# Copyright (C) 2008-2014 by
# Aric Hagberg <hagberg@lanl.gov>
# Dan Schult <dschult@colgate.edu>
# Pieter Swart <swart@lanl.gov>
# All rights reserved.
# BSD license.
#
# Authors: Aric Hagberg (hagberg@lanl.gov)
"""
*****
Pajek
*****
Read graphs in Pajek format.
This implementation handles directed and undirected graphs including
those with self loops and parallel edges.
Format
------
See http://vlado.fmf.uni-lj.si/pub/networks/pajek/doc/draweps.htm
for format information.
"""
import warnings
import networkx as nx
from networkx.utils import is_string_like, open_file, make_str
__all__ = ['read_pajek', 'parse_pajek', 'generate_pajek', 'write_pajek']
[docs]def generate_pajek(G):
"""Generate lines in Pajek graph format.
Parameters
----------
G : graph
A Networkx graph
References
----------
See http://vlado.fmf.uni-lj.si/pub/networks/pajek/doc/draweps.htm
for format information.
"""
if G.name == '':
name = 'NetworkX'
else:
name = G.name
# Apparently many Pajek format readers can't process this line
# So we'll leave it out for now.
# yield '*network %s'%name
# write nodes with attributes
yield '*vertices %s' % (G.order())
nodes = list(G)
# make dictionary mapping nodes to integers
nodenumber = dict(zip(nodes, range(1, len(nodes) + 1)))
for n in nodes:
# copy node attributes and pop mandatory attributes
# to avoid duplication.
na = G.nodes.get(n, {}).copy()
x = na.pop('x', 0.0)
y = na.pop('y', 0.0)
id = int(na.pop('id', nodenumber[n]))
nodenumber[n] = id
shape = na.pop('shape', 'ellipse')
s = ' '.join(map(make_qstr, (id, n, x, y, shape)))
# only optional attributes are left in na.
for k, v in na.items():
if is_string_like(v) and v.strip() != '':
s += ' %s %s' % (make_qstr(k), make_qstr(v))
else:
warnings.warn('Node attribute %s is not processed. %s.' %
(k,
'Empty attribute' if is_string_like(v) else
'Non-string attribute'))
yield s
# write edges with attributes
if G.is_directed():
yield '*arcs'
else:
yield '*edges'
for u, v, edgedata in G.edges(data=True):
d = edgedata.copy()
value = d.pop('weight', 1.0) # use 1 as default edge value
s = ' '.join(map(make_qstr, (nodenumber[u], nodenumber[v], value)))
for k, v in d.items():
if is_string_like(v) and v.strip() != '':
s += ' %s %s' % (make_qstr(k), make_qstr(v))
else:
warnings.warn('Edge attribute %s is not processed. %s.' %
(k,
'Empty attribute' if is_string_like(v) else
'Non-string attribute'))
yield s
[docs]@open_file(1, mode='wb')
def write_pajek(G, path, encoding='UTF-8'):
"""Write graph in Pajek format to path.
Parameters
----------
G : graph
A Networkx graph
path : file or string
File or filename to write.
Filenames ending in .gz or .bz2 will be compressed.
Examples
--------
>>> G=nx.path_graph(4)
>>> nx.write_pajek(G, "test.net")
Warnings
--------
Optional node attributes and edge attributes must be non-empty strings.
Otherwise it will not be written into the file. You will need to
convert those attributes to strings if you want to keep them.
References
----------
See http://vlado.fmf.uni-lj.si/pub/networks/pajek/doc/draweps.htm
for format information.
"""
for line in generate_pajek(G):
line += '\n'
path.write(line.encode(encoding))
[docs]@open_file(0, mode='rb')
def read_pajek(path, encoding='UTF-8'):
"""Read graph in Pajek format from path.
Parameters
----------
path : file or string
File or filename to write.
Filenames ending in .gz or .bz2 will be uncompressed.
Returns
-------
G : NetworkX MultiGraph or MultiDiGraph.
Examples
--------
>>> G=nx.path_graph(4)
>>> nx.write_pajek(G, "test.net")
>>> G=nx.read_pajek("test.net")
To create a Graph instead of a MultiGraph use
>>> G1=nx.Graph(G)
References
----------
See http://vlado.fmf.uni-lj.si/pub/networks/pajek/doc/draweps.htm
for format information.
"""
lines = (line.decode(encoding) for line in path)
return parse_pajek(lines)
[docs]def parse_pajek(lines):
"""Parse Pajek format graph from string or iterable.
Parameters
----------
lines : string or iterable
Data in Pajek format.
Returns
-------
G : NetworkX graph
See Also
--------
read_pajek()
"""
import shlex
# multigraph=False
if is_string_like(lines):
lines = iter(lines.split('\n'))
lines = iter([line.rstrip('\n') for line in lines])
G = nx.MultiDiGraph() # are multiedges allowed in Pajek? assume yes
labels = [] # in the order of the file, needed for matrix
while lines:
try:
l = next(lines)
except: # EOF
break
if l.lower().startswith("*network"):
try:
label, name = l.split(None, 1)
except ValueError:
# Line was not of the form: *network NAME
pass
else:
G.graph['name'] = name
elif l.lower().startswith("*vertices"):
nodelabels = {}
l, nnodes = l.split()
for i in range(int(nnodes)):
l = next(lines)
try:
splitline = [x.decode('utf-8') for x in
shlex.split(make_str(l).encode('utf-8'))]
except AttributeError:
splitline = shlex.split(str(l))
id, label = splitline[0:2]
labels.append(label)
G.add_node(label)
nodelabels[id] = label
G.nodes[label]['id'] = id
try:
x, y, shape = splitline[2:5]
G.nodes[label].update({'x': float(x),
'y': float(y),
'shape': shape})
except:
pass
extra_attr = zip(splitline[5::2], splitline[6::2])
G.nodes[label].update(extra_attr)
elif l.lower().startswith("*edges") or l.lower().startswith("*arcs"):
if l.lower().startswith("*edge"):
# switch from multidigraph to multigraph
G = nx.MultiGraph(G)
if l.lower().startswith("*arcs"):
# switch to directed with multiple arcs for each existing edge
G = G.to_directed()
for l in lines:
try:
splitline = [x.decode('utf-8') for x in
shlex.split(make_str(l).encode('utf-8'))]
except AttributeError:
splitline = shlex.split(str(l))
if len(splitline) < 2:
continue
ui, vi = splitline[0:2]
u = nodelabels.get(ui, ui)
v = nodelabels.get(vi, vi)
# parse the data attached to this edge and put in a dictionary
edge_data = {}
try:
# there should always be a single value on the edge?
w = splitline[2:3]
edge_data.update({'weight': float(w[0])})
except:
pass
# if there isn't, just assign a 1
# edge_data.update({'value':1})
extra_attr = zip(splitline[3::2], splitline[4::2])
edge_data.update(extra_attr)
# if G.has_edge(u,v):
# multigraph=True
G.add_edge(u, v, **edge_data)
elif l.lower().startswith("*matrix"):
G = nx.DiGraph(G)
adj_list = ((labels[row], labels[col], {'weight': int(data)})
for (row, line) in enumerate(lines)
for (col, data) in enumerate(line.split())
if int(data) != 0)
G.add_edges_from(adj_list)
return G
def make_qstr(t):
"""Returns the string representation of t.
Add outer double-quotes if the string has a space.
"""
if not is_string_like(t):
t = str(t)
if " " in t:
t = r'"%s"' % t
return t
# fixture for nose tests
def teardown_module(module):
import os
os.unlink('test.net')