python类average_shortest_path_length()的实例源码

def test_characteristic_path_length():
    """
    Pandit, Arka, and John C. Crittenden. "Index of network resilience
    (INR) for urban water distribution systems." Nature (2012).
    """

    raise SkipTest

    inp_file = join(datadir,'Anytown.inp')

    # Create a water network model for results object
    wn = wntr.network.WaterNetworkModel(inp_file)

    G = wn.get_graph_deep_copy()
    udG = G.to_undirected()

    CPL = nx.average_shortest_path_length(udG)

    print('CPL = ',CPL)
    print('expected CPL = ',1.24)
    error = abs(1.24-CPL)
    assert_less(error, 0.01)

def Attributes_of_Graph(G):
    print "*Statistic attributes of graphs:"
    print "N", nx.number_of_nodes(G)
    print "M", nx.number_of_edges(G)

    print "C", nx.average_clustering(G)
    #print "<d>", nx.average_shortest_path_length(G)
    print "r", nx.degree_assortativity_coefficient(G)

    degree_list = list(G.degree_iter())
    max_degree = 0
    min_degree = 0
    avg_degree_1 = 0.0
    avg_degree_2 = 0.0
    for node in degree_list:
        avg_degree_1 = avg_degree_1 + node[1]
        avg_degree_2 = avg_degree_2 + node[1]*node[1]
        if node[1] > max_degree:
            max_degree = node[1]
        if node[1] < min_degree:
            min_degree = node[1]
    #end for
    avg_degree = avg_degree_1/len(degree_list)
    avg_degree_square = (avg_degree_2/len(degree_list)) / (avg_degree*avg_degree)
    print "<k>", avg_degree
    print "k_max", max_degree
    print "H", avg_degree_square
    print "DH", float(max_degree-min_degree)/G.number_of_nodes()

#************************************************************************

def Attributes_of_Graph(G):
    print "*Statistic attributes of graphs:"
    print "N", nx.number_of_nodes(G)
    print "M", nx.number_of_edges(G)

    print "C", nx.average_clustering(G)
    #print "<d>", nx.average_shortest_path_length(G)
    print "r", nx.degree_assortativity_coefficient(G)

    degree_list = list(G.degree_iter())
    max_degree = 0
    min_degree = 0
    avg_degree_1 = 0.0
    avg_degree_2 = 0.0
    for node in degree_list:
        avg_degree_1 = avg_degree_1 + node[1]
        avg_degree_2 = avg_degree_2 + node[1]*node[1]
        if node[1] > max_degree:
            max_degree = node[1]
        if node[1] < min_degree:
            min_degree = node[1]
    #end for
    avg_degree = avg_degree_1/len(degree_list)
    avg_degree_square = (avg_degree_2/len(degree_list)) / (avg_degree*avg_degree)
    print "<k>", avg_degree
    print "k_max", max_degree
    print "H (degree heterogeneity)", avg_degree_square
    print "S (average span of degree distribution)", float(max_degree-min_degree)/G.number_of_nodes()



#*******************************************************************

def statistics(self):
        """Return some topological information about the experiment"""
        stat = {}
        stat["net diameter"] = nx.diameter(self.network)
        stat["net radius"]   = nx.radius(self.network)
        stat["net asp"]     = nx.average_shortest_path_length(self.network)
        stat["input asp"] = net.inputASL(self.network, self.inputc)
        for m in self.measures.values():
            distr = net.distances_to_roi(self.network, self.inputc,m.roi)
            stat["stim to roi distances, mean",m.name] = np.mean(distr)
            stat["stim to roi distances, var",m.name] = np.var(distr)
            centrs = nx.closeness_centrality(self.network)
            stat["roi centralities",m.name] = [centrs[tuple(node)]
                                                for node in np.transpose(m.roi.nonzero())]
        return stat

def main(filename, type, constructed_graph = -1):
    # 1. original graph
    original_graph_path = os.path.join("data",filename,"")
    original_graph = generate_graph(original_graph_path,filename,-1)
    plt.figure("original graph degree distribution")
    draw_degree(original_graph)
    print('original edge number: ',len(original_graph.edges()))


