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

"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"

"""
Algorithms for finding k-edge-connected components and subgraphs.

A k-edge-connected component (k-edge-cc) is a maximal set of nodes in G, such
that all pairs of node have an edge-connectivity of at least k.

A k-edge-connected subgraph (k-edge-subgraph) is a maximal set of nodes in G,
such that the subgraph of G defined by the nodes has an edge-connectivity at
least k.
"""
import networkx as nx
from networkx.utils import arbitrary_element
from networkx.utils import not_implemented_for
from networkx.algorithms import bridges
from functools import partial
import itertools as it

__all__ = [
    "k_edge_components",
    "k_edge_subgraphs",
    "bridge_components",
    "EdgeComponentAuxGraph",
]


@not_implemented_for("multigraph")
def k_edge_components(G, k):
    """Generates nodes in each maximal k-edge-connected component in G.

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

    k : Integer
        Desired edge connectivity

    Returns
    -------
    k_edge_components : a generator of k-edge-ccs. Each set of returned nodes
       will have k-edge-connectivity in the graph G.

    See Also
    -------
    :func:`local_edge_connectivity`
    :func:`k_edge_subgraphs` : similar to this function, but the subgraph
        defined by the nodes must also have k-edge-connectivity.
    :func:`k_components` : similar to this function, but uses node-connectivity
        instead of edge-connectivity

    Raises
    ------
    NetworkXNotImplemented
        If the input graph is a multigraph.

    ValueError:
        If k is less than 1

    Notes
    -----
    Attempts to use the most efficient implementation available based on k.
    If k=1, this is simply simply connected components for directed graphs and
    connected components for undirected graphs.
    If k=2 on an efficient bridge connected component algorithm from _[1] is
    run based on the chain decomposition.
    Otherwise, the algorithm from _[2] is used.

    Example
    -------
    >>> import itertools as it
    >>> from networkx.utils import pairwise
    >>> paths = [
    ...     (1, 2, 4, 3, 1, 4),
    ...     (5, 6, 7, 8, 5, 7, 8, 6),
    ... ]
    >>> G = nx.Graph()
    >>> G.add_nodes_from(it.chain(*paths))
    >>> G.add_edges_from(it.chain(*[pairwise(path) for path in paths]))
    >>> # note this returns {1, 4} unlike k_edge_subgraphs
    >>> sorted(map(sorted, nx.k_edge_components(G, k=3)))
    [[1, 4], [2], [3], [5, 6, 7, 8]]

    References
    ----------
    .. [1] https://en.wikipedia.org/wiki/Bridge_%28graph_theory%29
    .. [2] Wang, Tianhao, et al. (2015) A simple algorithm for finding all
        k-edge-connected components.
        http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0136264
    """
    # Compute k-edge-ccs using the most efficient algorithms available.
    if k < 1:
        raise ValueError("k cannot be less than 1")
    if G.is_directed():
        if k == 1:
            return nx.strongly_connected_components(G)
        else:
            # TODO: investigate https://arxiv.org/abs/1412.6466 for k=2
            aux_graph = EdgeComponentAuxGraph.construct(G)
            return aux_graph.k_edge_components(k)
    else:
        if k == 1:
            return nx.connected_components(G)
        elif k == 2:
            return bridge_components(G)
        else:
            aux_graph = EdgeComponentAuxGraph.construct(G)
            return aux_graph.k_edge_components(k)


@not_implemented_for("multigraph")
def k_edge_subgraphs(G, k):
    """Generates nodes in each maximal k-edge-connected subgraph in G.

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

    k : Integer
        Desired edge connectivity

    Returns
    -------
    k_edge_subgraphs : a generator of k-edge-subgraphs
        Each k-edge-subgraph is a maximal set of nodes that defines a subgraph
        of G that is k-edge-connected.

    See Also
    -------
    :func:`edge_connectivity`
    :func:`k_edge_components` : similar to this function, but nodes only
        need to have k-edge-connctivity within the graph G and the subgraphs
        might not be k-edge-connected.

    Raises
    ------
    NetworkXNotImplemented
        If the input graph is a multigraph.

