Python networkx.all_pairs_shortest_path_length() Examples

def _compute_distance_matrix(self):
        """Compute the full distance matrix on pairs of nodes.

        The distance map self._dist_matrix is computed from the graph using
        all_pairs_shortest_path_length.
        """
        if not self.is_connected():
            raise CouplingError("coupling graph not connected")
        lengths = nx.all_pairs_shortest_path_length(self.graph.to_undirected(as_view=True))
        lengths = dict(lengths)
        size = len(lengths)
        cmap = np.zeros((size, size))
        for idx in range(size):
            cmap[idx, np.fromiter(lengths[idx].keys(), dtype=int)] = np.fromiter(
                lengths[idx].values(), dtype=int)
        self._dist_matrix = cmap 

def shortest_path_matrix(G):
    """
    Return a matrix of pairwise shortest path lengths between nodes.

    Parameters
    ----------
    G (nx.Graph): the graph in question

    Returns
    -------
    pmat (np.ndarray): a matrix of shortest paths between nodes in G

    """

    N = G.number_of_nodes()
    pmat = np.zeros((N, N)) + N

    paths = nx.all_pairs_shortest_path_length(G)
    for node_i, node_ij in paths:
        for node_j, length_ij in node_ij.items():
            pmat[node_i, node_j] = length_ij

    pmat[pmat == np.inf] = N

    return pmat 

def precompute_dist_data(edge_index, num_nodes, approximate=0):
        '''
        Here dist is 1/real_dist, higher actually means closer, 0 means disconnected
        :return:
        '''
        graph = nx.Graph()
        edge_list = edge_index.transpose(1,0).tolist()
        graph.add_edges_from(edge_list)

        n = num_nodes
        dists_array = np.zeros((n, n))
        # dists_dict = nx.all_pairs_shortest_path_length(graph,cutoff=approximate if approximate>0 else None)
        # dists_dict = {c[0]: c[1] for c in dists_dict}
        dists_dict = all_pairs_shortest_path_length_parallel(graph,cutoff=approximate if approximate>0 else None)
        for i, node_i in enumerate(graph.nodes()):
            shortest_dist = dists_dict[node_i]
            for j, node_j in enumerate(graph.nodes()):
                dist = shortest_dist.get(node_j, -1)
                if dist!=-1:
                    # dists_array[i, j] = 1 / (dist + 1)
                    dists_array[node_i, node_j] = 1 / (dist + 1)
        return dists_array 

def test_all_pairs_shortest_path_length(self):
        ans = dict(nx.shortest_path_length(self.cycle))
        assert_equal(ans[0], {0: 0, 1: 1, 2: 2, 3: 3, 4: 3, 5: 2, 6: 1})
        assert_equal(ans, dict(nx.all_pairs_shortest_path_length(self.cycle)))
        ans = dict(nx.shortest_path_length(self.grid))
        assert_equal(ans[1][16], 6)
        # now with weights
        ans = dict(nx.shortest_path_length(self.cycle, weight='weight'))
        assert_equal(ans[0], {0: 0, 1: 1, 2: 2, 3: 3, 4: 3, 5: 2, 6: 1})
        assert_equal(ans, dict(nx.all_pairs_dijkstra_path_length(self.cycle)))
        ans = dict(nx.shortest_path_length(self.grid, weight='weight'))
        assert_equal(ans[1][16], 6)
        # weights and method specified
        ans = dict(nx.shortest_path_length(self.cycle, weight='weight',
                                           method='dijkstra'))
        assert_equal(ans[0], {0: 0, 1: 1, 2: 2, 3: 3, 4: 3, 5: 2, 6: 1})
        assert_equal(ans, dict(nx.all_pairs_dijkstra_path_length(self.cycle)))
        ans = dict(nx.shortest_path_length(self.cycle, weight='weight',
                                           method='bellman-ford'))
        assert_equal(ans[0], {0: 0, 1: 1, 2: 2, 3: 3, 4: 3, 5: 2, 6: 1})
        assert_equal(ans,
                     dict(nx.all_pairs_bellman_ford_path_length(self.cycle))) 