    # 2. reconstruct graph
    if constructed_graph == -1:
        reconstruct_graph_path = os.path.join("reconstruction", filename, type,"")
        reconstruct_graph_adj = pickle.load(open(glob.glob(reconstruct_graph_path+"*.adj")[0],'rb'))
    else:
        reconstruct_graph_adj = constructed_graph
    reconstruct_graph = adj2Graph(reconstruct_graph_adj, edgesNumber = len(original_graph.edges()))
    print('edge number: ', len(reconstruct_graph.edges()))
    plt.figure("reconstruct graph degree distribution")
    draw_degree(reconstruct_graph)

    print("Clustering: ",nx.average_clustering(original_graph), ' ', nx.average_clustering(reconstruct_graph))
    # print("Diameter: ", nx.average_shortest_path_length(original_graph), ' ', nx.average_shortest_path_length(reconstruct_graph))
    # print("degree centrality: ", nx.degree_centrality(original_graph), ' ',  nx.degree_centrality(reconstruct_graph))
    #print("closeness centrality: ", nx.closeness_centrality(original_graph), ' ', nx.closeness_centrality(reconstruct_graph))

    plt.show()

def run(self):
        ip_addresses = ['192.168.1.%s' % x for x in range(1, self._number_clients)]
        ports = [x for x in range(1, 2)]
        clients = []
        progress = 0
        for ip_addr in ip_addresses:
            print_progress(progress, self._number_clients, suffix="Running simulation")
            for port in ports:
                progress += 1
                client = Client(ip_addr, port, clients[0] if len(clients) > 0 else None,
                                max_chache_size=self._number_connections_per_client)
                clients.append(client)
                connection = Connection(client, clients[0])
                connection.initiate()

                bootstrapper_connections = clients[0].get_connections()
                for conn in bootstrapper_connections:
                    connection = Connection(client, conn.second_client)
                    connection.initiate()

        graph = networkx.nx.Graph()
        for client in clients:
            logging.error(client.get_ident())
            logging.error(client.get_connection_idents())
            for node in client.get_connections():
                graph.add_edge(node.first_client.get_ident(), node.second_client.get_ident())

        networkx.draw(graph, with_labels=False)
        plt.savefig("path_graph.pdf")
        print("Network is connected: %s" % networkx.is_connected(graph))
        print("Average shortest path length: %s" % networkx.average_shortest_path_length(graph))
        print("Average bipartite clustering coefficent %s" % networkx.average_clustering(graph))
        print("Bipartite clustering coefficent %s" % networkx.clustering(graph))
        print("degree_assortativity_coefficient %s" % networkx.degree_assortativity_coefficient(graph))

def graph_info(g):
    result = {}
    components = list(nx.strongly_connected_component_subgraphs(g))
    in_degrees = g.in_degree()
    out_degrees = g.out_degree()
    highest_in_degree_node = sorted(in_degrees, key = lambda x: in_degrees[x], reverse = True)[0]
    highest_out_degree_node = sorted(out_degrees, key = lambda x: out_degrees[x], reverse = True)[0]

    result['highest in_degree node'] = highest_in_degree_node
    result['highest out_degree_node'] = highest_out_degree_node

    result['numnber of components'] = len(components)
    result['number of nodes'] = g.number_of_nodes()
    result['number of edges'] = g.number_of_edges()
#Degree centrality
    in_degree_centrality = nx.in_degree_centrality(g)
    out_degree_centrality = nx.out_degree_centrality(g)
    result['sorted in_degree centrality'] = sorted([(el,in_degree_centrality[el]) for el in g.nodes()], key = lambda x: x[1], reverse = True)
    result['sorted out_degree centrality'] = sorted([(el,out_degree_centrality[el]) for el in g.nodes()], key = lambda x: x[1], reverse = True)

    result['closeness_centrality'] = sorted([(el,nx.closeness_centrality(g)[el]) for el in nx.closeness_centrality(g)], key = lambda x: x[1], reverse = True)
    result['highest in_degree node closeness'] = nx.closeness_centrality(g)[highest_in_degree_node]
    result['highest out_degree node closeness'] = nx.closeness_centrality(g)[highest_out_degree_node]


    result['betweenness centrality'] = sorted([(el,nx.betweenness_centrality(g)[el]) for el in nx.betweenness_centrality(g)], key = lambda x: x[1], reverse = True)
    result['highest in_degree node betweenness'] = nx.betweenness_centrality(g)[highest_in_degree_node]
    result['highest in_degree node betweenness'] = nx.betweenness_centrality(g)[highest_out_degree_node]


