def get_edge_list():
cn = barbell_graph(GC.barbell_m1, GC.barbell_m2)
out = GC.nx2favites(cn, 'u')
f = gopen(expanduser("%s/contact_network.txt.gz" % GC.out_dir), 'wb',
9)
f.write('\n'.join(out).encode())
f.write(b'\n')
f.close()
GC.cn_communities = [
{i
for i in range(GC.barbell_m1)},
{
i
for i in range(GC.barbell_m1 +
GC.barbell_m2, 2 * GC.barbell_m1 +
GC.barbell_m2)
}
] # only left and right communities, not the path
f = gopen(
expanduser("%s/contact_network_partitions.txt.gz" % GC.out_dir),
'wb', 9)
f.write(str(GC.cn_communities).encode())
f.write(b'\n')
f.close()
GC.cn_communities = [{str(i) for i in c} for c in GC.cn_communities]
return out
def get_edge_list():
cn = complete_graph(GC.num_cn_nodes)
out = GC.nx2favites(cn, 'u')
f = gopen(expanduser("%s/contact_network.txt.gz" % GC.out_dir), 'wb',
9)
f.write('\n'.join(out).encode())
f.write(b'\n')
f.close()
return out
def get_edge_list():
cn = barabasi_albert_graph(GC.num_cn_nodes,
GC.num_edges_from_new,
seed=GC.random_number_seed)
if GC.random_number_seed is not None:
GC.random_number_seed += 1
out = GC.nx2favites(cn, 'u')
f = gopen(expanduser("%s/contact_network.txt.gz" % GC.out_dir), 'wb',
9)
f.write('\n'.join(out).encode())
f.write(b'\n')
f.close()
return out
def get_edge_list():
cn = newman_watts_strogatz_graph(GC.num_cn_nodes,
GC.nws_k,
GC.nws_prob,
seed=GC.random_number_seed)
if GC.random_number_seed is not None:
GC.random_number_seed += 1
out = GC.nx2favites(cn, 'u')
f = gopen(expanduser("%s/contact_network.txt.gz" % GC.out_dir), 'wb',
9)
f.write('\n'.join(out).encode())
f.write(b'\n')
f.close()
return out
def get_edge_list():
du = GC.d_or_u == 'd'
cn = random_partition_graph(GC.rpg_sizes, GC.rpg_p_in, GC.rpg_p_out, directed=du, seed=GC.random_number_seed)
if GC.random_number_seed is not None:
GC.random_number_seed += 1
out = GC.nx2favites(cn, GC.d_or_u)
f = gopen(expanduser("%s/contact_network.txt.gz" % GC.out_dir),'wb',9)
f.write('\n'.join(out).encode()); f.write(b'\n')
f.close()
f = gopen(expanduser("%s/contact_network_partitions.txt.gz" % GC.out_dir),'wb',9)
f.write(str(cn.graph['partition']).encode()); f.write(b'\n')
f.close()
GC.cn_communities = [{str(n) for n in c} for c in cn.graph['partition']]
return out
def get_edge_list():
cn = relaxed_caveman_graph(GC.cave_num_cliques, GC.cave_clique_size, GC.cave_prob, seed=GC.random_number_seed)
if GC.random_number_seed is not None:
GC.random_number_seed += 1
out = GC.nx2favites(cn, 'u')
f = gopen(expanduser("%s/contact_network.txt.gz" % GC.out_dir),'wb',9)
f.write('\n'.join(out).encode()); f.write(b'\n')
f.close()
GC.cn_communities = [{c*GC.cave_clique_size+i for i in range(GC.cave_clique_size)} for c in range(GC.cave_num_cliques)]
f = gopen(expanduser("%s/contact_network_partitions.txt.gz" % GC.out_dir),'wb',9)
f.write(str(GC.cn_communities).encode()); f.write(b'\n')
f.close()
GC.cn_communities = [{str(i) for i in c} for c in GC.cn_communities]
return out
def get_edge_list():
du = GC.d_or_u == 'd'
cn = fast_gnp_random_graph(GC.num_cn_nodes,
GC.er_prob,
directed=du,
seed=GC.random_number_seed)
if GC.random_number_seed is not None:
GC.random_number_seed += 1
out = GC.nx2favites(cn, GC.d_or_u)
f = gopen(expanduser("%s/contact_network.txt.gz" % GC.out_dir), 'wb',
9)
f.write('\n'.join(out).encode())
f.write(b'\n')
f.close()
return out
def get_edge_list():
try:
cn = random_degree_sequence_graph(GC.cn_degree_sequence,
tries=GC.cn_tries,
seed=GC.random_number_seed)
except NetworkXUnfeasible:
from os import chdir
chdir(GC.START_DIR)
