Mercurial > repos > shellac > guppy_basecaller
diff env/lib/python3.7/site-packages/networkx/relabel.py @ 0:26e78fe6e8c4 draft
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
author | shellac |
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date | Sat, 02 May 2020 07:14:21 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/env/lib/python3.7/site-packages/networkx/relabel.py Sat May 02 07:14:21 2020 -0400 @@ -0,0 +1,225 @@ +# Copyright (C) 2006-2019 by +# Aric Hagberg <hagberg@lanl.gov> +# Dan Schult <dschult@colgate.edu> +# Pieter Swart <swart@lanl.gov> +# All rights reserved. +# BSD license. +import networkx as nx + +__all__ = ['convert_node_labels_to_integers', 'relabel_nodes'] + + +def relabel_nodes(G, mapping, copy=True): + """Relabel the nodes of the graph G. + + Parameters + ---------- + G : graph + A NetworkX graph + + mapping : dictionary + A dictionary with the old labels as keys and new labels as values. + A partial mapping is allowed. + + copy : bool (optional, default=True) + If True return a copy, or if False relabel the nodes in place. + + Examples + -------- + To create a new graph with nodes relabeled according to a given + dictionary: + + >>> G = nx.path_graph(3) + >>> sorted(G) + [0, 1, 2] + >>> mapping = {0: 'a', 1: 'b', 2: 'c'} + >>> H = nx.relabel_nodes(G, mapping) + >>> sorted(H) + ['a', 'b', 'c'] + + Nodes can be relabeled with any hashable object, including numbers + and strings: + + >>> import string + >>> G = nx.path_graph(26) # nodes are integers 0 through 25 + >>> sorted(G)[:3] + [0, 1, 2] + >>> mapping = dict(zip(G, string.ascii_lowercase)) + >>> G = nx.relabel_nodes(G, mapping) # nodes are characters a through z + >>> sorted(G)[:3] + ['a', 'b', 'c'] + >>> mapping = dict(zip(G, range(1, 27))) + >>> G = nx.relabel_nodes(G, mapping) # nodes are integers 1 through 26 + >>> sorted(G)[:3] + [1, 2, 3] + + To perform a partial in-place relabeling, provide a dictionary + mapping only a subset of the nodes, and set the `copy` keyword + argument to False: + + >>> G = nx.path_graph(3) # nodes 0-1-2 + >>> mapping = {0: 'a', 1: 'b'} # 0->'a' and 1->'b' + >>> G = nx.relabel_nodes(G, mapping, copy=False) + >>> sorted(G, key=str) + [2, 'a', 'b'] + + A mapping can also be given as a function: + + >>> G = nx.path_graph(3) + >>> H = nx.relabel_nodes(G, lambda x: x ** 2) + >>> list(H) + [0, 1, 4] + + Notes + ----- + Only the nodes specified in the mapping will be relabeled. + + The keyword setting copy=False modifies the graph in place. + Relabel_nodes avoids naming collisions by building a + directed graph from ``mapping`` which specifies the order of + relabelings. Naming collisions, such as a->b, b->c, are ordered + such that "b" gets renamed to "c" before "a" gets renamed "b". + In cases of circular mappings (e.g. a->b, b->a), modifying the + graph is not possible in-place and an exception is raised. + In that case, use copy=True. + + See Also + -------- + convert_node_labels_to_integers + """ + # you can pass a function f(old_label)->new_label + # but we'll just make a dictionary here regardless + if not hasattr(mapping, "__getitem__"): + m = {n: mapping(n) for n in G} + else: + m = mapping + if copy: + return _relabel_copy(G, m) + else: + return _relabel_inplace(G, m) + + +def _relabel_inplace(G, mapping): + old_labels = set(mapping.keys()) + new_labels = set(mapping.values()) + if len(old_labels & new_labels) > 0: + # labels sets overlap + # can we topological sort and still do the relabeling? + D = nx.DiGraph(list(mapping.items())) + D.remove_edges_from(nx.selfloop_edges(D)) + try: + nodes = reversed(list(nx.topological_sort(D))) + except nx.NetworkXUnfeasible: + raise nx.NetworkXUnfeasible('The