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+python-versions = "^3.9" +content-hash = "007ea72bba6c933e5af6a4466fb8e46e2d776c9717434086a47bf2022094bb33" diff --git a/pythonVtk/pyproject.toml b/python-vtk/pyproject.toml similarity index 94% rename from pythonVtk/pyproject.toml rename to python-vtk/pyproject.toml index 26ae66167c..a62efa3304 100644 --- a/pythonVtk/pyproject.toml +++ b/python-vtk/pyproject.toml @@ -1,5 +1,5 @@ [tool.poetry] -name = "pythonvtk" +name = "python-vtk" version = "0.1.0" description = "" authors = ["Jim Schaff "] diff --git a/pythonVtk/tests/dummy_test.py b/python-vtk/tests/dummy_test.py similarity index 100% rename from pythonVtk/tests/dummy_test.py rename to python-vtk/tests/dummy_test.py diff --git a/pythonVtk/vcellvismesh/__init__.py b/python-vtk/vcellvismesh/__init__.py similarity index 100% rename from pythonVtk/vcellvismesh/__init__.py rename to python-vtk/vcellvismesh/__init__.py diff --git a/pythonVtk/vcellvismesh/constants.py b/python-vtk/vcellvismesh/constants.py similarity index 100% rename from pythonVtk/vcellvismesh/constants.py rename to python-vtk/vcellvismesh/constants.py diff --git a/pythonVtk/vcellvismesh/ttypes.py b/python-vtk/vcellvismesh/ttypes.py similarity index 100% rename from pythonVtk/vcellvismesh/ttypes.py rename to python-vtk/vcellvismesh/ttypes.py diff --git a/pythonVtk/vtkService/__init__.py b/python-vtk/vtkService/__init__.py similarity index 100% rename from pythonVtk/vtkService/__init__.py rename to python-vtk/vtkService/__init__.py diff --git a/pythonVtk/vtkService/makeLittleVtk.py b/python-vtk/vtkService/makeLittleVtk.py similarity index 96% rename from pythonVtk/vtkService/makeLittleVtk.py rename to python-vtk/vtkService/makeLittleVtk.py index a697d8c162..fb4ff371c6 100644 --- a/pythonVtk/vtkService/makeLittleVtk.py +++ b/python-vtk/vtkService/makeLittleVtk.py @@ -1,30 +1,30 @@ -import vtk - -import vtkService.vtkService as vtkService - -x = [1, 2, 3, 4] -y = [1, 2, 3, 4] -ugrid = vtk.vtkUnstructuredGrid() -points = vtk.vtkPoints() -points.SetDataTypeToDouble() -xyToNode = [[] for i in range(len(x))] -index = 0 -for i, xCoord in enumerate(x): - for yCoord in y: - points.InsertNextPoint(xCoord, yCoord, 0.0) - xyToNode[i].append(index) - index += 1 -ugrid.SetPoints(points) - -# Add the volume elements -for i, xCoord in enumerate(x[:-1]): - for j, yCoord in enumerate(y[:-1]): - idList = vtk.vtkIdList() - idList.InsertNextId(xyToNode[i][j]) - idList.InsertNextId(xyToNode[i + 1][j]) - idList.InsertNextId(xyToNode[i + 1][j + 1]) - idList.InsertNextId(xyToNode[i][j + 1]) - ugrid.InsertNextCell(vtk.VTK_QUAD, idList) - -vtkService.writevtk(ugrid, "abc.vtu") -vtkService.writeDataArrayToNewVtkFile("abc.vtu", "var", [1., 2., 3., 4., 5., 6., 7., 8., 9.], "abc_var.vtu") +import vtk + +import vtkService.vtkService as vtkService + +x = [1, 2, 3, 4] +y = [1, 2, 3, 4] +ugrid = vtk.vtkUnstructuredGrid() +points = vtk.vtkPoints() +points.SetDataTypeToDouble() +xyToNode = [[] for i in range(len(x))] +index = 0 +for i, xCoord in enumerate(x): + for yCoord in y: + points.InsertNextPoint(xCoord, yCoord, 0.0) + xyToNode[i].append(index) + index += 1 +ugrid.SetPoints(points) + +# Add the volume elements +for i, xCoord in enumerate(x[:-1]): + for j, yCoord in enumerate(y[:-1]): + idList = vtk.vtkIdList() + idList.InsertNextId(xyToNode[i][j]) + idList.InsertNextId(xyToNode[i + 1][j]) + idList.InsertNextId(xyToNode[i + 1][j + 1]) + idList.InsertNextId(xyToNode[i][j + 1]) + ugrid.InsertNextCell(vtk.VTK_QUAD, idList) + +vtkService.writevtk(ugrid, "abc.vtu") +vtkService.writeDataArrayToNewVtkFile("abc.vtu", "var", [1., 2., 3., 4., 5., 6., 7., 8., 9.], "abc_var.vtu") diff --git a/pythonVtk/vtkService/vtkAddData_not_used.py b/python-vtk/vtkService/vtkAddData_not_used.py