497 lines
16 KiB
Python
497 lines
16 KiB
Python
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"""Functions to convert NetworkX graphs to and from other formats.
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The preferred way of converting data to a NetworkX graph is through the
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graph constructor. The constructor calls the to_networkx_graph() function
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which attempts to guess the input type and convert it automatically.
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Examples
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--------
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Create a graph with a single edge from a dictionary of dictionaries
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>>> d = {0: {1: 1}} # dict-of-dicts single edge (0,1)
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>>> G = nx.Graph(d)
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See Also
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--------
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nx_agraph, nx_pydot
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"""
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import warnings
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from collections.abc import Collection, Generator, Iterator
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import networkx as nx
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__all__ = [
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"to_networkx_graph",
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"from_dict_of_dicts",
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"to_dict_of_dicts",
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"from_dict_of_lists",
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"to_dict_of_lists",
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"from_edgelist",
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"to_edgelist",
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]
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def to_networkx_graph(data, create_using=None, multigraph_input=False):
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"""Make a NetworkX graph from a known data structure.
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The preferred way to call this is automatically
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from the class constructor
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>>> d = {0: {1: {"weight": 1}}} # dict-of-dicts single edge (0,1)
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>>> G = nx.Graph(d)
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instead of the equivalent
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>>> G = nx.from_dict_of_dicts(d)
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Parameters
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----------
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data : object to be converted
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Current known types are:
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any NetworkX graph
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dict-of-dicts
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dict-of-lists
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container (e.g. set, list, tuple) of edges
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iterator (e.g. itertools.chain) that produces edges
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generator of edges
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Pandas DataFrame (row per edge)
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2D numpy array
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scipy sparse array
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pygraphviz agraph
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create_using : NetworkX graph constructor, optional (default=nx.Graph)
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Graph type to create. If graph instance, then cleared before populated.
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multigraph_input : bool (default False)
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If True and data is a dict_of_dicts,
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try to create a multigraph assuming dict_of_dict_of_lists.
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If data and create_using are both multigraphs then create
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a multigraph from a multigraph.
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"""
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# NX graph
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if hasattr(data, "adj"):
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try:
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result = from_dict_of_dicts(
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data.adj,
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create_using=create_using,
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multigraph_input=data.is_multigraph(),
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)
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# data.graph should be dict-like
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result.graph.update(data.graph)
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# data.nodes should be dict-like
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# result.add_node_from(data.nodes.items()) possible but
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# for custom node_attr_dict_factory which may be hashable
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# will be unexpected behavior
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for n, dd in data.nodes.items():
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result._node[n].update(dd)
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return result
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except Exception as err:
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raise nx.NetworkXError("Input is not a correct NetworkX graph.") from err
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# pygraphviz agraph
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if hasattr(data, "is_strict"):
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try:
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return nx.nx_agraph.from_agraph(data, create_using=create_using)
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except Exception as err:
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raise nx.NetworkXError("Input is not a correct pygraphviz graph.") from err
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# dict of dicts/lists
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if isinstance(data, dict):
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try:
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return from_dict_of_dicts(
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data, create_using=create_using, multigraph_input=multigraph_input
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)
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except Exception as err1:
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if multigraph_input is True:
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raise nx.NetworkXError(
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f"converting multigraph_input raised:\n{type(err1)}: {err1}"
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)
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try:
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return from_dict_of_lists(data, create_using=create_using)
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except Exception as err2:
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raise TypeError("Input is not known type.") from err2
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# Pandas DataFrame
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try:
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import pandas as pd
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if isinstance(data, pd.DataFrame):
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if data.shape[0] == data.shape[1]:
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try:
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return nx.from_pandas_adjacency(data, create_using=create_using)
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except Exception as err:
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msg = "Input is not a correct Pandas DataFrame adjacency matrix."
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raise nx.NetworkXError(msg) from err
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else:
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try:
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return nx.from_pandas_edgelist(
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data, edge_attr=True, create_using=create_using
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)
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except Exception as err:
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msg = "Input is not a correct Pandas DataFrame edge-list."
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raise nx.NetworkXError(msg) from err
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except ImportError:
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warnings.warn("pandas not found, skipping conversion test.", ImportWarning)
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# numpy array
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try:
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import numpy as np
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if isinstance(data, np.ndarray):
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try:
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return nx.from_numpy_array(data, create_using=create_using)
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except Exception as err:
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raise nx.NetworkXError(
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f"Failed to interpret array as an adjacency matrix."
