def testLowerDimVtuToMesh(self): vtu = vtktools.vtu() points = vtk.vtkPoints() points.SetDataTypeToDouble() points.InsertNextPoint(0.0, 0.0, 0.0) points.InsertNextPoint(0.0, 0.0, 1.0) vtu.ugrid.SetPoints(points) mesh = VtuToMesh(vtu) self.assertEquals(mesh.GetDim(), 1) self.assertEquals(mesh.NodeCount(), 2) self.assertEquals(mesh.GetNodeCoord(0)[0], 0.0) self.assertEquals(mesh.GetNodeCoord(1)[0], 1.0) return
def testLowerDimVtuToMesh(self): vtu = vtktools.vtu() points = vtk.vtkPoints() points.SetDataTypeToDouble() points.InsertNextPoint(0.0, 0.0, 0.0) points.InsertNextPoint(0.0, 0.0, 1.0) vtu.ugrid.SetPoints(points) mesh = VtuToMesh(vtu) self.assertEquals(mesh.GetDim(), 1) self.assertEquals(mesh.NodeCount(), 2) self.assertEquals(mesh.GetNodeCoord(0)[0], 0.0) self.assertEquals(mesh.GetNodeCoord(1)[0], 1.0) return
basename = sys.argv[1]
debug.dprint("vtu basename: " + basename)
nPieces = fluiditytools.FindMaxVtuId(basename) + 1
debug.dprint("Number of pieces: " + str(nPieces))
# Write to a temporary directory so that the first piece isn't overwritten
tempDir = tempfile.mkdtemp()
# Create the parallel writer
writer = vtk.vtkXMLPUnstructuredGridWriter()
writer.SetNumberOfPieces(nPieces)
writer.WriteSummaryFileOn()
pvtuName = basename + ".pvtu"
writer.SetFileName(os.path.join(tempDir, pvtuName))
# Load in the first piece, so that the parallel writer has something to do (and
# knows which fields we have)
pieceName = fluiditytools.VtuFilenames(basename, 0)[0]
pieceVtu = vtktools.vtu(pieceName)
if vtk.vtkVersion.GetVTKMajorVersion() <= 5:
writer.SetInput(0, pieceVtu.ugrid)
else:
writer.SetInputData(0, pieceVtu.ugrid)
# Write
writer.Write()
# Move the output back and clean up
filehandling.Move(os.path.join(tempDir, pvtuName), pvtuName)
filehandling.Rmdir(tempDir, force=True)
basename = sys.argv[1]
debug.dprint("vtu basename: " + basename)
nPieces = fluiditytools.FindMaxVtuId(basename) + 1
debug.dprint("Number of pieces: " + str(nPieces))
# Write to a temporary directory so that the first piece isn't overwritten
tempDir = tempfile.mkdtemp()
# Create the parallel writer
writer = vtk.vtkXMLPUnstructuredGridWriter()
writer.SetNumberOfPieces(nPieces)
writer.WriteSummaryFileOn()
pvtuName = basename + ".pvtu"
writer.SetFileName(os.path.join(tempDir, pvtuName))
# Load in the first piece, so that the parallel writer has something to do (and
# knows which fields we have)
pieceName = fluiditytools.VtuFilenames(basename, 0)[0]
pieceVtu = vtktools.vtu(pieceName)
if vtk.vtkVersion.GetVTKMajorVersion() <= 5:
writer.SetInput(0, pieceVtu.ugrid)
else:
writer.SetInputData(0, pieceVtu.ugrid)
# Write
writer.Write()
# Move the output back and clean up
filehandling.Move(os.path.join(tempDir, pvtuName), pvtuName)
filehandling.Rmdir(tempDir, force = True)
if len(args) > 3:
debug.FatalError("Unrecognised trailing argument")
inputProject = args[0]
if len(args) == 2:
try:
firstId = int(args[1])
lastId = firstId
except ValueError:
debug.FatalError("Invalid first dump ID")
if len(args) == 3:
try:
firstId = int(args[1])
lastId = int(args[2])
assert(lastId >= firstId)
except:
debug.FatalError("Invalid last dump ID")
if len(args) == 1:
filenames = [inputProject + ".pvtu"]
else:
filenames = fluidity_tools.VtuFilenames(inputProject, firstId, lastId = lastId, extension = ".pvtu")
for filename in filenames:
debug.dprint("Processing file: " + filename)
vtu = vtktools.vtu(filename)
vtu = vtktools.VtuFromPvtu(vtu)
vtu.Write(filename[:-5] + ".vtu")
if len(args) < 2:
debug.FatalError("GMSH base name and vtu name required")
elif len(args) > 2:
debug.FatalError("Unrecognised trailing argument")
meshBasename = args[0]
vtuFilename = args[1]
possibleMeshBasenames = glob.glob(meshBasename + "_?*.msh")
meshBasenames = []
meshIds = []
for possibleMeshBasename in possibleMeshBasenames:
id = possibleMeshBasename[len(meshBasename) + 1:-4]
try:
id = int(id)
except ValueError:
continue
meshBasenames.append(possibleMeshBasename[:-4])
meshIds.append(id)
vtuBasename = os.path.basename(vtuFilename[:-len(vtuFilename.split(".")[-1]) -
1])
vtuExt = vtuFilename[-len(vtuFilename.split(".")[-1]):]
vtu = vtktools.vtu(vtuFilename)
for i, meshBasename in enumerate(meshBasenames):
debug.dprint("Processing mesh partition " + meshBasename)
meshVtu = gmshtools.ReadMsh(meshBasename).ToVtu(includeSurface=False)
partition = vtktools.RemappedVtu(vtu, meshVtu)
