def save(self, file_name, fmt="auto"):
""" overload Graph.save to make output dotfiles pretty.
This is entirely cosmetic. """
u = self
# add some properties to prettify dot output
if fmt is "dot" or fmt is "auto" and file_name.endswith(".dot"):
u = GraphView(self)
# add shape property according to vertex owners
shape = u.new_vertex_property("string")
for v in u.vertices():
if u.vp.owner[v] == 1:
shape[v] = "box"
else:
shape[v] = "diamond"
u.vp.shape = shape
# add label property according to priorities
#u.vertex_properties['label'] = u.vertex_properties['priority']
label = u.new_vertex_property("string")
for v in u.vertices():
prio = u.vertex_properties['priority'][v]
name = u.vertex_index[v]
label[v] = "%d (%d)" % (name, prio)
u.vp.label = label
Graph.save(u, file_name, fmt)
def test_fill_missing_time():
"""simple chain graph test
"""
g = Graph(directed=False)
g.add_vertex(4)
g.add_edge_list([(0, 1), (1, 2), (2, 3)])
t = GraphView(g, directed=True)
efilt = t.new_edge_property('bool')
efilt.a = True
efilt[t.edge(2, 3)] = False
t.set_edge_filter(efilt)
vfilt = t.new_vertex_property('bool')
vfilt.a = True
vfilt[3] = False
t.set_vertex_filter(vfilt)
root = 0
obs_nodes = {0, 2}
infection_times = [0, 1.5, 3, -1]
pt = fill_missing_time(g, t, root, obs_nodes, infection_times, debug=False)
for i in range(4):
assert pt[i] == infection_times[i]
def is_order_respected(tree, root, obs_nodes, infection_times):
tree = GraphView(tree)
obs_set = set(obs_nodes)
vfilt = tree.new_vertex_property('bool')
vfilt.a = True
tree.set_vertex_filter(vfilt)
leaves = [o for o in obs_nodes if tree.vertex(o).out_degree() == 0]
vis = init_visitor(tree, root)
pbfs_search(tree, root, terminals=leaves, visitor=vis, count_threshold=-1)
for l in leaves:
edges = extract_edges_from_pred(tree, root, l, vis.pred)
edges = edges[::-1]
path = list(edges[0]) + [u for _, u in edges[1:]]
useful_nodes_on_path = [v for v in path if v in obs_set]
for i in range(len(useful_nodes_on_path)-1):
u, v = useful_nodes_on_path[i: i+2]
if infection_times[u] > infection_times[v]:
return False
return True