def cluster_sp():
similaritymatrix = get_matrix("datasets/similaritymatrix.csv")
graph = add_graph(similaritymatrix, 1000)
dendo = get_dendrogram(graph)
bestpartition = best_partition(graph)
result = dictionaries_to_dataframe(bestpartition, dendo[0], 'SP ID',
'State', 'City')
result.to_csv('datasets/result.csv', sep=',', index=False)
cities_graph = community.induced_graph(dendo[0],
graph).edges(data='weight')
list_to_csv(cities_graph, 'cities_graph.csv')
states_graph = community.induced_graph(bestpartition,
graph).edges(data='weight')
list_to_csv(states_graph, 'states_graph.csv')
def makeCommunityInducedGraph(graph, partition, weight=True):
"""
Get Community Induced Graph of the partition
"""
induced_subgraph = None
if weight == True:
induced_subgraph = community.induced_graph(partition,
graph,
weight='weight')
else:
induced_subgraph = community.induced_graph(partition,
graph,
weight=None)
return induced_subgraph
def test_weight(self):
"""
Test that total edge weight does not change
"""
graph = nx.erdos_renyi_graph(50, 0.1)
part = dict([])
for node in graph.nodes():
part[node] = node % 5
self.assertEqual(graph.size(weight='weight'),
co.induced_graph(part, graph).size(weight='weight'))
for e1, e2 in graph.edges_iter():
graph[e1][e2]["test_weight"] = 2.
self.assertEqual(graph.size(weight='test_weight'),
co.induced_graph(part, graph, "test_weight").size(weight='test_weight'))
def plot_community_graph(graph,
partition,
figsize=(8, 8),
node_size=200,
plot_overlaps=False,
plot_labels=False,
cmap=None,
top_k=None,
min_size=None):
"""
Plot a algorithms-graph with node color coding for communities.
:param graph: NetworkX/igraph graph
:param partition: NodeClustering object
:param figsize: the figure size; it is a pair of float, default (8, 8)
:param node_size: int, default 200
:param plot_overlaps: bool, default False. Flag to control if multiple algorithms memberships are plotted.
:param plot_labels: bool, default False. Flag to control if node labels are plotted.
:param cmap: str or Matplotlib colormap, Colormap(Matplotlib colormap) for mapping intensities of nodes. If set to None, original colormap is used..
:param top_k: int, Show the top K influential communities. If set to zero or negative value indicates all.
:param min_size: int, Exclude communities below the specified minimum size.
Example:
>>> from cdlib import algorithms, viz
>>> import networkx as nx
>>> g = nx.karate_club_graph()
>>> coms = algorithms.louvain(g)
>>> viz.plot_community_graph(g, coms)
"""
cms = __filter(partition.communities, top_k, min_size)
node_to_com = {}
for cid, com in enumerate(cms):
for node in com:
if node not in node_to_com:
node_to_com[node] = cid
else:
# duplicating overlapped node
alias = "%s_%s" % (node, cid)
node_to_com[alias] = cid
edges = [(alias, y) for y in graph.neighbors(node)]
graph.add_edges_from(edges)
# handling partial coverage
s = nx.subgraph(graph, node_to_com.keys())
# algorithms graph construction
c_graph = induced_graph(node_to_com, s)
node_cms = [[node] for node in c_graph.nodes()]
return plot_network_clusters(c_graph,
NodeClustering(node_cms, None, ""),
nx.spring_layout(c_graph),
figsize=figsize,
node_size=node_size,
plot_overlaps=plot_overlaps,
plot_labels=plot_labels,
cmap=cmap)
def external_ec_coarsening(graph, sfdp_path, coarsening_scheme = 2, c_type = 'original'):
if c_type == 'louvain':
print("Coarsening with Louvain")
matrix = magicgraph.to_adjacency_matrix(graph)
nx_graph = nx.from_scipy_sparse_matrix(matrix)
dendro = community.generate_dendrogram(nx_graph)
coarse_graphs = [DoubleWeightedDiGraph(graph)]
merges = []
i = 0
for l in range(len(dendro)):
level = community.partition_at_level(dendro, l)
induced = community.induced_graph(level, nx_graph)
filename = 'induced'+str(l)+'.edgelist'
#nx.write_edgelist(induced, filename)
# write weighted graph to file
f = open(filename, 'w')
for u, v, a in induced.edges.data('weight', default = 1):
line = ' '.join([str(u), str(v), str(a)])
f.write(line + '\n')
f.close()
m_graph = magicgraph.load_weighted_edgelist(filename, undirected = True)
coarse_graphs.append(DoubleWeightedDiGraph(m_graph))
merges.append(level)
print('Level: ', i, 'N nodes: ', m_graph.number_of_nodes())
i+= 1
return coarse_graphs, merges
elif c_type == 'original':
return original_coarsening(graph, sfdp_path, coarsening_scheme)
def calc_louvain(adj_matrix, level=0, return_c_graph=False):
nx_G = nx.from_numpy_matrix(adj_matrix)
dendro = louvain.generate_dendrogram(
nx_G, randomize=False) #Maybe set tandomize True
if len(dendro) - level - 1 < 0:
raise Exception("The given Level is too deep. The maximum is: " +
str(len(dendro) - 1))
communities = louvain.partition_at_level(dendro, len(dendro) - level - 1)
number_communities = max(communities, key=lambda x: communities[x]) + 1
# Maybe unnecessary after some code rework and unification
community_list = []
for i in range(number_communities):
grp_list = []
for grp in communities:
if communities[grp] == i:
grp_list.append(grp)
else:
if grp_list:
community_list.append(grp_list)
community_level_G = louvain.induced_graph(communities, nx_G)
if return_c_graph:
c_level_graph = nx.adjacency_matrix(community_level_G)
else:
c_level_graph = None
return community_list, c_level_graph
def test_weight(self):
"""
Test that total edge weight does not change
"""
graph = nx.erdos_renyi_graph(50, 0.1)
part = dict([])
for node in graph.nodes():
part[node] = node % 5
self.assertEqual(graph.size(weight='weight'),
co.induced_graph(part, graph).size(weight='weight'))
for src, dst in graph.edges_iter():
graph[src][dst]["test_weight"] = 2.
induced = co.induced_graph(part, graph, "test_weight")
self.assertEqual(graph.size(weight='test_weight'),
induced.size(weight='test_weight'))
def test_nodes(self) :
"""
Test that result nodes are the communities
"""
g = nx.erdos_renyi_graph(50, 0.1)
part = dict([])
for node in g.nodes() :
part[node] = node % 5
self.assertSetEqual(set(part.values()), set(co.induced_graph(part, g).nodes()))
def test_weight(self) :
"""
Test that total edge weight does not change
"""
g = nx.erdos_renyi_graph(50, 0.1)
part = dict([])
for node in g.nodes() :
part[node] = node % 5
self.assertEqual(g.size(weight = 'weight'), co.induced_graph(part, g).size(weight = 'weight'))
def test_weight(self):
"""
Test that total edge weight does not change
"""
graph = nx.erdos_renyi_graph(50, 0.1)
part = dict([])
for node in graph.nodes():
part[node] = node % 5
self.assertEqual(graph.size(weight='weight'),
co.induced_graph(part, graph).size(weight='weight'))
for e1, e2 in graph.edges():
graph[e1][e2]["test_weight"] = 2.
