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#-*- coding: utf-8 -*-
"""
Mixing matrices for node attributes and degree.
"""
import networkx as nx
from networkx.utils import dict_to_numpy_array
from networkx.algorithms.assortativity.pairs import node_degree_xy, \
node_attribute_xy
__author__ = ' '.join(['Aric Hagberg <aric.hagberg@gmail.com>'])
__all__ = ['attribute_mixing_matrix',
'attribute_mixing_dict',
'degree_mixing_matrix',
'degree_mixing_dict',
'numeric_mixing_matrix',
'mixing_dict']
def attribute_mixing_dict(G,attribute,nodes=None,normalized=False):
"""Return dictionary representation of mixing matrix for attribute.
Parameters
----------
G : graph
NetworkX graph object.
attribute : string
Node attribute key.
nodes: list or iterable (optional)
Unse nodes in container to build the dict. The default is all nodes.
normalized : bool (default=False)
Return counts if False or probabilities if True.
Examples
--------
>>> G=nx.Graph()
>>> G.add_nodes_from([0,1],color='red')
>>> G.add_nodes_from([2,3],color='blue')
>>> G.add_edge(1,3)
>>> d=nx.attribute_mixing_dict(G,'color')
>>> print(d['red']['blue'])
1
>>> print(d['blue']['red']) # d symmetric for undirected graphs
1
Returns
-------
d : dictionary
Counts or joint probability of occurrence of attribute pairs.
"""
xy_iter=node_attribute_xy(G,attribute,nodes)
return mixing_dict(xy_iter,normalized=normalized)
def attribute_mixing_matrix(G,attribute,nodes=None,mapping=None,
normalized=True):
"""Return mixing matrix for attribute.
Parameters
----------
G : graph
NetworkX graph object.
attribute : string
Node attribute key.
nodes: list or iterable (optional)
Use only nodes in container to build the matrix. The default is
all nodes.
mapping : dictionary, optional
Mapping from node attribute to integer index in matrix.
If not specified, an arbitrary ordering will be used.
normalized : bool (default=False)
Return counts if False or probabilities if True.
Returns
-------
m: numpy array
Counts or joint probability of occurrence of attribute pairs.
"""
d=attribute_mixing_dict(G,attribute,nodes)
a=dict_to_numpy_array(d,mapping=mapping)
if normalized:
a=a/a.sum()
return a
def degree_mixing_dict(G, x='out', y='in', weight=None,
nodes=None, normalized=False):
"""Return dictionary representation of mixing matrix for degree.
Parameters
----------
G : graph
NetworkX graph object.
x: string ('in','out')
The degree type for source node (directed graphs only).
y: string ('in','out')
The degree type for target node (directed graphs only).
weight: string or None, optional (default=None)
The edge attribute that holds the numerical value used
as a weight. If None, then each edge has weight 1.
The degree is the sum of the edge weights adjacent to the node.
normalized : bool (default=False)
Return counts if False or probabilities if True.
Returns
-------
d: dictionary
Counts or joint probability of occurrence of degree pairs.
"""
xy_iter=node_degree_xy(G, x=x, y=y, nodes=nodes, weight=weight)
return mixing_dict(xy_iter,normalized=normalized)
def degree_mixing_matrix(G, x='out', y='in', weight=None,
nodes=None, normalized=True):
"""Return mixing matrix for attribute.
Parameters
----------
G : graph
NetworkX graph object.
x: string ('in','out')
The degree type for source node (directed graphs only).
y: string ('in','out')
The degree type for target node (directed graphs only).
nodes: list or iterable (optional)
Build the matrix using only nodes in container.
The default is all nodes.
weight: string or None, optional (default=None)
The edge attribute that holds the numerical value used
as a weight. If None, then each edge has weight 1.
The degree is the sum of the edge weights adjacent to the node.
normalized : bool (default=False)
Return counts if False or probabilities if True.
Returns
-------
m: numpy array
Counts, or joint probability, of occurrence of node degree.
"""
d=degree_mixing_dict(G, x=x, y=y, nodes=nodes, weight=weight)
s=set(d.keys())
for k,v in d.items():
s.update(v.keys())
m=max(s)
mapping=dict(zip(range(m+1),range(m+1)))
a=dict_to_numpy_array(d,mapping=mapping)
if normalized:
a=a/a.sum()
return a
def numeric_mixing_matrix(G,attribute,nodes=None,normalized=True):
"""Return numeric mixing matrix for attribute.
Parameters
----------
G : graph
NetworkX graph object.
attribute : string
Node attribute key.
nodes: list or iterable (optional)
Build the matrix only with nodes in container. The default is all nodes.
normalized : bool (default=False)
Return counts if False or probabilities if True.
Returns
-------
m: numpy array
Counts, or joint, probability of occurrence of node attribute pairs.
"""
d=attribute_mixing_dict(G,attribute,nodes)
s=set(d.keys())
for k,v in d.items():
s.update(v.keys())
m=max(s)
mapping=dict(zip(range(m+1),range(m+1)))
a=dict_to_numpy_array(d,mapping=mapping)
if normalized:
a=a/a.sum()
return a
def mixing_dict(xy,normalized=False):
"""Return a dictionary representation of mixing matrix.
Parameters
----------
xy : list or container of two-tuples
Pairs of (x,y) items.
attribute : string
Node attribute key
normalized : bool (default=False)
Return counts if False or probabilities if True.
Returns
-------
d: dictionary
Counts or Joint probability of occurrence of values in xy.
"""
d={}
psum=0.0
for x,y in xy:
if x not in d:
d[x]={}
if y not in d:
d[y]={}
v = d[x].get(y,0)
d[x][y] = v+1
psum+=1
if normalized:
for k,jdict in d.items():
for j in jdict:
jdict[j]/=psum
return d
# fixture for nose tests
def setup_module(module):
from nose import SkipTest
try:
import numpy
except:
raise SkipTest("NumPy not available")
try:
import scipy
except:
raise SkipTest("SciPy not available")
|
