer.InnerSurfaceCellEntityId = wallEntityOffset boundaryLayer.Execute() meshToSurface = vmtkscripts.vmtkMeshToSurface() meshToSurface.Mesh = boundaryLayer.InnerSurfaceMesh meshToSurface.Execute() innerSurface = meshToSurface.Surface if not self.BoundaryLayerOnCaps: self.PrintLog("Capping inner surface") capper = vmtkscripts.vmtkSurfaceCapper() capper.Surface = innerSurface capper.Interactive = 0 capper.Method = self.CappingMethod capper.TriangleOutput = 1 capper.CellEntityIdOffset = wallEntityOffset capper.Execute() self.PrintLog("Remeshing endcaps") remeshing = vmtkscripts.vmtkSurfaceRemeshing() remeshing.Surface = capper.Surface remeshing.CellEntityIdsArrayName = self.CellEntityIdsArrayName remeshing.TargetEdgeLength = self.TargetEdgeLength * self.EndcapsEdgeLengthFactor remeshing.MaxEdgeLength = self.MaxEdgeLength remeshing.MinEdgeLength = self.MinEdgeLength remeshing.TargetEdgeLengthFactor = self.TargetEdgeLengthFactor * self.EndcapsEdgeLengthFactor remeshing.TargetEdgeLengthArrayName = self.TargetEdgeLengthArrayName remeshing.TriangleSplitFactor = self.TriangleSplitFactor remeshing.ElementSizeMode = self.ElementSizeMode remeshing.ExcludeEntityIds = [wallEntityOffset] remeshing.Execute() innerSurface = remeshing.Surface self.PrintLog("Computing sizing function") sizingFunction = vtkvmtk.vtkvmtkPolyDataSizingFunction() sizingFunction.SetInputData(innerSurface) sizingFunction.SetSizingFunctionArrayName(self.SizingFunctionArrayName) sizingFunction.SetScaleFactor(self.VolumeElementScaleFactor) sizingFunction.Update() surfaceToMesh2 = vmtkscripts.vmtkSurfaceToMesh() surfaceToMesh2.Surface = sizingFunction.GetOutput() surfaceToMesh2.Execute() self.PrintLog("Generating volume mesh") tetgen = vmtkscripts.vmtkTetGen() tetgen.Mesh = surfaceToMesh2.Mesh tetgen.GenerateCaps = 0 tetgen.UseSizingFunction = 1 tetgen.SizingFunctionArrayName = self.SizingFunctionArrayName tetgen.CellEntityIdsArrayName = self.CellEntityIdsArrayName tetgen.Order = 1 tetgen.Quality = 1 tetgen.PLC = 1 tetgen.NoBoundarySplit = 1 tetgen.RemoveSliver = 1 tetgen.OutputSurfaceElements = 0 tetgen.OutputVolumeElements = 1 tetgen.Execute() #w = vtk.vtkXMLUnstructuredGridWriter() #w.SetInput(tetgen.Mesh) #w.SetFileName('tet.vtu') #w.Write() if tetgen.Mesh.GetNumberOfCells() == 0 and surfaceToMesh.Mesh.GetNumberOfCells() > 0: self.PrintLog('An error occurred during tetrahedralization. Will only output surface mesh and boundary layer.') if not self.BoundaryLayerOnCaps: surfaceToMesh.Mesh.GetCellData().GetArray(self.CellEntityIdsArrayName).FillComponent(0,wallEntityOffset) self.PrintLog("Assembling final mesh") appendFilter = vtkvmtk.vtkvmtkAppendFilter() appendFilter.AddInputData(surfaceToMesh.Mesh) appendFilter.AddInputData(boundaryLayer.Mesh) appendFilter.AddInputData(tetgen.Mesh) #appendFilter.AddInput(boundaryLayer.InnerSurfaceMesh) if not self.BoundaryLayerOnCaps: threshold = vtk.vtkThreshold() threshold.SetInputData(surfaceToMesh2.Mesh) threshold.ThresholdByUpper(1.5) threshold.SetInputArrayToProcess(0,0,0,1,self.CellEntityIdsArrayName) threshold.Update() endcaps = threshold.GetOutput() appendFilter.AddInputData(endcaps) appendFilter.Update() self.Mesh = appendFilter.GetOutput() if not self.BoundaryLayerOnCaps: cellEntityIdsArray = self.Mesh.GetCellData().GetArray(self.CellEntityIdsArrayName) def VisitNeighbors(i, cellEntityId): cellPointIds = vtk.vtkIdList() self.Mesh.GetCellPoints(i,cellPointIds) neighborPointIds = vtk.vtkIdList() neighborPointIds.SetNumberOfIds(1) pointNeighborCellIds = vtk.vtkIdList() neighborCellIds = vtk.vtkIdList() for j in range(cellPointIds.GetNumberOfIds()): neighborPointIds.SetId(0,cellPointIds.GetId(j)) self.Mesh.GetCellNeighbors(i,neighborPointIds,pointNeighborCellIds) for k in range(pointNeighborCellIds.GetNumberOfIds()): neighborCellIds.InsertNextId(pointNeighborCellIds.GetId(k)) for j in range(neighborCellIds.GetNumberOfIds()): cellId = neighborCellIds.GetId(j) neighborCellEntityId = cellEntityIdsArray.GetTuple1(cellId) neighborCellType = self.Mesh.GetCellType(cellId) if neighborCellType not in [vtk.VTK_TRIANGLE, vtk.VTK_QUADRATIC_TRIANGLE, vtk.VTK_QUAD]: continue if neighborCellEntityId != placeholderCellEntityId: continue cellEntityIdsArray.SetTuple1(cellId,cellEntityId) VisitNeighbors(cellId,cellEntityId) for i in range(self.Mesh.GetNumberOfCells()): cellEntityId = cellEntityIdsArray.GetTuple1(i) cellType = self.Mesh.GetCellType(i) if cellType not in [vtk.VTK_TRIANGLE, vtk.VTK_QUADRATIC_TRIANGLE, vtk.VTK_QUAD]: continue if cellEntityId in [0, 1, placeholderCellEntityId]: continue VisitNeighbors(i,cellEntityId) else: self.PrintLog("Computing sizing function") sizingFunction = vtkvmtk.vtkvmtkPolyDataSizingFunction() sizingFunction.SetInputData(remeshedSurface) sizingFunction.SetSizingFunctionArrayName(self.SizingFunctionArrayName) sizingFunction.SetScaleFactor(self.VolumeElementScaleFactor) sizingFunction.Update() self.PrintLog("Converting surface to mesh") surfaceToMesh = vmtkscripts.vmtkSurfaceToMesh() surfaceToMesh.Surface = sizingFunction.GetOutput() surfaceToMesh.Execute() self.PrintLog("Generating volume mesh") tetgen = vmtkscripts.vmtkTetGen() tetgen.Mesh = surfaceToMesh.Mesh tetgen.GenerateCaps = 0 tetgen.UseSizingFunction = 1 tetgen.SizingFunctionArrayName = self.SizingFunctionArrayName tetgen.CellEntityIdsArrayName = self.CellEntityIdsArrayName tetgen.Order = 1 tetgen.Quality = 1 tetgen.PLC = 1 tetgen.NoBoundarySplit = 1 tetgen.RemoveSliver = 1 tetgen.OutputSurfaceElements = 1 tetgen.OutputVolumeElements = 1 tetgen.Execute() self.Mesh = tetgen.Mesh if self.Mesh.GetNumberOfCells() == 0 and surfaceToMesh.Mesh.GetNumberOfCells() > 0: self.PrintLog('An error occurred during tetrahedralization. Will only output surface mesh.') self.Mesh = surfaceToMesh.Mesh if self.Tetrahedralize: tetrahedralize = vtkvmtk.vtkvmtkUnstructuredGridTetraFilter() tetrahedralize.SetInputData(self.Mesh) tetrahedralize.Update() self.Mesh = tetrahedralize.GetOutput() self.RemeshedSurface = remeshedSurface
def Execute(self): from vmtk import vmtkscripts if self.Surface == None: self.PrintError('Error: No input surface.') wallEntityOffset = 1 if self.SkipCapping or not self.BoundaryLayerOnCaps: self.PrintLog("Not capping surface") surface = self.Surface cellEntityIdsArray = vtk.vtkIntArray() cellEntityIdsArray.SetName(self.CellEntityIdsArrayName) cellEntityIdsArray.SetNumberOfTuples(surface.GetNumberOfCells()) cellEntityIdsArray.FillComponent(0,0.0) surface.GetCellData().AddArray(cellEntityIdsArray) else: self.PrintLog("Capping surface") capper = vmtkscripts.vmtkSurfaceCapper() capper.Surface = self.Surface capper.Interactive = 0 capper.Method = self.CappingMethod capper.TriangleOutput = 0 capper.CellEntityIdOffset = wallEntityOffset capper.Execute() surface = capper.Surface if self.SkipRemeshing: remeshedSurface = surface else: self.PrintLog("Remeshing surface") remeshing = vmtkscripts.vmtkSurfaceRemeshing() remeshing.Surface = surface remeshing.CellEntityIdsArrayName = self.CellEntityIdsArrayName remeshing.TargetEdgeLength = self.TargetEdgeLength