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) from err
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except ImportError:
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warnings.warn("numpy not found, skipping conversion test.", ImportWarning)
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# scipy sparse array - any format
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try:
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import scipy
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if hasattr(data, "format"):
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try:
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return nx.from_scipy_sparse_array(data, create_using=create_using)
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except Exception as err:
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raise nx.NetworkXError(
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"Input is not a correct scipy sparse array type."
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) from err
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except ImportError:
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warnings.warn("scipy not found, skipping conversion test.", ImportWarning)
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# Note: most general check - should remain last in order of execution
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# Includes containers (e.g. list, set, dict, etc.), generators, and
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# iterators (e.g. itertools.chain) of edges
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if isinstance(data, (Collection, Generator, Iterator)):
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try:
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return from_edgelist(data, create_using=create_using)
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except Exception as err:
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raise nx.NetworkXError("Input is not a valid edge list") from err
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raise nx.NetworkXError("Input is not a known data type for conversion.")
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@nx._dispatch
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def to_dict_of_lists(G, nodelist=None):
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"""Returns adjacency representation of graph as a dictionary of lists.
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Parameters
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----------
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G : graph
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A NetworkX graph
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nodelist : list
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Use only nodes specified in nodelist
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Notes
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-----
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Completely ignores edge data for MultiGraph and MultiDiGraph.
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"""
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if nodelist is None:
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nodelist = G
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d = {}
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for n in nodelist:
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d[n] = [nbr for nbr in G.neighbors(n) if nbr in nodelist]
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return d
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@nx._dispatch(graphs=None)
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def from_dict_of_lists(d, create_using=None):
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"""Returns a graph from a dictionary of lists.
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Parameters
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----------
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d : dictionary of lists
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A dictionary of lists adjacency representation.
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create_using : NetworkX graph constructor, optional (default=nx.Graph)
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Graph type to create. If graph instance, then cleared before populated.
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Examples
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--------
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>>> dol = {0: [1]} # single edge (0,1)
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>>> G = nx.from_dict_of_lists(dol)
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or
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>>> G = nx.Graph(dol) # use Graph constructor
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"""
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G = nx.empty_graph(0, create_using)
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G.add_nodes_from(d)
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if G.is_multigraph() and not G.is_directed():
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# a dict_of_lists can't show multiedges. BUT for undirected graphs,
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# each edge shows up twice in the dict_of_lists.
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# So we need to treat this case separately.
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seen = {}
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for node, nbrlist in d.items():
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for nbr in nbrlist:
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if nbr not in seen:
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G.add_edge(node, nbr)
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seen[node] = 1 # don't allow reverse edge to show up
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else:
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G.add_edges_from(
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((node, nbr) for node, nbrlist in d.items() for nbr in nbrlist)
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)
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return G
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def to_dict_of_dicts(G, nodelist=None, edge_data=None):
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"""Returns adjacency representation of graph as a dictionary of dictionaries.
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Parameters
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----------
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G : graph
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A NetworkX graph
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nodelist : list
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Use only nodes specified in nodelist
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edge_data : scalar, optional
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If provided, the value of the dictionary will be set to `edge_data` for
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all edges. Usual values could be `1` or `True`. If `edge_data` is
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`None` (the default), the edgedata in `G` is used, resulting in a
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dict-of-dict-of-dicts. If `G` is a MultiGraph, the result will be a
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dict-of-dict-of-dict-of-dicts. See Notes for an approach to customize
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handling edge data. `edge_data` should *not* be a container.
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Returns
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-------
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dod : dict
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A nested dictionary representation of `G`. Note that the level of
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nesting depends on the type of `G` and the value of `edge_data`
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(see Examples).
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See Also
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--------
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from_dict_of_dicts, to_dict_of_lists
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Notes
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-----
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For a more custom approach to handling edge data, try::
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dod = {
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n: {
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nbr: custom(n, nbr, dd) for nbr, dd in nbrdict.items()
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}
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for n, nbrdict in G.adj.items()
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}
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where `custom` returns the desired edge data for each edge between `n` and
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`nbr`, given existing edge data `dd`.
