def plot_co_x(cox, start, end, size = (20,20), title = '', weighted=False, weight_threshold=10):
""" Plotting function for keyword graphs
Parameters
--------------------
cox: the coword networkx graph; assumes that nodes have attribute 'topic'
start: start year
end: end year
"""
plt.figure(figsize=size)
plt.title(title +' %s - %s'%(start,end), fontsize=18)
if weighted:
elarge=[(u,v) for (u,v,d) in cox.edges(data=True) if d['weight'] >weight_threshold]
esmall=[(u,v) for (u,v,d) in cox.edges(data=True) if d['weight'] <=weight_threshold]
pos=nx.graphviz_layout(cox) # positions for all nodes
nx.draw_networkx_nodes(cox,pos,
node_color= [s*4500 for s in nx.eigenvector_centrality(cox).values()],
node_size = [s*6+20 for s in nx.degree(cox).values()],
alpha=0.7)
# edges
nx.draw_networkx_edges(cox,pos,edgelist=elarge,
width=1, alpha=0.5, edge_color='black') #, edge_cmap=plt.cm.Blues
nx.draw_networkx_edges(cox,pos,edgelist=esmall,
width=0.3,alpha=0.5,edge_color='yellow',style='dotted')
# labels
nx.draw_networkx_labels(cox,pos,font_size=10,font_family='sans-serif')
plt.axis('off')
else:
nx.draw_graphviz(cox, with_labels=True,
alpha = 0.8, width=0.1,
fontsize=9,
node_color = [s*4 for s in nx.eigenvector_centrality(cox).values()],
node_size = [s*6+20 for s in nx.degree(cox).values()])
def print_degree_distributions(dataset, context):
"""
Extracts degree distribution values from networks, and print them to
cvs-file.
**warning** overwrites if file exists.
"""
print '> Reading data..', dataset
corpus_path = '../data/'+dataset+'_text'
(documents, labels) = data.read_files(corpus_path)
degsfile = open('output/properties/cooccurrence/degrees_docs_'+dataset.replace('/','.'), 'w')
giant = nx.DiGraph()
print '> Building networks..'
for i, text in enumerate(documents):
if i%10==0: print ' ',str(i)+'/'+str(len(documents))
g = graph_representation.construct_cooccurrence_network(text,context=context)
giant.add_edges_from(g.edges())
degs = nx.degree(g).values()
degs = [str(d) for d in degs]
degsfile.write(','.join(degs)+'\n')
degsfile.close()
print '> Writing giant\'s distribution'
with open('output/properties/cooccurrence/degrees_giant_'+dataset.replace('/','.'), 'w') as f:
ds = nx.degree(giant).values()
ds = [str(d) for d in ds]
f.write(','.join(ds))
def draw_degree_rank_plot(orig_g, mG):
ori_degree_seq = sorted(nx.degree(orig_g).values(), reverse=True) # degree sequence
deg_seqs = []
for newg in mG:
deg_seqs.append(sorted(nx.degree(newg).values(), reverse=True)) # degree sequence
df = pd.DataFrame(deg_seqs)
plt.xscale("log")
plt.yscale("log")
plt.fill_between(df.columns, df.mean() - df.sem(), df.mean() + df.sem(), color="blue", alpha=0.2, label="se")
h, = plt.plot(df.mean(), color="blue", aa=True, linewidth=4, ls="--", label="H*")
orig, = plt.plot(ori_degree_seq, color="black", linewidth=4, ls="-", label="H")
plt.title("Degree Distribution")
plt.ylabel("Degree")
plt.ylabel("Ordered Vertices")
plt.tick_params(
axis="x", # changes apply to the x-axis
which="both", # both major and minor ticks are affected
bottom="off", # ticks along the bottom edge are off
top="off", # ticks along the top edge are off
labelbottom="off",
) # labels along the bottom edge are off
plt.legend([orig, h], ["$H$", "HRG $H^*$"], loc=3)
# fig = plt.gcf()
# fig.set_size_inches(5, 4, forward=True)
plt.show()
def PartitionGraph(graph,kc_nodes,anchor=EMPTY_SET,k=2):
G = graph.copy()
R_cand = set()
S_cand = set()
G_ccs = nx.connected_component_subgraphs(G)
for g_cc in G_ccs:
cc_nodes = set(g_cc.nodes())
kc_overlap = cc_nodes.intersection(kc_nodes)
if len(kc_overlap) > 0:
root = kc_overlap.pop()
R_nodes = set()
for n in cc_nodes:
d = nx.degree(G,n)
if n not in anchor and n not in kc_nodes and d > 0 and d < k:
R_nodes.add(n)
R_cand = R_cand.union(set((u,root) for u in R_nodes))
else:
S_nodes = set()
for n in cc_nodes:
d = nx.degree(G,n)
if n not in anchor and d > 0 and d < k:
S_nodes.add(n)
S_cand = S_cand.union(set((u,v) for u,v in combinations(S_nodes,2)))
return R_cand,S_cand
def RW_Size(G,r = 1000,m=100):
sampled = []
now_node = random.choice(G.nodes())
sampled.append(now_node)
while True:
next_node = random.choice(nx.neighbors(G,now_node))
now_node = next_node
sampled.append(now_node)
if len(sampled) >= r:
break
print(1)
lst = []
for i in range(0,r-m):
if i+m <= r-1:
for j in range(i+m,r):
# l1 = set(nx.neighbors(G,sampled[i]))
# l2 = set(nx.neighbors(G,sampled[j]))
# if len(list(l1 & l2)) >= 1:
lst.append((sampled[i],sampled[j]))
lst.append((sampled[j],sampled[i]))
sumA = 0.0
sumB = 0.0
print(len(lst))
for nodes in lst:
sumA += float(nx.degree(G,nodes[0]))/nx.degree(G,nodes[1])
l1 = set(nx.neighbors(G,nodes[0]))
l2 = set(nx.neighbors(G,nodes[1]))
count = len(list(l1&l2))
sumB += count/(float(nx.degree(G,nodes[0]))*nx.degree(G,nodes[1]))
return sumA/sumB
def compute_eps(G2, k, u, S1, S2):
max_deg_G2 = max(nx.degree(G2).itervalues())
print "max_deg_G2 =", max_deg_G2
deg_list = nx.degree(G2)
# start = time.clock()
X = compute_X(G2, max_deg_G2)
# print "compute_X: done"
# print "Elapsed ", (time.clock() - start
Y = compute_Y(X, G2.number_of_nodes(), max_deg_G2)
# print "compute_Y: done"
ent = compute_entropy(Y, G2.number_of_nodes(), max_deg_G2)
# print "len(ent) =", len(ent)
num_violated = 0
LOG2K = math.log(k,2)
print "LOG2K =", LOG2K
for (v, deg) in deg_list.iteritems(): # check the original graph
if (v == u or v in S1) and ent[deg] < LOG2K:
num_violated += 1
# check and update eps_min (if ok)
eps2 = float(num_violated)/G2.number_of_nodes()
#
return eps2
def compute_eps_deterministic_multi(G, G2, k_arr):
max_deg_G2 = max(nx.degree(G2).itervalues())
print "max_deg =", max_deg_G2
deg_list = nx.degree(G)
deg_list_G2 = nx.degree(G2)
deg_count_G2 = [0 for j in range(max_deg_G2+1)]
for deg in deg_list_G2.itervalues():
deg_count_G2[deg] += 1
ent = [0.0 for j in range(max_deg_G2+1)]
for j in range(max_deg_G2+1):
if deg_count_G2[j] > 0:
ent[j] = math.log(deg_count_G2[j],2) # simple
print "len(ent) =", len(ent)
# print "entropy =", ent
eps_arr = []
for k in k_arr:
num_violated = 0
LOG2K = math.log(k,2)
for (v, deg) in deg_list.iteritems(): # check the original graph
if deg <= max_deg_G2: # in the case of max_deg_G2 < max_deg_G
if ent[deg] > 0.0 and ent[deg] < LOG2K: # do not check zero-column of ent
num_violated += 1
# check and update eps_min (if ok)
eps2 = float(num_violated)/G2.number_of_nodes()
eps_arr.append(eps2)
#
return eps_arr
def RW_Size_col(G,r = 30000):
sampled = []
now_node = random.choice(G.nodes())
sampled.append(now_node)
sumA = 0.0
sumB = 0.0
sumA += nx.degree(G,now_node)
sumB += 1.0/nx.degree(G,now_node)
count = 0
while True:
next_node = random.choice(nx.neighbors(G,now_node))
now_node = next_node
sumA += nx.degree(G,now_node)
sumB += 1.0/nx.degree(G,now_node)
sampled.append(now_node)
count += 1
if count >= r:
break
count2 = 0
for i in range(0,len(sampled)-1):
for j in range(i+1,len(sampled)):
if(sampled[i] == sampled[j]):
count2 += 1
return sumA*sumB/(2*count2)
def compute_eps_multi(G, G2, k_arr):
max_deg_G2 = max(nx.degree(G2).itervalues())
print "max_deg_G2 =", max_deg_G2
deg_list = nx.degree(G) # G not G2
deg_list_G2 = nx.degree(G2)
X = compute_X(G2, G2.number_of_nodes(), max_deg_G2, deg_list_G2)
Y = compute_Y(X, G2.number_of_nodes(), max_deg_G2, deg_list_G2)
# check X, Y
check_X_and_Y(X, Y, G2.number_of_nodes(), max_deg_G2, deg_list_G2)
ent = compute_entropy(Y, G2.number_of_nodes(), max_deg_G2, deg_list_G2)
print "len(ent) =", len(ent)
# print "entropy =", ent
eps_arr = []
for k in k_arr:
num_violated = 0
LOG2K = math.log(k,2)
# print "LOG2K =", LOG2K
for (v, deg) in deg_list.iteritems(): # check the original graph
if deg <= max_deg_G2: # in the case of max_deg_G2 < max_deg_G
if ent[deg] > 0.0 and ent[deg] < LOG2K: # do not check zero-column of ent
num_violated += 1
# check and update eps_min (if ok)
eps2 = float(num_violated)/G2.number_of_nodes()
eps_arr.append(eps2)
#
return eps_arr
def cand_gen(G, k, a, c, cores=None):
'''
generate all the branch given a k-plex a
a: current k-plex
c: the block
'''
b = neighbors(G, a)
b.difference_update(c)
# the strict nodes
subg = G.subgraph(a)
strict_nodes = {node for node in a if nx.degree(subg, node) == len(a)-k }
for node in strict_nodes:
b.intersection_update(G.neighbors(node))
# always reshape by optimal
if cores is None:
b = {node for node in list(b) if nx.degree(G, node) >= len(optimal)-k}
else:
b = {node for node in list(b) if cores[node]>=len(optimal)-k}
# calculate the valid candidates
b = {node for node in b if len(set(G.neighbors(node)).intersection(a)) >= len(a)+1-k }
# sort the candidate list
b = list(b)
# b.sort(key = lambda x: len(set(G.neighbors(x)).intersection(a)), reverse=True)
return b
def leaf_removal(g, verbose=False):
G = g.copy()
stop = 0;
potential_mis = [];
isolated = [x for x in g.nodes() if nx.degree(g,x)==0];
potential_mis.extend(isolated);
G.remove_nodes_from(isolated);
while stop==0:
deg = G.degree();
if 1 in deg.values():
for n in G.nodes_iter():
if deg[n]==1:
L = n;
break;
nn = nx.neighbors(G,L)[0]
G.remove_node(L);
G.remove_node(nn);
potential_mis.append(L);
isolated = [x for x in G.nodes() if nx.degree(G,x)==0];
potential_mis.extend(isolated);
G.remove_nodes_from(isolated);
else:
stop=1;
core_mis = [];
if G.number_of_nodes()>=1:
core_mis = nx.maximal_independent_set(G);
if verbose==True:
print len(potential_mis), len(core_mis), N;
potential_mis.extend(core_mis);
else:
if verbose==True:
print len(potential_mis), len(core_mis), N;
return potential_mis, core_mis;
def __generate_paths(self):
self.__paths = []
graph = copy.deepcopy(self.__graph)
paths = []
if not graph.nodes():
return
start_nodes = [n for n in graph.nodes() if (n.style() != "curve" or (nx.degree(graph, n) == 1))]
start_nodes = sorted(start_nodes, key=lambda n: nx.degree(graph, n))
if start_nodes:
path = [start_nodes[0]]
else:
path = [graph.nodes()[0]]
while path:
neighbors = nx.neighbors(graph, path[-1])
if neighbors:
node = neighbors[0]
graph.remove_edge(path[-1], node)
path.append(node)
else:
paths.append(copy.copy(path))
while path and not graph.neighbors(path[-1]):
path.pop()
for path in paths:
self.__paths.append(reduce_path(path))
return
def nodeMaxDegree(G):
degree=0
for n in G.nodes():
if nx.degree(G,n)> degree :
degree=nx.degree(G,n)
node=n
return node
def _tester():
# think of this like a networkx scratchpad
G = nx.Graph() # this is an undirected graph
G.add_edge(1, 2)
G.add_edge(2, 3)
G.add_node(4)
print nx.degree(G)
print nx.info(G)
def mindeg_GSK(BG, variables_index=0, verbose=False):
Vprime1 = [];
Vprime2 = [];
layer = nx.get_node_attributes(BG,'bipartite');
var = [x for x in BG.nodes() if layer[x] == variables_index]
fac = [x for x in BG.nodes() if layer[x] != variables_index]
if verbose==True:
print 'Initial variable nodes:', var;
print 'Initial factor nodes:', fac;
isolated_variables = [x for x in BG.nodes() if nx.degree(BG,x)==0 and layer[x]==variables_index];
[var.remove(x) for x in isolated_variables]
G = BG.copy();
Vprime1.extend(isolated_variables);
G.remove_nodes_from(isolated_variables)
isolated_factors = [x for x in G.nodes() if nx.degree(BG,x)==0 and layer[x]!=variables_index];
[fac.remove(x) for x in isolated_factors]
G.remove_nodes_from(isolated_factors);
while len(var)>0:
if verbose==True:
print '#var:',len(var),'#fac:', len(fac), '#nodes in depleted graph:', G.number_of_nodes(),'#original BG:',BG.number_of_nodes();
pendant = return_mindeg_pendant(G,layer,variables_index);
if len(pendant)==0:
