import argparse import copy import os import sys import traceback import vtkmodules.all as vtk from thrift.TSerialization import TBinaryProtocol from thrift.TSerialization import deserialize from thrift.TSerialization import serialize from python_vtk.vcellvismesh.ttypes import ChomboIndexData from python_vtk.vcellvismesh.ttypes import FiniteVolumeIndexData from python_vtk.vcellvismesh.ttypes import MovingBoundaryIndexData from python_vtk.vcellvismesh.ttypes import PolyhedronFace from python_vtk.vcellvismesh.ttypes import VisIrregularPolyhedron from python_vtk.vcellvismesh.ttypes import VisLine from python_vtk.vcellvismesh.ttypes import VisMesh from python_vtk.vcellvismesh.ttypes import VisPolygon from python_vtk.vcellvismesh.ttypes import VisTetrahedron def writeChomboVolumeVtkGridAndIndexData(visMesh: VisMesh, domainname: str, vtkfile, indexfile) -> None: originalVisMesh = visMesh correctedVisMesh = originalVisMesh # same mesh if no irregularPolyhedra if originalVisMesh.irregularPolyhedra is not None: correctedVisMesh = copy.deepcopy(visMesh) if correctedVisMesh.tetrahedra is None: correctedVisMesh.tetrahedra = [] for irregularPolyhedron in correctedVisMesh.irregularPolyhedra: tets = createTetrahedra(irregularPolyhedron, correctedVisMesh) for tet in tets: correctedVisMesh.tetrahedra.append(tet) correctedVisMesh.irregularPolyhedra = None vtkgrid: vtk.vtkUnstructuredGrid = getVolumeVtkGrid(correctedVisMesh) writevtk(vtkgrid, vtkfile) chomboIndexData = ChomboIndexData() chomboIndexData.chomboVolumeIndices = [] chomboIndexData.domainName = domainname if correctedVisMesh.dimension == 2: if correctedVisMesh.polygons is not None: for polygon in correctedVisMesh.polygons: assert isinstance(polygon, VisPolygon) chomboIndexData.chomboVolumeIndices.append(polygon.chomboVolumeIndex) if chomboIndexData.chomboVolumeIndices is None: print("didn't find any indices ... bad") elif correctedVisMesh.dimension == 3: if correctedVisMesh.visVoxels is not None: for voxel in correctedVisMesh.visVoxels: chomboIndexData.chomboVolumeIndices.append(voxel.chomboVolumeIndex) if correctedVisMesh.irregularPolyhedra is not None: raise Exception("unexpected irregular polyhedra in mesh, should have been replaced with tetrahedra") if correctedVisMesh.tetrahedra is not None: for tetrahedron in correctedVisMesh.tetrahedra: assert isinstance(tetrahedron, VisTetrahedron) chomboIndexData.chomboVolumeIndices.append(tetrahedron.chomboVolumeIndex) if len(chomboIndexData.chomboVolumeIndices) == 0: print("didn't find any indices ... bad") writeChomboIndexData(indexfile, chomboIndexData) def writeChomboMembraneVtkGridAndIndexData(visMesh: VisMesh, domainname: str, vtkfile, indexfile) -> None: vtkgrid = getMembraneVtkGrid(visMesh) writevtk(vtkgrid, vtkfile) chomboIndexData = ChomboIndexData() chomboIndexData.chomboSurfaceIndices = [] if domainname.upper().endswith("MEMBRANE") is False: raise Exception("expecting domain name ending with membrane") chomboIndexData.domainName = domainname if visMesh.dimension == 3: if visMesh.surfaceTriangles is not None: for surfaceTriangle in visMesh.surfaceTriangles: chomboIndexData.chomboSurfaceIndices.append(surfaceTriangle.chomboSurfaceIndex) elif visMesh.dimension == 2: if visMesh.visLines is not None: for visLine in visMesh.visLines: assert