self.assertEqual(
graph.size(weight='test_weight'),
co.induced_graph(part, graph,
"test_weight").size(weight='test_weight'))
def ppl(diary):
# make people-event DataFrame
ppl_evt = diary[['Event', 'Participants']].dropna(subset=['Participants'])
evtXie = pd.DataFrame({
"Event": ppl_evt['Event'].unique(),
"Participants": "謝蘭生"
})
ppl_evt = ppl_evt.append(evtXie, ignore_index=True)
# make edgelist from people-event DF
el = ppl_evt.merge(ppl_evt, on="Event")
el = el.drop("Event", axis=1).rename(columns={
"Participants_x": "Source",
"Participants_y": "Target"
})
el = el.query("Source<Target")
el["Weight"] = 1
# Calculate Weight of edges with Groupby
edgelist = el.groupby(["Source", "Target"]).sum().reset_index()
# export edges into a graphml file
G = nx.from_pandas_dataframe(edgelist,
source="Source",
target="Target",
edge_attr="Weight")
nx.set_node_attributes(G, "k-core", nx.core_number(G))
communityDict = community.best_partition(G)
nx.set_node_attributes(G, "community", communityDict)
nx.set_node_attributes(
G, "betweenness",
nx.betweenness_centrality(G, 850, normalized=True, weight="Weight"))
nx.write_graphml(G, "Graph/Network/ppl.graphml", encoding="utf-8")
# export a graph of the relationship between communities
G_commun = community.induced_graph(communityDict, G)
nx.write_graphml(G_commun,
"Graph/Network/pplCommunity.graphml",
encoding="utf-8")
# export nodes with attributes into a csv
idx, attr = zip(*G.nodes(data=True))
core = [d['k-core'] for d in attr]
commun = [d['community'] for d in attr]
betwn = [d['betweenness'] for d in attr]
nodes_attr = pd.DataFrame(
{
'k-core': core,
'community': commun,
'betweenness centrality': betwn
},
index=idx)
nodes_attr.to_csv("csv/pplCoreCommunity.csv", encoding='utf-8')
return
def test_unique(self):
"""
Test that the induced graph is the same when all nodes are alone
"""
graph = nx.erdos_renyi_graph(50, 0.1)
part = dict([])
for node in graph.nodes():
part[node] = node
ind = co.induced_graph(part, graph)
self.assertTrue(nx.is_isomorphic(graph, ind))
def test_weight(self):
"""
Test that total edge weight does not change
"""
g = nx.erdos_renyi_graph(50, 0.1)
part = dict([])
for node in g.nodes():
part[node] = node % 5
self.assertEqual(g.size(weight='weight'),
co.induced_graph(part, g).size(weight='weight'))
def test_uniq(self) :
"""
Test that the induced graph is the same when all nodes are alone
"""
g = nx.erdos_renyi_graph(50, 0.1)
part = dict([])
for node in g.nodes() :
part[node] = node
ind = co.induced_graph(part, g)
self.assert_(nx.is_isomorphic(g, ind))
def test_nodes(self):
"""
Test that result nodes are the communities
"""
graph = nx.erdos_renyi_graph(50, 0.1)
part = dict([])
for node in graph.nodes():
part[node] = node % 5
self.assertSetEqual(set(part.values()),
set(co.induced_graph(part, graph).nodes()))
def plot_community_graph(graph,
partition,
figsize=(8, 8),
node_size=200,
plot_overlaps=False,
plot_labels=False):
"""
Plot a algorithms-graph with node color coding for communities.
:param graph: NetworkX/igraph graph
:param partition: NodeClustering object
:param figsize: the figure size; it is a pair of float, default (8, 8)
:param node_size: int, default 200
:param plot_overlaps: bool, default False. Flag to control if multiple algorithms memberships are plotted.
:param plot_labels: bool, default False. Flag to control if node labels are plotted.
Example:
>>> from cdlib import algorithms, viz
>>> import networkx as nx
>>> g = nx.karate_club_graph()
>>> coms = algorithms.louvain(g)
>>> viz.plot_community_graph(g, coms)
"""
cms = partition.communities
node_to_com = {}
for cid, com in enumerate(cms):
for node in com:
if node not in node_to_com:
node_to_com[node] = cid
else:
# duplicating overlapped node
alias = "%s_%s" % (node, cid)
node_to_com[alias] = cid
edges = [(alias, y) for y in graph.neighbors(node)]
graph.add_edges_from(edges)
# handling partial coverage
s = nx.subgraph(graph, node_to_com.keys())
# algorithms graph construction
c_graph = induced_graph(node_to_com, s)
node_cms = [[node] for node in c_graph.nodes()]
return plot_network_clusters(c_graph,
NodeClustering(node_cms, None, ""),
nx.spring_layout(c_graph),
figsize=figsize,
node_size=node_size,
plot_overlaps=plot_overlaps,
plot_labels=plot_labels)
def setup(g, num_players, num_seeds):
#first compute the best partition
partition = community.best_partition(g)
induced_graph = community.induced_graph(partition, g)
# Play around with picking the "best" community
# node boundary?
#print nx.current_flow_closeness_centrality(induced_graph) # not better
# print nx.katz_centrality(induced_graph) # doesn't converge
#print nx.eigenvector_centrality(induced_graph) # not as good
#print nx.communicability_centrality(induced_graph) # not as good
#{0: 8.451771641899612, 1: 9.041654401534407, 2: 9.321830560246685, 3: 8.79634625159723, 4: 7.512000387517644, 5: 9.319261339431147, 6: 8.635502364748598, 7: 9.182167514276696, 8: 8.812816793986622, 9: 5.955242238035001, 10: 7.224124906314186, 11: 8.598864555204745, 12: 1.3780813983087927, 13: 8.574141188778002, 14: 1.4894068385674029}
#{0: 0.03170498456257798, 1: 0.03351885293616147, 2: 0.982004394865475, 3: 0.009750044520081363, 4: 0.012642119637055598, 5: 0.08211419419246402, 6: 0.013202397926046897, 7: 0.15814666928657686, 8: 0.026268239793024895, 9: 0.0005523351650465954, 10: 0.0009839216844465231, 11: 0.019821817113884598, 12: 4.399697547690089e-05, 13: 0.016495461620553098, 14: 0.00022120782918811697}
#{0: 1670.2226290285078, 1: 3648.298186716118, 2: 4153.05229512053, 3: 3214.282455755265, 4: 561.0349179323383, 5: 4068.320908838754, 6: 2977.2760610270666, 7: 3474.488922208751, 8: 3493.8811964338947, 9: 1521.5720949300896, 10: 2520.2823105797784, 11: 1385.0884502097147, 12: 281.6674672972596, 13: 2306.8136315883607, 14: 358.98207498678886}
# viewer.draw_graph(induced_graph)
# try:
# plt.show()
# except:
# plt.hide()
# Choose the community with the most number of outgoing edges
#weights = nx.communicability_centrality(induced_graph) #weight='weight'
weights = nx.degree(induced_graph, weight='weight')
#print weights
best_com = max(weights, key=weights.__getitem__)
com = defaultdict(list)
for node, c in partition.iteritems():
com[c].append(node)
selected_comm = g.subgraph(com[best_com])
# get one node from every clique
#print selected_comm.number_of_nodes()
# max_size_clique = nx.graph_clique_number(selected_comm)
# print max_size_clique
# lst = []
# for cl in nx.find_cliques(selected_comm):
# if len(cl) >= max_size_clique/2:
# lst.append(r.choice(cl))
# #return cl
# #print len(cl), cl
# return lst
#print nx.find_cliques(selected_comm)
#setup = largest_clique.setup(selected_comm, num_players, num_seeds)
#return setup
return strat.setup(selected_comm, num_players, num_seeds)
def test_clique(self):
"""
Test that a complet graph of size 2*n has the right behavior when split in two
"""
n = 5
g = nx.complete_graph(2*n)
part = dict([])
for node in g.nodes() :
part[node] = node % 2
ind = co.induced_graph(part, g)
goal = nx.Graph()
goal.add_weighted_edges_from([(0,1,n*n),(0,0,n*(n-1)/2), (1, 1, n*(n-1)/2)])
self.assert_(nx.is_isomorphic(ind, goal))
def test_clique(self):
"""
Test that a complet graph of size 2*n has the right behavior when split in two
"""
n = 5
g = nx.complete_graph(2 * n)
part = dict([])
for node in g.nodes():
part[node] = node % 2
ind = co.induced_graph(part, g)
goal = nx.Graph()
goal.add_weighted_edges_from([(0, 1, n * n), (0, 0, n * (n - 1) / 2),
(1, 1, n * (n - 1) / 2)])
self.assert_(nx.is_isomorphic(ind, goal))
def ppl_plc(diary):
# make people-place DataFrame by merging on event
evt_plc = diary[['Event', 'Place']].dropna()
evt_ppl = diary[['Event', 'Participants']]
Xie = pd.DataFrame({'Event': diary['Event'], 'Participants': '謝蘭生'})
evt_ppl = evt_ppl.append(Xie, ignore_index=True)
ppl_plc = pd.merge(evt_plc, evt_ppl, how='left').dropna().drop('Event',
axis=1)
ppl_plc['Weight'] = 1
# make edgelist
edges = ppl_plc.groupby(['Place', 'Participants']).sum().reset_index()
ppl_dict = pd.Series('People',
index=edges['Participants'].unique()).to_dict()
plc_dict = pd.Series('Place', index=edges['Place'].unique()).to_dict()
type_dict = {**ppl_dict, **plc_dict}
edges.rename(columns={
'Participants': 'Source',
'Place': 'Target'
},