    ValueError:
        If k is less than 1

    Notes
    -----
    Attempts to use the most efficient implementation available based on k.
    If k=1, or k=2 and the graph is undirected, then this simply calls
    `k_edge_components`.  Otherwise the algorithm from _[1] is used.

    Example
    -------
    >>> import itertools as it
    >>> from networkx.utils import pairwise
    >>> paths = [
    ...     (1, 2, 4, 3, 1, 4),
    ...     (5, 6, 7, 8, 5, 7, 8, 6),
    ... ]
    >>> G = nx.Graph()
    >>> G.add_nodes_from(it.chain(*paths))
    >>> G.add_edges_from(it.chain(*[pairwise(path) for path in paths]))
    >>> # note this does not return {1, 4} unlike k_edge_components
    >>> sorted(map(sorted, nx.k_edge_subgraphs(G, k=3)))
    [[1], [2], [3], [4], [5, 6, 7, 8]]

    References
    ----------
    .. [1] Zhou, Liu, et al. (2012) Finding maximal k-edge-connected subgraphs
        from a large graph.  ACM International Conference on Extending Database
        Technology 2012 480-–491.
        https://openproceedings.org/2012/conf/edbt/ZhouLYLCL12.pdf
    """
    if k < 1:
        raise ValueError("k cannot be less than 1")
    if G.is_directed():
        if k <= 1:
            # For directed graphs ,
            # When k == 1, k-edge-ccs and k-edge-subgraphs are the same
            return k_edge_components(G, k)
        else:
            return _k_edge_subgraphs_nodes(G, k)
    else:
        if k <= 2:
            # For undirected graphs,
            # when k <= 2, k-edge-ccs and k-edge-subgraphs are the same
            return k_edge_components(G, k)
        else:
            return _k_edge_subgraphs_nodes(G, k)


def _k_edge_subgraphs_nodes(G, k):
    """Helper to get the nodes from the subgraphs.

    This allows k_edge_subgraphs to return a generator.
    """
    for C in general_k_edge_subgraphs(G, k):
        yield set(C.nodes())


@not_implemented_for("directed")
@not_implemented_for("multigraph")
def bridge_components(G):
    """Finds all bridge-connected components G.

    Parameters
    ----------
    G : NetworkX undirected graph

    Returns
    -------
    bridge_components : a generator of 2-edge-connected components


    See Also
    --------
    :func:`k_edge_subgraphs` : this function is a special case for an
        undirected graph where k=2.
    :func:`biconnected_components` : similar to this function, but is defined
        using 2-node-connectivity instead of 2-edge-connectivity.

    Raises
    ------
    NetworkXNotImplemented
        If the input graph is directed or a multigraph.

    Notes
    -----
    Bridge-connected components are also known as 2-edge-connected components.

    Example
    -------
    >>> # The barbell graph with parameter zero has a single bridge
    >>> G = nx.barbell_graph(5, 0)
    >>> from networkx.algorithms.connectivity.edge_kcomponents import bridge_components
    >>> sorted(map(sorted, bridge_components(G)))
    [[0, 1, 2, 3, 4], [5, 6, 7, 8, 9]]
    """
    H = G.copy()
    H.remove_edges_from(bridges(G))
    yield from nx.connected_components(H)


class EdgeComponentAuxGraph:
    r"""A simple algorithm to find all k-edge-connected components in a graph.

    Constructing the AuxillaryGraph (which may take some time) allows for the
    k-edge-ccs to be found in linear time for arbitrary k.

    Notes
    -----
    This implementation is based on [1]_. The idea is to construct an auxiliary
    graph from which the k-edge-ccs can be extracted in linear time. The
    auxiliary graph is constructed in $O(|V|\cdot F)$ operations, where F is the
    complexity of max flow. Querying the components takes an additional $O(|V|)$
    operations. This algorithm can be slow for large graphs, but it handles an
    arbitrary k and works for both directed and undirected inputs.

    The undirected case for k=1 is exactly connected components.
    The undirected case for k=2 is exactly bridge connected components.
    The directed case for k=1 is exactly strongly connected components.

