print "converting curves to vtk"
for i in range(matrix.getFirstCurve(),
matrix.numberOfCurves() - 1): # ! shift!!
nbp = matrix.getCurve(i).numberOfPoints()
if nbp == 2:
cell = vtk.vtkLine()
cell.GetPointIds().SetId(
0,
matrix.getCurve(i).getPointNumber(0) - matrix.getFirstPoint() -
1)
cell.GetPointIds().SetId(
1,
matrix.getCurve(i).getPointNumber(1) - matrix.getFirstPoint() -
1)
elif nbp == 3:
cell = vtk.vtkQuadraticEdge()
cell.GetPointIds().SetId(
0,
matrix.getCurve(i).getPointNumber(0) - matrix.getFirstPoint() -
1)
cell.GetPointIds().SetId(
1,
matrix.getCurve(i).getPointNumber(2) - matrix.getFirstPoint() -
1)
cell.GetPointIds().SetId(
2,
matrix.getCurve(i).getPointNumber(1) - matrix.getFirstPoint() -
1)
else:
raise Exception("curve with %d points" % nbp)
import backdrop # Contour every quadratic cell type # Create a scene with one of each cell type. # QuadraticEdge edgePoints = vtk.vtkPoints() edgePoints.SetNumberOfPoints(3) edgePoints.InsertPoint(0, 0, 0, 0) edgePoints.InsertPoint(1, 1.0, 0, 0) edgePoints.InsertPoint(2, 0.5, 0.25, 0) edgeScalars = vtk.vtkFloatArray() edgeScalars.SetNumberOfTuples(3) edgeScalars.InsertValue(0, 0.0) edgeScalars.InsertValue(1, 0.0) edgeScalars.InsertValue(2, 0.9) aEdge = vtk.vtkQuadraticEdge() aEdge.GetPointIds().SetId(0, 0) aEdge.GetPointIds().SetId(1, 1) aEdge.GetPointIds().SetId(2, 2) aEdgeGrid = vtk.vtkUnstructuredGrid() aEdgeGrid.Allocate(1, 1) aEdgeGrid.InsertNextCell(aEdge.GetCellType(), aEdge.GetPointIds()) aEdgeGrid.SetPoints(edgePoints) aEdgeGrid.GetPointData().SetScalars(edgeScalars) aEdgeMapper = vtk.vtkDataSetMapper() aEdgeMapper.SetInputData(aEdgeGrid) aEdgeMapper.ScalarVisibilityOff() aEdgeActor = vtk.vtkActor() aEdgeActor.SetMapper(aEdgeMapper) aEdgeActor.GetProperty().SetRepresentationToWireframe() aEdgeActor.GetProperty().SetAmbient(1.0)
import backdrop # Contour every quadratic cell type # Create a scene with one of each cell type. # QuadraticEdge edgePoints = vtk.vtkPoints() edgePoints.SetNumberOfPoints(3) edgePoints.InsertPoint(0, 0, 0, 0) edgePoints.InsertPoint(1, 1.0, 0, 0) edgePoints.InsertPoint(2, 0.5, 0.25, 0) edgeScalars = vtk.vtkFloatArray() edgeScalars.SetNumberOfTuples(3) edgeScalars.InsertValue(0, 0.0) edgeScalars.InsertValue(1, 0.0) edgeScalars.InsertValue(2, 0.9) aEdge = vtk.vtkQuadraticEdge() aEdge.GetPointIds().SetId(0, 0) aEdge.GetPointIds().SetId(1, 1) aEdge.GetPointIds().SetId(2, 2) aEdgeGrid = vtk.vtkUnstructuredGrid() aEdgeGrid.Allocate(1, 1) aEdgeGrid.InsertNextCell(aEdge.GetCellType(), aEdge.GetPointIds()) aEdgeGrid.SetPoints(edgePoints) aEdgeGrid.GetPointData().SetScalars(edgeScalars) aEdgeMapper = vtk.vtkDataSetMapper() aEdgeMapper.SetInputData(aEdgeGrid) aEdgeMapper.ScalarVisibilityOff() aEdgeActor = vtk.vtkActor() aEdgeActor.SetMapper(aEdgeMapper) aEdgeActor.GetProperty().SetRepresentationToWireframe() aEdgeActor.GetProperty().SetAmbient(1.0)
def write_vtu(filename, fns, index = None, t = None):
"""
Write the supplied Function or Function s to a vtu or pvtu file with the
supplied filename base. If the Function s are defined on multiple function
spaces then separate output files are written for each function space. The
optional integer index can be used to add an index to the output filenames.
