Python networkx.barabasi_albert_graph函数代码示例

def update_all_parameter(diff):
    #print 'each difference -  %s' % diff
    luc_node = int(30*diff)
    hcc_node = int(5)
    time = 10

    #parameter
    luc_gro = int(6*diff)
    hcc_gro = int(2)

    lucG = nx.barabasi_albert_graph(luc_node, luc_gro)
    hccG = nx.barabasi_albert_graph(hcc_node, hcc_gro)

    frequency = np.array([0.9, 0.1])
    G_combine =nx.Graph()
    G_combine = graph.merge_graph(G_combine, hccG, lucG, frequency)

    frequency_1 = np.array([0.5, 0.5])
    G_combine_1 =nx.Graph()
    G_combine_1 = graph.merge_graph(G_combine_1, hccG, lucG, frequency_1)


    #Time series cell volume
    LucN = []
    hccN = []

    #Number of initial cell 
    LucN0 = 100
    hccN0 = 100
    LucN_init = 100
    hccN_init = 100

    for t in range(time):
      LucN.append(calc.convert_volume(LucN0))
      lucG = graph.update_graph(lucG, luc_gro)
      LucN0 = LucN_init*calc.calc_entropy(lucG, t+1)

    for t in range(time):
      hccN.append(calc.convert_volume(hccN0))
      hccG = graph.update_graph(hccG, hcc_gro)
      hccN0 = hccN_init*calc.calc_entropy(hccG, t+1)

    #Mix Number of cell
    MixN0 = 100
    MixN_init = 100
    initial_populations = MixN0*frequency
    G_comb_gro = ((frequency*np.array([luc_gro, hcc_gro])).sum())/2
    MixN = []
    x = []
    for t in range(time):
      x.append(t)
      MixN.append(calc.convert_volume(MixN0))
      G_combine = graph.update_graph(G_combine, G_comb_gro)
      MixN0 = MixN_init*calc.calc_entropy(G_combine, t+1)
 
    sim_ratio =  np.array(LucN)/np.array(MixN)
    return sim_ratio


    """

 def setUp(self):
     self.G=nx.barabasi_albert_graph(1000, 10, 8)
     pth_graph=nx.path_graph(1000)
     edge=random.choice(pth_graph.edges())
     pth_graph.remove_edge(edge[0], edge[1])
     self.dG=pth_graph
     self.dG2=nx.barabasi_albert_graph(900, 10, 0)
     for i in xrange(900,1000):
         self.dG2.add_node(i)

def test_powerlaw_mle():
    print 'Testing Power law MLE estimator'
    G = nx.barabasi_albert_graph(100, 5)
    print 'nn: %d, alpha: %f'%(G.number_of_nodes(),powerlaw_mle(G))
    G = nx.barabasi_albert_graph(1000, 5)
    print 'nn: %d, alpha: %f'%(G.number_of_nodes(),powerlaw_mle(G))
    G = nx.barabasi_albert_graph(10000, 5)
    print 'nn: %d, alpha: %f'%(G.number_of_nodes(),powerlaw_mle(G))
    G = nx.barabasi_albert_graph(100000, 5)
    print 'nn: %d, alpha: %f'%(G.number_of_nodes(),powerlaw_mle(G))
    print 'Expected: 2.9 (or thereabout)'

def main():

    msg = "usage: ./p2p2012.py type r|g|g2 ttl par tries churn_rate"

    if len(sys.argv) < 7:
        print msg
        sys.exit(1)

    global out_file, churn_rate
    out_file = sys.stdout

    gtype = sys.argv[1]
    walk = sys.argv[2]
    ttl = int(sys.argv[3])
    par = int(sys.argv[4])
    tries = int(sys.argv[5])
    churn_rate = float(sys.argv[6])

    if gtype == "a":
        g = nx.barabasi_albert_graph(97134, 3)
    elif gtype == "b":
        g = nx.barabasi_albert_graph(905668, 12)
    elif gtype == "c":
        g = sm.randomWalk_mod(97134, 0.90, 0.23)
    elif gtype == "d":
        g = sm.randomWalk_mod(905668, 0.93, 0.98)
    elif gtype == "e":
        g = sm.nearestNeighbor_mod(97134, 0.53, 1)
    elif gtype == "f":
        g = sm.nearestNeighbor_mod(905668, 0.90, 5)
    elif gtype == "g":
        g = nx.random_regular_graph(6, 97134)
    elif gtype == "h":
        g = nx.random_regular_graph(20, 905668)
    elif gtype == "i":
        g = nx.read_edgelist(sys.argv[7])

    if walk == "r":
        lookup(g, ttl, tries, par, get_random_node)
    elif walk == "g":
        lookup(g, ttl, tries, par, get_greedy_node)
    elif walk == "g2":
        lookup(g, ttl, tries, par, get_greedy2_node)
    elif walk == "sum":
        sum_edges(g, int(sys.argv[3]))