inplace=True)
# make the people-place network
G = nx.from_pandas_dataframe(edges,
source="Source",
target="Target",
edge_attr="Weight")
nx.set_node_attributes(G, 'Type', type_dict)
nx.set_node_attributes(G, "k-core", nx.core_number(G))
communityDict = community.best_partition(G)
nx.set_node_attributes(G, "community", communityDict)
nx.write_graphml(G, "Graph/Network/ppl_plc.graphml", encoding="utf-8")
# make community network
G_commun = community.induced_graph(communityDict, G)
nx.write_graphml(G_commun,
"Graph/Network/ppl_plc_Community.graphml",
encoding="utf-8")
# export nodes with attributes into a csv
idx, attr = zip(*G.nodes(data=True))
core = [d['k-core'] for d in attr]
commun = [d['community'] for d in attr]
nodes_attr = pd.DataFrame({'k-core': core, 'community': commun}, index=idx)
nodes_attr.to_csv("csv/ppl_plc_CoreCommunity.csv", encoding='utf-8')
return
def test_clique(self):
"""
Test that a complete graph of size 2*graph_size has the right behavior
when split in two
"""
graph_size = 5
graph = nx.complete_graph(2 * graph_size)
part = dict([])
for node in graph.nodes():
part[node] = node % 2
ind = co.induced_graph(part, graph)
goal = nx.Graph()
edges = [(0, 1, graph_size**2),
(0, 0, graph_size * (graph_size - 1) / 2),
(1, 1, graph_size * (graph_size - 1) / 2)]
goal.add_weighted_edges_from(edges)
self.assertTrue(nx.is_isomorphic(ind, goal))
def test_clique(self):
"""
Test that a complete graph of size 2*graph_size has the right behavior
when split in two
"""
graph_size = 5
graph = nx.complete_graph(2 * graph_size)
part = dict([])
for node in graph.nodes():
part[node] = node % 2
ind = co.induced_graph(part, graph)
goal = nx.Graph()
edges = [(0, 1, graph_size ** 2),
(0, 0, graph_size * (graph_size - 1) / 2),
(1, 1, graph_size * (graph_size - 1) / 2)]
goal.add_weighted_edges_from(edges)
self.assertTrue(nx.is_isomorphic(ind, goal))
def calc_louvain(adj_matrix, level=0, return_c_graph=False):
nx_G = nx.from_numpy_array(adj_matrix)
dendro = louvain.generate_dendrogram(
nx_G, randomize=False, random_state=0) #Maybe set randomize True
#print(dendro)
#asdasd
level = len(dendro) - level - 1
if level < 0:
raise Exception("The given Level is too deep. The maximum is: " +
str(len(dendro) - 1))
communities = louvain.partition_at_level(dendro, level)
number_communities = max(communities, key=lambda x: communities[x]) + 1
# Maybe unnecessary after some code rework and unification
community_list = []
for i in range(number_communities):
grp_list = []
for grp in communities:
if communities[grp] == i:
grp_list.append(grp)
else:
if grp_list:
community_list.append(grp_list)
community_level_G = louvain.induced_graph(communities, nx_G)
if return_c_graph:
c_level_graph = nx.adjacency_matrix(community_level_G)
else:
c_level_graph = None
inv_dendro = []
for dct in dendro:
inv_dct = {}
for k, v in dct.items():
inv_dct.setdefault(v, []).append(k)
inv_dendro.append(inv_dct)
return community_list, c_level_graph, dendro, inv_dendro
def drawInducedGraph(g, subgraph, partition, algorithm, comm_to_plot, community_d):
# colors
comm_to_color_zip = zip(COLORS, comm_to_plot)
comm_to_color = [color for color, com in comm_to_color_zip]
fig, ax = plt.subplots()
# induced graph scoring
score = community.modularity(partition, subgraph)
print "Induced Community Score: ", score
# draw induced graph
new_er_partition = {node:comm for node, comm in partition.items() if comm in comm_to_plot}
comm_graph = community.induced_graph(new_er_partition, subgraph)
new_partition = {comm:comm for comm in comm_graph.nodes()}
new_pos = community_layout(comm_graph, new_partition, comm_scale=2000,node_scale=50)
weights = [comm_graph[u][v]['weight']/15.0 for u,v in comm_graph.edges()]
# node_degs = [val*35 for node,val in nx.degree(comm_graph)]
community_self_loops = [community_d[comm] for comm in comm_graph.nodes()]
nx.draw(comm_graph, new_pos, cmap=plt.get_cmap('jet'), with_labels=False, arrows=True, node_color=comm_to_color,node_size=community_self_loops,width=weights)
plt.title("Supernodes from Community Detection Using " + algorithm + " Algorithm \n Modularity Score: " + str(score))
plt.savefig('new_plots/induced_community_' + algorithm + '_' + LAYOUT_TYPE + '.png')
def induced_graph(original_graph,
partition,
induced_graph=None,
rescale_node_size=1.,
draw=True,
cmap=None,
words_map_inv=None,
pos=None,
betweenness_scaled=None):
"""
Returns the graph induced from the community partition of the graph
"""
if (induced_graph == None):
induced_graph = community.induced_graph(partition,
original_graph,
weight="weight")
if (draw and cmap):
if (pos == None):
pos = nx.spring_layout(induced_graph)
w = induced_graph.degree(weight="weight")
sizes = [w[node] * rescale_node_size for node in induced_graph.nodes()]
nx.draw(induced_graph,
pos=pos,
node_size=sizes,
node_color=[cmap[n] for n in induced_graph.nodes()])
labels = {}
for com in induced_graph.nodes():
rep = max([
nodes for nodes in partition.keys() if partition[nodes] == com
],
key=lambda n: original_graph.degree(n, weight="weight"))
labels[com] = words_map_inv[rep]
nx.draw_networkx_labels(induced_graph, pos, labels, font_size=16)
return induced_graph
def draw_graph(self, output_file=None, npmi_threshhold = .7):
"""Draw a graph of used-with connections between packages
@param output_file: file to save graph to; if None, then show graph
"""
G1 = self.G.copy()
for edge in self.G.edges_iter(data=True):
if edge[2]["weight"] < npmi_threshhold:
G1.remove_edge(edge[0], edge[1])
G1 = nx.subgraph(G1, [node for node in G1.nodes() if nx.degree(G1)[node] > 1])
partition = community.best_partition(G1)
partpos = nx.spring_layout(community.induced_graph(partition, G1), iterations=100)
forced_partpos = { n : partpos[partition[n]] for n in G1.nodes() }
print "between"
pos=nx.spring_layout(G1,pos =forced_partpos,iterations=200)
plt.clf()
plt.figure(figsize=(36,36))
plt.axis("off")
plt.title('usedwith')
labels = { node : self.names[node] for node in G1.nodes() }
nx.draw_networkx_edges(G1,pos, edge_color="#cccccc")
nx.draw_networkx_nodes(G1,pos,node_size=50, node_color=[hashColor(partition[n]) for n in G1.nodes()])
nx.draw_networkx_labels(G1,pos,labels=labels)
if output_file is None:
plt.show()
else:
plt.savefig(output_file, bbox_inches='tight')
import pdb
pdb.set_trace()
def network_plots(l, partition, out, temp):
# Projection colored and sized by communitu
pos = community_layout(l, partition)
min_comm_size = get_top_comm_len(partition, 3)
print('MIN COMM SIZE: ' + str(min_comm_size))
c = _color_nodes(l, partition, min_comm_size)
s = _size_nodes(l, partition, 3)
nx.draw(l, pos, node_color=c, node_size=s, width=0.3, alpha=0.7)
plt.savefig(out + '02_comms_projection.png')
plt.close()
# Induced network of communities
ind = induced_graph(partition, l)
node_size = []
for comm_node in ind.nodes:
size = temp[temp['community'] == comm_node]['nodecount'].values[0]
if size == 1:
node_size.append(0)
else:
node_size.append(np.exp(size))
nx.draw(ind, node_size=node_size, node_color='black', alpha=0.7, width=0.5)
plt.savefig(out + 'induced_projection.png')
plt.close()
pos = nx.spring_layout(l, k=0.50)
plt.axis('off')
nx.draw_networkx(l,
node_size=7,
with_labels=False,
node_color=c,
edge_color='black',
width=0.3,
alpha=0.7,
pos=pos)
plt.savefig(out + 'projection.png')
plt.close()
def induced_graph_viz(l, partition, partition_df, name):
partition_df = partition_df.reset_index()
partition_df = partition_df.groupby([0]).count()
print(partition_df.head())
partition_df = partition_df.reset_index()
print(partition_df.head())
partition_df.columns = ['community', 'nodecount']
# Induced network of communities
ind = induced_graph(partition, l)
node_size = []
for comm_node in ind.nodes:
size = partition_df[partition_df['community'] ==
comm_node]['nodecount'].values[0]
if size == 1:
node_size.append(0)
else:
node_size.append(size**2)
plt.figure(figsize=(14, 16))
nx.draw(ind, node_size=node_size, alpha=0.7)
plt.savefig(name + '_induced_projection.png')
plt.close()
return ind
def induce_graph_by_communities(graph: nx.Graph,
communities: Dict[Any, int],
weight_attribute: str = 'weight') -> nx.Graph:
"""
Creates a community graph with nodes from the communities dictionary
and using the edges of the original graph to form edges between communities.