remeshing.MaxEdgeLength = self.MaxEdgeLength remeshing.MinEdgeLength = self.MinEdgeLength remeshing.TargetEdgeLengthFactor = self.TargetEdgeLengthFactor remeshing.TargetEdgeLengthArrayName = self.TargetEdgeLengthArrayName remeshing.TriangleSplitFactor = self.TriangleSplitFactor remeshing.ElementSizeMode = self.ElementSizeMode if self.RemeshCapsOnly: remeshing.ExcludeEntityIds = [wallEntityOffset] remeshing.Execute() remeshedSurface = remeshing.Surface if self.BoundaryLayer: projection = vmtkscripts.vmtkSurfaceProjection() projection.Surface = remeshedSurface projection.ReferenceSurface = surface projection.Execute() normals = vmtkscripts.vmtkSurfaceNormals() normals.Surface = projection.Surface normals.NormalsArrayName = 'Normals' normals.Execute() surfaceToMesh = vmtkscripts.vmtkSurfaceToMesh() surfaceToMesh.Surface = normals.Surface surfaceToMesh.Execute() self.PrintLog("Generating boundary layer fluid") placeholderCellEntityId = 9999 boundaryLayer = vmtkscripts.vmtkBoundaryLayer() boundaryLayer.Mesh = surfaceToMesh.Mesh boundaryLayer.WarpVectorsArrayName = 'Normals' boundaryLayer.NegateWarpVectors = True boundaryLayer.ThicknessArrayName = self.TargetEdgeLengthArrayName if self.ElementSizeMode == 'edgelength': boundaryLayer.ConstantThickness = True else: boundaryLayer.ConstantThickness = False boundaryLayer.IncludeSurfaceCells = 0 boundaryLayer.NumberOfSubLayers = self.NumberOfSubLayers boundaryLayer.NumberOfSubsteps = self.NumberOfSubsteps boundaryLayer.Relaxation = self.Relaxation boundaryLayer.LocalCorrectionFactor = self.LocalCorrectionFactor boundaryLayer.SubLayerRatio = self.SubLayerRatio boundaryLayer.Thickness = self.BoundaryLayerThicknessFactor * self.TargetEdgeLength boundaryLayer.ThicknessRatio = self.BoundaryLayerThicknessFactor * self.TargetEdgeLengthFactor boundaryLayer.MaximumThickness = self.BoundaryLayerThicknessFactor * self.MaxEdgeLength if not self.BoundaryLayerOnCaps: boundaryLayer.SidewallCellEntityId = placeholderCellEntityId boundaryLayer.InnerSurfaceCellEntityId = wallEntityOffset boundaryLayer.VolumeCellEntityId = self.VolumeId_fluid boundaryLayer.Execute() self.PrintLog("Generating boundary layer solid") boundaryLayer2 = vmtkscripts.vmtkBoundaryLayer() boundaryLayer2.Mesh = surfaceToMesh.Mesh boundaryLayer2.WarpVectorsArrayName = 'Normals' boundaryLayer2.NegateWarpVectors = True boundaryLayer2.ThicknessArrayName = self.TargetEdgeLengthArrayName if self.ElementSizeMode == 'edgelength': boundaryLayer2.ConstantThickness = True else: boundaryLayer2.ConstantThickness = False boundaryLayer2.IncludeSurfaceCells = 1 boundaryLayer2.NumberOfSubLayers = self.NumberOfSubLayers boundaryLayer2.NumberOfSubsteps = self.NumberOfSubsteps boundaryLayer2.Relaxation = self.Relaxation boundaryLayer2.LocalCorrectionFactor = self.LocalCorrectionFactor boundaryLayer2.SubLayerRatio = self.SubLayerRatio boundaryLayer2.Thickness = self.BoundaryLayerThicknessFactor * self.TargetEdgeLength boundaryLayer2.ThicknessRatio = self.BoundaryLayerThicknessFactor * self.TargetEdgeLengthFactor boundaryLayer2.MaximumThickness = self.BoundaryLayerThicknessFactor * self.MaxEdgeLength if not self.BoundaryLayerOnCaps: boundaryLayer2.SidewallCellEntityId = self.SolidSideWallId #placeholderCellEntityId boundaryLayer2.InnerSurfaceCellEntityId = self.InterfaceId_fsi # wallEntityOffset boundaryLayer2.OuterSurfaceCellEntityId = self.InterfaceId_outer # wallEntityOffset boundaryLayer2.VolumeCellEntityId = self.VolumeId_solid boundaryLayer2.Execute() meshToSurface = vmtkscripts.vmtkMeshToSurface() meshToSurface.Mesh = boundaryLayer.InnerSurfaceMesh meshToSurface.Execute() innerSurface = meshToSurface.Surface if not self.BoundaryLayerOnCaps: self.PrintLog("Capping inner surface") capper = vmtkscripts.vmtkSurfaceCapper() capper.Surface = innerSurface capper.Interactive = 0 capper.Method = self.CappingMethod capper.TriangleOutput = 1 capper.CellEntityIdOffset = wallEntityOffset capper.Execute() self.PrintLog("Remeshing endcaps") remeshing = vmtkscripts.vmtkSurfaceRemeshing() remeshing.Surface = capper.Surface remeshing.CellEntityIdsArrayName = self.CellEntityIdsArrayName remeshing.TargetEdgeLength = self.TargetEdgeLength * self.EndcapsEdgeLengthFactor remeshing.MaxEdgeLength = self.MaxEdgeLength remeshing.MinEdgeLength = self.MinEdgeLength remeshing.TargetEdgeLengthFactor = self.TargetEdgeLengthFactor * self.EndcapsEdgeLengthFactor remeshing.TargetEdgeLengthArrayName = self.TargetEdgeLengthArrayName remeshing.TriangleSplitFactor = self.TriangleSplitFactor remeshing.ElementSizeMode = self.ElementSizeMode remeshing.ExcludeEntityIds = [wallEntityOffset] # [wallEntityOffset, InterfaceId] #[wallEntityOffset] remeshing.Execute() innerSurface = remeshing.Surface self.PrintLog("Computing sizing function") sizingFunction = vtkvmtk.vtkvmtkPolyDataSizingFunction() sizingFunction.SetInputData(innerSurface) sizingFunction.SetSizingFunctionArrayName(self.SizingFunctionArrayName) sizingFunction.SetScaleFactor(self.VolumeElementScaleFactor) sizingFunction.Update() surfaceToMesh2 = vmtkscripts.vmtkSurfaceToMesh() surfaceToMesh2.Surface = sizingFunction.GetOutput() surfaceToMesh2.Execute() self.PrintLog("Generating volume mesh") tetgen = vmtkscripts.vmtkTetGen() tetgen.Mesh = surfaceToMesh2.Mesh tetgen.GenerateCaps = 0 tetgen.UseSizingFunction = 1 tetgen.SizingFunctionArrayName = self.SizingFunctionArrayName tetgen.CellEntityIdsArrayName = self.CellEntityIdsArrayName tetgen.Order = 1 tetgen.Quality = 1 tetgen.PLC = 1 tetgen.NoBoundarySplit = 1 tetgen.RemoveSliver = 1 tetgen.OutputSurfaceElements = 1 tetgen.OutputVolumeElements = 1 tetgen.RegionAttrib = 0 tetgen.Execute() ##### ADDING CELL IDs #array = vtk.vtkDoubleArray() #array.SetNumberOfTuples(tetgen.Mesh.GetNumberOfCells()) #array.SetNumberOfComponents(1) #array.FillComponent(0, 1.0) #array.SetName('RegionIDs') #tetgen.Mesh.GetCellData().AddArray(array) #array = vtk.vtkDoubleArray() #array.SetNumberOfTuples(boundaryLayer.Mesh.GetNumberOfCells()) #array.SetNumberOfComponents(1) #array.FillComponent(0, 1.0) #array.SetName('RegionIDs') #boundaryLayer.Mesh.GetCellData().AddArray(array) #array = vtk.vtkDoubleArray() #array.SetNumberOfTuples(boundaryLayer2.Mesh.GetNumberOfCells()) #array.SetNumberOfComponents(1) #array.FillComponent(0, 2.0) #array.SetName('RegionIDs') #boundaryLayer2.Mesh.GetCellData().AddArray(array) ##### # w1 = vtk.vtkXMLUnstructuredGridWriter() # w1.SetInputData(boundaryLayer2.Mesh) # w1.SetFileName('BoundaryLayer2.vtu') # w1.Write() # # w2 = vtk.vtkXMLUnstructuredGridWriter() # w2.SetInputData(tetgen.Mesh) # w2.SetFileName('Tetgen.vtu') # w2.Write() # # w3 = vtk.vtkXMLUnstructuredGridWriter() # w3.SetInputData(boundaryLayer.Mesh) # w3.SetFileName('BoundaryLayer.vtu') # w3.Write() # # w4 = vtk.vtkXMLUnstructuredGridWriter() # w4.SetInputData(boundaryLayer.InnerSurfaceMesh) # w4.SetFileName('InnerLayer.vtu') # w4.Write() #from IPython import embed; embed() self.PrintLog("Assembling fluid mesh") appendFilter = vtkvmtk.vtkvmtkAppendFilter() appendFilter.AddInputData(boundaryLayer.Mesh) appendFilter.AddInputData(tetgen.Mesh) appendFilter.Update() self.Mesh = appendFilter.GetOutput() if not self.BoundaryLayerOnCaps: cellEntityIdsArray = self.Mesh.GetCellData().GetArray(self.CellEntityIdsArrayName) def VisitNeighbors(i, cellEntityId): cellPointIds = vtk.vtkIdList() self.Mesh.GetCellPoints(i,cellPointIds) neighborPointIds = vtk.vtkIdList() neighborPointIds.SetNumberOfIds(1) pointNeighborCellIds = vtk.vtkIdList() neighborCellIds = vtk.vtkIdList() for j in range(cellPointIds.GetNumberOfIds()): neighborPointIds.SetId(0,cellPointIds.GetId(j)) self.Mesh.GetCellNeighbors(i,neighborPointIds,pointNeighborCellIds) for k in range(pointNeighborCellIds.GetNumberOfIds()): neighborCellIds.InsertNextId(pointNeighborCellIds.GetId(k)) for j in range(neighborCellIds.GetNumberOfIds()): cellId = neighborCellIds.GetId(j) neighborCellEntityId = cellEntityIdsArray.GetTuple1(cellId) neighborCellType = self.Mesh.GetCellType(cellId) if neighborCellType not in [vtk.VTK_TRIANGLE, vtk.VTK_QUADRATIC_TRIANGLE, vtk.VTK_QUAD]: continue if neighborCellEntityId != placeholderCellEntityId: continue cellEntityIdsArray.SetTuple1(cellId,cellEntityId) VisitNeighbors(cellId,cellEntityId) for i in range(self.Mesh.GetNumberOfCells()): cellEntityId = cellEntityIdsArray.GetTuple1(i) cellType = self.Mesh.GetCellType(i) if cellType not in [vtk.VTK_TRIANGLE, vtk.VTK_QUADRATIC_TRIANGLE, vtk.VTK_QUAD]: continue if cellEntityId in [0, 1, placeholderCellEntityId]: continue VisitNeighbors(i,cellEntityId) self.PrintLog("Assembling final FSI mesh") appendFilter2 = vtkvmtk.vtkvmtkAppendFilter() appendFilter2.AddInputData(appendFilter.GetOutput()) appendFilter2.AddInputData(boundaryLayer2.Mesh) appendFilter2.Update() self.Mesh = appendFilter2.GetOutput() else: self.PrintLog("Computing sizing function") sizingFunction = vtkvmtk.vtkvmtkPolyDataSizingFunction() sizingFunction.SetInputData(remeshedSurface) sizingFunction.SetSizingFunctionArrayName(self.SizingFunctionArrayName) sizingFunction.SetScaleFactor(self.VolumeElementScaleFactor) sizingFunction.Update() self.PrintLog("Converting surface to mesh") surfaceToMesh = vmtkscripts.vmtkSurfaceToMesh() surfaceToMesh.Surface = sizingFunction.GetOutput() surfaceToMesh.Execute() self.PrintLog("Generating volume mesh") tetgen = vmtkscripts.vmtkTetGen() tetgen.Mesh = surfaceToMesh.Mesh tetgen.GenerateCaps = 0 tetgen.UseSizingFunction = 1 tetgen.SizingFunctionArrayName = self.SizingFunctionArrayName tetgen.CellEntityIdsArrayName = self.CellEntityIdsArrayName tetgen.Order = 1 tetgen.Quality = 1 tetgen.PLC = 1 tetgen.NoBoundarySplit = 1 tetgen.RemoveSliver = 1 tetgen.OutputSurfaceElements = 1 tetgen.OutputVolumeElements = 1 tetgen.Execute() self.Mesh = tetgen.Mesh if self.Mesh.GetNumberOfCells() == 0 and surfaceToMesh.Mesh.GetNumberOfCells() > 0: self.PrintLog('An error occurred during tetrahedralization. Will only output surface mesh.') self.Mesh = surfaceToMesh.Mesh if self.Tetrahedralize: tetrahedralize = vtkvmtk.vtkvmtkUnstructuredGridTetraFilter() tetrahedralize.SetInputData(self.Mesh) tetrahedralize.Update() self.Mesh = tetrahedralize.GetOutput() self.RemeshedSurface = remeshedSurface
