Python networkx.pagerank_numpy函数代码示例

	def personal_page_rank(self, p_vector, reverse=False):
		'''
			Personal_Page_Rank: Get the personal pagerank of the supplied input vector

			Input: 
				- p_vector: A hash-map of input values for a selection (or all) nodes
				(if supplied nodes aren't in the graph, they will be ignored)

			Output:
				- A vector of diffused heats in hash-map (key,value) format
		'''
		input_pvec = None
		#  without initializing this vector the initial probabilities will be flat
		# and this will be equivalent to standard page rank
		if p_vector:
			input_pvec = {}
			# doesn't seem to be necessary for a non-zero epsilon now, but 
			# leave this as a place holder
			epsilon = 0.0
			for node in self.G.nodes(data=False):
				if node in p_vector:
					input_pvec[node] = p_vector[node]
				else:
					input_pvec[node] = epsilon

		if reverse:	
			return nx.pagerank_numpy(self.G_reversed, 0.85, input_pvec)
		else:
			return nx.pagerank_numpy(self.G, 0.85, input_pvec)

 def test_numpy_pagerank(self):
     G = self.G
     p = networkx.pagerank_numpy(G, alpha=0.9)
     for n in G:
         assert_almost_equal(p[n], G.pagerank[n], places=4)
     personalize = dict((n, random.random()) for n in G)
     p = networkx.pagerank_numpy(G, alpha=0.9, personalization=personalize)

def main():
    disapprove, cooperate = build_graph(gdelt_data_iter())

    # Computer pagerank for disapprove Graph node
    print("Computing pagerank for disapprove graph")
    pagerank1 = nx.pagerank_numpy(disapprove, alpha=0.90)
    print("Computing pagerank for cooperate graph")
    pagerank2 = nx.pagerank_numpy(cooperate, alpha=0.90)

    max1 = max(pagerank1.values())

    key1 = ''
    key2 = ''
    for key in pagerank1.keys():
        if pagerank1[key] == max1:
            key1 = key

    max2 = max(pagerank2.values())
    for key in pagerank2.keys():
        if pagerank2[key] == max2:
            key2 = key

    with open('results/disapprove_graph_page_rank.csv', 'w') as f1:
        for line in str(pagerank1):
            f1.write(line)

    with open('results/cooperate_graph_page_rank.csv', 'w') as f2:
        for line in str(pagerank2):
            f2.write(line)

    print("Maximum Page rank for disapprove graph is: %s %s" % (key1, max1))
    print("Maximum Page rank for cooperate graph is:  %s %s" % (key2, max2))

 def test_numpy_pagerank(self):
     try:
         import numpy
     except ImportError:
         raise SkipTest('numpy not available.')
     G=self.G
     p=networkx.pagerank_numpy(G,alpha=0.9)
     for n in G:
         assert_almost_equal(p[n],G.pagerank[n],places=4)
     personalize = dict((n,random.random()) for n in G)
     p=networkx.pagerank_numpy(G,alpha=0.9, personalization=personalize)

def pagerank(graph, weighted=True):
    """ Pagerank algorithm with beta = 0.85.

    If unweighted, then every outgoing edge is considered uniformly.
    Otherwise, outgoing edges are weighted by their given weights.

    Returns:
        An array where the ith element corresponds to the pagerank score
        of agent i in the trust graph.
    """
    if weighted:
        return np.array(nx.pagerank_numpy(graph).values())
    else:
        return np.array(nx.pagerank_numpy(graph, weight=None).values())

 def OrigPagerank(self):
     ''' returns a 2d array containing the pagerank of the origin node for all edges
     ''' 
     probas = np.dot( 
                   np.array(nx.pagerank_numpy(self).values(),dtype=float).reshape(-1,1),
                   np.ones((1,self.number_of_nodes())))
     return probas

def draw_graph(nodes, edges, graphs_dir, default_lang='all'):
    lang_graph = nx.MultiDiGraph()
    lang_graph.add_nodes_from(nodes)
    for edge in edges:
        if edges[edge] == 0:
            lang_graph.add_edge(edge[0], edge[1])
        else:
            lang_graph.add_edge(edge[0], edge[1], weight=float(edges[edge]), label=str(edges[edge]))