## if not, choose randomly and do the game.
if verbose==True:
print var
m = G.number_of_nodes()*2;
degs = G.degree();
for e in G.edges():
if degs[e[0]] + degs[e[1]] < m:
m = degs[e[0]] + degs[e[1]];
v = e;
if e[0] in var:
v = e[0];
else:
v = e[1];
pendant = []
pendant.append(v);
pendant.extend(nx.neighbors(G,v));
Vprime2.append(pendant[0]);
else:
Vprime1.append(pendant[0]);
augmented_pendant = []
augmented_pendant.extend(pendant);
for n in pendant[1:]:
augmented_pendant.extend(nx.neighbors(G,n));
augmented_pendant = list(set(augmented_pendant));
G.remove_nodes_from(augmented_pendant);
[var.remove(x) for x in augmented_pendant if x in var];
[fac.remove(x) for x in augmented_pendant if x in fac];
return Vprime1,Vprime2;
def k_dependency_feats(self):
wordindex = self.index + 1
headindex = dep_head_of(self.deptree,wordindex)
D = {}
D["k_dist_to_root"] = len(dep_pathtoroot(self.deptree,wordindex))
D["k_deprel"] = self.deptree[headindex][wordindex]["deprel"]
D["k_headdist"] = abs(headindex - wordindex) # maybe do 0 for root?
D["k_head_degree"] = nx.degree(self.deptree,headindex)
D["k_child_degree"] = nx.degree(self.deptree,wordindex)
return D
def sub_by_degree(min_degree,net):
#return a subset of net by biger than min_degree
remove_node_list = [item for item in nx.degree(net) \
if nx.degree(net)[item] < min_degree]
new_net = nx.Graph()
new_net.add_nodes_from(net.nodes())
new_net.add_edges_from(net.edges())
for name in remove_node_list:
new_net.remove_node(name)
return new_net
def main():
LOG = True
#if (len(sys.argv) != 3):
# print "ERROR: genRandomGeorml <nodes> <raio>"
# sys.exit(1)
NMAX = int(sys.argv[1])
RAIO = float(sys.argv[2])
#NMAX=40
#RAIO=0.1
ALCANCE=250
G=nx.random_geometric_graph(NMAX,RAIO,2)
while not nx.is_connected(G):
RAIO=RAIO+.005
G=nx.random_geometric_graph(NMAX,RAIO,2)
if LOG: print "Graph is not full connected"
pos=nx.get_node_attributes(G,'pos')
network(G,pos,1)
#Remove vizinhos que estejam demasiado perto
while nodeNear(G)<1000 :
G.remove_node(nodeNear(G))
if nx.is_connected(G):
pos=nx.get_node_attributes(G,'pos')
network(G,pos,2)
#Remove no que tem mais vizinhos
T=G
if not nodeSolo(T,nodeMaxDegree(T)): T.remove_node(nodeMaxDegree(T))
if nx.is_connected(T):
G=T
pos=nx.get_node_attributes(G,'pos')
network(G,pos,3)
for n in G.neighbors(nodeMaxDegree(G)):
if nx.degree(G,n)== 2 :
degree=nx.degree(G,n)
node=n
print "node=",n
if not nodeSolo(G,n): G.remove_node(n)
break
pos=nx.get_node_attributes(G,'pos')
network(G,pos,4)
else:
if LOG: print "SubGraph is not full connected"
def remove_by_degree(G, d):
'''
remove nodes by degree
'''
nodes_to_be_delete = [i for i in G.nodes() if nx.degree(G, i) < d]
while len(nodes_to_be_delete) > 0:
print(nodes_to_be_delete)
if 164373 in nodes_to_be_delete:
a = input()
G.remove_nodes_from(nodes_to_be_delete)
nodes_to_be_delete = [i for i in G.nodes() if nx.degree(G, i) < d]
return
def compute_measures(bigDict):
""" Computes the measures for each network
Measures to compute:
nr_of_nodes
nr_of_edges
max_edge_value
min_edge_value
is_connected
number_connected_components
average_unweighted_node_degree
average_weighted_node_degree
average_clustering_coefficient
average_weighted_shortest_path_length
average_unweighted_shortest_path_length
To be added:
single node values, e.g. node degree of brainstem etc.
Non-scalar return values: (not used yet)
degree_distribution
edge_weight_distribution
"""
returnMeasures = {}
for key, netw in bigDict.items():
outm = {}
outm['nr_of_nodes'] = netw.number_of_nodes()
outm['nr_of_edges'] = netw.number_of_edges()
outm['max_edge_value'] = np.max([d['weight']for f,t,d in netw.edges(data=True)])
outm['min_edge_value'] = np.min([d['weight']for f,t,d in netw.edges(data=True)])
outm['is_connected'] = nx.is_connected(netw)
outm['number_connected_components'] = nx.number_connected_components(netw)
outm['average_unweighted_node_degree'] = np.mean(nx.degree(netw, weighted = False).values())
outm['average_weighted_node_degree'] = np.mean(nx.degree(netw, weighted = True).values())
outm['average_clustering_coefficient'] = nx.average_clustering(netw)
outm['average_weighted_shortest_path_length'] = nx.average_shortest_path_length(netw, weighted = True)
outm['average_unweighted_shortest_path_length'] = nx.average_shortest_path_length(netw, weighted = False)
returnMeasures[key] = outm
return returnMeasures
def apply_sifi_surcharge(self): degree_sum = 0 for bank in self.network.contracts: degree_sum += float(nx.degree(self.network.contracts)[bank]) average_degree = float(degree_sum / len(self.network.contracts.nodes())) for bank in self.network.contracts: # the sifi surcharge is the product of the sifiSurchargeFactor and the connectedness as measured # by degree/average_degree # the maximum ensures that no bank has to hold less than 1.0 times their banking capital sifiSurcharge = max(self.get_state(0).sifiSurchargeFactor*( float(nx.degree(self.network.contracts)[bank]) / average_degree), 1.0) bank.apply_sifi_surcharge(sifiSurcharge)
def construct_graph_list_und(graphs_to_const):
"""Construct and return a list of graphs so graph construction is easily
repeatable.
Can handle: Random, Small-world, Scale-free, SGPA, SGPA-random"""
graph_list = []
# Always construct and add Allen Institute mouse brain to list
G_brain = brain_graph.binary_undirected()[0]
graph_list.append(G_brain)
# Calculate degree & clustering coefficient distribution
n_nodes = G_brain.order()
brain_degree = nx.degree(G_brain).values()
brain_degree_mean = np.mean(brain_degree)
# Construct degree controlled random
if 'Random' in graphs_to_const:
G_RAND = und_graphs.random_simple_deg_seq(
sequence=brain_degree, brain_size=BRAIN_SIZE, tries=1000)[0]
graph_list.append(G_RAND)
# Construct small-world graph
if 'Small-world' in graphs_to_const:
graph_list.append(nx.watts_strogatz_graph(
n_nodes, int(round(brain_degree_mean)), SW_REWIRE_PROB))
# Construct scale-free graph
if 'Scale-free' in graphs_to_const:
graph_list.append(nx.barabasi_albert_graph(
n_nodes, int(round(brain_degree_mean / 2.))))
# Construct SGPA graph
if 'SGPA' in graphs_to_const:
G_SGPA = source_growth(bc.num_brain_nodes, bc.num_brain_edges_directed,
L=LENGTH_SCALE)[0]
graph_list.append(G_SGPA.to_undirected())
# Construct degree-controlled SGPA graph
if 'SGPA-random' in graphs_to_const:
SGPA_degree = nx.degree(G_SGPA).values()
G_SGPA_RAND = und_graphs.random_simple_deg_seq(
sequence=SGPA_degree, brain_size=BRAIN_SIZE, tries=1000)[0]
graph_list.append(G_SGPA_RAND)
# Error check that we created correct number of graphs
if len(graph_list) != len(graphs_to_const):
raise RuntimeError('Graph list/names don\'t match')
return graph_list
def make_hist(gnm, sw, rw):
degree_sequence1=sorted(nx.degree(gnm).values(),reverse=True)
degree_sequence2=sorted(nx.degree(sw).values(),reverse=True)
degree_sequence3=sorted(nx.degree(rw).values(),reverse=True)
counts1 = {}
counts2 = {}
counts3 = {}
for i in range(len(degree_sequence1)):
if(i in counts1):
counts1[i] += 1
else: counts1[i] = 1
for i in range(len(degree_sequence2)):
if(i in counts2):
counts2[i] += 1
else: counts2[i] = 1
for i in range(len(degree_sequence3)):
if(i in counts3):
counts3[i] += 1
else: counts3[i] = 1
counts = []
for i in range(len(counts1)):
counts.append(float(counts1[i]))
p1, = plt.loglog(counts,'b-',marker='o')
counts = []
for i in range(len(counts2)):
counts.append(float(counts2[i]))
p2, = plt.loglog(counts,'r-',marker='o')
counts = []
for i in range(len(counts3)):
counts.append(float(counts3[i]))
p3, = plt.loglog(counts,'y-',marker='o')
#p1, = plt.loglog(counts1,'b-',marker='o')
#p2, = plt.loglog(counts2,'r-',marker='o')
#p3, = plt.loglog(counts3,'y-',marker='o')
plt.title("Degree rank plot")
plt.ylabel("degree")
plt.xlabel("rank")
plt.legend([p1, p2, p3], ["Gnm", "Small-World", "Real-World"])
plt.savefig("test3.png")
plt.close()
def findEndpointsBifurcations(self, verbose = False):
"""For the current graph, identify all points that are either
endpoints (1 neighbor) or """+\
"""bifurcation points (3 neighbors)"""
endpoints = []
bifurcations = []
for n in self.cg.nodes_iter():
if( nx.degree(self.cg,n) == 1 ):
endpoints.append(n)
elif( nx.degree(self.cg,n) >= 3 ):
bifurcations.append(n)
self.endpoints[self.currentGraphKey] = endpoints
self.bifurcations[self.currentGraphKey] = bifurcations
def gp(G,edge_pro_dict,node_degree_dict):
Ggp=nx.Graph()
for each_node in G.nodes():
Ggp.add_node(each_node)
edge_pro_order=sorted(edge_pro_dict.iteritems(), key=lambda d:d[1],reverse=True)
for each_edge_order in edge_pro_order:
u=each_edge_order[0][0]
v=each_edge_order[0][1]
discrepency_u=nx.degree(Ggp)[u]-node_degree_dict[u]
discrepency_v=nx.degree(Ggp)[v]-node_degree_dict[v]
if(abs(discrepency_u+1)+abs(discrepency_v+1)<abs(discrepency_u)+abs(discrepency_v)):
Ggp.add_edge(u,v)
return Ggp
def RemoveCore(graph,k=2,anchor=EMPTY_SET):
G = graph.copy()
Gn = FindKCore(G,k,anchor)
for u,v in Gn.edges_iter():
if u != v:
G.remove_edge(u,v)
KC_nodes = set(filter(lambda n: nx.degree(G,n) > 0,Gn.nodes()))
G_small = G.copy()
for n in G.nodes_iter():
if nx.degree(G,n) == 0:
G_small.remove_node(n)
return G, G_small,KC_nodes
def participation_coefficient(graph, partition):
'''
Computes the participation coefficient for each node.
------
Inputs
------
graph = networkx graph
partition = modularity partition of graph
------
Output
------
List of the participation coefficient for each node.
