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Source code for networkx.algorithms.connectivity.kcomponents
# -*- coding: utf-8 -*-
"""
Moody and White algorithm for k-components
"""
from collections import defaultdict
from itertools import combinations
from operator import itemgetter
import networkx as nx
from networkx.utils import not_implemented_for
# Define the default maximum flow function.
from networkx.algorithms.flow import edmonds_karp
default_flow_func = edmonds_karp
__author__ = '\n'.join(['Jordi Torrents <jtorrents@milnou.net>'])
__all__ = ['k_components']
@not_implemented_for('directed')
[docs]def k_components(G, flow_func=None):
r"""Returns the k-component structure of a graph G.
A `k`-component is a maximal subgraph of a graph G that has, at least,
node connectivity `k`: we need to remove at least `k` nodes to break it
into more components. `k`-components have an inherent hierarchical
structure because they are nested in terms of connectivity: a connected
graph can contain several 2-components, each of which can contain
one or more 3-components, and so forth.
Parameters
----------
G : NetworkX graph
flow_func : function
Function to perform the underlying flow computations. Default value
:meth:`edmonds_karp`. This function performs better in sparse graphs with
right tailed degree distributions. :meth:`shortest_augmenting_path` will
perform better in denser graphs.
Returns
-------
k_components : dict
Dictionary with all connectivity levels `k` in the input Graph as keys
and a list of sets of nodes that form a k-component of level `k` as
values.
Raises
------
NetworkXNotImplemented:
If the input graph is directed.
Examples
--------
>>> # Petersen graph has 10 nodes and it is triconnected, thus all
>>> # nodes are in a single component on all three connectivity levels
>>> G = nx.petersen_graph()
>>> k_components = nx.k_components(G)
Notes
-----
Moody and White [1]_ (appendix A) provide an algorithm for identifying
k-components in a graph, which is based on Kanevsky's algorithm [2]_
for finding all minimum-size node cut-sets of a graph (implemented in
:meth:`all_node_cuts` function):
1. Compute node connectivity, k, of the input graph G.
2. Identify all k-cutsets at the current level of connectivity using
Kanevsky's algorithm.
3. Generate new graph components based on the removal of
these cutsets. Nodes in a cutset belong to both sides
of the induced cut.
4. If the graph is neither complete nor trivial, return to 1;
else end.
This implementation also uses some heuristics (see [3]_ for details)
to speed up the computation.
See also
--------
node_connectivity
all_node_cuts
References
----------
.. [1] Moody, J. and D. White (2003). Social cohesion and embeddedness:
A hierarchical conception of social groups.
American Sociological Review 68(1), 103--28.
http://www2.asanet.org/journals/ASRFeb03MoodyWhite.pdf
.. [2] Kanevsky, A. (1993). Finding all minimum-size separating vertex
sets in a graph. Networks 23(6), 533--541.
http://onlinelibrary.wiley.com/doi/10.1002/net.3230230604/abstract
.. [3] Torrents, J. and F. Ferraro (2015). Structural Cohesion:
Visualization and Heuristics for Fast Computation.
http://arxiv.org/pdf/1503.04476v1
"""
# Dictionary with connectivity level (k) as keys and a list of
# sets of nodes that form a k-component as values. Note that
# k-compoents can overlap (but only k - 1 nodes).
k_components = defaultdict(list)
# Define default flow function
if flow_func is None:
flow_func = default_flow_func
# Bicomponents as a base to check for higher order k-components
for component in nx.connected_components(G):
# isolated nodes have connectivity 0
comp = set(component)
if len(comp) > 1:
k_components[1].append(comp)
bicomponents = list(nx.biconnected_component_subgraphs(G))
for bicomponent in bicomponents:
bicomp = set(bicomponent)
# avoid considering dyads as bicomponents
if len(bicomp) > 2:
k_components[2].append(bicomp)
for B in bicomponents:
if len(B) <= 2:
continue
k = nx.node_connectivity(B, flow_func=flow_func)
if k > 2:
k_components[k].append(set(B.nodes_iter()))
# Perform cuts in a DFS like order.
cuts = list(nx.all_node_cuts(B, k=k, flow_func=flow_func))
stack = [(k, _generate_partition(B, cuts, k))]
while stack:
(parent_k, partition) = stack[-1]
try:
nodes = next(partition)
C = B.subgraph(nodes)
this_k = nx.node_connectivity(C, flow_func=flow_func)
if this_k > parent_k and this_k > 2:
k_components[this_k].append(set(C.nodes_iter()))
cuts = list(nx.all_node_cuts(C, k=this_k, flow_func=flow_func))
if cuts:
stack.append((this_k, _generate_partition(C, cuts, this_k)))
except StopIteration:
stack.pop()
# This is necessary because k-components may only be reported at their
# maximum k level. But we want to return a dictionary in which keys are
# connectivity levels and values list of sets of components, without
# skipping any connectivity level. Also, it's possible that subsets of
# an already detected k-component appear at a level k. Checking for this
# in the while loop above penalizes the common case. Thus we also have to
# _consolidate all connectivity levels in _reconstruct_k_components.
return _reconstruct_k_components(k_components)
def _consolidate(sets, k):
"""Merge sets that share k or more elements.
See: http://rosettacode.org/wiki/Set_consolidation
The iterative python implementation posted there is
faster than this because of the overhead of building a
Graph and calling nx.connected_components, but it's not
clear for us if we can use it in NetworkX because there
is no licence for the code.
"""
G = nx.Graph()
nodes = {i: s for i, s in enumerate(sets)}
G.add_nodes_from(nodes)
G.add_edges_from((u, v) for u, v in combinations(nodes, 2)
if len(nodes[u] & nodes[v]) >= k)
for component in nx.connected_components(G):
yield set.union(*[nodes[n] for n in component])
def _generate_partition(G, cuts, k):
def has_nbrs_in_partition(G, node, partition):
for n in G[node]:
if n in partition:
return True
return False
components = []
nodes = ({n for n, d in G.degree().items() if d > k} -
{n for cut in cuts for n in cut})
H = G.subgraph(nodes)
for cc in nx.connected_components(H):
component = set(cc)
for cut in cuts:
for node in cut:
if has_nbrs_in_partition(G, node, cc):
component.add(node)
if len(component) < G.order():
components.append(component)
for component in _consolidate(components, k+1):
yield component
def _reconstruct_k_components(k_comps):
result = dict()
max_k = max(k_comps)
for k in reversed(range(1, max_k+1)):
if k == max_k:
result[k] = list(_consolidate(k_comps[k], k))
elif k not in k_comps:
result[k] = list(_consolidate(result[k+1], k))
else:
nodes_at_k = set.union(*k_comps[k])
to_add = [c for c in result[k+1] if any(n not in nodes_at_k for n in c)]
if to_add:
result[k] = list(_consolidate(k_comps[k] + to_add, k))
else:
result[k] = list(_consolidate(k_comps[k], k))
return result
def build_k_number_dict(kcomps):
result = {}
for k, comps in sorted(kcomps.items(), key=itemgetter(0)):
for comp in comps:
for node in comp:
result[node] = k
return result