"""
*****
Pydot
*****
Import and export NetworkX graphs in Graphviz dot format using pydotplus.
Either this module or nx_agraph can be used to interface with graphviz.
See Also
--------
PyDotPlus: https://github.com/carlos-jenkins/pydotplus
Graphviz: http://www.research.att.com/sw/tools/graphviz/
DOT Language: http://www.graphviz.org/doc/info/lang.html
"""
# Author: Aric Hagberg (aric.hagberg@gmail.com)
# Copyright (C) 2004-2016 by
# Aric Hagberg <hagberg@lanl.gov>
# Dan Schult <dschult@colgate.edu>
# Pieter Swart <swart@lanl.gov>
# All rights reserved.
# BSD license.
import importlib
from networkx.utils import open_file, make_str
import networkx as nx
__all__ = ['write_dot', 'read_dot', 'graphviz_layout', 'pydot_layout',
'to_pydot', 'from_pydot']
# 2.x/3.x compatibility
try:
basestring
except NameError:
basestring = str
[docs]@open_file(1, mode='w')
def write_dot(G, path):
"""Write NetworkX graph G to Graphviz dot format on path.
Path can be a string or a file handle.
"""
P=to_pydot(G)
path.write(P.to_string())
return
[docs]@open_file(0, mode='r')
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(read_dot(path)) to return a Graph instead of a MultiGraph.
"""
import pydotplus
data = path.read()
P = pydotplus.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.nx_pydot.to_pydot(K5)
>>> G = nx.nx_pydot.from_pydot(A) # return MultiGraph
# make a Graph instead of MultiGraph
>>> G = nx.Graph(nx.nx_pydot.from_pydot(A))
"""
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:
N = nx.MultiGraph()
else:
N = nx.Graph()
else:
if multiedges:
N = nx.MultiDiGraph()
else:
N = nx.DiGraph()
# assign defaults
name=P.get_name().strip('"')
if name != '':
N.name = 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()
v=e.get_destination()
attr=e.get_attributes()
s=[]
d=[]
if isinstance(u, basestring):
s.append(u.strip('"'))
else:
for unodes in u['nodes']:
s.append(unodes.strip('"'))
if isinstance(v, basestring):
d.append(v.strip('"'))
else:
for vnodes in v['nodes']:
d.append(vnodes.strip('"'))
for source_node in s:
for destination_node in d:
N.add_edge(source_node,destination_node,**attr)
# add default attributes for graph, nodes, edges
pattr = P.get_attributes()
if pattr:
N.graph['graph'] = pattr
try:
N.graph['node']=P.get_node_defaults()[0]
except:# IndexError,TypeError:
pass #N.graph['node']={}
try:
N.graph['edge']=P.get_edge_defaults()[0]
except:# IndexError,TypeError:
pass #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.nx_pydot.to_pydot(K5)
Notes
-----
"""
import pydotplus
# 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.name
graph_defaults=N.graph.get('graph',{})
if name is '':
P = pydotplus.Dot('', graph_type=graph_type, strict=strict,
**graph_defaults)
else:
P = pydotplus.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,make_str(v)) for k,v in nodedata.items())
p=pydotplus.Node(make_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,make_str(v)) for k,v in edgedata.items())
edge=pydotplus.Edge(make_str(u), make_str(v),
key=make_str(key), **str_edgedata)
P.add_edge(edge)
else:
for u,v,edgedata in N.edges_iter(data=True):
str_edgedata=dict((k,make_str(v)) for k,v in edgedata.items())
edge=pydotplus.Edge(make_str(u),make_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.nx_pydot.graphviz_layout(G)
>>> pos = nx.nx_pydot.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.nx_pydot.pydot_layout(G)
>>> pos = nx.nx_pydot.pydot_layout(G, prog='dot')
"""
import pydotplus
P=to_pydot(G)
if root is not None :
P.set("root",make_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=pydotplus.graph_from_dot_data(D)
node_pos={}
for n in G.nodes():
pydot_node = pydotplus.Node(make_str(n)).get_name()
node=Q.get_node(pydot_node)
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 pydotplus
except ImportError:
raise SkipTest("pydotplus not available")