"""
*****
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.
Examples
--------
>>> G = nx.complete_graph(5)
>>> PG = nx.nx_pydot.to_pydot(G)
>>> H = nx.nx_pydot.from_pydot(PG)
See Also
--------
- pydot: https://github.com/erocarrera/pydot
- Graphviz: https://www.graphviz.org
- DOT Language: http://www.graphviz.org/doc/info/lang.html
"""
from locale import getpreferredencoding
import networkx as nx
from networkx.utils import open_file
__all__ = [
"write_dot",
"read_dot",
"graphviz_layout",
"pydot_layout",
"to_pydot",
"from_pydot",
]
[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")
@nx._dispatchable(name="pydot_read_dot", graphs=None, returns_graph=True)
def read_dot(path):
"""Returns 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(nx.nx_pydot.read_dot(path))` to return a :class:`Graph` instead of a
:class:`MultiGraph`.
"""
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]
@nx._dispatchable(graphs=None, returns_graph=True)
def from_pydot(P):
"""Returns 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, str):
s.append(u.strip('"'))
else:
for unodes in u["nodes"]:
s.append(unodes.strip('"'))
if isinstance(v, str):
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):
"""Returns 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
-----
"""
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 == "":
P = pydot.Dot("", graph_type=graph_type, strict=strict, **graph_defaults)
else:
P = pydot.Dot(
f'"{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 = {str(k): str(v) for k, v in nodedata.items()}
n = str(n)
p = pydot.Node(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 = {str(k): str(v) for k, v in edgedata.items() if k != "key"}
u, v = str(u), str(v)
edge = pydot.Edge(u, v, key=str(key), **str_edgedata)
P.add_edge(edge)
else:
for u, v, edgedata in N.edges(data=True):
str_edgedata = {str(k): str(v) for k, v in edgedata.items()}
u, v = str(u), str(v)
edge = pydot.Edge(u, v, **str_edgedata)
P.add_edge(edge)
return P
[docs]
def graphviz_layout(G, prog="neato", root=None):
"""Create node positions using Pydot and Graphviz.
Returns a dictionary of positions keyed by node.
Parameters
----------
G : NetworkX Graph
The graph for which the layout is computed.
prog : string (default: 'neato')
The name of the GraphViz program to use for layout.
Options depend on GraphViz version but may include:
'dot', 'twopi', 'fdp', 'sfdp', 'circo'
root : Node from G or None (default: None)
The node of G from which to start some layout algorithms.
Returns
-------
Dictionary of (x, y) 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)
[docs]
def pydot_layout(G, prog="neato", root=None):
"""Create node positions using :mod:`pydot` and Graphviz.
Parameters
----------
G : Graph
NetworkX graph to be laid out.
prog : string (default: 'neato')
Name of the GraphViz command to use for layout.
Options depend on GraphViz version but may include:
'dot', 'twopi', 'fdp', 'sfdp', 'circo'
root : Node from G or None (default: None)
The node of G from which to start some layout algorithms.
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")
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_pydot.pydot_layout(H, prog="dot")
G_layout = {H.nodes[n]["node_label"]: p for n, p in H_layout.items()}
"""
import pydot
P = to_pydot(G)
if root is not None:
P.set("root", 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 = str(D_bytes, encoding=getpreferredencoding())
if D == "": # no data returned
print(f"Graphviz layout with {prog} failed")
print()
print("To debug what happened try:")
print("P = nx.nx_pydot.to_pydot(G)")
print('P.write_dot("file.dot")')
print(f"And then run {prog} on file.dot")
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():
str_n = str(n)
node = Q.get_node(pydot.quote_id_if_necessary(str_n))
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
