321 lines
10 KiB
Python
321 lines
10 KiB
Python
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"""
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Tests for VF2 isomorphism algorithm.
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"""
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import os
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import struct
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import random
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import pytest
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import networkx as nx
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from networkx.algorithms import isomorphism as iso
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class TestWikipediaExample(object):
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# Source: https://en.wikipedia.org/wiki/Graph_isomorphism
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# Nodes 'a', 'b', 'c' and 'd' form a column.
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# Nodes 'g', 'h', 'i' and 'j' form a column.
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g1edges = [['a', 'g'], ['a', 'h'], ['a', 'i'],
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['b', 'g'], ['b', 'h'], ['b', 'j'],
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['c', 'g'], ['c', 'i'], ['c', 'j'],
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['d', 'h'], ['d', 'i'], ['d', 'j']]
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# Nodes 1,2,3,4 form the clockwise corners of a large square.
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# Nodes 5,6,7,8 form the clockwise corners of a small square
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g2edges = [[1, 2], [2, 3], [3, 4], [4, 1],
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[5, 6], [6, 7], [7, 8], [8, 5],
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[1, 5], [2, 6], [3, 7], [4, 8]]
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def test_graph(self):
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g1 = nx.Graph()
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g2 = nx.Graph()
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g1.add_edges_from(self.g1edges)
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g2.add_edges_from(self.g2edges)
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gm = iso.GraphMatcher(g1, g2)
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assert gm.is_isomorphic()
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#Just testing some cases
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assert gm.subgraph_is_monomorphic()
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mapping = sorted(gm.mapping.items())
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# this mapping is only one of the possibilies
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# so this test needs to be reconsidered
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# isomap = [('a', 1), ('b', 6), ('c', 3), ('d', 8),
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# ('g', 2), ('h', 5), ('i', 4), ('j', 7)]
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# assert_equal(mapping, isomap)
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def test_subgraph(self):
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g1 = nx.Graph()
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g2 = nx.Graph()
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g1.add_edges_from(self.g1edges)
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g2.add_edges_from(self.g2edges)
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g3 = g2.subgraph([1, 2, 3, 4])
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gm = iso.GraphMatcher(g1, g3)
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assert gm.subgraph_is_isomorphic()
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def test_subgraph_mono(self):
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g1 = nx.Graph()
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g2 = nx.Graph()
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g1.add_edges_from(self.g1edges)
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g2.add_edges_from([[1, 2], [2, 3], [3, 4]])
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gm = iso.GraphMatcher(g1, g2)
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assert gm.subgraph_is_monomorphic()
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class TestVF2GraphDB(object):
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# http://amalfi.dis.unina.it/graph/db/
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@staticmethod
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def create_graph(filename):
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"""Creates a Graph instance from the filename."""
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# The file is assumed to be in the format from the VF2 graph database.
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# Each file is composed of 16-bit numbers (unsigned short int).
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# So we will want to read 2 bytes at a time.
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# We can read the number as follows:
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# number = struct.unpack('<H', file.read(2))
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# This says, expect the data in little-endian encoding
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# as an unsigned short int and unpack 2 bytes from the file.
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fh = open(filename, mode='rb')
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# Grab the number of nodes.
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# Node numeration is 0-based, so the first node has index 0.
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nodes = struct.unpack('<H', fh.read(2))[0]
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graph = nx.Graph()
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for from_node in range(nodes):
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# Get the number of edges.
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edges = struct.unpack('<H', fh.read(2))[0]
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for edge in range(edges):
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# Get the terminal node.
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to_node = struct.unpack('<H', fh.read(2))[0]
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graph.add_edge(from_node, to_node)
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fh.close()
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return graph
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def test_graph(self):
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head, tail = os.path.split(__file__)
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g1 = self.create_graph(os.path.join(head, 'iso_r01_s80.A99'))
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g2 = self.create_graph(os.path.join(head, 'iso_r01_s80.B99'))
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gm = iso.GraphMatcher(g1, g2)
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assert gm.is_isomorphic()
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def test_subgraph(self):
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# A is the subgraph
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# B is the full graph
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head, tail = os.path.split(__file__)
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subgraph = self.create_graph(os.path.join(head, 'si2_b06_m200.A99'))
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graph = self.create_graph(os.path.join(head, 'si2_b06_m200.B99'))
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gm = iso.GraphMatcher(graph, subgraph)
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assert gm.subgraph_is_isomorphic()
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#Just testing some cases
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assert gm.subgraph_is_monomorphic()
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# There isn't a similar test implemented for subgraph monomorphism,
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# feel free to create one.
