def parse_p2g(lines):
"""Parse p2g format graph from string or iterable. Returns an XDiGraph."""
if is_string_like(lines): lines=iter(lines.split('\n'))
lines = iter([line.rstrip('\n') for line in lines])
description = lines.next()
# are multiedges (parallel edges) allowed?
G=networkx_v099.XDiGraph(name=description,selfloops=True)
nnodes,nedges=map(int,lines.next().split())
nodelabel={}
nbrs={}
# loop over the nodes keeping track of node labels and out neighbors
# defer adding edges until all node labels are known
for i in range(nnodes):
n=lines.next()
nodelabel[i]=n
G.add_node(n)
nbrs[n]=map(int,lines.next().split())
# now we know all of the node labels so we can add the edges
# with the correct labels
for n in G:
for nbr in nbrs[n]:
G.add_edge(n,nodelabel[nbr])
return G
def parse_p2g(lines):
"""Parse p2g format graph from string or iterable. Returns an XDiGraph."""
if is_string_like(lines): lines = iter(lines.split('\n'))
lines = iter([line.rstrip('\n') for line in lines])
description = lines.next()
# are multiedges (parallel edges) allowed?
G = networkx_v099.XDiGraph(name=description, selfloops=True)
nnodes, nedges = map(int, lines.next().split())
nodelabel = {}
nbrs = {}
# loop over the nodes keeping track of node labels and out neighbors
# defer adding edges until all node labels are known
for i in range(nnodes):
n = lines.next()
nodelabel[i] = n
G.add_node(n)
nbrs[n] = map(int, lines.next().split())
# now we know all of the node labels so we can add the edges
# with the correct labels
for n in G:
for nbr in nbrs[n]:
G.add_edge(n, nodelabel[nbr])
return G
def parse_pajek(lines):
"""Parse pajek format graph from string or iterable.."""
import shlex
if is_string_like(lines): lines = iter(lines.split('\n'))
lines = iter([line.rstrip('\n') for line in lines])
G = networkx_v099.XDiGraph(
selfloops=True) # are multiedges allowed in Pajek?
G.node_attr = {} # dictionary to hold node attributes
directed = True # assume this is a directed network for now
while lines:
try:
l = lines.next()
except: #EOF
break
if l.startswith("*network"):
label, name = l.split()
G.name = name
if l.startswith("*vertices"):
nodelabels = {}
l, nnodes = l.split()
for i in range(int(nnodes)):
splitline = shlex.split(lines.next())
id, label, x, y, shape = splitline[0:5]
G.add_node(label)
nodelabels[id] = label
G.node_attr[label] = {'id': id, 'x': x, 'y': y, 'shape': shape}
extra_attr = zip(splitline[5::2], splitline[6::2])
G.node_attr[label].update(extra_attr)
if l.startswith("*edges") or l.startswith("*arcs"):
if l.startswith("*edge"):
G = networkx_v099.XGraph(G) # switch from digraph to graph
for l in lines:
splitline = shlex.split(l)
ui, vi, w = splitline[0:3]
u = nodelabels.get(ui, ui)
v = nodelabels.get(vi, vi)
edge_data = {'value': float(w)}
extra_attr = zip(splitline[3::2], splitline[4::2])
edge_data.update(extra_attr)
G.add_edge(u, v, edge_data)
return G
def parse_pajek(lines):
"""Parse pajek format graph from string or iterable.."""
import shlex
if is_string_like(lines): lines=iter(lines.split('\n'))
lines = iter([line.rstrip('\n') for line in lines])
G=networkx_v099.XDiGraph(selfloops=True) # are multiedges allowed in Pajek?