def calc_shortest_path(protein_graph, prefix, generate_plots=True, xmgrace=False):
    num_nodes = len(protein_graph.nodes())
    nodes_axis = range(1, num_nodes + 1)

    path_dict = nx.all_pairs_shortest_path_length(protein_graph)
    dj_path_matrix = np.zeros((num_nodes, num_nodes))

    for i in range(num_nodes):
        for j in range(num_nodes):
            try:
                dj_path_matrix[i,j] = path_dict[i][j]
            except KeyError as ke:
                raise nx.exception.NetworkXNoPath("\nERROR::type=orphan_node:message=No link between %d and %d:exception=%s\n" % (i, j, str(ke)))

    np.savetxt("%s_L.dat" % prefix, dj_path_matrix)

    avg_L_per_node = np.sum(dj_path_matrix, axis=0)/(num_nodes - 1)

    if generate_plots:
        plt.plot(nodes_axis, avg_L_per_node)
        plt.title("%s L" % prefix, fontsize=18)
        plt.xlabel('Node Indices', fontsize=16)
        plt.ylabel('L', fontsize=16)
        plt.savefig("%s_L.png" % prefix, dpi=300, bbox_inches='tight')
        plt.close()

    avg_L_per_node = avg_L_per_node.reshape(1, num_nodes)
    np.savetxt("%s_avg_L.dat" % prefix, avg_L_per_node)
    if xmgrace:
        dat2xmgrace(avg_L_per_node, prefix, "L", traj=traj)

    return dj_path_matrix 

def path_length(self, from_node, to_node):
        if self._path_lengths is None:
            self._path_lengths = dict(nx.all_pairs_shortest_path_length(self, cutoff=None))
        if from_node not in self._path_lengths or to_node not in self._path_lengths[from_node]:
            return math.inf
        else:
            return self._path_lengths[from_node][to_node] 

def test_all_pairs_shortest_path_length(self):
        l=nx.shortest_path_length(self.cycle)
        assert_equal(l[0],{0:0,1:1,2:2,3:3,4:3,5:2,6:1})
        assert_equal(l,nx.all_pairs_shortest_path_length(self.cycle))
        l=nx.shortest_path_length(self.grid)
        assert_equal(l[1][16],6)
        # now with weights
        l=nx.shortest_path_length(self.cycle,weight='weight')
        assert_equal(l[0],{0:0,1:1,2:2,3:3,4:3,5:2,6:1})
        assert_equal(l,nx.all_pairs_dijkstra_path_length(self.cycle))
        l=nx.shortest_path_length(self.grid,weight='weight')
        assert_equal(l[1][16],6) 

def test_all_pairs_shortest_path_length(self):
        l=nx.all_pairs_shortest_path_length(self.cycle)
        assert_equal(l[0],{0:0,1:1,2:2,3:3,4:3,5:2,6:1})
        l=nx.all_pairs_shortest_path_length(self.grid)
        assert_equal(l[1][16],6) 

def all_pairs_shortest_path_length(G, cutoff=None):
    """Computes the shortest path lengths between all nodes in ``G``.

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

    cutoff : integer, optional
        Depth at which to stop the search. Only paths of length at most
        ``cutoff`` are returned.

    Returns
    -------
    lengths : dictionary
        Dictionary of shortest path lengths keyed by source and target.

    Notes
    -----
    The dictionary returned only has keys for reachable node pairs.