    nodes = g.number_of_nodes()
    edges = g.size()
    avg_cc = nx.average_clustering(g)

    print >> sys.stderr, nodes, edges, avg_cc

    def test_networkx_matrix(self):
        print('\n---------- Matrix Test Start -----------\n')

        g = nx.barabasi_albert_graph(30, 2)
        nodes = g.nodes()
        edges = g.edges()
        print(edges)

        mx1 = nx.adjacency_matrix(g)
        fp = tempfile.NamedTemporaryFile()
        file_name = fp.name
        sp.savetxt(file_name, mx1.toarray(), fmt='%d')

        # Load it back to matrix
        mx2 = sp.loadtxt(file_name)
        fp.close()

        g2 = nx.from_numpy_matrix(mx2)
        cyjs_g = util.from_networkx(g2)

        #print(json.dumps(cyjs_g, indent=4))

        self.assertIsNotNone(cyjs_g)
        self.assertIsNotNone(cyjs_g['data'])
        self.assertEqual(len(nodes), len(cyjs_g['elements']['nodes']))
        self.assertEqual(len(edges), len(cyjs_g['elements']['edges']))

        # Make sure all edges are reproduced
        print(set(edges))
        diff = compare_edge_sets(set(edges), cyjs_g['elements']['edges'])
        self.assertEqual(0, len(diff))

def compare_graphs(graph):
    n = nx.number_of_nodes(graph)
    m = nx.number_of_edges(graph)
    k = np.mean(list(nx.degree(graph).values()))
    erdos = nx.erdos_renyi_graph(n, p=m/float(n*(n-1)/2))
    barabasi = nx.barabasi_albert_graph(n, m=int(k)-7)
    small_world = nx.watts_strogatz_graph(n, int(k), p=0.04)
    print(' ')
    print('Compare the number of edges')
    print(' ')
    print('My network: ' + str(nx.number_of_edges(graph)))
    print('Erdos: ' + str(nx.number_of_edges(erdos)))
    print('Barabasi: ' + str(nx.number_of_edges(barabasi)))
    print('SW: ' + str(nx.number_of_edges(small_world)))
    print(' ')
    print('Compare average clustering coefficients')
    print(' ')
    print('My network: ' + str(nx.average_clustering(graph)))
    print('Erdos: ' + str(nx.average_clustering(erdos)))
    print('Barabasi: ' + str(nx.average_clustering(barabasi)))
    print('SW: ' + str(nx.average_clustering(small_world)))
    print(' ')
    print('Compare average path length')
    print(' ')
    print('My network: ' + str(nx.average_shortest_path_length(graph)))
    print('Erdos: ' + str(nx.average_shortest_path_length(erdos)))
    print('Barabasi: ' + str(nx.average_shortest_path_length(barabasi)))
    print('SW: ' + str(nx.average_shortest_path_length(small_world)))
    print(' ')
    print('Compare graph diameter')
    print(' ')
    print('My network: ' + str(nx.diameter(graph)))
    print('Erdos: ' + str(nx.diameter(erdos)))
    print('Barabasi: ' + str(nx.diameter(barabasi)))
    print('SW: ' + str(nx.diameter(small_world)))

def ba_network(p=25, n=150):
    """ Barabasi-Albert algorithm is used to generate a scale free network. The
    precision matrix is constructed as the above nearest neighbor based
    algorithm. We also set the degree as 5."""
    m = 5
    G = networkx.barabasi_albert_graph(p, m)  # obtain networkx library graph G
    A = np.array(networkx.adjacency_matrix(G))  # numpy matrix is returned

    # We weight the edges using a random number in [-1.0, -0.5] \cup [0.5, 1.0]
    for i in range(p):
        for j in range(p):
            if A[i, j] > 0:
                A[i, j] = A[i, j] * np.random.uniform(0.5, 1.0)
                A[j, i] = A[i, j]

    # ensure symmetry
    A = (A + A.T) / 2.0

    # Randomize sign
    A = A * pow(-1.0, np.random.random_integers(0, 1, [p, p]))

    # The diagonal entires are set to the sum of the absolute values of the row
    # then, we obtain precision matrix
    # I placed the factor 2 to ensure invertibility
    P = A + 0.25 * np.diag(np.sum(np.absolute(A), 1))