Weights are aggregated; you may need to normalize the resulting graph
after calling this function.
Note: logs a warning if the size of the community dictionary is less than
the size of the provided graph's vertexset.
:param networkx.Graph graph: The original graph that contains the edges that will be
used to formulate a new induced community graph
:param communities: The communities dictionary provides a mapping of
original vertex ID to new community ID.
:type communities: dict[Any, int]
:param str weight_attribute: The weight attribute on the original graph's edges to use
when aggregating the weights of the induced community graph. Default is `weight`.
:return: The induced community graph.
:rtype: networkx.Graph
:raises ValueError: If the graph is None
:raises ValueError: If the communities dictionary is None
"""
logger = logging.getLogger(__name__)
if graph is None:
raise ValueError("graph cannot be None")
if communities is None:
raise ValueError("communities cannot be None")
if len(communities) < len(graph.nodes()):
logger.warning(
f"Length of communities provided ({len(communities)}) is less than the "
+ f"total number of nodes in the graph ({len(graph.nodes())})")
return community.induced_graph(communities, graph, weight_attribute)
def augment_graph_data(data, max_groups):
total_nodes = len(data['nodes'])
#lowering the necessary node count
#since in some cases node count is greatly reduced after processing
# first author kurtz,m goes from ~60 to 19 for instance
if total_nodes < 15:
#just get rid of the sets
for i, l in enumerate(data["links"]):
data["links"][i]["overlap"] = list(l["overlap"])
return {"fullGraph": data}
#create the networkx graph
G = nx.Graph()
for i, x in enumerate(data['nodes']):
G.add_node(i,
node_name=x["nodeName"],
nodeWeight=x["nodeWeight"],
title=x["title"],
citation_count=x["citation_count"],
first_author=x["first_author"],
read_count=x["read_count"])
for i, x in enumerate(data['links']):
G.add_edge(x["source"],
x["target"],
weight=x["value"],
overlap=list(x["overlap"]))
all_nodes = G.nodes()
#partition is a dictionary with group names as keys
# and individual node indexes as values
partition = community.best_partition(G)
for g in G.nodes():
G.node[g]["group"] = partition[g]
#with new group info, create the summary group graph
summary_graph = community.induced_graph(partition, G)
#title container
titles = {}
#enhance the information that will be in the json handed off to d3
for x in summary_graph.nodes():
summary_graph.node[x]["total_citations"] = sum([
G.node[paper].get("citation_count", 0) for paper in G.nodes()
if G.node[paper]["group"] == x
])
summary_graph.node[x]["total_reads"] = sum([
G.node[paper].get("read_count", 0) for paper in G.nodes()
if G.node[paper]["group"] == x
])
papers = sorted([
G.node[paper] for paper in G.nodes() if G.node[paper]["group"] == x
],
key=lambda x: x.get("nodeWeight", 0),
reverse=True)
titles[x] = [p["title"] for p in papers]
summary_graph.node[x]["paper_count"] = len(papers)
#attaching title 'word clouds' to the nodes
significant_words = tf_idf.get_tf_idf_vals(titles)
for x in summary_graph.nodes():
#remove the ones with only 1 paper
if summary_graph.node[x]["paper_count"] == 1:
summary_graph.remove_node(x)
else:
#otherwise, give them a title
#how many words should we show on the group? max 6, otherwise 1 per every 2 papers
summary_graph.node[x]["node_label"] = dict(
sorted(significant_words[x].items(),
key=lambda x: x[1],
reverse=True)[:6])
#remove all but top n groups from summary graph
#where top n is measured by total citations from a group
top_nodes = sorted([n for n in summary_graph.nodes(data=True)],
key=lambda x: x[1]["total_citations"],
reverse=True)[:max_groups]
top_nodes = [t for t in top_nodes if t >= 1]
top_node_ids = [n[0] for n in top_nodes]
for group_id in summary_graph.nodes():
if group_id not in top_node_ids:
summary_graph.remove_node(group_id)
#remove nodes from full graph that aren't in top group
#this automatically takes care of edges, too
for node in G.nodes(data=True):
if node[1]["group"] not in top_node_ids:
G.remove_node(node[0])
#continuing to enhance the information: add to group info about the most common co-references
for x in summary_graph.nodes():
#make a float so division later to get a percent makes sense
num_papers = float(summary_graph.node[x]["paper_count"])
references = {}
#find all members of group x
indexes = [
paperIndex for paperIndex in G.nodes()
if G.node[paperIndex]["group"] == x
]
for edge in G.edges(data=True):
#if it passes, it's an inter-group connection
# [0] is source, [1] is target, [2] is data dict
paper_one = edge[0]
paper_two = edge[1]
if paper_one in indexes and paper_two in indexes:
for bib in edge[2]["overlap"]:
if bib in references:
references[bib].update([paper_one, paper_two])
else:
references[bib] = set([paper_one, paper_two])
count_references = sorted(references.items(),
key=lambda x: len(x[1]),
reverse=True)[:5]
top_common_references = [
(tup[0], float("{0:.2f}".format(len(tup[1]) / num_papers)))
for tup in count_references
]
top_common_references = dict(top_common_references)
summary_graph.node[x]["top_common_references"] = top_common_references
summary_json = json_graph.node_link_data(summary_graph)
# giving groups node_names based on size of groups
for i, n in enumerate(
sorted(summary_json["nodes"],
key=lambda x: x["paper_count"],
reverse=True)):
for possible_real_index, node in enumerate(summary_json["nodes"]):
if node == n:
real_index = possible_real_index
summary_json["nodes"][real_index]["node_name"] = i + 1
for i, n in enumerate(summary_json["nodes"]):
#cache this so graph manipulation later is easier
summary_json["nodes"][i]["stable_index"] = i
#find the node
final_data = {
"summaryGraph": summary_json,
"fullGraph": json_graph.node_link_data(G)
}
return final_data
#Create network layout for visualizations
spring_pos = nx.spring_layout(G_karate)
plt.axis("off")
nx.draw_networkx(G_karate, pos = spring_pos, with_labels = False, node_size = 80)
############### Community detection ###########
import community as com
parts = com.best_partition(G_karate)
values = [parts.get(node) for node in G_karate.nodes()]
plt.axis("off")
nx.draw_networkx(G_karate, pos = spring_pos, cmap = plt.get_cmap("jet"), node_color = values, font_size=20,node_size = 80, with_labels = False)
## Calculate the modularity ##
com.modularity(parts, G_karate)
## induced graph : each community is represented as one node ##
help(com)
G_induced=com.induced_graph(parts, G_karate)
plt.axis("off")
nx.draw_networkx(G_induced, cmap = plt.get_cmap("jet"), font_size=20,node_size = 80, with_labels = False)
import pubmed
from utils import *
import community
import networkx as net
import matplotlib.pyplot as plot
#articles = pubmed.get_articles('compu')
#open('articles.json','wb').write(json.dumps(articles))
articles = json.loads(open('articles.json','rb').read())
#articles2=[a for a in articles if parser.parse(a['DP'].replace('-',' ').split(' ')[0])>datetime.datetime(2000,1,1)]
aunet=pubmed.make_author_network(articles2)
