Python networkx.number_of_nodes方法代碼示例

# 需要導入模塊: import networkx [as 別名]
# 或者: from networkx import number_of_nodes [as 別名]
def tree(start, height, r=2, role_start=0):
    """Builds a balanced r-tree of height h
    INPUT:
    -------------
    start       :    starting index for the shape
    height      :    int height of the tree 
    r           :    int number of branches per node 
    role_start  :    starting index for the roles
    OUTPUT:
    -------------
    graph       :    a tree shape graph, with ids beginning at start
    roles       :    list of the roles of the nodes (indexed starting at role_start)
    """
    graph = nx.balanced_tree(r, height)
    roles = [0] * graph.number_of_nodes()
    return graph, roles 

# 需要導入模塊: import networkx [as 別名]
# 或者: from networkx import number_of_nodes [as 別名]
def as_tree(graph, root=OPENSTACK_CLUSTER, reverse=False):
        if nx.__version__ >= '2.0':
            linked_graph = json_graph.node_link_graph(
                graph, attrs={'name': 'graph_index'})
        else:
            linked_graph = json_graph.node_link_graph(graph)
        if 0 == nx.number_of_nodes(linked_graph):
            return {}
        if reverse:
            linked_graph = linked_graph.reverse()
        if nx.__version__ >= '2.0':
            return json_graph.tree_data(
                linked_graph,
                root=root,
                attrs={'id': 'graph_index', 'children': 'children'})
        else:
            return json_graph.tree_data(linked_graph, root=root) 

# 需要導入模塊: import networkx [as 別名]
# 或者: from networkx import number_of_nodes [as 別名]
def test_iterators(self):
        G=self.G()
        G.add_edges_from([('A', 'B'), ('A', 'C'), ('B', 'D'), 
                          ('C', 'B'), ('C', 'D')])
        G.add_nodes_from('GJK')
        assert_equal(sorted(G.nodes_iter()),
                     ['A', 'B', 'C', 'D', 'G', 'J', 'K'])
        assert_edges_equal(G.edges_iter(),
        [('A', 'B'), ('A', 'C'), ('B', 'D'), ('C', 'B'), ('C', 'D')])

        assert_equal(sorted([v for k,v in G.degree_iter()]),
                     [0, 0, 0, 2, 2, 3, 3])
        assert_equal(sorted(G.degree_iter(),key=str),
                     [('A', 2), ('B', 3), ('C', 3), ('D', 2), 
                      ('G', 0), ('J', 0), ('K', 0)])
        assert_equal(sorted(G.neighbors_iter('A')),['B', 'C'])
        assert_raises(nx.NetworkXError,G.neighbors_iter,'X')
        G.clear()
        assert_equal(nx.number_of_nodes(G),0)
        assert_equal(nx.number_of_edges(G),0) 

# 需要導入模塊: import networkx [as 別名]
# 或者: from networkx import number_of_nodes [as 別名]
def test_margulis_gabber_galil_graph():
    try:
        # Scipy is required for conversion to an adjacency matrix.
        # We also use scipy for computing the eigenvalues,
        # but this second use could be done using only numpy.
        import numpy as np
        import scipy.linalg
        has_scipy = True
    except ImportError as e:
        has_scipy = False
    for n in 2, 3, 5, 6, 10:
        g = margulis_gabber_galil_graph(n)
        assert_equal(number_of_nodes(g), n*n)
        for node in g:
            assert_equal(g.degree(node), 8)
            assert_equal(len(node), 2)
            for i in node:
                assert_equal(int(i), i)
                assert_true(0 <= i < n)
        if has_scipy:
            # Eigenvalues are already sorted using the scipy eigvalsh,
            # but the implementation in numpy does not guarantee order.
            w = sorted(scipy.linalg.eigvalsh(adjacency_matrix(g).A))
            assert_less(w[-2], 5*np.sqrt(2)) 

# 需要導入模塊: import networkx [as 別名]
# 或者: from networkx import number_of_nodes [as 別名]
def test_iterators(self):
        G = self.G()
        G.add_edges_from([('A', 'B'), ('A', 'C'), ('B', 'D'),
                          ('C', 'B'), ('C', 'D')])
        G.add_nodes_from('GJK')
        assert_equal(sorted(G.nodes()),
                     ['A', 'B', 'C', 'D', 'G', 'J', 'K'])
        assert_edges_equal(G.edges(),
                           [('A', 'B'), ('A', 'C'), ('B', 'D'), ('C', 'B'), ('C', 'D')])

        assert_equal(sorted([v for k, v in G.degree()]),
                     [0, 0, 0, 2, 2, 3, 3])
        assert_equal(sorted(G.degree(), key=str),
                     [('A', 2), ('B', 3), ('C', 3), ('D', 2),
                      ('G', 0), ('J', 0), ('K', 0)])
        assert_equal(sorted(G.neighbors('A')), ['B', 'C'])
        assert_raises(nx.NetworkXError, G.neighbors, 'X')
        G.clear()
        assert_equal(nx.number_of_nodes(G), 0)
        assert_equal(nx.number_of_edges(G), 0) 

