from collections import defaultdict import numpy as np from numpy.testing import assert_array_almost_equal from sklearn.utils.graph import (graph_shortest_path, single_source_shortest_path_length) def floyd_warshall_slow(graph, directed=False): N = graph.shape[0] #set nonzero entries to infinity graph[np.where(graph == 0)] = np.inf #set diagonal to zero graph.flat[::N + 1] = 0 if not directed: graph = np.minimum(graph, graph.T) for k in range(N): for i in range(N): for j in range(N): graph[i, j] = min(graph[i, j], graph[i, k] + graph[k, j]) graph[np.where(np.isinf(graph))] = 0 return graph def generate_graph(N=20): #sparse grid of distances rng = np.random.RandomState(0) dist_matrix = rng.random_sample((N, N)) #make symmetric: distances are not direction-dependent dist_matrix = dist_matrix + dist_matrix.T #make graph sparse i = (rng.randint(N, size=N * N // 2), rng.randint(N, size=N * N // 2)) dist_matrix[i] = 0 #set diagonal to zero dist_matrix.flat[::N + 1] = 0 return dist_matrix def test_floyd_warshall(): dist_matrix = generate_graph(20) for directed in (True, False): graph_FW = graph_shortest_path(dist_matrix, directed, 'FW') graph_py = floyd_warshall_slow(dist_matrix.copy(), directed) assert_array_almost_equal(graph_FW, graph_py) def test_dijkstra(): dist_matrix = generate_graph(20) for directed in (True, False): graph_D = graph_shortest_path(dist_matrix, directed, 'D') graph_py = floyd_warshall_slow(dist_matrix.copy(), directed) assert_array_almost_equal(graph_D, graph_py) def test_shortest_path(): dist_matrix = generate_graph(20) # We compare path length and not costs (-> set distances to 0 or 1) dist_matrix[dist_matrix != 0] = 1 for directed in (True, False): if not directed: dist_matrix = np.minimum(dist_matrix, dist_matrix.T) graph_py = floyd_warshall_slow(dist_matrix.copy(), directed) for i in range(dist_matrix.shape[0]): # Non-reachable nodes have distance 0 in graph_py dist_dict = defaultdict(int) dist_dict.update(single_source_shortest_path_length(dist_matrix, i)) for j in range(graph_py[i].shape[0]): assert_array_almost_equal(dist_dict[j], graph_py[i, j]) def test_dijkstra_bug_fix(): X = np.array([[0., 0., 4.], [1., 0., 2.], [0., 5., 0.]]) dist_FW = graph_shortest_path(X, directed=False, method='FW') dist_D = graph_shortest_path(X, directed=False, method='D') assert_array_almost_equal(dist_D, dist_FW)