"""
***************
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):
"""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 e:
raise ImportError("requires pygraphviz " "http://pygraphviz.github.io/") from e
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 e:
raise ImportError(
"read_dot() requires pygraphviz " "http://pygraphviz.github.io/"
) from e
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 e:
raise ImportError("requires pygraphviz " "http://pygraphviz.github.io/") from e
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 `networkx.utils.default_opener`,
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 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 = 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:
nx.utils.default_opener(path.name)
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.
"""
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 nx.utils.default_opener(filename).",
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()
nx.utils.default_opener(filename)