## removes single links; now will separate into research groups.
components=net.connected_component_subgraphs(trim_edges(aunet,2))
## separate the rest into communities. Plot the overall structure, individual clusters, macrostructure
community.plot_community(components[0], filename='images/largest_community.pdf')
subgraphs=community.plot_partitions(components[0],filename='images/community')
ind=community.induced_graph(community.best_partition(components[0]),components[0])
net.draw(ind)
plot.savefig('images/macrostructure.pdf')
# Matrix2 = [[0 for x in range(size2)] for y in range(size2)]
#
#
# for i in range(0, size2):
# for j in range(0, size2):
# if j == i or j < i:
# continue
#
# for node in clusters[i]:
# Matrix2[i][j] += helpers.num_edges(node, clusters[j], Matrix)
# Matrix2[j][i] += helpers.num_edges(node, clusters[j], Matrix)
#
# Matrix3 = helpers.flip_edge_ratio(Matrix2, size2)
# Matrix4 = helpers.edge_ratio(Matrix2, size2)
G2 = community.induced_graph(labels, G)
size2 = G2.number_of_nodes()
Matrix2 = helpers.create_shortest_path_matrix(G2, size2, "weight")
dFrame2 = DataFrame(Matrix2)
dFrame2.to_csv("Matrix_Files/M2.csv")
# save matrix to file for output to dipha
dipha_utils.writeDistBin(Matrix2, infile2)
#os.system("run_dipha.bat")
# nx.draw(G)
# plt.savefig("G.png")
# nx.draw(G2)
# plt.savefig("G2.png")
import networkx as nx
import community as c
import matplotlib.pyplot as plt
# import the graph
G = nx.read_graphml("test1.graphml")
# find communities
dendo = c.generate_dendrogram(G)
for level in range(len(dendo) - 1):
print("partition at level", level, "is", c.partition_at_level(dendo, level))
partition = c.best_partition(G)
m = c.modularity(partition, G)
print(m)
agglomerate = c.induced_graph(partition, G)
# draw the graph
colors = ["blue", "green", "yellow", "violet", "black", "orange", "cyan", "red", "indigo", "pink"]
plt.figure(1)
size = float(len(set(partition.values())))
pos = nx.spring_layout(G)
count = 0.
for community in set(partition.values()):
count = count + 1.
list_nodes = [nodes for nodes in partition.keys() if partition[nodes] == community]
nx.draw_networkx_nodes(G, pos, list_nodes, node_size=40, node_color=colors[int(count) % 10])
nx.draw_networkx_edges(G, pos, alpha=0.5)
nx.draw_networkx_nodes(G_fb, spring_pos, list_nodes, node_size = 15,
node_color = str(count / size))
nx.draw_networkx_edges(G_fb,spring_pos, alpha=0.5)
plt.show()
##### Dendo graph ######
dendo = community.generate_dendogram(G_fb)
for level in range(len(dendo) - 1) :
print "partition at level", level, "is", community.partition_at_level(dendo, level)
##### induced graph ####
G=community.induced_graph(parts, G_fb)
#nx.draw_networkx(G, pos = spring_pos, cmap = plt.get_cmap("jet"), node_color = values, node_size = 15, with_labels = False)
nx.draw_networkx(G)
def build_json(hierarchy_dict, h5_data, dataset_name, graph, json, threshold):
# data set dict
ds_dict = {}
# graph dict
g_dict = {}
# Maximum hierarchy size
hmax = len(hierarchy_dict["dendro"]) - 1
# Add pseudo entry to trigger single node dict creation
hierarchy_dict[hmax + 1] = {}
for hidx, hdict in hierarchy_dict.items():
if not isinstance(hidx, int):
continue
# Dendrogram list is sorted inversely to hierarchy dict. Therefore, the dendrogram index has to be recalculated.
didx = hmax - hidx
# edge dict
e_dict = {}
# node dict
n_dict = {}
# hierarchy dicr
h_dict = {}
if didx > -1:
# Nodes
for com, nodes in hierarchy_dict["inv_dendro"][didx].items():
# attribute dict
a_dict = {}
a_dict["index"] = com
a_dict["name"] = "h%in%i" % (hidx, com)
a_dict["childs"] = nodes
a_dict["mzs"] = list(
h5_data.columns[hdict["communities"][com]])
try:
a_dict["membership"] = hierarchy_dict["dendro"][didx +
1][com]
except Exception as e:
print(e)
n_dict["h%in%i" % (hidx, com)] = a_dict
else:
# single nodes are always first entry in dendro
for node, com in hierarchy_dict["dendro"][0].items():
a_dict = {}
a_dict["index"] = node
a_dict["name"] = h5_data.columns[node]
a_dict["membership"] = com
a_dict["mzs"] = [h5_data.columns[node]]
n_dict["h%in%i" % (hidx, node)] = a_dict
# Edges
if didx > -1:
community = louvain.partition_at_level(hierarchy_dict["dendro"],
didx)
edges = louvain.induced_graph(community, graph).edges(data=True)
else:
edges = graph.edges(data=True)
idx = 0
for source, target, weight in edges:
# Include source == target for inner edge weight.
#print(weight)
if source != target:
a_dict = {}
a_dict["index"] = idx
a_dict["name"] = "h%ie%i" % (hidx, idx)
a_dict["source"] = "h%in%i" % (hidx, source)
a_dict["target"] = "h%in%i" % (hidx, target)
try:
count = weight["count"]
except:
count = 1
#print(count)
a_dict["weight"] = weight["weight"] / count
e_dict["h%ie%i" % (hidx, idx)] = a_dict
idx += 1
h_dict["nodes"] = n_dict
h_dict["edges"] = e_dict
g_dict["hierarchy%i" % (hidx)] = h_dict
ds_dict["graph"] = g_dict
ds_dict["dataset"] = dataset_name
ds_dict["threshold"] = threshold
#mzs = [x for x in np.round(h5_data.columns, 3)]
mzs = [x for x in h5_data.columns]
mzs_dict = {}
for mz in mzs:
mzs_dict[str(mz)] = {}
for hy, vals in g_dict.items():
for nid, props in vals["nodes"].items():
try:
if mz in props["mzs"]:
mzs_dict[str(mz)][hy] = nid
break
# Last hierarchy has no "mzs" prop
except Exception as e:
print(e)
if mz == props["name"]:
mzs_dict[str(mz)][hy] = nid
ds_dict["mzs"] = mzs_dict
json["graphs"]["graph%i" % (hierarchy_dict["graph_idx"])] = ds_dict
return json
#
# # (b). 'coverage' - (note: have to turn partition into a list of sets.)
# # ???? NOT WORKING AND NOT SURE WHY.
# partsList = []
# numParts = part.get( max(part,key=part.get) )
# for p in range( numParts ):
# partsList.append( set([i for i,j in part.items() if j == p]) )
# coverage[i] = nx.community.coverage(G, partsList)
#
#
#
#
# Looking further into dendrogram. Makes sense.
try:
G2 = c.induced_graph(
dend[0], G,
weight='weight') # define graph turns clusters into nodes.
q_dend[1, i] = c.modularity(dend[1], G2, weight='weight')
pp = c.partition_at_level(
dend,
1) # express partition at a give layer in terms of all nodes.