    # normalize entries to make the diagonal elements equal to one
    P = P / np.diag(P)

    cov = np.linalg.inv(P)  # covariance matrix

    # Sample from the covariance matrix
    samples = np.random.multivariate_normal(np.zeros(p), cov, n)

    return samples, cov

def test_random_model():
    n_node = graph.number_of_nodes()
    n_edge = graph.number_of_edges()

    p = float(2 * n_edge) / (n_node*n_node - 2*n_node)
    #new_graph = networkx.erdos_renyi_graph(n_node, p)
    new_graph = networkx.barabasi_albert_graph(n_node, n_edge/n_node)
    mapping = dict(zip(new_graph.nodes(), graph.nodes()))
    new_graph = networkx.relabel_nodes(new_graph, mapping)

    return new_graph

    available_edges = graph.edges()

    for edge in new_graph.edges():
	if len(available_edges) > 0:
	    edge_org = available_edges.pop()
	    new_graph.add_edge(edge[0], edge[1], graph.get_edge(edge_org[0], edge_org[1]))
	else:
	    print "Removing:", edge
	    new_graph.remove_edge(edge[0], edge[1])

    for edge_org in available_edges:
	print "Adding:", edge_org
	new_graph.add_edge(edge_org[0], edge_org[1], graph.get_edge(edge_org[0], edge_org[1]))
    return new_graph

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 main():
    
    ### Undirected graph ###
    
    # Initialize model using the Petersen graph
    model=gmm.gmm(nx.petersen_graph())
    old_graph=model.get_base()
    model.set_termination(node_ceiling)
    model.set_rule(rand_add)
    
    # Run simualation with tau=4 and Poisson density for motifs
    gmm.algorithms.simulate(model,4)   

    # View results
    new_graph=model.get_base()
    print(nx.info(new_graph))
    
    # Draw graphs
    old_pos=nx.spring_layout(old_graph)
    new_pos=nx.spring_layout(new_graph,iterations=2000)
    fig1=plt.figure(figsize=(15,7))
    fig1.add_subplot(121)
    #fig1.text(0.1,0.9,"Base Graph")
    nx.draw(old_graph,pos=old_pos,node_size=25,with_labels=False)
    fig1.add_subplot(122)
    #fig1.text(0.1,0.45,"Simulation Results")
    nx.draw(new_graph,pos=new_pos,node_size=20,with_labels=False)
    fig1.savefig("undirected_model.png")
    
    ### Directed graph ###
    
    # Initialize model using random directed Barabasi-Albert model
    directed_base=nx.barabasi_albert_graph(25,2).to_directed()
    directed_model=gmm.gmm(directed_base)
    directed_model.set_termination(node_ceiling)
    directed_model.set_rule(rand_add)
    
    # Run simualation with tau=4 and Poisson density for motifs
    gmm.algorithms.simulate(directed_model,4)
    
    # View results
    new_directed=directed_model.get_base()
    print(nx.info(new_directed))
    
    # Draw directed graphs
    old_dir_pos=new_pos=nx.spring_layout(directed_base)
    new_dir_pos=new_pos=nx.spring_layout(new_directed,iterations=2000)
    fig2=plt.figure(figsize=(7,10))
    fig2.add_subplot(211)
    fig2.text(0.1,0.9,"Base Directed Graph")
    nx.draw(directed_base,pos=old_dir_pos,node_size=25,with_labels=False)
    fig2.add_subplot(212)
    fig2.text(0.1,0.45, "Simualtion Results")
    nx.draw(new_directed,pos=new_dir_pos,node_size=20,with_labels=False)
    fig2.savefig("directed_model.png")
    
    # Export files
    nx.write_graphml(model.get_base(), "base_model.graphml")
    nx.write_graphml(directed_model.get_base(), "directed_model.graphml")
    nx.write_graphml(nx.petersen_graph(), "petersen_graph.graphml")

	def generate(self):

		barabasi_albert = nx.barabasi_albert_graph(self.nodes, self.m, self.seed)
		self.nx_topology = nx.MultiDiGraph()
		self.nx_topology.clear()

		index = 0

		nodes = []
		for node in barabasi_albert.nodes():
			#SSnodes.append(node+1)
			nodes.append(str(node+1))

		self.nx_topology.add_nodes_from(nodes)

		for (n1, n2) in barabasi_albert.edges():

			n1 = n1 + 1
			n2 = n2 + 1
			self.sip.update(str(index))
			id_ = str(self.sip.hash())

			#SSself.nx_topology.add_edge(n1, n2, capacity=self.DEFAULT_SPEED, allocated=0.0, src_port="", dst_port="", src_port_no="", dst_port_no="", src_mac="", dst_mac="", flows=[], id=id_) 
			self.nx_topology.add_edge(str(n1), str(n2), capacity=self.DEFAULT_SPEED, allocated=0.0, src_port="", dst_port="", src_port_no="", dst_port_no="", src_mac="", dst_mac="", flows=[], id=id_) 

			index = index + 1
			self.sip.update(str(index))
			id_ = str(self.sip.hash())

