def is_isomorphic(self, g1, g2, approximate=False):
"""Check if two graphs are isomorphic.
To accelerate the process, we use an approximate algorithm,
whose False value means definitely not isomorphic while True
value does not guarantee isomorphic for 100%.
"""
if approximate:
return isomorphism.faster_could_be_isomorphic(g1, g2)
else:
if isomorphism.faster_could_be_isomorphic(g1, g2):
if isomorphism.is_isomorphic(g1, g2):
return True
return False
def is_isomorphic(self, g1, g2, approximate=False):
"""Check if two graphs are isomorphic.
To accelerate the process, we use an approximate algorithm,
whose False value means definitely not isomorphic while True
value does not guarantee isomorphic for 100%.
"""
if approximate:
return isomorphism.faster_could_be_isomorphic(g1, g2)
else:
if isomorphism.faster_could_be_isomorphic(g1, g2):
if isomorphism.is_isomorphic(g1, g2):
return True
return False
def are_equivalent_partitions(a, b):
"""Checks for partition equivalence by checking if the graphs are isomorphic."""
ga = a["graph"]
gb = b["graph"]
if not iso.faster_could_be_isomorphic(ga, gb):
return False
em = iso.categorical_edge_match("particle", "exotic")
return nx.is_isomorphic(ga, gb, edge_match=em)
def find_all_isomorphisms(home, other):
if iso.faster_could_be_isomorphic(home, other):
label_matcher = lambda x, y: x['distance_dependent_label'] == y['distance_dependent_label']
graph_label_matcher = iso.GraphMatcher(home, other, node_match=label_matcher)
for index, mapping in enumerate(graph_label_matcher.isomorphisms_iter()):
if index == 15: # give up ..
break
yield mapping
else:
logger.debug('faster iso check failed')
raise StopIteration
def getValue(self, graph):
''' Lookup polynomial evaluation or calculate value if graph size is 1.'''
if graph.number_of_edges() == 0:
return 1
try:
for candidate, value in self.knownGraphs[(graph.number_of_edges(), graph.number_of_nodes())]:
if isomorphism.faster_could_be_isomorphic(candidate, graph):
if isomorphism.is_isomorphic(candidate, graph):
return value
except KeyError:
raise KeyError
def is_isomorphic(graph1, graph2, ignore_active_bonds=False, timeout=5):
"""Check whether two NX graphs are isomorphic. Contains a timeout because
the gm.is_isomorphic() method occasionally gets stuck
Arguments:
graph1 (nx.Graph): graph 1
graph2 (nx.Graph): graph 2
Keyword Arguments:
ignore_active_bonds (bool):
timeout (float): Timeout in seconds
Returns:
(bool): if the graphs are isomorphic
"""
if ignore_active_bonds:
graph1, graph2 = get_graphs_ignoring_active_edges(graph1, graph2)
if not isomorphism.faster_could_be_isomorphic(graph1, graph2):
return False
# Always match on atom types
node_match = isomorphism.categorical_node_match('atom_label', 'C')
if ignore_active_bonds:
gm = isomorphism.GraphMatcher(graph1, graph2, node_match=node_match)
else:
# Also match on edges
edge_match = isomorphism.categorical_edge_match('active', False)
gm = isomorphism.GraphMatcher(graph1,
graph2,
node_match=node_match,
edge_match=edge_match)
# NX can hang here for not very large graphs, so kill after a timeout
def handler(signum, frame):
raise TimeoutError
signal.signal(signal.SIGALRM, handler)
signal.alarm(int(timeout))
try:
result = gm.is_isomorphic()
# Cancel the timer
signal.alarm(0)
return result
except TimeoutError:
logger.error('NX graph matching hanging')
return False
def find_all_isomorphisms(home, other):
if iso.faster_could_be_isomorphic(home, other):
ddl = 'distance_dependent_label'
label_matcher = lambda x, y: x[ddl] == y[ddl] and \
x.get('shard', 1) == y.get('shard', 1)
graph_label_matcher = iso.GraphMatcher(home, other, node_match=label_matcher)
for index, mapping in enumerate(graph_label_matcher.isomorphisms_iter()):
if index == 5:
logger.debug('lsgg_compose_util i checked more than 5 isomorphisms')
yield mapping
else:
logger.log(5, 'lsgg_compose_util faster iso check failed')
yield {} # iso.graphmatcher returns empty dict when nothing is found. i do the same :)
def test_faster_could_be_isomorphic(self):
assert_true(iso.faster_could_be_isomorphic(self.G3, self.G2))
def test_faster_could_be_isomorphic(self):
assert iso.faster_could_be_isomorphic(self.G3, self.G2)
assert not iso.faster_could_be_isomorphic(self.G3, self.G5)
assert not iso.faster_could_be_isomorphic(self.G1, self.G6)
def test_faster_could_be_isomorphic(self):
assert_true(iso.faster_could_be_isomorphic(self.G3,self.G2))
