"""
*****
Pydot
*****
Import and export NetworkX graphs in Graphviz dot format using pydot.
Either this module or nx_pygraphviz can be used to interface with graphviz.
See Also
--------
Pydot: http://code.google.com/p/pydot/
Graphviz: http://www.research.att.com/sw/tools/graphviz/
DOT Language: http://www.graphviz.org/doc/info/lang.html
"""
# Copyright (C) 2004-2011 by
# Aric Hagberg <hagberg@lanl.gov>
# Dan Schult <dschult@colgate.edu>
# Pieter Swart <swart@lanl.gov>
# All rights reserved.
# BSD license.
from networkx.utils import open_file
import networkx as nx
__author__ = """Aric Hagberg (hagberg@lanl.gov)"""
__all__ = ['write_dot', 'read_dot', 'graphviz_layout', 'pydot_layout',
'to_pydot', 'from_pydot']
@open_file(1,mode='w')
[docs]def write_dot(G,path):
"""Write NetworkX graph G to Graphviz dot format on path.
Path can be a string or a file handle.
"""
try:
import pydot
except ImportError:
raise ImportError("write_dot() requires pydot",
"http://code.google.com/p/pydot/")
P=to_pydot(G)
path.write(P.to_string())
return
@open_file(0,mode='r')
[docs]def read_dot(path):
"""Return a NetworkX MultiGraph or MultiDiGraph from a dot file on path.
Parameters
----------
path : filename or file handle
Returns
-------
G : NetworkX multigraph
A MultiGraph or MultiDiGraph.
Notes
-----
Use G=nx.Graph(nx.read_dot(path)) to return a Graph instead of a MultiGraph.
"""
try:
import pydot
except ImportError:
raise ImportError("read_dot() requires pydot",
"http://code.google.com/p/pydot/")
data=path.read()
P=pydot.graph_from_dot_data(data)
return from_pydot(P)
[docs]def from_pydot(P):
"""Return a NetworkX graph from a Pydot graph.
Parameters
----------
P : Pydot graph
A graph created with Pydot
Returns
-------
G : NetworkX multigraph
A MultiGraph or MultiDiGraph.
Examples
--------
>>> K5=nx.complete_graph(5)
>>> A=nx.to_pydot(K5)
>>> G=nx.from_pydot(A) # return MultiGraph
>>> G=nx.Graph(nx.from_pydot(A)) # make a Graph instead of MultiGraph
"""
if P.get_strict(None): # pydot bug: get_strict() shouldn't take argument
multiedges=False
else:
multiedges=True
if P.get_type()=='graph': # undirected
if multiedges:
create_using=nx.MultiGraph()
else:
create_using=nx.Graph()
else:
if multiedges:
create_using=nx.MultiDiGraph()
else:
create_using=nx.DiGraph()
# assign defaults
N=nx.empty_graph(0,create_using)
N.name=P.get_name()
# add nodes, attributes to N.node_attr
for p in P.get_node_list():
n=p.get_name().strip('"')
if n in ('node','graph','edge'):
continue
N.add_node(n,**p.get_attributes())
# add edges
for e in P.get_edge_list():
u=e.get_source().strip('"')
v=e.get_destination().strip('"')
attr=e.get_attributes()
N.add_edge(u,v,**attr)
# add default attributes for graph, nodes, edges
N.graph['graph']=P.get_attributes()
try:
N.graph['node']=P.get_node_defaults()[0]
except:# IndexError,TypeError:
N.graph['node']={}
try:
N.graph['edge']=P.get_edge_defaults()[0]
except:# IndexError,TypeError:
N.graph['edge']={}
return N
[docs]def to_pydot(N, strict=True):
"""Return a pydot graph from a NetworkX graph N.
