412 lines
12 KiB
Python
412 lines
12 KiB
Python
"""
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*****
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Pydot
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*****
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Import and export NetworkX graphs in Graphviz dot format using pydot.
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Either this module or nx_agraph can be used to interface with graphviz.
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Examples
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--------
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>>> G = nx.complete_graph(5)
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>>> PG = nx.nx_pydot.to_pydot(G)
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>>> H = nx.nx_pydot.from_pydot(PG)
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See Also
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--------
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- pydot: https://github.com/erocarrera/pydot
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- Graphviz: https://www.graphviz.org
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- DOT Language: http://www.graphviz.org/doc/info/lang.html
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"""
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from locale import getpreferredencoding
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import networkx as nx
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from networkx.utils import open_file
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__all__ = [
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"write_dot",
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"read_dot",
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"graphviz_layout",
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"pydot_layout",
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"to_pydot",
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"from_pydot",
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]
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@open_file(1, mode="w")
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def write_dot(G, path):
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"""Write NetworkX graph G to Graphviz dot format on path.
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Path can be a string or a file handle.
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"""
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P = to_pydot(G)
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path.write(P.to_string())
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return
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@open_file(0, mode="r")
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@nx._dispatchable(name="pydot_read_dot", graphs=None, returns_graph=True)
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def read_dot(path):
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"""Returns a NetworkX :class:`MultiGraph` or :class:`MultiDiGraph` from the
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dot file with the passed path.
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If this file contains multiple graphs, only the first such graph is
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returned. All graphs _except_ the first are silently ignored.
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Parameters
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----------
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path : str or file
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Filename or file handle.
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Returns
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-------
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G : MultiGraph or MultiDiGraph
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A :class:`MultiGraph` or :class:`MultiDiGraph`.
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Notes
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-----
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Use `G = nx.Graph(nx.nx_pydot.read_dot(path))` to return a :class:`Graph` instead of a
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:class:`MultiGraph`.
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"""
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import pydot
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data = path.read()
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# List of one or more "pydot.Dot" instances deserialized from this file.
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P_list = pydot.graph_from_dot_data(data)
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# Convert only the first such instance into a NetworkX graph.
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return from_pydot(P_list[0])
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@nx._dispatchable(graphs=None, returns_graph=True)
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def from_pydot(P):
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"""Returns a NetworkX graph from a Pydot graph.
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Parameters
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----------
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P : Pydot graph
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A graph created with Pydot
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Returns
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-------
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G : NetworkX multigraph
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A MultiGraph or MultiDiGraph.
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Examples
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--------
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>>> K5 = nx.complete_graph(5)
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>>> A = nx.nx_pydot.to_pydot(K5)
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>>> G = nx.nx_pydot.from_pydot(A) # return MultiGraph
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# make a Graph instead of MultiGraph
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>>> G = nx.Graph(nx.nx_pydot.from_pydot(A))
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"""
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if P.get_strict(None): # pydot bug: get_strict() shouldn't take argument
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multiedges = False
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else:
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multiedges = True
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if P.get_type() == "graph": # undirected
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if multiedges:
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N = nx.MultiGraph()
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else:
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N = nx.Graph()
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else:
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if multiedges:
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N = nx.MultiDiGraph()
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else:
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N = nx.DiGraph()
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# assign defaults
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name = P.get_name().strip('"')
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if name != "":
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N.name = name
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# add nodes, attributes to N.node_attr
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for p in P.get_node_list():
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n = p.get_name().strip('"')
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if n in ("node", "graph", "edge"):
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continue
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N.add_node(n, **p.get_attributes())
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# add edges
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for e in P.get_edge_list():
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u = e.get_source()
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v = e.get_destination()
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attr = e.get_attributes()
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s = []
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d = []
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if isinstance(u, str):
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s.append(u.strip('"'))
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else:
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for unodes in u["nodes"]:
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s.append(unodes.strip('"'))
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if isinstance(v, str):
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d.append(v.strip('"'))
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else:
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for vnodes in v["nodes"]:
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d.append(vnodes.strip('"'))
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for source_node in s:
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for destination_node in d:
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N.add_edge(source_node, destination_node, **attr)
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# add default attributes for graph, nodes, edges
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pattr = P.get_attributes()
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if pattr:
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N.graph["graph"] = pattr
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try:
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N.graph["node"] = P.get_node_defaults()[0]
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except (IndexError, TypeError):
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pass # N.graph['node']={}
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try:
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N.graph["edge"] = P.get_edge_defaults()[0]
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except (IndexError, TypeError):
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pass # N.graph['edge']={}
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return N
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def _check_colon_quotes(s):
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# A quick helper function to check if a string has a colon in it
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# and if it is quoted properly with double quotes.