    References
    ----------
    .. [1] Wang, Tianhao, et al. (2015) A simple algorithm for finding all
        k-edge-connected components.
        http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0136264

    Example
    -------
    >>> import itertools as it
    >>> from networkx.utils import pairwise
    >>> from networkx.algorithms.connectivity import EdgeComponentAuxGraph
    >>> # Build an interesting graph with multiple levels of k-edge-ccs
    >>> paths = [
    ...     (1, 2, 3, 4, 1, 3, 4, 2),  # a 3-edge-cc (a 4 clique)
    ...     (5, 6, 7, 5),  # a 2-edge-cc (a 3 clique)
    ...     (1, 5),  # combine first two ccs into a 1-edge-cc
    ...     (0,),  # add an additional disconnected 1-edge-cc
    ... ]
    >>> G = nx.Graph()
    >>> G.add_nodes_from(it.chain(*paths))
    >>> G.add_edges_from(it.chain(*[pairwise(path) for path in paths]))
    >>> # Constructing the AuxGraph takes about O(n ** 4)
    >>> aux_graph = EdgeComponentAuxGraph.construct(G)
    >>> # Once constructed, querying takes O(n)
    >>> sorted(map(sorted, aux_graph.k_edge_components(k=1)))
    [[0], [1, 2, 3, 4, 5, 6, 7]]
    >>> sorted(map(sorted, aux_graph.k_edge_components(k=2)))
    [[0], [1, 2, 3, 4], [5, 6, 7]]
    >>> sorted(map(sorted, aux_graph.k_edge_components(k=3)))
    [[0], [1, 2, 3, 4], [5], [6], [7]]
    >>> sorted(map(sorted, aux_graph.k_edge_components(k=4)))
    [[0], [1], [2], [3], [4], [5], [6], [7]]

    Example
    -------
    >>> # The auxiliary graph is primarilly used for k-edge-ccs but it
    >>> # can also speed up the queries of k-edge-subgraphs by refining the
    >>> # search space.
    >>> import itertools as it
    >>> from networkx.utils import pairwise
    >>> from networkx.algorithms.connectivity import EdgeComponentAuxGraph
    >>> paths = [
    ...     (1, 2, 4, 3, 1, 4),
    ... ]
    >>> G = nx.Graph()
    >>> G.add_nodes_from(it.chain(*paths))
    >>> G.add_edges_from(it.chain(*[pairwise(path) for path in paths]))
    >>> aux_graph = EdgeComponentAuxGraph.construct(G)
    >>> sorted(map(sorted, aux_graph.k_edge_subgraphs(k=3)))
    [[1], [2], [3], [4]]
    >>> sorted(map(sorted, aux_graph.k_edge_components(k=3)))
    [[1, 4], [2], [3]]
    """

    # @not_implemented_for('multigraph')  # TODO: fix decor for classmethods
    @classmethod
    def construct(EdgeComponentAuxGraph, G):
        """Builds an auxiliary graph encoding edge-connectivity between nodes.

        Notes
        -----
        Given G=(V, E), initialize an empty auxiliary graph A.
        Choose an arbitrary source node s.  Initialize a set N of available
        nodes (that can be used as the sink). The algorithm picks an
        arbitrary node t from N - {s}, and then computes the minimum st-cut
        (S, T) with value w. If G is directed the the minimum of the st-cut or
        the ts-cut is used instead. Then, the edge (s, t) is added to the
        auxiliary graph with weight w. The algorithm is called recursively
        first using S as the available nodes and s as the source, and then
        using T and t. Recursion stops when the source is the only available
        node.

