339 lines
13 KiB
Python
339 lines
13 KiB
Python
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"""
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Spherical Voronoi Code
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.. versionadded:: 0.18.0
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"""
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#
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# Copyright (C) Tyler Reddy, Ross Hemsley, Edd Edmondson,
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# Nikolai Nowaczyk, Joe Pitt-Francis, 2015.
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#
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# Distributed under the same BSD license as Scipy.
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#
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import numpy as np
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import numpy.matlib
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import scipy
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import itertools
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from . import _voronoi
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from scipy.spatial.distance import pdist
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__all__ = ['SphericalVoronoi']
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def sphere_check(points, radius, center):
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""" Determines distance of generators from theoretical sphere
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surface.
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"""
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actual_squared_radii = (((points[...,0] - center[0]) ** 2) +
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((points[...,1] - center[1]) ** 2) +
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((points[...,2] - center[2]) ** 2))
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max_discrepancy = (np.sqrt(actual_squared_radii) - radius).max()
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return abs(max_discrepancy)
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def calc_circumcenters(tetrahedrons):
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""" Calculates the cirumcenters of the circumspheres of tetrahedrons.
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An implementation based on
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http://mathworld.wolfram.com/Circumsphere.html
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Parameters
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----------
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tetrahedrons : an array of shape (N, 4, 3)
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consisting of N tetrahedrons defined by 4 points in 3D
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Returns
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----------
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circumcenters : an array of shape (N, 3)
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consisting of the N circumcenters of the tetrahedrons in 3D
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"""
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num = tetrahedrons.shape[0]
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a = np.concatenate((tetrahedrons, np.ones((num, 4, 1))), axis=2)
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sums = np.sum(tetrahedrons ** 2, axis=2)
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d = np.concatenate((sums[:, :, np.newaxis], a), axis=2)
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dx = np.delete(d, 1, axis=2)
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dy = np.delete(d, 2, axis=2)
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dz = np.delete(d, 3, axis=2)
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dx = np.linalg.det(dx)
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dy = -np.linalg.det(dy)
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dz = np.linalg.det(dz)
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a = np.linalg.det(a)
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nominator = np.vstack((dx, dy, dz))
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denominator = 2*a
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return (nominator / denominator).T
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def project_to_sphere(points, center, radius):
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"""
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Projects the elements of points onto the sphere defined
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by center and radius.
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Parameters
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----------
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points : array of floats of shape (npoints, ndim)
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consisting of the points in a space of dimension ndim
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center : array of floats of shape (ndim,)
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the center of the sphere to project on
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radius : float
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the radius of the sphere to project on
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returns: array of floats of shape (npoints, ndim)
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the points projected onto the sphere
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"""
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lengths = scipy.spatial.distance.cdist(points, np.array([center]))
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return (points - center) / lengths * radius + center
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class SphericalVoronoi:
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""" Voronoi diagrams on the surface of a sphere.
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.. versionadded:: 0.18.0
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Parameters
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----------
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points : ndarray of floats, shape (npoints, 3)
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Coordinates of points to construct a spherical
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Voronoi diagram from
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radius : float, optional
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Radius of the sphere (Default: 1)
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center : ndarray of floats, shape (3,)
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Center of sphere (Default: origin)
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threshold : float
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Threshold for detecting duplicate points and
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mismatches between points and sphere parameters.
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(Default: 1e-06)
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Attributes
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----------
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points : double array of shape (npoints, 3)
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the points in 3D to generate the Voronoi diagram from
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radius : double
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radius of the sphere
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Default: None (forces estimation, which is less precise)
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center : double array of shape (3,)
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center of the sphere
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Default: None (assumes sphere is centered at origin)
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vertices : double array of shape (nvertices, 3)
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Voronoi vertices corresponding to points
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regions : list of list of integers of shape (npoints, _ )
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the n-th entry is a list consisting of the indices
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of the vertices belonging to the n-th point in points
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Raises
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------
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ValueError
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If there are duplicates in `points`.
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If the provided `radius` is not consistent with `points`.
