def _from_arrays(self, vertices, faces, deep=True, verts=False):
"""Set polygons and points from numpy arrays.
Parameters
----------
vertices : np.ndarray of dtype=np.float32 or np.float64
Vertex array. 3D points.
faces : np.ndarray of dtype=np.int64
Face index array. Faces can contain any number of points.
verts : bool, optional
Faces array is a vertex array.
Examples
--------
>>> import numpy as np
>>> import pyvista
>>> vertices = np.array([[0, 0, 0],
... [1, 0, 0],
... [1, 1, 0],
... [0, 1, 0],
... [0.5, 0.5, 1]])
>>> faces = np.hstack([[4, 0, 1, 2, 3],
... [3, 0, 1, 4],
... [3, 1, 2, 4]]) # one square and two triangles
>>> surf = pyvista.PolyData(vertices, faces)
"""
self.SetPoints(pyvista.vtk_points(vertices, deep=deep))
if verts:
self.SetVerts(CellArray(faces))
else:
self.SetPolys(CellArray(faces))
def _from_arrays(self, x, y, z):
"""Create VTK structured grid directly from numpy arrays.
Parameters
----------
x : np.ndarray
Position of the points in x direction.
y : np.ndarray
Position of the points in y direction.
z : np.ndarray
Position of the points in z direction.
"""
if not (x.shape == y.shape == z.shape):
raise ValueError('Input point array shapes must match exactly')
# make the output points the same precision as the input arrays
points = np.empty((x.size, 3), x.dtype)
points[:, 0] = x.ravel('F')
points[:, 1] = y.ravel('F')
points[:, 2] = z.ravel('F')
# ensure that the inputs are 3D
dim = list(x.shape)
while len(dim) < 3:
dim.append(1)
# Create structured grid
self.SetDimensions(dim)
self.SetPoints(pyvista.vtk_points(points))
def points(self, points):
""" set points without copying """
if not isinstance(points, np.ndarray):
raise TypeError('Points must be a numpy array')
vtk_points = pyvista.vtk_points(points, False)
self.SetPoints(vtk_points)
self.GetPoints().Modified()
self.Modified()
def points(self) -> pyvista_ndarray:
"""Return a pointer to the points as a numpy object."""
_points = self.GetPoints()
try:
_points = _points.GetData()
except AttributeError:
# create an empty array
vtk_points = pyvista.vtk_points(np.empty((0, 3)), False)
self.SetPoints(vtk_points)
_points = self.GetPoints().GetData()
return pyvista_ndarray(_points, dataset=self)
def points(self, points):
"""Set points without copying."""
if not isinstance(points, np.ndarray):
raise TypeError('Points must be a numpy array')
vtk_points = pyvista.vtk_points(points, False)
pdata = self.GetPoints()
if not pdata:
self.SetPoints(vtk_points)
else:
pdata.SetData(vtk_points.GetData())
self.GetPoints().Modified()
self.Modified()
def Pyramid(points=None):
"""Create a pyramid defined by 5 points.
Parameters
----------
points : sequence, optional
Points of the pyramid. Points are ordered such that the first
four points are the four counterclockwise points on the
quadrilateral face, and the last point is the apex.
Defaults to pyramid in example.
Returns
-------
pyvista.UnstructuredGrid
Unstructured grid containing a single pyramid cell.