If t is supplied then a scalar field equal to t and with name "time" is added
to the output files.
All Function s should be on the same mesh and have unique names. In 1D all
Function s must have Lagrange basis functions (continuous or discontinous)
with degree 0 to 3. In 2D and 3D all Function s must have Lagrange basis
functions (continuous or discontinuous) with degree 0 to 2.
"""
if isinstance(fns, dolfin.Function):
return write_vtu(filename, [fns], index = index, t = t)
if not isinstance(filename, str):
raise InvalidArgumentException("filename must be a string")
if not isinstance(fns, list):
raise InvalidArgumentException("fns must be a Function or a list of Function s")
if len(fns) == 0:
raise InvalidArgumentException("fns must include at least one Function")
for fn in fns:
if not isinstance(fn, dolfin.Function):
raise InvalidArgumentException("fns must be a Function or a list of Function s")
if not index is None and not isinstance(index, int):
raise InvalidArgumentException("index must be an integer")
if not t is None and not isinstance(t, (float, dolfin.Constant)):
raise InvalidArgumentException("t must be a float or Constant")
mesh = fns[0].function_space().mesh()
dim = mesh.geometry().dim()
if not dim in [1, 2, 3]:
raise NotImplementedException("Mesh dimension %i not supported by write_vtu" % dim)
def expand_sub_fns(fn):
n_sub_spaces = fn.function_space().num_sub_spaces()
if n_sub_spaces > 1:
fns = fn.split(deepcopy = True)
for i, sfn in enumerate(copy.copy(fns)):
sfn.rename("%s_%i" % (fn.name(), i + 1), "%s_%i" % (fn.name(), i + 1))
if sfn.function_space().num_sub_spaces() > 0:
fns.remove(sfn)
fns += expand_sub_fns(sfn)
return fns
elif n_sub_spaces == 1:
e = fn.function_space().ufl_element().extract_component(0)[1]
space = dolfin.FunctionSpace(mesh, e.family(), e.degree())
sfn = dolfin.Function(space, name = "%s_1" % fn.name())
sfn.vector()[:] = fn.vector()
return [sfn]
else:
return [fn]
nfns = []
for i, fn in enumerate(fns):
space = fn.function_space()
if not space.mesh().id() == mesh.id():
raise InvalidArgumentException("Require exactly one mesh in write_vtu")
n_sub_spaces = space.num_sub_spaces()
nfns += expand_sub_fns(fn)
fns = nfns; del(nfns)
spaces = []
lfns = OrderedDict()
for fn in fns:
space = fn.function_space()
assert(space.mesh().id() == mesh.id())
e = space.ufl_element()
assert(e.cell().geometric_dimension() == dim)
assert(e.cell().topological_dimension() == dim)
if (not e.family() in ["Lagrange", "Discontinuous Lagrange"]
or not dim in [1, 2, 3]
or (dim == 1 and not e.degree() in [1, 2, 3])
or (dim in [2, 3] and not e.degree() in [1, 2])) and \
(not e.family() == "Discontinuous Lagrange"
or not dim in [1, 2, 3]
or not e.degree() == 0):
raise NotImplementedException('Element family "%s" with degree %i in %i dimension(s) not supported by write_vtu' % (e.family(), e.degree(), dim))
if e in lfns:
lfns[e].append(fn)
else:
spaces.append(space)
lfns[e] = [fn]
fns = lfns
if len(spaces) == 1:
filenames = [filename]
