Python networkx.shortest_simple_paths方法代碼示例

# 需要導入模塊: import networkx [as 別名]
# 或者: from networkx import shortest_simple_paths [as 別名]
def visualize_frags(outdir, graphs, options):
    from rpy2.robjects import r

    utilities.ensure_dir(outdir)

    for i, graph in enumerate(graphs):
        r.pdf(os.path.join(outdir, "fragments.cluster_{}.pdf".format(i)))

        for component in networkx.connected_components(graph):
            subgraph = graph.subgraph(component)
            
            ends = [node for node,degree in subgraph.degree_iter() if degree==1]
            breakends = [node for node in list(networkx.shortest_simple_paths(subgraph, ends[0], ends[1]))[0]]
            # breakends = [breakend_from_label(node) for node in breakends]
            breakends = breakends[:-1:2] + breakends[-1:]
            # print ")"*100, breakends

            for sample, dataset in sorted(options.iter_10xdatasets()):
                plot_frags(breakends, options, sample, dataset)
        # plot_frags(breakpoints, options, sample, dataset)
        r["dev.off"]() 

# 需要導入模塊: import networkx [as 別名]
# 或者: from networkx import shortest_simple_paths [as 別名]
def k_shortest_paths(self, source, target):
        """
        如果源宿點是None，則返回len為1的None數組
        :param source:
        :param target:
        :return:
        """
        if source is None:
            return [None]
        generator = shortest_simple_paths(self, source, target, weight=self.weight)
        rtn = []
        index = 0
        for i in generator:
            index += 1
            if index > self.k:
                break
            rtn.append(i)
        return rtn 

# 需要導入模塊: import networkx [as 別名]
# 或者: from networkx import shortest_simple_paths [as 別名]
def k_shortest_paths(self, source, target):
        """
        如果源宿點是None，則返回len為1的None數組
        :param source:
        :param target:
        :return:
        """
        if source is None:
            return [None]
        generator = shortest_simple_paths(self.net, source, target, weight=self.weight)
        rtn = []
        index = 0
        for i in generator:
            index += 1
            if index > self.k:
                break
            rtn.append(i)
        return rtn 

# 需要導入模塊: import networkx [as 別名]
# 或者: from networkx import shortest_simple_paths [as 別名]
def visualize_frag_cluster(breakpoints, options):
    """
    breakpoints are (chromx, x, chromy, y, orientation)
    """

    graph = networkx.Graph()
    for breakpoint in breakpoints:
        chromx, x, chromy, y, orientation = breakpoint
        graph.add_edge((chromx, x, orientation[0]), (chromy, y, orientation[1]))

    ends = [node for node,degree in graph.degree_iter() if degree==1]
    breakends = [node for node in list(networkx.shortest_simple_paths(graph, ends[0], ends[1]))[0]]
    # breakends = [breakend_from_label(node) for node in breakends]
    breakends = breakends[:-1:2] + breakends[-1:]
    # print ")"*100, breakends

    for sample, dataset in sorted(options.iter_10xdatasets()):
        plot_frags(breakends, options, sample, dataset) 

# 需要導入模塊: import networkx [as 別名]
# 或者: from networkx import shortest_simple_paths [as 別名]
def k_shortest_paths(G, source, target, k, weight=None):
    return list(islice(nx.shortest_simple_paths(G, source, target, weight=weight), k))

# DE PM! LO Ordena de menor a menos segun el weight 

# 需要導入模塊: import networkx [as 別名]
# 或者: from networkx import shortest_simple_paths [as 別名]
def nodes_in_order(self):
        ends = self.ends
        return list(networkx.shortest_simple_paths(self.graph, ends[0], ends[1]))[0] 

# 需要導入模塊: import networkx [as 別名]
# 或者: from networkx import shortest_simple_paths [as 別名]
def find_all_paths(self, max_paths=10, sort=True, score=True):
        """ Find all paths through DAG to End

            Params:
               max_paths (int :default:=10): Number of paths to find
                          If this is > 1000, all paths will be found
               sort (bool)                 : If True (default), sort paths
                                             in ascending order of length
        """
        if self.roots:
            self.lock_start()
        if score:
            self.score_graph()
        # shortest_simple_paths is slow for >1000 paths
        if max_paths <= 1000:
            if score:
                paths = list(six.moves.map(lambda x: x[1:-1],
                                           islice(nx.shortest_simple_paths(
                                                        self.G, self.start, self.end, weight='weight'),
                                                  max_paths)))
                scores = self.scorer.score_splits(paths)
                path_scores = zip(paths, scores)
                sorted_path_scores = sorted(path_scores, key=operator.itemgetter(1), reverse=True)
                logger.debug("Sorted paths with scores:\n %s", sorted_path_scores)
                # Strip the scores from the returned result, to be consistent with no-scoring option
                sorted_paths, _ = zip(*sorted_path_scores)
                return list(sorted_paths)
            else:
                paths = list(six.moves.map(lambda x: x[1:-1],
                                           islice(nx.shortest_simple_paths(
                                                        self.G, self.start, self.end),
                                                  max_paths)))
                return paths
        else:  # Fall back to all_simple_paths
            ps = list(six.moves.map(lambda x: x[1:-1],
                                    nx.all_simple_paths(self.G, self.start, self.end)))
            # If we do not intend to display paths, no need to sort them
            if sort:
                ps.sort(key=lambda x: len(x))
            return ps 

