Python networkx.ego_graph方法代碼示例

# 需要導入模塊: import networkx [as 別名]
# 或者: from networkx import ego_graph [as 別名]
def get_hub_vertices(self, num):
    """Get account vertices randomly (high-degree vertices are likely selected)

    :param num: Number of total account vertices
    :return: Account ID list
    """
    # if suspicious is None:
    #   candidates = self.g.nodes()
    # else:
    #   candidates = [n for n in self.g.nodes() if self.g.nodes[n]["suspicious"] == suspicious]  # True/False
    # candidates = [n for n in candidates if self.factor <= self.degrees[n]]
    # degrees = [self.degrees[n] for n in candidates]
    # probs = np.array(degrees) / float(sum(degrees))

    candidates = set()
    while len(candidates) < num:
      hub = random.choice(self.hubs)
      candidates.update([hub]+self.g.adj[hub].keys()) # candidates.update(nx.ego_graph(self.g, hub).nodes())
    return np.random.choice(list(candidates), num, False) 

# 需要導入模塊: import networkx [as 別名]
# 或者: from networkx import ego_graph [as 別名]
def ego_networks(g_original, level=1):
    """
    Ego-networks returns overlapping communities centered at each nodes within a given radius.

    :param g_original: a networkx/igraph object
    :param level: extrac communities with all neighbors of distance<=level from a node. Deafault 1
    :return: NodeClustering object


    :Example:

    >>> from cdlib import algorithms
    >>> import networkx as nx
    >>> G = nx.karate_club_graph()
    >>> coms = algorithms.ego_networks(G)
    """

    g = convert_graph_formats(g_original, nx.Graph)

    coms = []
    for n in g.nodes():
        coms.append(list(nx.ego_graph(g, n, radius=level).nodes()))
    return NodeClustering(coms, g_original, "Ego Network", method_parameters={"level": 1}, overlap=True) 

# 需要導入模塊: import networkx [as 別名]
# 或者: from networkx import ego_graph [as 別名]
def test_ego(self):
        G=nx.star_graph(3)
        H=nx.ego_graph(G,0)
        assert_true(nx.is_isomorphic(G,H))
        G.add_edge(1,11)
        G.add_edge(2,22)
        G.add_edge(3,33)
        H=nx.ego_graph(G,0)
        assert_true(nx.is_isomorphic(nx.star_graph(3),H))
        G=nx.path_graph(3)
        H=nx.ego_graph(G,0)
        assert_equal(H.edges(), [(0, 1)])
        H=nx.ego_graph(G,0,undirected=True)
        assert_equal(H.edges(), [(0, 1)])
        H=nx.ego_graph(G,0,center=False)
        assert_equal(H.edges(), []) 

# 需要導入模塊: import networkx [as 別名]
# 或者: from networkx import ego_graph [as 別名]
def test_ego(self):
        G = nx.star_graph(3)
        H = nx.ego_graph(G, 0)
        assert_true(nx.is_isomorphic(G, H))
        G.add_edge(1, 11)
        G.add_edge(2, 22)
        G.add_edge(3, 33)
        H = nx.ego_graph(G, 0)
        assert_true(nx.is_isomorphic(nx.star_graph(3), H))
        G = nx.path_graph(3)
        H = nx.ego_graph(G, 0)
        assert_edges_equal(H.edges(), [(0, 1)])
        H = nx.ego_graph(G, 0, undirected=True)
        assert_edges_equal(H.edges(), [(0, 1)])
        H = nx.ego_graph(G, 0, center=False)
        assert_edges_equal(H.edges(), []) 

# 需要導入模塊: import networkx [as 別名]
# 或者: from networkx import ego_graph [as 別名]
def citeseer_ego():
    _, _, G = data.Graph_load(dataset='citeseer')
    G = max(nx.connected_component_subgraphs(G), key=len)
    G = nx.convert_node_labels_to_integers(G)
    graphs = []
    for i in range(G.number_of_nodes()):
        G_ego = nx.ego_graph(G, i, radius=3)
        if G_ego.number_of_nodes() >= 50 and (G_ego.number_of_nodes() <= 400):
            graphs.append(G_ego)
    return graphs 

# 需要導入模塊: import networkx [as 別名]
# 或者: from networkx import ego_graph [as 別名]
def execute(self):
        """
        Execute Demon algorithm