isinstance(visLine, VisLine) chomboIndexData.chomboSurfaceIndices.append(visLine.chomboSurfaceIndex) if len(chomboIndexData.chomboSurfaceIndices) == 0: print("didn't find any indices ... bad") writeChomboIndexData(indexfile, chomboIndexData) def writeFiniteVolumeSmoothedVtkGridAndIndexData(visMesh: VisMesh, domainName: str, vtuFile, indexFile) -> None: vtkgrid = getVolumeVtkGrid(visMesh) if visMesh.dimension == 3: vtkgridSmoothed = smoothUnstructuredGridSurface(vtkgrid) else: vtkgridSmoothed = vtkgrid writevtk(vtkgridSmoothed, vtuFile) finiteVolumeIndexData = FiniteVolumeIndexData() finiteVolumeIndexData.finiteVolumeIndices = [] finiteVolumeIndexData.domainName = domainName if visMesh.dimension == 2: # if volume if visMesh.polygons is not None: for polygon in visMesh.polygons: finiteVolumeIndexData.finiteVolumeIndices.append(polygon.finiteVolumeIndex) # if membrane if visMesh.visLines is not None: for visLine in visMesh.visLines: finiteVolumeIndexData.finiteVolumeIndices.append(visLine.finiteVolumeIndex) elif visMesh.dimension == 3: # if volume if visMesh.visVoxels is not None: for voxel in visMesh.visVoxels: finiteVolumeIndexData.finiteVolumeIndices.append(voxel.finiteVolumeIndex) if visMesh.irregularPolyhedra is not None: raise Exception("unexpected irregular polyhedra in mesh, should have been replaced with tetrahedra") if visMesh.tetrahedra is not None: for tetrahedron in visMesh.tetrahedra: finiteVolumeIndexData.finiteVolumeIndices.append(tetrahedron.finiteVolumeIndex) # if membrane if visMesh.polygons is not None: for polygon in visMesh.polygons: finiteVolumeIndexData.finiteVolumeIndices.append(polygon.finiteVolumeIndex) if finiteVolumeIndexData.finiteVolumeIndices == None or len(finiteVolumeIndexData.finiteVolumeIndices) == 0: print("didn't find any indices ... bad") writeFiniteVolumeIndexData(indexFile, finiteVolumeIndexData) def writeFiniteVolumeIndexData(finiteVolumeIndexFile, finiteVolumeIndexData): assert isinstance(finiteVolumeIndexData, FiniteVolumeIndexData) blob = serialize(finiteVolumeIndexData, protocol_factory=TBinaryProtocol.TBinaryProtocolFactory()) ff = open(finiteVolumeIndexFile,'wb') ff.write(blob) ff.close() print("wrote finitevolume data to file "+str(finiteVolumeIndexFile)) def writeMovingBoundaryVolumeVtkGridAndIndexData(visMesh: VisMesh, domainName: str, vtuFile, indexFile): vtkgrid = getVolumeVtkGrid(visMesh) writevtk(vtkgrid, vtuFile) movingBoundaryIndexData = MovingBoundaryIndexData() movingBoundaryIndexData.movingBoundaryVolumeIndices = [] movingBoundaryIndexData.domainName = domainName movingBoundaryIndexData.timeIndex = 0 if visMesh.dimension == 2: # if volume if visMesh.polygons is not None: for polygon in visMesh.polygons: movingBoundaryIndexData.movingBoundaryVolumeIndices.append(polygon.movingBoundaryVolumeIndex) # if membrane if visMesh.visLines is not None: for visLine in visMesh.visLines: movingBoundaryIndexData.movingBoundarySurfaceIndices.append(visLine.movingBoundarySurfaceIndex) # elif visMesh.dimension == 3: # # if volume # if visMesh.visVoxels is not None: # for voxel in visMesh.visVoxels: # movingBoundaryIndexData.finiteVolumeIndices.append(voxel.finiteVolumeIndex) # if visMesh.irregularPolyhedra is not None: # raise Exception("unexpected irregular polyhedra in mesh, should have been replaced with tetrahedra") # if visMesh.tetrahedra is not None: # for tetrahedron in visMesh.tetrahedra: # movingBoundaryIndexData.finiteVolumeIndices.append(tetrahedron.finiteVolumeIndex) # # if membrane # if visMesh.polygons is not None: # for polygon in visMesh.polygons: # movingBoundaryIndexData.finiteVolumeIndices.append(polygon.finiteVolumeIndex) if movingBoundaryIndexData.movingBoundaryVolumeIndices == None and movingBoundaryIndexData.movingBoundarySurfaceIndices == None: print("didn't find any indices ... bad") if movingBoundaryIndexData.movingBoundaryVolumeIndices != None and len(movingBoundaryIndexData.movingBoundaryVolumeIndices) == 0: print("didn't find any indices ... bad") if movingBoundaryIndexData.movingBoundarySurfaceIndices != None and len(movingBoundaryIndexData.movingBoundarySurfaceIndices) == 0: print("didn't find any indices ... bad") writeMovingBoundaryIndexData(indexFile, movingBoundaryIndexData) def writeComsolVolumeVtkGridAndIndexData(visMesh, domainName, vtuFile, indexFile): assert isinstance(visMesh, VisMesh) vtkgrid = getVolumeVtkGrid(visMesh) writevtk(vtkgrid, vtuFile) # movingBoundaryIndexData = MovingBoundaryIndexData() # movingBoundaryIndexData.movingBoundaryVolumeIndices = [] # movingBoundaryIndexData.domainName = domainName # movingBoundaryIndexData.timeIndex = 0 # if visMesh.dimension == 2: # # if volume # if visMesh.polygons is not None: # for polygon in visMesh.polygons: # movingBoundaryIndexData.movingBoundaryVolumeIndices.append(polygon.movingBoundaryVolumeIndex) # # if membrane # if visMesh.visLines is not None: # for visLine in visMesh.visLines: # movingBoundaryIndexData.movingBoundarySurfaceIndices.append(visLine.movingBoundarySurfaceIndex) # elif visMesh.dimension == 3: # # if volume # if visMesh.visVoxels is not None: # for voxel in visMesh.visVoxels: # movingBoundaryIndexData.finiteVolumeIndices.append(voxel.finiteVolumeIndex) # if visMesh.irregularPolyhedra is not None: # raise Exception("unexpected irregular polyhedra in mesh, should have been replaced with tetrahedra") # if visMesh.tetrahedra is not None: # for tetrahedron in visMesh.tetrahedra: # movingBoundaryIndexData.finiteVolumeIndices.append(tetrahedron.finiteVolumeIndex) # # if membrane # if visMesh.polygons is not None: # for polygon in visMesh.polygons: # movingBoundaryIndexData.finiteVolumeIndices.append(polygon.finiteVolumeIndex) # if movingBoundaryIndexData.movingBoundaryVolumeIndices == None and movingBoundaryIndexData.movingBoundarySurfaceIndices == None: # print "didn't find any indices ... bad" # # if movingBoundaryIndexData.movingBoundaryVolumeIndices != None and len(movingBoundaryIndexData.movingBoundaryVolumeIndices) == 0: # print "didn't find any indices ... bad" # # if movingBoundaryIndexData.movingBoundarySurfaceIndices != None and len(movingBoundaryIndexData.movingBoundarySurfaceIndices) == 0: # print "didn't find any indices ... bad" # #writeMovingBoundaryIndexData(indexFile, None) def writeMovingBoundaryIndexData(movingBoundaryIndexFile, movingBoundaryIndexData): assert isinstance(movingBoundaryIndexData, MovingBoundaryIndexData) blob = serialize(movingBoundaryIndexData, protocol_factory=TBinaryProtocol.TBinaryProtocolFactory()) ff = open(movingBoundaryIndexFile,'wb') ff.write(blob) ff.close() print("wrote movingboundary data to file "+str(movingBoundaryIndexFile)) def writeChomboIndexData(chomboIndexFile, chomboIndexData): """ Returns: None: """ assert