'''
pc_dict = {}
all_nodes = set(graph.nodes())
paths = nx.shortest_path_length(G=graph)
for m in partition.keys():
mod_list = set(partition[m])
between_mod_list = list(set.difference(all_nodes, mod_list))
for source in mod_list:
degree = float(nx.degree(G=graph, nbunch=source))
count = 0
for target in between_mod_list:
if paths[source][target] == 1:
count += 1
bm_degree = count
pc = 1 - (bm_degree / degree)**2
pc_dict[source] = pc
return pc_dict
def give_output_list(self, game): """ This returns a list of the selected nodes. The twin attack player finds the highest degree nodes, and for each, it selects two neighbors of that node and""" nodes = nx.nodes(game.network) nodes.sort(key=lambda x : nx.degree(game.network, x), reverse=True) selections = set() for node in nodes: adjacents = list(nx.all_neighbors(game.network, node)) for adj_node in adjacents[:2]: selections.add(adj_node) if len(selections) == game.num_seeds: break if len(selections) == game.num_seeds: break assert len(selections) == game.num_seeds return list(selections)
def draw_graph(graph2):
plt.clf()
nodes = set([n1 for n1, n2 in graph2] + [n2 for n1, n2 in graph2]) # Extract nodes from graph
G = nx.Graph() # Graph - No Edges
for node in nodes: #Nodes
G.add_node(node)
for edge in graph2: #Edges
G.add_edge(edge[0], edge[1])
pos = nx.spring_layout(G) # Layout settings
nx.draw_networkx_nodes(G,pos,node_size=1500, node_color='w', font_size=6)
nx.draw_networkx_edges(G,pos,alpha=0.75,width=3)
nx.draw_networkx_labels(G,pos, font_color='b')
plt.title('Twitter Hashtag Graph')
plt.axis('off') # Show graph
plt.savefig(".\\images\\graph.png")
# Calculate average degree
average_degree = np.mean(nx.degree(G).values())
ft2 = open(sys.argv[2], 'a') # Write to ft2.txt
if np.isnan(average_degree): # NaN for no hashtags
ft2.write('0.00'+'\n')
else:
aver_deg = format(average_degree, '.2f')
ft2.write(str(aver_deg)+'\n')
ft2.close()
return
def draw_graph(username, password, filename='graph.txt', label_flag=True, remove_isolated=True, different_size=True, iso_level=10, node_size=40):
"""Reading data from file and draw the graph.If not exists, create the file and re-scratch data from net"""
print "Generating graph..."
try:
with open(filename, 'r') as f:
G = p.load(f)
except:
G = getgraph(username, password)
with open(filename, 'w') as f:
p.dump(G, f)
#nx.draw(G)
# Judge whether remove the isolated point from graph
if remove_isolated is True:
H = nx.empty_graph()
for SG in nx.connected_component_subgraphs(G):
if SG.number_of_nodes() > iso_level:
H = nx.union(SG, H)
G = H
# Ajust graph for better presentation
if different_size is True:
L = nx.degree(G)
G.dot_size = {}
for k, v in L.items():
G.dot_size[k] = v
node_size = [G.dot_size[v] * 10 for v in G]
pos = nx.spring_layout(G, iterations=50)
nx.draw_networkx_edges(G, pos, alpha=0.2)
nx.draw_networkx_nodes(G, pos, node_size=node_size, node_color='r', alpha=0.3)
# Judge whether shows label
if label_flag is True:
nx.draw_networkx_labels(G, pos, alpha=0.5)
#nx.draw_graphviz(G)
plt.show()
return G
import networkx as nx
import network_attack as na
graph = nx.erdos_renyi_graph(n=300, p=0.1)
print("the total number of edges:")
n_edges = nx.number_of_edges(graph)
print(n_edges)
print("the total number of nodes:")
n_nodes = nx.number_of_nodes(graph)
print(n_nodes)
n_cc = nx.number_connected_components(graph)
print("the total number of connected components:")
print(n_cc)
print("the density of the graph:")
print(nx.diameter(graph))
avg_deg = sum([d for (n, d) in nx.degree(graph)]) / float(graph.number_of_nodes())
print("the average degree is " + str(avg_deg))
closeness_centrality = nx.closeness_centrality
pagerank_centrality = nx.pagerank
betweenness_centrality = nx.betweenness_centrality
# GCC ATTACK
clo_gcc_att = na.gcc_attack(graph, closeness_centrality)
pgr_gcc_att = na.gcc_attack(graph, pagerank_centrality)
bet_gcc_att = na.gcc_attack(graph, betweenness_centrality)
rnd_gcc = na.rnd_gcc_attack(graph, 1)
na.attack_measures_plot("THe Giant Component Component Size", clo_gcc_att, pgr_gcc_att, bet_gcc_att, rnd_gcc)
# Diameter ATTACK
clo_dia_att = na.diameter_attack(graph, closeness_centrality)
graph.py
import networkx as nx
import matplotlib.pyplot as plt
from random import random
g = nx.read_edgelist('GraphData.txt',create_using=nx.DiGraph(),nodetype=int)
print nx.info(g)
d = nx.degree(g) #for node sizes
colors = [(random(), random(), random()) for _i in range(10)] #for different node colors
nx.draw(g,nx.random_layout(g),with_labels=True,node_size=[v * 300 for v in d.values()], node_color=colors,alpha=0.7)
plt.show()
nx.draw_networkx_nodes(G, pos, alpha = 0.6, node_size = 350)
# edges
nx.draw_networkx_edges(G, pos, edgelist = elarge,
width = 2, alpha = 0.9, edge_color = 'g')
nx.draw_networkx_edges(G, pos, edgelist = emidle,
width = 1.5, alpha = 0.6, edge_color = 'y')
nx.draw_networkx_edges(G, pos, edgelist = esmall,
width = 1, alpha = 0.3, edge_color = 'b', style = 'dashed')
# labels
nx.draw_networkx_labels(G, pos, font_size = 10)
plt.axis('off')
plt.title("《红楼梦》社交网络")
plt.show()
# 计算每个节点的度
Gdegree = nx.degree(G)
Gdegree = dict(Gdegree)
Gdegree = pd.DataFrame({"name": list(Gdegree.keys()),
"degree": list(Gdegree.values())})
Gdegree.sort_values(by = "degree", ascending = False).plot(x = "name",
y = "degree",
kind = "bar",
figsize = (12, 6),
legend = False)
plt.xticks(FontProperties = font, size = 5)
plt.ylabel("degree")
plt.show()
plt.figure(figsize = (12, 12))
# 生成社交网络图
G = nx.Graph()
def Find_CNP(G, mixed_label = False):
#Find all component of G
G_components = list(nx.connected_components(G))
G_temp = G.copy()
edge_cut = []
while len(G_components) != 0:
min_ratioN1 = float('inf')
min_ratioN2 = float('inf')
componentOfG = G.subgraph(G_components[0]).copy() #we get the first component and find cnp
if len(componentOfG.nodes()) <= 3:
del G_components[0]
continue
for v in G_components[0]:
neighbor1 = list(componentOfG.neighbors(v))
neighbor1.extend([v])
induced_N1 = componentOfG.subgraph(neighbor1)
#----------- Clustering Coefficient
length_n1 = len(neighbor1)
length_e1 = len(list(induced_N1.edges()))
if length_n1==1 or length_n1==0:
cc=0
else:
cc = 2*length_e1/(length_n1*(length_n1-1))
#-----Calculating clustering coefficient is finished here!-------
cutRatioN1_V4 = coherentCutRatio_V4(nx.degree(induced_N1),nx.degree(componentOfG,induced_N1.nodes()),cc)
cutRatioN1_V1 = coherentCutRatio_V1(nx.degree(induced_N1),nx.degree(componentOfG,induced_N1.nodes()))
cutRatioN1 = stat.mean([cutRatioN1_V4,cutRatioN1_V1])
if cutRatioN1 < min_ratioN1:
min_ratioN1 = cutRatioN1
#calculate edge cut for this minimum cut ratio
cnp_nodes1 = induced_N1.nodes()
edge_cutN1 = edgeCutSet_V2(induced_N1,componentOfG)
minN1_v4 = cutRatioN1_V4
minN1_v1 = cutRatioN1_V1
#Get neighbor2 for node v
neighbor2 = neighbor1[:]
[neighbor2.extend(list(componentOfG.neighbors(n))) for n in neighbor1]
neighbor2 = list(set(neighbor2))
induced_N2 = componentOfG.subgraph(neighbor2).copy()
induced_N2 = induced_N2.copy()
Complement_indN2 = nx.complement(induced_N2)
if(not nx.is_connected(Complement_indN2)):#we find the CNP
#----------- Clustering Coefficient
length_n2 = len(neighbor2)
length_e2 = len(list(induced_N2.edges()))
if length_n2==1 or length_n2==0:
cc=0
else:
cc = 2*length_e2/(length_n2*(length_n2-1))
#-----Calculating clustering coefficient is finished here!-------
cutRatioN2_V4 = coherentCutRatio_V4(nx.degree(induced_N2),nx.degree(componentOfG,induced_N2.nodes()),cc)
cutRatioN2_V1 = coherentCutRatio_V1(nx.degree(induced_N2),nx.degree(componentOfG,induced_N2.nodes()))
cutRatioN2 = stat.mean([cutRatioN2_V4,cutRatioN2_V1])
if cutRatioN2 < min_ratioN2:
min_ratioN2 = cutRatioN2
#calculate edge cut for this minimum cut ratio
cnp_nodes2 = induced_N2.nodes()
edge_cutN2 = edgeCutSet_V2(induced_N2,componentOfG)
minN2_v4 = cutRatioN2_V4
minN2_v1 = cutRatioN2_V4
else:
cut_node = my_cut_nodes(Complement_indN2, mixed_label)
if (len(cut_node)==0):
print("for node ",v,"removing ",cut_node," is not enough and we need to remove more than K nodes")
return
""""we may find differnt cut_node_set
if we have more than one choose a set with minimum weight"""
if (len(cut_node)>1):
minweight = float('inf')
for n in cut_node:
"""we calculate the score for each set seperately and then choose one with the minimum score"""
temp_N2 = induced_N2.copy()
temp_N2.remove_nodes_from(n)
#----------- Clustering Coefficient
length_n2 = len(temp_N2.nodes())
length_e2 = len(list(temp_N2.edges()))
if length_n2==1 or length_n2==0:
cc=0
else:
cc = 2*length_e2/(length_n2*(length_n2-1))
#-----Calculating clustering coefficient is finished here!-------
cutRatioN2_V4 = coherentCutRatio_V4(nx.degree(temp_N2),nx.degree(componentOfG,temp_N2.nodes()),cc)
cutRatioN2_V1 = coherentCutRatio_V1(nx.degree(temp_N2),nx.degree(componentOfG,temp_N2.nodes()))
temp_score = stat.mean([cutRatioN2_V4,cutRatioN2_V1])
if temp_score < minweight:
minweight = temp_score
minWeightNode = n
cut_node = minWeightNode
else:
#flatten the cut node
cut_node = [node for sublist in cut_node for node in sublist]
induced_N2.remove_nodes_from(cut_node)
#----------- Clustering Coefficient
length_n2 = len(induced_N2.nodes())
length_e2 = len(list(induced_N2.edges()))
if length_n2==1 or length_n2==0:
cc=0
else:
cc = 2*length_e2/(length_n2*(length_n2-1))
#-----Calculating clustering coefficient is finished here!-------
cutRatioN2_V4 = coherentCutRatio_V4(nx.degree(induced_N2),nx.degree(componentOfG,induced_N2.nodes()),cc)
cutRatioN2_V1 = coherentCutRatio_V1(nx.degree(induced_N2),nx.degree(componentOfG,induced_N2.nodes()))
cutRatioN2 = stat.mean([cutRatioN2_V4,cutRatioN2_V1])
if cutRatioN2 < min_ratioN2:
min_ratioN2 = cutRatioN2
#calculate edge cut for this minimum cut ratio
cnp_nodes2 = induced_N2.nodes()
edge_cutN2 = edgeCutSet_V2(induced_N2,componentOfG)
minN2_v4 = cutRatioN2_V4
minN2_v1 = cutRatioN2_V4
if min_ratioN1 < min_ratioN2:
edge_cut.append(edge_cutN1)
cnp_nodes = cnp_nodes1
else:
edge_cut.append(edge_cutN2)
cnp_nodes = cnp_nodes2
G_temp.remove_nodes_from(cnp_nodes)
G_components = list(nx.connected_components(G_temp))
edge_cut = [edge for sublist in edge_cut for edge in sublist]
if not mixed_label:
edge_cut = list(set(tuple(sorted(x)) for x in edge_cut))
else:
sorted_x = []
for i in range(len(edge_cut)):
intList=sorted([i for i in edge_cut[i] if type(i) is int])
strList=sorted([i for i in edge_cut[i] if type(i) is str])
sorted_x.append(intList + strList)
edge_cut = list(set(tuple(i) for i in (sorted_x)))
return(edge_cut)
for asin, metadata in amazonBooks.items():
copurchaseGraph.add_node(asin)
for a in metadata['Copurchased'].split():
copurchaseGraph.add_node(a.strip())
similarity = 0
n1 = set((amazonBooks[asin]['Categories']).split())
n2 = set((amazonBooks[a]['Categories']).split())
n1In2 = n1 & n2
n1Un2 = n1 | n2
if (len(n1Un2)) > 0:
similarity = round(len(n1In2) / len(n1Un2), 2)
copurchaseGraph.add_edge(asin, a.strip(), weight=similarity)
# get degree centrality and clustering coefficients
# of each ASIN and add it to amazonBooks metadata
dc = networkx.degree(copurchaseGraph)
for asin in networkx.nodes(copurchaseGraph):
metadata = amazonBooks[asin]
metadata['DegreeCentrality'] = int(dc[asin])
ego = networkx.ego_graph(copurchaseGraph, asin, radius=1)
metadata['ClusteringCoeff'] = round(networkx.average_clustering(ego), 2)
amazonBooks[asin] = metadata
# write amazonBooks data to file
# (all except copurchase data - becuase that data is now in the graph)
fhw = open('./amazon-books.txt', 'w', encoding='utf-8', errors='ignore')
fhw.write("Id\t" + "ASIN\t" + "Title\t" + "Categories\t" +
"Group\t" #+ "Copurchased\t" +
"SalesRank\t" + "TotalReviews\t" + "AvgRating\t"
"DegreeCentrality\t" + "ClusteringCoeff\n")
for asin, metadata in amazonBooks.items():
def cal_nei_sim(disease, edges, save_nei_sim=False):
print("begin to calculate similarity based on neighbours...")