else:
filenames = []
for space in spaces:
e = space.ufl_element()
lfilename = "%s_P%i" % (filename, e.degree())
if e.family() == "Discontinuous Lagrange":
lfilename = "%s_DG" % lfilename
filenames.append(lfilename)
if not t is None:
for space in spaces:
lt = dolfin.Function(space, name = "time")
if isinstance(t, float):
lt.vector()[:] = t
else:
lt.assign(t)
fns[space.ufl_element()].append(lt)
names = {e:[] for e in fns}
for e in fns:
for fn in fns[e]:
name = fn.name()
if name in names[e]:
raise InvalidArgumentException("Duplicate Function name: %s" % name)
names[e].append(name)
for filename, space in zip(filenames, spaces):
e = space.ufl_element()
degree = e.degree()
vtu = vtk.vtkUnstructuredGrid()
dof = space.dofmap()
nodes = set()
for i in xrange(mesh.num_cells()):
cell = dof.cell_dofs(i)
for node in cell:
nodes.add(node)
nodes = numpy.array(sorted(list(nodes)), dtype = numpy.intc)
if degree == 0:
xspace = dolfin.FunctionSpace(mesh, "CG", 1)
xdof = xspace.dofmap()
xnodes = set()
for i in xrange(mesh.num_cells()):
cell = xdof.cell_dofs(i)
for node in cell:
xnodes.add(node)
xnodes = numpy.array(sorted(list(xnodes)), dtype = numpy.intc)
else:
xspace = space
xdof = dof
xnodes = nodes
xnode_map = {node:i for i, node in enumerate(xnodes)}
x = dolfin.interpolate(dolfin.Expression("x[0]"), xspace).vector().gather(xnodes)
if dim > 1:
y = dolfin.interpolate(dolfin.Expression("x[1]"), xspace).vector().gather(xnodes)
if dim > 2:
z = dolfin.interpolate(dolfin.Expression("x[2]"), xspace).vector().gather(xnodes)
n = x.shape[0]
points = vtk.vtkPoints()
points.SetDataTypeToDouble()
points.SetNumberOfPoints(n)
if dim == 1:
for i in xrange(n):
points.SetPoint(i, x[i], 0.0, 0.0)
elif dim == 2:
for i in xrange(n):
points.SetPoint(i, x[i], y[i], 0.0)
else:
for i in xrange(n):
points.SetPoint(i, x[i], y[i], z[i])
vtu.SetPoints(points)
id_list = vtk.vtkIdList()
if dim == 1:
if degree in [0, 1]:
cell_type = vtk.vtkLine().GetCellType()
id_list.SetNumberOfIds(2)
cell_map = None
elif degree == 2:
cell_type = vtk.vtkQuadraticEdge().GetCellType()
id_list.SetNumberOfIds(3)
cell_map = None
else:
cell_type = vtk.vtkCubicLine().GetCellType()
id_list.SetNumberOfIds(4)
cell_map = None
elif dim == 2:
if degree in [0, 1]:
cell_type = vtk.vtkTriangle().GetCellType()
id_list.SetNumberOfIds(3)
cell_map = None
else:
cell_type = vtk.vtkQuadraticTriangle().GetCellType()
id_list.SetNumberOfIds(6)
cell_map = {0:0, 1:1, 2:2, 3:5, 4:3, 5:4}
else:
if degree in [0, 1]:
cell_type = vtk.vtkTetra().GetCellType()
id_list.SetNumberOfIds(4)
cell_map = None
else:
cell_type = vtk.vtkQuadraticTetra().GetCellType()
id_list.SetNumberOfIds(10)
cell_map = {0:0, 1:1, 2:2, 3:3, 4:9, 5:6, 6:8, 7:7, 8:5, 9:4}
for i in xrange(mesh.num_cells()):
cell = xdof.cell_dofs(i)
assert(len(cell) == id_list.GetNumberOfIds())
if not cell_map is None:
cell = [cell[cell_map[j]] for j in xrange(len(cell))]
for j in xrange(len(cell)):
id_list.SetId(j, xnode_map[cell[j]])
vtu.InsertNextCell(cell_type, id_list)
