import os import copy import numpy as np from numpy.testing import (assert_equal, assert_almost_equal, assert_, assert_allclose, assert_array_equal) import pytest from pytest import raises as assert_raises import scipy.spatial._qhull as qhull from scipy.spatial import cKDTree as KDTree from scipy.spatial import Voronoi import itertools def sorted_tuple(x): return tuple(sorted(x)) def sorted_unique_tuple(x): return tuple(np.unique(x)) def assert_unordered_tuple_list_equal(a, b, tpl=tuple): if isinstance(a, np.ndarray): a = a.tolist() if isinstance(b, np.ndarray): b = b.tolist() a = list(map(tpl, a)) a.sort() b = list(map(tpl, b)) b.sort() assert_equal(a, b) np.random.seed(1234) points = [(0,0), (0,1), (1,0), (1,1), (0.5, 0.5), (0.5, 1.5)] pathological_data_1 = np.array([ [-3.14,-3.14], [-3.14,-2.36], [-3.14,-1.57], [-3.14,-0.79], [-3.14,0.0], [-3.14,0.79], [-3.14,1.57], [-3.14,2.36], [-3.14,3.14], [-2.36,-3.14], [-2.36,-2.36], [-2.36,-1.57], [-2.36,-0.79], [-2.36,0.0], [-2.36,0.79], [-2.36,1.57], [-2.36,2.36], [-2.36,3.14], [-1.57,-0.79], [-1.57,0.79], [-1.57,-1.57], [-1.57,0.0], [-1.57,1.57], [-1.57,-3.14], [-1.57,-2.36], [-1.57,2.36], [-1.57,3.14], [-0.79,-1.57], [-0.79,1.57], [-0.79,-3.14], [-0.79,-2.36], [-0.79,-0.79], [-0.79,0.0], [-0.79,0.79], [-0.79,2.36], [-0.79,3.14], [0.0,-3.14], [0.0,-2.36], [0.0,-1.57], [0.0,-0.79], [0.0,0.0], [0.0,0.79], [0.0,1.57], [0.0,2.36], [0.0,3.14], [0.79,-3.14], [0.79,-2.36], [0.79,-0.79], [0.79,0.0], [0.79,0.79], [0.79,2.36], [0.79,3.14], [0.79,-1.57], [0.79,1.57], [1.57,-3.14], [1.57,-2.36], [1.57,2.36], [1.57,3.14], [1.57,-1.57], [1.57,0.0], [1.57,1.57], [1.57,-0.79], [1.57,0.79], [2.36,-3.14], [2.36,-2.36], [2.36,-1.57], [2.36,-0.79], [2.36,0.0], [2.36,0.79], [2.36,1.57], [2.36,2.36], [2.36,3.14], [3.14,-3.14], [3.14,-2.36], [3.14,-1.57], [3.14,-0.79], [3.14,0.0], [3.14,0.79], [3.14,1.57], [3.14,2.36], [3.14,3.14], ]) pathological_data_2 = np.array([ [-1, -1], [-1, 0], [-1, 1], [0, -1], [0, 0], [0, 1], [1, -1 - np.finfo(np.float_).eps], [1, 0], [1, 1], ]) bug_2850_chunks = [np.random.rand(10, 2), np.array([[0,0], [0,1], [1,0], [1,1]]) # add corners ] # same with some additional chunks bug_2850_chunks_2 = (bug_2850_chunks + [np.random.rand(10, 2), 0.25 + np.array([[0,0], [0,1], [1,0], [1,1]])]) DATASETS = { 'some-points': np.asarray(points), 'random-2d': np.random.rand(30, 2), 'random-3d': np.random.rand(30, 3), 'random-4d': np.random.rand(30, 4), 'random-5d': np.random.rand(30, 5), 'random-6d': np.random.rand(10, 6), 'random-7d': np.random.rand(10, 7), 'random-8d': np.random.rand(10, 8), 'pathological-1': pathological_data_1, 'pathological-2': pathological_data_2 } INCREMENTAL_DATASETS = { 'bug-2850': (bug_2850_chunks, None), 'bug-2850-2': (bug_2850_chunks_2, None), } def _add_inc_data(name, chunksize): """ Generate incremental datasets from basic data sets """ points = DATASETS[name] ndim = points.shape[1] opts = None nmin = ndim + 2 if name == 'some-points': # since Qz is not allowed, use QJ opts = 'QJ Pp' elif name == 'pathological-1': # include enough points so that we get different x-coordinates nmin = 12 chunks = [points[:nmin]] for j in range(nmin, len(points), chunksize): chunks.append(points[j:j+chunksize]) new_name = "%s-chunk-%d" % (name, chunksize) assert new_name not in INCREMENTAL_DATASETS INCREMENTAL_DATASETS[new_name] = (chunks, opts) for name in DATASETS: for chunksize in 1, 4, 16: _add_inc_data(name, chunksize) class Test_Qhull: def test_swapping(self): # Check that Qhull state swapping works x = qhull._Qhull(b'v', np.array([[0,0],[0,1],[1,0],[1,1.],[0.5,0.5]]), b'Qz') xd = copy.deepcopy(x.get_voronoi_diagram()) y = qhull._Qhull(b'v', np.array([[0,0],[0,1],[1,0],[1,2.]]), b'Qz') yd = copy.deepcopy(y.get_voronoi_diagram()) xd2 = copy.deepcopy(x.get_voronoi_diagram()) x.close() yd2 = copy.deepcopy(y.get_voronoi_diagram()) y.close() assert_raises(RuntimeError, x.get_voronoi_diagram) assert_raises(RuntimeError, y.get_voronoi_diagram) assert_allclose(xd[0], xd2[0]) assert_unordered_tuple_list_equal(xd[1], xd2[1], tpl=sorted_tuple) assert_unordered_tuple_list_equal(xd[2], xd2[2], tpl=sorted_tuple) assert_unordered_tuple_list_equal(xd[3], xd2[3], tpl=sorted_tuple) assert_array_equal(xd[4], xd2[4]) assert_allclose(yd[0], yd2[0]) assert_unordered_tuple_list_equal(yd[1], yd2[1], tpl=sorted_tuple) assert_unordered_tuple_list_equal(yd[2], yd2[2], tpl=sorted_tuple) assert_unordered_tuple_list_equal(yd[3], yd2[3], tpl=sorted_tuple) assert_array_equal(yd[4], yd2[4]) x.close() assert_raises(RuntimeError, x.get_voronoi_diagram) y.close() assert_raises(RuntimeError, y.get_voronoi_diagram) def test_issue_8051(self): points = np.array([[0, 0], [0, 1], [0, 2], [1, 0], [1, 1], [1, 2],[2, 0], [2, 1], [2, 2]]) Voronoi(points) class TestUtilities: """ Check that utility functions work. """ def test_find_simplex(self): # Simple check that simplex finding works points = np.array([(0,0), (0,1), (1,1), (1,0)], dtype=np.double) tri = qhull.Delaunay(points) # +---+ # |\ 0| # | \ | # |1 \| # +---+ assert_equal(tri.simplices, [[1, 3, 2], [3, 1, 0]]) for p in [(0.25, 0.25, 1), (0.75, 0.75, 0), (0.3, 0.2, 1)]: i = tri.find_simplex(p[:2]) assert_equal(i, p[2], err_msg='%r' % (p,)) j = qhull.tsearch(tri, p[:2]) assert_equal(i, j) def test_plane_distance(self): # Compare plane distance from hyperplane equations obtained from Qhull # to manually computed plane equations x = np.array([(0,0), (1, 1), (1, 0), (0.99189033, 0.37674127), (0.99440079, 0.45182168)], dtype=np.double) p = np.array([0.99966555, 0.15685619], dtype=np.double) tri = qhull.Delaunay(x) z = tri.lift_points(x) pz = tri.lift_points(p) dist = tri.plane_distance(p) for j, v in enumerate(tri.simplices): x1 = z[v[0]] x2 = z[v[1]] x3 = z[v[2]] n = np.cross(x1 - x3, x2 - x3) n /= np.sqrt(np.dot(n, n)) n *= -np.sign(n[2]) d = np.dot(n, pz - x3) assert_almost_equal(dist[j], d) def test_convex_hull(self): # Simple check that the convex hull seems to works points = np.array([(0,0), (0,1), (1,1), (1,0)], dtype=np.double) tri = qhull.Delaunay(points) # +---+ # |\ 0| # | \ | # |1 \| # +---+ assert_equal(tri.convex_hull, [[3, 2], [1, 2], [1, 0], [3, 0]]) def test_volume_area(self): #Basic check that we get back the correct volume and area for a cube points = np.array([(0, 0, 0), (0, 1, 0), (1, 0, 0), (1, 1, 0), (0, 0, 1), (0, 1, 1), (1, 0, 1), (1, 1, 1)]) hull = qhull.ConvexHull(points) assert_allclose(hull.volume, 1., rtol=1e-14, err_msg="Volume of cube is incorrect") assert_allclose(hull.area, 6., rtol=1e-14, err_msg="Area of cube is incorrect") def test_random_volume_area(self): #Test that the results for a random 10-point convex are #coherent with the output of qconvex Qt s FA points = np.array([(0.362568364506, 0.472712355305, 0.347003084477), (0.733731893414, 0.634480295684, 0.950513180209), (0.511239955611, 0.876839441267, 0.418047827863), (0.0765906233393, 0.527373281342, 0.6509863541), (0.146694972056, 0.596725793348, 0.894860986685), (0.513808585741, 0.069576205858, 0.530890338876), (0.512343805118, 0.663537132612, 0.037689295973), (0.47282965018, 0.462176697655, 0.14061843691), (0.240584597123, 0.778660020591, 0.722913476339), (0.951271745935, 0.967000673944, 0.890661319684)]) hull = qhull.ConvexHull(points) assert_allclose(hull.volume, 0.14562013, rtol=1e-07, err_msg="Volume of random polyhedron is incorrect") assert_allclose(hull.area, 1.6670425, rtol=1e-07, err_msg="Area of random polyhedron is incorrect") def test_incremental_volume_area_random_input(self): """Test that incremental mode gives the same volume/area as non-incremental mode and incremental mode with restart""" nr_points = 20 dim = 3 points = np.random.random((nr_points, dim)) inc_hull = qhull.ConvexHull(points[:dim+1, :], incremental=True) inc_restart_hull = qhull.ConvexHull(points[:dim+1, :], incremental=True) for i in range(dim+1, nr_points): hull = qhull.ConvexHull(points[:i+1, :]) inc_hull.add_points(points[i:i+1, :]) inc_restart_hull.add_points(points[i:i+1, :], restart=True) assert_allclose(hull.volume, inc_hull.volume, rtol=1e-7) assert_allclose(hull.volume, inc_restart_hull.volume, rtol=1e-7) assert_allclose(hull.area, inc_hull.area, rtol=1e-7) assert_allclose(hull.area, inc_restart_hull.area, rtol=1e-7) def _check_barycentric_transforms(self, tri, err_msg="", unit_cube=False, unit_cube_tol=0): """Check that a triangulation has reasonable barycentric transforms""" vertices = tri.points[tri.simplices] sc = 1/(tri.ndim + 1.0) centroids = vertices.sum(axis=1) * sc # Either: (i) the simplex has a `nan` barycentric transform, # or, (ii) the centroid is in the simplex def barycentric_transform(tr, x): r = tr[:,-1,:] Tinv = tr[:,:-1,:] return np.einsum('ijk,ik->ij', Tinv, x - r) eps = np.finfo(float).eps c = barycentric_transform(tri.transform, centroids) with np.errstate(invalid="ignore"): ok = np.isnan(c).all(axis=1) | (abs(c - sc)/sc < 0.1).all(axis=1) assert_(ok.all(), "%s %s" % (err_msg, np.nonzero(~ok))) # Invalid simplices must be (nearly) zero volume q = vertices[:,:-1,:] - vertices[:,-1,None,:] volume = np.array([np.linalg.det(q[k,:,:]) for k in range(tri.nsimplex)]) ok = np.isfinite(tri.transform[:,0,0]) | (volume < np.sqrt(eps)) assert_(ok.all(), "%s %s" % (err_msg, np.nonzero(~ok))) # Also, find_simplex for the centroid should end up in some # simplex for the non-degenerate cases j = tri.find_simplex(centroids) ok = (j != -1) | np.isnan(tri.transform[:,0,0]) assert_(ok.all(), "%s %s" % (err_msg, np.nonzero(~ok))) if unit_cube: # If in unit cube, no interior point should be marked out of hull at_boundary = (centroids <= unit_cube_tol).any(axis=1) at_boundary |= (centroids >= 1 - unit_cube_tol).any(axis=1) ok = (j != -1) | at_boundary assert_(ok.all(), "%s %s" % (err_msg, np.nonzero(~ok))) def test_degenerate_barycentric_transforms(self): # The triangulation should not produce invalid barycentric # transforms that stump the simplex finding data = np.load(os.path.join(os.path.dirname(__file__), 'data', 'degenerate_pointset.npz')) points = data['c'] data.close() tri = qhull.Delaunay(points) # Check that there are not too many invalid simplices bad_count = np.isnan(tri.transform[:,0,0]).sum() assert_(bad_count < 23, bad_count) # Check the transforms self._check_barycentric_transforms(tri) @pytest.mark.slow def test_more_barycentric_transforms(self): # Triangulate some "nasty" grids eps = np.finfo(float).eps npoints = {2: 70, 3: 11, 4: 5, 5: 3} for ndim in range(2, 6): # Generate an uniform grid in n-d unit cube x = np.linspace(0, 1, npoints[ndim]) grid = np.c_[list(map(np.ravel, np.broadcast_arrays(*np.ix_(*([x]*ndim)))))].T err_msg = "ndim=%d" % ndim # Check using regular grid tri = qhull.Delaunay(grid) self._check_barycentric_transforms(tri, err_msg=err_msg, unit_cube=True) # Check with eps-perturbations np.random.seed(1234) m = (np.random.rand(grid.shape[0]) < 0.2) grid[m,:] += 2*eps*(np.random.rand(*grid[m,:].shape) - 0.5) tri = qhull.Delaunay(grid) self._check_barycentric_transforms(tri, err_msg=err_msg, unit_cube=True, unit_cube_tol=2*eps) # Check with duplicated data tri = qhull.Delaunay(np.r_[grid, grid]) self._check_barycentric_transforms(tri, err_msg=err_msg, unit_cube=True, unit_cube_tol=2*eps) class TestVertexNeighborVertices: def _check(self, tri): expected = [set() for j in range(tri.points.shape[0])] for s in tri.simplices: for a in s: for b in s: if a != b: expected[a].add(b) indptr, indices = tri.vertex_neighbor_vertices got = [set(map(int, indices[indptr[j]:indptr[j+1]])) for j in range(tri.points.shape[0])] assert_equal(got, expected, err_msg="%r != %r" % (got, expected)) def test_triangle(self): points = np.array([(0,0), (0,1), (1,0)], dtype=np.double) tri = qhull.Delaunay(points) self._check(tri) def test_rectangle(self): points = np.array([(0,0), (0,1), (1,1), (1,0)], dtype=np.double) tri = qhull.Delaunay(points) self._check(tri) def test_complicated(self): points = np.array([(0,0), (0,1), (1,1), (1,0), (0.5, 0.5), (0.9, 0.5)], dtype=np.double) tri = qhull.Delaunay(points) self._check(tri) class TestDelaunay: """ Check that triangulation works. """ def test_masked_array_fails(self): masked_array = np.ma.masked_all(1) assert_raises(ValueError, qhull.Delaunay, masked_array) def test_array_with_nans_fails(self): points_with_nan = np.array([(0,0), (0,1), (1,1), (1,np.nan)], dtype=np.double) assert_raises(ValueError, qhull.Delaunay, points_with_nan) def test_nd_simplex(self): # simple smoke test: triangulate a n-dimensional simplex for nd in range(2, 8): points = np.zeros((nd+1, nd)) for j in range(nd): points[j,j] = 1.0 points[-1,:] = 1.0 tri = qhull.Delaunay(points) tri.simplices.sort() assert_equal(tri.simplices, np.arange(nd+1, dtype=int)[None, :]) assert_equal(tri.neighbors, -1 + np.zeros((nd+1), dtype=int)[None,:]) def test_2d_square(self): # simple smoke test: 2d square points = np.array([(0,0), (0,1), (1,1), (1,0)], dtype=np.double) tri = qhull.Delaunay(points) assert_equal(tri.simplices, [[1, 3, 2], [3, 1, 0]]) assert_equal(tri.neighbors, [[-1, -1, 1], [-1, -1, 0]]) def test_duplicate_points(self): x = np.array([0, 1, 0, 1], dtype=np.float64) y = np.array([0, 0, 1, 1], dtype=np.float64) xp = np.r_[x, x] yp = np.r_[y, y] # shouldn't fail on duplicate points qhull.Delaunay(np.c_[x, y]) qhull.Delaunay(np.c_[xp, yp]) def test_pathological(self): # both should succeed points = DATASETS['pathological-1'] tri = qhull.Delaunay(points) assert_equal(tri.points[tri.simplices].max(), points.max()) assert_equal(tri.points[tri.simplices].min(), points.min()) points = DATASETS['pathological-2'] tri = qhull.Delaunay(points) assert_equal(tri.points[tri.simplices].max(), points.max()) assert_equal(tri.points[tri.simplices].min(), points.min()) def test_joggle(self): # Check that the option QJ indeed guarantees that all input points # occur as vertices of the triangulation points = np.random.rand(10, 2) points = np.r_[points, points] # duplicate input data tri = qhull.Delaunay(points, qhull_options="QJ Qbb Pp") assert_array_equal(np.unique(tri.simplices.ravel()), np.arange(len(points))) def test_coplanar(self): # Check that the coplanar point output option indeed works points = np.random.rand(10, 2) points = np.r_[points, points] # duplicate input data tri = qhull.Delaunay(points) assert_(len(np.unique(tri.simplices.ravel())) == len(points)//2) assert_(len(tri.coplanar) == len(points)//2) assert_(len(np.unique(tri.coplanar[:,2])) == len(points)//2) assert_(np.all(tri.vertex_to_simplex >= 0)) def test_furthest_site(self): points = [(0, 0), (0, 1), (1, 0), (0.5, 0.5), (1.1, 1.1)] tri = qhull.Delaunay(points, furthest_site=True) expected = np.array([(1, 4, 0), (4, 2, 0)]) # from Qhull assert_array_equal(tri.simplices, expected) @pytest.mark.parametrize("name", sorted(INCREMENTAL_DATASETS)) def test_incremental(self, name): # Test incremental construction of the triangulation chunks, opts = INCREMENTAL_DATASETS[name] points = np.concatenate(chunks, axis=0) obj = qhull.Delaunay(chunks[0], incremental=True, qhull_options=opts) for chunk in chunks[1:]: obj.add_points(chunk) obj2 = qhull.Delaunay(points) obj3 = qhull.Delaunay(chunks[0], incremental=True, qhull_options=opts) if len(chunks) > 1: obj3.add_points(np.concatenate(chunks[1:], axis=0), restart=True) # Check that the incremental mode agrees with upfront mode if name.startswith('pathological'): # XXX: These produce valid but different triangulations. # They look OK when plotted, but how to check them? assert_array_equal(np.unique(obj.simplices.ravel()), np.arange(points.shape[0])) assert_array_equal(np.unique(obj2.simplices.ravel()), np.arange(points.shape[0])) else: assert_unordered_tuple_list_equal(obj.simplices, obj2.simplices, tpl=sorted_tuple) assert_unordered_tuple_list_equal(obj2.simplices, obj3.simplices, tpl=sorted_tuple) def test_vertices_deprecation(self): tri = qhull.Delaunay([(0, 0), (0, 1), (1, 0)]) msg = ("Delaunay attribute 'vertices' is deprecated in favour of " "'simplices' and will be removed in Scipy 1.11.0.") with pytest.warns(DeprecationWarning, match=msg): tri.vertices def assert_hulls_equal(points, facets_1, facets_2): # Check that two convex hulls constructed from the same point set # are equal facets_1 = set(map(sorted_tuple, facets_1)) facets_2 = set(map(sorted_tuple, facets_2)) if facets_1 != facets_2 and points.shape[1] == 2: # The direct check fails for the pathological cases # --- then the convex hull from Delaunay differs (due # to rounding error etc.) from the hull computed # otherwise, by the question whether (tricoplanar) # points that lie almost exactly on the hull are # included as vertices of the hull or not. # # So we check the result, and accept it if the Delaunay # hull line segments are a subset of the usual hull. eps = 1000 * np.finfo(float).eps for a, b in facets_1: for ap, bp in facets_2: t = points[bp] - points[ap] t /= np.linalg.norm(t) # tangent