G = nx.Graph()
G.add_edges_from(edges) # 将多种生物信息构造成异构矩阵
print(
"step 1: epsilon -> 2, calculate first degree sequence and second degree sequence..."
)
DegreeSequence1 = []
DegreeSequence2 = []
for di in disease:
neighboursOne = G.neighbors(di) #获取节点的第一层邻居
degreeOfOne = []
neghboursTwo = []
for indexOfNeighbours in neighboursOne:
degreeOfOne.append(nx.degree(G,
indexOfNeighbours)) #保存第一层邻居的degree
neghboursTwo.extend(G.neighbors(indexOfNeighbours)) #获取第一层邻居节点的邻居
sortedDegreeOfOne = sorted(degreeOfOne) #对第一层邻居的degree进行排序
DegreeSequence1.append(sortedDegreeOfOne)
neghboursTwo = set(neghboursTwo)
neghboursTwo.remove(di) #去除二层邻居节点的自己
degreeOfTwo = []
for indexOfNeighbours in neghboursTwo:
degreeOfTwo.append(nx.degree(G,
indexOfNeighbours)) #保存第二层邻居的degree
sortedDegreeOfTwo = sorted(degreeOfTwo) #对第一层邻居的degree进行排序
DegreeSequence2.append(sortedDegreeOfTwo)
cores = multiprocessing.cpu_count() # 获取计算机CPU数目
pool = multiprocessing.Pool(cores) # 构造一个线程池
print("step 2: compute neighbour_sim in parallel with {} cpus...".format(
cores))
# 构造一个多线程的任务
resultsOne = [
pool.apply_async(dtw_distance_fast,
(DegreeSequence1[i], DegreeSequence1[j]))
for i in range(0, len(DegreeSequence1))
for j in range(i + 1, len(DegreeSequence1))
]
# 将成对的第一层degree sequence计算结果存储到数组中
arrOne = np.zeros((len(DegreeSequence1), len(DegreeSequence1)))
i = 0
j = 1
for r in resultsOne:
if j == len(DegreeSequence1):
i += 1
j = i + 1
arrOne[i][j] = float(r.get())
j += 1
# 构造一个多线程任务
resultsTwo = [
pool.apply_async(dtw_distance_fast,
(DegreeSequence2[i], DegreeSequence2[j]))
for i in range(0, len(DegreeSequence2))
for j in range(i + 1, len(DegreeSequence2))
]
# 将成对的第二层degree sequence计算结果存储到数组中
arrTwo = np.zeros((len(DegreeSequence2), len(DegreeSequence2)))
i = 0
j = 1
for r in resultsTwo:
if j == len(DegreeSequence2):
i += 1
j = i + 1
arrTwo[i][j] = float(r.get())
j += 1
# ----------------------------------------------------------------------------
print("step 3: construct similarity matrix...")
alpha = 0.5 # a decaying weight factor α in the range between 0 and 1
NeiSim = {}
sim_matrix = np.zeros((len(disease), len(disease)))
for i in range(0, len(disease)):
for j in range(i + 1, len(disease)):
distance = math.pow(alpha, 1) * arrOne[i][j] + math.pow(
alpha, 2) * arrTwo[i][j]
NeiSim["{}\t{}".format(disease[i],
disease[j])] = math.exp(-distance)
sim_matrix[i][j] = math.exp(-distance)
sim_matrix[j][i] = math.exp(-distance)
if save_nei_sim:
print("sort the path similarity and save...")
res = sorted(NeiSim.items(), key=lambda x: x[1], reverse=True)
FileUtil.writeSortedDic2File(res, "./nei_Sim.txt")
return sim_matrix
jet_grad = np.linspace(0, 1, 256) # Jet gradient for Old->New
cbar_ax.imshow(np.vstack((jet_grad, jet_grad)), aspect='auto', cmap=cm.jet)
fig.savefig(SAVE_FILE_NAME_IN_OUT, dpi=300)
fig.savefig(SAVE_FILE_NAME_IN_OUT_PNG, dpi=300)
# plot clustering vs degree and nodal efficiency
fig, axs = plt.subplots(1,
2,
figsize=(8, 3.75),
tight_layout=True,
facecolor='white')
cc_full = nx.clustering(G.to_undirected())
deg_full = nx.degree(G.to_undirected())
cc = [cc_full[node] for node in nodes]
deg = [deg_full[node] for node in nodes]
# calculate nodal efficiency
G.efficiency_matrix = metrics_bd.efficiency_matrix(G)
nodal_efficiency = np.sum(G.efficiency_matrix, axis=1) / (len(G.nodes()) - 1)
labels = ('a', 'b')
axs[0].scatter(deg, cc, c=node_ages, cmap=cm.jet, lw=0)
axs[0].set_xlim(0, 150)
axs[0].set_ylim(-0.025, 1.025)
axs[0].set_xlabel('Degree')
axs[0].set_ylabel('Clustering coefficient')
axs[0].locator_params(axis='x', nbins=6)
print(random_node)
print("Executing MHRW...")
sample = MHRW()
sample.mhrw(G, random_node, size)
print("Writing sample network...")
nx.write_edgelist(sample.G1,
"data/JS_sample_network_75.csv",
delimiter=",",
data=False)
G.clear()
G = sample.G1
DG = nx.degree(G)
num_nodes = 0
sum_degree = 0
for i in DG:
num_nodes += 1
sum_degree += i[1]
print("Grau da rede:", sum_degree)
print("Grau médio:", (sum_degree / num_nodes))
print("Nodes:", nx.number_of_nodes(G))
print("Edges:", nx.number_of_edges(G))
print("Density:", nx.density(G))
AC = nx.average_clustering(G)
def _dissolve_adjacent(_target_graph: nx.Graph,
_parent_node_name: str,
_node_group: Union[set, list, tuple],
highest_degree=False) -> nx.Graph:
# set the new centroid from the centroid of the node group's Multipoint:
node_geoms = []
if not highest_degree:
for n_uid in _node_group:
x = _target_graph.nodes[n_uid]['x']
y = _target_graph.nodes[n_uid]['y']
node_geoms.append(geometry.Point(x, y))
# if by highest_degree, then find the centroid of the highest degree nodes
else:
highest_degree = 0
for n_uid in _node_group:
if n_uid in _target_graph:
if nx.degree(_target_graph, n_uid) > highest_degree:
highest_degree = nx.degree(_target_graph, n_uid)
# aggregate the highest degree nodes
node_geoms = []
for n_uid in _node_group:
if n_uid not in _target_graph:
continue
if nx.degree(_target_graph, n_uid) != highest_degree:
continue
x = _target_graph.nodes[n_uid]['x']
y = _target_graph.nodes[n_uid]['y']
# append geom
node_geoms.append(geometry.Point(x, y))
# find the new centroid
c = geometry.MultiPoint(node_geoms).centroid
_target_graph.add_node(_parent_node_name, x=c.x, y=c.y)
# remove old nodes and reassign to new parent node
# first determine new edges
new_edges = []
for uid in _node_group:
for nb_uid in nx.neighbors(_target_graph, uid):
# drop geoms between merged nodes
# watch for self-loop edge cases
if uid in _node_group and nb_uid in _node_group and uid != nb_uid:
continue
else:
if 'geom' not in _target_graph[uid][nb_uid]:
raise KeyError(
f'Missing "geom" attribute for edge {uid}-{nb_uid}')
line_geom = _target_graph[uid][nb_uid]['geom']
if line_geom.type != 'LineString':
raise TypeError(
f'Expecting LineString geometry but found {line_geom.type} geometry for edge {uid}-{nb_uid}.'
)
# first orient geom in correct direction
s_x = _target_graph.nodes[uid]['x']
s_y = _target_graph.nodes[uid]['y']
# check geom coordinates directionality - flip if facing backwards direction
if not np.allclose(
(s_x, s_y), line_geom.coords[0][:2], atol=0.001, rtol=0):
line_geom = geometry.LineString(line_geom.coords[::-1])
# double check that coordinates now face the forwards direction
if not np.allclose(
(s_x, s_y), line_geom.coords[0][:2], atol=0.001, rtol=0):
raise ValueError(
f'Edge geometry endpoint coordinate mismatch for edge {uid}-{nb_uid}'
)
# update geom starting point to new parent node's coordinates
coords = list(line_geom.coords)
coords[0] = (c.x, c.y)
# if self-loop, then the end also needs updating
if uid == nb_uid:
coords[-1] = (c.x, c.y)
target_uid = _parent_node_name
else:
target_uid = nb_uid
new_line_geom = geometry.LineString(coords)
new_edges.append(
(_parent_node_name, target_uid, new_line_geom))
# remove the nodes from the target graph, this will also implicitly drop related edges
_target_graph.remove_nodes_from(_node_group)
# add the edges
for s, e, geom in new_edges:
# when dealing with a collapsed linestring, this should be a rare occurance
if geom.length == 0:
logger.warning(
f'Encountered a geom of length 0m: check edge {s}-{e}.')
continue
# don't add edge duplicates from respectively merged nodes
if (s, e) not in _target_graph.edges():
_target_graph.add_edge(s, e, geom=geom)
# however, do add if substantially different geom...
else:
diff = _target_graph[s][e]['geom'].length / geom.length
if abs(diff) > 1.25:
_target_graph.add_edge(s, e, geom=geom)
return _target_graph
def de_clip(filename, n_nodes, hinge_list, gt_file):
n_iter = 5
f = open(filename)
line1 = f.readline()
print line1
f.close()
extension = filename.split('.')[-1]
if extension == 'graphml':
g = input3(filename)
elif len(line1.split()) != 2:
g = input1(filename)
else:
g = input2(filename)
print nx.info(g)
degree_sequence = sorted(g.degree().values(), reverse=True)
print Counter(degree_sequence)
degree_sequence = sorted(nx.degree(g).values(), reverse=True)
print Counter(degree_sequence)
try:
import ujson
mapping = ujson.load(open(gt_file))
print 'getting mapping'
mapped_nodes = 0
print str(len(mapping))
print str(len(g.nodes()))
for node in g.nodes():
# print node
node_base = node.split("_")[0]
# print node_base
#print node
if mapping.has_key(node_base):
g.node[node]['aln_start'] = min(mapping[node_base][0][0],
mapping[node_base][0][1])
g.node[node]['aln_end'] = max(mapping[node_base][0][1],
mapping[node_base][0][0])
g.node[node]['chr'] = mapping[node_base][0][2]
mapped_nodes += 1
else:
# pass
g.node[node]['aln_start'] = 0
g.node[node]['aln_end'] = 0
g.node[node]['aln_strand'] = 0
for edge in g.edges_iter():
in_node = edge[0]
out_node = edge[1]
# print 'akjdfakjhfakljh'
if ((g.node[in_node]['aln_start'] < g.node[out_node]['aln_start']
and
g.node[out_node]['aln_start'] < g.node[in_node]['aln_end']) or
(g.node[in_node]['aln_start'] < g.node[out_node]['aln_end'] and
g.node[out_node]['aln_end'] < g.node[in_node]['aln_end'])):
g.edge[in_node][out_node]['false_positive'] = 0
else:
g.edge[in_node][out_node]['false_positive'] = 1
except:
raise
# print "json "+filename.split('.')[0]+'.mapping.json'+" not found. exiting."
print hinge_list
print str(mapped_nodes) + " out of " + str(len(
g.nodes())) + " nodes mapped."
