def infomap(self, inter_edge, threshold, update_method = None, **kwargs):
'''
Infomap helper function.
'''
im = Infomap("--two-level --directed --silent")
######### Make Network
## add intra edges
thresholded_adjacency = []
for l in range(self.length):
thresholded_adjacency.append(self.threshold(self.list_adjacency[l], thresh = threshold))
for n1,e in enumerate(thresholded_adjacency[l]):## list of length 2 corresponding to the adjacency matrices in each layer
for n2,w in enumerate(e):
s = MultilayerNode(layer_id = l, node_id = n1)
t = MultilayerNode(layer_id = l, node_id = n2)
im.add_multilayer_link(s, t, w)
im.add_multilayer_link(t, s, w)
## add inter edges
if update_method == 'local' or update_method == 'global':
updated_interlayer = self.update_interlayer(kwargs['spikes'], 0, inter_edge, 0.1, update_method)
for l in range(self.length-1):
for k in range(self.size):# number of nodes which is 60 in the multilayer network
s = MultilayerNode(layer_id = l, node_id = k)
t = MultilayerNode(layer_id = l+1, node_id = k)
im.add_multilayer_link(s, t, updated_interlayer[l][k])
im.add_multilayer_link(t, s, updated_interlayer[l][k])
elif update_method == 'neighborhood':
updated_interlayer_indices, updated_interlayer_weights = self.get_normalized_outlinks(thresholded_adjacency, inter_edge)
for l in range(self.length-1):
for k in range(self.size):
w, nbr = self.neighborhood_flow(l, k, updated_interlayer_indices, updated_interlayer_weights, threshold)
for n in nbr:
s = MultilayerNode(layer_id = l, node_id = k)
t = MultilayerNode(layer_id = l+1, node_id = n)
im.add_multilayer_link(s, t, w)
im.add_multilayer_link(t, s, w)
elif update_method == None:
for l in range(self.length-1):
for k in range(self.size):# number of nodes which is 60 in the multilayer network
s = MultilayerNode(layer_id = l, node_id = k)
t = MultilayerNode(layer_id = l+1, node_id = k)
im.add_multilayer_link(s, t, inter_edge)
im.add_multilayer_link(t, s, inter_edge)
im.run()
return(im)
def print_result(im):
print(
f"Found {im.num_top_modules} modules with codelength {im.codelength:.8f} bits"
)
print("#layer_id node_id module_id:")
for node in im.nodes:
print(f"{node.layer_id} {node.node_id} {node.module_id}")
im = Infomap(silent=True)
print("\nAdding multilayer network...")
# from (layer1, node1) to (layer2, node2) with optional weight
im.add_multilayer_link((2, 1), (1, 2), 1.0)
im.add_multilayer_link((1, 2), (2, 1), 1.0)
im.add_multilayer_link((3, 2), (2, 3), 1.0)
im.run()
print_result(im)
# Add only intra-layer links and let Infomap provide
# inter-layer links by relaxing the random walker's
# constraint to its current layer
im = Infomap(silent=True)
print("\nAdding intra-layer network...")
# Add layer_id, source_node_id, target_node_id and optional weight
im.add_multilayer_intra_link(1, 1, 2)