if degree == 0:
for fn in fns[e]:
if not fn.value_rank() == 0:
raise NotImplementException("Function rank %i not supported by write_vtu" % fn.value_rank())
data = fn.vector().gather(nodes)
cell_data = vtk.vtkDoubleArray()
cell_data.SetNumberOfComponents(1)
cell_data.SetNumberOfValues(mesh.num_cells())
cell_data.SetName(fn.name())
for i, datum in enumerate(data):
cell_data.SetValue(i, datum)
vtu.GetCellData().AddArray(cell_data)
vtu.GetCellData().SetActiveScalars(names[e][0])
else:
for fn in fns[e]:
if not fn.value_rank() == 0:
raise NotImplementException("Function rank %i not supported by write_vtu" % fn.value_rank())
data = fn.vector().gather(nodes)
point_data = vtk.vtkDoubleArray()
point_data.SetNumberOfComponents(1)
point_data.SetNumberOfValues(n)
point_data.SetName(fn.name())
for i, datum in enumerate(data):
point_data.SetValue(i, datum)
vtu.GetPointData().AddArray(point_data)
vtu.GetPointData().SetActiveScalars(names[e][0])
if dolfin.MPI.num_processes() > 1:
writer = vtk.vtkXMLPUnstructuredGridWriter()
writer.SetNumberOfPieces(dolfin.MPI.num_processes())
writer.SetStartPiece(dolfin.MPI.process_number())
writer.SetEndPiece(dolfin.MPI.process_number())
ext = ".pvtu"
else:
writer = vtk.vtkXMLUnstructuredGridWriter()
ext = ".vtu"
if index is None:
filename = "%s%s" % (filename, ext)
else:
filename = "%s_%i%s" % (filename, index, ext)
writer.SetFileName(filename)
writer.SetDataModeToAppended()
writer.EncodeAppendedDataOff()
writer.SetCompressorTypeToZLib()
writer.GetCompressor().SetCompressionLevel(9)
writer.SetBlockSize(2 ** 15)
writer.SetInput(vtu)
writer.Write()
if not writer.GetProgress() == 1.0 or not writer.GetErrorCode() == 0:
raise IOException("Failed to write vtu file: %s" % filename)
return
newNodes = nodes
if type.GetElementTypeId() == elements.ELEMENT_QUAD:
newNodes = copy.deepcopy(nodes)
newNodes[2] = nodes[3]
newNodes[3] = nodes[2]
return newNodes
if VtkSupport():
VTK_UNKNOWN = None
VTK_EMPTY_CELL = vtk.vtkEmptyCell().GetCellType()
VTK_VERTEX = vtk.vtkVertex().GetCellType()
VTK_LINE = vtk.vtkLine().GetCellType()
VTK_QUADRATIC_LINE = vtk.vtkQuadraticEdge().GetCellType()
VTK_TRIANGLE = vtk.vtkTriangle().GetCellType()
VTK_QUADRATIC_TRIANGLE = vtk.vtkQuadraticTriangle().GetCellType()
VTK_TETRAHEDRON = vtk.vtkTetra().GetCellType()
VTK_QUADRATIC_TETRAHEDRON = vtk.vtkQuadraticTetra().GetCellType()
VTK_QUAD = vtk.vtkQuad().GetCellType()
VTK_HEXAHEDRON = vtk.vtkHexahedron().GetCellType()
vtkTypeIds = ( \
VTK_UNKNOWN, \
VTK_EMPTY_CELL, \
VTK_VERTEX, \
VTK_LINE, VTK_QUADRATIC_LINE, \
VTK_TRIANGLE, VTK_QUADRATIC_TRIANGLE, VTK_QUAD, \
VTK_TETRAHEDRON, VTK_QUADRATIC_TETRAHEDRON, VTK_HEXAHEDRON \
)
newNodes = nodes
if type.GetElementTypeId() == elements.ELEMENT_QUAD:
newNodes = copy.deepcopy(nodes)
newNodes[2] = nodes[3]
newNodes[3] = nodes[2]
return newNodes
if VtkSupport():
VTK_UNKNOWN = None
VTK_EMPTY_CELL = vtk.vtkEmptyCell().GetCellType()
VTK_VERTEX = vtk.vtkVertex().GetCellType()
VTK_LINE = vtk.vtkLine().GetCellType()
