annotate env/lib/python3.9/site-packages/networkx/algorithms/centrality/current_flow_closeness.py @ 0:4f3585e2f14b draft default tip

"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"

"""Current-flow closeness centrality measures."""
import networkx as nx

from networkx.utils import not_implemented_for, reverse_cuthill_mckee_ordering
from networkx.algorithms.centrality.flow_matrix import (
    CGInverseLaplacian,
    FullInverseLaplacian,
    laplacian_sparse_matrix,
    SuperLUInverseLaplacian,
)

__all__ = ["current_flow_closeness_centrality", "information_centrality"]


@not_implemented_for("directed")
def current_flow_closeness_centrality(G, weight=None, dtype=float, solver="lu"):
    """Compute current-flow closeness centrality for nodes.

    Current-flow closeness centrality is variant of closeness
    centrality based on effective resistance between nodes in
    a network. This metric is also known as information centrality.

    Parameters
    ----------
    G : graph
      A NetworkX graph.

    weight : None or string, optional (default=None)
      If None, all edge weights are considered equal.
      Otherwise holds the name of the edge attribute used as weight.

    dtype: data type (default=float)
      Default data type for internal matrices.
      Set to np.float32 for lower memory consumption.

    solver: string (default='lu')
       Type of linear solver to use for computing the flow matrix.
       Options are "full" (uses most memory), "lu" (recommended), and
       "cg" (uses least memory).

    Returns
    -------
    nodes : dictionary
       Dictionary of nodes with current flow closeness centrality as the value.

    See Also
    --------
    closeness_centrality

    Notes
    -----
    The algorithm is from Brandes [1]_.

    See also [2]_ for the original definition of information centrality.

    References
    ----------
    .. [1] Ulrik Brandes and Daniel Fleischer,
       Centrality Measures Based on Current Flow.
       Proc. 22nd Symp. Theoretical Aspects of Computer Science (STACS '05).
       LNCS 3404, pp. 533-544. Springer-Verlag, 2005.
       http://algo.uni-konstanz.de/publications/bf-cmbcf-05.pdf

    .. [2] Karen Stephenson and Marvin Zelen:
       Rethinking centrality: Methods and examples.
       Social Networks 11(1):1-37, 1989.
       https://doi.org/10.1016/0378-8733(89)90016-6
    """
    if not nx.is_connected(G):
        raise nx.NetworkXError("Graph not connected.")
    solvername = {
        "full": FullInverseLaplacian,
        "lu": SuperLUInverseLaplacian,
        "cg": CGInverseLaplacian,
    }
    n = G.number_of_nodes()
    ordering = list(reverse_cuthill_mckee_ordering(G))
    # make a copy with integer labels according to rcm ordering
    # this could be done without a copy if we really wanted to
    H = nx.relabel_nodes(G, dict(zip(ordering, range(n))))
    betweenness = dict.fromkeys(H, 0.0)  # b[v]=0 for v in H
    n = H.number_of_nodes()
    L = laplacian_sparse_matrix(
        H, nodelist=range(n), weight=weight, dtype=dtype, format="csc"
    )
    C2 = solvername[solver](L, width=1, dtype=dtype)  # initialize solver
    for v in H:
        col = C2.get_row(v)
        for w in H:
            betweenness[v] += col[v] - 2 * col[w]
            betweenness[w] += col[v]
    for v in H:
        betweenness[v] = 1.0 / (betweenness[v])
    return {ordering[k]: float(v) for k, v in betweenness.items()}


information_centrality = current_flow_closeness_centrality