def compute_local_community(self, g):
r = []
for i in xrange(3):
r.append(minimize(lambda x: -1*(gt.modularity(g, gt.community_structure(g, 100, x)))
, 0, method='COBYLA', options={'disp': True}).x)
print "Optimal global Modularity: ", np.mean(r)
b = gt.community_structure(g, 100, np.mean(r))
return b
def compute_global_community(self):
r = []
for i in xrange(3):
r.append(minimize(self.optimize_global_modularity, 0, method='COBYLA', options={'disp': False}).x)
print "Optimal global group number: ", np.mean(r)
b = gt.community_structure(self.g, 100, np.mean(r))
return b
def community():
g = gt.load_graph(filename)
print 'Graph loaded, now finding community'
# state = gt.BlockState(g, B=blocks)
# for i in xrange(iterations):
# if i < iterations / 2:
# gt.mcmc_sweep(state)
# else:
# gt.mcmc_sweep(state, beta=float('inf'))
# g.vp['blocks'] = state.get_blocks()
spins = {}
if 'blocks' in g.vp:
spins = {'spins': g.vp['blocks']}
g.vp['blocks'] = gt.community_structure(g, n_iter=iterations, n_spins=blocks, **spins)
if 'pos' in g.vp:
gt.sfdp_layout(g, groups=g.vp['blocks'], pos=g.vp['pos'])
for i in xrange(blocks):
print '%d nodes in block %d' % (len(gt.find_vertex(g, g.vp['blocks'], i)), i)
g.save(filename)
def optimize_global_modularity(self, x):
b = gt.community_structure(self.g, 100, x)
return -1*(gt.modularity(self.g, b))
if f_g.edge(s_i,t_i) is not None:
e = f_g.edge(s_i, t_i)
e_w[e] +=1
else:
e = f_g.add_edge(s_i, t_i)
e_w[e] = 0
f_g.edge_properties['cofield'] = e_w
# <codecell>
print f_g.num_edges()
f_g.num_vertices()
# <codecell>
v_comm = gt.community_structure(f_g, 1000, 5)
#v_comm = gt.betweenness(f_g)
# <codecell>
import numpy
u = gt.GraphView(f_g, vfilt=gt.label_largest_component(f_g))
deg = u.degree_property_map('total', weight = f_g.edge_properties['cofield'])
deg.fa = 2*(numpy.sqrt(deg.fa)*0.5 + 0.4)
edg = f_g.edge_properties['cofield']
edg.fa = (numpy.sqrt(edg.fa)*0.6+1)
ebet = gt.betweenness(f_g)[1]
# <codecell>