    # print graph info in stdout
    # degree centrality
    print('-----------------\n\n')
    print(default_lang)
    print(nx.info(lang_graph))
    try:
        # When ties are associated to some positive aspects such as friendship or collaboration,
        #  indegree is often interpreted as a form of popularity, and outdegree as gregariousness.
        DC = nx.degree_centrality(lang_graph)
        max_dc = max(DC.values())
        max_dc_list = [item for item in DC.items() if item[1] == max_dc]
    except ZeroDivisionError:
        max_dc_list = []
    # https://ru.wikipedia.org/wiki/%D0%9A%D0%BE%D0%BC%D0%BF%D0%BB%D0%B5%D0%BA%D1%81%D0%BD%D1%8B%D0%B5_%D1%81%D0%B5%D1%82%D0%B8
    print('maxdc', str(max_dc_list), sep=': ')
    # assortativity coef
    AC = nx.degree_assortativity_coefficient(lang_graph)
    print('AC', str(AC), sep=': ')
    # connectivity
    print("Слабо-связный граф: ", nx.is_weakly_connected(lang_graph))
    print("количество слабосвязанных компонент: ", nx.number_weakly_connected_components(lang_graph))
    print("Сильно-связный граф: ", nx.is_strongly_connected(lang_graph))
    print("количество сильносвязанных компонент: ", nx.number_strongly_connected_components(lang_graph))
    print("рекурсивные? компоненты: ", nx.number_attracting_components(lang_graph))
    print("число вершинной связности: ", nx.node_connectivity(lang_graph))
    print("число рёберной связности: ", nx.edge_connectivity(lang_graph))
    # other info
    print("average degree connectivity: ", nx.average_degree_connectivity(lang_graph))
    print("average neighbor degree: ", sorted(nx.average_neighbor_degree(lang_graph).items(),
                                              key=itemgetter(1), reverse=True))
    # best for small graphs, and our graphs are pretty small
    print("pagerank: ", sorted(nx.pagerank_numpy(lang_graph).items(), key=itemgetter(1), reverse=True))

    plt.figure(figsize=(16.0, 9.0), dpi=80)
    plt.axis('off')
    pos = graphviz_layout(lang_graph)
    nx.draw_networkx_edges(lang_graph, pos, alpha=0.5, arrows=True)
    nx.draw_networkx(lang_graph, pos, node_size=1000, font_size=12, with_labels=True, node_color='green')
    nx.draw_networkx_edge_labels(lang_graph, pos, edges)

    # saving file to draw it with dot-graphviz
    # changing overall graph view, default is top-bottom
    lang_graph.graph['graph'] = {'rankdir': 'LR'}
    # marking with blue nodes with maximum degree centrality
    for max_dc_node in max_dc_list:
        lang_graph.node[max_dc_node[0]]['fontcolor'] = 'blue'
    write_dot(lang_graph, os.path.join(graphs_dir, default_lang + '_links.dot'))

    # plt.show()
    plt.savefig(os.path.join(graphs_dir, 'python_' + default_lang + '_graph.png'), dpi=100)
    plt.close()

def getRandomPageRanks(filename):
	Ga=nx.read_graphml(sys.argv[1])

	# create a copy of the graph and extract giant component
	# get component size distribution
	cc=nx.connected_components(Ga)
	cc_dict={}
	for x in range(0,len(cc)):
		try:
			cc_dict[len(cc[x])].append(x)
		except KeyError:
			cc_dict[len(cc[x])]=[]
			cc_dict[len(cc[x])].append(x)

	isolates=nx.isolates(Ga)

	rg=nx.fast_gnp_random_graph(Ga.number_of_nodes(),2.0*Ga.number_of_edges()/(Ga.number_of_nodes()*(Ga.number_of_nodes()-1)))
	c_rg=nx.average_clustering(rg)
	rg_cc=nx.connected_component_subgraphs(rg)[0]
	rg_asp=nx.algorithms.shortest_paths.generic.average_shortest_path_length(rg_cc)

	p_rg=community.best_partition(rg_cc)
	m_rg=community.modularity(p_rg,rg_cc)

	pageranks = nx.pagerank_numpy(rg)
	return pageranks

def features_matrix(graph, anchors, use_dist=True, use_pgrs=True,
                    use_pgr=True, use_comm=False, use_comm_centr=False):
    node_feats = []
    n = len(graph)
    if use_dist:
        dists = nx.all_pairs_shortest_path_length(graph)
    if use_pgr:
        pageranks = nx.pagerank_numpy(graph)
    if use_pgrs:
        pgr_anchor = [anchored_pagerank(graph, anchor) for anchor in anchors]
    if use_comm_centr:
        communicability_centrality = nx.communicability_centrality(graph)
    if use_comm:
        communicability = nx.communicability(graph)