G.node_attr={} # dictionary to hold node attributes
directed=True # assume this is a directed network for now
while lines:
try:
l=lines.next()
except: #EOF
break
if l.startswith("*network"):
label,name=l.split()
G.name=name
if l.startswith("*vertices"):
nodelabels={}
l,nnodes=l.split()
for i in range(int(nnodes)):
splitline=shlex.split(lines.next())
id,label,x,y,shape=splitline[0:5]
G.add_node(label)
nodelabels[id]=label
G.node_attr[label]={'id':id,'x':x,'y':y,'shape':shape}
extra_attr=zip(splitline[5::2],splitline[6::2])
G.node_attr[label].update(extra_attr)
if l.startswith("*edges") or l.startswith("*arcs"):
if l.startswith("*edge"):
G=networkx_v099.XGraph(G) # switch from digraph to graph
for l in lines:
splitline=shlex.split(l)
ui,vi,w=splitline[0:3]
u=nodelabels.get(ui,ui)
v=nodelabels.get(vi,vi)
edge_data={'value':float(w)}
extra_attr=zip(splitline[3::2],splitline[4::2])
edge_data.update(extra_attr)
G.add_edge(u,v,edge_data)
return G
def parse_leda(lines):
"""Parse LEDA.GRAPH format from string or iterable.
Returns an Graph or DiGraph."""
if is_string_like(lines): lines = iter(lines.split('\n'))
lines = iter([line.rstrip('\n') for line in lines \
if not (line.startswith('#') or line.startswith('\n') or line=='')])
for i in range(3):
lines.next()
# Graph
du = int(lines.next()) # -1 directed, -2 undirected
if du == -1:
G = networkx_v099.DiGraph()
else:
G = networkx_v099.Graph()
# Nodes
n = int(lines.next()) # number of vertices
node = {}
for i in range(1, n + 1): # LEDA counts from 1 to n
symbol = lines.next()[2:-3] # strip out data from |{data}|
if symbol == "":
symbol = str(i) # use int if no label - could be trouble
node[i] = symbol
G.add_nodes_from([s for i, s in node.items()])
# Edges
m = int(lines.next()) # number of edges
for i in range(m):
try:
s, t, reversal, label = lines.next().split()
except:
raise NetworkXError,\
'Too few fields in LEDA.GRAPH edge %d' % (i+1)
# BEWARE: no handling of reversal edges
G.add_edge(node[int(s)], node[int(t)], label[2:-2])
return G
def parse_leda(lines):
"""Parse LEDA.GRAPH format from string or iterable.
Returns an Graph or DiGraph."""
if is_string_like(lines): lines=iter(lines.split('\n'))
lines = iter([line.rstrip('\n') for line in lines \
if not (line.startswith('#') or line.startswith('\n') or line=='')])
for i in range(3):
lines.next()
# Graph
du = int(lines.next()) # -1 directed, -2 undirected
if du==-1:
G = networkx_v099.DiGraph()
else:
G = networkx_v099.Graph()
# Nodes
n =int(lines.next()) # number of vertices
node={}
for i in range(1,n+1): # LEDA counts from 1 to n
symbol=lines.next()[2:-3] # strip out data from |{data}|
if symbol=="": symbol=str(i) # use int if no label - could be trouble
node[i]=symbol
G.add_nodes_from([s for i,s in node.items()])
# Edges
m = int(lines.next()) # number of edges
for i in range(m):
try:
s,t,reversal,label=lines.next().split()
except:
raise NetworkXError,\
'Too few fields in LEDA.GRAPH edge %d' % (i+1)
# BEWARE: no handling of reversal edges
G.add_edge(node[int(s)],node[int(t)],label[2:-2])
return G
def make_str(t):
if is_string_like(t): return t
return str(t)
def union(G,H,create_using=None,rename=False,name=None):
""" Return the union of graphs G and H.
Graphs G and H must be disjoint, otherwise an exception is raised.
Node names of G and H can be changed be specifying the tuple
rename=('G-','H-') (for example).
Node u in G is then renamed "G-u" and v in H is renamed "H-v".
To force a disjoint union with node relabeling, use
disjoint_union(G,H) or convert_node_labels_to integers().
Optional create_using=R returns graph R filled in with the
union of G and H. Otherwise a new graph is created, of the
same class as G. It is recommended that G and H be either
both directed or both undirected.
