Python networkx.degree_centrality函数代码示例

def degree_removal(g, recalculate=False):
    """
    Performs robustness analysis based on degree centrality,
    on the network specified by infile using sequential (recalculate = True)
    or simultaneous (recalculate = False) approach. Returns a list
    with fraction of nodes removed, a list with the corresponding sizes of
    the largest component of the network, and the overall vulnerability
    of the network.
    """

    m = nx.degree_centrality(g)
    l = sorted(m.items(), key=operator.itemgetter(1), reverse=True)
    x = []
    y = []
    dimension = fd.fractal_dimension(g, iterations=100, debug=False)
    n = len(g.nodes())
    x.append(0)
    y.append(dimension)

    for i in range(1, n-1):
        g.remove_node(l.pop(0)[0])
        if recalculate:
            m = nx.degree_centrality(g)
            l = sorted(m.items(), key=operator.itemgetter(1),
                       reverse=True)
        dimension = fd.fractal_dimension(g, iterations=100, debug=False)
        x.append(i * 1. / n)
        y.append(dimension)

    return x, y

def degree_fracture(infile, outfile, fraction, recalculate = False):
    """
    Removes given fraction of nodes from infile network in reverse order of 
    degree centrality (with or without recalculation of centrality values 
    after each node removal) and saves the network in outfile.
    """

    g = networkx.read_gml(infile)
    m = networkx.degree_centrality(g)
    l = sorted(m.items(), key = operator.itemgetter(1), reverse = True)
    largest_component = max(networkx.connected_components(g), key = len)
    n = len(g.nodes())
    for i in range(1, n - 1):
        g.remove_node(l.pop(0)[0])
        if recalculate:
            m = networkx.degree_centrality(g)
            l = sorted(m.items(), key = operator.itemgetter(1), 
                       reverse = True)
        largest_component = max(networkx.connected_components(g), key = len)
        if i * 1. / n >= fraction:
            break
    components = networkx.connected_components(g)
    component_id = 1
    for component in components:
        for node in component:
            g.node[node]["component"] = component_id
        component_id += 1
    networkx.write_gml(g, outfile)

def degree(infile, recalculate = False):
    """
    Performs robustness analysis based on degree centrality,  
    on the network specified by infile using sequential (recalculate = True) 
    or simultaneous (recalculate = False) approach. Returns a list 
    with fraction of nodes removed, a list with the corresponding sizes of 
    the largest component of the network, and the overall vulnerability 
    of the network.
    """

    g = networkx.read_gml(infile)
    m = networkx.degree_centrality(g)
    l = sorted(m.items(), key = operator.itemgetter(1), reverse = True)
    x = []
    y = []
    largest_component = max(networkx.connected_components(g), key = len)
    n = len(g.nodes())
    x.append(0)
    y.append(len(largest_component) * 1. / n)
    R = 0.0
    for i in range(1, n - 1):
        g.remove_node(l.pop(0)[0])
        if recalculate:
            m = networkx.degree_centrality(g)
            l = sorted(m.items(), key = operator.itemgetter(1), 
                       reverse = True)
        largest_component = max(networkx.connected_components(g), key = len)
        x.append(i * 1. / n)
        R += len(largest_component) * 1. / n
        y.append(len(largest_component) * 1. / n)
    return x, y, 0.5 - R / n

def degree_component(seed_num, graph=None, graph_json_filename=None, graph_json_str=None):
  if graph_json_filename is None and graph_json_str is None and graph is None:
    return []

  G = None
  if graph is not None:
    G = graph
  elif graph_json_str is None:
    G = util.load_graph(graph_json_filename=graph_json_filename)
  else:
    G = util.load_graph(graph_json_str=graph_json_str)

  components = list(nx.connected_components(G))
  components = filter(lambda x: len(x) > 0.1 * len(G), components)
  total_size = sum(map(lambda x: len(x), components))
  total_nodes = 0
  rtn = []
  for comp in components[1:]:
    num_nodes = int(float(len(comp)) / total_size * seed_num)
    component = G.subgraph(list(comp))
    clse_cent = nx.degree_centrality(component)
    collector = collections.Counter(clse_cent)
    clse_cent = collector.most_common(num_nodes)
    rtn += map(lambda (x, y): x, clse_cent)
    total_nodes += num_nodes

  num_nodes = seed_num - total_nodes
  component = G.subgraph(list(components[0]))
  clse_cent = nx.degree_centrality(component)
  collector = collections.Counter(clse_cent)
  clse_cent = collector.most_common(num_nodes)
  rtn += map(lambda (x, y): x, clse_cent)
  return rtn