# 需要導入模塊: import networkx [as 別名]
# 或者: from networkx import number_of_nodes [as 別名]
def test_margulis_gabber_galil_graph():
    try:
        # Scipy is required for conversion to an adjacency matrix.
        # We also use scipy for computing the eigenvalues,
        # but this second use could be done using only numpy.
        import numpy as np
        import scipy.linalg
        has_scipy = True
    except ImportError as e:
        has_scipy = False
    for n in 2, 3, 5, 6, 10:
        g = margulis_gabber_galil_graph(n)
        assert_equal(number_of_nodes(g), n * n)
        for node in g:
            assert_equal(g.degree(node), 8)
            assert_equal(len(node), 2)
            for i in node:
                assert_equal(int(i), i)
                assert_true(0 <= i < n)
        if has_scipy:
            # Eigenvalues are already sorted using the scipy eigvalsh,
            # but the implementation in numpy does not guarantee order.
            w = sorted(scipy.linalg.eigvalsh(adjacency_matrix(g).A))
            assert_less(w[-2], 5 * np.sqrt(2)) 

# 需要導入模塊: import networkx [as 別名]
# 或者: from networkx import number_of_nodes [as 別名]
def _modularity_generator(self):
        """Calculating the sparse modularity matrix."""
        degs = nx.degree(self._graph)
        e_count = self._graph.number_of_edges()
        n_count = self._graph.number_of_nodes()
        modularity_mat_shape = (n_count, n_count)
        indices_1 = np.array([edge[0] for edge in self._graph.edges()] + [edge[1] for edge in self._graph.edges()])
        indices_2 = np.array([edge[1] for edge in self._graph.edges()] + [edge[0] for edge in self._graph.edges()])
        scores = [1.0-(float(degs[e[0]]*degs[e[1]])/(2*e_count)) for e in self._graph.edges()]
        scores = scores + [1.0-(float(degs[e[1]]*degs[e[0]])/(2*e_count)) for e in self._graph.edges()]
        mod_matrix = coo_matrix((scores, (indices_1, indices_2)), shape=modularity_mat_shape)
        return mod_matrix 

# 需要導入模塊: import networkx [as 別名]
# 或者: from networkx import number_of_nodes [as 別名]
def _setup_matrices(self):
        """Creating parameter matrices and target matrices."""
        self._number_of_nodes = nx.number_of_nodes(self._graph)
        self._M = np.random.uniform(0, 1, (self._number_of_nodes, self.dimensions))
        self._U = np.random.uniform(0, 1, (self._number_of_nodes, self.dimensions))
        self._H = np.random.uniform(0, 1, (self._number_of_nodes, self.clusters))
        self._C = np.random.uniform(0, 1, (self.clusters, self.dimensions))
        self._B1 = nx.adjacency_matrix(self._graph, nodelist=range(self._graph.number_of_nodes()))
        self._B2 = self._modularity_generator()
        self._X = np.transpose(self._U)
        overlaps = self._B1.dot(self._B1)
        self._S = self._B1 + self.eta*self._B1*(overlaps) 

# 需要導入模塊: import networkx [as 別名]
# 或者: from networkx import number_of_nodes [as 別名]
def watts_strogatz_graph(N, deg, dia, dim, domain):
    '''
    Parameters of the graph:
    n (int) – The number of nodes
    k (int) – Each node is joined with its k nearest neighbors in a ring topology.
    p (float) – The probability of rewiring each edge

    Average Degree is solely decided by k
    Diameter depends on the value of p
    :return: Graph Object
    '''
    strt_time = time()

    p = 0.2

    G = nx.watts_strogatz_graph(n=N, k=deg, p=p)

    lcc, _ = graph_util.get_nk_lcc_undirected(G)

    best_G = lcc

    best_diam = nx.algorithms.diameter(best_G)

    best_avg_deg = np.mean(list(dict(nx.degree(best_G)).values()))

    end_time = time()

    print('Graph_Name: Watts_Strogatz_Graph')
    print('Num_Nodes: ', nx.number_of_nodes(best_G), ' Avg_Deg : ', best_avg_deg, ' Diameter: ', best_diam)
    print('TIME: ', end_time - strt_time)

    return best_G, best_avg_deg, best_diam

######################################################################## 

# 需要導入模塊: import networkx [as 別名]
# 或者: from networkx import number_of_nodes [as 別名]
def powerlaw_cluster_graph(N, deg, dia, dim, domain):
    '''
    Parameters of the graph:
    n (int) – the number of nodes
    m (int) – the number of random edges to add for each new node
    p (float,) – Probability of adding a triangle after adding a random edge
    Formula for m:  (m^2)- (Nm)/2 + avg_deg * (N/2) = 0  =>  From this equation we need to find m :
    p : Does not vary the average degree or diameter so much. : Higher value of p may cause average degree to overshoot intended average_deg
    so we give the control of average degree to parameter m: by setting a lower value of p: 0.1
    :return: Graph Object
    '''