    for node in graph.nodes():
        assert node == len(node_feats)
        feats = []
        if use_dist:
            feats += [dists[node][anchor] for anchor in anchors]
        if use_pgrs:
            feats += [pgr[node]*n for pgr in pgr_anchor]
        if use_pgr:
            feats.append(pageranks[node]*n)
        if use_comm_centr:
            feats.append(communicability_centrality[node])
        if use_comm:
            feats += [communicability[node][anchor] for anchor in anchors]


        node_feats.append(np.array(feats))
    return node_feats

def features_dict(graph, anchors, use_dist=True, use_pgrs=True,
                    use_pgr=True, use_comm=False, use_comm_centr=False):
    node_feats = {}
    n = len(graph)
    if use_dist:
        # dists = nx.all_pairs_shortest_path_length(graph)
        dists = dists_to_anchors(graph, anchors)
    if use_pgr:
        pageranks = nx.pagerank_numpy(graph)
    if use_pgrs:
        # pgr_anchor = [anchored_pagerank(graph, anchor) for anchor in anchors]
        pgr_anchor = pageranks_to_anchors(graph, anchors)
    if use_comm_centr:
        communicability_centrality = nx.communicability_centrality(graph)
    if use_comm:
        communicability = nx.communicability(graph)

    for node in graph.nodes():
        feats = []
        if use_dist:
            feats += [dists[node][anchor] for anchor in anchors]
        if use_pgrs:
            feats += [pgr_anchor[anchor][node]*n
                      for anchor in range(len(anchors))]
            # feats += [pgr[node]*n for pgr in pgr_anchor]
        if use_pgr:
            feats.append(pageranks[node]*n)
        if use_comm_centr:
            feats.append(communicability_centrality[node])
        if use_comm:
            feats += [communicability[node][anchor] for anchor in anchors]


        node_feats[node] = np.array(feats)
    return node_feats

 def TargPagerank(self):
     ''' returns a 2d array containing the pagerank of the target node for all edges
     ''' 
     probas =  np.dot( 
                   np.ones((self.number_of_nodes(),1)),
                   np.array(nx.pagerank_numpy(self).values(),dtype=float).reshape(1,-1)
                   )       
     return probas

def parse_nci(graph_name='nci1.graph', with_structural_features=False):
    path = "%s/data/nci/" % (current_dir,)

    if graph_name == 'nci1.graph':
        maxval = 37
    elif graph_name == 'nci109.graph':
        maxval = 38

    with open(path+graph_name,'r') as f:
        raw = cp.load(f)

        n_classes = 2
        n_graphs = len(raw['graph'])

        A = []
        rX = []
        Y = np.zeros((n_graphs, n_classes), dtype='int32')

        for i in range(n_graphs):
            # Set label
            Y[i][raw['labels'][i]] = 1

            # Parse graph
            G = raw['graph'][i]

            n_nodes = len(G)

            a = np.zeros((n_nodes,n_nodes), dtype='float32')
            x = np.zeros((n_nodes,maxval), dtype='float32')

            for node, meta in G.iteritems():
                x[node,meta['label'][0] - 1] = 1
                for neighbor in meta['neighbors']:
                    a[node, neighbor] = 1

            A.append(a)
            rX.append(x)

    if with_structural_features:
        import networkx as nx

        for i in range(len(rX)):
            struct_feat = np.zeros((rX[i].shape[0], 3))
            # degree
            struct_feat[:,0] = A[i].sum(1)

            G = nx.from_numpy_matrix(A[i])
            # pagerank
            prank = nx.pagerank_numpy(G)
            struct_feat[:,1] = np.asarray([prank[k] for k in range(A[i].shape[0])])

            # clustering
            clust = nx.clustering(G)
            struct_feat[:,2] = np.asarray([clust[k] for k in range(A[i].shape[0])])

            rX[i] = np.hstack((rX[i],struct_feat))

    return A, rX, Y

    def get_pagerank(self, damping_factor=0.85):
        """ Computes normalized page rank of current graph
        """
        pagerank = np.array(nx.pagerank_numpy(self.graph.graph, alpha=damping_factor)).tolist()

        vals = list(pagerank.values())
        vals /= npl.norm(vals)

        return vals

 def test_numpy_pagerank(self):
     try:
         import numpy
     except ImportError:
         raise SkipTest('numpy not available.')
     G=self.G
     p=networkx.pagerank_numpy(G,alpha=0.9)
     for n in G:
         assert_almost_equal(p[n],G.pagerank[n],places=4)    

 def test_numpy_pagerank(self):
     G=self.G
     try:
         p=networkx.pagerank_numpy(G,alpha=0.9,
                                                        tol=1.e-08)
         for (a,b) in zip(p,self.G.pagerank):
             assert_almost_equal(a,b)
     except ImportError:
         print "Skipping pagerank_numpy test"