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

"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"

"""
Adjacency matrix and incidence matrix of graphs.
"""
import networkx as nx

__all__ = ["incidence_matrix", "adj_matrix", "adjacency_matrix"]


def incidence_matrix(G, nodelist=None, edgelist=None, oriented=False, weight=None):
    """Returns incidence matrix of G.

    The incidence matrix assigns each row to a node and each column to an edge.
    For a standard incidence matrix a 1 appears wherever a row's node is
    incident on the column's edge.  For an oriented incidence matrix each
    edge is assigned an orientation (arbitrarily for undirected and aligning to
    direction for directed).  A -1 appears for the source (tail) of an edge and
    1 for the destination (head) of the edge.  The elements are zero otherwise.

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

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

    edgelist : list, optional (default= all edges in G)
       The columns are ordered according to the edges in edgelist.
       If edgelist is None, then the ordering is produced by G.edges().

    oriented: bool, optional (default=False)
       If True, matrix elements are +1 or -1 for the head or tail node
       respectively of each edge.  If False, +1 occurs at both nodes.

    weight : string or None, optional (default=None)
       The edge data key used to provide each value in the matrix.
       If None, then each edge has weight 1.  Edge weights, if used,
       should be positive so that the orientation can provide the sign.

    Returns
    -------
    A : SciPy sparse matrix
      The incidence matrix of G.

    Notes
    -----
    For MultiGraph/MultiDiGraph, the edges in edgelist should be
    (u,v,key) 3-tuples.

    "Networks are the best discrete model for so many problems in
    applied mathematics" [1]_.

    References
    ----------
    .. [1] Gil Strang, Network applications: A = incidence matrix,
       http://academicearth.org/lectures/network-applications-incidence-matrix
    """
    import scipy.sparse

    if nodelist is None:
        nodelist = list(G)
    if edgelist is None:
        if G.is_multigraph():
            edgelist = list(G.edges(keys=True))
        else:
            edgelist = list(G.edges())
    A = scipy.sparse.lil_matrix((len(nodelist), len(edgelist)))
    node_index = {node: i for i, node in enumerate(nodelist)}
    for ei, e in enumerate(edgelist):
        (u, v) = e[:2]
        if u == v:
            continue  # self loops give zero column
        try:
            ui = node_index[u]
            vi = node_index[v]
        except KeyError as e:
            raise nx.NetworkXError(
                f"node {u} or {v} in edgelist " f"but not in nodelist"
            ) from e
        if weight is None:
            wt = 1
        else:
            if G.is_multigraph():
                ekey = e[2]
                wt = G[u][v][ekey].get(weight, 1)
            else:
                wt = G[u][v].get(weight, 1)
        if oriented:
            A[ui, ei] = -wt
            A[vi, ei] = wt
        else:
            A[ui, ei] = wt
            A[vi, ei] = wt
    return A.asformat("csc")


def adjacency_matrix(G, nodelist=None, weight="weight"):
    """Returns adjacency matrix of G.

    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 provide each value in the matrix.
       If None, then each edge has weight 1.

    Returns
    -------
    A : SciPy sparse matrix
      Adjacency matrix representation of G.

    Notes
    -----
    For directed graphs, entry i,j corresponds to an edge from i to j.

    If you want a pure Python adjacency matrix representation try
    networkx.convert.to_dict_of_dicts which will return a
    dictionary-of-dictionaries format that can be addressed as a
    sparse matrix.

    For MultiGraph/MultiDiGraph with parallel edges the weights are summed.
    See `to_numpy_array` for other options.

    The convention used for self-loop edges in graphs is to assign the
    diagonal matrix entry value to the edge weight attribute
    (or the number 1 if the edge has no weight attribute).  If the
    alternate convention of doubling the edge weight is desired the
    resulting Scipy sparse matrix can be modified as follows:

    >>> import scipy as sp
    >>> G = nx.Graph([(1, 1)])
    >>> A = nx.adjacency_matrix(G)
    >>> print(A.todense())
    [[1]]
    >>> A.setdiag(A.diagonal() * 2)
    >>> print(A.todense())
    [[2]]

    See Also
    --------
    to_numpy_array
    to_scipy_sparse_matrix
    to_dict_of_dicts
    adjacency_spectrum
    """
    return nx.to_scipy_sparse_matrix(G, nodelist=nodelist, weight=weight)


adj_matrix = adjacency_matrix