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class TestAtlas(object):
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@classmethod
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def setup_class(cls):
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global atlas
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import platform
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if platform.python_implementation() == 'Jython':
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pytest.mark.skip('graph atlas not available under Jython.')
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import networkx.generators.atlas as atlas
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cls.GAG = atlas.graph_atlas_g()
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def test_graph_atlas(self):
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# Atlas = nx.graph_atlas_g()[0:208] # 208, 6 nodes or less
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Atlas = self.GAG[0:100]
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alphabet = list(range(26))
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for graph in Atlas:
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nlist = list(graph)
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labels = alphabet[:len(nlist)]
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for s in range(10):
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random.shuffle(labels)
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d = dict(zip(nlist, labels))
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relabel = nx.relabel_nodes(graph, d)
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gm = iso.GraphMatcher(graph, relabel)
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assert gm.is_isomorphic()
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def test_multiedge():
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# Simple test for multigraphs
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# Need something much more rigorous
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edges = [(0, 1), (1, 2), (2, 3), (3, 4), (4, 5),
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(5, 6), (6, 7), (7, 8), (8, 9), (9, 10),
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(10, 11), (10, 11), (11, 12), (11, 12),
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(12, 13), (12, 13), (13, 14), (13, 14),
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(14, 15), (14, 15), (15, 16), (15, 16),
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(16, 17), (16, 17), (17, 18), (17, 18),
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(18, 19), (18, 19), (19, 0), (19, 0)]
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nodes = list(range(20))
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for g1 in [nx.MultiGraph(), nx.MultiDiGraph()]:
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g1.add_edges_from(edges)
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for _ in range(10):
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new_nodes = list(nodes)
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random.shuffle(new_nodes)
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d = dict(zip(nodes, new_nodes))
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g2 = nx.relabel_nodes(g1, d)
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if not g1.is_directed():
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gm = iso.GraphMatcher(g1, g2)
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else:
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gm = iso.DiGraphMatcher(g1, g2)
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assert gm.is_isomorphic()
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#Testing if monomorphism works in multigraphs
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assert gm.subgraph_is_monomorphic()
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def test_selfloop():
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# Simple test for graphs with selfloops
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edges = [(0, 1), (0, 2), (1, 2), (1, 3), (2, 2),
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(2, 4), (3, 1), (3, 2), (4, 2), (4, 5), (5, 4)]
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nodes = list(range(6))
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for g1 in [nx.Graph(), nx.DiGraph()]:
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g1.add_edges_from(edges)
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for _ in range(100):
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new_nodes = list(nodes)
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random.shuffle(new_nodes)
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d = dict(zip(nodes, new_nodes))
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g2 = nx.relabel_nodes(g1, d)
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if not g1.is_directed():
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gm = iso.GraphMatcher(g1, g2)
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else:
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gm = iso.DiGraphMatcher(g1, g2)
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assert gm.is_isomorphic()
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def test_selfloop_mono():
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# Simple test for graphs with selfloops
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edges0 = [(0, 1), (0, 2), (1, 2), (1, 3),
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(2, 4), (3, 1), (3, 2), (4, 2), (4, 5), (5, 4)]
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edges = edges0 + [(2, 2)]
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nodes = list(range(6))
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for g1 in [nx.Graph(), nx.DiGraph()]:
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g1.add_edges_from(edges)
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for _ in range(100):
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new_nodes = list(nodes)
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random.shuffle(new_nodes)
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d = dict(zip(nodes, new_nodes))
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g2 = nx.relabel_nodes(g1, d)
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g2.remove_edges_from(nx.selfloop_edges(g2))
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if not g1.is_directed():
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gm = iso.GraphMatcher(g2, g1)
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else:
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gm = iso.DiGraphMatcher(g2, g1)
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assert not gm.subgraph_is_monomorphic()
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def test_isomorphism_iter1():
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# As described in:
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# http://groups.google.com/group/networkx-discuss/browse_thread/thread/2ff65c67f5e3b99f/d674544ebea359bb?fwc=1
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g1 = nx.DiGraph()
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g2 = nx.DiGraph()