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Notes
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----------
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The spherical Voronoi diagram algorithm proceeds as follows. The Convex
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Hull of the input points (generators) is calculated, and is equivalent to
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their Delaunay triangulation on the surface of the sphere [Caroli]_.
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A 3D Delaunay tetrahedralization is obtained by including the origin of
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the coordinate system as the fourth vertex of each simplex of the Convex
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Hull. The circumcenters of all tetrahedra in the system are calculated and
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projected to the surface of the sphere, producing the Voronoi vertices.
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The Delaunay tetrahedralization neighbour information is then used to
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order the Voronoi region vertices around each generator. The latter
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approach is substantially less sensitive to floating point issues than
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angle-based methods of Voronoi region vertex sorting.
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The surface area of spherical polygons is calculated by decomposing them
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into triangles and using L'Huilier's Theorem to calculate the spherical
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excess of each triangle [Weisstein]_. The sum of the spherical excesses is
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multiplied by the square of the sphere radius to obtain the surface area
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of the spherical polygon. For nearly-degenerate spherical polygons an area
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of approximately 0 is returned by default, rather than attempting the
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unstable calculation.
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Empirical assessment of spherical Voronoi algorithm performance suggests
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quadratic time complexity (loglinear is optimal, but algorithms are more
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challenging to implement). The reconstitution of the surface area of the
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sphere, measured as the sum of the surface areas of all Voronoi regions,
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is closest to 100 % for larger (>> 10) numbers of generators.
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References
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----------
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.. [Caroli] Caroli et al. Robust and Efficient Delaunay triangulations of
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points on or close to a sphere. Research Report RR-7004, 2009.
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.. [Weisstein] "L'Huilier's Theorem." From MathWorld -- A Wolfram Web
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Resource. http://mathworld.wolfram.com/LHuiliersTheorem.html
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See Also
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--------
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Voronoi : Conventional Voronoi diagrams in N dimensions.
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Examples
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--------
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>>> from matplotlib import colors
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>>> from mpl_toolkits.mplot3d.art3d import Poly3DCollection
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>>> import matplotlib.pyplot as plt
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>>> from scipy.spatial import SphericalVoronoi
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>>> from mpl_toolkits.mplot3d import proj3d
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>>> # set input data
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>>> points = np.array([[0, 0, 1], [0, 0, -1], [1, 0, 0],
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... [0, 1, 0], [0, -1, 0], [-1, 0, 0], ])
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>>> center = np.array([0, 0, 0])
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>>> radius = 1
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>>> # calculate spherical Voronoi diagram
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>>> sv = SphericalVoronoi(points, radius, center)
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>>> # sort vertices (optional, helpful for plotting)
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>>> sv.sort_vertices_of_regions()
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>>> # generate plot
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>>> fig = plt.figure()
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>>> ax = fig.add_subplot(111, projection='3d')
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>>> # plot the unit sphere for reference (optional)
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>>> u = np.linspace(0, 2 * np.pi, 100)
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>>> v = np.linspace(0, np.pi, 100)
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>>> x = np.outer(np.cos(u), np.sin(v))
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>>> y = np.outer(np.sin(u), np.sin(v))
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>>> z = np.outer(np.ones(np.size(u)), np.cos(v))
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>>> ax.plot_surface(x, y, z, color='y', alpha=0.1)
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>>> # plot generator points
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>>> ax.scatter(points[:, 0], points[:, 1], points[:, 2], c='b')
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>>> # plot Voronoi vertices
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>>> ax.scatter(sv.vertices[:, 0], sv.vertices[:, 1], sv.vertices[:, 2],
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... c='g')
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>>> # indicate Voronoi regions (as Euclidean polygons)
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>>> for region in sv.regions:
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... random_color = colors.rgb2hex(np.random.rand(3))
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... polygon = Poly3DCollection([sv.vertices[region]], alpha=1.0)
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... polygon.set_color(random_color)
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... ax.add_collection3d(polygon)
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>>> plt.show()
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"""
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def __init__(self, points, radius=None, center=None, threshold=1e-06):
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"""
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Initializes the object and starts the computation of the Voronoi
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diagram.