        Parameters
        ----------
        G : NetworkX graph
        """
        # workaround for classmethod decorator
        not_implemented_for("multigraph")(lambda G: G)(G)

        def _recursive_build(H, A, source, avail):
            # Terminate once the flow has been compute to every node.
            if {source} == avail:
                return
            # pick an arbitrary node as the sink
            sink = arbitrary_element(avail - {source})
            # find the minimum cut and its weight
            value, (S, T) = nx.minimum_cut(H, source, sink)
            if H.is_directed():
                # check if the reverse direction has a smaller cut
                value_, (T_, S_) = nx.minimum_cut(H, sink, source)
                if value_ < value:
                    value, S, T = value_, S_, T_
            # add edge with weight of cut to the aux graph
            A.add_edge(source, sink, weight=value)
            # recursively call until all but one node is used
            _recursive_build(H, A, source, avail.intersection(S))
            _recursive_build(H, A, sink, avail.intersection(T))

        # Copy input to ensure all edges have unit capacity
        H = G.__class__()
        H.add_nodes_from(G.nodes())
        H.add_edges_from(G.edges(), capacity=1)

        # A is the auxiliary graph to be constructed
        # It is a weighted undirected tree
        A = nx.Graph()

        # Pick an arbitrary node as the source
        if H.number_of_nodes() > 0:
            source = arbitrary_element(H.nodes())
            # Initialize a set of elements that can be chosen as the sink
            avail = set(H.nodes())

            # This constructs A
            _recursive_build(H, A, source, avail)

        # This class is a container the holds the auxiliary graph A and
        # provides access the the k_edge_components function.
        self = EdgeComponentAuxGraph()
        self.A = A
        self.H = H
        return self

    def k_edge_components(self, k):
        """Queries the auxiliary graph for k-edge-connected components.

        Parameters
        ----------
        k : Integer
            Desired edge connectivity

        Returns
        -------
        k_edge_components : a generator of k-edge-ccs

        Notes
        -----
        Given the auxiliary graph, the k-edge-connected components can be
        determined in linear time by removing all edges with weights less than
        k from the auxiliary graph.  The resulting connected components are the
        k-edge-ccs in the original graph.
        """
        if k < 1:
            raise ValueError("k cannot be less than 1")
        A = self.A
        # "traverse the auxiliary graph A and delete all edges with weights less
        # than k"
        aux_weights = nx.get_edge_attributes(A, "weight")
        # Create a relevant graph with the auxiliary edges with weights >= k
        R = nx.Graph()
        R.add_nodes_from(A.nodes())
        R.add_edges_from(e for e, w in aux_weights.items() if w >= k)

        # Return the nodes that are k-edge-connected in the original graph
        yield from nx.connected_components(R)

    def k_edge_subgraphs(self, k):
        """Queries the auxiliary graph for k-edge-connected subgraphs.

        Parameters
        ----------
        k : Integer
            Desired edge connectivity

        Returns
        -------
        k_edge_subgraphs : a generator of k-edge-subgraphs

        Notes
        -----
        Refines the k-edge-ccs into k-edge-subgraphs. The running time is more
        than $O(|V|)$.

        For single values of k it is faster to use `nx.k_edge_subgraphs`.
        But for multiple values of k, it can be faster to build AuxGraph and
        then use this method.
        """
        if k < 1:
            raise ValueError("k cannot be less than 1")
        H = self.H
        A = self.A
        # "traverse the auxiliary graph A and delete all edges with weights less
        # than k"
        aux_weights = nx.get_edge_attributes(A, "weight")
        # Create a relevant graph with the auxiliary edges with weights >= k
        R = nx.Graph()
        R.add_nodes_from(A.nodes())
        R.add_edges_from(e for e, w in aux_weights.items() if w >= k)

        # Return the components whose subgraphs are k-edge-connected
        for cc in nx.connected_components(R):
            if len(cc) < k:
                # Early return optimization
                for node in cc:
                    yield {node}
            else:
                # Call subgraph solution to refine the results
                C = H.subgraph(cc)
                yield from k_edge_subgraphs(C, k)


def _low_degree_nodes(G, k, nbunch=None):
    """Helper for finding nodes with degree less than k."""
    # Nodes with degree less than k cannot be k-edge-connected.
    if G.is_directed():
        # Consider both in and out degree in the directed case
        seen = set()
        for node, degree in G.out_degree(nbunch):
            if degree < k:
                seen.add(node)
                yield node
        for node, degree in G.in_degree(nbunch):
            if node not in seen and degree < k:
                seen.add(node)
                yield node
    else:
        # Only the degree matters in the undirected case
        for node, degree in G.degree(nbunch):
            if degree < k:
                yield node


def _high_degree_components(G, k):
    """Helper for filtering components that can't be k-edge-connected.