q_dend[2, i] = c.modularity(pp, G, weight='weight')
except:
continue
# Plot modularity metric for different partitions at different resolution parameters.
if False:
plt.plot(res, q_bp, 'b')
plt.plot(res, q_dend[0], 'r')
plt.plot(res, q_dend[1], 'g')
plt.plot(res, q_dend[2], 'k')
plt.axis("off")
nx.draw_networkx(G_lesmis, pos=spring_pos, with_labels=False, node_size=15)
############### Community detection ###########
import community as com
parts = com.best_partition(G_lesmis)
values = [parts.get(node) for node in G_lesmis.nodes()]
plt.axis("off")
nx.draw_networkx(G_lesmis,
pos=spring_pos,
cmap=plt.get_cmap("jet"),
node_color=values,
font_size=20,
node_size=80,
with_labels=False)
## Calculate the modularity ##
com.modularity(parts, G_lesmis)
## induced graph : each community is represented as one node ##
help(com)
G_induced = com.induced_graph(parts, G_lesmis)
plt.axis("off")
nx.draw_networkx(G_induced,
cmap=plt.get_cmap("jet"),
font_size=20,
node_size=80,
with_labels=False)
def extraction(self):
'''Extract adjacency lists,mats,user and community centrality and communities bags'''
#Compute the first derivative and the point of timeslot separation
firstderiv,mentionLimit=self.timeslotselection(self.authors,self.mentions,self.alltime)
#Split time according to the first derivative of the users' activity#
sesStart,timeslot,timeLimit=0,0,[self.alltime[0]]
print("Forming timeslots")
for k in range(len(mentionLimit)):
if firstderiv[k]<0 and firstderiv[k+1]>=0:
#make timeslot timelimit array
timeLimit.append(self.alltime[int(mentionLimit[k])])
fileNum='{0}'.format(str(timeslot).zfill(2))
# print("Forming Timeslot Data "+str(timeslot)+" at point "+str(k))
sesEnd=int(mentionLimit[k]+1)
#Make pairs of users with weights
usersPair=list(zip(self.authors[sesStart:sesEnd],self.mentions[sesStart:sesEnd]))
#Create weighted adjacency list
weighted=collections.Counter(usersPair)
weighted=list(weighted.items())
adjusrs,weights=zip(*weighted)
adjauthors,adjments=zip(*adjusrs)
adjList=list(zip(adjauthors,adjments,weights))
#Write pairs of users to txt file for Gephi
my_txt=open(self.dataset_path+"/data/GDD/results/forGephi/usersPairs_"+fileNum+".txt","w")
my_txt.write("Source,Target,Weight"+"\n")
for line in adjList:
my_txt.write(",".join(str(x) for x in line) + "\n")
my_txt.close()
#Create dictionary of tags per user
tmptags=self.tags[sesStart:sesEnd]
self.tagBag[timeslot]={}
for authIdx,auth in enumerate(self.authors[sesStart:sesEnd]):
if auth not in self.tagBag[timeslot]:
self.tagBag[timeslot][auth]=[]
elif tmptags[authIdx]:
self.tagBag[timeslot][auth].append(tmptags[authIdx])
#create dictionary of urls per user
tmpUrls=self.tweetUrls[sesStart:sesEnd]
self.urlBag[timeslot]={}
for authIdx,auth in enumerate(self.authors[sesStart:sesEnd]):
if auth not in self.urlBag[timeslot]:
self.urlBag[timeslot][auth]=[]
elif tmpUrls[authIdx]:
self.urlBag[timeslot][auth].append(tmpUrls[authIdx])
#create dictionary of tweet Ids per user
tmptweetids=self.tweetIds[sesStart:sesEnd]
self.tweetIdBag[timeslot]={}
for authIdx,auth in enumerate(self.authors[sesStart:sesEnd]):
if auth not in self.tweetIdBag[timeslot]:
self.tweetIdBag[timeslot][auth]=[]
elif tmptweetids[authIdx]:
self.tweetIdBag[timeslot][auth].append(tmptweetids[authIdx])
for mentIdx,ment in enumerate(self.mentions[sesStart:sesEnd]):
if ment not in self.tweetIdBag[timeslot]:
self.tweetIdBag[timeslot][ment]=[]
elif tmptweetids[mentIdx]:
self.tweetIdBag[timeslot][ment].append(tmptweetids[mentIdx])
#create dictionary of text per user
tmptweetText=self.twText[sesStart:sesEnd]
self.tweetTextBag[timeslot]={}
for authIdx,auth in enumerate(self.authors[sesStart:sesEnd]):
if auth not in self.tweetTextBag[timeslot]:
self.tweetTextBag[timeslot][auth]=[]
elif tmptweetText[authIdx]:
self.tweetTextBag[timeslot][auth].append(tmptweetText[authIdx])
for mentIdx,ment in enumerate(self.mentions[sesStart:sesEnd]):
if ment not in self.tweetTextBag[timeslot]:
self.tweetTextBag[timeslot][ment]=[]
elif tmptweetText[mentIdx]:
self.tweetTextBag[timeslot][ment].append(tmptweetText[mentIdx])
#Create dictionary of text
#Construct networkX graph
tempDiGraph=nx.DiGraph()
tempDiGraph.add_weighted_edges_from(adjList)
tempDiGraph.remove_edges_from(tempDiGraph.selfloop_edges())
tempGraph=nx.Graph()
tempGraph.add_weighted_edges_from(adjList)
tempGraph.remove_edges_from(tempGraph.selfloop_edges())
#Extract the centrality of each user using the PageRank algorithm
tempUserPgRnk=nx.pagerank(tempDiGraph,alpha=0.85,max_iter=100,tol=0.001)
maxPGR=max((pgr for k,(pgr) in tempUserPgRnk.items()))
for k in tempUserPgRnk.items():
tempUserPgRnk[k[0]]/=maxPGR
self.userPgRnkBag[timeslot]=tempUserPgRnk
#Detect Communities using the louvain algorithm#
partition = community.best_partition(tempGraph)
inv_partition = {}
for k, v in partition.items():
inv_partition[v] = inv_partition.get(v, [])
inv_partition[v].append(k)
inv_partition[v].sort()
strComms=[inv_partition[x] for x in inv_partition]
strComms.sort(key=len,reverse=True)
#Construct Communities of uniqueUsers indices and new community dict with size sorted communities
numComms,new_partition=[],{}
for c1,comms in enumerate(strComms):
numpart=[]
for ids in comms:
numpart.extend(self.uniqueUsers[ids])
new_partition[ids]=c1
numComms.append(numpart)
newinv_partition = {}
for k, v in new_partition.items():
newinv_partition[v] = newinv_partition.get(v, [])
newinv_partition[v].append(k)
newinv_partition[v].sort()
#Construct a graph using the communities as users
tempCommGraph=community.induced_graph(new_partition,tempDiGraph)
#Detect the centrality of each community using the PageRank algorithm
commPgRnk=nx.pagerank(tempCommGraph,alpha=0.85,max_iter=100,tol=0.001)
maxCPGR=max((cpgr for k,(cpgr) in commPgRnk.items()))
commPgRnkList=[]
for key,value in commPgRnk.items():
commPgRnkList.append(value/maxCPGR)
self.commPgRnkBag[timeslot]=commPgRnkList
'''Construct Community Dictionary'''
self.commStrBag[timeslot]=strComms
self.commNumBag[timeslot]=numComms
sesStart=sesEnd
timeslot+=1
day_month=[datetime.datetime.fromtimestamp(int(x)).strftime('%d/%m') for x in timeLimit]
self.day_month=day_month
self.timeLimit=[time.ctime(int(x)) for x in timeLimit]
edge_colors = 'red'
pos = nx.spring_layout(G)
nx.draw(G, pos, width=0.5, alpha=0.5)
plt.savefig("First_Graph.png")
nx.draw_networkx_edges(G, pos, width=0.5, alpha=0.5)
partition = community.best_partition(G)
print len(partition)
partition_set = set()
for item in partition.values():
partition_set.add(item)
induced_graph = community.induced_graph(partition, G)
print induced_graph.edges(data='weight')
pos = nx.spring_layout(induced_graph)
nx.draw(induced_graph, pos, width=0.5, alpha=0.5)
plt.savefig("Induced_Graph.png")
nx.draw_networkx_edges(induced_graph, pos, width=0.5, alpha=0.5)
cluster_size = []
for i in range(168):
cluster_size.append(0)
for i in range(1, len(partition) + 1):
cluster_size[partition[i]] += 1
print partition[i]
def augment_graph_data(data, max_groups):
total_nodes = len(data['nodes'])
#lowering the necessary node count
#since in some cases node count is greatly reduced after processing
# first author kurtz,m goes from ~60 to 19 for instance
if total_nodes < 15:
#just get rid of the sets
for i, l in enumerate(data["links"]):
data["links"][i]["overlap"] = list(l["overlap"])
return {"fullGraph" :data}
#create the networkx graph
G = nx.Graph()
for i,x in enumerate(data['nodes']):