VTK_QUADRATIC_LINE = vtk.vtkQuadraticEdge().GetCellType()
VTK_TRIANGLE = vtk.vtkTriangle().GetCellType()
VTK_QUADRATIC_TRIANGLE = vtk.vtkQuadraticTriangle().GetCellType()
VTK_TETRAHEDRON = vtk.vtkTetra().GetCellType()
VTK_QUADRATIC_TETRAHEDRON = vtk.vtkQuadraticTetra().GetCellType()
VTK_QUAD = vtk.vtkQuad().GetCellType()
VTK_HEXAHEDRON = vtk.vtkHexahedron().GetCellType()
vtkTypeIds = ( \
VTK_UNKNOWN, \
VTK_EMPTY_CELL, \
VTK_VERTEX, \
VTK_LINE, VTK_QUADRATIC_LINE, \
VTK_TRIANGLE, VTK_QUADRATIC_TRIANGLE, VTK_QUAD, \
VTK_TETRAHEDRON, VTK_QUADRATIC_TETRAHEDRON, VTK_HEXAHEDRON \
)
def main():
titles = list()
textMappers = list()
textActors = list()
uGrids = list()
mappers = list()
actors = list()
renderers = list()
uGrids.append(MakeUnstructuredGrid(vtk.vtkQuadraticEdge()))
titles.append("VTK_QUADRATIC_EDGE (= 21)")
uGrids.append(MakeUnstructuredGrid(vtk.vtkQuadraticTriangle()))
titles.append("VTK_QUADRATIC_TRIANGLE (= 22)")
uGrids.append(MakeUnstructuredGrid(vtk.vtkQuadraticQuad()))
titles.append("VTK_QUADRATIC_QUAD (= 23)")
uGrids.append(MakeQuadraticPolygon())
titles.append("VTK_QUADRATIC_POLYGON (= 36)")
uGrids.append(MakeUnstructuredGrid(vtk.vtkQuadraticTetra()))
titles.append("VTK_QUADRATIC_TETRA (= 24)")
uGrids.append(MakeUnstructuredGrid(vtk.vtkQuadraticHexahedron()))
titles.append("VTK_QUADRATIC_HEXAHEDRON (= 25)")
uGrids.append(MakeUnstructuredGrid(vtk.vtkQuadraticWedge()))
titles.append("VTK_QUADRATIC_WEDGE (= 26)")
uGrids.append(MakeUnstructuredGrid(vtk.vtkQuadraticPyramid()))
titles.append("VTK_QUADRATIC_PYRAMID (= 27)")
uGrids.append(MakeUnstructuredGrid(vtk.vtkBiQuadraticQuad()))
titles.append("VTK_BIQUADRATIC_QUAD (= 28)")
uGrids.append(MakeUnstructuredGrid(vtk.vtkTriQuadraticHexahedron()))
titles.append("VTK_TRIQUADRATIC_HEXAHEDRON (= 29)")
uGrids.append(MakeUnstructuredGrid(vtk.vtkQuadraticLinearQuad()))
titles.append("VTK_QUADRATIC_LINEAR_QUAD (= 30)")
uGrids.append(MakeUnstructuredGrid(vtk.vtkQuadraticLinearWedge()))
titles.append("VTK_QUADRATIC_LINEAR_WEDGE (= 31)")
uGrids.append(MakeUnstructuredGrid(vtk.vtkBiQuadraticQuadraticWedge()))
titles.append("VTK_BIQUADRATIC_QUADRATIC_WEDGE (= 32)")
uGrids.append(MakeUnstructuredGrid(
vtk.vtkBiQuadraticQuadraticHexahedron()))
titles.append("VTK_BIQUADRATIC_QUADRATIC_HEXAHEDRON (= 33)")
uGrids.append(MakeUnstructuredGrid(vtk.vtkBiQuadraticTriangle()))
titles.append("VTK_BIQUADRATIC_TRIANGLE (= 34)")
uGrids.append(MakeUnstructuredGrid(vtk.vtkCubicLine()))
titles.append("VTK_CUBIC_LINE (= 35)")
colors = vtk.vtkNamedColors()
renWin = vtk.vtkRenderWindow()
renWin.SetSize(600, 600)
renWin.SetWindowName("Isoparametric Cell")
iRen = vtk.vtkRenderWindowInteractor()
iRen.SetRenderWindow(renWin)
# Create one sphere for all
sphere = vtk.vtkSphereSource()
sphere.SetPhiResolution(21)
sphere.SetThetaResolution(21)
sphere.SetRadius(.08)
# Create one text property for all
textProperty = vtk.vtkTextProperty()
textProperty.SetFontSize(10)
textProperty.SetJustificationToCentered()