        """

        for n in self.g.nodes():
            self.g.nodes[n]['communities'] = [n]

        all_communities = {}

        for ego in tqdm.tqdm(nx.nodes(self.g), ncols=35, bar_format='Exec: {l_bar}{bar}'):

            ego_minus_ego = nx.ego_graph(self.g, ego, 1, False)
            community_to_nodes = self.__overlapping_label_propagation(ego_minus_ego, ego)

            # merging phase
            for c in community_to_nodes.keys():
                if len(community_to_nodes[c]) > self.min_community_size:
                    actual_community = community_to_nodes[c]
                    all_communities = self.__merge_communities(all_communities, actual_community)

        # write output on file
        if self.file_output:
            with open(self.file_output, "w") as out_file_com:
                for idc, c in enumerate(all_communities.keys()):
                    out_file_com.write("%d\t%s\n" % (idc, str(sorted(c))))

        return list(all_communities.keys()) 

# 需要導入模塊: import networkx [as 別名]
# 或者: from networkx import ego_graph [as 別名]
def _get_egonet_features(self) -> pd.DataFrame:
        """
        Return egonet features for each node in the graph
        """
        egonet_features = {}
        for node in self.G.nodes:
            ego = nx.ego_graph(self.G, node, radius=1)
            ego_boundary = list(nx.edge_boundary(self.G, ego.nodes))
            egonet_features[node] = {
                'internal_edges': self._get_edge_sum(ego.edges),
                'external_edges': self._get_edge_sum(ego_boundary)
            }
        return pd.DataFrame.from_dict(egonet_features, orient='index')

    ### helpers ### 

# 需要導入模塊: import networkx [as 別名]
# 或者: from networkx import ego_graph [as 別名]
def test_ego_distance(self):
        G=nx.Graph()                                                            
        G.add_edge(0,1,weight=2,distance=1)
        G.add_edge(1,2,weight=2,distance=2)
        G.add_edge(2,3,weight=2,distance=1) 
        assert_equal(sorted(nx.ego_graph(G,0,radius=3).nodes()),[0,1,2,3])
        eg=nx.ego_graph(G,0,radius=3,distance='weight')
        assert_equal(sorted(eg.nodes()),[0,1])
        eg=nx.ego_graph(G,0,radius=3,distance='weight',undirected=True)
        assert_equal(sorted(eg.nodes()),[0,1])
        eg=nx.ego_graph(G,0,radius=3,distance='distance')
        assert_equal(sorted(eg.nodes()),[0,1,2]) 

# 需要導入模塊: import networkx [as 別名]
# 或者: from networkx import ego_graph [as 別名]
def test_ego_distance(self):
        G = nx.Graph()
        G.add_edge(0, 1, weight=2, distance=1)
        G.add_edge(1, 2, weight=2, distance=2)
        G.add_edge(2, 3, weight=2, distance=1)
        assert_nodes_equal(nx.ego_graph(G, 0, radius=3).nodes(), [0, 1, 2, 3])
        eg = nx.ego_graph(G, 0, radius=3, distance='weight')
        assert_nodes_equal(eg.nodes(), [0, 1])
        eg = nx.ego_graph(G, 0, radius=3, distance='weight', undirected=True)
        assert_nodes_equal(eg.nodes(), [0, 1])
        eg = nx.ego_graph(G, 0, radius=3, distance='distance')
        assert_nodes_equal(eg.nodes(), [0, 1, 2]) 

# 需要導入模塊: import networkx [as 別名]
# 或者: from networkx import ego_graph [as 別名]
def local_efficiency(G):
    """Returns the average local efficiency of the graph.

    The *efficiency* of a pair of nodes in a graph is the multiplicative
    inverse of the shortest path distance between the nodes. The *local
    efficiency* of a node in the graph is the average global efficiency of the
    subgraph induced by the neighbors of the node. The *average local
    efficiency* is the average of the local efficiencies of each node [1]_.

    Parameters
    ----------
    G : :class:`networkx.Graph`
        An undirected graph for which to compute the average local efficiency.

    Returns
    -------
    float
        The average local efficiency of the graph.

    Notes
    -----
    Edge weights are ignored when computing the shortest path distances.

