474 lines
14 KiB
Python
474 lines
14 KiB
Python
|
# Copyright (C) 2004-2019 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']
|
||
|
|
|
||
|
|
|
||
|
|
def from_agraph(A, create_using=None):
|
||
|
|
"""Returns 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
|
||
|
|
|
||
|
|
|
||
|
|
def to_agraph(N):
|
||
|
|
"""Returns 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
|
||
|
|
|
||
|
|
|
||
|
|
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
|
||
|
|
|
||
|
|
|
||
|
|
def read_dot(path):
|
||
|
|
"""Returns 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)
|
||
|
|
|
||
|
|
|
||
|
|
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 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)
|
||
|
|
|
||
|
|
|
||
|
|
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:
|
||
|
|
xs = node.attr["pos"].split(',')
|
||
|
|
node_pos[n] = tuple(float(x) for x in xs)
|
||
|
|
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 pytest
|
||
|
|
def setup_module(module):
|
||
|
|
import pytest
|
||
|
|
pygraphviz = pytest.importorskip('pygraphviz')
|