A new name can be specified in the form
X=union(G,H,name="new_name")
Implemented for Graph, DiGraph, XGraph, XDiGraph.
"""
if name is None:
name="union( %s, %s )"%(G.name,H.name)
if create_using is None:
R=G.__class__()
else:
R=create_using
R.clear()
R.name=name
# rename graph to obtain disjoint node labels
# note that for objects w/o succinct __name__,
# the new labels can be quite verbose
# See also disjoint_union
if rename: # create new string labels
Gname={}
Hname={}
for v in G:
if is_string_like(v):
Gname[v]=rename[0]+v
else:
Gname[v]=rename[0]+repr(v)
for v in H:
if is_string_like(v):
Hname[v]=rename[1]+v
else:
Hname[v]=rename[1]+repr(v)
else:
Gname=dict( ((v,v) for v in G) )
Hname=dict( ((v,v) for v in H) )
# node name check
Hnames=set(Hname.values())
Gnames=set(Gname.values())
if Gnames & Hnames:
raise networkx_v099.NetworkXError,\
"node sets of G and H are not disjoint. Use appropriate rename=('Gprefix','Hprefix')"
# node names OK, now build union
R.add_nodes_from(Gnames)
R.add_edges_from( ( (Gname[u],Gname[v],x) for u,v,x in G.edges_iter(data=True) ))
R.add_nodes_from(Hnames)
R.add_edges_from( ( (Hname[u],Hname[v],x) for u,v,x in H.edges_iter(data=True) ))
return R
def make_str(t):
if is_string_like(t): return t
return str(t)
def write_gml(G, path):
"""
Write the graph G in GML format to the file or file handle path.
Examples
---------
>>> G=nx.path_graph(4)
>>> nx.write_gml(G,"test.gml")
path can be a filehandle or a string with the name of the file.
>>> fh=open("test.gml",'w')
>>> nx.write_gml(G,fh)
Filenames ending in .gz or .bz2 will be compressed.
>>> nx.write_gml(G,"test.gml.gz")
The output file will use the default text encoding on your system.
It is possible to write files in other encodings by opening
the file with the codecs module. See doc/examples/unicode.py
for hints.
>>> import codecs
>>> fh=codecs.open("test.gml",'w',encoding='iso8859-1')# use iso8859-1
>>> nx.write_gml(G,fh)
GML specifications indicate that the file should only use
7bit ASCII text encoding.iso8859-1 (latin-1).
Only a single level of attributes for graphs, nodes, and edges,
is supported.
"""
fh = _get_fh(path, mode='w')
# comments="#"
# pargs=comments+" "+' '.join(sys.argv)
# fh.write("%s\n" % (pargs))
# fh.write(comments+" GMT %s\n" % (time.asctime(time.gmtime())))
# fh.write(comments+" %s\n" % (G.name))
# check for attributes or assign empty dict
if hasattr(G, 'graph_attr'):
graph_attr = G.graph_attr
else:
graph_attr = {}
if hasattr(G, 'node_attr'):
node_attr = G.node_attr
else:
node_attr = {}
indent = 2 * ' '
count = iter(range(G.number_of_nodes()))
node_id = {}
fh.write("graph [\n")
# write graph attributes
for k, v in graph_attr.items():
if is_string_like(v):
v = '"' + v + '"'
fh.write(indent + "%s %s\n" % (k, v))
# write nodes
for n in G:
fh.write(indent + "node [\n")
# get id or assign number
if n in node_attr:
nid = node_attr[n].get('id', count.next())
else:
nid = count.next()
node_id[n] = nid
fh.write(2 * indent + "id %s\n" % nid)
fh.write(2 * indent + "label \"%s\"\n" % n)
if n in node_attr:
for k, v in node_attr[n].items():
if is_string_like(v): v = '"' + v + '"'
if k == 'id': continue
fh.write(2 * indent + "%s %s\n" % (k, v))
fh.write(indent + "]\n")
# write edges
for e in G.edges_iter():
if len(e) == 3:
u, v, d = e
# try to guess what is on the edge and do something reasonable
edgedata = {}
if d is None: # no data
pass
elif hasattr(d, 'iteritems'): # try dict-like
edgedata = dict(d.iteritems())
elif hasattr(d, '__iter__'): # some kind of container
edgedata['data'] = d.__repr__()
else: # something else - string, number
edgedata['data'] = d
else:
u, v = e
edgedata = {}
fh.write(indent + "edge [\n")
fh.write(2 * indent + "source %s\n" % node_id[u])
fh.write(2 * indent + "target %s\n" % node_id[v])
for k, v in edgedata.items():
if k == 'source': continue
if k == 'target': continue
if is_string_like(v): v = '"' + v + '"'
fh.write(2 * indent + "%s %s\n" % (k, v))
fh.write(indent + "]\n")
fh.write("]\n")
def write_gml(G, path):
"""
Write the graph G in GML format to the file or file handle path.
