def node_betweenness_centrality(tree):
'''Returns betweenness centrality of all nodes in tree.
INPUT
-----
tree : networkx graph
'''
utils.check_spanning_tree(tree)
return nx.betweenness_centrality(tree)
def tree_diameter(tree):
'''Returns largest distance between any two nodes in tree.
INPUT
-----
tree : networkx graph
'''
utils.check_spanning_tree(tree)
M = len(tree.edges())
return max(max(nx.shortest_path_length(tree).values()).values()) / M
def tree_degree_divergence(tree):
'''Returns kappa, a metric representing the broadness of the degree distribution
of the tree.
INPUT
-----
tree : networkx graph
'''
utils.check_spanning_tree(tree)
degrees = np.array(node_degree(tree).values())
return np.mean(degrees ** 2) / np.mean(degrees)
def tree_leaf_number(tree):
'''Returns number of leaves of tree.
INPUT
-----
tree : networkx graph
'''
utils.check_spanning_tree(tree)
degrees = np.array(nx.degree(tree).values())
M = len(tree.edges())
return len(degrees[degrees == 1]) / M
def tree_heirarchy(tree):
'''Returns a metric representing the trade-off between integrating and overload
of central nodes of the tree.
INPUT
-----
tree : networkx graph
'''
utils.check_spanning_tree(tree)
n_leaf = tree_leaf_number(tree)
M = len(tree.edges())
bc_max = max(node_betweenness_centrality(tree).values())
return n_leaf / (2 * M * bc_max)
def tree_radius(tree, norm=False):
'''Returns the value of the node with the smallest average shortest path length.
INPUT
-----
tree : networkx graph
'''
utils.check_spanning_tree(tree)
if norm:
M = len(tree.edges())
return tree_radius(tree) / M
else:
return min(node_eccentricity(tree).values())
def tree_max_degree(tree, norm=False):
'''Returns maximum degree centrality of tree.
INPUT
-----
tree : networkx graph
'''
utils.check_spanning_tree(tree)
if norm:
M = len(tree.edges())
return tree_max_degree(tree) / M
else:
return max(node_degree(tree).values())
def node_degree(tree, norm=False):
'''Returns degree centrality of all nodes in tree.
INPUT
-----
tree : networkx graph
'''
utils.check_spanning_tree(tree)
if norm:
M = len(tree.edges())
return node_degree(tree) / M
else:
return nx.degree(tree)
def tree_eccentricity_difference(tree, norm=False):
'''Returns the difference in values between the nodes with the smallest and
largest average shortest path lengths.
INPUT
-----
tree : networkx graph
'''
utils.check_spanning_tree(tree)
ecc = node_eccentricity(tree).values()
if norm:
M = len(tree.edges())
return max(ecc / M) - min(ecc / M)
else:
return max(ecc) - min(ecc)
def node_eccentricity(tree, norm=False):
'''Returns average shortest path length of all nodes in tree.
INPUT
-----
tree : networkx graph
'''
utils.check_spanning_tree(tree)
lengths = nx.shortest_path_length(tree)
avg_lengths = []
for n in tree.nodes():
lengths[n].pop(n)
avg_lengths.append(np.mean(lengths[n].values()))
if norm:
M = len(tree.edges())
return node_eccentricity(tree) / M
else:
return dict(zip(range(len(avg_lengths)), avg_lengths))
def kruskals_minimum_spanning_tree(g):
''' Find minimum spanning tree based on distance edge attribute.
Parameters
----------
g: weighted undirected networkx graph
Returns
-------
mst_g : weighted undirected networkx graph
mimimum spanning tree graph
mst_mat : ndarray
minimum spanning tree adjacency matrix
'''
if not g.get_edge_data(0,1)['distance']:
utils.add_distance_edge_attr(g)
mst_g = nx.minimum_spanning_tree(g, weight='distance')
mst_mat = nx.to_numpy_matrix(mst_g)
utils.check_spanning_tree(mst_g)
return mst_g, mst_mat
def prims_minimum_spanning_tree(input_g, seed=None):
"""
Prim's Algorithm : Finds order of nodes added to minimum spanning tree.
Parameters
----------
input_g : weighted networkx graph
seed : int
starting seed node of networkx graph
if None, seed node randomly selected
Returns
-------
mst_g : networkx graph
minimum spanning tree graph
curr_nodes : list
order nodes added to the tree
"""
if not seed:
seed = int(np.random.choice(input_g.nodes(),1))
if not input_g.get_edge_data(0,1)['distance']:
utils.add_distance_edge_attr(input_g)
g = input_g.copy()
curr_nodes, curr_edges = [seed], []
nodes = g.nodes()
while len(curr_nodes) < len(nodes):
curr_close, curr_dist, curr_edge = 1, np.inf, (0, 0)
for node in curr_nodes:
for edge in g.edges(node, data = True):
if edge[1] in curr_nodes:
continue
else:
if edge[2]['distance'] < curr_dist:
g.remove_edge(edge[0], edge[1])
curr_close, curr_dist, curr_edge = edge[1], edge[2]['distance'], edge
curr_nodes.append(curr_close)
curr_edges.append(curr_edge)
mst_g = nx.Graph()
mst_g.add_edges_from(curr_edges)
utils.check_spanning_tree(mst_g)
return mst_g, curr_nodes