G.add_node(i, node_name= x["nodeName"], nodeWeight = x["nodeWeight"], title=x["title"], citation_count=x["citation_count"], first_author = x["first_author"], read_count = x["read_count"])
for i,x in enumerate(data['links']):
G.add_edge(x["source"], x["target"], weight = x["value"], overlap = list(x["overlap"]))
all_nodes = G.nodes()
#partition is a dictionary with group names as keys
# and individual node indexes as values
partition = community.best_partition(G)
for g in G.nodes():
G.node[g]["group"] = partition[g]
#with new group info, create the summary group graph
summary_graph = community.induced_graph(partition, G)
#title container
titles = {}
#enhance the information that will be in the json handed off to d3
for x in summary_graph.nodes():
summary_graph.node[x]["total_citations"] = sum([G.node[paper].get("citation_count", 0) for paper in G.nodes() if G.node[paper]["group"] == x])
summary_graph.node[x]["total_reads"] = sum([G.node[paper].get("read_count", 0) for paper in G.nodes() if G.node[paper]["group"] == x])
papers = sorted([G.node[paper] for paper in G.nodes() if G.node[paper]["group"] == x], key = lambda x: x.get("nodeWeight", 0), reverse = True)
titles[x] = [p["title"]for p in papers]
summary_graph.node[x]["paper_count"] = len(papers)
#attaching title 'word clouds' to the nodes
significant_words = tf_idf.get_tf_idf_vals(titles)
for x in summary_graph.nodes():
#remove the ones with only 1 paper
if summary_graph.node[x]["paper_count"] == 1:
summary_graph.remove_node(x)
else:
#otherwise, give them a title
#how many words should we show on the group? max 6, otherwise 1 per every 2 papers
summary_graph.node[x]["node_label"] = dict(sorted(significant_words[x].items(), key = lambda x: x[1], reverse = True)[:6])
#remove all but top n groups from summary graph
#where top n is measured by total citations from a group
top_nodes = sorted([n for n in summary_graph.nodes(data = True)], key= lambda x : x[1]["total_citations"], reverse = True )[:max_groups]
top_nodes = [t for t in top_nodes if t >=1]
top_node_ids = [n[0] for n in top_nodes]
for group_id in summary_graph.nodes():
if group_id not in top_node_ids:
summary_graph.remove_node(group_id)
#remove nodes from full graph that aren't in top group
#this automatically takes care of edges, too
for node in G.nodes(data = True):
if node[1]["group"] not in top_node_ids:
G.remove_node(node[0])
#continuing to enhance the information: add to group info about the most common co-references
for x in summary_graph.nodes():
#make a float so division later to get a percent makes sense
num_papers = float(summary_graph.node[x]["paper_count"])
references = {}
#find all members of group x
indexes = [paperIndex for paperIndex in G.nodes() if G.node[paperIndex]["group"] == x]
for edge in G.edges(data=True):
#if it passes, it's an inter-group connection
# [0] is source, [1] is target, [2] is data dict
paper_one = edge[0]
paper_two = edge[1]
if paper_one in indexes and paper_two in indexes:
for bib in edge[2]["overlap"]:
if bib in references:
references[bib].update([paper_one, paper_two])
else:
references[bib] = set([paper_one, paper_two])
count_references = sorted(references.items(), key=lambda x:len(x[1]), reverse = True)[:5]
top_common_references = [(tup[0], float("{0:.2f}".format(len(tup[1])/num_papers))) for tup in count_references]
top_common_references = dict(top_common_references)
summary_graph.node[x]["top_common_references"] = top_common_references
summary_json = json_graph.node_link_data(summary_graph)
# giving groups node_names based on size of groups
for i, n in enumerate(sorted(summary_json["nodes"], key=lambda x:x["paper_count"], reverse=True)):
for possible_real_index, node in enumerate(summary_json["nodes"]):
if node == n:
real_index = possible_real_index
summary_json["nodes"][real_index]["node_name"] = i +1
for i, n in enumerate(summary_json["nodes"]):
#cache this so graph manipulation later is easier
summary_json["nodes"][i]["stable_index"] = i
#find the node
final_data = {"summaryGraph" : summary_json, "fullGraph" : json_graph.node_link_data(G) }
return final_data
plt.axis("off")
nx.draw_networkx(G_karate, pos=spring_pos, with_labels=False, node_size=80)
############### Community detection ###########
import community as com
parts = com.best_partition(G_karate)
values = [parts.get(node) for node in G_karate.nodes()]
plt.axis("off")
nx.draw_networkx(G_karate,
pos=spring_pos,
cmap=plt.get_cmap("jet"),
node_color=values,
font_size=20,
node_size=80,
with_labels=False)
## Calculate the modularity ##
com.modularity(parts, G_karate)
## induced graph : each community is represented as one node ##
help(com)
G_induced = com.induced_graph(parts, G_karate)
plt.axis("off")
nx.draw_networkx(G_induced,
cmap=plt.get_cmap("jet"),
font_size=20,
node_size=80,
with_labels=False)
plt.axis("off")
nx.draw_networkx(G_lesmis, pos = spring_pos, with_labels = False, node_size = 15)
############### Community detection ###########
import community as com
parts = com.best_partition(G_lesmis)
values = [parts.get(node) for node in G_lesmis.nodes()]
plt.axis("off")
nx.draw_networkx(G_lesmis, pos = spring_pos, cmap = plt.get_cmap("jet"), node_color = values, font_size=20,node_size = 80, with_labels = False)
## Calculate the modularity ##
com.modularity(parts, G_lesmis)
## induced graph : each community is represented as one node ##
help(com)
G_induced=com.induced_graph(parts, G_lesmis)
plt.axis("off")
nx.draw_networkx(G_induced, cmap = plt.get_cmap("jet"), font_size=20,node_size = 80, with_labels = False)
def extraction(self):
'''Extract adjacency lists,mats,user and community centrality and communities bags'''
import community
#Compute the first derivative and the point of timeslot separation
firstderiv, mentionLimit = self.timeslotselection(self.authors, self.mentions, self.alltime)
self.commPgRnkBag = {}
#Split time according to the first derivative of the users' activity#
sesStart, timeslot, timeLimit,commCount = 0, 0, [self.alltime[0]],0
print("Forming timeslots")
for tmplim in mentionLimit:
#make timeslot timelimit array
timeLimit.append(self.alltime[int(tmplim)])
fileNum = '{0}'.format(str(timeslot).zfill(2))
# print("Forming Timeslot Data "+str(timeslot)+" at point "+str(tmplim))
sesEnd = int(tmplim + 1)
#Make pairs of users with weights
usersPair = list(zip(self.authors[sesStart:sesEnd], self.mentions[sesStart:sesEnd]))
#Create weighted adjacency list
weighted = collections.Counter(usersPair)
weighted = list(weighted.items())
adjusrs, weights = zip(*weighted)
adjauthors, adjments = zip(*adjusrs)
adjList = list(zip(adjauthors, adjments, weights))
'''Write pairs of users to txt file for Gephi'''
my_txt = open(self.dataset_path + "/data/nonadaptive/results/forGephi/usersPairs_" + fileNum + ".txt", "w")#
my_txt.write("Source,Target,Weight" + "\n")
for line in adjList:
my_txt.write(",".join(str(x) for x in line) + "\n")
my_txt.close()
'''create dictionaries of text per user, of urls per user,
of tweet Ids per user and of tags per user'''
tmptweetText = self.twText[sesStart:sesEnd]
self.tweetTextBag[timeslot] = {}
tmpUrls = self.tweetUrls[sesStart:sesEnd]
self.urlBag[timeslot] = {}
tmptweetids = self.tweetIds[sesStart:sesEnd]
self.tweetIdBag[timeslot] = {}
tmptags = self.tags[sesStart:sesEnd]
self.tagBag[timeslot] = {}
for authIdx, auth in enumerate(self.authors[sesStart:sesEnd]):
if auth not in self.tweetTextBag[timeslot]:
self.tweetTextBag[timeslot][auth] = []
if tmptweetText[authIdx]:
self.tweetTextBag[timeslot][auth].append(tmptweetText[authIdx])