def sna_calculations(g, play_file):
    """
    :param g: a NetworkX graph object
    :type g: object
    :param play_file: the location of a play in .txt format
    :type play_file: string
    :return: returns a dictionary containing various network related figures
    :rtype: dict
    :note: also writes into results/file_name-snaCalculations.csv and results/allCharacters.csv
    """
    file_name = os.path.splitext(os.path.basename(play_file))[0]
    sna_calculations_list = dict()
    sna_calculations_list['playType'] = file_name[0]
    sna_calculations_list['avDegreeCentrality'] = numpy.mean(numpy.fromiter(iter(nx.degree_centrality(g).values()),
                                                                            dtype=float))
    sna_calculations_list['avDegreeCentralityStd'] = numpy.std(
        numpy.fromiter(iter(nx.degree_centrality(g).values()), dtype=float))
    sna_calculations_list['avInDegreeCentrality'] = numpy.mean(
        numpy.fromiter(iter(nx.in_degree_centrality(g).values()), dtype=float))
    sna_calculations_list['avOutDegreeCentrality'] = numpy.mean(
        numpy.fromiter(iter(nx.out_degree_centrality(g).values()), dtype=float))

    try:
        sna_calculations_list['avShortestPathLength'] = nx.average_shortest_path_length(g)
    except:
        sna_calculations_list['avShortestPathLength'] = 'not connected'

    sna_calculations_list['density'] = nx.density(g)
    sna_calculations_list['avEigenvectorCentrality'] = numpy.mean(
        numpy.fromiter(iter(nx.eigenvector_centrality(g).values()), dtype=float))
    sna_calculations_list['avBetweennessCentrality'] = numpy.mean(
        numpy.fromiter(iter(nx.betweenness_centrality(g).values()), dtype=float))
    sna_calculations_list['DegreeCentrality'] = nx.degree_centrality(g)
    sna_calculations_list['EigenvectorCentrality'] = nx.eigenvector_centrality(g)
    sna_calculations_list['BetweennessCentrality'] = nx.betweenness_centrality(g)

    # sna_calculations.txt file
    sna_calc_file = csv.writer(open('results/' + file_name + '-snaCalculations.csv', 'wb'), quoting=csv.QUOTE_ALL,
                               delimiter=';')
    for key, value in sna_calculations_list.items():
        sna_calc_file.writerow([key, value])

    # all_characters.csv file
    if not os.path.isfile('results/allCharacters.csv'):
        with open('results/allCharacters.csv', 'w') as f:
            f.write(
                'Name;PlayType;play_file;DegreeCentrality;EigenvectorCentrality;BetweennessCentrality;speech_amount;AverageUtteranceLength\n')

    all_characters = open('results/allCharacters.csv', 'a')
    character_speech_amount = speech_amount(play_file)
    for character in sna_calculations_list['DegreeCentrality']:
        all_characters.write(character + ';' + str(sna_calculations_list['playType']) + ';' + file_name + ';' + str(
            sna_calculations_list['DegreeCentrality'][character]) + ';' + str(
            sna_calculations_list['EigenvectorCentrality'][character]) + ';' + str(
            sna_calculations_list['BetweennessCentrality'][character]) + ';' + str(
            character_speech_amount[0][character]) + ';' + str(character_speech_amount[1][character]) + '\n')
    all_characters.close()

    return sna_calculations

    def __init__(self, time, voteomat):

        self.foldername = voteomat.network_func_name + voteomat.distribution_func_name
        self.foldertime = time
        self.path = "Statistics//"+self.foldername+"//"
        self.path += g_candidates_affecting_nodes + "=" + str(voteomat.candidates_affecting) + "_"
        self.path += g_candidates_affected_by_median + "=" + str(voteomat.candidates_affected) + "_"
        self.path += g_neighbours_affecting_each_other + "=" + str(voteomat.affecting_neighbours) + "_"
        self.path += g_counterforce_affecting_candidates + "=" + str(voteomat.counter_force_affecting) + "_"
        self.path += "counterforce_left="+str(voteomat.counter_force_left)+"_"+"counterforce_right="+str(voteomat.counter_force_right)+ "_" + time
        self.make_sure_path_exists(self.path)
        self.file = open(self.path + "//statistic.csv", 'w')
        self.statistic = {}
        self.statistic["networkfunc"] = voteomat.network_func_name
        self.statistic["distributionfunc"] = voteomat.distribution_func_name
        self.statistic["acceptance"] = voteomat.acceptance
        median, avg, std = voteomat.get_statistic()
        self.statistic["median"] = []
        self.statistic["median"].append(median)
        self.statistic["avg"] = []
        self.statistic["avg"].append(avg)
        self.statistic["std"] = []
        self.statistic["std"].append(std)