similarity index 96% rename from pythonVtk/vtkService/vtkAddData_not_used.py rename to python-vtk/vtkService/vtkAddData_not_used.py index 1d2407b429..f5cd87c8cd 100644 --- a/pythonVtk/vtkService/vtkAddData_not_used.py +++ b/python-vtk/vtkService/vtkAddData_not_used.py @@ -1,41 +1,41 @@ -import argparse - -import numpy as np -import vtk - -from vtkService.vtkService import writeDataArrayToNewVtkFile - - -def main(): - # try: - parser = argparse.ArgumentParser() - parser.add_argument("invtkfile", help="filename of input vtk mesh (VTK XML unstructured grid") - parser.add_argument("varname", help="name of cell data variable") - parser.add_argument("outvtkfile", help="filename of output vtk mesh (VTK XML unstructured grid") - args = parser.parse_args() - - # deserialize raw bytes into VarDataAdd - reader = vtk.vtkXMLUnstructuredGridReader() - reader.SetFileName(args.invtkfile) - reader.Update() - mesh = reader.GetOutput() - assert isinstance(mesh, vtk.vtkUnstructuredGrid) - num_cells = mesh.GetCells().GetSize() - - # write 0..N-1 into data - npdata = np.arange(0, num_cells, 0.1) - - writeDataArrayToNewVtkFile(args.invtkfile, args.varname, npdata, args.outvtkfile) - print("done") - - -# except: -# e = sys.exc_info()[0] -# print("exception "+e) -# sys.exit(-1) -# else: -# sys.exit(0) - - -if __name__ == '__main__': - main() +import argparse + +import numpy as np +import vtk + +from vtkService.vtkService import writeDataArrayToNewVtkFile + + +def main(): + # try: + parser = argparse.ArgumentParser() + parser.add_argument("invtkfile", help="filename of input vtk mesh (VTK XML unstructured grid") + parser.add_argument("varname", help="name of cell data variable") + parser.add_argument("outvtkfile", help="filename of output vtk mesh (VTK XML unstructured grid") + args = parser.parse_args() + + # deserialize raw bytes into VarDataAdd + reader = vtk.vtkXMLUnstructuredGridReader() + reader.SetFileName(args.invtkfile) + reader.Update() + mesh = reader.GetOutput() + assert isinstance(mesh, vtk.vtkUnstructuredGrid) + num_cells = mesh.GetCells().GetSize() + + # write 0..N-1 into data + npdata = np.arange(0, num_cells, 0.1) + + writeDataArrayToNewVtkFile(args.invtkfile, args.varname, npdata, args.outvtkfile) + print("done") + + +# except: +# e = sys.exc_info()[0] +# print("exception "+e) +# sys.exit(-1) +# else: +# sys.exit(0) + + +if __name__ == '__main__': + main() diff --git a/pythonVtk/vtkService/vtkService.py b/python-vtk/vtkService/vtkService.py similarity index 97% rename from pythonVtk/vtkService/vtkService.py rename to python-vtk/vtkService/vtkService.py index 074a705b60..42c5562a8f 100644 --- a/pythonVtk/vtkService/vtkService.py +++ b/python-vtk/vtkService/vtkService.py @@ -1,660 +1,660 @@ -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 vcellvismesh.ttypes import ChomboIndexData -from vcellvismesh.ttypes import FiniteVolumeIndexData -from vcellvismesh.ttypes import MovingBoundaryIndexData -from vcellvismesh.ttypes import PolyhedronFace -from vcellvismesh.ttypes import VisIrregularPolyhedron -from vcellvismesh.ttypes import VisLine -from vcellvismesh.ttypes import VisMesh -from vcellvismesh.ttypes import VisPolygon -from 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() +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 vcellvismesh.ttypes import ChomboIndexData +from vcellvismesh.ttypes import FiniteVolumeIndexData +from vcellvismesh.ttypes import MovingBoundaryIndexData +from vcellvismesh.ttypes import PolyhedronFace +from vcellvismesh.ttypes import VisIrregularPolyhedron +from vcellvismesh.ttypes import VisLine +from vcellvismesh.ttypes import VisMesh +from vcellvismesh.ttypes import VisPolygon +from 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 = 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