def Execute(self): from vmtk import vmtkscripts if self.Surface == None: self.PrintError('Error: No input surface.') wallEntityOffset = 1 if self.SkipCapping or not self.BoundaryLayerOnCaps: self.PrintLog("Not capping surface") surface = self.Surface cellEntityIdsArray = vtk.vtkIntArray() cellEntityIdsArray.SetName(self.CellEntityIdsArrayName) cellEntityIdsArray.SetNumberOfTuples(surface.GetNumberOfCells()) cellEntityIdsArray.FillComponent(0, 0.0) surface.GetCellData().AddArray(cellEntityIdsArray) else: self.PrintLog("Capping surface") capper = vmtkscripts.vmtkSurfaceCapper() capper.Surface = self.Surface capper.Interactive = 0 capper.Method = self.CappingMethod capper.TriangleOutput = 0 capper.CellEntityIdOffset = self.Vessel_inlet_outlet capper.Execute() surface = capper.Surface if self.SkipRemeshing: remeshedSurface = surface else: self.PrintLog("Remeshing surface") remeshing = vmtkscripts.vmtkSurfaceRemeshing() remeshing.Surface = surface remeshing.CellEntityIdsArrayName = self.CellEntityIdsArrayName remeshing.TargetEdgeLength = self.TargetEdgeLength remeshing.MaxEdgeLength = self.MaxEdgeLength remeshing.MinEdgeLength = self.MinEdgeLength remeshing.TargetEdgeLengthFactor = self.TargetEdgeLengthFactor remeshing.TargetEdgeLengthArrayName = self.TargetEdgeLengthArrayName remeshing.TriangleSplitFactor = self.TriangleSplitFactor remeshing.ElementSizeMode = self.ElementSizeMode if self.RemeshCapsOnly: remeshing.ExcludeEntityIds = [self.Vessel_wall] remeshing.Execute() remeshedSurface = remeshing.Surface if self.BoundaryLayer: projection = vmtkscripts.vmtkSurfaceProjection() projection.Surface = remeshedSurface projection.ReferenceSurface = surface projection.Execute() normals = vmtkscripts.vmtkSurfaceNormals() normals.Surface = projection.Surface normals.NormalsArrayName = 'Normals' normals.Execute() surfaceToMesh = vmtkscripts.vmtkSurfaceToMesh() surfaceToMesh.Surface = normals.Surface surfaceToMesh.Execute() self.PrintLog("Generating 1st boundary layer -- PVS") placeholderCellEntityId = 9999 boundaryLayer = vmtkscripts.vmtkBoundaryLayer() boundaryLayer.Mesh = surfaceToMesh.Mesh boundaryLayer.WarpVectorsArrayName = 'Normals' boundaryLayer.NegateWarpVectors = True boundaryLayer.ThicknessArrayName = self.TargetEdgeLengthArrayName if self.ElementSizeMode == 'edgelength': boundaryLayer.ConstantThickness = True else: boundaryLayer.ConstantThickness = False boundaryLayer.IncludeSurfaceCells = 0 boundaryLayer.NumberOfSubLayers = self.NumberOfSubLayers boundaryLayer.NumberOfSubsteps = self.NumberOfSubsteps boundaryLayer.Relaxation = self.Relaxation boundaryLayer.LocalCorrectionFactor = self.LocalCorrectionFactor boundaryLayer.SubLayerRatio = self.SubLayerRatio boundaryLayer.Thickness = self.BoundaryLayerThicknessFactor * self.TargetEdgeLength boundaryLayer.ThicknessRatio = self.BoundaryLayerThicknessFactor * self.TargetEdgeLengthFactor boundaryLayer.MaximumThickness = self.BoundaryLayerThicknessFactor * self.MaxEdgeLength if not self.BoundaryLayerOnCaps: boundaryLayer.SidewallCellEntityId = placeholderCellEntityId boundaryLayer.InnerSurfaceCellEntityId = self.Vessel_wall boundaryLayer.VolumeCellEntityId = self.PVS boundaryLayer.Execute() # We need a second boundary layer to make sure we have the right OuterSurface self.PrintLog("Generating 2nd boundary layer -- PVS") placeholderCellEntityId2 = 99999 boundaryLayer2 = vmtkscripts.vmtkBoundaryLayer() boundaryLayer2.Mesh = surfaceToMesh.Mesh boundaryLayer2.WarpVectorsArrayName = 'Normals' boundaryLayer2.NegateWarpVectors = True boundaryLayer2.ThicknessArrayName = self.TargetEdgeLengthArrayName if self.ElementSizeMode == 'edgelength': boundaryLayer2.ConstantThickness = True else: boundaryLayer2.ConstantThickness = False boundaryLayer2.IncludeSurfaceCells = 1 boundaryLayer2.NumberOfSubLayers = self.NumberOfSubLayers boundaryLayer2.NumberOfSubsteps = self.NumberOfSubsteps boundaryLayer2.Relaxation = self.Relaxation boundaryLayer2.LocalCorrectionFactor = self.LocalCorrectionFactor boundaryLayer2.SubLayerRatio = self.SubLayerRatio boundaryLayer2.Thickness = self.BoundaryLayerThicknessFactor * self.TargetEdgeLength boundaryLayer2.ThicknessRatio = self.BoundaryLayerThicknessFactor * self.TargetEdgeLengthFactor boundaryLayer2.MaximumThickness = self.BoundaryLayerThicknessFactor * self.MaxEdgeLength if not self.BoundaryLayerOnCaps: boundaryLayer2.SidewallCellEntityId = placeholderCellEntityId2 boundaryLayer2.OuterSurfaceCellEntityId = self.PVS_wall boundaryLayer2.VolumeCellEntityId = self.PVS boundaryLayer2.Execute() meshToSurface = vmtkscripts.vmtkMeshToSurface() meshToSurface.Mesh = boundaryLayer.InnerSurfaceMesh meshToSurface.Execute() innerSurface = meshToSurface.Surface if not self.BoundaryLayerOnCaps: self.PrintLog("Capping inner surface") capper = vmtkscripts.vmtkSurfaceCapper() capper.Surface = innerSurface capper.Interactive = 0 capper.Method = self.CappingMethod capper.TriangleOutput = 1 capper.CellEntityIdOffset = self.Vessel_inlet_outlet capper.Execute() self.PrintLog("Remeshing endcaps") remeshing = vmtkscripts.vmtkSurfaceRemeshing() remeshing.Surface = capper.Surface remeshing.CellEntityIdsArrayName = self.CellEntityIdsArrayName remeshing.TargetEdgeLength = self.TargetEdgeLength * self.EndcapsEdgeLengthFactor remeshing.MaxEdgeLength = self.MaxEdgeLength remeshing.MinEdgeLength = self.MinEdgeLength remeshing.TargetEdgeLengthFactor = self.TargetEdgeLengthFactor * self.EndcapsEdgeLengthFactor remeshing.TargetEdgeLengthArrayName = self.TargetEdgeLengthArrayName remeshing.TriangleSplitFactor = self.TriangleSplitFactor remeshing.ElementSizeMode = self.ElementSizeMode remeshing.ExcludeEntityIds = [self.Vessel_wall] remeshing.Execute() innerSurface = remeshing.Surface self.PrintLog("Computing sizing function") sizingFunction = vtkvmtk.vtkvmtkPolyDataSizingFunction() sizingFunction.SetInputData(innerSurface) sizingFunction.SetSizingFunctionArrayName( self.SizingFunctionArrayName) sizingFunction.SetScaleFactor(self.VolumeElementScaleFactor) sizingFunction.Update() surfaceToMesh2 = vmtkscripts.vmtkSurfaceToMesh() surfaceToMesh2.Surface = sizingFunction.GetOutput() surfaceToMesh2.Execute() self.PrintLog("Generating volume mesh") tetgen = vmtkscripts.vmtkTetGen() tetgen.Mesh = surfaceToMesh2.Mesh tetgen.GenerateCaps = 0 tetgen.UseSizingFunction = 1 tetgen.SizingFunctionArrayName = self.SizingFunctionArrayName tetgen.CellEntityIdsArrayName = self.CellEntityIdsArrayName tetgen.Order = 1 tetgen.Quality = 1 tetgen.PLC = 1 tetgen.NoBoundarySplit = 1 tetgen.RemoveSliver = 1 tetgen.OutputSurfaceElements = 1 tetgen.OutputVolumeElements = 1 tetgen.RegionAttrib = 1 tetgen.Execute() # Define VisitNeighbors used to differenciate markers in Sidewall areas def VisitNeighbors(i, cellEntityId, cellEntityIdsArray, placeholderTag): cellPointIds = vtk.vtkIdList() self.Mesh.GetCellPoints(i, cellPointIds) neighborPointIds = vtk.vtkIdList() neighborPointIds.SetNumberOfIds(1) pointNeighborCellIds = vtk.vtkIdList() neighborCellIds = vtk.vtkIdList() for j in range(cellPointIds.GetNumberOfIds()): neighborPointIds.SetId(0, cellPointIds.GetId(j)) self.Mesh.GetCellNeighbors(i, neighborPointIds, pointNeighborCellIds) for k in range(pointNeighborCellIds.GetNumberOfIds()): neighborCellIds.InsertNextId( pointNeighborCellIds.GetId(k)) for j in range(neighborCellIds.GetNumberOfIds()): cellId = neighborCellIds.GetId(j) neighborCellEntityId = cellEntityIdsArray.GetTuple1(cellId) neighborCellType = self.Mesh.GetCellType(cellId) if neighborCellType not in [ vtk.VTK_TRIANGLE, vtk.VTK_QUADRATIC_TRIANGLE, vtk.VTK_QUAD ]: continue if neighborCellEntityId != placeholderTag: continue cellEntityIdsArray.SetTuple1(cellId, cellEntityId) VisitNeighbors(cellId, cellEntityId, cellEntityIdsArray, placeholderTag) self.PrintLog("Assembling PVS mesh - 1st layer") appendFilter = vtkvmtk.vtkvmtkAppendFilter() appendFilter.AddInputData(boundaryLayer.Mesh) appendFilter.AddInputData(tetgen.Mesh) appendFilter.Update() self.Mesh = appendFilter.GetOutput() # Use placeholderCellEntityId - inlet/outlet for the PVS-1 if not self.BoundaryLayerOnCaps: cellEntityIdsArray = self.Mesh.GetCellData().GetArray( self.CellEntityIdsArrayName) for i in range(self.Mesh.GetNumberOfCells()): cellEntityId = cellEntityIdsArray.GetTuple1(i) cellType = self.Mesh.GetCellType(i) if cellType not in [ vtk.VTK_TRIANGLE, vtk.VTK_QUADRATIC_TRIANGLE, vtk.VTK_QUAD ]: continue if cellEntityId in [ 0, 1, placeholderCellEntityId, self.Vessel_wall ]: continue VisitNeighbors( i, cellEntityId + self.PVS_inlet_outlet - self.Vessel_inlet_outlet, cellEntityIdsArray, placeholderCellEntityId) appendFilter.Update() self.Mesh = appendFilter.GetOutput() self.PrintLog("Assembling PVS mesh - 2nd layer") appendFilter2 = vtkvmtk.vtkvmtkAppendFilter() appendFilter2.AddInputData(appendFilter.GetOutput()) appendFilter2.AddInputData(boundaryLayer2.Mesh) appendFilter2.Update() self.Mesh = appendFilter2.GetOutput() # Use placeholderCellEntityId2 - inlet/outlet for the PVS-2 if not self.BoundaryLayerOnCaps: cellEntityIdsArray = self.Mesh.GetCellData().GetArray( self.CellEntityIdsArrayName) for i in range(self.Mesh.GetNumberOfCells()): cellEntityId = cellEntityIdsArray.GetTuple1(i) cellType = self.Mesh.GetCellType(i) if cellType not in [ vtk.VTK_TRIANGLE, vtk.VTK_QUADRATIC_TRIANGLE, vtk.VTK_QUAD ]: continue if cellEntityId in [ 0, 1, placeholderCellEntityId2, self.Vessel_wall ]: continue VisitNeighbors(i, cellEntityId, cellEntityIdsArray, placeholderCellEntityId2) self.PrintLog("Assembling final mesh") appendFilter2.Update() self.Mesh = appendFilter2.GetOutput() else: self.PrintLog("Computing sizing function") sizingFunction = vtkvmtk.vtkvmtkPolyDataSizingFunction() sizingFunction.SetInputData(remeshedSurface) sizingFunction.SetSizingFunctionArrayName( self.SizingFunctionArrayName) sizingFunction.SetScaleFactor(self.VolumeElementScaleFactor) sizingFunction.Update() self.PrintLog("Converting surface to mesh") surfaceToMesh = vmtkscripts.vmtkSurfaceToMesh() surfaceToMesh.Surface = sizingFunction.GetOutput() surfaceToMesh.Execute() self.PrintLog("Generating volume mesh") tetgen = vmtkscripts.vmtkTetGen() tetgen.Mesh = surfaceToMesh.Mesh tetgen.GenerateCaps = 0 tetgen.UseSizingFunction = 1 tetgen.SizingFunctionArrayName = self.SizingFunctionArrayName tetgen.CellEntityIdsArrayName = self.CellEntityIdsArrayName tetgen.Order = 1 tetgen.Quality = 1 tetgen.PLC = 1 tetgen.NoBoundarySplit = 1 tetgen.RemoveSliver = 1 tetgen.OutputSurfaceElements = 1 tetgen.OutputVolumeElements = 1 tetgen.Execute() self.Mesh = tetgen.Mesh if self.Mesh.GetNumberOfCells( ) == 0 and surfaceToMesh.Mesh.GetNumberOfCells() > 0: self.PrintLog( 'An error occurred during tetrahedralization. Will only output surface mesh.' ) self.Mesh = surfaceToMesh.Mesh if self.Tetrahedralize: tetrahedralize = vtkvmtk.vtkvmtkUnstructuredGridTetraFilter() tetrahedralize.SetInputData(self.Mesh) tetrahedralize.Update() self.Mesh = tetrahedralize.GetOutput() self.RemeshedSurface = remeshedSurface