def KMeansClustering_Iterative(self, step=False):
'''
Integrate orange here
actually it is a little subtle here:
1. I dont think kmeans is a good way to decide which community a node(user) should be
however it is the most generalized one
2.TODO maybe change the number of clusters(rather than make it automatically...) is better, but you have to check to result first
'''
eig_data = self.build_orange_data_from_eig_vector()
# clustering
self.km = Orange.clustering.kmeans.Clustering(data=eig_data,
centroids=5,
distance=EigDistance)
# you had better construct it into a vertex_clustering in order to compute modularity, it is not reasonable to use orange to insert into database any more
clusters = self.km.clusters
d = {}
for idx, c in enumerate(clusters):
if not d.has_key(c):
d[c] = [idx]
else:
d[c].append(idx)
import Queue
q = Queue.Queue()
for v in d.values():
q.put(v)
res_list = []
import CommunityExtraction as ce
while q.qsize() > 0:
v = q.get()
print 'qsize:%s cluster size: %s res list size: %s' % (
q.qsize(), len(v), len(res_list))
if len(v) < ce.CRITERION_CLUSTER_NODES_LOWER_BOUND:
res_list.append(v)
pass
elif len(v) > ce.CRITERION_CLUSTER_NODES_UPPER_BOUND:
# may be it can be iterative
sub_data = eig_data.get_items(v)
sub_km = Orange.clustering.kmeans.Clustering(
data=sub_data, centroids=5, distance=EigDistance)
sub_clusters = sub_km.clusters
temp_d = dict()
for idx, c in enumerate(sub_clusters):
if not temp_d.has_key(c):
temp_d[c] = [v[idx]]
else:
temp_d[c].append(v[idx])
for sub_v in temp_d.values():
q.put(sub_v)
pass
else:
res_list.append(v)
pass
pass
clusters = [0] * len(eig_data)
for idx, res in enumerate(res_list):
for r in res:
clusters[r] = idx
pass
import igraph
self.vertex_clustering = igraph.clustering.VertexClustering(
self.g, clusters)
print 'writing vertex_clustering'
FSDao.write_pickle(self.expr_dir,
SQLDao.ce.properties['vertex_clustering_file_name'],
self.vertex_clustering)
print 'finished writing vertex_clustering'
