def Mesh2VTKUGrid(mesh): vtkcelltypes=((),(vtk.VTK_EMPTY_CELL,vtk.VTK_VERTEX,vtk.VTK_LINE),(vtk.VTK_EMPTY_CELL,vtk.VTK_VERTEX,vtk.VTK_LINE,vtk.VTK_TRIANGLE,vtk.VTK_QUAD,vtk.VTK_POLYGON,vtk.VTK_POLYGON),(vtk.VTK_EMPTY_CELL,vtk.VTK_VERTEX,vtk.VTK_LINE,vtk.VTK_TRIANGLE,vtk.VTK_TETRA,vtk.VTK_CONVEX_POINT_SET,vtk.VTK_CONVEX_POINT_SET,vtk.VTK_CONVEX_POINT_SET,vtk.VTK_HEXAHEDRON)) npoints=mesh.num_vertices() geom=mesh.geometry() pts=vtk.vtkPoints() pts.SetNumberOfPoints(npoints) for i in xrange(npoints): p=geom.point(i) pts.SetPoint(i,p.x(),p.y(),p.z()) dim = mesh.topology().dim() ncells=mesh.num_cells() cells=vtk.vtkCellArray() cellTypes=vtk.vtkUnsignedCharArray() cellTypes.SetNumberOfTuples(ncells) cellLocations=vtk.vtkIdTypeArray() cellLocations.SetNumberOfTuples(ncells) loc=0 for (cell,i) in zip(mesh.cells(),xrange(ncells)) : ncellpoints=len(cell) cells.InsertNextCell(ncellpoints) for cpoint in cell: cells.InsertCellPoint(cpoint) cellTypes.SetTuple1(i,vtkcelltypes[dim][ncellpoints]) cellLocations.SetTuple1(i,loc) loc+=1+ncellpoints ugrid = vtk.vtkUnstructuredGrid() ugrid.SetPoints(pts) ugrid.SetCells(cellTypes,cellLocations,cells) return ugrid
def Mesh2VTKUGrid(mesh):
vtkcelltypes=((),(vtk.VTK_EMPTY_CELL,vtk.VTK_VERTEX,vtk.VTK_LINE),(vtk.VTK_EMPTY_CELL,vtk.VTK_VERTEX,vtk.VTK_LINE,vtk.VTK_TRIANGLE,vtk.VTK_QUAD,vtk.VTK_POLYGON,vtk.VTK_POLYGON),(vtk.VTK_EMPTY_CELL,vtk.VTK_VERTEX,vtk.VTK_LINE,vtk.VTK_TRIANGLE,vtk.VTK_TETRA,vtk.VTK_CONVEX_POINT_SET,vtk.VTK_CONVEX_POINT_SET,vtk.VTK_CONVEX_POINT_SET,vtk.VTK_HEXAHEDRON))
npoints=mesh.num_vertices()
geom=mesh.geometry()
pts=vtk.vtkPoints()
pts.SetNumberOfPoints(npoints)
for i in xrange(npoints):
p=geom.point(i)
pts.SetPoint(i,p.x(),p.y(),p.z())
dim = mesh.topology().dim()
ncells=mesh.num_cells()
cells=vtk.vtkCellArray()
cellTypes=vtk.vtkUnsignedCharArray()
cellTypes.SetNumberOfTuples(ncells)
cellLocations=vtk.vtkIdTypeArray()
cellLocations.SetNumberOfTuples(ncells)
loc=0
for (cell,i) in zip(mesh.cells(),xrange(ncells)) :
ncellpoints=len(cell)
cells.InsertNextCell(ncellpoints)
for cpoint in cell:
cells.InsertCellPoint(cpoint)
cellTypes.SetTuple1(i,vtkcelltypes[dim][ncellpoints])
cellLocations.SetTuple1(i,loc)
loc+=1+ncellpoints
ugrid = vtk.vtkUnstructuredGrid()
ugrid.SetPoints(pts)
ugrid.SetCells(cellTypes,cellLocations,cells)
return ugrid
def RequestData(self, request, inInfo, outInfo):
logger.debug("Requesting data...")
input = self.GetInputDataObject(0, 0)
trajectory_data = dsa.WrapDataObject(input)
output = dsa.WrapDataObject(vtkPolyData.GetData(outInfo))
# Retrieve current time
time = timesteps_util.get_timestep(self, logger=logger)
# Retrieve trajectory data
trajectory_times = trajectory_data.PointData["Time"]
trajectory_points = trajectory_data.Points
# Interpolate along the trajectory to find current position
current_position = [
np.interp(time, trajectory_times, trajectory_points[:, i])
for i in range(3)
]
# Expose to VTK
points_vtk = vtk.vtkPoints()
verts_vtk = vtk.vtkCellArray()
verts_vtk.InsertNextCell(1)
points_vtk.InsertPoint(0, *current_position)
verts_vtk.InsertCellPoint(0)
output.SetPoints(points_vtk)
output.SetVerts(verts_vtk)
# Interpolate remaining point data along the trajectory
for dataset in trajectory_data.PointData.keys():
if dataset == "Time":
continue
point_data = trajectory_data.PointData[dataset]
data_at_position = np.zeros(point_data.shape[1:])
if len(data_at_position.shape) > 0:
for i in itertools.product(
*map(range, data_at_position.shape)):
point_data_i = point_data[(slice(None), ) + i]
if len(trajectory_times) == len(point_data_i):
data_at_position[i] = np.interp(
time, trajectory_times, point_data_i)
else:
logger.warning(
"Unable to interpolate trajectory dataset"
f" {dataset}[{i}]: Length of dataset"
f" ({len(point_data_i)}) does not match length of"
f" trajectory times ({len(trajectory_times)}).")
else:
data_at_position = np.interp(time, trajectory_times,
point_data)
data_vtk = vtknp.numpy_to_vtk(np.array([data_at_position]))
data_vtk.SetName(dataset)
output.GetPointData().AddArray(data_vtk)
return 1
def _particles2poly_data(cuds):
particle2index = {}
points = vtk.vtkPoints()
lines = vtk.vtkCellArray()
poly_data = vtk.vtkPolyData()
point_data = poly_data.GetPointData()
data_collector = CUBADataAccumulator(container=point_data)
for index, particle in enumerate(cuds.iter(item_type=CUBA.PARTICLE)):
particle2index[particle.uid] = index
points.InsertPoint(index, *particle.coordinates)
data_collector.append(particle.data)
cell_data = poly_data.GetCellData()
data_collector = CUBADataAccumulator(container=cell_data)
for bond in cuds.iter(item_type=CUBA.BOND):
lines.InsertNextCell(len(bond.particles))
for uuid in bond.particles:
lines.InsertCellPoint(particle2index[uuid])
data_collector.append(bond.data)
poly_data.SetPoints(points)
poly_data.SetLines(lines)
return poly_data