# Copyright (C) 2004-2018 by
# Aric Hagberg <hagberg@lanl.gov>
# Dan Schult <dschult@colgate.edu>
# Pieter Swart <swart@lanl.gov>
# All rights reserved.
# BSD license.
#
# Author: Aric Hagberg (hagberg@lanl.gov)
"""
***************
Graphviz AGraph
***************
Interface to pygraphviz AGraph class.
Examples
--------
>>> G = nx.complete_graph(5)
>>> A = nx.nx_agraph.to_agraph(G)
>>> H = nx.nx_agraph.from_agraph(A)
See Also
--------
Pygraphviz: http://pygraphviz.github.io/
"""
import os
import tempfile
import networkx as nx
__all__ = ['from_agraph', 'to_agraph',
'write_dot', 'read_dot',
'graphviz_layout',
'pygraphviz_layout',
'view_pygraphviz']
[docs]def from_agraph(A, create_using=None):
"""Return a NetworkX Graph or DiGraph from a PyGraphviz graph.
Parameters
----------
A : PyGraphviz AGraph
A graph created with PyGraphviz
create_using : NetworkX graph constructor, optional (default=nx.Graph)
Graph type to create. If graph instance, then cleared before populated.
Examples
--------
>>> K5 = nx.complete_graph(5)
>>> A = nx.nx_agraph.to_agraph(K5)
>>> G = nx.nx_agraph.from_agraph(A)
Notes
-----
The Graph G will have a dictionary G.graph_attr containing
the default graphviz attributes for graphs, nodes and edges.
Default node attributes will be in the dictionary G.node_attr
which is keyed by node.
Edge attributes will be returned as edge data in G. With
edge_attr=False the edge data will be the Graphviz edge weight
attribute or the value 1 if no edge weight attribute is found.
"""
if create_using is None:
if A.is_directed():
if A.is_strict():
create_using = nx.DiGraph
else:
create_using = nx.MultiDiGraph
else:
if A.is_strict():
create_using = nx.Graph
else:
create_using = nx.MultiGraph
# assign defaults
N = nx.empty_graph(0, create_using)
if A.name is not None:
N.name = A.name
# add graph attributes
N.graph.update(A.graph_attr)
# add nodes, attributes to N.node_attr
for n in A.nodes():
str_attr = {str(k): v for k, v in n.attr.items()}
N.add_node(str(n), **str_attr)
# add edges, assign edge data as dictionary of attributes
for e in A.edges():
u, v = str(e[0]), str(e[1])
attr = dict(e.attr)
str_attr = {str(k): v for k, v in attr.items()}
if not N.is_multigraph():
if e.name is not None:
str_attr['key'] = e.name
N.add_edge(u, v, **str_attr)
else:
N.add_edge(u, v, key=e.name, **str_attr)
# add default attributes for graph, nodes, and edges
# hang them on N.graph_attr
N.graph['graph'] = dict(A.graph_attr)
N.graph['node'] = dict(A.node_attr)
N.graph['edge'] = dict(A.edge_attr)
return N
[docs]def to_agraph(N):
"""Return a pygraphviz graph from a NetworkX graph N.
Parameters
----------
N : NetworkX graph
A graph created with NetworkX
Examples
--------
>>> K5 = nx.complete_graph(5)
>>> A = nx.nx_agraph.to_agraph(K5)
Notes
-----
If N has an dict N.graph_attr an attempt will be made first
to copy properties attached to the graph (see from_agraph)
and then updated with the calling arguments if any.
"""
try:
import pygraphviz
except ImportError:
raise ImportError('requires pygraphviz ',
'http://pygraphviz.github.io/')
directed = N.is_directed()
strict = nx.number_of_selfloops(N) == 0 and not N.is_multigraph()
A = pygraphviz.AGraph(name=N.name, strict=strict, directed=directed)
# default graph attributes
A.graph_attr.update(N.graph.get('graph', {}))
A.node_attr.update(N.graph.get('node', {}))
A.edge_attr.update(N.graph.get('edge', {}))
A.graph_attr.update((k, v) for k, v in N.graph.items()
if k not in ('graph', 'node', 'edge'))
# add nodes
for n, nodedata in N.nodes(data=True):
A.add_node(n)
if nodedata is not None:
a = A.get_node(n)
a.attr.update({k: str(v) for k, v in nodedata.items()})
# loop over edges
if N.is_multigraph():
for u, v, key, edgedata in N.edges(data=True, keys=True):
str_edgedata = {k: str(v) for k, v in edgedata.items()
if k != 'key'}
A.add_edge(u, v, key=str(key))
if edgedata is not None:
a = A.get_edge(u, v)
a.attr.update(str_edgedata)
else:
for u, v, edgedata in N.edges(data=True):
str_edgedata = {k: str(v) for k, v in edgedata.items()}
A.add_edge(u, v)
if edgedata is not None:
a = A.get_edge(u, v)
a.attr.update(str_edgedata)
return A
[docs]def write_dot(G, path):
"""Write NetworkX graph G to Graphviz dot format on path.