Parameters
----------
N : NetworkX graph
A graph created with NetworkX
Examples
--------
>>> K5=nx.complete_graph(5)
>>> P=nx.to_pydot(K5)
Notes
-----
"""
try:
import pydot
except ImportError:
raise ImportError('to_pydot() requires pydot: '
'http://code.google.com/p/pydot/')
# set Graphviz graph type
if N.is_directed():
graph_type='digraph'
else:
graph_type='graph'
strict=N.number_of_selfloops()==0 and not N.is_multigraph()
name = N.graph.get('name')
graph_defaults=N.graph.get('graph',{})
if name is None:
P = pydot.Dot(graph_type=graph_type,strict=strict,**graph_defaults)
else:
P = pydot.Dot('"%s"'%name,graph_type=graph_type,strict=strict,
**graph_defaults)
try:
P.set_node_defaults(**N.graph['node'])
except KeyError:
pass
try:
P.set_edge_defaults(**N.graph['edge'])
except KeyError:
pass
for n,nodedata in N.nodes_iter(data=True):
str_nodedata=dict((k,str(v)) for k,v in nodedata.items())
p=pydot.Node(str(n),**str_nodedata)
P.add_node(p)
if N.is_multigraph():
for u,v,key,edgedata in N.edges_iter(data=True,keys=True):
str_edgedata=dict((k,str(v)) for k,v in edgedata.items())
edge=pydot.Edge(str(u),str(v),key=str(key),**str_edgedata)
P.add_edge(edge)
else:
for u,v,edgedata in N.edges_iter(data=True):
str_edgedata=dict((k,str(v)) for k,v in edgedata.items())
edge=pydot.Edge(str(u),str(v),**str_edgedata)
P.add_edge(edge)
return P
def pydot_from_networkx(N):
"""Create a Pydot graph from a NetworkX graph."""
from warnings import warn
warn('pydot_from_networkx is replaced by to_pydot', DeprecationWarning)
return to_pydot(N)
def networkx_from_pydot(D, create_using=None):
"""Create a NetworkX graph from a Pydot graph."""
from warnings import warn
warn('networkx_from_pydot is replaced by from_pydot',
DeprecationWarning)
return from_pydot(D)
[docs]def graphviz_layout(G,prog='neato',root=None, **kwds):
"""Create node positions using Pydot and Graphviz.
Returns a dictionary of positions keyed by node.
Examples
--------
>>> G=nx.complete_graph(4)
>>> pos=nx.graphviz_layout(G)
>>> pos=nx.graphviz_layout(G,prog='dot')
Notes
-----
This is a wrapper for pydot_layout.
"""
return pydot_layout(G=G,prog=prog,root=root,**kwds)
[docs]def pydot_layout(G,prog='neato',root=None, **kwds):
"""Create node positions using Pydot and Graphviz.
Returns a dictionary of positions keyed by node.
Examples
--------
>>> G=nx.complete_graph(4)
>>> pos=nx.pydot_layout(G)
>>> pos=nx.pydot_layout(G,prog='dot')
"""
try:
import pydot
except ImportError:
raise ImportError('pydot_layout() requires pydot ',
'http://code.google.com/p/pydot/')
P=to_pydot(G)
if root is not None :
P.set("root",str(root))
D=P.create_dot(prog=prog)
if D=="": # no data returned
print("Graphviz layout with %s failed"%(prog))
print()
print("To debug what happened try:")
print("P=pydot_from_networkx(G)")
print("P.write_dot(\"file.dot\")")
print("And then run %s on file.dot"%(prog))
return
Q=pydot.graph_from_dot_data(D)
node_pos={}
for n in G.nodes():
node=Q.get_node(pydot.Node(str(n)).get_name())
if isinstance(node,list):
node=node[0]
pos=node.get_pos()[1:-1] # strip leading and trailing double quotes
if pos != None:
xx,yy=pos.split(",")
node_pos[n]=(float(xx),float(yy))
return node_pos
# fixture for nose tests
def setup_module(module):
from nose import SkipTest
try:
import pydot
except:
raise SkipTest("pydot not available")