node label sets are overlapping ' + 'and no ordering can resolve the ' + 'mapping. Use copy=True.') + else: + # non-overlapping label sets + nodes = old_labels + + multigraph = G.is_multigraph() + directed = G.is_directed() + + for old in nodes: + try: + new = mapping[old] + except KeyError: + continue + if new == old: + continue + try: + G.add_node(new, **G.nodes[old]) + except KeyError: + raise KeyError("Node %s is not in the graph" % old) + if multigraph: + new_edges = [(new, new if old == target else target, key, data) + for (_, target, key, data) + in G.edges(old, data=True, keys=True)] + if directed: + new_edges += [(new if old == source else source, new, key, data) + for (source, _, key, data) + in G.in_edges(old, data=True, keys=True)] + else: + new_edges = [(new, new if old == target else target, data) + for (_, target, data) in G.edges(old, data=True)] + if directed: + new_edges += [(new if old == source else source, new, data) + for (source, _, data) in G.in_edges(old, data=True)] + G.remove_node(old) + G.add_edges_from(new_edges) + return G + + +def _relabel_copy(G, mapping): + H = G.__class__() + H.add_nodes_from(mapping.get(n, n) for n in G) + H._node.update((mapping.get(n, n), d.copy()) for n, d in G.nodes.items()) + if G.is_multigraph(): + H.add_edges_from((mapping.get(n1, n1), mapping.get(n2, n2), k, d.copy()) + for (n1, n2, k, d) in G.edges(keys=True, data=True)) + else: + H.add_edges_from((mapping.get(n1, n1), mapping.get(n2, n2), d.copy()) + for (n1, n2, d) in G.edges(data=True)) + H.graph.update(G.graph) + return H + + +def convert_node_labels_to_integers(G, first_label=0, ordering="default", + label_attribute=None): + """Returns a copy of the graph G with the nodes relabeled using + consecutive integers. + + Parameters + ---------- + G : graph + A NetworkX graph + + first_label : int, optional (default=0) + An integer specifying the starting offset in numbering nodes. + The new integer labels are numbered first_label, ..., n-1+first_label. + + ordering : string + "default" : inherit node ordering from G.nodes() + "sorted" : inherit node ordering from sorted(G.nodes()) + "increasing degree" : nodes are sorted by increasing degree + "decreasing degree" : nodes are sorted by decreasing degree + + label_attribute : string, optional (default=None) + Name of node attribute to store old label. If None no attribute + is created. + + Notes + ----- + Node and edge attribute data are copied to the new (relabeled) graph. + + There is no guarantee that the relabeling of nodes to integers will + give the same two integers for two (even identical graphs). + Use the `ordering` argument to try to preserve the order. + + See Also + -------- + relabel_nodes + """ + N = G.number_of_nodes() + first_label + if ordering == "default": + mapping = dict(zip(G.nodes(), range(first_label, N))) + elif ordering == "sorted": + nlist = sorted(G.nodes()) + mapping = dict(zip(nlist, range(first_label, N))) + elif ordering == "increasing degree": + dv_pairs = [(d, n) for (n, d) in G.degree()] + dv_pairs.sort() # in-place sort from lowest to highest degree + mapping = dict(zip([n for d, n in dv_pairs], range(first_label, N))) + elif ordering == "decreasing degree": + dv_pairs = [(d, n) for (n, d) in G.degree()] + dv_pairs.sort() # in-place sort from lowest to highest degree + dv_pairs.reverse() + mapping = dict(zip([n for d, n in dv_pairs], range(first_label, N))) + else: + raise nx.NetworkXError('Unknown node ordering: %s' % ordering) + H = relabel_nodes(G, mapping) + # create node attribute with the old label + if label_attribute is not None: + nx.set_node_attributes(H, {v: k for k, v in mapping.items()}, + label_attribute) + return H