"""
***************
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/
- Graphviz: https://www.graphviz.org
- DOT Language: http://www.graphviz.org/doc/info/lang.html
"""
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):
"""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=None)
Graph type to create. If graph instance, then cleared before populated.
If `None`, then the appropriate Graph type is inferred from `A`.
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):
"""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 as err:
raise ImportError(
"requires pygraphviz " "http://pygraphviz.github.io/"
) from err
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)
# Add node data
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))
# Add edge data
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)
# Add edge data
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
"""
A = to_agraph(G)
A.write(path)
A.clear()
return
[docs]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 as err:
raise ImportError(
"read_dot() requires pygraphviz " "http://pygraphviz.github.io/"
) from err
A = pygraphviz.AGraph(file=path)
gr = from_agraph(A)
A.clear()
return gr
[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 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
-------
node_pos : dict
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 as err:
raise ImportError(
"requires pygraphviz " "http://pygraphviz.github.io/"
) from err
if root is not None:
args += f"-Groot={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, show=True
):
"""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.
show : bool, default = True
Whether to display the graph with :mod:`PIL.Image.show`,
default is `True`. If `False`, the rendered graph is still available
at `path`.
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.")
# 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 callable(edgelabel):
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 = f"_{suffix}.{ext}"
else:
suffix = f".{ext}"
path = tempfile.NamedTemporaryFile(suffix=suffix, delete=False)
else:
# Assume the decorator worked and it is a file-object.
pass
# Write graph to file
A.draw(path=path, format=None, prog=prog, args=args)
path.close()
# Show graph in a new window (depends on platform configuration)
if show:
from PIL import Image
Image.open(path.name).show()
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.
"""
from PIL import Image
import warnings
warnings.warn(
"display_pygraphviz is deprecated and will be removed in NetworkX 3.0. "
"To view a graph G using pygraphviz, use nx.nx_agraph.view_pygraphviz(G). "
"To view a graph from file, consider an image processing libary like "
"`Pillow`, e.g. ``PIL.Image.open(path.name).show()``",
DeprecationWarning,
)
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()
Image.open(filename).show()