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g3 = nx.DiGraph()
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g1.add_edge('A', 'B')
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g1.add_edge('B', 'C')
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g2.add_edge('Y', 'Z')
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g3.add_edge('Z', 'Y')
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gm12 = iso.DiGraphMatcher(g1, g2)
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gm13 = iso.DiGraphMatcher(g1, g3)
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x = list(gm12.subgraph_isomorphisms_iter())
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y = list(gm13.subgraph_isomorphisms_iter())
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assert {'A': 'Y', 'B': 'Z'} in x
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assert {'B': 'Y', 'C': 'Z'} in x
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assert {'A': 'Z', 'B': 'Y'} in y
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assert {'B': 'Z', 'C': 'Y'} in y
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assert len(x) == len(y)
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assert len(x) == 2
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def test_monomorphism_iter1():
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g1 = nx.DiGraph()
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g2 = nx.DiGraph()
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g1.add_edge('A', 'B')
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g1.add_edge('B', 'C')
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g1.add_edge('C', 'A')
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g2.add_edge('X', 'Y')
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g2.add_edge('Y', 'Z')
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gm12 = iso.DiGraphMatcher(g1, g2)
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x = list(gm12.subgraph_monomorphisms_iter())
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assert {'A': 'X', 'B': 'Y', 'C': 'Z'} in x
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assert {'A': 'Y', 'B': 'Z', 'C': 'X'} in x
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assert {'A': 'Z', 'B': 'X', 'C': 'Y'} in x
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assert len(x) == 3
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gm21 = iso.DiGraphMatcher(g2, g1)
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#Check if StopIteration exception returns False
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assert not gm21.subgraph_is_monomorphic()
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def test_isomorphism_iter2():
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# Path
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for L in range(2, 10):
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g1 = nx.path_graph(L)
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gm = iso.GraphMatcher(g1, g1)
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s = len(list(gm.isomorphisms_iter()))
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assert s == 2
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# Cycle
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for L in range(3, 10):
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g1 = nx.cycle_graph(L)
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gm = iso.GraphMatcher(g1, g1)
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s = len(list(gm.isomorphisms_iter()))
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assert s == 2 * L
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def test_multiple():
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# Verify that we can use the graph matcher multiple times
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edges = [('A', 'B'), ('B', 'A'), ('B', 'C')]
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for g1, g2 in [(nx.Graph(), nx.Graph()), (nx.DiGraph(), nx.DiGraph())]:
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g1.add_edges_from(edges)
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g2.add_edges_from(edges)
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g3 = nx.subgraph(g2, ['A', 'B'])
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if not g1.is_directed():
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gmA = iso.GraphMatcher(g1, g2)
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gmB = iso.GraphMatcher(g1, g3)
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else:
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gmA = iso.DiGraphMatcher(g1, g2)
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gmB = iso.DiGraphMatcher(g1, g3)
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assert gmA.is_isomorphic()
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g2.remove_node('C')
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if not g1.is_directed():
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gmA = iso.GraphMatcher(g1, g2)
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else:
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gmA = iso.DiGraphMatcher(g1, g2)
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assert gmA.subgraph_is_isomorphic()
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assert gmB.subgraph_is_isomorphic()
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assert gmA.subgraph_is_monomorphic()
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assert gmB.subgraph_is_monomorphic()
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# for m in [gmB.mapping, gmB.mapping]:
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# assert_true(m['A'] == 'A')
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# assert_true(m['B'] == 'B')
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# assert_true('C' not in m)
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def test_noncomparable_nodes():
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node1 = object()
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node2 = object()
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node3 = object()
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# Graph
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G = nx.path_graph([node1, node2, node3])
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gm = iso.GraphMatcher(G, G)
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assert gm.is_isomorphic()
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#Just testing some cases
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assert gm.subgraph_is_monomorphic()
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# DiGraph
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G = nx.path_graph([node1, node2, node3], create_using=nx.DiGraph)
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H = nx.path_graph([node3, node2, node1], create_using=nx.DiGraph)
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dgm = iso.DiGraphMatcher(G, H)
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assert dgm.is_isomorphic()
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#Just testing some cases
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assert gm.subgraph_is_monomorphic()
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