view SmallWorldGraph.py @ 33:cfb7f28678c7

bisection() wasn't returning the index like it should. Added some simple tests.
author Brian Neal <bgneal@gmail.com>
date Wed, 09 Jan 2013 20:11:53 -0600
parents f6073c187926
children 305cc03c2750
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"""This module contains the SmallWorldGraph class for 4.4, exercise 4.

"""
import heapq
import itertools
import random

from Graph import Edge
from RandomGraph import RandomGraph


INFINITY = float('Inf')

class SmallWorldGraph(RandomGraph):
    """A small world graph for 4.4, exercise 4 in Think Complexity."""

    def __init__(self, vs, k, p):
        """Create a small world graph. Parameters:
            vs - a list of vertices
            k - regular graph parameter k: the number of edges between vertices
            p - probability for rewiring.

        First a regular graph is created from the list of vertices and parameter
        k, which specifies how many edges each vertex should have. Then the
        rewire() method is called with parameter p to rewire the graph according
        to the algorithm by Watts and Strogatz.

        """
        super(SmallWorldGraph, self).__init__(vs=vs)
        self.add_regular_edges(k)
        self.rewire(p)

        # give each edge a default length of 1; this is used by the
        # shortest_path_tree() method
        for e in self.edges():
            e.length = 1

    def rewire(self, p):
        """Assuming the graph is initially a regular graph, rewires the graph
        using the Watts and Strogatz algorithm.

        """
        # We iterate over the edges in a random order:
        edges = self.edges()
        random.shuffle(edges)
        vertices = self.vertices()

        for e in edges:
            if random.random() < p:
                v, w = e    # remember the 2 vertices this edge connected
                self.remove_edge(e)     # remove from graph

                # pick another vertex to connect to v; duplicate edges are
                # forbidden
                while True:
                    x = random.choice(vertices)
                    if v is not x and not self.get_edge(v, x):
                        self.add_edge(Edge(v, x))
                        break

    def clustering_coefficient(self):
        """Compute the clustering coefficient for this graph as defined by Watts
        and Strogatz.

        """
        cv = {}
        for v in self:
            # consider a node and its neighbors
            nodes = self.out_vertices(v)
            nodes.append(v)

            # compute the maximum number of possible edges between these nodes
            # if they were all connected to each other:
            n = len(nodes)
            if n == 1:
                # edge case of only 1 node; handle this case to avoid division
                # by zero in the general case
                cv[v] = 1.0
                continue

            possible = n * (n - 1) / 2.0

            # now compute how many edges actually exist between the nodes
            actual = 0
            for x, y in itertools.combinations(nodes, 2):
                if self.get_edge(x, y):
                    actual += 1

            # the fraction of actual / possible is this nodes C sub v value
            cv[v] = actual / possible

        # The clustering coefficient is the average of all C sub v values
        if len(cv):
            return sum(cv.values()) / float(len(cv))
        return 0.0

    def shortest_path_tree(self, source, hint=None):
        """Finds the length of the shortest path from the source vertex to all
        other vertices in the graph. This length is stored on the vertices as an
        attribute named 'dist'. The algorithm used is Dijkstra's.

        hint: if provided, must be a dictionary mapping tuples to already known
        shortest path distances. This can be used to speed up the algorithm.

        """
        if not hint:
            hint = {}

        for v in self.vertices():
            v.dist = hint.get((source, v), INFINITY)
        source.dist = 0

        queue = [v for v in self.vertices() if v.dist < INFINITY]
        sort_flag = True
        while len(queue):

            if sort_flag:
                queue.sort(key=lambda v: v.dist)
                sort_flag = False

            v = queue.pop(0)

            # for each neighbor of v, see if we found a new shortest path
            for w, e in self[v].iteritems():
                d = v.dist + e.length
                if d < w.dist:
                    w.dist = d
                    queue.append(w)
                    sort_flag = True

    def shortest_path_tree2(self, source):
        """Finds the length of the shortest path from the source vertex to all
        other vertices in the graph. This length is stored on the vertices as an
        attribute named 'dist'. The algorithm used is Dijkstra's with a Heap
        used to sort/store pending nodes to be examined.

        """
        for v in self.vertices():
            v.dist = INFINITY
        source.dist = 0

        queue = []
        heapq.heappush(queue, (0, source))
        while len(queue):

            _, v = heapq.heappop(queue)

            # for each neighbor of v, see if we found a new shortest path
            for w, e in self[v].iteritems():
                d = v.dist + e.length
                if d < w.dist:
                    w.dist = d
                    heapq.heappush(queue, (d, w))

    def all_pairs_floyd_warshall(self):
        """Finds the shortest paths between all pairs of vertices using the
        Floyd-Warshall algorithm.

        http://en.wikipedia.org/wiki/Floyd-Warshall_algorithm

        """
        vertices = self.vertices()
        dist = {}
        for i in vertices:
            for j in vertices:
                if i is j:
                    dist[i, j] = 0.0
                else:
                    e = self.get_edge(i, j)
                    dist[i, j] = e.length if e else INFINITY

        for k in vertices:
            for i in vertices:
                for j in vertices:
                    d_ik = dist[i, k]
                    d_kj = dist[k, j]
                    new_cost = d_ik + d_kj
                    if new_cost < dist[i, j]:
                        dist[i, j] = new_cost

        return dist

    def big_l(self):
        """Computes the "big-L" value for the graph as per Watts & Strogatz.

        L is defined as the number of edges in the shortest path between
        two vertices, averaged over all vertices.

        Uses the shortest_path_tree() method, called once for every node.

        """
        d = {}
        for v in self.vertices():
            self.shortest_path_tree(v, d)
            t = [((w, v), w.dist) for w in self.vertices() if v is not w]
            d.update(t)

        if len(d):
            return sum(d.values()) / float(len(d))
        return 0.0

    def big_l2(self):
        """Computes the "big-L" value for the graph as per Watts & Strogatz.

        L is defined as the number of edges in the shortest path between
        two vertices, averaged over all vertices.

        Uses the all_pairs_floyd_warshall() method.

        """
        dist = self.all_pairs_floyd_warshall()
        vertices = self.vertices()
        result = [dist[i, j] for i in vertices for j in vertices if i is not j]

        if len(result):
            return sum(result) / float(len(result))
        return 0.0

    def big_l3(self):
        """Computes the "big-L" value for the graph as per Watts & Strogatz.

        L is defined as the number of edges in the shortest path between
        two vertices, averaged over all vertices.

        Uses the shortest_path_tree2() method, called once for every node.

        """
        d = {}
        for v in self.vertices():
            self.shortest_path_tree2(v)
            t = [((v, w), w.dist) for w in self.vertices() if v is not w]
            d.update(t)

        if len(d):
            return sum(d.values()) / float(len(d))
        return 0.0