Python networkx.powerlaw_cluster_graph函数代码示例

def initialize():
    global g
    global wr
    global f
    global initialConditions
    initialConditions=0
    # Inicialite file for saving data
    cola= dt.datetime.now().strftime('%H%M')
    outputfilename = 'competicion_01_{}.csv'.format( cola)
    fileOut = open(outputfilename, 'w')
    wr = csv.writer(fileOut,quoting = csv.QUOTE_NONE)
    wr.writerow(['Tipo 1','Tipo 2','Tipo 3','Patogeno'])
    f = open( 'competicion_01_{}.ini'.format( cola), "w")
    
 #   g = nx.karate_club_graph()
    g=nx.powerlaw_cluster_graph(100,3,0.3)
    g.pos = nx.spring_layout(g)

    for i in g.nodes_iter():
        if random() < .33:
            g.node[i]['tipo'] = 0
        elif random() < .33:
            g.node[i]['tipo'] = 1
        elif random() < .33:
            g.node[i]['tipo'] = 2
        elif random() < .33:
            g.node[i]['tipo'] = 3
        else:
            g.node[i]['tipo'] = 4

def get_graph(objects, properties):
    graph_type = properties['graph_type']
    n = len(objects)-1
    if 'num_nodes_to_attach' in properties.keys():
        k = properties['num_nodes_to_attach']
    else:
        k = 3
    r = properties['connection_probability']

    tries = 0
    while(True):
        if graph_type == 'random':
            x = nx.fast_gnp_random_graph(n,r)
        elif graph_type == 'erdos_renyi_graph':
            x = nx.erdos_renyi_graph(n,r)
        elif graph_type == 'watts_strogatz_graph':
            x = nx.watts_strogatz_graph(n, k, r)
        elif graph_type == 'newman_watts_strogatz_graph':
            x = nx.newman_watts_strogatz_graph(n, k, r)
        elif graph_type == 'barabasi_albert_graph':
            x = nx.barabasi_albert_graph(n, k, r)
        elif graph_type == 'powerlaw_cluster_graph':
            x = nx.powerlaw_cluster_graph(n, k, r)
        elif graph_type == 'cycle_graph':
            x = nx.cycle_graph(n)
        else: ##Star by default
            x = nx.star_graph(len(objects)-1)
        tries += 1
        cc_conn = nx.connected_components(x)
        if len(cc_conn) == 1 or tries > 5: 
            ##best effort to create a connected graph!
            break
    return x, cc_conn

    def fromPowerLaw(cls, specs):
        '''
        :param specs: a tupple containing (n, m, p, seed, bw, delay, cpu)
        :return: a substrate
        '''
        n, m, p, seed, bw, delay, cpu = specs
        n = int(n)
        m = int(m)
        p = float(p)
        seed = int(seed)
        g = nx.powerlaw_cluster_graph(n, m, p, seed)
        session = Session()
        nodes = [Node(name=str(n), cpu_capacity=cpu) for n in g.nodes()]

        session.add_all(nodes)
        session.flush()

        edges = [Edge
                 (node_1=session.query(Node).filter(Node.name == str(e[0])).one(),
                  node_2=session.query(Node).filter(Node.name == str(e[1])).one(),
                  bandwidth=bw,
                  delay=delay
                  )
                 for e in g.edges()

                 ]
        session.add_all(edges)
        session.flush()

        return cls(edges, nodes
                   )

	def __update_structure(self):
		self.structure = nx.powerlaw_cluster_graph(
			self.num_nodes,
			self.node_degree,
			self.prob_triad,
			self.seed
		)

		if nx.is_connected(self.structure):
			return

		components = nx.connected_components(self.structure)

		biggest_comp = []
		comp_index = -1
		for i, component in enumerate(components):
			if len(component) > len(biggest_comp):
				biggest_comp = component
				comp_index = i

		if self.seed:
			random.seed(self.seed)

		del components[comp_index]
		for component in components:
			for left_node in component:
				right_node = random.choice(biggest_comp)
				self.structure.add_edge(left_node, right_node)

def add_edges_to_groups(output_graph, groups_list, edges_to_add, prob, level):
    global template_created
    total_groups = len(groups_list)
    edges_per_node = max((3 - level), 1)
    triangle_prob = 0.1*level
    if False:
        random_graph = nx.random_regular_graph(int(total_groups/3), total_groups)
    else:
        random_graph = nx.powerlaw_cluster_graph(total_groups, edges_per_node, triangle_prob, random.random()*10)

