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