Examples
--------
>>> import pyvista
>>> pointa = [1.0, 1.0, 0.0]
>>> pointb = [-1.0, 1.0, 0.0]
>>> pointc = [-1.0, -1.0, 0.0]
>>> pointd = [1.0, -1.0, 0.0]
>>> pointe = [0.0, 0.0, 1.608]
>>> pyramid = pyvista.Pyramid([pointa, pointb, pointc, pointd, pointe])
>>> pyramid.plot(show_edges=True, line_width=5)
"""
if points is None:
points = [[1.0, 1.0, 0.0], [-1.0, 1.0, 0.0], [-1.0, -1.0, 0.0],
[1.0, -1.0, 0.0], [0.0, 0.0, (4 - 2**0.5)**0.5]]
if len(points) != 5:
raise TypeError('Points must be given as length 5 np.ndarray or list')
check_valid_vector(points[0], 'points[0]')
check_valid_vector(points[1], 'points[1]')
check_valid_vector(points[2], 'points[2]')
check_valid_vector(points[3], 'points[3]')
check_valid_vector(points[4], 'points[4]')
pyramid = _vtk.vtkPyramid()
pyramid.GetPointIds().SetId(0, 0)
pyramid.GetPointIds().SetId(1, 1)
pyramid.GetPointIds().SetId(2, 2)
pyramid.GetPointIds().SetId(3, 3)
pyramid.GetPointIds().SetId(4, 4)
ug = _vtk.vtkUnstructuredGrid()
ug.SetPoints(pyvista.vtk_points(np.array(points), False))
ug.InsertNextCell(pyramid.GetCellType(), pyramid.GetPointIds())
return pyvista.wrap(ug)
def Pyramid(points):
"""Create a pyramid defined by 5 points.
Parameters
----------
points : np.ndarray or list
Points of the pyramid. Points are ordered such that the first
four points are the four counterclockwise points on the
quadrilateral face, and the last point is the apex.
Returns
-------
pyramid : pyvista.UnstructuredGrid
Examples
--------
>>> import pyvista
>>> pointa = [1.0, 1.0, 1.0]
>>> pointb = [-1.0, 1.0, 1.0]
>>> pointc = [-1.0, -1.0, 1.0]
>>> pointd = [1.0, -1.0, 1.0]
>>> pointe = [0.0, 0.0, 0.0]
>>> pyramid = pyvista.Pyramid([pointa, pointb, pointc, pointd, pointe])
>>> pyramid.plot() # doctest:+SKIP
"""
if len(points) != 5:
raise TypeError('Points must be given as length 5 np.ndarray or list')
check_valid_vector(points[0], 'points[0]')
check_valid_vector(points[1], 'points[1]')
check_valid_vector(points[2], 'points[2]')
check_valid_vector(points[3], 'points[3]')
check_valid_vector(points[4], 'points[4]')
pyramid = _vtk.vtkPyramid()
pyramid.GetPointIds().SetId(0, 0)
pyramid.GetPointIds().SetId(1, 1)
pyramid.GetPointIds().SetId(2, 2)
pyramid.GetPointIds().SetId(3, 3)
pyramid.GetPointIds().SetId(4, 4)
ug = _vtk.vtkUnstructuredGrid()
ug.SetPoints(pyvista.vtk_points(np.array(points), False))
ug.InsertNextCell(pyramid.GetCellType(), pyramid.GetPointIds())
return pyvista.wrap(ug)
def Spline(points, n_points=None):
"""Create a spline from points.
Parameters
----------
points : np.ndarray
Array of points to build a spline out of. Array must be 3D
and directionally ordered.
n_points : int, optional
Number of points to interpolate along the points array.
Returns
-------
pyvista.PolyData
Line mesh of spline.
Examples
--------
Construct a spline.
>>> import numpy as np
>>> import pyvista as pv
>>> theta = np.linspace(-4 * np.pi, 4 * np.pi, 100)
>>> z = np.linspace(-2, 2, 100)
>>> r = z**2 + 1
>>> x = r * np.sin(theta)
>>> y = r * np.cos(theta)
>>> points = np.column_stack((x, y, z))
>>> spline = pv.Spline(points, 1000)
>>> spline.plot(render_lines_as_tubes=True, line_width=10, show_scalar_bar=False)
"""
spline_function = _vtk.vtkParametricSpline()
spline_function.SetPoints(pyvista.vtk_points(points, False))
# get interpolation density
u_res = n_points
if u_res is None:
u_res = points.shape[0]
u_res -= 1
spline = surface_from_para(spline_function, u_res)
return spline.compute_arc_length()
def polygon_to_vtk(polygon, topo_points):
"""Converts a polygon shape to a pyvista.PolyData object.
This assumes the points are ordered.