# 需要導入模塊: import networkx [as 別名]
# 或者: from networkx import shortest_simple_paths [as 別名]
def _get_single_path(  # pylint: disable=too-many-arguments, too-many-locals
        self,
        graph: DiGraph,
        source: Address,
        target: Address,
        value: PaymentAmount,
        reachability_state: AddressReachabilityProtocol,
        visited: Dict[ChannelID, float],
        disallowed_paths: List[List[Address]],
        fee_penalty: float,
    ) -> Optional[Path]:
        # update edge weights
        for node1, node2 in graph.edges():
            edge = graph[node1][node2]
            backwards_edge = graph[node2][node1]
            edge["weight"] = self.edge_weight(
                visited=visited,
                view=edge["view"],
                view_from_partner=backwards_edge["view"],
                amount=value,
                fee_penalty=fee_penalty,
            )

        # find next path
        all_paths: Iterable[List[Address]] = nx.shortest_simple_paths(
            G=graph, source=source, target=target, weight="weight"
        )
        try:
            # skip duplicates and invalid paths
            path = next(
                p
                for p in (Path(self.G, nodes, value, reachability_state) for nodes in all_paths)
                if p.is_valid and p.nodes not in disallowed_paths
            )
            return path
        except StopIteration:
            return None 

# 需要導入模塊: import networkx [as 別名]
# 或者: from networkx import shortest_simple_paths [as 別名]
def test_shortest_simple_paths():
    G = cnlti(nx.grid_2d_graph(4, 4), first_label=1, ordering="sorted")
    paths = nx.shortest_simple_paths(G, 1, 12)
    assert_equal(next(paths), [1, 2, 3, 4, 8, 12])
    assert_equal(next(paths), [1, 5, 6, 7, 8, 12])
    assert_equal([len(path) for path in nx.shortest_simple_paths(G, 1, 12)],
                 sorted([len(path) for path in nx.all_simple_paths(G, 1, 12)])) 

# 需要導入模塊: import networkx [as 別名]
# 或者: from networkx import shortest_simple_paths [as 別名]
def test_shortest_simple_paths_directed():
    G = nx.cycle_graph(7, create_using=nx.DiGraph())
    paths = nx.shortest_simple_paths(G, 0, 3)
    assert_equal([path for path in paths], [[0, 1, 2, 3]]) 

# 需要導入模塊: import networkx [as 別名]
# 或者: from networkx import shortest_simple_paths [as 別名]
def test_Greg_Bernstein():
    g1 = nx.Graph()
    g1.add_nodes_from(["N0", "N1", "N2", "N3", "N4"])
    g1.add_edge("N4", "N1", weight=10.0, capacity=50, name="L5")
    g1.add_edge("N4", "N0", weight=7.0, capacity=40, name="L4")
    g1.add_edge("N0", "N1", weight=10.0, capacity=45, name="L1")
    g1.add_edge("N3", "N0", weight=10.0, capacity=50, name="L0")
    g1.add_edge("N2", "N3", weight=12.0, capacity=30, name="L2")
    g1.add_edge("N1", "N2", weight=15.0, capacity=42, name="L3")
    solution = [['N1', 'N0', 'N3'], ['N1', 'N2', 'N3'], ['N1', 'N4', 'N0', 'N3']]
    result = list(nx.shortest_simple_paths(g1, 'N1', 'N3', weight='weight'))
    assert_equal(result, solution) 

# 需要導入模塊: import networkx [as 別名]
# 或者: from networkx import shortest_simple_paths [as 別名]
def test_weighted_shortest_simple_path():
    def cost_func(path):
        return sum(G.edge[u][v]['weight'] for (u, v) in zip(path, path[1:]))
    G = nx.complete_graph(5)
    weight = {(u, v): random.randint(1, 100) for (u, v) in G.edges()}
    nx.set_edge_attributes(G, 'weight', weight)
    cost = 0
    for path in nx.shortest_simple_paths(G, 0, 3, weight='weight'):
        this_cost = cost_func(path)
        assert_true(cost <= this_cost)
        cost = this_cost 

# 需要導入模塊: import networkx [as 別名]
# 或者: from networkx import shortest_simple_paths [as 別名]
def test_directed_weighted_shortest_simple_path():
    def cost_func(path):
        return sum(G.edge[u][v]['weight'] for (u, v) in zip(path, path[1:]))
    G = nx.complete_graph(5)
    G = G.to_directed()
    weight = {(u, v): random.randint(1, 100) for (u, v) in G.edges()}
    nx.set_edge_attributes(G, 'weight', weight)
    cost = 0
    for path in nx.shortest_simple_paths(G, 0, 3, weight='weight'):
        this_cost = cost_func(path)
        assert_true(cost <= this_cost)
        cost = this_cost 

# 需要導入模塊: import networkx [as 別名]
# 或者: from networkx import shortest_simple_paths [as 別名]
def test_ssp_source_missing():
    G = nx.Graph()
    G.add_path([1,2,3])
    paths = list(nx.shortest_simple_paths(G, 0, 3)) 

# 需要導入模塊: import networkx [as 別名]
# 或者: from networkx import shortest_simple_paths [as 別名]
def test_ssp_target_missing():
    G = nx.Graph()
    G.add_path([1,2,3])
    paths = list(nx.shortest_simple_paths(G, 1, 4))