import pytest import networkx as nx from networkx.generators.classic import barbell_graph, cycle_graph, path_graph from networkx.testing.utils import assert_graphs_equal #numpy = pytest.importorskip("numpy") class TestConvertNumpy(object): @classmethod def setup_class(cls): global np global np_assert_equal try: import numpy as np np_assert_equal = np.testing.assert_equal except ImportError: pytest.skip('Numpy not available', allow_module_level=True) def setup_method(self): self.G1 = barbell_graph(10, 3) self.G2 = cycle_graph(10, create_using=nx.DiGraph) self.G3 = self.create_weighted(nx.Graph()) self.G4 = self.create_weighted(nx.DiGraph()) def test_exceptions(self): G = np.array("a") pytest.raises(nx.NetworkXError, nx.to_networkx_graph, G) def create_weighted(self, G): g = cycle_graph(4) G.add_nodes_from(g) G.add_weighted_edges_from((u, v, 10 + u) for u, v in g.edges()) return G def assert_equal(self, G1, G2): assert sorted(G1.nodes()) == sorted(G2.nodes()) assert sorted(G1.edges()) == sorted(G2.edges()) def identity_conversion(self, G, A, create_using): assert(A.sum() > 0) GG = nx.from_numpy_matrix(A, create_using=create_using) self.assert_equal(G, GG) GW = nx.to_networkx_graph(A, create_using=create_using) self.assert_equal(G, GW) GI = nx.empty_graph(0, create_using).__class__(A) self.assert_equal(G, GI) def test_shape(self): "Conversion from non-square array." A = np.array([[1, 2, 3], [4, 5, 6]]) pytest.raises(nx.NetworkXError, nx.from_numpy_matrix, A) def test_identity_graph_matrix(self): "Conversion from graph to matrix to graph." A = nx.to_numpy_matrix(self.G1) self.identity_conversion(self.G1, A, nx.Graph()) def test_identity_graph_array(self): "Conversion from graph to array to graph." A = nx.to_numpy_matrix(self.G1) A = np.asarray(A) self.identity_conversion(self.G1, A, nx.Graph()) def test_identity_digraph_matrix(self): """Conversion from digraph to matrix to digraph.""" A = nx.to_numpy_matrix(self.G2) self.identity_conversion(self.G2, A, nx.DiGraph()) def test_identity_digraph_array(self): """Conversion from digraph to array to digraph.""" A = nx.to_numpy_matrix(self.G2) A = np.asarray(A) self.identity_conversion(self.G2, A, nx.DiGraph()) def test_identity_weighted_graph_matrix(self): """Conversion from weighted graph to matrix to weighted graph.""" A = nx.to_numpy_matrix(self.G3) self.identity_conversion(self.G3, A, nx.Graph()) def test_identity_weighted_graph_array(self): """Conversion from weighted graph to array to weighted graph.""" A = nx.to_numpy_matrix(self.G3) A = np.asarray(A) self.identity_conversion(self.G3, A, nx.Graph()) def test_identity_weighted_digraph_matrix(self): """Conversion from weighted digraph to matrix to weighted digraph.""" A = nx.to_numpy_matrix(self.G4) self.identity_conversion(self.G4, A, nx.DiGraph()) def test_identity_weighted_digraph_array(self): """Conversion from weighted digraph to array to weighted digraph.""" A = nx.to_numpy_matrix(self.G4) A = np.asarray(A) self.identity_conversion(self.G4, A, nx.DiGraph()) def test_nodelist(self): """Conversion from graph to matrix to graph with nodelist.""" P4 = path_graph(4) P3 = path_graph(3) nodelist = list(P3) A = nx.to_numpy_matrix(P4, nodelist=nodelist) GA = nx.Graph(A) self.assert_equal(GA, P3) # Make nodelist ambiguous by containing duplicates. nodelist += [nodelist[0]] pytest.raises(nx.NetworkXError, nx.to_numpy_matrix, P3, nodelist=nodelist) def test_weight_keyword(self): WP4 = nx.Graph() WP4.add_edges_from((n, n + 1, dict(weight=0.5, other=0.3)) for n in range(3)) P4 = path_graph(4) A = nx.to_numpy_matrix(P4) np_assert_equal(A, nx.to_numpy_matrix(WP4, weight=None)) np_assert_equal(0.5 * A, nx.to_numpy_matrix(WP4)) np_assert_equal(0.3 * A, nx.to_numpy_matrix(WP4, weight='other')) def test_from_numpy_matrix_type(self): A = np.matrix([[1]]) G = nx.from_numpy_matrix(A) assert type(G[0][0]['weight']) == int A = np.matrix([[1]]).astype(np.float) G = nx.from_numpy_matrix(A) assert type(G[0][0]['weight']) == float A = np.matrix([[1]]).astype(np.str) G = nx.from_numpy_matrix(A) assert type(G[0][0]['weight']) == str A = np.matrix([[1]]).astype(np.bool) G = nx.from_numpy_matrix(A) assert type(G[0][0]['weight']) == bool A = np.matrix([[1]]).astype(np.complex) G = nx.from_numpy_matrix(A) assert type(G[0][0]['weight']) == complex A = np.matrix([[1]]).astype(np.object) pytest.raises(TypeError, nx.from_numpy_matrix, A) G = nx.cycle_graph(3) A = nx.adj_matrix(G).todense() H = nx.from_numpy_matrix(A) assert all(type(m) == int and type(n) == int for m, n in H.edges()) H = nx.from_numpy_array(A) assert all(type(m) == int and type(n) == int for m, n in H.edges()) def test_from_numpy_matrix_dtype(self): dt = [('weight', float), ('cost', int)] A = np.matrix([[(1.0, 2)]], dtype=dt) G = nx.from_numpy_matrix(A) assert type(G[0][0]['weight']) == float assert type(G[0][0]['cost']) == int assert G[0][0]['cost'] == 2 assert G[0][0]['weight'] == 1.0 def test_to_numpy_recarray(self): G = nx.Graph() G.add_edge(1, 2, weight=7.0, cost=5) A = nx.to_numpy_recarray(G, dtype=[('weight', float), ('cost', int)]) assert sorted(A.dtype.names) == ['cost', 'weight'] assert A.weight[0, 1] == 7.0 assert A.weight[0, 0] == 0.0 assert A.cost[0, 1] == 5 assert A.cost[0, 0] == 0 def test_numpy_multigraph(self): G = nx.MultiGraph() G.add_edge(1, 2, weight=7) G.add_edge(1, 2, weight=70) A = nx.to_numpy_matrix(G) assert A[1, 0] == 77 A = nx.to_numpy_matrix(G, multigraph_weight=min) assert A[1, 0] == 7 A = nx.to_numpy_matrix(G, multigraph_weight=max) assert A[1, 0] == 70 def test_from_numpy_matrix_parallel_edges(self): """Tests that the :func:`networkx.from_numpy_matrix` function interprets integer weights as the number of parallel edges when creating a multigraph. """ A = np.matrix([[1, 1], [1, 2]]) # First, with a simple graph, each integer entry in the adjacency # matrix is interpreted as the weight of a single edge in the graph. expected = nx.DiGraph() edges = [(0, 0), (0, 1), (1, 0)] expected.add_weighted_edges_from([(u, v, 1) for (u, v) in edges]) expected.add_edge(1, 1, weight=2) actual = nx.from_numpy_matrix(A, parallel_edges=True, create_using=nx.DiGraph) assert_graphs_equal(actual, expected) actual = nx.from_numpy_matrix(A, parallel_edges=False, create_using=nx.DiGraph) assert_graphs_equal(actual, expected) # Now each integer entry in the adjacency matrix is interpreted as the # number of parallel edges in the graph if the appropriate keyword # argument is specified. edges = [(0, 0), (0, 1), (1, 0), (1, 1), (1, 1)] expected = nx.MultiDiGraph() expected.add_weighted_edges_from([(u, v, 1) for (u, v) in edges]) actual = nx.from_numpy_matrix(A, parallel_edges=True, create_using=nx.MultiDiGraph) assert_graphs_equal(actual, expected) expected = nx.MultiDiGraph() expected.add_edges_from(set(edges), weight=1) # The sole self-loop (edge 0) on vertex 1 should have weight 2. expected[1][1][0]['weight'] = 2 actual = nx.from_numpy_matrix(A, parallel_edges=False, create_using=nx.MultiDiGraph) assert_graphs_equal(actual, expected) def test_symmetric(self): """Tests that a symmetric matrix has edges added only once to an undirected