# for i in range(5):
# merge_simple_path(g)
# degree_sequence=sorted(nx.degree(g).values(),reverse=True)
# print Counter(degree_sequence)
in_hinges = set()
out_hinges = set()
num_iter = 10000
iter_done = 0
if hinge_list != None:
print "Found hinge list."
with open(hinge_list, 'r') as f:
for lines in f:
lines1 = lines.split()
if lines1[2] == '1':
in_hinges.add(lines1[0] + '_0')
out_hinges.add(lines1[0] + '_1')
elif lines1[2] == '-1':
in_hinges.add(lines1[0] + '_1')
out_hinges.add(lines1[0] + '_0')
print str(len(in_hinges)) + ' hinges found.'
for node in g.nodes():
if node in in_hinges and node in out_hinges:
g.node[node]['hinge'] = 100
elif node in in_hinges:
g.node[node]['hinge'] = 10
elif node in out_hinges:
g.node[node]['hinge'] = -10
else:
g.node[node]['hinge'] = 0
while len(g.nodes()) > n_nodes and iter_done < num_iter:
node = g.nodes()[random.randrange(len(g.nodes()))]
iter_done += 1
# print iter_done
if g.in_degree(node) == 1 and g.out_degree(node) == 1:
base_node = node.split("_")[0]
orintation = node.split("_")[1]
# if orintation=='1':
# node2=base_node+'_0'
# else:
# node2=base_node+'_1'
# print node,node2
in_node = g.in_edges(node)[0][0]
out_node = g.out_edges(node)[0][1]
if g.node[node]['hinge'] == 0 and g.node[in_node][
'hinge'] == 0 and g.node[out_node]['hinge'] == 0:
if g.out_degree(in_node) == 1 and g.in_degree(
out_node) == 1:
if in_node != node and out_node != node and in_node != out_node:
bad_node = False
# print g.in_edges(node)
# print g.edge[g.in_edges(node)[0][0]][g.in_edges(node)[0][1]]
# print g.out_edges(node)
for in_edge in g.in_edges(node):
if g.edge[in_edge[0]][
in_edge[1]]['false_positive'] == 1:
bad_node = True
for out_edge in g.out_edges(node):
if g.edge[out_edge[0]][
out_edge[1]]['false_positive'] == 1:
bad_node = True
if not bad_node:
#print in_node, node, out_node
merge_path(g, in_node, node, out_node)
# print g.edge[edge1[0]][edge1[1]]['hinge_edge']
for nd in g.nodes():
if len(nd.split("_")) == 1:
print nd + " in trouble"
# in_node = g.in_edges(node2)[0][0]
# out_node = g.out_edges(node2)[0][1]
# if g.node[node2]['hinge']==0 and g.node[in_node]['hinge']==0 and g.node[out_node]['hinge']==0:
# if g.out_degree(in_node) == 1 and g.in_degree(out_node) == 1:
# if in_node != node2 and out_node != node2 and in_node != out_node:
# bad_node=False
# for in_edge in g.in_edges(node2):
# if g.edge[in_edge]==1:
# bad_node=True
# for out_edge in g.out_edges(node2):
# if g.edge[out_edge]==1:
# bad_node=True
# if not bad_node:
# #print in_node, node, out_node
# merge_path(g,in_node,node2,out_node)
# for nd in g.nodes():
# print nd
else:
while len(g.nodes()) > n_nodes:
node = g.nodes()[random.randrange(len(g.nodes()))]
if g.in_degree(node) == 1 and g.out_degree(node) == 1:
# assert g.in_degree(node2) == 1 and g.out_degree(node2) == 1
# edge_1 = g.out_edges(node)[0]
# edge_2 = g.in_edges(node)[0]
edge1 = g.out_edges(node)[0]
edge2 = g.in_edges(node)[0]
# print g.edge[edge1[0]][edge1[1]]['hinge_edge']
if (g.edge[edge1[0]][edge1[1]]['hinge_edge'] == -1
and g.edge[edge2[0]][edge2[1]]['hinge_edge'] == -1):
in_node = g.in_edges(node)[0][0]
out_node = g.out_edges(node)[0][1]
if g.out_degree(in_node) == 1 and g.in_degree(
out_node) == 1:
if in_node != node and out_node != node and in_node != out_node:
#print in_node, node, out_node
merge_path(g, in_node, node, out_node)
degree_sequence = sorted(nx.degree(g).values(), reverse=True)
print Counter(degree_sequence)
nx.write_graphml(g, filename.split('.')[0] + '.sparse3.graphml')
print nx.number_weakly_connected_components(g)
print nx.number_strongly_connected_components(g)
def calculate_preferential_bias_on_node(network, node):
return (float((nx.degree(network, node) + 1)) / (
float(sum(nx.degree(network).values()) + nx.number_of_nodes(network))))
def main():
event_data = np.genfromtxt('data/events_US_air_traffic_GMT.txt',
names=True,
dtype=int)
event_data.sort(order=['StartTime'])
network = nx.read_weighted_edgelist(
'data/aggregated_US_air_traffic_network_undir.edg')
n_nodes = network.number_of_nodes()
# creation of bins for the plots
min_timestemp = min(event_data, key=lambda item: item["StartTime"])[2]
max_timestemp = max(event_data, key=lambda item: item["EndTime"])[3]
n_bins = 50
bins = create_bins(min_timestemp, max_timestemp, n_bins)
######################################
# task 1 #
######################################
print("-------------- TASK 1 --------------")
infection_times, infection_list = infection_time(event_data, 1, 0)
print("Node 41 infection time: " + str(infection_times['41']) + " (" +
str(datetime.fromtimestamp(infection_times['41'])) + ")")
# animation of the infection
# visualize_si(np.array(infection_list), save_fname="./simulations/infection_simulation_prob1_seed0.mp4")
######################################
# task 2 #
######################################
print("-------------- TASK 2 --------------")
seed_node = 0
infection_prob = [0.01, 0.05, 0.1, 0.5, 1.0]
infection_times_list_avg = []
infection_times_list_probs = []
for prob in infection_prob:
for i in range(10):
_, infection_list = infection_time(event_data, prob, seed_node)
infection_times_list_avg.append(infection_list)
infection_times_list_probs.append(infection_times_list_avg)
infection_times_list_avg = []
plot_avg_prevalence_probs(infection_times_list_probs, infection_prob,
n_nodes, bins)
######################################
# task 3 #
######################################
print("-------------- TASK 3 --------------")
infection_prob = 0.1
seed_nodes = [0, 4, 41, 100, 200]
seed_nodes_labels = ['ABE', 'ATL', 'ACN', 'HSV', 'DBQ']
infection_times_list_avg = []
infection_times_list_nodes = []
for seed_node in seed_nodes:
for i in range(10):
_, infection_list = infection_time(event_data, infection_prob,
seed_node)
infection_times_list_avg.append(infection_list)
infection_times_list_nodes.append(infection_times_list_avg)
infection_times_list_avg = []
plot_avg_prevalence_nodes(infection_times_list_nodes, seed_nodes_labels,
n_nodes, bins)
######################################
# task 4 #
######################################
print("-------------- TASK 4 --------------")
# ----- task 4 and 5 ----- #
clustering_coefficient_net = nx.clustering(network)
degree_net = nx.degree(network)
strength_net = nx.degree(network, weight="weight")
betweenness_centrality_net = nx.betweenness_centrality(network)
# ------------------------ #
infection_prob = 0.5
infection_times_list = []
for i in range(50):
seed_node = random.randint(0, n_nodes)
infection_times, _ = infection_time(event_data, infection_prob,
seed_node)
infection_times_list.append(infection_times)
infection_times_df = pd.DataFrame(infection_times_list)
infection_times_median = dict(infection_times_df.median())
plot_and_spearman_task4(infection_times_median, clustering_coefficient_net,
degree_net, strength_net,
betweenness_centrality_net, n_nodes)
######################################
# task 5 #
######################################
print("-------------- TASK 5 --------------")
# nodes immunized
imm_neighbour = []
range_nodes = set(range(0, n_nodes))
while len(imm_neighbour) < 10:
rand_node = random.choice(list(range_nodes))
rand_neighbour = random.choice(list(network.neighbors(str(rand_node))))
if (int(rand_neighbour) not in imm_neighbour):
imm_neighbour.append(int(rand_neighbour))
imm_random_node = []
range_nodes = set(range(0, n_nodes))
for i in range(10):
rand_node = random.choice(list(range_nodes))
imm_random_node.append(rand_node)
range_nodes.remove(rand_node)
imm_clustering_coefficient = []
d = Counter(clustering_coefficient_net)
for k, _ in d.most_common(10):
imm_clustering_coefficient.append(int(k))
imm_degree = []
highest_degree = sorted(degree_net, key=lambda x: x[1], reverse=True)[:10]
for k, _ in highest_degree:
imm_degree.append(int(k))
imm_strength = []
highest_strength = sorted(strength_net, key=lambda x: x[1],
reverse=True)[:10]
for k, _ in highest_strength:
imm_strength.append(int(k))
imm_betweenness_centrality = []
d = Counter(betweenness_centrality_net)
for k, _ in d.most_common(10):
imm_betweenness_centrality.append(int(k))
# create a set of all the immunized nodes
imm_nodes = set(imm_neighbour) | set(imm_random_node) | set(
imm_clustering_coefficient) | set(imm_degree) | set(
imm_strength) | set(imm_betweenness_centrality)
range_seed = set(range(0, n_nodes)) - imm_nodes
# extract the seed nodes from a set of nodes not part of the immunized ones
seed_nodes = []
for i in range(20):
rand_seed = random.choice(list(range_seed))
seed_nodes.append(rand_seed)
range_seed.remove(rand_seed)
immunized_nodes_list = []
immunized_nodes_list.append(imm_neighbour)
immunized_nodes_list.append(imm_random_node)
immunized_nodes_list.append(imm_clustering_coefficient)
immunized_nodes_list.append(imm_degree)
immunized_nodes_list.append(imm_strength)
immunized_nodes_list.append(imm_betweenness_centrality)
immunization_strategy_labels = [
'random neighbour', 'random node', 'clustering coefficient', 'degree',
'strength', 'betweenness centrality'
]
infection_prob = 0.5
infection_times_list_avg = []
infection_times_list_immunization = []
for immunized_nodes, imm_strategy in zip(immunized_nodes_list,
immunization_strategy_labels):
print("Calculating " + imm_strategy)
for seed_node in seed_nodes:
_, infection_list = infection_time(event_data, infection_prob,
seed_node, immunized_nodes)
infection_times_list_avg.append(infection_list)
infection_times_list_immunization.append(infection_times_list_avg)
infection_times_list_avg = []
plot_avg_prevalence_immunization(infection_times_list_immunization,
immunization_strategy_labels, n_nodes,
bins)
######################################
# task 6 #
######################################
print("-------------- TASK 6 --------------")
id_data = np.genfromtxt('data/US_airport_id_info.csv',
delimiter=',',
dtype=None,
names=True,
encoding=None)
xycoords = {}
for row in id_data:
xycoords[str(row['id'])] = (row['xcoordviz'], row['ycoordviz'])
edge_list = []
for edge in network.edges():
if int(edge[0]) > int(edge[1]):
edge = (edge[1], edge[0])
edge_list.append(edge) # edge_list created to maintain the right order
infection_prob = 0.5
infecting_edges_fraction = []
for i in range(20):
seed_node = random.randint(0, n_nodes)
infecting_edges = infection_edges(event_data, infection_prob,
seed_node, edge_list)
infecting_edges_fraction.append(infecting_edges)
# calculation of the fraction of times that each link is used for infecting the disease from the results of 20 runs
infecting_edges_fraction = (np.sum(np.array(infecting_edges_fraction), 0) /
20).tolist()
# print Transmission links - fraction
fig, ax = plot_network_usa(network,
xycoords,
edges=edge_list,
linewidths=infecting_edges_fraction)
plt.suptitle(r'Transmission links ($f_{ij}$)')
fig.savefig("./plots/t6_map_fraction.pdf")
# print Transmission links - mst
maximum_spanning_tree = nx.maximum_spanning_tree(network)
fig, ax = plot_network_usa(maximum_spanning_tree,
xycoords,
edges=list(maximum_spanning_tree.edges))
plt.suptitle(r'Transmission links (maximal spanning tree)')
fig.savefig("./plots/t6_map_mst.pdf")
link_weights = nx.get_edge_attributes(network, 'weight')
link_betweenness_centrality = nx.edge_betweenness_centrality(network)
# ordered lists (following the order of edge_list)
link_weights_list = []
link_betweenness_centrality_list = []
for edge in edge_list:
if edge in link_weights:
link_weights_list.append(link_weights[edge])
else:
link_weights_list.append(link_weights[(edge[1], edge[0])])
if edge in link_betweenness_centrality:
link_betweenness_centrality_list.append(
link_betweenness_centrality[edge])
else:
link_betweenness_centrality_list.append(
link_betweenness_centrality[(edge[1], edge[0])])
# scatter plot of the transmission fraction as a function of the link weight
fig, ax = plot_scatterplot(link_weights_list, infecting_edges_fraction)
plt.suptitle(r'Transmission fraction as a function of the link weight')
ax.set_xlabel(r'link weight $w_{ij}$')
ax.set_ylabel(r'transmission fraction $f_{ij}$')
fig.savefig("./plots/t6_scatter_weight.pdf")
# scatter plot of the transmission fraction as a function of the link betweenness centrality
fig, ax = plot_scatterplot(link_betweenness_centrality_list,
infecting_edges_fraction)
plt.suptitle(
r'Transmission fraction as a function of the link betweenness centrality'
)
ax.set_xlabel(r'unweighted link betweenness centrality $eb_{ij}$')
ax.set_ylabel(r'transmission fraction $f_{ij}$')
fig.savefig("./plots/t6_scatter_bet_centr.pdf")
# Spearman rank-correlation coefficient
print(
"Spearman rank-correlation coefficient between transmission fraction and: "
)
print("- link weight: " + str(
spearmanr(link_weights_list, infecting_edges_fraction).correlation))
print("- betweenness centrality: " + str(
spearmanr(link_betweenness_centrality_list,
infecting_edges_fraction).correlation))
#print(most_corelated_taxon[i][0], most_corelated_taxon[j][0])
if not G.has_edge(i + 1, j + 1):
G.add_edge(i + 1, j + 1)
#print(scipy.stats.spearmanr(predicted_data.loc[:, most_corelated_taxon[i][0]], predicted_data.loc[:,most_corelated_taxon[j][0]])[1],
# scipy.stats.spearmanr(predicted_data.loc[:, most_corelated_taxon[i][0]],
# predicted_data.loc[:, most_corelated_taxon[j][0]])[0])
#nx.draw(G, with_labels = True)
#print(nx.connected_components(G))
#print(nx.degree(G))
#print(sorted(i[1] for i in nx.degree(G)))
#print(nx.clustering(G))
#plt.show()
#print(G)
rel_dict = []
for i in nx.degree(G):
#if i[1] != 0:
print(i)
print(labeldict[i[0]])
rel_dict.append(labeldict[i[0]])
new_data = preproccessed_data[rel_dict]
#visualize_pca(new_data)
otu_after_pca, _ = apply_pca(new_data, n_components=2)
merged_data = otu_after_pca.join(OtuMf.mapping_file['DiagnosisGroup'])
merged_data.fillna(0)
mapping_disease_for_labels = {
'Control': 0,
'Cirrhosis/HCC': 1,
for node in nx.nodes(G):
for tup in G.node[node]['conferences']:
try:
if tup[0] != conf:
G2a.remove_node(node)
except:
continue
print("Done!")