    if template_created:
        template_created = False
        plt.axis('off')
        position = nx.graphviz_layout(random_graph, prog='sfdp')
        nx.draw_networkx_nodes(random_graph, position, node_size=30, node_color='r') #output_graph.degree().values())
        nx.draw_networkx_edges(random_graph, position, alpha=0.3)
        plt.savefig(dataset_name2 +"/"+ "template_" + image_name, bbox_inches='tight', dpi=500)
        print "plot saved as ", image_name
    
    random_edges = random_graph.edges()
    
    for edge in random_edges:
        e0 = edge[0]
        e1 = edge[1]
        if random.random() > 0.3:
            e0, e1 = e1, e0
        print("adding level{} edges between group{} and group{}".format(level, e0, e1))
        add_edges_to_two_groups(output_graph, groups_list[e0], groups_list[e1], edges_to_add, prob)

 def test_pagerank(self):
     size = 1000
     g = nx.DiGraph(nx.powerlaw_cluster_graph(size, 3, 0.001))
     N = len(g.nodes())
     tmp_file = tempfile.NamedTemporaryFile(delete=False)
     for node in g.nodes():
         outlinks = g.out_edges(nbunch=[node])
         outlinks = map(str, [n2 for n1, n2 in outlinks])
         if not outlinks:
             value = 'pr_results,%s,%s' % (1.0/N, N)
             tmp_file.write('%s\t%s\n' % (node, value))
         else:
             outlinks_str = ','.join(outlinks)
             value = 'pr_results,%s,%s,' % (1.0/N, N)
             value += outlinks_str
             tmp_file.write('%s\t%s\n' % (node, value))
     tmp_file.flush()
     input_path = tmp_file.name
     job_id = 'unittest'
     sorted_ids = pagerank(job_id, self.iter_count, input_path, self.top_n)
     fs = HadoopFS()
     fs.rmr('%s/hat_results' % job_id)
     if self.top_n <= size: 
         self.assertEqual(len(sorted_ids), self.top_n, 'some ids is missing')
     id_ranges = range(0, 1000)
     for _id in sorted_ids:
         self.assertIn(int(_id), id_ranges, 'node should in graph')

def createGraphsAndCommunities():
	g = nx.scale_free_graph(500, alpha=0.40, beta=0.40, gamma=0.20)
	g1 = nx.powerlaw_cluster_graph(500, 10, 0.2)
	g2 = nx.barabasi_albert_graph(500, 10)
	g3 = nx.newman_watts_strogatz_graph(500, 10, 0.2)
	nx.write_graphml (g, direc+"sfg.graphml")
	nx.write_graphml(g1, direc+"pcg.graphml")
	nx.write_graphml(g2, direc+"bag.graphml")
	nx.write_graphml(g3, direc+"nwsg.graphml")

	graphs = {}
	graphs["sfg"] = graph_tool.load_graph(direc+"sfg.graphml")
	graphs["pcg"] = graph_tool.load_graph(direc+"pcg.graphml")
	graphs["bag"] = graph_tool.load_graph(direc+"bag.graphml")
	graphs["nwsg"] = graph_tool.load_graph(direc+"nwsg.graphml")
	graphs["price"] = graph_tool.generation.price_network(1000)
	
	for i,h in graphs.iteritems():
		s = graph_tool.community.minimize_blockmodel_dl(h)
		b = s.b
		graph_tool.draw.graph_draw(h, vertex_fill_color=b, vertex_shape=b, output=direc+"block"+str(i)+".pdf")
		
		com = graph_tool.community.community_structure(h, 10000, 20)
		graph_tool.draw.graph_draw(h, vertex_fill_color=com, vertex_shape=com, output=direc+"community"+str(i)+".pdf")

		state = graph_tool.community.minimize_nested_blockmodel_dl(h)
		graph_tool.draw.draw_hierarchy(state, output=direc+"nestedblock"+str(i)+".pdf")

		pagerank = graph_tool.centrality.pagerank(h)
		graph_tool.draw.graph_draw(h, vertex_fill_color=pagerank, vertex_size = graph_tool.draw.prop_to_size(pagerank, mi=5, ma=15), vorder=pagerank, output=direc+"pagerank"+str(i)+".pdf")
		h.set_reversed(is_reversed=True)
		pagerank = graph_tool.centrality.pagerank(h)
		graph_tool.draw.graph_draw(h, vertex_fill_color=pagerank, vertex_size = graph_tool.draw.prop_to_size(pagerank, mi=5, ma=15), vorder=pagerank, output=direc+"reversed_pagerank"+str(i)+".pdf")

def RandomHolmeKim(n, m, p, seed=None):
    """
    Returns a random graph generated by the Holme and Kim algorithm for
    graphs with power law degree distribution and approximate average
    clustering.

    INPUT:


    -  ``n`` - number of vertices.

    -  ``m`` - number of random edges to add for each new
       node.