multigraph when using :func:`networkx.from_numpy_matrix`. """ A = np.matrix([[0, 1], [1, 0]]) G = nx.from_numpy_matrix(A, create_using=nx.MultiGraph) expected = nx.MultiGraph() expected.add_edge(0, 1, weight=1) assert_graphs_equal(G, expected) def test_dtype_int_graph(self): """Test that setting dtype int actually gives an integer matrix. For more information, see GitHub pull request #1363. """ G = nx.complete_graph(3) A = nx.to_numpy_matrix(G, dtype=int) assert A.dtype == int def test_dtype_int_multigraph(self): """Test that setting dtype int actually gives an integer matrix. For more information, see GitHub pull request #1363. """ G = nx.MultiGraph(nx.complete_graph(3)) A = nx.to_numpy_matrix(G, dtype=int) assert A.dtype == int class TestConvertNumpyArray(object): @classmethod def setup_class(cls): global np global np_assert_equal np = pytest.importorskip('numpy') np_assert_equal = np.testing.assert_equal def setup_method(self): self.G1 = barbell_graph(10, 3) self.G2 = cycle_graph(10, create_using=nx.DiGraph) self.G3 = self.create_weighted(nx.Graph()) self.G4 = self.create_weighted(nx.DiGraph()) def create_weighted(self, G): g = cycle_graph(4) G.add_nodes_from(g) G.add_weighted_edges_from((u, v, 10 + u) for u, v in g.edges()) return G def assert_equal(self, G1, G2): assert sorted(G1.nodes()) == sorted(G2.nodes()) assert sorted(G1.edges()) == sorted(G2.edges()) def identity_conversion(self, G, A, create_using): assert(A.sum() > 0) GG = nx.from_numpy_array(A, create_using=create_using) self.assert_equal(G, GG) GW = nx.to_networkx_graph(A, create_using=create_using) self.assert_equal(G, GW) GI = nx.empty_graph(0, create_using).__class__(A) self.assert_equal(G, GI) def test_shape(self): "Conversion from non-square array." A = np.array([[1, 2, 3], [4, 5, 6]]) pytest.raises(nx.NetworkXError, nx.from_numpy_array, A) def test_identity_graph_array(self): "Conversion from graph to array to graph." A = nx.to_numpy_array(self.G1) self.identity_conversion(self.G1, A, nx.Graph()) def test_identity_digraph_array(self): """Conversion from digraph to array to digraph.""" A = nx.to_numpy_array(self.G2) self.identity_conversion(self.G2, A, nx.DiGraph()) def test_identity_weighted_graph_array(self): """Conversion from weighted graph to array to weighted graph.""" A = nx.to_numpy_array(self.G3) self.identity_conversion(self.G3, A, nx.Graph()) def test_identity_weighted_digraph_array(self): """Conversion from weighted digraph to array to weighted digraph.""" A = nx.to_numpy_array(self.G4) self.identity_conversion(self.G4, A, nx.DiGraph()) def test_nodelist(self): """Conversion from graph to array to graph with nodelist.""" P4 = path_graph(4) P3 = path_graph(3) nodelist = list(P3) A = nx.to_numpy_array(P4, nodelist=nodelist) GA = nx.Graph(A) self.assert_equal(GA, P3) # Make nodelist ambiguous by containing duplicates. nodelist += [nodelist[0]] pytest.raises(nx.NetworkXError, nx.to_numpy_array, P3, nodelist=nodelist) def test_weight_keyword(self): WP4 = nx.Graph() WP4.add_edges_from((n, n + 1, dict(weight=0.5, other=0.3)) for n in range(3)) P4 = path_graph(4) A = nx.to_numpy_array(P4) np_assert_equal(A, nx.to_numpy_array(WP4, weight=None)) np_assert_equal(0.5 * A, nx.to_numpy_array(WP4)) np_assert_equal(0.3 * A, nx.to_numpy_array(WP4, weight='other')) def test_from_numpy_array_type(self): A = np.array([[1]]) G = nx.from_numpy_array(A) assert type(G[0][0]['weight']) == int A = np.array([[1]]).astype(np.float) G = nx.from_numpy_array(A) assert type(G[0][0]['weight']) == float A = np.array([[1]]).astype(np.str) G = nx.from_numpy_array(A) assert type(G[0][0]['weight']) == str A = np.array([[1]]).astype(np.bool) G = nx.from_numpy_array(A) assert type(G[0][0]['weight']) == bool A = np.array([[1]]).astype(np.complex) G = nx.from_numpy_array(A) assert type(G[0][0]['weight']) == complex A = np.array([[1]]).astype(np.object) pytest.raises(TypeError, nx.from_numpy_array, A) def test_from_numpy_array_dtype(self): dt = [('weight', float), ('cost', int)] A = np.array([[(1.0, 2)]], dtype=dt) G = nx.from_numpy_array(A) assert type(G[0][0]['weight']) == float assert type(G[0][0]['cost']) == int assert G[0][0]['cost'] == 2 assert G[0][0]['weight'] == 1.0 def test_to_numpy_recarray(self): G = nx.Graph() G.add_edge(1, 2, weight=7.0, cost=5) A = nx.to_numpy_recarray(G, dtype=[('weight', float), ('cost', int)]) assert sorted(A.dtype.names) == ['cost', 'weight'] assert A.weight[0, 1] == 7.0 assert A.weight[0, 0] == 0.0 assert A.cost[0, 1] == 5 assert A.cost[0, 0] == 0 def test_numpy_multigraph(self): G = nx.MultiGraph() G.add_edge(1, 2, weight=7) G.add_edge(1, 2, weight=70) A = nx.to_numpy_array(G) assert A[1, 0] == 77 A = nx.to_numpy_array(G, multigraph_weight=min) assert A[1, 0] == 7 A = nx.to_numpy_array(G, multigraph_weight=max) assert A[1, 0] == 70 def test_from_numpy_array_parallel_edges(self): """Tests that the :func:`networkx.from_numpy_array` function interprets integer weights as the number of parallel edges when creating a multigraph. """ A = np.array([[1, 1], [1, 2]]) # First, with a simple graph, each integer entry in the adjacency # matrix is interpreted as the weight of a single edge in the graph. expected = nx.DiGraph() edges = [(0, 0), (0, 1), (1, 0)] expected.add_weighted_edges_from([(u, v, 1) for (u, v) in edges]) expected.add_edge(1, 1, weight=2) actual = nx.from_numpy_array(A, parallel_edges=True, create_using=nx.DiGraph) assert_graphs_equal(actual, expected) actual = nx.from_numpy_array(A, parallel_edges=False, create_using=nx.DiGraph) assert_graphs_equal(actual, expected) # Now each integer entry in the adjacency matrix is interpreted as the # number of parallel edges in the graph if the appropriate keyword # argument is specified. edges = [(0, 0), (0, 1), (1, 0), (1, 1), (1, 1)] expected = nx.MultiDiGraph() expected.add_weighted_edges_from([(u, v, 1) for (u, v) in edges]) actual = nx.from_numpy_array(A, parallel_edges=True, create_using=nx.MultiDiGraph) assert_graphs_equal(actual, expected) expected = nx.MultiDiGraph() expected.add_edges_from(set(edges), weight=1) # The sole self-loop (edge 0) on vertex 1 should have weight 2. expected[1][1][0]['weight'] = 2 actual = nx.from_numpy_array(A, parallel_edges=False, create_using=nx.MultiDiGraph) assert_graphs_equal(actual, expected) def test_symmetric(self): """Tests that a symmetric array has edges added only once to an undirected multigraph when using :func:`networkx.from_numpy_array`. """ A = np.array([[0, 1], [1, 0]]) G = nx.from_numpy_array(A, create_using=nx.MultiGraph) expected = nx.MultiGraph() expected.add_edge(0, 1, weight=1) assert_graphs_equal(G, expected) def test_dtype_int_graph(self): """Test that setting dtype int actually gives an integer array. For more information, see GitHub pull request #1363. """ G = nx.complete_graph(3) A = nx.to_numpy_array(G, dtype=int) assert A.dtype == int def test_dtype_int_multigraph(self): """Test that setting dtype int actually gives an integer array. For more information, see GitHub pull request #1363. """ G = nx.MultiGraph(nx.complete_graph(3)) A = nx.to_numpy_array(G, dtype=int) assert A.dtype == int