"""
*****
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.
"""
# 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.
import networkx as nx
from networkx.utils import is_string_like, open_file, make_str
__author__ = """Aric Hagberg <aric.hagberg@gmail.com>"""
__all__ = ['read_pajek', 'parse_pajek', 'generate_pajek', 'write_pajek']
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 = G.nodes()
# make dictionary mapping nodes to integers
nodenumber=dict(zip(nodes,range(1,len(nodes)+1)))
for n in nodes:
na=G.node.get(n,{})
x=na.get('x',0.0)
y=na.get('y',0.0)
id=int(na.get('id',nodenumber[n]))
nodenumber[n]=id
shape=na.get('shape','ellipse')
s=' '.join(map(make_qstr,(id,n,x,y,shape)))
for k,v in na.items():
s+=' %s %s'%(make_qstr(k),make_qstr(v))
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():
s+=' %s %s'%(make_qstr(k),make_qstr(v))
s+=' %s %s'%(k,v)
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")
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
while lines:
try:
l=next(lines)
except: #EOF
break
if l.lower().startswith("*network"):
try:
label, name = l.split()
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]
G.add_node(label)
nodelabels[id]=label
G.node[label]={'id':id}
try:
x,y,shape=splitline[2:5]
G.node[label].update({'x':float(x),
'y':float(y),
'shape':shape})
except:
pass
extra_attr=zip(splitline[5::2],splitline[6::2])
G.node[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)
return G
def make_qstr(t):
"""Return 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')