    See also
    --------
    global_efficiency

    References
    ----------
    .. [1] Latora, Vito, and Massimo Marchiori.
           "Efficient behavior of small-world networks."
           *Physical Review Letters* 87.19 (2001): 198701.
           <http://dx.doi.org/10.1103/PhysRevLett.87.198701>

    """
    # TODO This summation can be trivially parallelized.
    return sum(global_efficiency(nx.ego_graph(G, v)) for v in G) / len(G) 

# 需要導入模塊: import networkx [as 別名]
# 或者: from networkx import ego_graph [as 別名]
def Graph_load(dataset = 'cora'):
    '''
    Load a single graph dataset
    :param dataset: dataset name
    :return:
    '''
    names = ['x', 'tx', 'allx', 'graph']
    objects = []
    for i in range(len(names)):
        load = pkl.load(open("dataset/ind.{}.{}".format(dataset, names[i]), 'rb'), encoding='latin1')
        # print('loaded')
        objects.append(load)
        # print(load)
    x, tx, allx, graph = tuple(objects)
    test_idx_reorder = parse_index_file("dataset/ind.{}.test.index".format(dataset))
    test_idx_range = np.sort(test_idx_reorder)

    if dataset == 'citeseer':
        # Fix citeseer dataset (there are some isolated nodes in the graph)
        # Find isolated nodes, add them as zero-vecs into the right position
        test_idx_range_full = range(min(test_idx_reorder), max(test_idx_reorder) + 1)
        tx_extended = sp.lil_matrix((len(test_idx_range_full), x.shape[1]))
        tx_extended[test_idx_range - min(test_idx_range), :] = tx
        tx = tx_extended

    features = sp.vstack((allx, tx)).tolil()
    features[test_idx_reorder, :] = features[test_idx_range, :]
    G = nx.from_dict_of_lists(graph)
    adj = nx.adjacency_matrix(G)
    return adj, features, G


######### code test ########
# adj, features,G = Graph_load()
# print(adj)
# print(G.number_of_nodes(), G.number_of_edges())

# _,_,G = Graph_load(dataset='citeseer')
# G = max(nx.connected_component_subgraphs(G), key=len)
# G = nx.convert_node_labels_to_integers(G)
#
# count = 0
# max_node = 0
# for i in range(G.number_of_nodes()):
#     G_ego = nx.ego_graph(G, i, radius=3)
#     # draw_graph(G_ego,prefix='test'+str(i))
#     m = G_ego.number_of_nodes()
#     if m>max_node:
#         max_node = m
#     if m>=50:
#         print(i, G_ego.number_of_nodes(), G_ego.number_of_edges())
#         count += 1
# print('count', count)
# print('max_node', max_node) 

# 需要導入模塊: import networkx [as 別名]
# 或者: from networkx import ego_graph [as 別名]
def meshedness(graph, radius=5, name="meshedness", distance=None):
    """
    Calculates meshedness for subgraph around each node if radius is set, or for
    whole graph, if ``radius=None``.

    Subgraph is generated around each node within set radius. If ``distance=None``,
    radius will define topological distance, otherwise it uses values in distance
    attribute.

    .. math::
        \\alpha=\\frac{e-v+1}{2 v-5}

    where :math:`e` is the number of edges in subgraph and :math:`v` is the number of nodes in subgraph.

    Adapted from :cite:`feliciotti2018`.


    Parameters
    ----------
    graph : networkx.Graph
        Graph representing street network.
        Ideally generated from GeoDataFrame using :func:`momepy.gdf_to_nx`
    radius: int, optional
        Include all neighbors of distance <= radius from n
    name : str, optional
        calculated attribute name
    distance : str, optional
        Use specified edge data key as distance.
        For example, setting ``distance=’weight’`` will use the edge ``weight`` to
        measure the distance from the node n.

    Returns
    -------
    Graph
        networkx.Graph if radius is set
    float
        meshedness for graph if ``radius=None``

    Examples
    --------
    >>> network_graph = mm.meshedness(network_graph, radius=800, distance='edge_length')
    """
    netx = graph.copy()

    if radius:
        for n in tqdm(netx, total=len(netx)):
            sub = nx.ego_graph(
                netx, n, radius=radius, distance=distance
            )  # define subgraph of steps=radius
            netx.nodes[n][name] = _meshedness(
                sub
            )  # save value calulated for subgraph to node

        return netx

    return _meshedness(netx) 

# 需要導入模塊: import networkx [as 別名]
# 或者: from networkx import ego_graph [as 別名]
def mean_node_degree(graph, radius=5, name="mean_nd", degree="degree", distance=None):
    """
    Calculates mean node degree for subgraph around each node if radius is set, or for
    whole graph, if ``radius=None``.

    Subgraph is generated around each node within set radius. If ``distance=None``,
    radius will define topological distance, otherwise it uses values in ``distance``
    attribute.