			#SSself.nx_topology.add_edge(n2, n1, capacity=self.DEFAULT_SPEED, allocated=0.0, src_port="", dst_port="", src_port_no="", dst_port_no="", src_mac="", dst_mac="", flows=[], id=id_) 
			self.nx_topology.add_edge(str(n2), str(n1), capacity=self.DEFAULT_SPEED, allocated=0.0, src_port="", dst_port="", src_port_no="", dst_port_no="", src_mac="", dst_mac="", flows=[], id=id_) 

			index = index + 1	

def generate_graph(type = 'PL', n = 100, seed = 1.0, parameter = 2.1):
    if type == 'ER':
        G = nx.erdos_renyi_graph(n, p=parameter, seed=seed, directed=True)
        G = nx.DiGraph(G)
        G.remove_edges_from(G.selfloop_edges())
    elif type == 'PL':
        z = nx.utils.create_degree_sequence(n, nx.utils.powerlaw_sequence, exponent = parameter)
        while not nx.is_valid_degree_sequence(z):
            z = nx.utils.create_degree_sequence(n, nx.utils.powerlaw_sequence, exponent = parameter)
        G = nx.configuration_model(z)
        G = nx.DiGraph(G)
        G.remove_edges_from(G.selfloop_edges())
    elif type == 'BA':
        G = nx.barabasi_albert_graph(n, 3, seed=None)
        G = nx.DiGraph(G)
    elif type == 'grid':
        G = nx.grid_2d_graph(int(np.ceil(np.sqrt(n))), int(np.ceil(np.sqrt(n))))
        G = nx.DiGraph(G)
    elif type in ['facebook', 'enron', 'twitter', 'students', 'tumblr', 'facebookBig']:
        #print 'start reading'
        #_, G, _, _ = readRealGraph(os.path.join("..","..","Data", type+".txt"))
        _, G, _, _ = readRealGraph(os.path.join("..","Data", type+".txt"))
        print 'size of graph', G.number_of_nodes()
        #Gcc = sorted(nx.connected_component_subgraphs(G.to_undirected()), key = len, reverse=True)
        #print Gcc[0].number_of_nodes()
        #print 'num of connected components', len(sorted(nx.connected_component_subgraphs(G.to_undirected()), key = len, reverse=True))
        #exit()
        if G.number_of_nodes() > n:
            G = getSubgraph(G, n)
        #G = getSubgraphSimulation(G, n, infP = 0.3)
    #nx.draw(G)
    #plt.show()
    return G

    def __init__(self, N = 10000, m_0 = 3):
        """
        :Purpose:
            This is the base class used to generate the social network 
            for the other agents, i.e. . The class inherits from the PopulationClass.

        :Input:	
            N : int
              Number of agents. Default: 10000

            m_0: int	
              Number of nodes each node is connected to in preferential
              attachment step
        """
        if type(N) is not int:			
            raise ValueError(('Population size must be integer,\
                                      n = %s, not %s')%(string(N), type(N)))	
        else: pass
        if m_0 not in range(10):
            raise ValueError('m_0 must be integer smaller than 10')
        else: self.m_0 = m_0

        PopulationClass.__init__(self, n = N)	# Create population
        SpecialAgents = set(self.IDU_agents).union(set(self.MSM_agents))
        SpecialAgents = SpecialAgents.union(set(self.NIDU_agents))
        NormalAgents = set(range(self.PopulationSize)).difference(SpecialAgents)
        NormalAgents = list(NormalAgents)
        self.NetworkSize = len(NormalAgents)
        # scale free Albert Barabsai Graph
        self.G = nx.barabasi_albert_graph(self.NetworkSize,m_0)

def correlation_betweenness_degree_on_BA():
    n = 1000
    m = 2
    G = nx.barabasi_albert_graph(n, m)

    print nx.info(G)
    ND, ND_lambda = ECT.get_number_of_driver_nodes(G)
    print "ND = ", ND
    print "ND lambda:", ND_lambda
    ND, driverNodes = ECT.get_driver_nodes(G)
    print "ND =", ND

    degrees = []
    betweenness = []
    tot_degree = nx.degree_centrality(G)
    tot_betweenness = nx.betweenness_centrality(G,weight=None)

    for node in driverNodes:
        degrees.append(tot_degree[node])
        betweenness.append(tot_betweenness[node])

    with open("results/driver_degree_BA.txt", "w") as f:
        for x in degrees:
            print >> f, x
    with open("results/driver_betweenness_BA.txt", "w") as f:
        for x in betweenness:
            print >> f, x
    with open("results/tot_degree_BA.txt", "w") as f:
        for key, value in tot_degree.iteritems():
            print >> f, value

    with open("results/tot_betweenness_BA.txt", "w") as f:
        for key, value in tot_betweenness.iteritems():
            print >> f, value

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")