n = np.array([-t[1], t[0]]) # normal # check that the two line segments are parallel # to the same line c1 = np.dot(n, points[b] - points[ap]) c2 = np.dot(n, points[a] - points[ap]) if not np.allclose(np.dot(c1, n), 0): continue if not np.allclose(np.dot(c2, n), 0): continue # Check that the segment (a, b) is contained in (ap, bp) c1 = np.dot(t, points[a] - points[ap]) c2 = np.dot(t, points[b] - points[ap]) c3 = np.dot(t, points[bp] - points[ap]) if c1 < -eps or c1 > c3 + eps: continue if c2 < -eps or c2 > c3 + eps: continue # OK: break else: raise AssertionError("comparison fails") # it was OK return assert_equal(facets_1, facets_2) class TestConvexHull: def test_masked_array_fails(self): masked_array = np.ma.masked_all(1) assert_raises(ValueError, qhull.ConvexHull, masked_array) def test_array_with_nans_fails(self): points_with_nan = np.array([(0,0), (1,1), (2,np.nan)], dtype=np.double) assert_raises(ValueError, qhull.ConvexHull, points_with_nan) @pytest.mark.parametrize("name", sorted(DATASETS)) def test_hull_consistency_tri(self, name): # Check that a convex hull returned by qhull in ndim # and the hull constructed from ndim delaunay agree points = DATASETS[name] tri = qhull.Delaunay(points) hull = qhull.ConvexHull(points) assert_hulls_equal(points, tri.convex_hull, hull.simplices) # Check that the hull extremes are as expected if points.shape[1] == 2: assert_equal(np.unique(hull.simplices), np.sort(hull.vertices)) else: assert_equal(np.unique(hull.simplices), hull.vertices) @pytest.mark.parametrize("name", sorted(INCREMENTAL_DATASETS)) def test_incremental(self, name): # Test incremental construction of the convex hull chunks, _ = INCREMENTAL_DATASETS[name] points = np.concatenate(chunks, axis=0) obj = qhull.ConvexHull(chunks[0], incremental=True) for chunk in chunks[1:]: obj.add_points(chunk) obj2 = qhull.ConvexHull(points) obj3 = qhull.ConvexHull(chunks[0], incremental=True) if len(chunks) > 1: obj3.add_points(np.concatenate(chunks[1:], axis=0), restart=True) # Check that the incremental mode agrees with upfront mode assert_hulls_equal(points, obj.simplices, obj2.simplices) assert_hulls_equal(points, obj.simplices, obj3.simplices) def test_vertices_2d(self): # The vertices should be in counterclockwise order in 2-D np.random.seed(1234) points = np.random.rand(30, 2) hull = qhull.ConvexHull(points) assert_equal(np.unique(hull.simplices), np.sort(hull.vertices)) # Check counterclockwiseness x, y = hull.points[hull.vertices].T angle = np.arctan2(y - y.mean(), x - x.mean()) assert_(np.all(np.diff(np.unwrap(angle)) > 0)) def test_volume_area(self): # Basic check that we get back the correct volume and area for a cube points = np.array([(0, 0, 0), (0, 1, 0), (1, 0, 0), (1, 1, 0), (0, 0, 1), (0, 1, 1), (1, 0, 1), (1, 1, 1)]) tri = qhull.ConvexHull(points) assert_allclose(tri.volume, 1., rtol=1e-14) assert_allclose(tri.area, 6., rtol=1e-14) @pytest.mark.parametrize("incremental", [False, True]) def test_good2d(self, incremental): # Make sure the QGn option gives the correct value of "good". points = np.array([[0.2, 0.2], [0.2, 0.4], [0.4, 0.4], [0.4, 0.2], [0.3, 0.6]]) hull = qhull.ConvexHull(points=points, incremental=incremental, qhull_options='QG4') expected = np.array([False, True, False, False], dtype=bool) actual = hull.good assert_equal(actual, expected) @pytest.mark.parametrize("visibility", [ "QG4", # visible=True "QG-4", # visible=False ]) @pytest.mark.parametrize("new_gen, expected", [ # add generator that places QG4 inside hull # so all facets are invisible (np.array([[0.3, 0.7]]), np.array([False, False, False, False, False], dtype=bool)), # adding a generator on the opposite side of the square # should preserve the single visible facet & add one invisible # facet (np.array([[0.3, -0.7]]), np.array([False, True, False, False, False], dtype=bool)), # split the visible facet on top of the square into two # visible facets, with visibility at the end of the array # because add_points concatenates (np.array([[0.3, 0.41]]), np.array([False, False, False, True, True], dtype=bool)), # with our current Qhull options, coplanarity will not count # for visibility; this case shifts one visible & one invisible # facet & adds a coplanar facet # simplex at index position 2 is the shifted visible facet # the final simplex is the coplanar facet (np.array([[0.5, 0.6], [0.6, 0.6]]), np.array([False, False, True, False, False], dtype=bool)), # place the new generator such that it envelops the query # point within the convex hull, but only just barely within # the double precision limit # NOTE: testing exact degeneracy is less predictable than this # scenario, perhaps because of the default Qt option we have # enabled for Qhull to handle precision matters (np.array([[0.3, 0.6 + 1e-16]]), np.array([False, False, False, False, False], dtype=bool)), ]) def test_good2d_incremental_changes(self, new_gen, expected, visibility): # use the usual square convex hull # generators from test_good2d points = np.array([[0.2, 0.2], [0.2, 0.4], [0.4, 0.4], [0.4, 0.2], [0.3, 0.6]]) hull = qhull.ConvexHull(points=points, incremental=True, qhull_options=visibility) hull.add_points(new_gen) actual = hull.good if '-' in visibility: expected = np.invert(expected) assert_equal(actual, expected) @pytest.mark.parametrize("incremental", [False, True]) def test_good2d_no_option(self, incremental): # handle case where good attribue doesn't exist # because Qgn or Qg-n wasn't specified points = np.array([[0.2, 0.2], [0.2, 0.4], [0.4, 0.4], [0.4, 0.2], [0.3, 0.6]]) hull = qhull.ConvexHull(points=points, incremental=incremental) actual = hull.good assert actual is None # preserve None after incremental addition if incremental: hull.add_points(np.zeros((1, 2))) actual = hull.good assert actual is None @pytest.mark.parametrize("incremental", [False, True]) def test_good2d_inside(self, incremental): # Make sure the QGn option gives the correct value of "good". # When point n is inside the convex hull of the rest, good is # all False. points = np.array([[0.2, 0.2], [0.2, 0.4], [0.4, 0.4], [0.4, 0.2], [0.3, 0.3]]) hull = qhull.ConvexHull(points=points, incremental=incremental, qhull_options='QG4') expected = np.array([False, False, False, False], dtype=bool) actual = hull.good assert_equal(actual, expected) @pytest.mark.parametrize("incremental", [False, True]) def test_good3d(self, incremental): # Make sure the QGn option gives the correct value of "good" # for a 3d figure points = np.array([[0.0, 0.0, 0.0], [0.90029516, -0.39187448, 0.18948093], [0.48676420, -0.72627633, 0.48536925], [0.57651530, -0.81179274, -0.09285832], [0.67846893, -0.71119562, 0.18406710]]) hull = qhull.ConvexHull(points=points, incremental=incremental, qhull_options='QG0') expected = np.array([True, False, False, False], dtype=bool) assert_equal(hull.good, expected) class TestVoronoi: @pytest.mark.parametrize("qhull_opts, extra_pts", [ # option Qz (default for SciPy) will add # an extra point at infinity ("Qbb Qc Qz", 1), ("Qbb Qc", 0), ]) @pytest.mark.parametrize("n_pts", [50, 100]) @pytest.mark.parametrize("ndim", [2, 3]) def test_point_region_structure(self, qhull_opts, n_pts, extra_pts, ndim): # see gh-16773 rng = np.random.default_rng(7790) points = rng.random((n_pts, ndim)) vor = Voronoi(points, qhull_options=qhull_opts) pt_region = vor.point_region assert pt_region.max() == n_pts - 1 + extra_pts assert pt_region.size == len(vor.regions) - extra_pts assert len(vor.regions) == n_pts + extra_pts assert vor.points.shape[0] == n_pts # if there is an empty sublist in the Voronoi # regions data structure, it should never be # indexed because it corresponds to an internally # added point at infinity and is not a member of the # generators (input points) if extra_pts: sublens = [len(x) for x in vor.regions] # only one point at infinity (empty region) # is allowed assert sublens.count(0) == 1 assert sublens.index(0) not in pt_region def test_masked_array_fails(self): masked_array = np.ma.masked_all(1) assert_raises(ValueError, qhull.Voronoi, masked_array) def test_simple(self): # Simple case with known Voronoi diagram points = [(0, 0), (0, 1), (0, 2), (1, 0), (1, 1), (1, 2), (2, 0), (2, 1), (2, 2)] # qhull v o Fv Qbb Qc Qz < dat output = """ 2 5 10 1 -10.101 -10.101 0.5 0.5 0.5 1.5 1.5 0.5 1.5 1.5 2 0 1 3 2 0 1 2 0 2 3 3 0 1 4 1 2 4 3 3 4 0 2 2 0 3 3 4 0 3 2 0 4 0 12 4 0 3 0 1 4 0 1 0 1 4 1 4 1 2 4 1 2 0 2 4 2 5 