view env/lib/python3.9/site-packages/networkx/linalg/laplacianmatrix.py @ 0:4f3585e2f14b draft default tip

"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"

"""Laplacian matrix of graphs.
"""
import networkx as nx
from networkx.utils import not_implemented_for

__all__ = [
    "laplacian_matrix",
    "normalized_laplacian_matrix",
    "directed_laplacian_matrix",
    "directed_combinatorial_laplacian_matrix",
]


@not_implemented_for("directed")
def laplacian_matrix(G, nodelist=None, weight="weight"):
    """Returns the Laplacian matrix of G.

    The graph Laplacian is the matrix L = D - A, where
    A is the adjacency matrix and D is the diagonal matrix of node degrees.

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

    nodelist : list, optional
       The rows and columns are ordered according to the nodes in nodelist.
       If nodelist is None, then the ordering is produced by G.nodes().

    weight : string or None, optional (default='weight')
       The edge data key used to compute each value in the matrix.
       If None, then each edge has weight 1.

    Returns
    -------
    L : SciPy sparse matrix
      The Laplacian matrix of G.

    Notes
    -----
    For MultiGraph/MultiDiGraph, the edges weights are summed.

    See Also
    --------
    to_numpy_array
    normalized_laplacian_matrix
    laplacian_spectrum
    """
    import scipy.sparse

    if nodelist is None:
        nodelist = list(G)
    A = nx.to_scipy_sparse_matrix(G, nodelist=nodelist, weight=weight, format="csr")
    n, m = A.shape
    diags = A.sum(axis=1)
    D = scipy.sparse.spdiags(diags.flatten(), [0], m, n, format="csr")
    return D - A


@not_implemented_for("directed")
def normalized_laplacian_matrix(G, nodelist=None, weight="weight"):
    r"""Returns the normalized Laplacian matrix of G.

    The normalized graph Laplacian is the matrix

    .. math::

        N = D^{-1/2} L D^{-1/2}

    where `L` is the graph Laplacian and `D` is the diagonal matrix of
    node degrees.

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

    nodelist : list, optional
       The rows and columns are ordered according to the nodes in nodelist.
       If nodelist is None, then the ordering is produced by G.nodes().

    weight : string or None, optional (default='weight')
       The edge data key used to compute each value in the matrix.
       If None, then each edge has weight 1.

    Returns
    -------
    N : Scipy sparse matrix
      The normalized Laplacian matrix of G.

    Notes
    -----
    For MultiGraph/MultiDiGraph, the edges weights are summed.
    See to_numpy_array for other options.

    If the Graph contains selfloops, D is defined as diag(sum(A,1)), where A is
    the adjacency matrix [2]_.

    See Also
    --------
    laplacian_matrix
    normalized_laplacian_spectrum

    References
    ----------
    .. [1] Fan Chung-Graham, Spectral Graph Theory,
       CBMS Regional Conference Series in Mathematics, Number 92, 1997.
    .. [2] Steve Butler, Interlacing For Weighted Graphs Using The Normalized
       Laplacian, Electronic Journal of Linear Algebra, Volume 16, pp. 90-98,
       March 2007.
    """
    import numpy as np
    import scipy
    import scipy.sparse

    if nodelist is None:
        nodelist = list(G)
    A = nx.to_scipy_sparse_matrix(G, nodelist=nodelist, weight=weight, format="csr")
    n, m = A.shape
    diags = A.sum(axis=1).flatten()
    D = scipy.sparse.spdiags(diags, [0], m, n, format="csr")
    L = D - A
    with scipy.errstate(divide="ignore"):
        diags_sqrt = 1.0 / np.sqrt(diags)
    diags_sqrt[np.isinf(diags_sqrt)] = 0
    DH = scipy.sparse.spdiags(diags_sqrt, [0], m, n, format="csr")
    return DH.dot(L.dot(DH))


###############################################################################
# Code based on
# https://bitbucket.org/bedwards/networkx-community/src/370bd69fc02f/networkx/algorithms/community/


@not_implemented_for("undirected")
@not_implemented_for("multigraph")
def directed_laplacian_matrix(
    G, nodelist=None, weight="weight", walk_type=None, alpha=0.95
):
    r"""Returns the directed Laplacian matrix of G.

    The graph directed Laplacian is the matrix

    .. math::

        L = I - (\Phi^{1/2} P \Phi^{-1/2} + \Phi^{-1/2} P^T \Phi^{1/2} ) / 2

    where `I` is the identity matrix, `P` is the transition matrix of the
    graph, and `\Phi` a matrix with the Perron vector of `P` in the diagonal and
    zeros elsewhere.

    Depending on the value of walk_type, `P` can be the transition matrix
    induced by a random walk, a lazy random walk, or a random walk with
    teleportation (PageRank).

    Parameters
    ----------
    G : DiGraph
       A NetworkX graph

    nodelist : list, optional
       The rows and columns are ordered according to the nodes in nodelist.
       If nodelist is None, then the ordering is produced by G.nodes().

    weight : string or None, optional (default='weight')
       The edge data key used to compute each value in the matrix.
       If None, then each edge has weight 1.

    walk_type : string or None, optional (default=None)
       If None, `P` is selected depending on the properties of the
       graph. Otherwise is one of 'random', 'lazy', or 'pagerank'

    alpha : real
       (1 - alpha) is the teleportation probability used with pagerank

    Returns
    -------
    L : NumPy matrix
      Normalized Laplacian of G.

