453 lines
14 KiB
Python
453 lines
14 KiB
Python
"""
|
|
*****
|
|
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
|
|
"""
|
|
import warnings
|
|
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",
|
|
]
|
|
|
|
|
|
@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.
|
|
"""
|
|
msg = (
|
|
"nx.nx_pydot.write_dot depends on the pydot package, which has"
|
|
"known issues and is not actively maintained. Consider using"
|
|
"nx.nx_agraph.write_dot instead.\n\n"
|
|
"See https://github.com/networkx/networkx/issues/5723"
|
|
)
|
|
warnings.warn(msg, PendingDeprecationWarning, stacklevel=2)
|
|
P = to_pydot(G)
|
|
path.write(P.to_string())
|
|
return
|
|
|
|
|
|
@open_file(0, mode="r")
|
|
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
|
|
|
|
msg = (
|
|
"nx.nx_pydot.read_dot depends on the pydot package, which has"
|
|
"known issues and is not actively maintained. Consider using"
|
|
"nx.nx_agraph.read_dot instead.\n\n"
|
|
"See https://github.com/networkx/networkx/issues/5723"
|
|
)
|
|
warnings.warn(msg, PendingDeprecationWarning, stacklevel=2)
|
|
|
|
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])
|
|
|
|
|
|
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))
|
|
|
|
"""
|
|
msg = (
|
|
"nx.nx_pydot.from_pydot depends on the pydot package, which has"
|
|
"known issues and is not actively maintained.\n\n"
|
|
"See https://github.com/networkx/networkx/issues/5723"
|
|
)
|
|
warnings.warn(msg, PendingDeprecationWarning, stacklevel=2)
|
|
|
|
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
|
|
|
|
|
|
def _check_colon_quotes(s):
|
|
# A quick helper function to check if a string has a colon in it
|
|
# and if it is quoted properly with double quotes.
|
|
# refer https://github.com/pydot/pydot/issues/258
|
|
return ":" in s and (s[0] != '"' or s[-1] != '"')
|
|
|
|
|
|
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
|
|
|
|
msg = (
|
|
"nx.nx_pydot.to_pydot depends on the pydot package, which has"
|
|
"known issues and is not actively maintained.\n\n"
|
|
"See https://github.com/networkx/networkx/issues/5723"
|
|
)
|
|
warnings.warn(msg, PendingDeprecationWarning, stacklevel=2)
|
|
|
|
# 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()}
|
|
# Explicitly catch nodes with ":" in node names or nodedata.
|
|
n = str(n)
|
|
raise_error = _check_colon_quotes(n) or (
|
|
any(
|
|
(_check_colon_quotes(k) or _check_colon_quotes(v))
|
|
for k, v in str_nodedata.items()
|
|
)
|
|
)
|
|
if raise_error:
|
|
raise ValueError(
|
|
f'Node names and attributes should not contain ":" unless they are quoted with "".\
|
|
For example the string \'attribute:data1\' should be written as \'"attribute:data1"\'.\
|
|
Please refer https://github.com/pydot/pydot/issues/258'
|
|
)
|
|
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)
|
|
raise_error = (
|
|
_check_colon_quotes(u)
|
|
or _check_colon_quotes(v)
|
|
or (
|
|
any(
|
|
(_check_colon_quotes(k) or _check_colon_quotes(val))
|
|
for k, val in str_edgedata.items()
|
|
)
|
|
)
|
|
)
|
|
if raise_error:
|
|
raise ValueError(
|
|
f'Node names and attributes should not contain ":" unless they are quoted with "".\
|
|
For example the string \'attribute:data1\' should be written as \'"attribute:data1"\'.\
|
|
Please refer https://github.com/pydot/pydot/issues/258'
|
|
)
|
|
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)
|
|
raise_error = (
|
|
_check_colon_quotes(u)
|
|
or _check_colon_quotes(v)
|
|
or (
|
|
any(
|
|
(_check_colon_quotes(k) or _check_colon_quotes(val))
|
|
for k, val in str_edgedata.items()
|
|
)
|
|
)
|
|
)
|
|
if raise_error:
|
|
raise ValueError(
|
|
f'Node names and attributes should not contain ":" unless they are quoted with "".\
|
|
For example the string \'attribute:data1\' should be written as \'"attribute:data1"\'.\
|
|
Please refer https://github.com/pydot/pydot/issues/258'
|
|
)
|
|
edge = pydot.Edge(u, v, **str_edgedata)
|
|
P.add_edge(edge)
|
|
return P
|
|
|
|
|
|
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.
|
|
"""
|
|
msg = (
|
|
"nx.nx_pydot.graphviz_layout depends on the pydot package, which has"
|
|
"known issues and is not actively maintained. Consider using"
|
|
"nx.nx_agraph.graphviz_layout instead.\n\n"
|
|
"See https://github.com/networkx/networkx/issues/5723"
|
|
)
|
|
warnings.warn(msg, PendingDeprecationWarning, stacklevel=2)
|
|
|
|
return pydot_layout(G=G, prog=prog, root=root)
|
|
|
|
|
|
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(G, prog='dot')
|
|
G_layout = {H.nodes[n]['node_label']: p for n, p in H_layout.items()}
|
|
|
|
"""
|
|
import pydot
|
|
|
|
msg = (
|
|
"nx.nx_pydot.pydot_layout depends on the pydot package, which has"
|
|
"known issues and is not actively maintained.\n\n"
|
|
"See https://github.com/networkx/networkx/issues/5723"
|
|
)
|
|
warnings.warn(msg, PendingDeprecationWarning, stacklevel=2)
|
|
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)
|
|
# Explicitly catch nodes with ":" in node names or nodedata.
|
|
if _check_colon_quotes(str_n):
|
|
raise ValueError(
|
|
f'Node names and node attributes should not contain ":" unless they are quoted with "".\
|
|
For example the string \'attribute:data1\' should be written as \'"attribute:data1"\'.\
|
|
Please refer https://github.com/pydot/pydot/issues/258'
|
|
)
|
|
pydot_node = pydot.Node(str_n).get_name()
|
|
node = Q.get_node(pydot_node)
|
|
|
|
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
|