Parameters
----------
G : graph
A networkx graph
path : filename
Filename or file handle to write
"""
try:
import pygraphviz
except ImportError:
raise ImportError('requires pygraphviz ',
'http://pygraphviz.github.io/')
A = to_agraph(G)
A.write(path)
A.clear()
return
[docs]def read_dot(path):
"""Return a NetworkX graph from a dot file on path.
Parameters
----------
path : file or string
File name or file handle to read.
"""
try:
import pygraphviz
except ImportError:
raise ImportError('read_dot() requires pygraphviz ',
'http://pygraphviz.github.io/')
A = pygraphviz.AGraph(file=path)
return from_agraph(A)
[docs]def graphviz_layout(G, prog='neato', root=None, args=''):
"""Create node positions for G using Graphviz.
Parameters
----------
G : NetworkX graph
A graph created with NetworkX
prog : string
Name of Graphviz layout program
root : string, optional
Root node for twopi layout
args : string, optional
Extra arguments to Graphviz layout program
Returns : dictionary
Dictionary of x, y, positions keyed by node.
Examples
--------
>>> G = nx.petersen_graph()
>>> pos = nx.nx_agraph.graphviz_layout(G)
>>> pos = nx.nx_agraph.graphviz_layout(G, prog='dot')
Notes
-----
This is a wrapper for pygraphviz_layout.
"""
return pygraphviz_layout(G, prog=prog, root=root, args=args)
[docs]def pygraphviz_layout(G, prog='neato', root=None, args=''):
"""Create node positions for G using Graphviz.
Parameters
----------
G : NetworkX graph
A graph created with NetworkX
prog : string
Name of Graphviz layout program
root : string, optional
Root node for twopi layout
args : string, optional
Extra arguments to Graphviz layout program
Returns : dictionary
Dictionary of x, y, positions keyed by node.
Examples
--------
>>> G = nx.petersen_graph()
>>> pos = nx.nx_agraph.graphviz_layout(G)
>>> pos = nx.nx_agraph.graphviz_layout(G, prog='dot')
Notes
-----
If you use complex node objects, they may have the same string
representation and GraphViz could treat them as the same node.
The layout may assign both nodes a single location. See Issue #1568
If this occurs in your case, consider relabeling the nodes just
for the layout computation using something similar to:
H = nx.convert_node_labels_to_integers(G, label_attribute='node_label')
H_layout = nx.nx_agraph.pygraphviz_layout(G, prog='dot')
G_layout = {H.nodes[n]['node_label']: p for n, p in H_layout.items()}
"""
try:
import pygraphviz
except ImportError:
raise ImportError('requires pygraphviz ',
'http://pygraphviz.github.io/')
if root is not None:
args += "-Groot=%s" % root
A = to_agraph(G)
A.layout(prog=prog, args=args)
node_pos = {}
for n in G:
node = pygraphviz.Node(A, n)
try:
xx, yy = node.attr["pos"].split(',')
node_pos[n] = (float(xx), float(yy))
except:
print("no position for node", n)
node_pos[n] = (0.0, 0.0)
return node_pos
@nx.utils.open_file(5, 'w+b')
def view_pygraphviz(G, edgelabel=None, prog='dot', args='',
suffix='', path=None):
"""Views the graph G using the specified layout algorithm.
Parameters
----------
G : NetworkX graph
The machine to draw.
edgelabel : str, callable, None
If a string, then it specifes the edge attribute to be displayed
on the edge labels. If a callable, then it is called for each
edge and it should return the string to be displayed on the edges.
