def test_brandes_erlebach():
# Figure 1 chapter 7: Connectivity
# http://www.informatik.uni-augsburg.de/thi/personen/kammer/Graph_Connectivity.pdf
G = nx.Graph()
G.add_edges_from([(1, 2), (1, 3), (1, 4), (1, 5), (2, 3), (2, 6), (3, 4),
(3, 6), (4, 6), (4, 7), (5, 7), (6, 8), (6, 9), (7, 8),
(7, 10), (8, 11), (9, 10), (9, 11), (10, 11)])
for flow_func in flow_funcs:
kwargs = dict(flow_func=flow_func)
assert_equal(3,
local_edge_connectivity(G, 1, 11, **kwargs),
msg=msg.format(flow_func.__name__))
assert_equal(3,
nx.edge_connectivity(G, 1, 11, **kwargs),
msg=msg.format(flow_func.__name__))
assert_equal(2,
local_node_connectivity(G, 1, 11, **kwargs),
msg=msg.format(flow_func.__name__))
assert_equal(2,
nx.node_connectivity(G, 1, 11, **kwargs),
msg=msg.format(flow_func.__name__))
assert_equal(
2,
nx.edge_connectivity(G, **kwargs), # node 5 has degree 2
msg=msg.format(flow_func.__name__))
assert_equal(2,
nx.node_connectivity(G, **kwargs),
msg=msg.format(flow_func.__name__))
def avg_node_connectivity(G, I, s):
total_connectivity = 0
for t in I:
if t != s:
total_connectivity += local_node_connectivity(G, s, t)
avg_connectivity = total_connectivity / (len(I) - 1)
# TODO: normalize
return avg_connectivity
def chcekConnectivity(G, startNode):
ret = None
for u, v in itertools.combinations(startNode, 2):
k = local_node_connectivity(G, u, v)
if k == 0:
ret = False
if ret is None:
ret = True
return ret
def Connectivity(overlap, graph, baseoutput):
coverage = 30.0
H = build_auxiliary_node_connectivity(graph)
R = build_residual_network(H, 'capacity')
with open(baseoutput + '-Connectivity', 'w') as output:
for ov in overlap:
connect = local_node_connectivity(
graph, ov.read1, ov.read2, auxiliary=H,
residual=R) / float(coverage)
output.write(str(connect) + '\n')
def test_brandes_erlebach():
# Figure 1 chapter 7: Connectivity
# http://www.informatik.uni-augsburg.de/thi/personen/kammer/Graph_Connectivity.pdf
G = nx.Graph()
G.add_edges_from([(1, 2), (1, 3), (1, 4), (1, 5), (2, 3), (2, 6), (3, 4),
(3, 6), (4, 6), (4, 7), (5, 7), (6, 8), (6, 9), (7, 8),
(7, 10), (8, 11), (9, 10), (9, 11), (10, 11)])
for flow_func in flow_funcs:
kwargs = dict(flow_func=flow_func)
assert_equal(3, local_edge_connectivity(G, 1, 11, **kwargs),
msg=msg.format(flow_func.__name__))
assert_equal(3, nx.edge_connectivity(G, 1, 11, **kwargs),
msg=msg.format(flow_func.__name__))
assert_equal(2, local_node_connectivity(G, 1, 11, **kwargs),
msg=msg.format(flow_func.__name__))
assert_equal(2, nx.node_connectivity(G, 1, 11, **kwargs),
msg=msg.format(flow_func.__name__))
assert_equal(2, nx.edge_connectivity(G, **kwargs), # node 5 has degree 2
msg=msg.format(flow_func.__name__))
assert_equal(2, nx.node_connectivity(G, **kwargs),
msg=msg.format(flow_func.__name__))
def test_brandes_erlebach():
# Figure 1 chapter 7: Connectivity
# http://www.informatik.uni-augsburg.de/thi/personen/kammer/Graph_Connectivity.pdf
G = nx.Graph()
G.add_edges_from([
(1, 2),
(1, 3),
(1, 4),
(1, 5),
(2, 3),
(2, 6),
(3, 4),
(3, 6),
(4, 6),
(4, 7),
(5, 7),
(6, 8),
(6, 9),
(7, 8),
(7, 10),
(8, 11),
(9, 10),
(9, 11),
(10, 11),
])
for flow_func in flow_funcs:
kwargs = dict(flow_func=flow_func)
errmsg = f"Assertion failed in function: {flow_func.__name__}"
assert 3 == local_edge_connectivity(G, 1, 11, **kwargs), errmsg
assert 3 == nx.edge_connectivity(G, 1, 11, **kwargs), errmsg
assert 2 == local_node_connectivity(G, 1, 11, **kwargs), errmsg
assert 2 == nx.node_connectivity(G, 1, 11, **kwargs), errmsg
assert 2 == nx.edge_connectivity(G, **kwargs), errmsg
assert 2 == nx.node_connectivity(G, **kwargs), errmsg
if flow_func is flow.preflow_push:
assert 3 == nx.edge_connectivity(G, 1, 11, cutoff=2,
**kwargs), errmsg
else:
assert 2 == nx.edge_connectivity(G, 1, 11, cutoff=2,
**kwargs), errmsg
pf_dict[last] += 0
pf_dict[splits[1]] += 0
print
# print pf_dict
print
# Remove nodes with low neighbour count
# Donot remove if its destination node.
for node in G.nodes():
if len(G.neighbors(node)) < 1 and (not node in dest_as_list):
G.remove_node(node)
#Save complete graph copy for plotting purposes
G_copy = G.copy()
print local_node_connectivity(G, "1680", "8867")
print minimum_st_node_cut(G, "1680", "8867")
# find_cuts(G)
fo = open("temp.txt", "w")
for mm in all_cut_vertex:
fo.write(mm+"\n");
print "number of cuts " + str(len(all_cut_vertex))