# Create and link the mappers actors and renderers together.
for i in range(0, len(uGrids)):
print("Creating:", titles[i])
textMappers.append(vtk.vtkTextMapper())
textActors.append(vtk.vtkActor2D())
textMappers[i].GetTextProperty().SetFontSize(10)
textMappers[i].GetTextProperty().ShadowOn()
mappers.append(vtk.vtkDataSetMapper())
actors.append(vtk.vtkActor())
renderers.append(vtk.vtkRenderer())
mappers[i].SetInputData(uGrids[i])
actors[i].SetMapper(mappers[i])
actors[i].GetProperty().SetColor(colors.GetColor3d("Tomato"))
actors[i].GetProperty().EdgeVisibilityOn()
actors[i].GetProperty().SetLineWidth(3)
actors[i].GetProperty().SetOpacity(.5)
renderers[i].AddViewProp(actors[i])
textMappers[i].SetInput(titles[i])
textActors[i].SetMapper(textMappers[i])
textActors[i].SetPosition(50, 10)
renderers[i].AddViewProp(textActors[i])
# Label the points
labelMapper = vtk.vtkLabeledDataMapper()
labelMapper.SetInputData(uGrids[i])
labelActor = vtk.vtkActor2D()
labelActor.SetMapper(labelMapper)
renderers[i].AddViewProp(labelActor)
# Glyph the points
pointMapper = vtk.vtkGlyph3DMapper()
pointMapper.SetInputData(uGrids[i])
pointMapper.SetSourceConnection(sphere.GetOutputPort())
pointMapper.ScalingOff()
pointMapper.ScalarVisibilityOff()
pointActor = vtk.vtkActor()
pointActor.SetMapper(pointMapper)
pointActor.GetProperty().SetDiffuseColor(colors.GetColor3d("Banana"))
pointActor.GetProperty().SetSpecular(.6)
pointActor.GetProperty().SetSpecularColor(1.0, 1.0, 1.0)
pointActor.GetProperty().SetSpecularPower(100)
renderers[i].AddViewProp(pointActor)
renWin.AddRenderer(renderers[i])
# Setup the viewports
xGridDimensions = 4
yGridDimensions = 4
rendererSize = 240
renWin.SetSize(rendererSize * xGridDimensions,
rendererSize * yGridDimensions)
for row in range(0, yGridDimensions):
for col in range(0, xGridDimensions):
index = row * xGridDimensions + col
# (xmin, ymin, xmax, ymax)
viewport = [
float(col) / xGridDimensions,
float(yGridDimensions - (row + 1)) / yGridDimensions,
float(col + 1) / xGridDimensions,
float(yGridDimensions - row) / yGridDimensions
]
if index > (len(actors) - 1):
# Add a renderer even if there is no actor.
# This makes the render window background all the same color.
ren = vtk.vtkRenderer()
ren.SetBackground(colors.GetColor3d("SlateGray"))
ren.SetViewport(viewport)
renWin.AddRenderer(ren)
continue
renderers[index].SetViewport(viewport)
renderers[index].SetBackground(colors.GetColor3d("SlateGray"))
renderers[index].ResetCamera()
renderers[index].GetActiveCamera().Azimuth(30)
renderers[index].GetActiveCamera().Elevation(-30)
renderers[index].ResetCameraClippingRange()
iRen.Initialize()
renWin.Render()
iRen.Start()
def write_vtu(filename, fns, index=None, t=None):
"""
Write the supplied Function or Function s to a vtu or pvtu file with the
supplied filename base. If the Function s are defined on multiple function
spaces then separate output files are written for each function space. The
optional integer index can be used to add an index to the output filenames.
If t is supplied then a scalar field equal to t and with name "time" is added
to the output files.
All Function s should be on the same mesh and have unique names. In 1D all
Function s must have Lagrange basis functions (continuous or discontinous)
with degree 0 to 3. In 2D and 3D all Function s must have Lagrange basis
functions (continuous or discontinuous) with degree 0 to 2.