assert False, "Contact network degree sequence is not graphical"
except NetworkXError:
from os import chdir
chdir(GC.START_DIR)
assert False, "NetworkX failed to produce graph after %d tries" % GC.cn_tries
if GC.random_number_seed is not None:
GC.random_number_seed += 1
out = GC.nx2favites(cn, 'u')
f = gopen(expanduser("%s/contact_network.txt.gz" % GC.out_dir), 'wb',
9)
f.write('\n'.join(out).encode())
f.write(b'\n')
f.close()
return out
def get_edge_list():
# set things up
a = (GC.cng_m + 1) / (2 * GC.cng_m)
probs = [0] + [
2 * a / (i * (i + 1)) for i in range(1, GC.cng_m + 1)
] # prepend 0 to make non-zero probabilities be indices 1 through M
M = [
m for m, n in enumerate(
multinomial(len(GC.cng_N), probs, size=1)[0]) for _ in range(n)
]
com = list()
for i in range(len(M)):
com.append(
GC.nx2favites(
barabasi_albert_graph(GC.cng_N[i],
M[i],
seed=GC.random_number_seed), 'u'))
if GC.random_number_seed is not None:
GC.random_number_seed += 1
# process disconnected BA graphs (one per community)
nodes = list()
node_lines = list()
edge_lines = list()
for i, g in enumerate(com):
nodes.append(list())
node_prefix = 'COM%d' % i
for l in g:
if len(l) == 0 or l[0] == '#':
continue
parts = l.split()
assert parts[0] in {'NODE', 'EDGE'
}, "Invalid FAVITES edge list encountered"
if parts[0] == 'NODE':
name = "%s-%s" % (node_prefix, parts[1])
nodes[-1].append(name)
node_lines.append("NODE\t%s\t%s" % (name, parts[2]))
else:
u = "%s-%s" % (node_prefix, parts[1])
v = "%s-%s" % (node_prefix, parts[2])
edge_lines.append("EDGE\t%s\t%s\t%s\t%s" %
(u, v, parts[3], parts[4]))
# add edges between communities
possible_num_er_edges = sum(len(c) for c in nodes)**2 - sum(
len(c)**2 for c in nodes)
if len(nodes) == 1:
num_er_edges = 0 # only 1 community
else:
num_er_edges = 2 * binomial(
possible_num_er_edges,
GC.cng_p) # multiply by 2 for bidirectionality
er_edges = set()
er_choice_indices = list(range(len(nodes)))
while len(er_edges) != 2 * num_er_edges:
i = choice(er_choice_indices)
j = choice(er_choice_indices)
while i == j:
j = choice(er_choice_indices)
u = choice(nodes[i])
v = choice(nodes[j])
er_edges.add((u, v))
er_edges.add((v, u))
edge_lines.append("EDGE\t%s\t%s\t.\tu" % (u, v))
# output final graph
out = node_lines + edge_lines
f = gopen(expanduser("%s/contact_network.txt.gz" % GC.out_dir), 'wb',
9)
f.write('\n'.join(out).encode())
f.write(b'\n')
f.close()
return out
'''
edgelists = []
for cng_i, cng in enumerate(local_cn_generators):
MF.modules['ContactNetworkGenerator'] = MF.module_implementations['ContactNetworkGenerator'][cng['ContactNetworkGenerator']]['class']
for param in MF.module_implementations['ContactNetworkGenerator'][cng['ContactNetworkGenerator']]['req']:
setattr(GC,param,cng[param])
MF.modules['ContactNetworkGenerator'].init()
edgelists.append(MF.modules['ContactNetworkGenerator'].get_edge_list())
g = {} # g[node]['attributes' or 'edges']
GC.cn_communities = []
total_num_nodes = 0
out = []
for edgelist_i,edgelist in enumerate(edgelists):
GC.cn_communities.append([])
node_prefix = "CNG%d-COM%d"%(GC.cng_community_num,edgelist_i)
for line in edgelist:
if len(line) == 0 or line[0] == '#':
continue
parts = line.split()
assert parts[0] in {'NODE','EDGE'}, "Invalid FAVITES edge list encountered"
if parts[0] == 'NODE':
name = "%s-%s" % (node_prefix,parts[1])
assert name not in g, "Duplicate node name encountered"
g[name] = {'edges':[], 'attributes':parts[2]}
out.append("NODE\t%s\t%s" % (name,parts[2]))
GC.cn_communities[-1].append(name)
else:
u = "%s-%s" % (node_prefix,parts[1])
assert u in g, "Encountered non-existant node name"
v = "%s-%s" % (node_prefix,parts[2])
assert v in g, "Encountered non-existant node name"
g[u]['edges'].append((v,parts[3],parts[4]))
assert len(GC.cn_communities[-1]) != 0, "Encountered empty community"
total_num_nodes += len(GC.cn_communities[-1])
for u in g:
for v,attr,du in g[u]['edges']:
out.append("EDGE\t%s\t%s\t%s\t%s" % (u,v,attr,du))
possible_across_edges = 0
for i in range(len(GC.cn_communities)-1):
for j in range(i+1,len(GC.cn_communities)):
possible_across_edges += len(GC.cn_communities[i])*len(GC.cn_communities[j])
num_across_edges = binomial(possible_across_edges,GC.cn_p_across)
done = set()
for _ in range(num_across_edges):
i,j = sample(range(len(GC.cn_communities)),2)
u,v = choice(GC.cn_communities[i]),choice(GC.cn_communities[j])
while (u,v) in done:
i,j = sample(range(len(GC.cn_communities)),2)
u,v = choice(GC.cn_communities[i]),choice(GC.cn_communities[j])
done.add((u,v))
out.append("EDGE\t%s\t%s\t.\tu" % (u,v))
f = gopen(expanduser("%s/contact_network.txt.gz" % GC.out_dir),'wb',9)
f.write('\n'.join(out).encode()); f.write(b'\n')
f.close()
f = gopen(expanduser("%s/contact_network_partitions.txt.gz" % GC.out_dir),'wb',9)
f.write(str(GC.cn_communities).encode()); f.write(b'\n')
f.close()
return out'''
exit()
def get_edge_list():
# set things up
a = (GC.cng_m + 1) / (2 * GC.cng_m)
probs = [0] + [
2 * a / (i * (i + 1)) for i in range(1, GC.cng_m + 1)
] # prepend 0 to make non-zero probabilities be indices 1 through M
M = [
m for m, n in enumerate(
multinomial(len(GC.cng_N), probs, size=1)[0]) for _ in range(n)
]
com = list()
for i in range(len(M)):
com.append(
GC.nx2favites(
barabasi_albert_graph(GC.cng_N[i],
M[i],
seed=GC.random_number_seed), 'u'))
if GC.random_number_seed is not None:
GC.random_number_seed += 1
# process disconnected BA graphs (one per community)
nodes = list()
node_lines = list()
edge_lines = list()
GC.cn_communities = list()
for i, g in enumerate(com):
nodes.append(list())
GC.cn_communities.append(set())
node_prefix = 'COM%d' % i
for l in g:
if len(l) == 0 or l[0] == '#':
continue
parts = l.split()
assert parts[0] in {'NODE', 'EDGE'
}, "Invalid FAVITES edge list encountered"
if parts[0] == 'NODE':
name = "%s-%s" % (node_prefix, parts[1])
nodes[-1].append(name)
GC.cn_communities[-1].add(name)
node_lines.append("NODE\t%s\t%s" % (name, parts[2]))
else:
u = "%s-%s" % (node_prefix, parts[1])
v = "%s-%s" % (node_prefix, parts[2])
edge_lines.append("EDGE\t%s\t%s\t%s\t%s" %
(u, v, parts[3], parts[4]))
# add edges between communities
possible_num_er_edges = sum(len(c) for c in nodes)**2 - sum(
len(c)**2 for c in nodes)
if len(nodes) == 1:
num_er_edges = 0 # only 1 community
else:
num_er_edges = 2 * binomial(
possible_num_er_edges,
GC.cng_p) # multiply by 2 for bidirectionality
er_edges = set()
er_choice_indices = list(range(len(nodes)))
while len(er_edges) != 2 * num_er_edges:
i = choice(er_choice_indices)
j = choice(er_choice_indices)
while i == j:
j = choice(er_choice_indices)
u = choice(nodes[i])
v = choice(nodes[j])
er_edges.add((u, v))
er_edges.add((v, u))
edge_lines.append("EDGE\t%s\t%s\t.\tu" % (u, v))
# output final graph
out = node_lines + edge_lines
f = gopen(expanduser("%s/contact_network.txt.gz" % GC.out_dir), 'wb',
9)
f.write('\n'.join(out).encode())
f.write(b'\n')
f.close()
f = gopen(
expanduser("%s/contact_network_partitions.txt.gz" % GC.out_dir),
'wb', 9)
f.write(str(GC.cn_communities).encode())
f.write(b'\n')
f.close()
return out