    Parameters
    ----------
    graph : networkx.Graph
        Graph representing street network.
        Ideally generated from GeoDataFrame using :func:`momepy.gdf_to_nx`
    radius: int
        radius defining the extent of subgraph
    name : str, optional
        calculated attribute name
    degree : str
        name of attribute of node degree (:py:func:`momepy.node_degree`)
    distance : str, optional
        Use specified edge data key as distance.
        For example, setting ``distance=’weight’`` will use the edge ``weight`` to
        measure the distance from the node n.

    Returns
    -------
    Graph
        networkx.Graph if radius is set
    float
        mean node degree for graph if ``radius=None``

    Examples
    --------
    >>> network_graph = mm.mean_node_degree(network_graph, radius=3)
    """
    netx = graph.copy()

    if radius:
        for n in tqdm(netx, total=len(netx)):
            sub = nx.ego_graph(
                netx, n, radius=radius, distance=distance
            )  # define subgraph of steps=radius
            netx.nodes[n][name] = _mean_node_degree(sub, degree=degree)

        return netx

    return _mean_node_degree(netx, degree=degree) 

# 需要導入模塊: import networkx [as 別名]
# 或者: from networkx import ego_graph [as 別名]
def cyclomatic(graph, radius=5, name="cyclomatic", distance=None):
    """
    Calculates cyclomatic complexity for subgraph around each node if radius is set, or for
    whole graph, if ``radius=None``.

    Subgraph is generated around each node within set radius. If ``distance=None``,
    radius will define topological distance, otherwise it uses values in ``distance``
    attribute.

    .. math::
        \\alpha=e-v+1

    where :math:`e` is the number of edges in subgraph and :math:`v` is the number of nodes in subgraph.

    Adapted from :cite:`bourdic2012`.

    Parameters
    ----------
    graph : networkx.Graph
        Graph representing street network.
        Ideally generated from GeoDataFrame using :func:`momepy.gdf_to_nx`
    radius: int
        Include all neighbors of distance <= radius from n
    name : str, optional
        calculated attribute name
    distance : str, optional
        Use specified edge data key as distance.
        For example, setting ``distance=’weight’`` will use the edge ``weight`` to
        measure the distance from the node n.

    Returns
    -------
    Graph
        networkx.Graph if radius is set
    float
        cyclomatic complexity for graph if ``radius=None``

    Examples
    --------
    >>> network_graph = mm.cyclomatic(network_graph, radius=3)
    """
    netx = graph.copy()

    if radius:
        for n in tqdm(netx, total=len(netx)):
            sub = nx.ego_graph(
                netx, n, radius=radius, distance=distance
            )  # define subgraph of steps=radius
            netx.nodes[n][name] = _cyclomatic(
                sub
            )  # save value calulated for subgraph to node

        return netx

    return _cyclomatic(netx) 

# 需要導入模塊: import networkx [as 別名]
# 或者: from networkx import ego_graph [as 別名]
def edge_node_ratio(graph, radius=5, name="edge_node_ratio", distance=None):
    """
    Calculates edge / node ratio for subgraph around each node if radius is set, or for
    whole graph, if ``radius=None``.

    Subgraph is generated around each node within set radius. If ``distance=None``,
    radius will define topological distance, otherwise it uses values in ``distance``
    attribute.

    .. math::
        \\alpha=e/v

    where :math:`e` is the number of edges in subgraph and :math:`v` is the number of nodes in subgraph.

    Adapted from :cite:`dibble2017`.

    Parameters
    ----------
    graph : networkx.Graph
        Graph representing street network.
        Ideally generated from GeoDataFrame using :func:`momepy.gdf_to_nx`
    radius: int
        Include all neighbors of distance <= radius from n
    name : str, optional
        calculated attribute name
    distance : str, optional
        Use specified edge data key as distance.
        For example, setting ``distance=’weight’`` will use the edge ``weight`` to
        measure the distance from the node n.

    Returns
    -------
    Graph
        networkx.Graph if radius is set
    float
        edge / node ratio for graph if ``radius=None``

    Examples
    --------
    >>> network_graph = mm.edge_node_ratio(network_graph, radius=3)
    """
    netx = graph.copy()

    if radius:
        for n in tqdm(netx, total=len(netx)):
            sub = nx.ego_graph(
                netx, n, radius=radius, distance=distance
            )  # define subgraph of steps=radius
            netx.nodes[n][name] = _edge_node_ratio(
                sub
            )  # save value calulated for subgraph to node

        return netx

    return _edge_node_ratio(netx)