# In[28]:
nx.info(G2a)
# In[41]:
'''Compute the degree for nodes which is the number of edges each node has.'''
dg_values = list(nx.degree(G2a))
# In[55]:
print(min(dg_values))
print(max(dg_values))
# In[44]:
#Degree histogram
sns.set_style("darkgrid")
sns.set_context({"figure.figsize": (6, 4)})
fig, ax = plt.subplots()
sns.distplot(dg_values, color="dodgerblue", bins=8, hist=True, kde=False)
plt.xlabel("Degree", fontsize=12)
plt.ylabel("Node frequences", fontsize=12)
def process(graph):
if (not isinstance(graph, networkx.Graph)):
raise ValueError(
"invalid object; must be a NetworkX Graph class or subclass")
if (isinstance(graph, networkx.DiGraph)):
node_to_neighbors = lambda node: graph.successors(
node) + graph.predecessors(node)
else:
node_to_neighbors = lambda node: graph.neighbors(node)
node_to_degree = networkx.degree(graph)
# phase 1: node assignment
node_to_row, row_to_node = {}, []
def node_to_row_(node):
if (node in node_to_row):
return node_to_row[node]
row_idx = len(node_to_row)
node_to_row[node] = row_idx
row_to_node.append(node)
return row_idx
while True:
# find the node with highest degree that has not been assigned a row
hub, hub_degree = _key_with_max_value(node_to_degree, node_to_row)
if (hub == None):
break
# add it as a new row
node_to_row_(hub)
# list its direct neighbors by decreasing degree
hub_neighbors = reversed(
sorted(node_to_neighbors(hub),
key=lambda node: node_to_degree[node]))
# add them as new rows, if not assigned already
for node in hub_neighbors:
node_to_row_(node)
assert len(node_to_row) == graph.number_of_nodes() ###
# phase 2: edge assignment
edge_to_col, col_to_edge = {}, []
def edge_to_col_(edge):
if (edge in edge_to_col):
return edge_to_col[edge]
if (_order(*edge) in edge_to_col):
return edge_to_col[_order(*edge)]
edge_idx = len(edge_to_col)
edge_to_col[edge] = edge_idx
col_to_edge.append(edge)
return edge_idx
min_col, max_col = {}, {}
for i, node_a in enumerate(row_to_node):
for node_b in row_to_node[i + 1:]:
if graph.has_edge(node_a, node_b):
edge_idx = edge_to_col_((node_a, node_b))
for node in (node_a, node_b):
min_col[node] = min(min_col.get(node, POS_INF), edge_idx)
max_col[node] = max(max_col.get(node, NEG_INF), edge_idx)
assert len(edge_to_col) == graph.number_of_edges() ###
return (row_to_node, node_to_row), (col_to_edge,
edge_to_col), min_col, max_col
def select_observers(network, strategy, proportion=0.1, tread_off=0.1):
"""
:param network:
:param strategy:
"max_degree":
"min_degree":
"max_k_shell":
"min_k_shell":
"max_betweenness":
"min_betweenness":
"max_closeness":
"min_closeness":
"random":
:param proportion: percentage of observers
:param tread_off: mix strategy of max_degree and min_degree
:return:
"""
observer_nodes_size = int(nx.number_of_nodes(G=network) * proportion)
observers = []
if strategy == "max_degree":
degree_dict = dict(nx.degree(network))
degree_sorted_by_value = sorted(degree_dict.items(),
key=lambda x: x[1],
reverse=True)
observers = [x[0]
for x in degree_sorted_by_value][:observer_nodes_size]
elif strategy == "min_degree":
degree_dict = dict(nx.degree(network))
degree_sorted_by_value = sorted(degree_dict.items(),
key=lambda x: x[1])
observers = [x[0]
for x in degree_sorted_by_value][:observer_nodes_size]
elif strategy == "max_k_shell":
k_core_dict = dict(nx.core_number(G=network))
k_core_sorted = sorted(k_core_dict.items(),
key=lambda x: x[1],
reverse=True)
observers = [x[0] for x in k_core_sorted][:observer_nodes_size]
elif strategy == "min_k_shell":
k_core_dict = dict(nx.core_number(G=network))
k_core_sorted = sorted(k_core_dict.items(), key=lambda x: x[1])
observers = [x[0] for x in k_core_sorted][:observer_nodes_size]
elif strategy == "max_betweenness":
between_centrality = dict(nx.betweenness_centrality(G=network))
between_centrality_stored = sorted(between_centrality.items(),
key=lambda x: x[1],
reverse=True)
observers = [x[0]
for x in between_centrality_stored][:observer_nodes_size]
elif strategy == "min_betweenness":
between_centrality = dict(nx.betweenness_centrality(G=network))
between_centrality_stored = sorted(between_centrality.items(),
key=lambda x: x[1])
observers = [x[0]
for x in between_centrality_stored][:observer_nodes_size]
elif strategy == "max_closeness":
closeness_centrality = dict(nx.closeness_centrality(G=network))
closeness_centrality_stored = sorted(closeness_centrality.items(),
key=lambda x: x[1],
reverse=True)
observers = [x[0] for x in closeness_centrality_stored
][:observer_nodes_size]
elif strategy == "min_closeness":
closeness_centrality = dict(nx.closeness_centrality(G=network))
closeness_centrality_stored = sorted(closeness_centrality.items(),
key=lambda x: x[1])
observers = [x[0] for x in closeness_centrality_stored
][:observer_nodes_size]
elif strategy == "random":
observers = np.random.randint(0, nx.number_of_nodes(network),
observer_nodes_size)
return observers
def fullSizeGraph(request):
import pandas as pd
import networkx
import matplotlib.pyplot as plt
import numpy as np
df_enron = filterDataByTime(pd.read_csv(request,
request.FILES['csv_data']))
#from bokeh.io import output_notebook, show, save
from bokeh.models import Range1d, Circle, ColumnDataSource, MultiLine
from bokeh.plotting import figure
from bokeh.models.graphs import from_networkx
from bokeh.palettes import Category10
from bokeh.transform import linear_cmap
from bokeh.embed import json_item
#output_notebook() #remove this when not using notebook
G = networkx.from_pandas_edgelist(df_enron,
'fromId',
'toId',
edge_attr=True)
di = {
'CEO': 1,
'Director': 2,
'Employee': 3,
'In House Lawyer': 4,
'Manager': 5,
'Managing Director': 6,
'President': 7,
'Trader': 8,
'Unknown': 9,
'Vice President': 10
}
df_rejob = df_enron.replace({"fromJobtitle": di})
df_attributes = df_enron[['fromId', 'fromJobtitle']].drop_duplicates()
df_attributes.columns = ['fromId', 'job']
df_attributesx = df_rejob[['fromId', 'fromJobtitle']].drop_duplicates()
job = df_attributes.set_index('fromId').to_dict('i')
jobx = df_attributesx.set_index('fromId').to_dict('i')
networkx.set_node_attributes(G, job)
networkx.set_node_attributes(G, jobx)
#jobs = ['Employee','Vice President','Unknown','Manager','CEO','Trader','Director','President','Managing Director','In House Lawyer']
degrees = dict(networkx.degree(G))
networkx.set_node_attributes(G, name='degree', values=degrees)
adjusted_node_size = dict([(node, (degree + 5) - ((degree + 5) * 0.3))
for node, degree in networkx.degree(G)])
networkx.set_node_attributes(G,
name='adjusted_node_size',
values=adjusted_node_size)
size_by_this_attribute = 'adjusted_node_size'
color_by_this_attribute = 'fromJobtitle'
color_palette = Category10[10]
TOOLTIPS = [
("Person ID", "@index"),
("people communicated with", "@degree"),
("Jobtitle", "@job"),
]
plot = figure(tooltips=TOOLTIPS,
tools="pan,zoom_in,wheel_zoom,save,reset,box_select,undo",
active_scroll='wheel_zoom',
x_range=Range1d(-20, 20),
y_range=Range1d(-20, 20),
title='Enron Emails',
plot_width=950,
plot_height=950)
plot.axis.visible = False
N_graph = from_networkx(G, networkx.spring_layout, scale=100)
N_graph.node_renderer.glyph = Circle(size=size_by_this_attribute,
fill_color=linear_cmap(
color_by_this_attribute,
color_palette, 1, 10))
N_graph.edge_renderer.glyph = MultiLine(line_alpha=10, line_width=1)
plot.renderers.append(N_graph)
item_text = json.dumps(json_item(plot))
return django.http.JsonResponse(item_text, safe=False)
def make_interactive_network(G,
labels=False,
title='My Network',
color_palette=Blues8,
node_size='degree',
node_color='modularity_class'):
from networkx.algorithms import community
# Get network info
degrees = dict(networkx.degree(G))
networkx.set_node_attributes(G, name='degree', values=degrees)
betweenness_centrality = networkx.betweenness_centrality(G)
networkx.set_node_attributes(G,
name='betweenness',
values=betweenness_centrality)
communities = community.greedy_modularity_communities(G)
# Create empty dictionaries
modularity_color = {}
modularity_class = {}
#Loop through each community in the network
for community_number, community in enumerate(communities):
#For each member of the community, add their community number and a distinct color
for name in community:
modularity_color[name] = Spectral8[community_number]
modularity_class[name] = community_number
networkx.set_node_attributes(G, modularity_color, 'modularity_color')
networkx.set_node_attributes(G, modularity_class, 'modularity_class')
#Choose colors for node and edge highlighting
node_highlight_color = node_color
edge_highlight_color = 'black'
#Choose attributes from G network to size and color by — setting manual size (e.g. 10) or color (e.g. 'skyblue') also allowed
#Pick a color palette — Blues8, Reds8, Purples8, Oranges8, Viridis8
#color_palette = Blues8
#Choose a title!
