209 lines
7.6 KiB
Python
209 lines
7.6 KiB
Python
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r"""
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Compressed sparse graph routines (:mod:`scipy.sparse.csgraph`)
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==============================================================
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.. currentmodule:: scipy.sparse.csgraph
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Fast graph algorithms based on sparse matrix representations.
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Contents
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--------
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.. autosummary::
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:toctree: generated/
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connected_components -- determine connected components of a graph
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laplacian -- compute the laplacian of a graph
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shortest_path -- compute the shortest path between points on a positive graph
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dijkstra -- use Dijkstra's algorithm for shortest path
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floyd_warshall -- use the Floyd-Warshall algorithm for shortest path
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bellman_ford -- use the Bellman-Ford algorithm for shortest path
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johnson -- use Johnson's algorithm for shortest path
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breadth_first_order -- compute a breadth-first order of nodes
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depth_first_order -- compute a depth-first order of nodes
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breadth_first_tree -- construct the breadth-first tree from a given node
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depth_first_tree -- construct a depth-first tree from a given node
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minimum_spanning_tree -- construct the minimum spanning tree of a graph
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reverse_cuthill_mckee -- compute permutation for reverse Cuthill-McKee ordering
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maximum_flow -- solve the maximum flow problem for a graph
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maximum_bipartite_matching -- compute a maximum matching of a bipartite graph
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min_weight_full_bipartite_matching - compute a minimum weight full matching of a bipartite graph
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structural_rank -- compute the structural rank of a graph
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NegativeCycleError
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.. autosummary::
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:toctree: generated/
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construct_dist_matrix
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csgraph_from_dense
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csgraph_from_masked
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csgraph_masked_from_dense
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csgraph_to_dense
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csgraph_to_masked
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reconstruct_path
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Graph Representations
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---------------------
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This module uses graphs which are stored in a matrix format. A
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graph with N nodes can be represented by an (N x N) adjacency matrix G.
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If there is a connection from node i to node j, then G[i, j] = w, where
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w is the weight of the connection. For nodes i and j which are
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not connected, the value depends on the representation:
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- for dense array representations, non-edges are represented by
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G[i, j] = 0, infinity, or NaN.
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- for dense masked representations (of type np.ma.MaskedArray), non-edges
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are represented by masked values. This can be useful when graphs with
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zero-weight edges are desired.
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- for sparse array representations, non-edges are represented by
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non-entries in the matrix. This sort of sparse representation also
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allows for edges with zero weights.
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As a concrete example, imagine that you would like to represent the following
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undirected graph::
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G
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(0)
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/ \
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1 2
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/ \
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(2) (1)
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This graph has three nodes, where node 0 and 1 are connected by an edge of
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weight 2, and nodes 0 and 2 are connected by an edge of weight 1.
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We can construct the dense, masked, and sparse representations as follows,
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keeping in mind that an undirected graph is represented by a symmetric matrix::
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>>> import numpy as np
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>>> G_dense = np.array([[0, 2, 1],
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... [2, 0, 0],
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... [1, 0, 0]])
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>>> G_masked = np.ma.masked_values(G_dense, 0)
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>>> from scipy.sparse import csr_matrix
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>>> G_sparse = csr_matrix(G_dense)
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This becomes more difficult when zero edges are significant. For example,
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consider the situation when we slightly modify the above graph::
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G2
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(0)
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/ \
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0 2
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/ \
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(2) (1)
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This is identical to the previous graph, except nodes 0 and 2 are connected
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by an edge of zero weight. In this case, the dense representation above
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leads to ambiguities: how can non-edges be represented if zero is a meaningful
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value? In this case, either a masked or sparse representation must be used
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to eliminate the ambiguity::
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>>> import numpy as np
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>>> G2_data = np.array([[np.inf, 2, 0 ],
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... [2, np.inf, np.inf],
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... [0, np.inf, np.inf]])
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>>> G2_masked = np.ma.masked_invalid(G2_data)
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>>> from scipy.sparse.csgraph import csgraph_from_dense
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>>> # G2_sparse = csr_matrix(G2_data) would give the wrong result
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>>> G2_sparse = csgraph_from_dense(G2_data, null_value=np.inf)
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>>> G2_sparse.data
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array([ 2., 0., 2., 0.])
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Here we have used a utility routine from the csgraph submodule in order to
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convert the dense representation to a sparse representation which can be
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understood by the algorithms in submodule. By viewing the data array, we
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can see that the zero values are explicitly encoded in the graph.
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Directed vs. undirected
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^^^^^^^^^^^^^^^^^^^^^^^
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Matrices may represent either directed or undirected graphs. This is
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specified throughout the csgraph module by a boolean keyword. Graphs are
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assumed to be directed by default. In a directed graph, traversal from node
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i to node j can be accomplished over the edge G[i, j], but not the edge
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G[j, i]. Consider the following dense graph::
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>>> import numpy as np
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>>> G_dense = np.array([[0, 1, 0],
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... [2, 0, 3],
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... [0, 4, 0]])
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When ``directed=True`` we get the graph::
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---1--> ---3-->
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(0) (1) (2)
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<--2--- <--4---
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In a non-directed graph, traversal from node i to node j can be
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accomplished over either G[i, j] or G[j, i]. If both edges are not null,
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and the two have unequal weights, then the smaller of the two is used.
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So for the same graph, when ``directed=False`` we get the graph::
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(0)--1--(1)--3--(2)
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Note that a symmetric matrix will represent an undirected graph, regardless
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of whether the 'directed' keyword is set to True or False. In this case,
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using ``directed=True`` generally leads to more efficient computation.
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The routines in this module accept as input either scipy.sparse representations
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(csr, csc, or lil format), masked representations, or dense representations
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with non-edges indicated by zeros, infinities, and NaN entries.
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""" # noqa: E501
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__docformat__ = "restructuredtext en"
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__all__ = ['connected_components',
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'laplacian',
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'shortest_path',
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'floyd_warshall',
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'dijkstra',
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'bellman_ford',
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'johnson',
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'breadth_first_order',
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'depth_first_order',
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'breadth_first_tree',
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'depth_first_tree',
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'minimum_spanning_tree',
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'reverse_cuthill_mckee',
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'maximum_flow',
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'maximum_bipartite_matching',
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'min_weight_full_bipartite_matching',
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'structural_rank',
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'construct_dist_matrix',
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'reconstruct_path',
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'csgraph_masked_from_dense',
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'csgraph_from_dense',
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'csgraph_from_masked',
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'csgraph_to_dense',
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'csgraph_to_masked',
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'NegativeCycleError']
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from ._laplacian import laplacian
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from ._shortest_path import (
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shortest_path, floyd_warshall, dijkstra, bellman_ford, johnson,
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NegativeCycleError
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)
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from ._traversal import (
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breadth_first_order, depth_first_order, breadth_first_tree,
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depth_first_tree, connected_components
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)
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from ._min_spanning_tree import minimum_spanning_tree
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from ._flow import maximum_flow
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from ._matching import (
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maximum_bipartite_matching, min_weight_full_bipartite_matching
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)
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from ._reordering import reverse_cuthill_mckee, structural_rank
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from ._tools import (
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construct_dist_matrix, reconstruct_path, csgraph_from_dense,
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csgraph_to_dense, csgraph_masked_from_dense, csgraph_from_masked,
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csgraph_to_masked
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)
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from scipy._lib._testutils import PytestTester
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test = PytestTester(__name__)
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del PytestTester
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