def __init__(self, pos, cell):
"""Construct basic VTK-representation of a set of atomic positions.
pos: NumPy array of dtype float and shape ``(n,3)``
Cartesian positions of the atoms.
cell: Instance of vtkUnitCellModule of subclass thereof
Holds information equivalent to that of atoms.get_cell().
"""
# Make sure position argument is a valid array
if not isinstance(pos, np.ndarray):
pos = np.array(pos)
assert pos.dtype == float and pos.shape[1:] == (3, )
vtkBaseGrid.__init__(self, len(pos), cell)
# Convert positions to VTK array
npy2da = vtkDoubleArrayFromNumPyArray(pos)
vtk_pda = npy2da.get_output()
del npy2da
# Transfer atomic positions to VTK points
self.vtk_pts = vtkPoints()
self.vtk_pts.SetData(vtk_pda)
# Create a VTK unstructured grid of these points
self.vtk_ugd = vtkUnstructuredGrid()
self.vtk_ugd.SetWholeBoundingBox(self.cell.get_bounding_box())
self.vtk_ugd.SetPoints(self.vtk_pts)
# Extract the VTK point data set
self.set_point_data(self.vtk_ugd.GetPointData())
def __init__(self, pos, cell):
"""Construct basic VTK-representation of a set of atomic positions.
pos: NumPy array of dtype float and shape ``(n,3)``
Cartesian positions of the atoms.
cell: Instance of vtkUnitCellModule of subclass thereof
Holds information equivalent to that of atoms.get_cell().
"""
# Make sure position argument is a valid array
if not isinstance(pos, np.ndarray):
pos = np.array(pos)
assert pos.dtype == float and pos.shape[1:] == (3,)
vtkBaseGrid.__init__(self, len(pos), cell)
# Convert positions to VTK array
npy2da = vtkDoubleArrayFromNumPyArray(pos)
vtk_pda = npy2da.get_output()
del npy2da
# Transfer atomic positions to VTK points
self.vtk_pts = vtkPoints()
self.vtk_pts.SetData(vtk_pda)
# Create a VTK unstructured grid of these points
self.vtk_ugd = vtkUnstructuredGrid()
self.vtk_ugd.SetWholeBoundingBox(self.cell.get_bounding_box())
self.vtk_ugd.SetPoints(self.vtk_pts)
# Extract the VTK point data set
self.set_point_data(self.vtk_ugd.GetPointData())
def add_scalar_property(self, data, name=None, active=True):
"""Add VTK-representation of scalar data at the atomic positions.
data: NumPy array of dtype float and shape ``(n,)``
Scalar values corresponding to the atomic positions.
name=None: str
Unique identifier for the scalar data.
active=True: bool
Flag indicating whether to use as active scalar data.
"""
# Make sure data argument is a valid array
if not isinstance(data, np.ndarray):
data = np.array(data)
assert data.dtype == float and data.shape == (self.npoints, )
# Convert scalar properties to VTK array
npa2da = vtkDoubleArrayFromNumPyArray(data)
return vtkBaseGrid.add_scalar_data_array(self, npa2da, name, active)
def add_vector_property(self, data, name=None, active=True):
"""Add VTK-representation of vector data at the atomic positions.
data: NumPy array of dtype float and shape ``(n,3)``
Vector components corresponding to the atomic positions.
name=None: str
Unique identifier for the vector data.
active=True: bool
Flag indicating whether to use as active vector data.
"""
# Make sure data argument is a valid array
if not isinstance(data, np.ndarray):
data = np.array(data)
assert data.dtype == float and data.shape == (self.npoints,3,)
# Convert vector properties to VTK array
npa2da = vtkDoubleArrayFromNumPyArray(data)
return vtkBaseGrid.add_vector_data_array(self, npa2da, name, active)