0 2 4 3 4 1 3 4 3 6 0 3 4 4 5 2 4 4 4 7 3 4 4 5 8 0 4 4 6 7 0 3 4 7 8 0 4 """ self._compare_qvoronoi(points, output) def _compare_qvoronoi(self, points, output, **kw): """Compare to output from 'qvoronoi o Fv < data' to Voronoi()""" # Parse output output = [list(map(float, x.split())) for x in output.strip().splitlines()] nvertex = int(output[1][0]) vertices = list(map(tuple, output[3:2+nvertex])) # exclude inf nregion = int(output[1][1]) regions = [[int(y)-1 for y in x[1:]] for x in output[2+nvertex:2+nvertex+nregion]] ridge_points = [[int(y) for y in x[1:3]] for x in output[3+nvertex+nregion:]] ridge_vertices = [[int(y)-1 for y in x[3:]] for x in output[3+nvertex+nregion:]] # Compare results vor = qhull.Voronoi(points, **kw) def sorttuple(x): return tuple(sorted(x)) assert_allclose(vor.vertices, vertices) assert_equal(set(map(tuple, vor.regions)), set(map(tuple, regions))) p1 = list(zip(list(map(sorttuple, ridge_points)), list(map(sorttuple, ridge_vertices)))) p2 = list(zip(list(map(sorttuple, vor.ridge_points.tolist())), list(map(sorttuple, vor.ridge_vertices)))) p1.sort() p2.sort() assert_equal(p1, p2) @pytest.mark.parametrize("name", sorted(DATASETS)) def test_ridges(self, name): # Check that the ridges computed by Voronoi indeed separate # the regions of nearest neighborhood, by comparing the result # to KDTree. points = DATASETS[name] tree = KDTree(points) vor = qhull.Voronoi(points) for p, v in vor.ridge_dict.items(): # consider only finite ridges if not np.all(np.asarray(v) >= 0): continue ridge_midpoint = vor.vertices[v].mean(axis=0) d = 1e-6 * (points[p[0]] - ridge_midpoint) dist, k = tree.query(ridge_midpoint + d, k=1) assert_equal(k, p[0]) dist, k = tree.query(ridge_midpoint - d, k=1) assert_equal(k, p[1]) def test_furthest_site(self): points = [(0, 0), (0, 1), (1, 0), (0.5, 0.5), (1.1, 1.1)] # qhull v o Fv Qbb Qc Qu < dat output = """ 2 3 5 1 -10.101 -10.101 0.6000000000000001 0.5 0.5 0.6000000000000001 3 0 2 1 2 0 1 2 0 2 0 3 0 2 1 5 4 0 2 0 2 4 0 4 1 2 4 0 1 0 1 4 1 4 0 1 4 2 4 0 2 """ self._compare_qvoronoi(points, output, furthest_site=True) def test_furthest_site_flag(self): points = [(0, 0), (0, 1), (1, 0), (0.5, 0.5), (1.1, 1.1)] vor = Voronoi(points) assert_equal(vor.furthest_site,False) vor = Voronoi(points,furthest_site=True) assert_equal(vor.furthest_site,True) @pytest.mark.parametrize("name", sorted(INCREMENTAL_DATASETS)) def test_incremental(self, name): # Test incremental construction of the triangulation if INCREMENTAL_DATASETS[name][0][0].shape[1] > 3: # too slow (testing of the result --- qhull is still fast) return chunks, opts = INCREMENTAL_DATASETS[name] points = np.concatenate(chunks, axis=0) obj = qhull.Voronoi(chunks[0], incremental=True, qhull_options=opts) for chunk in chunks[1:]: obj.add_points(chunk) obj2 = qhull.Voronoi(points) obj3 = qhull.Voronoi(chunks[0], incremental=True, qhull_options=opts) if len(chunks) > 1: obj3.add_points(np.concatenate(chunks[1:], axis=0), restart=True) # -- Check that the incremental mode agrees with upfront mode assert_equal(len(obj.point_region), len(obj2.point_region)) assert_equal(len(obj.point_region), len(obj3.point_region)) # The vertices may be in different order or duplicated in # the incremental map for objx in obj, obj3: vertex_map = {-1: -1} for i, v in enumerate(objx.vertices): for j, v2 in enumerate(obj2.vertices): if np.allclose(v, v2): vertex_map[i] = j def remap(x): if hasattr(x, '__len__'): return tuple(set([remap(y) for y in x])) try: return vertex_map[x] except KeyError as e: raise AssertionError("incremental result has spurious vertex at %r" % (objx.vertices[x],)) from e def simplified(x): items = set(map(sorted_tuple, x)) if () in items: items.remove(()) items = [x for x in items if len(x) > 1] items.sort() return items assert_equal( simplified(remap(objx.regions)), simplified(obj2.regions) ) assert_equal( simplified(remap(objx.ridge_vertices)), simplified(obj2.ridge_vertices) ) # XXX: compare ridge_points --- not clear exactly how to do this class Test_HalfspaceIntersection: def assert_unordered_allclose(self, arr1, arr2, rtol=1e-7): """Check that every line in arr1 is only once in arr2""" assert_equal(arr1.shape, arr2.shape) truths = np.zeros((arr1.shape[0],), dtype=bool) for l1 in arr1: indexes = np.nonzero((abs(arr2 - l1) < rtol).all(axis=1))[0] assert_equal(indexes.shape, (1,)) truths[indexes[0]] = True assert_(truths.all()) @pytest.mark.parametrize("dt", [np.float64, int]) def test_cube_halfspace_intersection(self, dt): halfspaces = np.array([[-1, 0, 0], [0, -1, 0], [1, 0, -2], [0, 1, -2]], dtype=dt) feasible_point = np.array([1, 1], dtype=dt) points = np.array([[0.0, 0.0], [2.0, 0.0], [0.0, 2.0], [2.0, 2.0]]) hull = qhull.HalfspaceIntersection(halfspaces, feasible_point) assert_allclose(hull.intersections, points) def test_self_dual_polytope_intersection(self): fname = os.path.join(os.path.dirname(__file__), 'data', 'selfdual-4d-polytope.txt') ineqs = np.genfromtxt(fname) halfspaces = -np.hstack((ineqs[:, 1:], ineqs[:, :1])) feas_point = np.array([0., 0., 0., 0.]) hs = qhull.HalfspaceIntersection(halfspaces, feas_point) assert_equal(hs.intersections.shape, (24, 4)) assert_almost_equal(hs.dual_volume, 32.0) assert_equal(len(hs.dual_facets), 24) for facet in hs.dual_facets: assert_equal(len(facet), 6) dists = halfspaces[:, -1] + halfspaces[:, :-1].dot(feas_point) self.assert_unordered_allclose((halfspaces[:, :-1].T/dists).T, hs.dual_points) points = itertools.permutations([0., 0., 0.5, -0.5]) for point in points: assert_equal(np.sum((hs.intersections == point).all(axis=1)), 1) def test_wrong_feasible_point(self): halfspaces = np.array([[-1.0, 0.0, 0.0], [0.0, -1.0, 0.0], [1.0, 0.0, -1.0], [0.0, 1.0, -1.0]]) feasible_point = np.array([0.5, 0.5, 0.5]) #Feasible point is (ndim,) instead of (ndim-1,) assert_raises(ValueError, qhull.HalfspaceIntersection, halfspaces, feasible_point) feasible_point = np.array([[0.5], [0.5]]) #Feasible point is (ndim-1, 1) instead of (ndim-1,) assert_raises(ValueError, qhull.HalfspaceIntersection, halfspaces, feasible_point) feasible_point = np.array([[0.5, 0.5]]) #Feasible point is (1, ndim-1) instead of (ndim-1,) assert_raises(ValueError, qhull.HalfspaceIntersection, halfspaces, feasible_point) feasible_point = np.array([-0.5, -0.5]) #Feasible point is outside feasible region assert_raises(qhull.QhullError, qhull.HalfspaceIntersection, halfspaces, feasible_point) def test_incremental(self): #Cube halfspaces = np.array([[0., 0., -1., -0.5], [0., -1., 0., -0.5], [-1., 0., 0., -0.5], [1., 0., 0., -0.5], [0., 1., 0., -0.5], [0., 0., 1., -0.5]]) #Cut each summit extra_normals = np.array([[1., 1., 1.], [1., 1., -1.], [1., -1., 1.], [1, -1., -1.]]) offsets = np.array([[-1.]]*8) extra_halfspaces = np.hstack((np.vstack((extra_normals, -extra_normals)), offsets)) feas_point = np.array([0., 0., 0.]) inc_hs = qhull.HalfspaceIntersection(halfspaces, feas_point, incremental=True) inc_res_hs = qhull.HalfspaceIntersection(halfspaces, feas_point, incremental=True) for i, ehs in enumerate(extra_halfspaces): inc_hs.add_halfspaces(ehs[np.newaxis, :]) inc_res_hs.add_halfspaces(ehs[np.newaxis, :], restart=True) total = np.vstack((halfspaces, extra_halfspaces[:i+1, :])) hs = qhull.HalfspaceIntersection(total, feas_point) assert_allclose(inc_hs.halfspaces, inc_res_hs.halfspaces) assert_allclose(inc_hs.halfspaces, hs.halfspaces) #Direct computation and restart should have points in same order assert_allclose(hs.intersections, inc_res_hs.intersections) #Incremental will have points in different order than direct computation self.assert_unordered_allclose(inc_hs.intersections, hs.intersections) inc_hs.close() def test_cube(self): # Halfspaces of the cube: halfspaces = np.array([[-1., 0., 0., 0.], # x >= 0 [1., 0., 0., -1.], # x <= 1 [0., -1., 0., 0.], # y >= 0 [0., 1., 0., -1.], # y <= 1 [0., 0., -1., 0.], # z >= 0 [0., 0., 1., -1.]]) # z <= 1 point = np.array([0.5, 0.5, 0.5]) hs = qhull.HalfspaceIntersection(halfspaces, point) # qhalf H0.5,0.5,0.5 o < input.txt qhalf_points = np.array([ [-2, 0, 0], [2, 0, 0], [0, -2, 0], [0, 2, 0], [0, 0, -2], [0, 0, 2]]) qhalf_facets = [ [2, 4, 0], [4, 2, 1], [5, 2, 0], [2, 5, 1], [3, 4, 1], [4, 3, 0], [5, 3, 1], [3, 5, 0]] assert len(qhalf_facets) == len(hs.dual_facets) for a, b in zip(qhalf_facets, hs.dual_facets): assert set(a) == set(b) # facet orientation can differ assert_allclose(hs.dual_points, qhalf_points)