Examples
---------
>>> G=nx.path_graph(4)
>>> nx.write_gml(G,"test.gml")
path can be a filehandle or a string with the name of the file.
>>> fh=open("test.gml",'w')
>>> nx.write_gml(G,fh)
Filenames ending in .gz or .bz2 will be compressed.
>>> nx.write_gml(G,"test.gml.gz")
The output file will use the default text encoding on your system.
It is possible to write files in other encodings by opening
the file with the codecs module. See doc/examples/unicode.py
for hints.
>>> import codecs
>>> fh=codecs.open("test.gml",'w',encoding='iso8859-1')# use iso8859-1
>>> nx.write_gml(G,fh)
GML specifications indicate that the file should only use
7bit ASCII text encoding.iso8859-1 (latin-1).
Only a single level of attributes for graphs, nodes, and edges,
is supported.
"""
fh=_get_fh(path,mode='w')
# comments="#"
# pargs=comments+" "+' '.join(sys.argv)
# fh.write("%s\n" % (pargs))
# fh.write(comments+" GMT %s\n" % (time.asctime(time.gmtime())))
# fh.write(comments+" %s\n" % (G.name))
# check for attributes or assign empty dict
if hasattr(G,'graph_attr'):
graph_attr=G.graph_attr
else:
graph_attr={}
if hasattr(G,'node_attr'):
node_attr=G.node_attr
else:
node_attr={}
indent=2*' '
count=iter(range(G.number_of_nodes()))
node_id={}
fh.write("graph [\n")
# write graph attributes
for k,v in graph_attr.items():
if is_string_like(v):
v='"'+v+'"'
fh.write(indent+"%s %s\n"%(k,v))
# write nodes
for n in G:
fh.write(indent+"node [\n")
# get id or assign number
if n in node_attr:
nid=node_attr[n].get('id',count.next())
else:
nid=count.next()
node_id[n]=nid
fh.write(2*indent+"id %s\n"%nid)
fh.write(2*indent+"label \"%s\"\n"%n)
if n in node_attr:
for k,v in node_attr[n].items():
if is_string_like(v): v='"'+v+'"'
if k=='id': continue
fh.write(2*indent+"%s %s\n"%(k,v))
fh.write(indent+"]\n")
# write edges
for e in G.edges_iter():
if len(e)==3:
u,v,d=e
# try to guess what is on the edge and do something reasonable
edgedata={}
if d is None: # no data
pass
elif hasattr(d,'iteritems'): # try dict-like
edgedata=dict(d.iteritems())
elif hasattr(d,'__iter__'): # some kind of container
edgedata['data']=d.__repr__()
else: # something else - string, number
edgedata['data']=d
else:
u,v=e
edgedata={}
fh.write(indent+"edge [\n")
fh.write(2*indent+"source %s\n"%node_id[u])
fh.write(2*indent+"target %s\n"%node_id[v])
for k,v in edgedata.items():
if k=='source': continue
if k=='target': continue
if is_string_like(v): v='"'+v+'"'
fh.write(2*indent+"%s %s\n"%(k,v))
fh.write(indent+"]\n")
fh.write("]\n")