    Removes and generates each node with degree less than k.  Then generates
    remaining components where all nodes have degree at least k.
    """
    # Iteravely remove parts of the graph that are not k-edge-connected
    H = G.copy()
    singletons = set(_low_degree_nodes(H, k))
    while singletons:
        # Only search neighbors of removed nodes
        nbunch = set(it.chain.from_iterable(map(H.neighbors, singletons)))
        nbunch.difference_update(singletons)
        H.remove_nodes_from(singletons)
        for node in singletons:
            yield {node}
        singletons = set(_low_degree_nodes(H, k, nbunch))

    # Note: remaining connected components may not be k-edge-connected
    if G.is_directed():
        yield from nx.strongly_connected_components(H)
    else:
        yield from nx.connected_components(H)


def general_k_edge_subgraphs(G, k):
    """General algorithm to find all maximal k-edge-connected subgraphs in G.

    Returns
    -------
    k_edge_subgraphs : a generator of nx.Graphs that are k-edge-subgraphs
        Each k-edge-subgraph is a maximal set of nodes that defines a subgraph
        of G that is k-edge-connected.

    Notes
    -----
    Implementation of the basic algorithm from _[1].  The basic idea is to find
    a global minimum cut of the graph. If the cut value is at least k, then the
    graph is a k-edge-connected subgraph and can be added to the results.
    Otherwise, the cut is used to split the graph in two and the procedure is
    applied recursively. If the graph is just a single node, then it is also
    added to the results. At the end, each result is either guaranteed to be
    a single node or a subgraph of G that is k-edge-connected.

    This implementation contains optimizations for reducing the number of calls
    to max-flow, but there are other optimizations in _[1] that could be
    implemented.

    References
    ----------
    .. [1] Zhou, Liu, et al. (2012) Finding maximal k-edge-connected subgraphs
        from a large graph.  ACM International Conference on Extending Database
        Technology 2012 480-–491.
        https://openproceedings.org/2012/conf/edbt/ZhouLYLCL12.pdf

    Example
    -------
    >>> from networkx.utils import pairwise
    >>> paths = [
    ...     (11, 12, 13, 14, 11, 13, 14, 12),  # a 4-clique
    ...     (21, 22, 23, 24, 21, 23, 24, 22),  # another 4-clique
    ...     # connect the cliques with high degree but low connectivity
    ...     (50, 13),
    ...     (12, 50, 22),
    ...     (13, 102, 23),
    ...     (14, 101, 24),
    ... ]
    >>> G = nx.Graph(it.chain(*[pairwise(path) for path in paths]))
    >>> sorted(map(len, k_edge_subgraphs(G, k=3)))
    [1, 1, 1, 4, 4]
    """
    if k < 1:
        raise ValueError("k cannot be less than 1")

    # Node pruning optimization (incorporates early return)
    # find_ccs is either connected_components/strongly_connected_components
    find_ccs = partial(_high_degree_components, k=k)

    # Quick return optimization
    if G.number_of_nodes() < k:
        for node in G.nodes():
            yield G.subgraph([node]).copy()
        return

    # Intermediate results
    R0 = {G.subgraph(cc).copy() for cc in find_ccs(G)}
    # Subdivide CCs in the intermediate results until they are k-conn
    while R0:
        G1 = R0.pop()
        if G1.number_of_nodes() == 1:
            yield G1
        else:
            # Find a global minimum cut
            cut_edges = nx.minimum_edge_cut(G1)
            cut_value = len(cut_edges)
            if cut_value < k:
                # G1 is not k-edge-connected, so subdivide it
                G1.remove_edges_from(cut_edges)
                for cc in find_ccs(G1):
                    R0.add(G1.subgraph(cc).copy())
            else:
                # Otherwise we found a k-edge-connected subgraph
                yield G1