        self.statistic["node_with_highest_degree_centrality"] = []
        self.max_degree_node = max( nx.degree_centrality(voteomat.get_network()).items(),key = lambda x: x[1])[0]

        self.statistic["node_with_highest_degree_centrality"].append(voteomat.get_network().nodes(data = True)[self.max_degree_node][1]["orientation"])
        self.statistic["node_with_minimum_degree_centrality"] = []
        self.min_degree_node = min(nx.degree_centrality(voteomat.get_network()).items(), key = lambda x: x[1])[0]
        self.statistic["node_with_minimum_degree_centrality"].append(voteomat.get_network().nodes(data = True)[self.min_degree_node][1]["orientation"])
        self.statistic["node_with_highest_closeness_centrality"] = []
        self.max_closeness_node = max( nx.closeness_centrality(voteomat.get_network()).items(),key = lambda x: x[1])[0]
        self.statistic["node_with_highest_closeness_centrality"].append(voteomat.get_network().nodes(data = True)[self.max_closeness_node][1]["orientation"])
        self.statistic["node_with_highest_betweenness_centrality"] = []
        self.max_betweenness_node = max(nx.betweenness_centrality(voteomat.get_network()).items() ,key = lambda x: x[1])[0]
        self.statistic["node_with_highest_betweenness_centrality"].append(voteomat.get_network().nodes(data = True)[self.max_betweenness_node][1]["orientation"])
        try:
            self.statistic["node_with_highest_eigenvector_centrality"] = []
            self.max_eigenvector_node = max( nx.eigenvector_centrality(voteomat.get_network(), max_iter = 1000).items(),key = lambda x: x[1])[0]
            self.statistic["node_with_highest_eigenvector_centrality"].append(voteomat.get_network().nodes(data = True)[self.max_eigenvector_node][1]["orientation"])
        except nx.NetworkXError:
            print "Eigenvector centrality not possible."

        freeman = self.freeman_centrality([x[1] for x in nx.degree_centrality(voteomat.get_network()).items()], max( nx.degree_centrality(voteomat.get_network()).items(),key = lambda x: x[1])[1])
        self.statistic["freeman_centrality"] = round(freeman,2)

        self.statistic["affecting_neighbours"] = voteomat.affecting_neighbours
        self.statistic["affecting_candidates"] = voteomat.candidates_affecting
        self.statistic["affected_canddiates"] = voteomat.candidates_affected
        self.statistic["affecting_counter_force"] = voteomat.counter_force_affecting
        self.statistic["affecting_counter_force_left"] = voteomat.counter_force_left
        self.statistic["affecting_counter_force_right"] = voteomat.counter_force_right

        self.statistic["candidates"] = []
        for candidate in voteomat.candidates:
            self.statistic["candidates"].append(candidate.to_save())
        self.statistic["network"] = voteomat.get_network().nodes(data=True);

def degree_apl(g, recalculate=False):
    """
    Performs robustness analysis based on degree centrality,
    on the network specified by infile using sequential (recalculate = True)
    or simultaneous (recalculate = False) approach. Returns a list
    with fraction of nodes removed, a list with the corresponding sizes of
    the largest component of the network, and the overall vulnerability
    of the network.
    """

    m = networkx.degree_centrality(g)
    l = sorted(m.items(), key=operator.itemgetter(1), reverse=True)
    x = []
    y = []

    average_path_length = 0.0
    number_of_components = 0
    n = len(g.nodes())

    for sg in networkx.connected_component_subgraphs(g):
        average_path_length += networkx.average_shortest_path_length(sg)
        number_of_components += 1

    average_path_length = average_path_length / number_of_components
    initial_apl = average_path_length

    x.append(0)
    y.append(average_path_length * 1. / initial_apl)

    r = 0.0
    for i in range(1, n - 2):
        g.remove_node(l.pop(0)[0])
        if recalculate:
            m = networkx.degree_centrality(g)
            l = sorted(m.items(), key=operator.itemgetter(1),
                       reverse=True)

        average_path_length = 0.0
        number_of_components = 0

        for sg in networkx.connected_component_subgraphs(g):
            if len(sg.nodes()) > 1:
                average_path_length += networkx.average_shortest_path_length(sg)
            number_of_components += 1


        average_path_length = average_path_length / number_of_components

        x.append(i * 1. / initial_apl)
        r += average_path_length * 1. / initial_apl
        y.append(average_path_length * 1. / initial_apl)
    return x, y, r / initial_apl

def labels(G, threshhold = 95):
    '''return labels(dictionary) for nodes with high centrality for a given percentile'''
    labels = {}
    