isinstance(chomboIndexData, ChomboIndexData) blob = serialize(chomboIndexData, protocol_factory=TBinaryProtocol.TBinaryProtocolFactory()) ff = open(chomboIndexFile,'wb') ff.write(blob) ff.close() print("wrote chomboIndex data to file "+str(chomboIndexFile)) # # read a vtkUnstructuredGrid from the XML format # def readvtk(vtkfile): if not os.path.isfile(vtkfile): raise Exception("unstructured grid " + str(vtkfile) + " not found") tester = vtk.vtkXMLFileReadTester() tester.SetFileName(str(vtkfile)) if tester.TestReadFile() != 1: raise Exception("expecting XML formatted VTK unstructured grid") reader = vtk.vtkXMLUnstructuredGridReader() reader.SetFileName(vtkfile) reader.Update() vtkgrid = reader.GetOutput() assert isinstance(vtkgrid, vtk.vtkUnstructuredGrid) print("read from file " + str(vtkfile)) vtkgrid.BuildLinks() return vtkgrid # # write a vtkUnstructuredGrid to the XML format # def writevtk(vtkgrid, filename): writer = vtk.vtkXMLUnstructuredGridWriter() bASCII = False if bASCII: writer.SetDataModeToAscii() else: writer.SetCompressorTypeToNone() writer.SetDataModeToBinary() try: writer.SetInputData(vtkgrid) except AttributeError: writer.SetInput(vtkgrid) writer.SetFileName(filename) writer.Update() print("wrote to file "+str(filename)) # # create a single-variable vtu file # def writeDataArrayToNewVtkFile(emptyMeshFile, varName, data, newMeshFile): assert type(emptyMeshFile) is str assert type(varName) is str assert type(newMeshFile) is str try: #raise ImportError("dummy exception") import numpy as np from vtk.util import numpy_support print("writing varData using numpy") data = np.array(data) vtkgrid = readvtk(emptyMeshFile) assert isinstance(vtkgrid, vtk.vtkUnstructuredGrid) # # add cell data array to the empty mesh for this variable # dataArray = vtk.vtkDoubleArray() dataArray = numpy_support.numpy_to_vtk(data) assert isinstance(dataArray, ) dataArray.SetName(varName) cellData: vtk.vtkCellData = vtkgrid.GetCellData() cellData.AddArray(dataArray) # # write mesh and data to the file for that domain and time # writevtk(vtkgrid, newMeshFile) except ImportError as nonumpy: import array print("writing varData using array package") print(type(data)) print(str(data)) data = array.array('d', data) vtkgrid = readvtk(emptyMeshFile) # # add cell data array to the empty mesh for this variable # dataArray = vtk.vtkDoubleArray() dataArray.SetVoidArray(data, len(data), 1) dataArray.SetNumberOfComponents(1) dataArray.SetName(varName) cellData: vtk.vtkCellData = vtkgrid.GetCellData() cellData.AddArray(dataArray) # # write mesh and data to the file for that domain and time # writevtk(vtkgrid, newMeshFile) def getMembraneVtkGrid(visMesh: VisMesh) -> vtk.vtkUnstructuredGrid: vtkpoints = vtk.vtkPoints() for visPoint in visMesh.surfacePoints: vtkpoints.InsertNextPoint(visPoint.x,visPoint.y,visPoint.z) vtkgrid = vtk.vtkUnstructuredGrid() vtkgrid.Allocate(len(visMesh.surfacePoints), len(visMesh.surfacePoints)) vtkgrid.SetPoints(vtkpoints) if visMesh.dimension == 2: vtkline = vtk.vtkLine() lineType = vtkline.GetCellType() for line in visMesh.visLines: pts = vtk.vtkIdList() pts.InsertNextId(line.p1) pts.InsertNextId(line.p2) vtkgrid.InsertNextCell(lineType, pts) else: vtktriangle = vtk.vtkTriangle() triangleType = vtktriangle.GetCellType() for surfaceTriangle in visMesh.surfaceTriangles: pts = vtk.vtkIdList() for pi in surfaceTriangle.pointIndices: pts.InsertNextId(pi) # each triangle is a cell vtkgrid.InsertNextCell(triangleType, pts) vtkgrid.BuildLinks() return vtkgrid def getVolumeVtkGrid(visMesh: VisMesh) -> vtk.vtkUnstructuredGrid: bClipPolyhedra = True vtkpoints = vtk.vtkPoints() for visPoint in visMesh.points: vtkpoints.InsertNextPoint(visPoint.x, visPoint.y, visPoint.z) vtkgrid = vtk.vtkUnstructuredGrid() vtkgrid.Allocate(len(visMesh.points), len(visMesh.points)) vtkgrid.SetPoints(vtkpoints) quadType = vtk.vtkQuad().GetCellType() # lineType = vtk.vtkLine().GetCellType() polygonType = vtk.vtkPolygon().GetCellType() polyhedronType = vtk.vtkPolyhedron().GetCellType() triangleType = vtk.vtkTriangle().GetCellType() voxelType = vtk.vtkVoxel().GetCellType() tetraType = vtk.vtkTetra().GetCellType() if visMesh.polygons != None: for visPolygon in visMesh.polygons: pts = vtk.vtkIdList() polygonPoints = visPolygon.pointIndices for p in polygonPoints: pts.InsertNextId(p) numPoints = len(polygonPoints) if numPoints == 4: vtkgrid.InsertNextCell(quadType, pts) elif numPoints == 3: vtkgrid.InsertNextCell(triangleType, pts) else: vtkgrid.InsertNextCell(polygonType, pts) # # replace any VisIrregularPolyhedron with a list of VisTetrahedron # if visMesh.visVoxels != None: for voxel in visMesh.visVoxels: pts = vtk.vtkIdList() polyhedronPoints = voxel.pointIndices for p in polyhedronPoints: pts.InsertNextId(p) vtkgrid.InsertNextCell(voxelType, pts) if visMesh.tetrahedra != None: for visTet in visMesh.tetrahedra: assert isinstance(visTet, VisTetrahedron) pts = vtk.vtkIdList() tetPoints = visTet.pointIndices for p in tetPoints: pts.InsertNextId(p) vtkgrid.InsertNextCell(tetraType, pts) bInitializedFaces = False if visMesh.irregularPolyhedra != None: for clippedPolyhedron in visMesh.irregularPolyhedra: if bClipPolyhedra == True: tets = createTetrahedra(clippedPolyhedron, visMesh) for visTet in tets: pts = vtk.vtkIdList() tetPoints = visTet.getPointIndices() for p in tetPoints: pts.InsertNextId(p) vtkgrid.InsertNextCell(tetraType, pts) else: faceStreamList = vtk.vtkIdList() faceStream = getVtkFaceStream(clippedPolyhedron) for p in faceStream: faceStreamList.InsertNextId(p) if bInitializedFaces == False and vtkgrid.GetNumberOfCells() > 0: vtkgrid.InitializeFacesRepresentation(vtkgrid.GetNumberOfCells()) bInitializedFaces = True vtkgrid.InsertNextCell(polyhedronType, faceStreamList) vtkgrid.BuildLinks() # vtkgrid.Squeeze() return vtkgrid def getVtkFaceStream(irregularPolyhedron: VisIrregularPolyhedron) -> list[int]: faceStream = [len(irregularPolyhedron.polyhedronFaces), ] for polyhedronFace in irregularPolyhedron.polyhedronFaces: faceStream.append(len(polyhedronFace.getVertices())) for v in polyhedronFace.vertices: faceStream.append(v) intFaceStream = [int(v) for v in faceStream] return intFaceStream def smoothUnstructuredGridSurface(vtkGrid: vtk.vtkUnstructuredGrid) -> vtk.vtkUnstructuredGrid: ugGeometryFilter = vtk.vtkUnstructuredGridGeometryFilter() ugGeometryFilter.PassThroughPointIdsOn() ugGeometryFilter.MergingOff() try: ugGeometryFilter.SetInputData(vtkGrid) except AttributeError: ugGeometryFilter.SetInput(vtkGrid) ugGeometryFilter.Update() surfaceUnstructuredGrid: vtk.vtkUnstructuredGrid = ugGeometryFilter.GetOutput() originalPointsIdsName = ugGeometryFilter.GetOriginalPointIdsName() cellData = surfaceUnstructuredGrid.GetCellData() numCellArrays = cellData.GetNumberOfArrays() for i in range(0, numCellArrays): cellArrayName = cellData.GetArrayName(i) print("CellArray(" + str(i) + ") '" + cellArrayName + "')") pointData: vtk.vtkPointData = surfaceUnstructuredGrid.GetPointData() numPointArrays = pointData.GetNumberOfArrays() for i in range(0, numPointArrays): pointArrayName = pointData.GetArrayName(i) print("PointArray(" + str(i) + ") '" + pointArrayName + "'") geometryFilter = vtk.vtkGeometryFilter() try: geometryFilter.SetInputData(surfaceUnstructuredGrid) except AttributeError: geometryFilter.SetInput(surfaceUnstructuredGrid) geometryFilter.Update() polyData: vtk.vtkPolyData = geometryFilter.GetOutput() filter = vtk.vtkWindowedSincPolyDataFilter() try: filter.SetInputData(polyData) except AttributeError: filter.SetInput(polyData) filter.SetNumberOfIterations(15) filter.BoundarySmoothingOff() filter.FeatureEdgeSmoothingOff() filter.SetFeatureAngle(120.0) filter.SetPassBand(0.001) filter.NonManifoldSmoothingOff() filter.NormalizeCoordinatesOn() filter.Update() smoothedPolydata = filter.GetOutput() smoothedPoints: vtk.vtkPoints = smoothedPolydata.GetPoints() smoothedPointData: vtk.vtkPointData = smoothedPolydata.GetPointData() pointIdsArray: vtk.vtkIdTypeArray = smoothedPointData.GetArray(originalPointsIdsName) pointsIdsArraySize = pointIdsArray.GetSize() origPoints = vtkGrid.GetPoints() for i in range(0, pointsIdsArraySize): pointId = pointIdsArray.GetValue(i) smoothedPoint = smoothedPoints.GetPoint(i) origPoints.SetPoint(pointId, smoothedPoint) return vtkGrid def getPointIndices(irregularPolyhedron: VisIrregularPolyhedron) -> list[int]: assert isinstance(irregularPolyhedron, VisIrregularPolyhedron) pointIndicesSet = set() for face in irregularPolyhedron.polyhedronFaces: assert(isinstance(face, PolyhedronFace)) for pointIndex in face.vertices: pointIndicesSet.add(pointIndex) pointArray = [int(x) for x in pointIndicesSet] return pointArray def createTetrahedra(clippedPolyhedron: VisIrregularPolyhedron, visMesh: VisMesh): vtkpolydata = vtk.vtkPolyData() vtkpoints = vtk.vtkPoints() polygonType = vtk.vtkPolygon().GetCellType() uniquePointIndices = getPointIndices(clippedPolyhedron) for point in uniquePointIndices: visPoint = visMesh.points[point] vtkpoints.InsertNextPoint(visPoint.x, visPoint.y, visPoint.z) vtkpolydata.Allocate(100, 100) vtkpolydata.SetPoints(vtkpoints) for face in clippedPolyhedron.polyhedronFaces: faceIdList = vtk.vtkIdList() for visPointIndex in face.vertices: vtkpointid = -1 for i in range(0, len(uniquePointIndices)): if uniquePointIndices[i] == visPointIndex: vtkpointid = i faceIdList.InsertNextId(vtkpointid) vtkpolydata.InsertNextCell(polygonType, faceIdList) delaunayFilter = vtk.vtkDelaunay3D() try: delaunayFilter.SetInputData(vtkpolydata) except AttributeError: delaunayFilter.SetInput(vtkpolydata) delaunayFilter.Update() delaunayFilter.SetAlpha(0.1) vtkgrid2: vtk.vtkUnstructuredGrid = delaunayFilter.GetOutput() assert isinstance(vtkgrid2, vtk.vtkUnstructuredGrid) # runtime check, remove later visTets = [] numTets = vtkgrid2.GetNumberOfCells() if numTets < 1: if len(uniquePointIndices)==4: visTet = VisTetrahedron(uniquePointIndices) visTet.chomboVolumeIndex = clippedPolyhedron.chomboVolumeIndex visTet.finiteVolumeIndex = clippedPolyhedron.finiteVolumeIndex