"""
pts = np.array(polygon.points)
pts = np.c_[pts, np.zeros(pts.shape[0])]
pts = _fix_to_topography(topo_points, pts)
cells = vtk.vtkCellArray()
for i in range(pts.shape[0]-1):
cell = _makeLineCell(i, i+1)
cells.InsertNextCell(cell)
# Add in last connection to make complete polygon
cell = _makeLineCell(i, 0)
cells.InsertNextCell(cell)
# Build the output
pdo = vtk.vtkPolyData()
pdo.SetPoints(pyvista.vtk_points(pts))
pdo.SetLines(cells)
return pyvista.wrap(pdo)
def points(self, points: np.ndarray):
"""Set points without copying."""
if isinstance(points, pyvista_ndarray):
# simply set the underlying data
if points.VTKObject is not None:
self.GetPoints().SetData(points.VTKObject)
self.GetPoints().Modified()
self.Modified()
return
# otherwise, wrap and use the array
if not isinstance(points, np.ndarray):
raise TypeError('Points must be a numpy array')
vtk_points = pyvista.vtk_points(points, False)
pdata = self.GetPoints()
if not pdata:
self.SetPoints(vtk_points)
else:
pdata.SetData(vtk_points.GetData())
self.GetPoints().Modified()
self.Modified()
def create_polyhedron(polyhedron_data):
"""
create the vtk grid containing all points and faces
"""
points = pv.vtk_points(np.array(polyhedron_data.vertex_list))
polyhedron_faces = polyhedron_data.polyhedron_faces
polyhedron_faces_id_list = vtk.vtkIdList()
# Number faces that make up the cell.
polyhedron_faces_id_list.InsertNextId(len(polyhedron_faces))
for face in polyhedron_faces:
# Number of points in the face == numberOfFaceVertices
polyhedron_faces_id_list.InsertNextId(len(face))
# Insert the pointIds for that face.
[polyhedron_faces_id_list.InsertNextId(i) for i in face]
polyhedron_grid = vtk.vtkUnstructuredGrid()
polyhedron_grid.InsertNextCell(
vtk.VTK_POLYHEDRON, polyhedron_faces_id_list)
polyhedron_grid.SetPoints(points)
return polyhedron_grid
def _from_arrays(self, offset, cells, cell_type, points, deep=True):
"""Create VTK unstructured grid from numpy arrays.
Parameters
----------
offset : np.ndarray dtype=np.int64
Array indicating the start location of each cell in the cells
array. Set to ``None`` when using VTK 9+.
cells : np.ndarray dtype=np.int64
Array of cells. Each cell contains the number of points in the
cell and the node numbers of the cell.
cell_type : np.uint8
Cell types of each cell. Each cell type numbers can be found from
vtk documentation. See example below.
points : np.ndarray
Numpy array containing point locations.
Examples
--------
>>> import numpy
>>> import vtk
>>> import pyvista
>>> offset = np.array([0, 9])
>>> cells = np.array([8, 0, 1, 2, 3, 4, 5, 6, 7, 8, 8, 9, 10, 11, 12, 13, 14, 15])
>>> cell_type = np.array([vtk.VTK_HEXAHEDRON, vtk.VTK_HEXAHEDRON], np.int8)
>>> cell1 = np.array([[0, 0, 0],
... [1, 0, 0],
... [1, 1, 0],
... [0, 1, 0],
... [0, 0, 1],
... [1, 0, 1],
... [1, 1, 1],
... [0, 1, 1]])
>>> cell2 = np.array([[0, 0, 2],
... [1, 0, 2],
... [1, 1, 2],
... [0, 1, 2],
... [0, 0, 3],
... [1, 0, 3],
... [1, 1, 3],
... [0, 1, 3]])
>>> points = np.vstack((cell1, cell2))
>>> grid = pyvista.UnstructuredGrid(offset, cells, cell_type, points)
"""
# Convert to vtk arrays
vtkcells = CellArray(cells, cell_type.size, deep)
if cell_type.dtype != np.uint8:
cell_type = cell_type.astype(np.uint8)
cell_type = numpy_to_vtk(cell_type, deep=deep)
# Convert points to vtkPoints object
points = pyvista.vtk_points(points, deep=deep)
self.SetPoints(points)
# vtk9 does not require an offset array
if VTK9:
if offset is not None:
warnings.warn('VTK 9 no longer accepts an offset array',
stacklevel=3)
self.SetCells(cell_type, vtkcells)
else:
self.SetCells(cell_type, numpy_to_idarr(offset), vtkcells)
def _from_arrays(self, offset, cells, cell_type, points, deep=True):
"""Create VTK unstructured grid from numpy arrays.