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Examples
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--------
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>>> G = nx.path_graph(3)
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>>> nx.to_dict_of_dicts(G)
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{0: {1: {}}, 1: {0: {}, 2: {}}, 2: {1: {}}}
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Edge data is preserved by default (``edge_data=None``), resulting
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in dict-of-dict-of-dicts where the innermost dictionary contains the
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edge data:
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>>> G = nx.Graph()
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>>> G.add_edges_from(
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... [
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... (0, 1, {'weight': 1.0}),
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... (1, 2, {'weight': 2.0}),
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... (2, 0, {'weight': 1.0}),
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... ]
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... )
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>>> d = nx.to_dict_of_dicts(G)
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>>> d # doctest: +SKIP
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{0: {1: {'weight': 1.0}, 2: {'weight': 1.0}},
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1: {0: {'weight': 1.0}, 2: {'weight': 2.0}},
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2: {1: {'weight': 2.0}, 0: {'weight': 1.0}}}
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>>> d[1][2]['weight']
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2.0
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If `edge_data` is not `None`, edge data in the original graph (if any) is
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replaced:
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>>> d = nx.to_dict_of_dicts(G, edge_data=1)
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>>> d
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{0: {1: 1, 2: 1}, 1: {0: 1, 2: 1}, 2: {1: 1, 0: 1}}
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>>> d[1][2]
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1
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This also applies to MultiGraphs: edge data is preserved by default:
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>>> G = nx.MultiGraph()
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>>> G.add_edge(0, 1, key='a', weight=1.0)
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'a'
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>>> G.add_edge(0, 1, key='b', weight=5.0)
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'b'
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>>> d = nx.to_dict_of_dicts(G)
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>>> d # doctest: +SKIP
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{0: {1: {'a': {'weight': 1.0}, 'b': {'weight': 5.0}}},
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1: {0: {'a': {'weight': 1.0}, 'b': {'weight': 5.0}}}}
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>>> d[0][1]['b']['weight']
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5.0
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But multi edge data is lost if `edge_data` is not `None`:
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>>> d = nx.to_dict_of_dicts(G, edge_data=10)
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>>> d
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{0: {1: 10}, 1: {0: 10}}
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"""
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dod = {}
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if nodelist is None:
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if edge_data is None:
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for u, nbrdict in G.adjacency():
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dod[u] = nbrdict.copy()
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else: # edge_data is not None
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for u, nbrdict in G.adjacency():
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dod[u] = dod.fromkeys(nbrdict, edge_data)
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else: # nodelist is not None
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if edge_data is None:
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for u in nodelist:
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dod[u] = {}
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for v, data in ((v, data) for v, data in G[u].items() if v in nodelist):
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dod[u][v] = data
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else: # nodelist and edge_data are not None
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for u in nodelist:
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dod[u] = {}
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for v in (v for v in G[u] if v in nodelist):
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dod[u][v] = edge_data
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return dod
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@nx._dispatch(graphs=None)
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def from_dict_of_dicts(d, create_using=None, multigraph_input=False):
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"""Returns a graph from a dictionary of dictionaries.
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Parameters
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----------
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d : dictionary of dictionaries
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A dictionary of dictionaries adjacency representation.
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create_using : NetworkX graph constructor, optional (default=nx.Graph)
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Graph type to create. If graph instance, then cleared before populated.
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multigraph_input : bool (default False)
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|
When True, the dict `d` is assumed
|
||
|
|
to be a dict-of-dict-of-dict-of-dict structure keyed by
|
||
|
|
node to neighbor to edge keys to edge data for multi-edges.
|
||
|
|
Otherwise this routine assumes dict-of-dict-of-dict keyed by
|
||
|
|
node to neighbor to edge data.
|
||
|
|
|
||
|
|
Examples
|
||
|
|
--------
|
||
|
|
>>> dod = {0: {1: {"weight": 1}}} # single edge (0,1)
|
||
|
|
>>> G = nx.from_dict_of_dicts(dod)
|
||
|
|
|
||
|
|
or
|
||
|
|
|
||
|
|
>>> G = nx.Graph(dod) # use Graph constructor
|
||
|
|
|
||
|
|
"""
|
||
|
|
G = nx.empty_graph(0, create_using)
|
||
|
|
G.add_nodes_from(d)