"""
if isinstance(fns, dolfin.Function):
return write_vtu(filename, [fns], index=index, t=t)
if not isinstance(filename, str):
raise InvalidArgumentException("filename must be a string")
if not isinstance(fns, list):
raise InvalidArgumentException(
"fns must be a Function or a list of Function s")
if len(fns) == 0:
raise InvalidArgumentException(
"fns must include at least one Function")
for fn in fns:
if not isinstance(fn, dolfin.Function):
raise InvalidArgumentException(
"fns must be a Function or a list of Function s")
if not index is None and not isinstance(index, int):
raise InvalidArgumentException("index must be an integer")
if not t is None and not isinstance(t, (float, dolfin.Constant)):
raise InvalidArgumentException("t must be a float or Constant")
mesh = fns[0].function_space().mesh()
dim = mesh.geometry().dim()
if not dim in [1, 2, 3]:
raise NotImplementedException(
"Mesh dimension %i not supported by write_vtu" % dim)
def expand_sub_fns(fn):
n_sub_spaces = fn.function_space().num_sub_spaces()
if n_sub_spaces > 1:
fns = fn.split(deepcopy=True)
for i, sfn in enumerate(copy.copy(fns)):
sfn.rename("%s_%i" % (fn.name(), i + 1),
"%s_%i" % (fn.name(), i + 1))
if sfn.function_space().num_sub_spaces() > 0:
fns.remove(sfn)
fns += expand_sub_fns(sfn)
return fns
elif n_sub_spaces == 1:
e = fn.function_space().ufl_element().extract_component(0)[1]
space = dolfin.FunctionSpace(mesh, e.family(), e.degree())
sfn = dolfin.Function(space, name="%s_1" % fn.name())
sfn.vector()[:] = fn.vector()
return [sfn]
else:
return [fn]
nfns = []
for i, fn in enumerate(fns):
space = fn.function_space()
if not space.mesh().id() == mesh.id():
raise InvalidArgumentException(
"Require exactly one mesh in write_vtu")
n_sub_spaces = space.num_sub_spaces()
nfns += expand_sub_fns(fn)
fns = nfns
del (nfns)
spaces = []
lfns = OrderedDict()
for fn in fns:
space = fn.function_space()
assert (space.mesh().id() == mesh.id())
e = space.ufl_element()
assert (e.cell().geometric_dimension() == dim)
assert (e.cell().topological_dimension() == dim)
if (not e.family() in ["Lagrange", "Discontinuous Lagrange"]
or not dim in [1, 2, 3]
or (dim == 1 and not e.degree() in [1, 2, 3])
or (dim in [2, 3] and not e.degree() in [1, 2])) and \
(not e.family() == "Discontinuous Lagrange"
or not dim in [1, 2, 3]
or not e.degree() == 0):
raise NotImplementedException(
'Element family "%s" with degree %i in %i dimension(s) not supported by write_vtu'
% (e.family(), e.degree(), dim))
if e in lfns:
lfns[e].append(fn)
else:
spaces.append(space)
lfns[e] = [fn]
fns = lfns
if len(spaces) == 1:
filenames = [filename]
else:
filenames = []
for space in spaces:
e = space.ufl_element()
lfilename = "%s_P%i" % (filename, e.degree())
if e.family() == "Discontinuous Lagrange":
lfilename = "%s_DG" % lfilename
filenames.append(lfilename)
if not t is None:
for space in spaces:
lt = dolfin.Function(space, name="time")
if isinstance(t, float):
lt.vector()[:] = t
else:
lt.assign(t)
fns[space.ufl_element()].append(lt)
names = {e: [] for e in fns}
for e in fns:
for fn in fns[e]:
name = fn.name()
if name in names[e]:
raise InvalidArgumentException("Duplicate Function name: %s" %
name)
names[e].append(name)
for filename, space in zip(filenames, spaces):
e = space.ufl_element()
degree = e.degree()
vtu = vtk.vtkUnstructuredGrid()
dof = space.dofmap()
nodes = set()
for i in range(mesh.num_cells()):
cell = dof.cell_dofs(i)
for node in cell:
nodes.add(node)
nodes = numpy.array(sorted(list(nodes)), dtype=numpy.intc)
if degree == 0:
xspace = dolfin.FunctionSpace(mesh, "CG", 1)
xdof = xspace.dofmap()
xnodes = set()
for i in range(mesh.num_cells()):
cell = xdof.cell_dofs(i)
for node in cell:
xnodes.add(node)