Parameters
----------
offset : np.ndarray dtype=np.int64
Array indicating the start location of each cell in the cells
array.
cells : np.ndarray dtype=np.int64
Array of cells. Each cell contains the number of points in the
cell and the node numbers of the cell.
cell_type : np.uint8
Cell types of each cell. Each cell type numbers can be found from
vtk documentation. See example below.
points : np.ndarray
Numpy array containing point locations.
Examples
--------
>>> import numpy
>>> import vtk
>>> import pyvista
>>> offset = np.array([0, 9])
>>> cells = np.array([8, 0, 1, 2, 3, 4, 5, 6, 7, 8, 8, 9, 10, 11, 12, 13, 14, 15])
>>> cell_type = np.array([vtk.VTK_HEXAHEDRON, vtk.VTK_HEXAHEDRON], np.int8)
>>> cell1 = np.array([[0, 0, 0],
... [1, 0, 0],
... [1, 1, 0],
... [0, 1, 0],
... [0, 0, 1],
... [1, 0, 1],
... [1, 1, 1],
... [0, 1, 1]])
>>> cell2 = np.array([[0, 0, 2],
... [1, 0, 2],
... [1, 1, 2],
... [0, 1, 2],
... [0, 0, 3],
... [1, 0, 3],
... [1, 1, 3],
... [0, 1, 3]])
>>> points = np.vstack((cell1, cell2))
>>> grid = pyvista.UnstructuredGrid(offset, cells, cell_type, points)
"""
if offset.dtype != pyvista.ID_TYPE:
offset = offset.astype(pyvista.ID_TYPE)
if cells.dtype != pyvista.ID_TYPE:
cells = cells.astype(pyvista.ID_TYPE)
if not cells.flags['C_CONTIGUOUS']:
cells = np.ascontiguousarray(cells)
# if cells.ndim != 1:
# cells = cells.ravel()
if cell_type.dtype != np.uint8:
cell_type = cell_type.astype(np.uint8)
# Get number of cells
ncells = cell_type.size
# Convert to vtk arrays
cell_type = numpy_to_vtk(cell_type, deep=deep)
offset = numpy_to_vtkIdTypeArray(offset, deep=deep)
vtkcells = vtk.vtkCellArray()
vtkcells.SetCells(ncells, numpy_to_vtkIdTypeArray(cells.ravel(), deep=deep))
# Convert points to vtkPoints object
points = pyvista.vtk_points(points, deep=deep)
# Create unstructured grid
self.SetPoints(points)
self.SetCells(cell_type, offset, vtkcells)
def __init__(self,
var_inp=None,
faces=None,
n_faces=None,
lines=None,
n_lines=None,
deep=False) -> None:
"""Initialize the polydata."""
local_parms = locals()
super().__init__()
# allow empty input
if var_inp is None:
return
# filename
opt_kwarg = ['faces', 'n_faces', 'lines', 'n_lines']
if isinstance(var_inp, (str, pathlib.Path)):
for kwarg in opt_kwarg:
if local_parms[kwarg]:
raise ValueError(
'No other arguments should be set when first '
'parameter is a string')
self._from_file(var_inp) # is filename
# When loading files with just point arrays, create and
# set the polydata vertices
if self.n_points > 0 and self.n_cells == 0:
verts = self._make_vertex_cells(self.n_points)
self.verts = CellArray(verts, self.n_points, deep)
return
# PolyData-like
if isinstance(var_inp, _vtk.vtkPolyData):
for kwarg in opt_kwarg:
if local_parms[kwarg]:
raise ValueError(
'No other arguments should be set when first '
'parameter is a PolyData')
if deep:
self.deep_copy(var_inp)
else:
self.shallow_copy(var_inp)
return
# First parameter is points
if isinstance(var_inp, (np.ndarray, list)):
self.SetPoints(pyvista.vtk_points(var_inp, deep=deep))
else:
msg = f"""
Invalid Input type:
Expected first argument to be either a:
- vtk.PolyData
- pyvista.PolyData
- numeric numpy.ndarray (1 or 2 dimensions)
- List (flat or nested with 3 points per vertex)
Instead got: {type(var_inp)}"""
raise TypeError(dedent(msg.strip('\n')))
# At this point, points have been setup, add faces and/or lines
if faces is None and lines is None:
# one cell per point (point cloud case)
verts = self._make_vertex_cells(self.n_points)
self.verts = CellArray(verts, self.n_points, deep)
elif faces is not None:
# here we use CellArray since we must specify deep and n_faces
self.faces = CellArray(faces, n_faces, deep)
# can always set lines
if lines is not None:
# here we use CellArray since we must specify deep and n_lines
self.lines = CellArray(lines, n_lines, deep)
def KochanekSpline(points,
tension=None,
bias=None,
continuity=None,
n_points=None):
"""Create a Kochanek spline from points.
