def make_tree(graph, source, edge_weight = None):
parent = ydict(backend=graph)
distance = ydict(backend=graph)
queue = ydeque(backend=graph)
queue_members = ydict(backend=graph)
queue.append(source)
queue_members[source] = True
distance[source] = 0
curr_pass = 0
curr_last = source
num_vertices = sum(1 for v in graph.vertices())
while queue:
v = queue.popleft()
del queue_members[v]
for e in graph.edges(source = v):
w = other_vertex(e, v)
dw, dv, e_weight = distance.get(w), distance[v], edge_weight[e]
if dw is None or dv + e_weight < dw:
distance[w] = dv + e_weight
parent[w] = e
if w not in queue_members:
queue.append(w)
queue_members[w] = True
if v == curr_last and queue:
curr_pass += 1
curr_last = queue[-1]
if curr_pass >= num_vertices:
raise NegativeCycleError
return parent
def make_tree(graph, source, edge_weight = None):
parent = ydict(backend=graph)
heap = yheap(backend=graph)
distance = ydict(backend=graph)
u, distance[u] = source, 0
while True:
for e in graph.edges(source = u):
if edge_weight[e] < 0:
raise NegativeEdgeWeightError(e)
v = other_vertex(e,u)
distance_to_v = distance.get(v)
relaxed_length = distance[u] + edge_weight[e]
if distance_to_v is None or relaxed_length < distance_to_v:
parent[v] = e
distance[v] = relaxed_length
if v in heap:
heap.modifykey(v, relaxed_length)
else:
heap.insert(v, relaxed_length)
try:
u = heap.deletemin()
except:
return parent
def connected_component_signature(g):
components = connected_components.compile(g)
component_size = ydict(g)
for v in g.vertices():
c = components(v)
component_size[c] = component_size.setdefault(c,0) + 1
return ydict(g, ((v, component_size[components(v)]) for v in g.vertices()))
def reachability_signature(g, reach):
sig = ydict(backend=g)
for v in g.vertices():
sig[v] = ydeque(sig, [1])
for i in range(reach):
for u in g.vertices():
val = sum(sig[v][i] for x,v in g.edges(source=u))
sig[u].append(val)
return ydict(g, ((k,v[-1]) for k,v in sig.iteritems()))
def __init__(self, graph):
self.description = 'depth-first search topological sort'
finished_vertices = ydict(backend=graph)
generator = depth_first_generator(graph)
# Bootstrap the depth-first search generator with all vertices
# of indegree 0. If there are no such vertices, raise an exception.
found_starting_vertex = False
for v in graph.vertices():
try:
graph.edges(target=v).next()
except StopIteration:
generator.bootstrap(v)
found_starting_vertex = True
if not found_starting_vertex:
raise NoIndegreeZeroVertices
# Topological ordering is now the reverse of the postorder. But
# a topological ordering still might not be possible if there are
# cycles, so we'll check for those here and raise an exception
# if there is one.
self.topological_order = ydeque(backend=graph)
# TODO: don't use the generator directly here, use a visitor
for e in generator.events():
if e['type'] == 'VERTEX' and e['state'] == 'FINISHED':
self.topological_order.append(e['vertex'])
elif e['type'] == 'EDGE' and e['target_state'] == 'DISCOVERED':
raise CycleExists
def isomorphism(g1, g2):
if sum(1 for v in g1.vertices()) != sum(1 for v in g2.vertices()) or \
sum(1 for e in g1.edges()) != sum(1 for e in g2.edges()):
return None
test_funcs = [partial(reachability_signature, reach=1),
partial(reachability_signature, reach=2),
partial(reachability_signature, reach=4)]
g1cf = canonical_form(g1, test_funcs)
g2cf = canonical_form(g2, test_funcs)
sorted_g1cf = ysorted(g1, g1cf.itervalues())
sorted_g2cf = ysorted(g2, g2cf.itervalues())
for x,y in izip(sorted_g1cf, sorted_g2cf):
if x != y:
return None
g2_cform_inv = function_inverse(g2cf, g2)
iso = ydict(backend=g1)
contexts = ydeque(backend=g1)
for v in g1.vertices():
g2_inv_image = ydeque(backend=contexts)
for image_element in g2_cform_inv[g1cf[v]]:
g2_inv_image.append(image_element)
contexts.append((v, g2_inv_image))
index = 0
while index >= 0 and index < len(contexts):
vertex = contexts[index][0]
if contexts[index][1]:
v_prime = contexts[index][1].popleft()
iso[vertex] = v_prime
if is_a_partial_isomorphism(g1, g2, iso):
index += 1
else:
if vertex in iso:
del iso[vertex]