|
||
|
|
# does dict d represent a MultiGraph or MultiDiGraph?
|
||
|
|
if multigraph_input:
|
||
|
|
if G.is_directed():
|
||
|
|
if G.is_multigraph():
|
||
|
|
G.add_edges_from(
|
||
|
|
(u, v, key, data)
|
||
|
|
for u, nbrs in d.items()
|
||
|
|
for v, datadict in nbrs.items()
|
||
|
|
for key, data in datadict.items()
|
||
|
|
)
|
||
|
|
else:
|
||
|
|
G.add_edges_from(
|
||
|
|
(u, v, data)
|
||
|
|
for u, nbrs in d.items()
|
||
|
|
for v, datadict in nbrs.items()
|
||
|
|
for key, data in datadict.items()
|
||
|
|
)
|
||
|
|
else: # Undirected
|
||
|
|
if G.is_multigraph():
|
||
|
|
seen = set() # don't add both directions of undirected graph
|
||
|
|
for u, nbrs in d.items():
|
||
|
|
for v, datadict in nbrs.items():
|
||
|
|
if (u, v) not in seen:
|
||
|
|
G.add_edges_from(
|
||
|
|
(u, v, key, data) for key, data in datadict.items()
|
||
|
|
)
|
||
|
|
seen.add((v, u))
|
||
|
|
else:
|
||
|
|
seen = set() # don't add both directions of undirected graph
|
||
|
|
for u, nbrs in d.items():
|
||
|
|
for v, datadict in nbrs.items():
|
||
|
|
if (u, v) not in seen:
|
||
|
|
G.add_edges_from(
|
||
|
|
(u, v, data) for key, data in datadict.items()
|
||
|
|
)
|
||
|
|
seen.add((v, u))
|
||
|
|
|
||
|
|
else: # not a multigraph to multigraph transfer
|
||
|
|
if G.is_multigraph() and not G.is_directed():
|
||
|
|
# d can have both representations u-v, v-u in dict. Only add one.
|
||
|
|
# We don't need this check for digraphs since we add both directions,
|
||
|
|
# or for Graph() since it is done implicitly (parallel edges not allowed)
|
||
|
|
seen = set()
|
||
|
|
for u, nbrs in d.items():
|
||
|
|
for v, data in nbrs.items():
|
||
|
|
if (u, v) not in seen:
|
||
|
|
G.add_edge(u, v, key=0)
|
||
|
|
G[u][v][0].update(data)
|
||
|
|
seen.add((v, u))
|
||
|
|
else:
|
||
|
|
G.add_edges_from(
|
||
|
|
((u, v, data) for u, nbrs in d.items() for v, data in nbrs.items())
|
||
|
|
)
|
||
|
|
return G
|
||
|
|
|
||
|
|
|
||
|
|
@nx._dispatch(preserve_edge_attrs=True)
|
||
|
|
def to_edgelist(G, nodelist=None):
|
||
|
|
"""Returns a list of edges in the graph.
|
||
|
|
|
||
|
|
Parameters
|
||
|
|
----------
|
||
|
|
G : graph
|
||
|
|
A NetworkX graph
|
||
|
|
|
||
|
|
nodelist : list
|
||
|
|
Use only nodes specified in nodelist
|
||
|
|
|
||
|
|
"""
|
||
|
|
if nodelist is None:
|
||
|
|
return G.edges(data=True)
|
||
|
|
return G.edges(nodelist, data=True)
|
||
|
|
|
||
|
|
|
||
|
|
@nx._dispatch(graphs=None)
|
||
|
|
def from_edgelist(edgelist, create_using=None):
|
||
|
|
"""Returns a graph from a list of edges.
|
||
|
|
|
||
|
|
Parameters
|
||
|
|
----------
|
||
|
|
edgelist : list or iterator
|
||
|
|
Edge tuples
|
||
|
|
|
||
|
|
create_using : NetworkX graph constructor, optional (default=nx.Graph)
|
||
|
|
Graph type to create. If graph instance, then cleared before populated.
|
||
|
|
|
||
|
|
Examples
|
||
|
|
--------
|
||
|
|
>>> edgelist = [(0, 1)] # single edge (0,1)
|
||
|
|
>>> G = nx.from_edgelist(edgelist)
|
||
|
|
|
||
|
|
or
|
||
|
|
|
||
|
|
>>> G = nx.Graph(edgelist) # use Graph constructor
|
||
|
|
|
||
|
|
"""
|
||
|
|
G = nx.empty_graph(0, create_using)
|
||
|
|
G.add_edges_from(edgelist)
|
||
|
|
return G
|