def findCommunities(G):
    """
	Partition network with the Infomap algorithm.
	Annotates nodes with 'community' id and return number of communities found.
	"""
    conf = infomap.init("--two-level")
    # Input data
    network = infomap.Network(conf)
    # Output data
    tree = infomap.HierarchicalNetwork(conf)

    print("Building network...")
    for e in G.edges_iter():
        network.addLink(*e)

    network.finalizeAndCheckNetwork(True, nx.number_of_nodes(G))

    # Cluster network
    infomap.run(network, tree)

    print("Found %d top modules with codelength: %f" % (tree.numTopModules(), tree.codelength()))

    communities = {}
    clusterIndexLevel = 1  # 1, 2, ... or -1 for top, second, ... or lowest cluster level
    for node in tree.leafIter(clusterIndexLevel):
        communities[node.originalLeafIndex] = node.clusterIndex()

    nx.set_node_attributes(G, "community", communities)
    return tree.numTopModules()
Exemple #2
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def findCommunities(G):
	"""
	Partition network with the Infomap algorithm.
	Annotates nodes with 'community' id and return number of communities found.
	"""
	conf = infomap.init("--two-level");
	# Input data
	network = infomap.Network(conf);
	# Output data
	tree = infomap.HierarchicalNetwork(conf)

	print "Building network..."
	for e in G.edges_iter():
		network.addLink(*e)

	network.finalizeAndCheckNetwork(True, nx.number_of_nodes(G));
	
	# Cluster network
	infomap.run(network, tree);
	codelength = tree.codelength()
	print "Codelength:", codelength

	communities = {}
	for leaf in tree.leafIter():
		communities[leaf.originalLeafIndex] = leaf.parentNode.parentIndex

	nx.set_node_attributes(G, 'community', communities)
	return tree.numTopModules()
Exemple #3
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def findCommunities(G):
	"""
	Partition network with the Infomap algorithm.
	Annotates nodes with 'community' id and return number of communities found.
	"""
	conf = infomap.init("--two-level");
	# Input data
	network = infomap.Network(conf);
	# Output data
	tree = infomap.HierarchicalNetwork(conf)

	print "Building network..."
	for e in G.edges_iter():
		network.addLink(*e)

	network.finalizeAndCheckNetwork(True, nx.number_of_nodes(G));

	# Cluster network
	infomap.run(network, tree);

	print "Found %d top modules with codelength: %f" % (tree.numTopModules(), tree.codelength())

	communities = {}
	clusterIndexLevel = 1 # 1, 2, ... or -1 for top, second, ... or lowest cluster level
	for node in tree.leafIter(clusterIndexLevel):
		communities[node.originalLeafIndex] = node.clusterIndex()

	nx.set_node_attributes(G, 'community', communities)
	return tree.numTopModules()
Exemple #4
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print "Creating network..."
network = infomap.Network(conf)

network.addLink(0, 1)
network.addLink(0, 2)
network.addLink(0, 3)
network.addLink(1, 0)
network.addLink(1, 2)
network.addLink(2, 1)
network.addLink(2, 0)
network.addLink(3, 0)
network.addLink(3, 4)
network.addLink(3, 5)
network.addLink(4, 3)
network.addLink(4, 5)
network.addLink(5, 4)
network.addLink(5, 3)

print "Num links:", network.numLinks()

network.finalizeAndCheckNetwork()

tree = infomap.HierarchicalNetwork(conf)

infomap.run(network, tree)

codelength = tree.codelength()

print "Codelength:", codelength
#!/usr/bin/env python
import os.path
from infomap import infomap

conf = infomap.init("--silent -N5")
# Add output directory (and output name) to automatically write result to file
# conf = infomap.init("--silent -N5 . --out-name test")

filename = "../../ninetriangles.net"
name = os.path.splitext(os.path.basename(filename))[0]
print("Loading network from '%s'..." % filename)
network = infomap.Network(conf)
network.readInputData(filename)

print("Running Infomap...")
tree = infomap.HierarchicalNetwork(conf)
infomap.run(network, tree)

print("Found %d top modules with codelength: %f" % (tree.numTopModules(), tree.codelength()))

print("Writing top level clusters to %s_level1.clu..." % name)
tree.writeClu("%s_level1.clu" % name, 1)
print("Writing second level clusters to %s_level2.clu..." % name)
tree.writeClu("%s_level2.clu" % name, 2)

print("Writing tree to %s.tree..." % name)
tree.writeHumanReadableTree("%s.tree" % name)

print("Done!")