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 min_steiner_tree(g,
obs_nodes,
p=None,
return_type='tree',
debug=False,
verbose=False):
assert len(obs_nodes) > 0, 'no terminals'
if g.num_vertices() == len(obs_nodes):
print('it\'s a minimum spanning tree problem')
gc, eweight, r2pred = build_closure(g,
obs_nodes,
p=p,
debug=debug,
verbose=verbose)
# print('gc', gc)
tree_map = min_spanning_tree(gc, eweight, root=None)
tree = GraphView(gc, directed=False, efilt=tree_map)
tree_edges = set()
for e in tree.edges():
u, v = map(int, e)
recovered_edges = extract_edges_from_pred(u, v, r2pred[u])
assert recovered_edges, 'empty!'
for i, j in recovered_edges:
tree_edges.add((i, j))
tree_nodes = list(set(itertools.chain(*tree_edges)))
if return_type == 'nodes':
return tree_nodes
elif return_type == 'edges':
return list(map(edge2tuple, tree_edges))
elif return_type == 'tree':
vfilt = g.new_vertex_property('bool')
vfilt.set_value(False)
for n in tree_nodes:
vfilt[n] = True
efilt = g.new_edge_property('bool')
for i, j in tree_edges:
efilt[g.edge(i, j)] = 1
subg = GraphView(g, efilt=efilt, vfilt=vfilt, directed=False)
if p is not None:
weights = subg.new_edge_property('float')
for e in subg.edges():
weights[e] = p[e]
else:
weights = None
# remove cycles
tree_map = min_spanning_tree(subg, weights, root=None)
t = GraphView(g, directed=False, vfilt=vfilt, efilt=tree_map)
return t