visTets.append(visTet) print("made trivial tet ... maybe inside out") else: print("found no tets, there are "+str(len(uniquePointIndices))+" unique point indices") # print("numFaces = "+str(vtkpolydata.GetNumberOfCells())+", numTets = "+str(numTets)); for cellIndex in range(0, numTets): cell = vtkgrid2.GetCell(cellIndex) if isinstance(cell, vtk.vtkTetra): vtkTet: vtk.vtkTetra = cell tetPointIds: vtk.vtkIdList = vtkTet.GetPointIds() assert isinstance(tetPointIds, vtk.vtkIdList) # # translate from vtkgrid pointids to visMesh point ids # numPoints = tetPointIds.GetNumberOfIds() visPointIds = [] for p in range(0, numPoints): visPointIds.append(uniquePointIndices[tetPointIds.GetId(p)]) visTet = VisTetrahedron(visPointIds) if clippedPolyhedron.chomboVolumeIndex != None: visTet.chomboVolumeIndex = clippedPolyhedron.chomboVolumeIndex if clippedPolyhedron.finiteVolumeIndex != None: visTet.finiteVolumeIndex = clippedPolyhedron.finiteVolumeIndex visTets.append(visTet) else: print("ChomboMeshMapping.createTetrahedra(): expecting a tet, found a " + cell.__type__) return visTets def main(): # sys.setrecursionlimit(100000) try: parser = argparse.ArgumentParser() list_of_meshtypes = ["chombovolume", "chombomembrane", "finitevolume", "movingboundary", "comsolvolume"] parser.add_argument("meshtype", help="type of visMesh processing required and index file generated", choices=list_of_meshtypes) parser.add_argument("domainname", help="domain name for output mesh") parser.add_argument("vismeshfile", help="filename of input visMesh to be processed (thrift serialization via TBinaryProtocol)") parser.add_argument("vtkfile", help="filename of output vtk mesh (VTK XML unstructured grid") parser.add_argument("indexfile", help="filename of output ChomboIndexData or FiniteVolumeIndexData (thrift serialization via TBinaryProtocol)") args = parser.parse_args() f_vismesh = open(args.vismeshfile, "rb") blob_vismesh = f_vismesh.read() print("read "+str(len(blob_vismesh))+" bytes from "+args.vismeshfile) f_vismesh.close() visMesh = VisMesh() protocol_factory = TBinaryProtocol.TBinaryProtocolFactory # deserialize(visMesh, blob_vismesh, protocol_factory = protocol_factory()) print("starting deserialization") deserialize(visMesh, blob_vismesh, protocol_factory=protocol_factory()) print("done with deserialization") if args.meshtype == "chombovolume": writeChomboVolumeVtkGridAndIndexData(visMesh, args.domainname, args.vtkfile, args.indexfile) elif args.meshtype == "chombomembrane": writeChomboMembraneVtkGridAndIndexData(visMesh, args.domainname, args.vtkfile, args.indexfile) elif args.meshtype == "finitevolume": writeFiniteVolumeSmoothedVtkGridAndIndexData(visMesh, args.domainname, args.vtkfile, args.indexfile) elif args.meshtype == "movingboundary": writeMovingBoundaryVolumeVtkGridAndIndexData(visMesh, args.domainname, args.vtkfile, args.indexfile) elif args.meshtype == "comsolvolume": writeComsolVolumeVtkGridAndIndexData(visMesh, args.domainname, args.vtkfile, args.indexfile) else: raise Exception("meshtype "+str(args.meshtype)+" not supported") except: e_info = sys.exc_info() traceback.print_exception(e_info[0], e_info[1], e_info[2], file=sys.stdout) sys.stderr.write("exception: "+str(e_info[0])+": "+str(e_info[1])+"\n") sys.stderr.flush() sys.exit(-1) else: sys.exit(0) if __name__ == '__main__': main()