    ## Calculating thof nodes: 10\nNumber of edges: 16\nAverage degree:   3.2000'
    strt_time = time()

    m = int(round((N - np.sqrt(N ** 2 - 4 * deg * N)) / 4))
    p = 0.2

    ## G at center:
    G = nx.powerlaw_cluster_graph(n=N, m=m, p=p)

    lcc, _ = graph_util.get_nk_lcc_undirected(G)

    best_G = lcc

    best_diam = nx.algorithms.diameter(best_G)

    best_avg_deg = np.mean(list(dict(nx.degree(best_G)).values()))


    end_time = time()
    print('Graph_Name: powerlaw_cluster_graph')
    print('Num_Nodes: ', nx.number_of_nodes(best_G), ' Avg_Deg : ', best_avg_deg, ' Diameter: ', best_diam)
    print('TIME: ', end_time - strt_time)
    return best_G, best_avg_deg, best_diam

##################################################################### 

# 需要導入模塊: import networkx [as 別名]
# 或者: from networkx import number_of_nodes [as 別名]
def get_clustering_coeff(edge_list):
    G = nx.from_edgelist(edgelist=edge_list)
    clust_coeff = nx.average_clustering(G)
    # print(nx.number_of_nodes(G), ' : ',clust_coeff)
    return clust_coeff 

# 需要導入模塊: import networkx [as 別名]
# 或者: from networkx import number_of_nodes [as 別名]
def test_size(self):
        num_nodes = nx.number_of_nodes(self.graph)
        self.assertEqual(num_nodes, 3971, "Should be 3971.")
        num_edges = nx.number_of_edges(self.graph)
        self.assertEqual(num_edges, 28202, "Should be 28202.") 

# 需要導入模塊: import networkx [as 別名]
# 或者: from networkx import number_of_nodes [as 別名]
def write_summary_file(self,path,append=True):
        '''
        Writes summary information about this network to a file
        
        **Optional Arguments**
         - *append* = True if summary information should be appended to the file. If so the file is written as a csv spreadsheet. 
           Default is true. If False is passed, a single, detailed summary is written for this network.
        '''
        if append: #write summary information in spreadsheet formant
            exists = os.path.exists(path)
            f = open(path,"a")
            
            if not exists: #write header
                f.write("name,#nodes,#edges\n") #todo add other stuff here
                
            #write data
            f.write("%s,%s,%s\n" % (self.basename,self.graph.number_of_nodes(),self.graph.number_of_edges()))
        
            f.close()
        else: #write detailed information
            import networkx as nx
            
            f = open(path,"w")
            f.write("Summary:")
            f.write("Name: %s\n" % self.basename)
            f.write("#nodes: %s\n" % self.graph.number_of_nodes())
            f.write("#edges: %s\n" % self.graph.number_of_edges())
            f.write("Detail")
            f.write("Degree sequence: %s" % str(list(nx.degree(self.graph).values())))
            f.write("Node list: %s" % str(self.graph.nodes(data=False)))
            f.write("Edge list: %s" % str(self.graph.edges(data=False)))
            f.write("Node attributes: %s" % str(self.graph.nodes(data=True)))
            f.write("Edge attributes: %s" % str(self.graph.edges(data=True)))
            
            f.close() 

# 需要導入模塊: import networkx [as 別名]
# 或者: from networkx import number_of_nodes [as 別名]
def __len__(self):
        """
        :return: the number of nodes in the graph
        """
        return nx.number_of_nodes(self.graph) 

# 需要導入模塊: import networkx [as 別名]
# 或者: from networkx import number_of_nodes [as 別名]
def skeleton_to_swc(skeleton, offset, resolution):
    import networkx as nx

    g = nx.Graph()
    g.add_nodes_from(skeleton.nodes())
    g.add_edges_from((e.u, e.v) for e in skeleton.edges())

    # Find a directed tree for mapping to a skeleton.
    if nx.number_of_nodes(g) > 1:
        # This discards cyclic edges in the graph.
        t = nx.bfs_tree(nx.minimum_spanning_tree(g), g.nodes()[0])
    else:
        t = nx.DiGraph()
        t.add_nodes_from(g)
    # Copy node attributes
    for n in t.nodes_iter():
        loc = skeleton.locations(n)
        # skeletopyze is z, y, x (as it should be).
        loc = np.array(loc)
        loc = np.multiply(loc + offset, resolution)
        t.node[n].update({'x': loc[0],
                          'y': loc[1],
                          'z': loc[2],
                          'radius': skeleton.diameters(n) / 2.0})

    # Set parent node ID
    for n, nbrs in t.adjacency_iter():
        for nbr in nbrs:
            t.node[nbr]['parent_id'] = n
            if 'radius' not in t.node[nbr]:
                t.node[nbr]['radius'] = -1

    return [[
        node_id,
        0,
        n['x'], n['y'], n['z'],
        n['radius'],
        n.get('parent_id', -1)] for node_id, n in t.nodes(data=True)]