    Examples
    --------
    >>> G = nx.path_graph(5)
    >>> length = nx.all_pairs_shortest_path_length(G)
    >>> print(length[1][4])
    3
    >>> length[1]
    {0: 1, 1: 0, 2: 1, 3: 2, 4: 3}

    """
    length = single_source_shortest_path_length
    # TODO This can be trivially parallelized.
    return {n: length(G, n, cutoff=cutoff) for n in G} 

def test_all_pairs_shortest_path_length(self):
        l = dict(nx.all_pairs_shortest_path_length(self.cycle))
        assert_equal(l[0], {0: 0, 1: 1, 2: 2, 3: 3, 4: 3, 5: 2, 6: 1})
        l = dict(nx.all_pairs_shortest_path_length(self.grid))
        assert_equal(l[1][16], 6) 

def test_all_pairs_shortest_path_length(self):
        l=dict(nx.shortest_path_length(self.cycle))
        assert_equal(l[0],{0:0,1:1,2:2,3:3,4:3,5:2,6:1})
        assert_equal(l, dict(nx.all_pairs_shortest_path_length(self.cycle)))
        l=dict(nx.shortest_path_length(self.grid))
        assert_equal(l[1][16],6)
        # now with weights
        l = dict(nx.shortest_path_length(self.cycle, weight='weight'))
        assert_equal(l[0], {0: 0, 1: 1, 2: 2, 3: 3, 4: 3, 5: 2, 6: 1})
        assert_equal(l, dict(nx.all_pairs_dijkstra_path_length(self.cycle)))
        l = dict(nx.shortest_path_length(self.grid, weight='weight'))
        assert_equal(l[1][16], 6) 

def test_all_pairs_shortest_path_length(self):
        l = dict(nx.all_pairs_shortest_path_length(self.cycle))
        assert_equal(l[0],{0:0,1:1,2:2,3:3,4:3,5:2,6:1})
        l = dict(nx.all_pairs_shortest_path_length(self.grid))
        assert_equal(l[1][16],6) 

def all_pairs_shortest_path_length(G, cutoff=None):
    """Computes the shortest path lengths between all nodes in `G`.

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

    cutoff : integer, optional
        Depth at which to stop the search. Only paths of length at most
        `cutoff` are returned.

    Returns
    -------
    lengths : iterator
        (source, dictionary) iterator with dictionary keyed by target and
        shortest path length as the key value.

    Notes
    -----
    The iterator returned only has reachable node pairs.

    Examples
    --------
    >>> G = nx.path_graph(5)
    >>> length = dict(nx.all_pairs_shortest_path_length(G))
    >>> for node in [0, 1, 2, 3, 4]:
    ...     print('1 - {}: {}'.format(node, length[1][node]))
    1 - 0: 1
    1 - 1: 0
    1 - 2: 1
    1 - 3: 2
    1 - 4: 3
    >>> length[3][2]
    1
    >>> length[2][2]
    0

    """
    length = single_source_shortest_path_length
    # TODO This can be trivially parallelized.
    for n in G:
        yield (n, length(G, n, cutoff=cutoff)) 

def all_pairs_shortest_path_length(G, cutoff=None):
    """Computes the shortest path lengths between all nodes in `G`.

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

    cutoff : integer, optional
        Depth at which to stop the search. Only paths of length at most
        `cutoff` are returned.

    Returns
    -------
    lengths : iterator
        (source, dictionary) iterator with dictionary keyed by target and
        shortest path length as the key value.

    Notes
    -----
    The iterator returned only has reachable node pairs.

    Examples
    --------
    >>> G = nx.path_graph(5)
    >>> length = dict(nx.all_pairs_shortest_path_length(G))
    >>> for node in [0, 1, 2, 3, 4]:
    ...     print('1 - {}: {}'.format(node, length[1][node]))
    1 - 0: 1
    1 - 1: 0
    1 - 2: 1
    1 - 3: 2
    1 - 4: 3
    >>> length[3][2]
    1
    >>> length[2][2]
    0

    """
    length = single_source_shortest_path_length
    # TODO This can be trivially parallelized.
    for n in G:
        yield (n, length(G, n, cutoff=cutoff))