if auth not in self.urlBag[timeslot]:
self.urlBag[timeslot][auth] = []
if tmpUrls[authIdx]:
for multUrls in tmpUrls[authIdx]:
self.urlBag[timeslot][auth].append(multUrls)
if auth not in self.tweetIdBag[timeslot]:
self.tweetIdBag[timeslot][auth] = []
if tmptweetids[authIdx]:
self.tweetIdBag[timeslot][auth].append(tmptweetids[authIdx])
if auth not in self.tagBag[timeslot]:
self.tagBag[timeslot][auth] = []
if tmptags[authIdx]:
self.tagBag[timeslot][auth].append(tmptags[authIdx])
for mentIdx, ment in enumerate(self.mentions[sesStart:sesEnd]):
if ment not in self.tweetTextBag[timeslot]:
self.tweetTextBag[timeslot][ment] = []
if tmptweetText[mentIdx]:
self.tweetTextBag[timeslot][ment].append(tmptweetText[mentIdx])
if ment not in self.tweetIdBag[timeslot]:
self.tweetIdBag[timeslot][ment] = []
if tmptweetids[mentIdx]:
self.tweetIdBag[timeslot][ment].append(tmptweetids[mentIdx])
'''Construct networkX graph'''
tempDiGraph = nx.DiGraph()
tempDiGraph.add_weighted_edges_from(adjList)
tempDiGraph.remove_edges_from(tempDiGraph.selfloop_edges())
tempGraph = nx.Graph()
tempGraph.add_weighted_edges_from(adjList)
tempGraph.remove_edges_from(tempGraph.selfloop_edges())
'''Extract the centrality of each user using the PageRank algorithm'''
tempUserPgRnk = nx.pagerank(tempDiGraph, alpha=0.85, max_iter=100, tol=0.001)
maxPGR=max((pgr for k,(pgr) in tempUserPgRnk.items()))
for k in tempUserPgRnk.items():
tempUserPgRnk[k[0]]/=maxPGR
self.userPgRnkBag[timeslot] = tempUserPgRnk
'''Detect Communities using the louvain algorithm'''
partition = community.best_partition(tempGraph)
inv_partition = {}
for k, v in partition.items():
inv_partition[v] = inv_partition.get(v, [])
inv_partition[v].append(k)
inv_partition[v].sort()
strComms = [inv_partition[x] for x in inv_partition]
strComms.sort(key=len, reverse=True)
commCount+=len(strComms)
'''Construct Communities of uniqueUsers indices and new community dict with size sorted communities'''
numComms, new_partition = [], {}
for c1, comms in enumerate(strComms):
numpart = []
for ids in comms:
numpart.extend(self.uniqueUsers[ids])
new_partition[ids] = c1
numpart.sort()
numComms.append(numpart)
newinv_partition = {}
for k, v in new_partition.items():
newinv_partition[v] = newinv_partition.get(v, [])
newinv_partition[v].append(k)
newinv_partition[v].sort()
'''Construct a graph using the communities as users'''
tempCommGraph = community.induced_graph(new_partition, tempDiGraph)
self.commGraph=tempCommGraph
'''Detect the centrality of each community using the PageRank algorithm'''
commPgRnk = nx.pagerank(tempCommGraph, alpha=0.85, max_iter=100, tol=0.001)
maxCPGR = max((cpgr for k, (cpgr) in commPgRnk.items()))
commPgRnkList = []
for key, value in commPgRnk.items():
commPgRnkList.append(value/maxCPGR)
self.commPgRnkBag[timeslot] = commPgRnkList
# #Detect the centrality of each community using the degree centrality algorithm
# commDegreeness = nx.degree_centrality(tempCommGraph)
# maxCDeg = max((cpgr for k, (cpgr) in commDegreeness.items()))
# commDegreenessList = []
# for key, value in commDegreeness.items():
# commDegreenessList.append(value/maxCDeg)
# self.commDegreenessBag[timeslot] = commDegreenessList
# #Detect the centrality of each community using the betweeness centrality algorithm
# commBetweeness = nx.betweenness_centrality(tempCommGraph)
# maxCBet = max((cpgr for k, (cpgr) in commBetweeness.items()))
# commBetweennessList = []
# for key, value in commBetweeness.items():
# commBetweennessList.append(value/maxCDeg)
# self.commBetweenessBag[timeslot] = commBetweennessList
# #Extract community degree
# degreelist=[]
# for k in range(len(tempCommGraph.edge)):
# tmpdeg=tempCommGraph.degree(k)
# degreelist.append(tmpdeg)
# degreelist=[x/max(degreelist) for x in degreelist]
# self.degreeBag[timeslot]=degreelist
'''Construct Community Dictionary'''
self.commStrBag[timeslot] = strComms
self.commNumBag[timeslot] = numComms
sesStart = sesEnd
timeslot += 1
day_month = [datetime.datetime.fromtimestamp(int(x)).strftime(self.labelstr) for x in timeLimit]
self.day_month = day_month
self.timeLimit = [datetime.datetime.fromtimestamp(int(x)).strftime(self.labelstr) for x in timeLimit]
statement = '\nTotal # of communities is '+str(commCount) + '\n'
statsfile = open(self.dataset_path + "/data/nonadaptive/results/basicstats.txt",'a')
print(statement)
statsfile.write(statement)
statsfile.close()
dataCommPck = open(self.dataset_path + '/data/nonadaptive/tmp/dataComm_'+str(self.fileTitle)+'.pck','wb')
pickle.dump(self, dataCommPck , protocol = 2)
dataCommPck.close()
def run_comm(inputcID,subids):
con = mdb.connect(user= '******', passwd='X', db='X',unix_socket='X',charset='utf8')
with con:
cur = con.cursor()
cur.execute("SELECT cID,tocID FROM CommenterSubs WHERE inputID=%s and tocID<>'NotShared'",(inputcID))# (tocID<>'None' AND cID<>'None')")# limit 1000")
edges = cur.fetchall()
cur.close()
edges_pulled = [list(x) for x in set(tuple(x) for x in edges)]
print "Number of edges pulled from the database", len(edges_pulled)
uedges=[]
for i,edge_i in enumerate(edges_pulled):
if edge_i[0] in subids:
uedges.append(edge_i)
print "Number of relevant edges for the inputcID",len(uedges)
G=nx.Graph()
for edge in uedges:
G.add_edge(edge[0],edge[1],weight=0.5)
#print edge[0],edge[1]
print "Number of edges", G.number_of_edges(),", number of nodes",G.number_of_nodes()
import community as comm
#dendo = comm.generate_dendogram(G) #takes a long time and unnecessary
part = comm.best_partition(G)
modularity=comm.modularity(part, G)
print "Number of communities found",max(part.values())+1, ", modularity:",modularity
count = 0.
commf=0; #community to which input channel belongs
nodesf=[] #nodes of the community to which input channel belongs
nodepcom=[]
label_prep=["" for x in range(len(part.values()))]
for com in set(part.values()) :
count = count + 1.
list_nodes = [nodes for nodes in part.keys() if part[nodes] == com]
nodepcom.append(len(list_nodes))
label_prep[int(com)]=str(len(list_nodes))
if inputcID in list_nodes:
print "Input Channel is in the community #", com
commf=com
nodesf=list_nodes
label_prep[int(com)]="Target community: "+str(len(list_nodes))
labs=dict(zip(set(part.values()), label_prep))
plt.figure()
h1=plt.hist(nodepcom,bins=20,normed=False,color='steelblue')
h2=plt.axvline(int(np.average(nodepcom)),0,1,color='navy',linewidth=10, label='average community size = '+str(int(np.average(nodepcom))))
plt.legend(fontsize=22)
plt.title('Network modularity Q = %.4f ' % (modularity),fontsize=30)
plt.xlabel('Number of channels per community', fontsize=26)
plt.ylabel('Frequency', fontsize=26)
plt.savefig('./static/img/'+inputcID+'/'+inputcID+'_com_size_distrib_1.png', dpi=300, format='png')#,transparent=True)
com1=comm.induced_graph(part, G)
# plt.figure()
# pos = nx.spring_layout(com1)
# nx.draw_networkx_edges(com1,pos,width=1.0, edge_color='g', style='solid', alpha=0.2)
# nx.draw_networkx_labels(com1, pos, labels=labs, font_size=12, font_color='r', font_family='sans-serif', font_weight='normal', alpha=1.0)
# plt.draw()
# plt.savefig('./static/img/'+inputcID+'/'+inputcID + '_v3_com_plot_all_1.png', dpi=300, format='png',transparent=True)
# #export to json for d3 graph plot
i=0
comfin=com1
for node in com1.nodes():
comfin.node[i]['group'] = i
comfin.node[i]['label'] = label_prep[i]
i=i+1
comfin.nodes(data=True)
nld=json_graph.node_link_data(comfin)
json.dump(nld,open('./static/img/'+inputcID+'/'+inputcID+'_community_graph_comsub2.json','w'))
return nodesf