title = title
#Establish which categories will appear when hovering over each node
HOVER_TOOLTIPS = [
("Character", "@index"),
("Degree", "@degree"),
("Modularity Class", "@modularity_class"),
("Modularity Color", "$color[swatch]:modularity_color"),
]
#Create a plot — set dimensions, toolbar, and title
plot = figure(tooltips=HOVER_TOOLTIPS,
tools="pan,wheel_zoom,save,reset",
active_scroll='wheel_zoom',
x_range=Range1d(-10.1, 10.1),
y_range=Range1d(-10.1, 10.1),
title=title)
#Create a network graph object
# https://networkx.github.io/documentation/networkx-1.9/reference/generated/networkx.drawing.layout.spring_layout.html
network_graph = from_networkx(G,
networkx.spring_layout,
scale=10,
center=(0, 0))
#Set node sizes and colors according to node degree (color as category from attribute)
if node_color == 'degree':
#Set node sizes and colors according to node degree (color as spectrum of color palette)
minimum_value_color = min(
network_graph.node_renderer.data_source.data[node_color])
maximum_value_color = max(
network_graph.node_renderer.data_source.data[node_color])
network_graph.node_renderer.glyph = Circle(
size=node_size,
fill_color=linear_cmap(node_color, color_palette,
minimum_value_color, maximum_value_color))
elif node_color == 'modularity_color':
#node_color='modularity_color'
network_graph.node_renderer.glyph = Circle(size=node_size,
fill_color=node_color)
#Set node highlight colors
network_graph.node_renderer.hover_glyph = Circle(
size=node_size, fill_color=node_highlight_color, line_width=2)
network_graph.node_renderer.selection_glyph = Circle(
size=node_size, fill_color=node_highlight_color, line_width=2)
#Set edge opacity and width
network_graph.edge_renderer.glyph = MultiLine(line_alpha=0.3, line_width=1)
#Set edge highlight colors
network_graph.edge_renderer.selection_glyph = MultiLine(
line_color=edge_highlight_color, line_width=2)
network_graph.edge_renderer.hover_glyph = MultiLine(
line_color=edge_highlight_color, line_width=2)
#Highlight nodes and edges
network_graph.selection_policy = NodesAndLinkedEdges()
network_graph.inspection_policy = NodesAndLinkedEdges()
plot.renderers.append(network_graph)
if labels == True:
#Add Labels
x, y = zip(*network_graph.layout_provider.graph_layout.values())
node_labels = list(G.nodes())
source = ColumnDataSource({
'x':
x,
'y':
y,
'name': [node_labels[i] for i in range(len(x))]
})
labels = LabelSet(x='x',
y='y',
text='name',
source=source,
background_fill_color='white',
text_font_size='10px',
background_fill_alpha=.7)
plot.renderers.append(labels)
show(plot)
#save(plot, filename=f"{title}.html")
def build(Time, dis, window, in_case):
location = '/Users/Abduljaleel/Desktop/project/USA/' + Time + '/' + dis + '/'
location_Time = '/Users/Abduljaleel/Desktop/project/USA/' + Time + '/'
st = open(location_Time + 'log_where.txt', 'a')
st.write(str(dis + '_' + Time) + '\n')
db = '/Users/Abduljaleel/Desktop/project/USA/SQLite/USA_' + dis
ddb = sqlite3.connect(db)
cc = ddb.cursor()
cc.execute("SELECT * FROM NODES order by date")
ddb.commit()
results = cc.fetchall()
all = len(results)
limit_1 = firstdate(ddb, cc)
window_time = add_time(limit_1, window)
limit_2 = add_time(limit_1, in_case)
last_tweet_date = lastdate(ddb, cc)
start = time.time()
w = 1
while True:
cc.execute("select * from nodes where date between " + str(limit_1) +
" and " + str(limit_2) + " order by date")
ddb.commit()
rs = cc.fetchall()
aa = []
for i in range(0, len(rs)):
aa.append(rs[i][0])
# w = loop(Net1,aa,w)
w = fib3.loop(Net1, aa, w)
limit_2 = add_time(limit_2, in_case)
if limit_2 > window_time:
break
limit_1 = next_event(limit_1, ddb, cc)
w = 1
while True:
cc.execute("select * from nodes where date between " + str(limit_1) +
" and " + str(limit_2) + " order by date")
ddb.commit()
rs = cc.fetchall()
aa = []
try:
d = int(rs[0][0])
e = float(d * 100) / all
print int(e)
except:
pr = 1
for i in range(0, len(rs)):
aa.append(rs[i][0])
# w = loop(Net1,aa,w)
w = fib3.loop(Net1, aa, w)
limit_1 = add_time(limit_1, in_case)
limit_2 = add_time(limit_1, window)
if limit_1 >= last_tweet_date:
break
print 'finish creating'
threshold = w * 0.79
H = nx.Graph([(u, v, d) for (u, v, d) in Net1.edges_iter(data=True)
if d['weight'] > threshold])
print '------degree start------'
deg = open(location + 'degree.txt', 'w')
DD = open(location + 'DD.txt', 'w')
data = []
DDD = H.degree()
for s in DDD:
deg.write(str(nx.degree(H, s)) + "\n")
data.append(nx.degree(H, s))
for i in range(0, max(data)):
j = i + 1
count = 0
for k in range(0, len(data)):
if data[k] == j:
count += 1
DD.write(str(j) + '\t' + str(count) + '\n')
print '------degree finsished------'
# st = open(location+'statistics.txt', 'a')
# print 'cluster start'
# cluster = nx.average_clustering(Net2)
# print 'pl start'
# pl = Net22.average_path_length()
# n=0
# summ=0
# for g in nx.connected_component_subgraphs(Net2):
# summ+=float(nx.average_shortest_path_length(g))
# n+=1
# summ = float(summ)/n
# st.write('cluster :'+str(cluster)+'\n')
# st.write('path_Len :'+str(summ)+'\n')
print '------Writing Graphml start------'
nx.write_graphml(H, location + dis + "_graph.graphml")
sts = open(location_Time + 'log_sec.txt', 'a')
end = time.time() - start
sts.write(str(dis + '_' + Time) + '\t' + str(end) + '\n')
def read_a_graph(path):
print path
type = str(path[-4:])
onlyfiles = [f for f in listdir(path) if isfile(join(path, f))]
# print onlyfiles
all_graphs = {}
for f in onlyfiles:
G = nx.read_edgelist(path + '/' + f, delimiter=" ")
print "---------" + f + "----------"
print "BEFORE"
print "nodes:", len(G)
print "edges:", G.number_of_edges()
if G.has_node('-1'):
G.remove_node('-1')
print "AFTER"
print "nodes:", len(G)
print "edges:", G.number_of_edges()
if G.number_of_edges() >= (len(G) / 4):
print "TAKE THIS ONE: ", "-", type, "-", f
###########CHECK HOW MANY ACCOUNTS OF OUR LIST IS IN THE TWEET CHAIN##########
involved = []
if type == "fake":
accounts = fake_accounts
else:
accounts = real_accounts
for node in G.nodes():
if int(node) in accounts:
involved.append(int(node))
print "INVOLVED USERS:", len(involved)
print involved
#######################################################
density = nx.density(G)
degree = nx.degree(G)
bc = nx.betweenness_centrality(G)
cc = nx.closeness_centrality(G)
graph = {"density": density, "degree": degree, "bc": bc, "cc": cc}
all_graphs[f] = graph
print "--------------------------"
# plt.title(f)
# nx.draw(G)
# plt.show()
# print all_graphs
for g in all_graphs:
print g
cc_low = []
cc_mid = []
cc_high = []
bc_low = []
bc_mid = []
bc_high = []
degree_low = []
degree_mid = []
degree_high = []
list_of_nodes = []
for n in all_graphs[g]['cc']:
list_of_nodes.append(n.encode("utf-8"))
# for every characteristic split in 4
for char in all_graphs[g]:
if char is not 'density':
low, mid, high = get_four_split(char, all_graphs[g][char])
if char is 'cc':
cc_low = low
cc_mid = mid
cc_high = high
elif char is 'bc':
bc_low = low
bc_mid = mid
bc_high = high
elif char is 'degree':
degree_low = low
degree_mid = mid
degree_high = high
classified = []
for n in list_of_nodes:
if n in get_a_list_of_the_first_of_a_tuple(
cc_low) and n in get_a_list_of_the_first_of_a_tuple(
degree_high):
classified.append((n, "A"))
elif n in get_a_list_of_the_first_of_a_tuple(
degree_high) and n in get_a_list_of_the_first_of_a_tuple(
bc_low):
classified.append((n, "B"))
elif n in get_a_list_of_the_first_of_a_tuple(
cc_high) and n in get_a_list_of_the_first_of_a_tuple(
degree_low):
classified.append((n, "C"))
elif n in get_a_list_of_the_first_of_a_tuple(
cc_high) and n in get_a_list_of_the_first_of_a_tuple(
bc_low):
classified.append((n, "D"))
elif n in get_a_list_of_the_first_of_a_tuple(
bc_high) and n in get_a_list_of_the_first_of_a_tuple(
degree_low):
classified.append((n, "E"))
elif n in get_a_list_of_the_first_of_a_tuple(
bc_high) and n in get_a_list_of_the_first_of_a_tuple(
cc_low):
classified.append((n, "F"))
elif n in get_a_list_of_the_first_of_a_tuple(bc_high):
classified.append((n, "G"))
else:
classified.append((n, "-"))
with open(g + ".txt", "w") as text_file:
for n in classified:
print n
text_file.write(str(n) + '\n')
print "______________________________"
counter = 0
sum = 0
for g in all_graphs:
sum = all_graphs[g]['density']
counter = counter + 1
avg = sum / counter
print "average density is", avg
def get_link_measures(net):
"""
Compute weights and edges betweenness centralities
:param net: network
:return: w: list of weights
eb: list of edge betweeenness centralities
"""
w, eb, eb_w, eb_w2, eb_pr, eb_cl, eb_ev, eb_s = [], [], [], [], [], [], [], []
# Edge weight and unweighted betweenness centrality
edges = net.edges(data=True)
betweenness_centr = nx.edge_betweenness_centrality(net, normalized=True)
for e in edges:
w.append(e[2]['weight'])
eb.append(betweenness_centr[(e[0], e[1])])
# Create a copy of the graph with inverse weights, square root is used to reduce the impact of high weights
net1 = net.copy()
edges1 = net1.edges(data=True)
for e in edges1:
w_e = e[2]['weight']
net1[e[0]][e[1]]['weight'] = 1 / (w_e**(1 / 3))
# Weighted betweenness centrality on net1
betweenness_centr_w = nx.edge_betweenness_centrality(net1,
normalized=True,
weight='weight')
for e in edges1:
eb_w.append(betweenness_centr_w[(e[0], e[1])])
# Node dictionary for k-shells
dict_k_shell = {}
max_degree = max([net.degree(n) for n in net.nodes])
for k in reversed(range(max_degree + 1)):
k_shell = nx.k_shell(net1, k=k)
k_shell_nodes = k_shell.nodes()
for i in k_shell_nodes:
if i not in dict_k_shell:
dict_k_shell[i] = k
# node dict for pagerank
dict_page_rank = nx.pagerank(net1, weight='weight')
# closeness centrality
closeness_centr = nx.closeness_centrality(net, distance='weight')
closeness_centr = dict(
sorted(closeness_centr.items(),
key=lambda pair: list(nodes).index(pair[0])))
# eigenvector centrality
eigenvector_centr = nx.eigenvector_centrality(net,
tol=10**-1,
weight='weight')
eigenvector_centr = dict(
sorted(eigenvector_centr.items(),
key=lambda pair: list(nodes).index(pair[0])))
# strengths of nodes
strengths = dict(nx.degree(net1, weight='weight'))
# For each edge, take lower value of centrality measureof the two nodes and use it to normalize previously
# computed weighted betweenness
j = 0
for e in edges:
eb_w2.append(eb_w[j] / min(dict_k_shell[e[0]], dict_k_shell[e[1]]))
eb_pr.append(eb_w[j] / min(dict_page_rank[e[0]], dict_page_rank[e[1]]))
eb_cl.append(eb_w[j] /
min(closeness_centr[e[0]], closeness_centr[e[1]]))
eb_ev.append(eb_w[j] /
min(eigenvector_centr[e[0]], eigenvector_centr[e[1]]))
eb_s.append(eb_w[j] / min(strengths[e[0]], strengths[e[1]]))
j = j + 1
return w, eb, eb_w, eb_w2, eb_pr, eb_cl, eb_ev, eb_s
import networkx as nx
import matplotlib.pyplot as plt
from examples.drawing.plot_edge_colormap import colors
n = 10 # 10 nodes
m = 20 # 20 edges
G = nx.gnm_random_graph(n, m)
# some properties
print("node degree clustering")
for v in nx.nodes(G):
print('%s %d %f' % (v, nx.degree(G, v), nx.clustering(G, v)))
# print the adjacency list
print("print the adjacency list")
for line in nx.generate_adjlist(G):
print(line)
nx.draw(G, node_size=250, with_labels=True)
plt.show()
# %%
with open('direct_conections_df.pkl', 'rb') as file:
data = pickle.load(file)
Conexiones = pd.DataFrame(data)
Conex_1 = Conexiones.iloc[0:200, 0:6]
# %%
G = nx.from_pandas_edgelist(Conex_1,
source='p_cty_code',
target='d_cty_code',
create_using=nx.DiGraph())
from matplotlib.pyplot import figure
figure(figsize=(12, 9))
#nx.draw_shell(G,with_labels=True)
#nx.draw_circular(G)
nx.degree(G)
#si quisieramos crear otro df que muestre los nodos y su numero de conexiones usamos:
conexion = {}
for x in G.nodes:
conexion[x] = len(G[x])
s = pd.Series(conexion, name='Conexiones')
df2 = s.to_frame().sort_values('Conexiones', ascending=False)
#%%
# Density
nx.density(G)
# Clustering
nx.clustering(G)
# Similar al comando anterior
for i in nx.clustering(G).items():
def most_similar_result_with_newwork(self, data_size, topn):
print(' -> creating most similar job matrix with network')
df = pd.DataFrame()
G = nx.karate_club_graph()
i = 0
keys_list = list(self.doc2idx.keys())
nodes = [] ## node list
edges = [] ## edge list(튜플의 형태로 저장)
for job_id in keys_list:
node_id = str(job_id).split('_')[2]
job_id = 'Job_ID_' + str(job_id).split('_')[2]
title = self.get_job_title(job_id)[0]
title = f'{title}({str(job_id)})'
similar_jobs = self.model.docvecs.most_similar(job_id,
topn=len(keys_list))
sim_list = []
for sim_job_id, score in similar_jobs:
if score >= 0.8:
nodes.append(node_id) ## node list
sim_job_titles = self.get_job_title(sim_job_id)[0]
sim_job_id = sim_job_id.split('_')[2]
input = f'{sim_job_titles}({sim_job_id})'
sim_list.append(input)
temp_tuple = (node_id, sim_job_id, score)
edges.append(temp_tuple)
else:
sim_list.append('')
i = i + 1
df.loc[:, title] = pd.Series(sim_list)
df.to_csv(self.model_path + self.data_name + '_sim_title_result.csv',
mode='w',
encoding='utf-8')
nodes = set(nodes)
nodes = list(nodes)
print(len(nodes))
print(nodes[:])
print(edges[:])
G.add_nodes_from(nodes)
G.add_weighted_edges_from(edges)
degree = nx.degree(G)
print(degree)
plt.figure(figsize=(20, 10))
graph_pos = nx.spring_layout(G, k=0.42, iterations=17)
nx.draw_networkx_labels(G,
graph_pos,
font_size=10,
font_family='sans-serif')
# nx.draw_networkx_nodes(G, graph_pos, node_size=[ var * 50 for var in degree], cmap='jet')
nx.draw_networkx_edges(G, graph_pos, edge_color='gray')
nx.draw(G,
node_size=[100 + v[1] * 100 for v in degree],
with_labels=True)
plt.show()
return df
@author: samic
"""
import networkx as nx
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
#block = pd.read_csv('block1.csv')
#block = pd.read_csv('block2.csv')
#block = pd.read_csv('block3.csv')
block = pd.read_csv('block4.csv')
block.drop(block.columns[[1]], axis=1, inplace=True)
toGraph = block.stack().reset_index()
del block
toGraph.columns = ['var1', 'var2', 'value']
toGraph_filtered = toGraph.loc[(toGraph['value'] > .8)
& (toGraph['var1'] != toGraph['var2'])]
G = nx.from_pandas_edgelist(toGraph_filtered, 'var1', 'var2')
#g = nx.draw(G, node_size=10)
# centrality
dictNodes = nx.eigenvector_centrality(G, max_iter=1000)
deg = nx.degree(G)
#sys.exit(1)
# basic graphs checks
small_graph = Gp.networkx_graph(data_vertices, data_adjacency)
big_graph = Gp.networkx_graph(struct_vertices, struct_adjacency)
Gp.check_graphs_size(small_graph, big_graph)
Gp.check_graphs_labels(small_graph, big_graph)
print "Basic NOE graph analysis:\n"
print "N (nodes, NOE graph) = ", len(small_graph.nodes())
print "N (edges, NOE graph) = ", len(small_graph.edges())
print "N (nodes, PDB graph) = ", len(big_graph.nodes())
print "N (edge, PDB graph) = ", len(big_graph.edges())
print "NOE sparsity >> ", len(small_graph.edges()) / float(
len(big_graph.edges()))
print "average degree >> ", np.mean(nx.degree(small_graph).values())
print "median degree >>", np.median(nx.degree(small_graph).values())
return data_vertices, data_adjacency, struct_vertices, struct_adjacency
def subgraph_isomorphism(self, noe_vertices, noe_adjacency,
structure_vertices, structure_adjacency, Gp, tag):
graph_noe, graph_noe_indexing = Gp.igraph_graph(
noe_vertices, noe_adjacency)
graph_structure, graph_structure_indexing = Gp.igraph_graph(
structure_vertices, structure_adjacency)
EP = IgraphSubIso(
) # instance of a class for subgraph isomorphism check and extraction
start_vf2 = time.time(
) # measure how long it takes for subgraph isomorphism to be evaluated
def bethe_hessian_matrix(G, r=None, nodelist=None):
r"""Returns the Bethe Hessian matrix of G.