    # create cutoff based on the given percentile
    cen_cutoff = np.percentile(list(nx.degree_centrality(G).values()), threshhold)
    
    # put nodes label in the dictionary if the centrality passes the threshold
    for key,value in nx.degree_centrality(G).items():
        if value >= cen_cutoff:
            labels[key] = key
    
    return labels

 def __init__(self) :
     self.g = nx.barabasi_albert_graph(random.randint(100,1000),random.randint(2,7))
     self.degree_centrality = nx.degree_centrality(self.g)
     self.deg = nx.degree_centrality(self.g)
     self.sorted_deg = sorted(self.deg.items(), key=operator.itemgetter(1))
     self.nodes = len(self.g.nodes())
     self.edges = len(self.g.edges())
     self.degree_rank()
     self.degree_dict = self.g.degree()
     self.avg_deg = sum(self.g.degree().values())/float(len(self.g.nodes()))
     #print self.rank
     #print self.degree_dict
     self.form_dataset()

	def degree_centrality(self, withme=True, node=None, average=False):

		if node==None:
			if withme:
				my_dict = nx.degree_centrality(self.mynet)
				new = {}
				new2={}
				for i in my_dict:
					new[self.id_to_name(i)] = my_dict[i]
					new2[i] = my_dict[i]
				if average:
					print "The average is " + str(round(sum(new.values())/float(len(new.values())),4))
				else:
					for i,j in new.items():
						print i, round(j,4)
					return new2
	 		else:
				my_dict = nx.degree_centrality(self.no_ego_net)

				new = {}
				new2={}
				for i in my_dict:
					new[self.id_to_name(i)] = my_dict[i]
					new2[i] = my_dict[i]
				if average:
					print "The average is " + str(round(sum(new.values())/float(len(new.values())),4))
				else:
					for i,j in new.items():
						print i, round(j,4)
					return new2
	
		else:
			if withme:
				my_dict = nx.degree_centrality(self.mynet)
				try:
					print "The coefficient for node "+str(node)+ "is "+ str(round(my_dict[node],4))
				except:
					try:
						return my_dict [self.name_to_id(node)]
					except:
						print "Invalid node name"
			else:
				my_dict = nx.degree_centrality(self.no_ego_net)
				try:
					print "The coefficient for node "+str(node)+ "is "+ str(round(my_dict[node],4))
				except:
					try:
						print "The coefficient for node "+str(node)+ "is "+ str(round(my_dict[[self.name_to_id(node)]],4))
					except:
						print "Invalid node name"

 def centralities(self):
     '''
     Get info on centralities of data
     Params:
         None
     Returns:
         dictionary of centrality metrics with keys(centralities supported):
             degree - degree centrality
             betweeness - betweeness centrality
             eigenvector - eigenvector centrality
             hub - hub scores - not implemented
             authority - authority scores - not implemented
             katz - katz centrality with params X Y
             pagerank - pagerank centrality with params X Y
     '''
     output = {}
     output['degree'] = nx.degree_centrality(self.G)
     output['betweeness'] = nx.betweenness_centrality(self.G)
     try:
         output['eigenvector'] = nx.eigenvector_centrality(self.G)
         output['katz'] = nx.katz_centrality(self.G)
     except:
         output['eigenvector'] = 'empty or exception'
         output['katz'] = 'empty or exception'
     # output['hub'] = 'Not implemented'
     # output['authority'] = 'Not implemented'
     # output['pagerank'] = 'Not implemented'
     return output

def run_main(file):

    NumberOfStations=465
    print file
    adjmatrix = np.loadtxt(file,delimiter=' ',dtype=np.dtype('int32'))