    -  ``p`` - probability of adding a triangle after
       adding a random edge.

    -  ``seed`` - for the random number generator.


    From the NetworkX documentation: The average clustering has a hard
    time getting above a certain cutoff that depends on m. This cutoff
    is often quite low. Note that the transitivity (fraction of
    triangles to possible triangles) seems to go down with network
    size. It is essentially the Barabasi-Albert growth model with an
    extra step that each random edge is followed by a chance of making
    an edge to one of its neighbors too (and thus a triangle). This
    algorithm improves on B-A in the sense that it enables a higher
    average clustering to be attained if desired. It seems possible to
    have a disconnected graph with this algorithm since the initial m
    nodes may not be all linked to a new node on the first iteration
    like the BA model.

    EXAMPLE: We show the edge list of a random graph on 8 nodes with 2
    random edges per node and a probability `p = 0.5` of
    forming triangles.

    ::

        sage: graphs.RandomHolmeKim(8, 2, 0.5).edges(labels=False)
        [(0, 2), (0, 5), (1, 2), (1, 3), (2, 3), (2, 4), (2, 6), (2, 7),
         (3, 4), (3, 6), (3, 7), (4, 5)]

    ::

        sage: G = graphs.RandomHolmeKim(12, 3, .3)
        sage: G.show()  # long time

    REFERENCE:

    - [1] Holme, P. and Kim, B.J. Growing scale-free networks with
      tunable clustering, Phys. Rev. E (2002). vol 65, no 2,
      026107.
    """
    if seed is None:
        seed = current_randstate().long_seed()
    import networkx

    return graph.Graph(networkx.powerlaw_cluster_graph(n, m, p, seed=seed))

def generate_topo(n):
    topo = nx.powerlaw_cluster_graph(n,2,0.08)
    # topo = fnss.waxman_1_topology(n=50,alpha=0.6,beta=0.3)
    # topo = fnss.fat_tree_topology(n)
    fnss.set_weights_constant(topo,1)
    fnss.set_delays_constant(topo, 1, 'ms')
    fnss.set_capacities_edge_betweenness(topo,[100,500,1000],'Mbps')
    fnss.write_topology(topo,'topo_pl_50.xml')

def generate_graph():
    # Try these included graphs! Play around with the constants!
    # Feel free to define your own graph for testing.

    #return nx.random_regular_graph(5, GRAPH_SIZE, seed=GRAPH_SEED)
    #return nx.barabasi_albert_graph(GRAPH_SIZE, 5)
    #return grid_graph()
    return nx.powerlaw_cluster_graph(GRAPH_SIZE, 5, 0.7)

def graph_space_iter():
    i = 20
    n = 0
    while n < 1000000:
        G = nx.powerlaw_cluster_graph(i, 10, 0.1)
        G = nx.convert_node_labels_to_integers(G)
        n = G.number_of_edges()
        i *= 2
        yield G.number_of_nodes(), G

def pl_cluster_new(n, m, p, random_seed=None):
	Gw=nx.powerlaw_cluster_graph(n, m, p, seed=random_seed)
	
	Gs=nx.Graph()
	Gs.add_nodes_from(Gw.nodes(),state=1.0)
	Gs.add_edges_from(Gw.edges(),weight=1.0)
	##remove self-edges
	Gs.remove_edges_from(Gs.selfloop_edges())
	
	return Gs

def create_scale_free_graph(N_nodes,p_edge,n_infected):
    #scale free and small world
    #Growing Scale-Free Networks with Tunable Clustering
    n = N_nodes
    m = int(0.5*p_edge*N_nodes)
    p = 1.0
    #Random graph
    #p_coop is the fraction of cooperators
    G = nx.powerlaw_cluster_graph(n,m,p)
    return set_graph_strategies(G, n_infected)

def topo_pl(nodes):
    bws = [1,2,3,4,5,6,7,8,9]
    network = nx.powerlaw_cluster_graph(nodes,2,0.13)
    g = nx.Graph()
    g.add_nodes_from(network.nodes())
    for link in network.edges():
        bw = random.choice(bws)
        g.add_edge(link[0],link[1],{'weight':bw})
        g.add_edge(link[1],link[0],{'weight':bw})
    return g

def initialize():
    global g
 #   g = nx.karate_club_graph()
    g=nx.powerlaw_cluster_graph(100,3,0.3)
    g.pos = nx.spring_layout(g)
    for i in g.nodes_iter():
        if random() < .3:
            g.node[i]['state'] = 1
        elif random() < .3:
            g.node[i]['state'] = 2
        elif random() < .3:
            g.node[i]['state'] = 3
        else:
            g.node[i]['state'] = 0