g2_inv_image = ydeque(backend=contexts)
for image_element in g2_cform_inv[g1cf[vertex]]:
g2_inv_image.append(image_element)
(index, vertex, str([x for x in g2_inv_image]))
contexts[index] = (vertex, g2_inv_image)
index -= 1
if index < 0:
return None
else:
return iso
def __call__(self, width=None, height=None):
if width is None:
width = 400
if height is None:
height = 400
p = ydict(memory_usage=self.graph.MemoryUsage)
p = fruchterman_reingold_drawing(self.graph, position = p,
min_x = 10, max_x = width + 10,
min_y = 10, max_y = height + 10,
iterations = 500, temp = 100,
cool = lambda t : max(0, t - 0.1))
p = fruchterman_reingold_drawing(self.graph, position = p,
min_x = 10, max_x = width + 10,
min_y = 10, max_y = height + 10,
iterations = 100, temp = 20,
cool = lambda t : max(0, t - 1))
return p
def forest_isomorphism(f1, f2):
#TODO: do this at a higher level, since both iso testers need it
if sum(1 for v in f1.vertices()) != sum(1 for v in f2.vertices()) or \
sum(1 for e in f1.edges()) != sum(1 for e in f2.edges()):
return None
results = []
for forest in (f1,f2):
generator = depth_first_generator(forest)
visitor = AggregateVisitor(backend=forest,
visitors={Depth:None})
traverse(root_vertices=graph.vertices(),
visitor=visitor,
generator=depth_first_generator(forest))
results.append(visitor.Depth)
f1_depth, f2_depth = results
f1_by_depths = ydict(backend=f1)
f2_by_depths = ydict(backend=f2)
max_depth = 0
for forest, depth, index_by_depths in [(f1, f1_depth, f1_by_depths),
(f2, f2_depth, f2_by_depths)]:
for v in forest.vertices():
d = depth[v]
max_depth = max(d, max_depth)
index_by_depths[d] = index_by_depths.setdefault(d, ydeque(backend=forest)).append(v)
prev_f1_canonical_id = ydict(backend=f1)
prev_f2_canonical_id = ydict(backend=f2)
if len(f1_by_depths[max_depth]) != len(f2_by_depths[max_depth]):
return
for v in f1_by_depths[max_depth]:
prev_f1_canonical_id[v] = 0
for v in f2_by_depths[max_depth]:
prev_f2_canonical_id[v] = 0
for depth in xrange(max_depth - 1, -1, -1):
f1_vertex_id = ydict(backend=f1)
f2_vertex_id = ydict(backend=f2)
if len(f1_by_depths[depth]) != len(f2_by_depths[depth]):
return
# don't do two-phase canonical id -> id transformation. instead, compute canonical ids
# on the fly by storing a lexicographically sorted list of ids and binary searching for
# existing ids each time
for v in f1_by_depths[depth]:
f1_vertex_id[v] = ydeque(backend=f2_vertex_id,
ysorted(backend=f2_vertex_id,
(prev_f1_canonical_id[w] for u,w in f1.edges(source=v))))
for v in f2_by_depths[depth]:
f2_vertex_id[v] = ydeque(backend=f2_vertex_id,
ysorted(backend=f2_vertex_id,
(prev_f2_canonical_id[w] for u,w in f2.edges(source=v))))
def is_a_partial_isomorphism(g1, g2, iso):
"""
Precondition: len(g1.vertices()) == len(g2.vertices()) and
len(g1.edges()) == len(g2.edges())
"""
g2_edges_mapped = ydict(backend=g1)
for u,v in g1.edges():
is_a_partial_iso = False
try:
u_image, v_image = iso[u], iso[v]
except KeyError:
continue
chosen_edge = None
for edge in g2.edges(source=u_image, target=v_image):
if g2_edges_mapped.get(edge) is None:
g2_edges_mapped[edge] = True
chosen_edge = edge
break
if chosen_edge is None:
return False
return True
def function_inverse(f, backend):
inverse = ydict(backend=backend)
for key, value in f.iteritems():
inverse.setdefault(value,ydeque(backend=inverse)).append(key)
return inverse
def canonical_form(g, test_funcs):
result_dicts = [func(g) for func in test_funcs]
return ydict(g, ((v,tuple(d[v] for d in result_dicts))
for v in g.vertices()))
def __init__(self, agg):
TraversalVisitor.__init__(self)
self.properties = agg
self.value = ydict(backend=agg)
def __init__(self, graph):
self.__vertex_state = ydict(backend=graph)
self.graph = graph
def __init__(self, graph, edge_weight):
self.__graph = graph
self.__edge_weight = edge_weight
self.__priority_queue = yheap(backend=graph)
self.__vertex_state = ydict(backend=graph)
def __init__(self, graph, vertex_heuristic):
self.__graph = graph
self.__h = vertex_heuristic
self.__priority_queue = yheap(backend=graph)
self.__vertex_state = ydict(backend=graph)