partition.Write(vtuBasename + "_" + str(meshIds[i]) + "." + vtuExt)
def ToVtu(self, includeSurface = True, includeVolume = True, idsName = "IDs"):
dim = self.GetDim()
assert(dim <= 3)
ugrid = vtk.vtkUnstructuredGrid()
# Add the points
points = vtk.vtkPoints()
points.SetDataTypeToDouble()
for nodeCoord in self.GetNodeCoords():
x = 0.0
y = 0.0
z = 0.0
if dim > 0:
x = nodeCoord[0]
if dim > 1:
y = nodeCoord[1]
if dim > 2:
z = nodeCoord[2]
points.InsertNextPoint(x, y, z)
ugrid.SetPoints(points)
if includeSurface or includeVolume:
cellData = vtk.vtkDoubleArray()
cellData.SetNumberOfComponents(1)
cellData.SetName(idsName)
if includeSurface:
# Add the surface elements
for element in self.GetSurfaceElements():
idList = vtk.vtkIdList()
type = vtktools.VtkType(dim = dim - 1, nodeCount = element.NodeCount())
for node in vtktools.ToVtkNodeOrder(element.GetNodes(), type):
idList.InsertNextId(node)
cell = ugrid.InsertNextCell(type.GetVtkTypeId(), idList)
if len(element.GetIds()) > 0:
# Add just the first ID
cellData.InsertTuple1(cell, element.GetIds()[0])
else:
cellData.InsertTuple1(cell, 0.0)
if includeVolume:
# Add the volume elements
for element in self.GetVolumeElements():
idList = vtk.vtkIdList()
type = vtktools.VtkType(dim = dim, nodeCount = element.NodeCount())
for node in vtktools.ToVtkNodeOrder(element.GetNodes(), type):
idList.InsertNextId(node)
cellId = ugrid.InsertNextCell(type.GetVtkTypeId(), idList)
if len(element.GetIds()) > 0:
# Add just the first ID
cellData.InsertTuple1(cellId, element.GetIds()[0])
else:
cellData.InsertTuple1(cellId, 0.0)
# Add the boundary and/or region IDs
ugrid.GetCellData().AddArray(cellData)
# Construct the vtu
vtu = vtktools.vtu()
vtu.ugrid = ugrid
return vtu
if len(args) < 2:
debug.FatalError("GMSH base name and vtu name required")
elif len(args) > 2:
debug.FatalError("Unrecognised trailing argument")
meshBasename = args[0]
vtuFilename = args[1]
possibleMeshBasenames = glob.glob(meshBasename + "_?*.msh")
meshBasenames = []
meshIds = []
for possibleMeshBasename in possibleMeshBasenames:
id = possibleMeshBasename[len(meshBasename) + 1:-4]
try:
id = int(id)
except ValueError:
continue
meshBasenames.append(possibleMeshBasename[:-4])
meshIds.append(id)
vtuBasename = os.path.basename(vtuFilename[:-len(vtuFilename.split(".")[-1]) - 1])
vtuExt = vtuFilename[-len(vtuFilename.split(".")[-1]):]
vtu = vtktools.vtu(vtuFilename)
for i, meshBasename in enumerate(meshBasenames):
debug.dprint("Processing mesh partition " + meshBasename)
meshVtu = gmshtools.ReadMsh(meshBasename).ToVtu(includeSurface = False)
partition = vtktools.RemappedVtu(vtu, meshVtu)
partition.Write(vtuBasename + "_" + str(meshIds[i]) + "." + vtuExt)
def ToVtu(self, includeSurface = True, includeVolume = True, idsName = "IDs"):
dim = self.GetDim()
assert(dim <= 3)
ugrid = vtk.vtkUnstructuredGrid()
# Add the points
points = vtk.vtkPoints()
points.SetDataTypeToDouble()
for nodeCoord in self.GetNodeCoords():
x = 0.0
y = 0.0
z = 0.0
if dim > 0:
x = nodeCoord[0]
if dim > 1:
y = nodeCoord[1]
if dim > 2:
z = nodeCoord[2]
points.InsertNextPoint(x, y, z)
ugrid.SetPoints(points)
if includeSurface or includeVolume:
cellData = vtk.vtkDoubleArray()
cellData.SetNumberOfComponents(1)
cellData.SetName(idsName)
if includeSurface:
# Add the surface elements
for element in self.GetSurfaceElements():
idList = vtk.vtkIdList()
type = vtktools.VtkType(dim = dim - 1, nodeCount = element.NodeCount())
for node in vtktools.ToVtkNodeOrder(element.GetNodes(), type):
idList.InsertNextId(node)
cell = ugrid.InsertNextCell(type.GetVtkTypeId(), idList)
if len(element.GetIds()) > 0:
# Add just the first ID
cellData.InsertTuple1(cell, element.GetIds()[0])
else:
cellData.InsertTuple1(cell, 0.0)
if includeVolume:
# Add the volume elements
for element in self.GetVolumeElements():
idList = vtk.vtkIdList()
type = vtktools.VtkType(dim = dim, nodeCount = element.NodeCount())
for node in vtktools.ToVtkNodeOrder(element.GetNodes(), type):
idList.InsertNextId(node)
cellId = ugrid.InsertNextCell(type.GetVtkTypeId(), idList)
if len(element.GetIds()) > 0:
# Add just the first ID
cellData.InsertTuple1(cellId, element.GetIds()[0])
else:
cellData.InsertTuple1(cellId, 0.0)
# Add the boundary and/or region IDs
ugrid.GetCellData().AddArray(cellData)
# Construct the vtu
vtu = vtktools.vtu()
vtu.ugrid = ugrid
return vtu