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points : The generator points of the Voronoi diagram assumed to be
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all on the sphere with radius supplied by the radius parameter and
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center supplied by the center parameter.
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radius : The radius of the sphere. Will default to 1 if not supplied.
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center : The center of the sphere. Will default to the origin if not
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supplied.
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"""
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self.points = points
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if np.any(center):
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self.center = center
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else:
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self.center = np.zeros(3)
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if radius:
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self.radius = radius
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else:
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self.radius = 1
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if pdist(self.points).min() <= threshold * self.radius:
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raise ValueError("Duplicate generators present.")
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max_discrepancy = sphere_check(self.points,
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self.radius,
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self.center)
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if max_discrepancy >= threshold * self.radius:
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raise ValueError("Radius inconsistent with generators.")
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self.vertices = None
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self.regions = None
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self._tri = None
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self._calc_vertices_regions()
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def _calc_vertices_regions(self):
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"""
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Calculates the Voronoi vertices and regions of the generators stored
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in self.points. The vertices will be stored in self.vertices and the
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regions in self.regions.
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This algorithm was discussed at PyData London 2015 by
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Tyler Reddy, Ross Hemsley and Nikolai Nowaczyk
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"""
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# perform 3D Delaunay triangulation on data set
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# (here ConvexHull can also be used, and is faster)
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self._tri = scipy.spatial.ConvexHull(self.points)
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# add the center to each of the simplices in tri to get the same
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# tetrahedrons we'd have gotten from Delaunay tetrahedralization
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# tetrahedrons will have shape: (2N-4, 4, 3)
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tetrahedrons = self._tri.points[self._tri.simplices]
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tetrahedrons = np.insert(
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tetrahedrons,
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3,
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np.array([self.center]),
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axis=1
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)
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# produce circumcenters of tetrahedrons from 3D Delaunay
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# circumcenters will have shape: (2N-4, 3)
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circumcenters = calc_circumcenters(tetrahedrons)
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# project tetrahedron circumcenters to the surface of the sphere
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# self.vertices will have shape: (2N-4, 3)
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self.vertices = project_to_sphere(
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circumcenters,
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self.center,
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self.radius
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)
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# calculate regions from triangulation
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# simplex_indices will have shape: (2N-4,)
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simplex_indices = np.arange(self._tri.simplices.shape[0])
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# tri_indices will have shape: (6N-12,)
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tri_indices = np.column_stack([simplex_indices, simplex_indices,
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simplex_indices]).ravel()
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# point_indices will have shape: (6N-12,)
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point_indices = self._tri.simplices.ravel()
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# array_associations will have shape: (6N-12, 2)
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array_associations = np.dstack((point_indices, tri_indices))[0]
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array_associations = array_associations[np.lexsort((
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array_associations[...,1],
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array_associations[...,0]))]
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array_associations = array_associations.astype(np.intp)
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# group by generator indices to produce
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# unsorted regions in nested list
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groups = []
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for k, g in itertools.groupby(array_associations,
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lambda t: t[0]):
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groups.append(list(list(zip(*list(g)))[1]))
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self.regions = groups
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def sort_vertices_of_regions(self):
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"""
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For each region in regions, it sorts the indices of the Voronoi
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vertices such that the resulting points are in a clockwise or
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counterclockwise order around the generator point.
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This is done as follows: Recall that the n-th region in regions
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surrounds the n-th generator in points and that the k-th
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Voronoi vertex in vertices is the projected circumcenter of the
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tetrahedron obtained by the k-th triangle in _tri.simplices (and the
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origin). For each region n, we choose the first triangle (=Voronoi
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vertex) in _tri.simplices and a vertex of that triangle not equal to
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the center n. These determine a unique neighbor of that triangle,
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which is then chosen as the second triangle. The second triangle
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will have a unique vertex not equal to the current vertex or the
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center. This determines a unique neighbor of the second triangle,
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which is then chosen as the third triangle and so forth. We proceed
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through all the triangles (=Voronoi vertices) belonging to the
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generator in points and obtain a sorted version of the vertices
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of its surrounding region.
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"""
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_voronoi.sort_vertices_of_regions(self._tri.simplices,
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self.regions)
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