The Bethe Hessian is a family of matrices parametrized by r, defined as
H(r) = (r^2 - 1) I - r A + D where A is the adjacency matrix, D is the
diagonal matrix of node degrees, and I is the identify matrix. It is equal
to the graph laplacian when the regularizer r = 1.
The default choice of regularizer should be the ratio [2]
.. math::
r_m = \left(\sum k_i \right)^{-1}\left(\sum k_i^2 \right) - 1
Parameters
----------
G : Graph
A NetworkX graph
r : float
Regularizer parameter
nodelist : list, optional
The rows and columns are ordered according to the nodes in nodelist.
If nodelist is None, then the ordering is produced by G.nodes().
Returns
-------
H : scipy.sparse.csr_matrix
The Bethe Hessian matrix of G, with paramter r.
Examples
--------
>>> k = [3, 2, 2, 1, 0]
>>> G = nx.havel_hakimi_graph(k)
>>> H = nx.modularity_matrix(G)
See Also
--------
bethe_hessian_spectrum
adjacency_matrix
laplacian_matrix
References
----------
.. [1] A. Saade, F. Krzakala and L. Zdeborová
"Spectral clustering of graphs with the bethe hessian",
Advances in Neural Information Processing Systems. 2014.
.. [2] C. M. Lee, E. Levina
"Estimating the number of communities in networks by spectral methods"
arXiv:1507.00827, 2015.
"""
import scipy as sp
import scipy.sparse # call as sp.sparse
if nodelist is None:
nodelist = list(G)
if r is None:
r = sum(d**2
for v, d in nx.degree(G)) / sum(d for v, d in nx.degree(G)) - 1
A = nx.to_scipy_sparse_array(G, nodelist=nodelist, format="csr")
n, m = A.shape
# TODO: Rm csr_array wrapper when spdiags array creation becomes available
D = sp.sparse.csr_array(
sp.sparse.spdiags(A.sum(axis=1), 0, m, n, format="csr"))
# TODO: Rm csr_array wrapper when eye array creation becomes available
I = sp.sparse.csr_array(sp.sparse.eye(m, n, format="csr"))
import warnings
warnings.warn(
"bethe_hessian_matrix will return a scipy.sparse array instead of a matrix in Networkx 3.0",
FutureWarning,
stacklevel=2,
)
# TODO: Remove the csr_matrix wrapper in NetworkX 3.0
return sp.sparse.csr_matrix((r**2 - 1) * I - r * A + D)
# ------ 网络挖掘 ------
# 通常我们分析的数据是以网络结构存储的，我们可以使用点和边描述之间的关系
# 本章中我们将会介绍分析此类数据的基本步骤，称为图论，一个帮助我们创造、处理和研究网络的类库
# 尤其我们将会介绍如何使用特定方法建立有意义的数据可视化，以及如何建立一组关联稠密的点
# 使用图论可以让我们很容易的导入用于描述数据结构的最常用结构
import networkx as nx
G = nx.read_gml("/Users/liding/E/Bdata/ptemp/liding/lesmiserables.gml") # networkx 必须要下载 1.9.1 版本才行
# 在上述代码我们导入了《悲惨世界》同时出现的单词组成的网络，可以通过https://gephi.org/datasets/lesmiserables.gml.zip免费
# 下载，数据以GML格式存储。我们还可以使用下面的命令导入并可视化网络：
nx.draw(G, node_size=0, edge_color="b", alpha=.2, font_size=7)
import igraph.test
#链接度
deg = nx.degree(G)
from numpy import percentile, mean, median
print min(deg.values())
print percentile(deg.values(),25) # computes the 1st quartile
print median(deg.values())
print percentile(deg.values(),75) # computes the 3rd quartile
print max(deg.values())10
#挑选连接度大于10的案例
Gt = G.copy()
dn = nx.degree(Gt)
for n in Gt.nodes():
if dn[n] <= 10:
Gt.remove_node(n)
nx.draw(Gt,node_size=0,edge_color='b',alpha=.2,font_size=12)
def nX_remove_filler_nodes(networkX_graph: nx.Graph) -> nx.Graph:
if not isinstance(networkX_graph, nx.Graph):
raise TypeError('This method requires an undirected networkX graph.')
logger.info(f'Removing filler nodes.')
g_copy = networkX_graph.copy()
removed_nodes = set()
def manual_weld(_G, _start_node, _geom_a, _geom_b):
s_x = _G.nodes[_start_node]['x']
s_y = _G.nodes[_start_node]['y']
# check geom coordinates directionality - flip to wind in same direction
# i.e. _geom_a should start at _start_node whereas _geom_b should end at _start_node
if not np.allclose(
(s_x, s_y), _geom_a.coords[0][:2], atol=0.001, rtol=0):
_geom_a = geometry.LineString(_geom_a.coords[::-1])
if not np.allclose(
(s_x, s_y), _geom_b.coords[-1][:2], atol=0.001, rtol=0):
_geom_b = geometry.LineString(_geom_b.coords[::-1])
# now concatenate
_new_agg_geom = geometry.LineString(
list(_geom_a.coords) + list(_geom_b.coords))
# check
assert np.allclose(_new_agg_geom.coords[0], (s_x, s_y),
atol=0.001,
rtol=0)
assert np.allclose(_new_agg_geom.coords[-1], (s_x, s_y),
atol=0.001,
rtol=0)
return _new_agg_geom
def recursive_weld(_G, start_node, agg_geom, agg_del_nodes, curr_node,
next_node):
# if the next node has a degree of 2, then follow the chain
# for disconnected components, check that the next node is not back at the start node...
if nx.degree(_G, next_node) == 2 and next_node != start_node:
# next node becomes new current
_new_curr = next_node
# add next node to delete list
agg_del_nodes.append(next_node)
# get its neighbours
_a, _b = list(nx.neighbors(networkX_graph, next_node))
# proceed to the new_next node
if _a == curr_node:
_new_next = _b
else:
_new_next = _a
# get the geom and weld
if 'geom' not in _G[_new_curr][_new_next]:
raise KeyError(
f'Missing "geom" attribute for edge {_new_curr}-{_new_next}'
)
new_geom = _G[_new_curr][_new_next]['geom']
if new_geom.type != 'LineString':
raise TypeError(
f'Expecting LineString geometry but found {new_geom.type} geometry.'
)
# when welding an isolated circular component, the ops linemerge will potentially weld onto the wrong end
# i.e. start-side instead of end-side... so orient and merge manually
if _new_next == start_node:
_new_agg_geom = manual_weld(_G, start_node, new_geom, agg_geom)
else:
_new_agg_geom = ops.linemerge([agg_geom, new_geom])
if _new_agg_geom.type != 'LineString':
raise TypeError(
f'Found {_new_agg_geom.type} geometry instead of "LineString" for new geom {_new_agg_geom.wkt}.'
f'Check that the adjacent LineStrings in the vicinity of {curr_node}-{next_node} are not corrupted.'
)
return recursive_weld(_G, start_node, _new_agg_geom, agg_del_nodes,
_new_curr, _new_next)
else:
end_node = next_node
return agg_geom, agg_del_nodes, end_node
# iterate the nodes and weld edges where encountering simple intersections
# use the original graph so as to write changes to new graph
for n in tqdm(networkX_graph.nodes(), disable=checks.quiet_mode):
# some nodes will already have been removed via recursive function
if n in removed_nodes:
continue
if nx.degree(networkX_graph, n) == 2:
# get neighbours and geoms either side
nb_a, nb_b = list(nx.neighbors(networkX_graph, n))
# geom A
if 'geom' not in networkX_graph[n][nb_a]:
raise KeyError(f'Missing "geom" attribute for edge {n}-{nb_a}')
geom_a = networkX_graph[n][nb_a]['geom']
if geom_a.type != 'LineString':
raise TypeError(
f'Expecting LineString geometry but found {geom_a.type} geometry.'
)
# start the A direction recursive weld
agg_geom_a, agg_del_nodes_a, end_node_a = recursive_weld(
networkX_graph, n, geom_a, [], n, nb_a)
# only follow geom B if geom A doesn't return an isolated (disconnected) looping component
# e.g. circular disconnected walkway
if end_node_a == n:
logger.warning(
f'Disconnected looping component encountered around {n}')
# in this case, do not remove the starting node because it suspends the loop
g_copy.remove_nodes_from(agg_del_nodes_a)
removed_nodes.update(agg_del_nodes_a)
g_copy.add_edge(n, n, geom=agg_geom_a)
continue
# geom B
if 'geom' not in networkX_graph[n][nb_b]:
raise KeyError(f'Missing "geom" attribute for edge {n}-{nb_b}')
geom_b = networkX_graph[n][nb_b]['geom']
if geom_b.type != 'LineString':
raise TypeError(
f'Expecting LineString geometry but found {geom_b.type} geometry.'
)
# start the B direction recursive weld
agg_geom_b, agg_del_nodes_b, end_node_b = recursive_weld(
networkX_graph, n, geom_b, [], n, nb_b)
# remove old nodes - edges are removed implicitly
agg_del_nodes = agg_del_nodes_a + agg_del_nodes_b
# also remove origin node n
agg_del_nodes.append(n)
g_copy.remove_nodes_from(agg_del_nodes)
removed_nodes.update(agg_del_nodes)
# merge the lines
# disconnected self-loops are caught above per geom a, i.e. where the whole loop is degree == 2
# however, lollipop scenarios are not, so weld manually
# lollipop scenarios are where a looping component (all degrees == 2) suspends off a node with degree > 2
if end_node_a == end_node_b:
merged_line = manual_weld(networkX_graph, end_node_a,
agg_geom_a, agg_geom_b)
else:
merged_line = ops.linemerge([agg_geom_a, agg_geom_b])
# run checks
if merged_line.type != 'LineString':
raise TypeError(
f'Found {merged_line.type} geometry instead of "LineString" for new geom {merged_line.wkt}. '
f'Check that the adjacent LineStrings for {nb_a}-{n} and {n}-{nb_b} actually touch.'
)
# add new edge
g_copy.add_edge(end_node_a, end_node_b, geom=merged_line)
return g_copy
try:
E[rA, rB] += 1
E[rB, rA] += 1
except KeyError:
E[rA, rB] = 1
E[rB, rA] = 1
if rA and rB:
try:
N.edge[rA][rB]['fweight'] += data['occurrence']
N.edge[rA][rB]['weight'] += 1
except KeyError:
N.add_edge(rA, rB, fweight=data['occurrence'], weight=1)
write_gml(N, 'networks/rimes.gml')
deg = nx.degree(N, weight='weight')
with open('stats/rime_degree.tsv', 'w') as f:
f.write('Rime\tDegree\n')
for n,w in sorted(deg.items(), key=lambda x: x[1], reverse=True):
f.write(n+'\t'+str(w)+'\n')
with open('stats/edges_rimes.tsv', 'w') as f:
f.write('RimeA\tRimeB\tOccurrence\n')
for (a,b),c in sorted(E.items(), key=lambda x: x[1], reverse=True):
f.write(a+'\t'+b+'\t'+str(c)+'\n')
if 'triples' in argv:
triples = []
visited = []
# make subgraph consisting only of nrj-cases
for nA,dA in G.nodes(data=True):