    # for i in range (0,NumberOfStations):
    #     if(adjmatrix[i,i]==1):
    #         print "posicion: ["+str(i)+","+str(i)+"]"


    g = nx.from_numpy_matrix(adjmatrix, create_using = nx.MultiGraph())
    degree = g.degree()
    density = nx.density(g)
    degree_centrality = nx.degree_centrality(g)
    clossness_centrality = nx.closeness_centrality(g)
    betweenless_centrality = nx.betweenness_centrality(g)

    print degree
    print density
    print degree_centrality
    print clossness_centrality
    print betweenless_centrality
    #nx.draw(g)
#    np.savetxt(OutputFile, Matrix, delimiter=' ',newline='\n',fmt='%i')

def calculate_network_measures(net, analyser):
    deg=nx.degree_centrality(net)
    clust=[]

    if(net.is_multigraph()):
        net = analyser.flatGraph(net)

    if(nx.is_directed(net)):
        tmp_net=net.to_undirected()
        clust=nx.clustering(tmp_net)
    else:
        clust=nx.clustering(net)



    if(nx.is_directed(net)):
        tmp_net=net.to_undirected()
        paths=nx.shortest_path(tmp_net, source=None, target=None, weight=None)
    else:
        paths=nx.shortest_path(net, source=None, target=None, weight=None)

    lengths = [map(lambda a: len(a[1]), x[1].items()[1:]) for x in paths.items()]
    all_lengths=[]
    for a in lengths:
        all_lengths.extend(a)
    max_value=max(all_lengths)
    #all_lengths = [x / float(max_value) for x in all_lengths]

    return deg.values(),clust.values(),all_lengths

def mean_degree_centrality(pg, normalize=0):
    """
    mean_degree_centrality(pg) calculates mean in- and out-degree
    centralities for directed graphs and simple degree-centralities
    for undirected graphs. If the normalize flag is set, each node's
    centralities are weighted by the number of edges in the (di)graph.
    """
    centrality = {}
    try:
        if networkx.is_directed_acyclic_graph(pg):
            cent_sum_in, cent_sum_out = 0, 0
            for n in pg.nodes():
                n_cent_in = pg.in_degree(n)
                n_cent_out = pg.out_degree(n)
                if normalize:
                    n_cent_in = float(n_cent_in) / float(pg.size()-1)
                    n_cent_out = float(n_cent_out) / float(pg.size()-1)
                cent_sum_in = cent_sum_in + n_cent_in
                cent_sum_out = cent_sum_out + n_cent_out
            centrality['in'] = cent_sum_in / float(pg.order())
            centrality['out'] = cent_sum_out / float(pg.order())
        else:
            cent_sum = 0
            for n in pg.nodes():
                if not normalize:
                    n_cent = pg.degree(n)
                else:
                    n_cent = networkx.degree_centrality(pg,n)
                cent_sum = cent_sum + n_cent
            centrality['all'] = cent_sum / float(pg.order())
    except:
        logging.error('pyp_network.mean_degree_centrality() failed!')
    return centrality

def allocate(G_phy, G_bgp):
    log.info("Allocating route reflectors")
    graph_phy = G_phy._graph
    for asn, devices in G_phy.groupby("asn").items():
        routers = [d for d in devices if d.is_router]
        router_ids = ank_utils.unwrap_nodes(routers)

        subgraph_phy = graph_phy.subgraph(router_ids)
        if len(subgraph_phy) == 1:  
                continue # single node in graph, no ibgp

        betw_cen = nx.degree_centrality(subgraph_phy)

        ordered = sorted(subgraph_phy.nodes(), key = lambda x: betw_cen[x], reverse = True)

        rr_count = len(subgraph_phy)/5 # Take top 20% to be route reflectors
        route_reflectors = ordered[:rr_count] # most connected 20%
        rr_clients = ordered[rr_count:] # the other routers
        route_reflectors = list(ank_utils.wrap_nodes(G_bgp, route_reflectors))
        rr_clients = list(ank_utils.wrap_nodes(G_bgp, rr_clients))

        G_bgp.update(route_reflectors, route_reflector = True) # mark as route reflector
        # rr <-> rr
        over_links = [(rr1, rr2) for rr1 in route_reflectors for rr2 in route_reflectors if rr1 != rr2] 
        G_bgp.add_edges_from(over_links, type = 'ibgp', direction = 'over')
        # client -> rr
        up_links = [(client, rr) for (client, rr) in itertools.product(rr_clients, route_reflectors)]
        G_bgp.add_edges_from(up_links, type = 'ibgp', direction = 'up')
        # rr -> client
        down_links = [(rr, client) for (client, rr) in up_links] # opposite of up
        G_bgp.add_edges_from(down_links, type = 'ibgp', direction = 'down')

    log.debug("iBGP done")