The function signature of `edgelabel` should be edgelabel(data),
where `data` is the edge attribute dictionary.
prog : string
Name of Graphviz layout program.
args : str
Additional arguments to pass to the Graphviz layout program.
suffix : str
If `filename` is None, we save to a temporary file. The value of
`suffix` will appear at the tail end of the temporary filename.
path : str, None
The filename used to save the image. If None, save to a temporary
file. File formats are the same as those from pygraphviz.agraph.draw.
Returns
-------
path : str
The filename of the generated image.
A : PyGraphviz graph
The PyGraphviz graph instance used to generate the image.
Notes
-----
If this function is called in succession too quickly, sometimes the
image is not displayed. So you might consider time.sleep(.5) between
calls if you experience problems.
"""
if not len(G):
raise nx.NetworkXException("An empty graph cannot be drawn.")
import pygraphviz
# If we are providing default values for graphviz, these must be set
# before any nodes or edges are added to the PyGraphviz graph object.
# The reason for this is that default values only affect incoming objects.
# If you change the default values after the objects have been added,
# then they inherit no value and are set only if explicitly set.
# to_agraph() uses these values.
attrs = ['edge', 'node', 'graph']
for attr in attrs:
if attr not in G.graph:
G.graph[attr] = {}
# These are the default values.
edge_attrs = {'fontsize': '10'}
node_attrs = {'style': 'filled',
'fillcolor': '#0000FF40',
'height': '0.75',
'width': '0.75',
'shape': 'circle'}
graph_attrs = {}
def update_attrs(which, attrs):
# Update graph attributes. Return list of those which were added.
added = []
for k, v in attrs.items():
if k not in G.graph[which]:
G.graph[which][k] = v
added.append(k)
def clean_attrs(which, added):
# Remove added attributes
for attr in added:
del G.graph[which][attr]
if not G.graph[which]:
del G.graph[which]
# Update all default values
update_attrs('edge', edge_attrs)
update_attrs('node', node_attrs)
update_attrs('graph', graph_attrs)
# Convert to agraph, so we inherit default values
A = to_agraph(G)
# Remove the default values we added to the original graph.
clean_attrs('edge', edge_attrs)
clean_attrs('node', node_attrs)
clean_attrs('graph', graph_attrs)
# If the user passed in an edgelabel, we update the labels for all edges.
if edgelabel is not None:
if not hasattr(edgelabel, '__call__'):
def func(data):
return ''.join([" ", str(data[edgelabel]), " "])
else:
func = edgelabel
# update all the edge labels
if G.is_multigraph():
for u, v, key, data in G.edges(keys=True, data=True):
# PyGraphviz doesn't convert the key to a string. See #339
edge = A.get_edge(u, v, str(key))
edge.attr['label'] = str(func(data))
else:
for u, v, data in G.edges(data=True):
edge = A.get_edge(u, v)
edge.attr['label'] = str(func(data))
if path is None:
ext = 'png'
if suffix:
suffix = '_%s.%s' % (suffix, ext)
else:
suffix = '.%s' % (ext,)
path = tempfile.NamedTemporaryFile(suffix=suffix, delete=False)
else:
# Assume the decorator worked and it is a file-object.
pass
display_pygraphviz(A, path=path, prog=prog, args=args)
return path.name, A
def display_pygraphviz(graph, path, format=None, prog=None, args=''):
"""Internal function to display a graph in OS dependent manner.
Parameters
----------
graph : PyGraphviz graph
A PyGraphviz AGraph instance.
path : file object
An already opened file object that will be closed.
format : str, None
An attempt is made to guess the output format based on the extension
of the filename. If that fails, the value of `format` is used.
prog : string
Name of Graphviz layout program.
args : str
Additional arguments to pass to the Graphviz layout program.
Notes
-----
If this function is called in succession too quickly, sometimes the
image is not displayed. So you might consider time.sleep(.5) between
calls if you experience problems.
"""
if format is None:
filename = path.name
format = os.path.splitext(filename)[1].lower()[1:]
if not format:
# Let the draw() function use its default
format = None
# Save to a file and display in the default viewer.
# We must close the file before viewing it.
graph.draw(path, format, prog, args)
path.close()
nx.utils.default_opener(filename)
# fixture for nose tests
def setup_module(module):
from nose import SkipTest
try:
import pygraphviz
except:
raise SkipTest("pygraphviz not available")