def vtu_readvf3d(name):
#generate reader and read file
reader = vtk.vtkXMLUnstructuredGridReader()
reader.SetFileName(name)
reader.Update()
vtkdata = reader.GetOutput()
#Obtain vectors and points from data in file
nPoints = vtkdata.GetNumberOfPoints()
pointData = vtkdata.GetPointData()
vectorData = pointData.GetVectors()
scalarData = pointData.GetScalars()
try:
vect_list = vtk2np(vectorData)
except AttributeError:
print 'there is no vector data'
vect_list = None
try:
scal_list = vtk2np(scalarData)
except AttributeError:
#print 'there is no scalar data'
scal_list = None
pnts_list = N.array([vtkdata.GetPoint(i) for i in range(nPoints)])
#rearange data to 3d matices
bounds = vtkdata.GetBounds()#(Xmin,Xmax,Ymin,Ymax,Zmin,Zmax)
[X,Y,Z,U,V,W] = ijk(pnts_list,bounds,vect_list)
return [X,Y,Z,U,V,W]
def _get_cells(obj):
"""Extract cells and cell_data from a vtkDataSet and sort it by types."""
cells, cell_data = {}, {}
data = _get_data(obj.GetCellData())
arr = vtk2np(obj.GetCells().GetData())
loc = vtk2np(obj.GetCellLocationsArray())
types = vtk2np(obj.GetCellTypesArray())
for typ in VTK_TYP:
if not isinstance(typ, int):
continue
cell_name = VTK_TYP[typ]
n_no = NODE_NO[cell_name]
cell_loc_i = np.where(types == typ)[0]
loc_i = loc[cell_loc_i]
# if there are no cells of the actual type continue
if len(loc_i) == 0:
# if not loc_i:
continue
arr_i = np.empty((len(loc_i), n_no), dtype=int)
for i in range(n_no):
arr_i[:, i] = arr[loc_i + i + 1]
cells[cell_name] = arr_i
cell_data_i = {}
for data_i in data:
cell_data_i[data_i] = data[data_i][cell_loc_i]
if cell_data_i != {}:
cell_data[cell_name] = cell_data_i
return cells, cell_data
def vtu_readvf3d(name):
#generate reader and read file
reader = vtk.vtkXMLUnstructuredGridReader()
reader.SetFileName(name)
reader.Update()
vtkdata = reader.GetOutput()
#Obtain vectors and points from data in file
nPoints = vtkdata.GetNumberOfPoints()
pointData = vtkdata.GetPointData()
vectorData = pointData.GetVectors()
scalarData = pointData.GetScalars()
try:
vect_list = vtk2np(vectorData)
except AttributeError:
print 'there is no vector data'
vect_list = None
try:
scal_list = vtk2np(scalarData)
except AttributeError:
#print 'there is no scalar data'
scal_list = None
pnts_list = N.array([vtkdata.GetPoint(i) for i in range(nPoints)])
#rearange data to 3d matices
bounds = vtkdata.GetBounds() #(Xmin,Xmax,Ymin,Ymax,Zmin,Zmax)
[X, Y, Z, U, V, W] = ijk(pnts_list, bounds, vect_list)
return [X, Y, Z, U, V, W]
def _poly_data_read(obj):
"""Reader for vtk polygonal data objects."""
output = {}
output["points"] = vtk2np(obj.GetPoints().GetData())
output["verts"] = _deflat_data(vtk2np(obj.GetVerts().GetData()))
output["lines"] = _deflat_data(vtk2np(obj.GetLines().GetData()))
output["polygons"] = _deflat_data(vtk2np(obj.GetPolys().GetData()))
output["strips"] = _deflat_data(vtk2np(obj.GetStrips().GetData()))
output["point_data"] = _get_data(obj.GetPointData())
output["cell_data"] = _get_data(obj.GetCellData())
output["field_data"] = _get_data(obj.GetFieldData())
return output
def _unst_grid_read(obj):
"""Reader for vtk unstructured grid objects."""
output = {}
output["field_data"] = _get_data(obj.GetFieldData())
output["points"] = vtk2np(obj.GetPoints().GetData())
output["point_data"] = _get_data(obj.GetPointData())
output["cells"], output["cell_data"] = _get_cells(obj)
return output
def _get_data(data):
"""Extract data as numpy arrays from a vtkObject."""
arr_dict = {}
no_of_arr = data.GetNumberOfArrays()
for i in range(no_of_arr):
arr = data.GetArray(i)
if arr:
arr_dict[arr.GetName()] = vtk2np(arr)
return arr_dict
def _rect_grid_read(obj):
"""Reader for vtk rectangular grid objects."""
output = {}
output["dimensions"] = np.array(obj.GetDimensions())
output["x"] = vtk2np(obj.GetXCoordinates())
output["y"] = vtk2np(obj.GetYCoordinates())
output["z"] = vtk2np(obj.GetZCoordinates())
output["field_data"] = _get_data(obj.GetFieldData())
output["point_data"] = _get_data(obj.GetPointData())
output["cell_data"] = _get_data(obj.GetCellData())
# reshape cell and point data according to the give dimensions
dim = output["dimensions"]
for arr in output["cell_data"]:
output["cell_data"][arr] = np.squeeze(
np.reshape(output["cell_data"][arr],
np.maximum(dim - 1, 1),
order="F"))
for arr in output["point_data"]:
output["point_data"][arr] = np.reshape(output["point_data"][arr],
dim,
order="F")
return output
def translate_mesh_points(mesh, r):
coords = vtk2np(mesh.GetPoints().GetData())
coords += np.array(r, dtype=np.float32).reshape(1, 3)
mesh.GetPoints().SetData(np2vtk(coords))
return mesh