1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
|
"""
*****
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
@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))
@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)
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')
|