    largest_component = sorted (components, key = lambda x: x.number_of_nodes(), reverse = True)[0]

    result['largest strongly component percent'] = largest_component.number_of_nodes()/float(g.number_of_nodes())
    result['largest strongly component diameter'] = nx.diameter(largest_component)
    result['largest strongly component average path length'] = nx.average_shortest_path_length(largest_component)
    result['average_degree (undireceted)'] = sum(g.degree().values())/float(g.number_of_nodes())
    result['avg_cluster_coefficient (transitivity)'] = nx.transitivity(g)
    return result

def structure_dependent_index(G, ebunch=None):
    if ebunch is None:
        ebunch = nx.non_edges(G)

    #C = nx.average_clustering(G)
    #d = nx.average_shortest_path_length(G)
    path_range = max(2, math.ceil(nx.average_shortest_path_length(G)))
    #print path_range

    def predict(u, v):
        #NeighborSet = nx.all_neighbors(G, u)
        #len( sorted(nx.common_neighbors(G, u, v) ))
        SD_Index = {}
        #Generate all simple paths in the graph G from source to target,  length <= cutoff .
        paths = list( nx.all_simple_paths(G, source=u, target=v, cutoff = path_range))
        print paths
        for path in paths:
            if SD_Index.has_key( len(path) ):
                SD_Index[len(path)] = SD_Index[len(path)] + 1.0
            else:
                SD_Index[len(path)] = 1.0
        #end for
        print SD_Index

        #Sum up the num of paths with different length
        Coefficient = 0.6
        SD_Value = 0.0
        key_Sequence = list(sorted(SD_Index.keys()))
        for key in key_Sequence:
            if key != 2:
                SD_Value = SD_Value + math.pow(Coefficient, key-2.0) * SD_Index[key]
        #end for
        return  SD_Value #Coefficient = 0.6

    Rank_List = []
    for u, v in ebunch:
        Rank_List.append((u, v, predict(u, v)))
    return Rank_List #((u, v, predict(u, v)) for u, v in ebunch)



##======================================================================##

def Prediction_LinkScores_Ratio(G, Predictor, Proportion, Toleration, Predict_Gap):
    print "Prediction_LinkScores_Ratio!"
    Rank_List_Set = {}
    OK_Value = float(G.number_of_edges())/Proportion

    if nx.is_connected(G) == True:
        Edge_Set = G.edges(data='True')

        Total = 0
        Error = 0
        Rank_List_Set[0] = [Link_Predictors.Wighted_Link_Prediction(Predictor, G), nx.average_clustering(G), nx.average_shortest_path_length(G) ]  ##Running time !!!!!
        '''
        while 1:
            #print i,len(Edge_Set),
            Tep_Edge = []
            Del = random.randint(0, len(Edge_Set)-1)
            Tep_Edge.append(Edge_Set[Del])

            #print "random range:", len(Edge_Set)-1
            #print Del,

            #Prediction with different training set
            G.remove_edge(Edge_Set[Del][0], Edge_Set[Del][1])
            if nx.is_connected(G) != True:
                G.add_edges_from(Tep_Edge)
                Error = Error + 1
                #print "Error:", Error
            else:
                #print Edge_Set[Del],
                Error = 0
                Total = Total + 1
                #print "Total:", Total

                if Total%Predict_Gap == 0:
                    V1 = Link_Predictors.Wighted_Link_Prediction(Predictor, G)
                    V2 = nx.average_clustering(G)
                    V3 = nx.average_shortest_path_length(G)
                    #V4 = Performance_Evaluation_AUC(Predictor, G, Probe_Set, Non_existing_links)
                    Rank_List_Set[Total] = [V1,V2,V3]
                Edge_Set = G.edges(data='True')
            #end if
            if Total > OK_Value or Error == Toleration:
                #print "complete with Total, Error:", Total, Error
                return Rank_List_Set
        #end while
        '''
        return Rank_List_Set
    #end if
    #return Rank_List_Set

##==========================================================================================
#Native_Prediction_Experiment(G, 'WSD', Probe_Set, Top_L, 3) #Top_K, Deleted_Ratio