xnodes = numpy.array(sorted(list(xnodes)), dtype=numpy.intc)
else:
xspace = space
xdof = dof
xnodes = nodes
xnode_map = {node: i for i, node in enumerate(xnodes)}
x = dolfin.interpolate(dolfin.Expression("x[0]"),
xspace).vector().gather(xnodes)
if dim > 1:
y = dolfin.interpolate(dolfin.Expression("x[1]"),
xspace).vector().gather(xnodes)
if dim > 2:
z = dolfin.interpolate(dolfin.Expression("x[2]"),
xspace).vector().gather(xnodes)
n = x.shape[0]
points = vtk.vtkPoints()
points.SetDataTypeToDouble()
points.SetNumberOfPoints(n)
if dim == 1:
for i in range(n):
points.SetPoint(i, x[i], 0.0, 0.0)
elif dim == 2:
for i in range(n):
points.SetPoint(i, x[i], y[i], 0.0)
else:
for i in range(n):
points.SetPoint(i, x[i], y[i], z[i])
vtu.SetPoints(points)
id_list = vtk.vtkIdList()
if dim == 1:
if degree in [0, 1]:
cell_type = vtk.vtkLine().GetCellType()
id_list.SetNumberOfIds(2)
cell_map = None
elif degree == 2:
cell_type = vtk.vtkQuadraticEdge().GetCellType()
id_list.SetNumberOfIds(3)
cell_map = None
else:
cell_type = vtk.vtkCubicLine().GetCellType()
id_list.SetNumberOfIds(4)
cell_map = None
elif dim == 2:
if degree in [0, 1]:
cell_type = vtk.vtkTriangle().GetCellType()
id_list.SetNumberOfIds(3)
cell_map = None
else:
cell_type = vtk.vtkQuadraticTriangle().GetCellType()
id_list.SetNumberOfIds(6)
cell_map = {0: 0, 1: 1, 2: 2, 3: 5, 4: 3, 5: 4}
else:
if degree in [0, 1]:
cell_type = vtk.vtkTetra().GetCellType()
id_list.SetNumberOfIds(4)
cell_map = None
else:
cell_type = vtk.vtkQuadraticTetra().GetCellType()
id_list.SetNumberOfIds(10)
cell_map = {
0: 0,
1: 1,
2: 2,
3: 3,
4: 9,
5: 6,
6: 8,
7: 7,
8: 5,
9: 4
}
for i in range(mesh.num_cells()):
cell = xdof.cell_dofs(i)
assert (len(cell) == id_list.GetNumberOfIds())
if not cell_map is None:
cell = [cell[cell_map[j]] for j in range(len(cell))]
for j in range(len(cell)):
id_list.SetId(j, xnode_map[cell[j]])
vtu.InsertNextCell(cell_type, id_list)
if degree == 0:
for fn in fns[e]:
if not fn.value_rank() == 0:
raise NotImplementedException(
"Function rank %i not supported by write_vtu" %
fn.value_rank())
data = fn.vector().gather(nodes)
cell_data = vtk.vtkDoubleArray()
cell_data.SetNumberOfComponents(1)
cell_data.SetNumberOfValues(mesh.num_cells())
cell_data.SetName(fn.name())
for i, datum in enumerate(data):
cell_data.SetValue(i, datum)
vtu.GetCellData().AddArray(cell_data)
vtu.GetCellData().SetActiveScalars(names[e][0])
else:
for fn in fns[e]:
if not fn.value_rank() == 0:
raise NotImplementedException(
"Function rank %i not supported by write_vtu" %
fn.value_rank())
data = fn.vector().gather(nodes)
point_data = vtk.vtkDoubleArray()
point_data.SetNumberOfComponents(1)
point_data.SetNumberOfValues(n)
point_data.SetName(fn.name())
for i, datum in enumerate(data):
point_data.SetValue(i, datum)
vtu.GetPointData().AddArray(point_data)
vtu.GetPointData().SetActiveScalars(names[e][0])
if dolfin.MPI.size(dolfin.mpi_comm_world()) > 1:
writer = vtk.vtkXMLPUnstructuredGridWriter()
writer.SetNumberOfPieces(dolfin.MPI.size(dolfin.mpi_comm_world()))
writer.SetStartPiece(dolfin.MPI.rank(dolfin.mpi_comm_world()))
writer.SetEndPiece(dolfin.MPI.rank(dolfin.mpi_comm_world()))
ext = ".pvtu"
else:
writer = vtk.vtkXMLUnstructuredGridWriter()
ext = ".vtu"
if index is None:
filename = "%s%s" % (filename, ext)
else:
filename = "%s_%i%s" % (filename, index, ext)
writer.SetFileName(filename)
writer.SetDataModeToAppended()
writer.EncodeAppendedDataOff()
writer.SetCompressorTypeToZLib()
writer.GetCompressor().SetCompressionLevel(9)
writer.SetBlockSize(2**15)
writer.SetInput(vtu)
writer.Write()
if not writer.GetProgress() == 1.0 or not writer.GetErrorCode() == 0:
raise IOException("Failed to write vtu file: %s" % filename)
return