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# refer https://github.com/pydot/pydot/issues/258
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return ":" in s and (s[0] != '"' or s[-1] != '"')
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def to_pydot(N):
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"""Returns a pydot graph from a NetworkX graph N.
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Parameters
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----------
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N : NetworkX graph
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A graph created with NetworkX
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Examples
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--------
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>>> K5 = nx.complete_graph(5)
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>>> P = nx.nx_pydot.to_pydot(K5)
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Notes
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-----
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"""
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import pydot
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# set Graphviz graph type
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if N.is_directed():
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graph_type = "digraph"
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else:
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graph_type = "graph"
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strict = nx.number_of_selfloops(N) == 0 and not N.is_multigraph()
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name = N.name
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graph_defaults = N.graph.get("graph", {})
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if name == "":
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P = pydot.Dot("", graph_type=graph_type, strict=strict, **graph_defaults)
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else:
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P = pydot.Dot(
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f'"{name}"', graph_type=graph_type, strict=strict, **graph_defaults
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)
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try:
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P.set_node_defaults(**N.graph["node"])
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except KeyError:
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pass
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try:
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P.set_edge_defaults(**N.graph["edge"])
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except KeyError:
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pass
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for n, nodedata in N.nodes(data=True):
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str_nodedata = {str(k): str(v) for k, v in nodedata.items()}
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# Explicitly catch nodes with ":" in node names or nodedata.
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n = str(n)
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raise_error = _check_colon_quotes(n) or (
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any(
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(_check_colon_quotes(k) or _check_colon_quotes(v))
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for k, v in str_nodedata.items()
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)
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)
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if raise_error:
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raise ValueError(
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f'Node names and attributes should not contain ":" unless they are quoted with "".\
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For example the string \'attribute:data1\' should be written as \'"attribute:data1"\'.\
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Please refer https://github.com/pydot/pydot/issues/258'
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)
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p = pydot.Node(n, **str_nodedata)
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P.add_node(p)
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if N.is_multigraph():
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for u, v, key, edgedata in N.edges(data=True, keys=True):
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str_edgedata = {str(k): str(v) for k, v in edgedata.items() if k != "key"}
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u, v = str(u), str(v)
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raise_error = (
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_check_colon_quotes(u)
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or _check_colon_quotes(v)
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or (
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any(
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(_check_colon_quotes(k) or _check_colon_quotes(val))
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for k, val in str_edgedata.items()
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)
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)
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)
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if raise_error:
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raise ValueError(
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f'Node names and attributes should not contain ":" unless they are quoted with "".\
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For example the string \'attribute:data1\' should be written as \'"attribute:data1"\'.\
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Please refer https://github.com/pydot/pydot/issues/258'
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)
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edge = pydot.Edge(u, v, key=str(key), **str_edgedata)
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P.add_edge(edge)
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else:
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for u, v, edgedata in N.edges(data=True):
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str_edgedata = {str(k): str(v) for k, v in edgedata.items()}
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u, v = str(u), str(v)
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raise_error = (
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_check_colon_quotes(u)
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or _check_colon_quotes(v)
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or (
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any(
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(_check_colon_quotes(k) or _check_colon_quotes(val))
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for k, val in str_edgedata.items()
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)
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)
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)
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if raise_error:
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raise ValueError(
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f'Node names and attributes should not contain ":" unless they are quoted with "".\
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For example the string \'attribute:data1\' should be written as \'"attribute:data1"\'.\
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Please refer https://github.com/pydot/pydot/issues/258'
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)
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edge = pydot.Edge(u, v, **str_edgedata)
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P.add_edge(edge)
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return P
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def graphviz_layout(G, prog="neato", root=None):
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"""Create node positions using Pydot and Graphviz.
