"""
*****
Pydot
*****
Import and export NetworkX graphs in Graphviz dot format using pydot.
Either this module or nx_agraph can be used to interface with graphviz.
See Also
--------
pydot: https://github.com/erocarrera/pydot
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) 2004-2017 by
# Aric Hagberg <hagberg@lanl.gov>
# Dan Schult <dschult@colgate.edu>
# Pieter Swart <swart@lanl.gov>
# Cecil Curry <leycec@gmail.com>
# All rights reserved.
# BSD license.
from locale import getpreferredencoding
from networkx.utils import open_file, make_str
from pkg_resources import parse_version
import networkx as nx
__all__ = ['write_dot', 'read_dot', 'graphviz_layout', 'pydot_layout',
'to_pydot', 'from_pydot']
# Minimum required version of pydot, which broke backwards API compatibility in
# non-trivial ways and is thus a hard NetworkX requirement. Note that, although
# pydot 1.2.0 was the first to do so, pydot 1.2.3 resolves a critical long-
# standing Python 2.x issue required for sane NetworkX operation. See also:
# https://github.com/erocarrera/pydot/blob/master/ChangeLog
PYDOT_VERSION_MIN = '1.2.3'
# 2.x/3.x compatibility
try:
basestring
except NameError:
basestring = str
unicode = 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 :class:`MultiGraph` or :class:`MultiDiGraph` from the
dot file with the passed path.
If this file contains multiple graphs, only the first such graph is
returned. All graphs _except_ the first are silently ignored.
Parameters
----------
path : str or file
Filename or file handle.
Returns
-------
G : MultiGraph or MultiDiGraph
A :class:`MultiGraph` or :class:`MultiDiGraph`.
Notes
-----
Use `G = nx.Graph(read_dot(path))` to return a :class:`Graph` instead of a
:class:`MultiGraph`.
"""
pydot = _import_pydot()
data = path.read()
# List of one or more "pydot.Dot" instances deserialized from this file.
P_list = pydot.graph_from_dot_data(data)
# Convert only the first such instance into a NetworkX graph.
return from_pydot(P_list[0])
[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
-----
"""
pydot = _import_pydot()
# set Graphviz graph type
if N.is_directed():
graph_type = 'digraph'
else:
graph_type = 'graph'
strict = nx.number_of_selfloops(N) == 0 and not N.is_multigraph()
name = N.name
graph_defaults = N.graph.get('graph', {})
if name is '':
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(data=True):
str_nodedata = dict((k, make_str(v)) for k, v in nodedata.items())
p = pydot.Node(make_str(n), **str_nodedata)
P.add_node(p)
if N.is_multigraph():
for u, v, key, edgedata in N.edges(data=True, keys=True):
str_edgedata = dict((k, make_str(v)) for k, v in edgedata.items() if k != 'key')
edge = pydot.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(data=True):
str_edgedata = dict((k, make_str(v)) for k, v in edgedata.items())
edge = pydot.Edge(make_str(u), make_str(v), **str_edgedata)
P.add_edge(edge)
return P
[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)
# FIXME: Document the "root" parameter.
# FIXME: Why does this function accept a variadic dictionary of keyword arguments
# (i.e., "**kwds") but fail to do anything with those arguments? This is probably
# wrong, as unrecognized keyword arguments will be silently ignored.
[docs]def pydot_layout(G, prog='neato', root=None, **kwds):
"""Create node positions using :mod:`pydot` and Graphviz.
Parameters
--------
G : Graph
NetworkX graph to be laid out.
prog : optional[str]
Basename of the GraphViz command with which to layout this graph.
Defaults to `neato`, the default GraphViz command for undirected graphs.
Returns
--------
dict
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')
"""
pydot = _import_pydot()
P = to_pydot(G)
if root is not None:
P.set("root", make_str(root))
# List of low-level bytes comprising a string in the dot language converted
# from the passed graph with the passed external GraphViz command.
D_bytes = P.create_dot(prog=prog)
# Unique string decoded from these bytes with the preferred locale encoding.
D = unicode(D_bytes, encoding=getpreferredencoding())
if D == "": # no data returned
print("Graphviz layout with %s failed" % (prog))
print()
print("To debug what happened try:")
print("P = nx.nx_pydot.to_pydot(G)")
print("P.write_dot(\"file.dot\")")
print("And then run %s on file.dot" % (prog))
return
# List of one or more "pydot.Dot" instances deserialized from this string.
Q_list = pydot.graph_from_dot_data(D)
assert len(Q_list) == 1
# The first and only such instance, as guaranteed by the above assertion.
Q = Q_list[0]
node_pos = {}
for n in G.nodes():
pydot_node = pydot.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 is not None:
xx, yy = pos.split(",")
node_pos[n] = (float(xx), float(yy))
return node_pos
def _import_pydot():
'''
Import and return the `pydot` module if the currently installed version of
this module satisfies NetworkX requirements _or_ raise an exception.
Returns
--------
:mod:`pydot`
Imported `pydot` module object.
Raises
--------
ImportError
If the `pydot` module is either unimportable _or_ importable but of
insufficient version.
'''
import pydot
# If the currently installed version of pydot is older than this minimum,
# raise an exception. The pkg_resources.parse_version() function bundled
# with setuptools is commonly regarded to be the most robust means of
# comparing version strings. (Your mileage may vary.)
if parse_version(pydot.__version__) < parse_version(PYDOT_VERSION_MIN):
raise ImportError(
'pydot %s < %s' % (pydot.__version__, PYDOT_VERSION_MIN))
return pydot
# fixture for nose tests
def setup_module(module):
from nose import SkipTest
try:
return _import_pydot()
except ImportError:
raise SkipTest("pydot not available")