    Notes
    -----
    Only implemented for DiGraphs

    See Also
    --------
    laplacian_matrix

    References
    ----------
    .. [1] Fan Chung (2005).
       Laplacians and the Cheeger inequality for directed graphs.
       Annals of Combinatorics, 9(1), 2005
    """
    import numpy as np
    from scipy.sparse import spdiags, linalg

    P = _transition_matrix(
        G, nodelist=nodelist, weight=weight, walk_type=walk_type, alpha=alpha
    )

    n, m = P.shape

    evals, evecs = linalg.eigs(P.T, k=1)
    v = evecs.flatten().real
    p = v / v.sum()
    sqrtp = np.sqrt(p)
    Q = spdiags(sqrtp, [0], n, n) * P * spdiags(1.0 / sqrtp, [0], n, n)
    I = np.identity(len(G))

    return I - (Q + Q.T) / 2.0


@not_implemented_for("undirected")
@not_implemented_for("multigraph")
def directed_combinatorial_laplacian_matrix(
    G, nodelist=None, weight="weight", walk_type=None, alpha=0.95
):
    r"""Return the directed combinatorial Laplacian matrix of G.

    The graph directed combinatorial Laplacian is the matrix

    .. math::

        L = \Phi - (\Phi P + P^T \Phi) / 2

    where `P` is the transition matrix of the graph and and `\Phi` a matrix
    with the Perron vector of `P` in the diagonal and zeros elsewhere.

    Depending on the value of walk_type, `P` can be the transition matrix
    induced by a random walk, a lazy random walk, or a random walk with
    teleportation (PageRank).

    Parameters
    ----------
    G : DiGraph
       A NetworkX graph

    nodelist : list, optional
       The rows and columns are ordered according to the nodes in nodelist.
       If nodelist is None, then the ordering is produced by G.nodes().

    weight : string or None, optional (default='weight')
       The edge data key used to compute each value in the matrix.
       If None, then each edge has weight 1.

    walk_type : string or None, optional (default=None)
       If None, `P` is selected depending on the properties of the
       graph. Otherwise is one of 'random', 'lazy', or 'pagerank'

    alpha : real
       (1 - alpha) is the teleportation probability used with pagerank

    Returns
    -------
    L : NumPy matrix
      Combinatorial Laplacian of G.

    Notes
    -----
    Only implemented for DiGraphs

    See Also
    --------
    laplacian_matrix

    References
    ----------
    .. [1] Fan Chung (2005).
       Laplacians and the Cheeger inequality for directed graphs.
       Annals of Combinatorics, 9(1), 2005
    """
    from scipy.sparse import spdiags, linalg

    P = _transition_matrix(
        G, nodelist=nodelist, weight=weight, walk_type=walk_type, alpha=alpha
    )

    n, m = P.shape

    evals, evecs = linalg.eigs(P.T, k=1)
    v = evecs.flatten().real
    p = v / v.sum()
    Phi = spdiags(p, [0], n, n)

    Phi = Phi.todense()

    return Phi - (Phi * P + P.T * Phi) / 2.0


def _transition_matrix(G, nodelist=None, weight="weight", walk_type=None, alpha=0.95):
    """Returns the transition matrix of G.

    This is a row stochastic giving the transition probabilities while
    performing a random walk on the graph. Depending on the value of walk_type,
    P can be the transition matrix induced by a random walk, a lazy random walk,
    or a random walk with teleportation (PageRank).

    Parameters
    ----------
    G : DiGraph
       A NetworkX graph

    nodelist : list, optional
       The rows and columns are ordered according to the nodes in nodelist.
       If nodelist is None, then the ordering is produced by G.nodes().

    weight : string or None, optional (default='weight')
       The edge data key used to compute each value in the matrix.
       If None, then each edge has weight 1.

    walk_type : string or None, optional (default=None)
       If None, `P` is selected depending on the properties of the
       graph. Otherwise is one of 'random', 'lazy', or 'pagerank'

    alpha : real
       (1 - alpha) is the teleportation probability used with pagerank

    Returns
    -------
    P : NumPy matrix
      transition matrix of G.

    Raises
    ------
    NetworkXError
        If walk_type not specified or alpha not in valid range
    """
    import numpy as np
    from scipy.sparse import identity, spdiags

    if walk_type is None:
        if nx.is_strongly_connected(G):
            if nx.is_aperiodic(G):
                walk_type = "random"
            else:
                walk_type = "lazy"
        else:
            walk_type = "pagerank"

    M = nx.to_scipy_sparse_matrix(G, nodelist=nodelist, weight=weight, dtype=float)
    n, m = M.shape
    if walk_type in ["random", "lazy"]:
        DI = spdiags(1.0 / np.array(M.sum(axis=1).flat), [0], n, n)
        if walk_type == "random":
            P = DI * M
        else:
            I = identity(n)
            P = (I + DI * M) / 2.0

    elif walk_type == "pagerank":
        if not (0 < alpha < 1):
            raise nx.NetworkXError("alpha must be between 0 and 1")
        # this is using a dense representation
        M = M.todense()
        # add constant to dangling nodes' row
        dangling = np.where(M.sum(axis=1) == 0)
        for d in dangling[0]:
            M[d] = 1.0 / n
        # normalize
        M = M / M.sum(axis=1)
        P = alpha * M + (1 - alpha) / n
    else:
        raise nx.NetworkXError("walk_type must be random, lazy, or pagerank")

    return P