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Returns a dictionary of positions keyed by node.
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Parameters
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----------
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G : NetworkX Graph
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The graph for which the layout is computed.
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prog : string (default: 'neato')
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The name of the GraphViz program to use for layout.
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Options depend on GraphViz version but may include:
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'dot', 'twopi', 'fdp', 'sfdp', 'circo'
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root : Node from G or None (default: None)
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The node of G from which to start some layout algorithms.
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Returns
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-------
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Dictionary of (x, y) positions keyed by node.
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Examples
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--------
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>>> G = nx.complete_graph(4)
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>>> pos = nx.nx_pydot.graphviz_layout(G)
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>>> pos = nx.nx_pydot.graphviz_layout(G, prog="dot")
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Notes
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-----
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This is a wrapper for pydot_layout.
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"""
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return pydot_layout(G=G, prog=prog, root=root)
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def pydot_layout(G, prog="neato", root=None):
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"""Create node positions using :mod:`pydot` and Graphviz.
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Parameters
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----------
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G : Graph
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NetworkX graph to be laid out.
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prog : string (default: 'neato')
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Name of the GraphViz command to use for layout.
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Options depend on GraphViz version but may include:
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'dot', 'twopi', 'fdp', 'sfdp', 'circo'
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root : Node from G or None (default: None)
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The node of G from which to start some layout algorithms.
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Returns
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-------
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dict
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Dictionary of positions keyed by node.
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Examples
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--------
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>>> G = nx.complete_graph(4)
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>>> pos = nx.nx_pydot.pydot_layout(G)
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>>> pos = nx.nx_pydot.pydot_layout(G, prog="dot")
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Notes
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-----
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If you use complex node objects, they may have the same string
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representation and GraphViz could treat them as the same node.
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The layout may assign both nodes a single location. See Issue #1568
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If this occurs in your case, consider relabeling the nodes just
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for the layout computation using something similar to::
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H = nx.convert_node_labels_to_integers(G, label_attribute="node_label")
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H_layout = nx.nx_pydot.pydot_layout(G, prog="dot")
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G_layout = {H.nodes[n]["node_label"]: p for n, p in H_layout.items()}
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"""
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import pydot
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P = to_pydot(G)
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if root is not None:
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P.set("root", str(root))
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# List of low-level bytes comprising a string in the dot language converted
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# from the passed graph with the passed external GraphViz command.
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D_bytes = P.create_dot(prog=prog)
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# Unique string decoded from these bytes with the preferred locale encoding
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D = str(D_bytes, encoding=getpreferredencoding())
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if D == "": # no data returned
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print(f"Graphviz layout with {prog} failed")
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print()
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print("To debug what happened try:")
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print("P = nx.nx_pydot.to_pydot(G)")
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print('P.write_dot("file.dot")')
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print(f"And then run {prog} on file.dot")
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return
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# List of one or more "pydot.Dot" instances deserialized from this string.
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Q_list = pydot.graph_from_dot_data(D)
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assert len(Q_list) == 1
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# The first and only such instance, as guaranteed by the above assertion.
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Q = Q_list[0]
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node_pos = {}
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for n in G.nodes():
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str_n = str(n)
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# Explicitly catch nodes with ":" in node names or nodedata.
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if _check_colon_quotes(str_n):
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raise ValueError(
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f'Node names and node attributes should not contain ":" unless they are quoted with "".\
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For example the string \'attribute:data1\' should be written as \'"attribute:data1"\'.\
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Please refer https://github.com/pydot/pydot/issues/258'
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)
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pydot_node = pydot.Node(str_n).get_name()
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node = Q.get_node(pydot_node)
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if isinstance(node, list):
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node = node[0]
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pos = node.get_pos()[1:-1] # strip leading and trailing double quotes
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if pos is not None:
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xx, yy = pos.split(",")
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node_pos[n] = (float(xx), float(yy))
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return node_pos
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