Parameters
----------
points : sequence
Array of points to build a Kochanek spline out of. Array must
be 3D and directionally ordered.
tension : sequence, optional
Changes the length of the tangent vector. Defaults to ``[0.0,
0.0, 0.0]``.
bias : sequence, optional
Primarily changes the direction of the tangent vector.
Defaults to ``[0.0, 0.0, 0.0]``.
continuity : sequence, optional
Changes the sharpness in change between tangents. Defaults to
``[0.0, 0.0, 0.0]``.
n_points : int, optional
Number of points on the spline. Defaults to the number of
points in ``points``.
Returns
-------
pyvista.PolyData
Kochanek spline.
Examples
--------
Construct a Kochanek spline.
>>> import numpy as np
>>> import pyvista as pv
>>> theta = np.linspace(-4 * np.pi, 4 * np.pi, 100)
>>> z = np.linspace(-2, 2, 100)
>>> r = z ** 2 + 1
>>> x = r * np.sin(theta)
>>> y = r * np.cos(theta)
>>> points = np.column_stack((x, y, z))
>>> kochanek_spline = pv.KochanekSpline(points, n_points=6)
>>> kochanek_spline.plot(line_width=4, color="k")
See :ref:`create_kochanek_spline_example` for an additional example.
"""
if tension is None:
tension = np.array([0.0, 0.0, 0.0])
check_valid_vector(tension, "tension")
if not np.all(np.abs(tension) <= 1.0):
raise ValueError(
"The absolute value of all values of the tension array elements must be <= 1.0 "
)
if bias is None:
bias = np.array([0.0, 0.0, 0.0])
check_valid_vector(bias, "bias")
if not np.all(np.abs(bias) <= 1.0):
raise ValueError(
"The absolute value of all values of the bias array elements must be <= 1.0 "
)
if continuity is None:
continuity = np.array([0.0, 0.0, 0.0])
check_valid_vector(continuity, "continuity")
if not np.all(np.abs(continuity) <= 1.0):
raise ValueError(
"The absolute value of all values continuity array elements must be <= 1.0 "
)
spline_function = _vtk.vtkParametricSpline()
spline_function.SetPoints(pyvista.vtk_points(points, False))
# set Kochanek spline for each direction
xspline = _vtk.vtkKochanekSpline()
yspline = _vtk.vtkKochanekSpline()
zspline = _vtk.vtkKochanekSpline()
xspline.SetDefaultBias(bias[0])
yspline.SetDefaultBias(bias[1])
zspline.SetDefaultBias(bias[2])
xspline.SetDefaultTension(tension[0])
yspline.SetDefaultTension(tension[1])
zspline.SetDefaultTension(tension[2])
xspline.SetDefaultContinuity(continuity[0])
yspline.SetDefaultContinuity(continuity[1])
zspline.SetDefaultContinuity(continuity[2])
spline_function.SetXSpline(xspline)
spline_function.SetYSpline(yspline)
spline_function.SetZSpline(zspline)
# get interpolation density
u_res = n_points
if u_res is None:
u_res = points.shape[0]
u_res -= 1
spline = surface_from_para(spline_function, u_res)
return spline.compute_arc_length()
