view Graph.py @ 24:5c2c4ce095ef

A stab at the L(p)/L(0) plot. I still don't quite get how the graphs in the Watts and Strogatz paper were generated. My results have basically the same shape, but don't converge to 0. I'm not sure how this is possible if the rewire function does not remove edges.
author Brian Neal <bgneal@gmail.com>
date Thu, 03 Jan 2013 18:41:13 -0600
parents 84e183b40c63
children 10db8c3a6b83
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""" Code example from Complexity and Computation, a book about
exploring complexity science with Python.  Available free from

http://greenteapress.com/complexity

Copyright 2011 Allen B. Downey.
Distributed under the GNU General Public License at gnu.org/licenses/gpl.html.
"""
import itertools
from collections import deque


class GraphError(Exception):
    """Exception for Graph errors"""
    pass


class Vertex(object):
    """A Vertex is a node in a graph."""

    def __init__(self, label=''):
        self.label = label

    def __repr__(self):
        """Returns a string representation of this object that can
        be evaluated as a Python expression."""
        return 'Vertex(%s)' % repr(self.label)

    __str__ = __repr__
    """The str and repr forms of this object are the same."""


class Edge(tuple):
    """An Edge is a list of two vertices."""

    def __new__(cls, *vs):
        """The Edge constructor takes two vertices."""
        if len(vs) != 2:
            raise ValueError, 'Edges must connect exactly two vertices.'
        return tuple.__new__(cls, vs)

    def __repr__(self):
        """Return a string representation of this object that can
        be evaluated as a Python expression."""
        return 'Edge(%s, %s)' % (repr(self[0]), repr(self[1]))

    __str__ = __repr__
    """The str and repr forms of this object are the same."""


class Graph(dict):
    """A Graph is a dictionary of dictionaries.  The outer
    dictionary maps from a vertex to an inner dictionary.
    The inner dictionary maps from other vertices to edges.

    For vertices a and b, graph[a][b] maps
    to the edge that connects a->b, if it exists."""

    def __init__(self, vs=None, es=None):
        """Creates a new graph.
        vs: list of vertices;
        es: list of edges.
        """
        if vs:
            for v in vs:
                self.add_vertex(v)

        if es:
            for e in es:
                self.add_edge(e)

    def add_vertex(self, v):
        """Add a vertex to the graph."""
        self[v] = {}

    def add_edge(self, e):
        """Adds and edge to the graph by adding an entry in both directions.

        If there is already an edge connecting these Vertices, the
        new edge replaces it.
        """
        v, w = e
        self[v][w] = e
        self[w][v] = e

    def get_edge(self, v, w):
        """Returns the edge object that exists between the two vertices v & w,
        or None if no such edge exists.

        """
        try:
            return self[v][w]
        except KeyError:
            return None

    def remove_edge(self, e):
        """Removes the edge e from the graph."""

        v, w = e
        del self[v][w]
        del self[w][v]

    def vertices(self):
        """Returns a list of the vertices in the graph."""

        return self.keys()

    def edges(self):
        """"Returns a list of the edges in the graph."""

        edge_set = set()
        for d in self.itervalues():
            edge_set.update(d.itervalues())

        return list(edge_set)

    def out_vertices(self, v):
        """Returns a list of vertices that are adjacent to the given vertex v.

        """
        return self[v].keys()

    def out_edges(self, v):
        """Returns a list of edges connected to a given vertex v."""

        return self[v].values()

    def remove_all_edges(self):
        """Removes all edges in the graph."""
        for v in self.iterkeys():
            self[v] = {}

    def add_all_edges(self):
        """Makes the graph complete by adding edges between all pairs of
        vertices.

        """
        # Clear all edges first
        self.remove_all_edges()

        # For each combination of 2 vertices, create an edge between them:
        for v, w in itertools.combinations(self.iterkeys(), 2):
            self.add_edge(Edge(v, w))

    def add_regular_edges(self, k):
        """Makes the graph regular by making every vertex have k edges.

        It is not always possible to create a regular graph with a given degree.
        If a graph has n vertices, then a regular graph can be constructed with
        degree k if n >= k + 1 and n * k is even. If these conditions are not
        met a GraphError exception is raised.

        """
        n = len(self.vertices())
        if n < k + 1:
            raise GraphError("Can't make a regular graph with degree >= number"
                             " of vertices")
        if (n * k) % 2 != 0:
            raise GraphError("Can't make a regular graph of degree k and"
                             " order n where k * n is odd")

        # Remove all edges first
        self.remove_all_edges()

        if k % 2 != 0:      # if k is odd
            self._add_regular_edges_even(k - 1)
            self._add_regular_edges_odd()
        else:
            self._add_regular_edges_even(k)

    def _add_regular_edges_even(self, k):
        """Make a regular graph with degree k. k must be even."""

        vs = self.vertices()
        vs2 = vs * 2

        for i, v in enumerate(vs):
            for j in range(1, k / 2 + 1):
                w = vs2[i + j]
                self.add_edge(Edge(v, w))

    def _add_regular_edges_odd(self):
        """Adds an extra edge across the graph to finish off a regular graph
        with odd degree. The number of vertices must be even.

        """
        vs = self.vertices()
        vs2 = vs * 2
        n = len(vs)

        for i in range(n / 2):
            v = vs2[i]
            w = vs2[i + n / 2]
            self.add_edge(Edge(v, w))

    def bfs(self, start, visit_func=None):
        """Perform a breadth first search starting at node start.

        The function visit_func, if supplied, is invoked on each node.

        The set of visited nodes is returned.

        """
        visited = set()

        # Create a work queue consisting initially of the starting node
        queue = deque([start])

        while queue:
            # retrieve first item from the queue
            v = queue.popleft()

            if v in visited:
                continue            # Skip this one if we've seen it before

            # Mark it as visited and invoke user's function on it
            visited.add(v)
            if visit_func:
                visit_func(v)

            # Add the adjacent neigbors to the node to the queue
            queue.extend(c for c in self.out_vertices(v) if c not in visited)

        return visited

    def is_connected(self):
        """Returns True if the graph is connected (there is a path from every
        node to every other node) and False otherwise.

        """
        vs = self.vertices()
        if len(vs):
            visited = self.bfs(vs[0])
            # See if all nodes have been visited
            return len(vs) == len(visited)

        return False        # Graph is empty


def main(script, *args):
    import pprint

    v = Vertex('v')
    print v
    w = Vertex('w')
    print w
    e = Edge(v, w)
    print e
    g = Graph([v,w], [e])
    pprint.pprint(g)

    print "g.get_edge(v, w): ", g.get_edge(v, w)
    x = Vertex('x')
    print "g.get_edge(v, x): ", g.get_edge(v, x)

    g.remove_edge(e)
    pprint.pprint(g)

    print "vertices: ", g.vertices()
    print "edges: ", g.edges()

    g.add_edge(e)
    u = Vertex('u')
    e1 = Edge(u, v)
    e2 = Edge(u, w)
    g.add_vertex(u)
    g.add_edge(e1)
    g.add_edge(e2)
    print "Adding vertex u and edges:"
    pprint.pprint(g)
    print "vertices: ", g.vertices()
    print "edges: ", g.edges()

    print "Out vertices for v: ", g.out_vertices(v)
    print "Out edges for v: ", g.out_edges(v)

    x = Vertex('x')
    g.add_vertex(x)
    g.add_all_edges()
    pprint.pprint(g)

    print "g is connected?", g.is_connected()
    edges = g.out_edges(v)
    for e in edges:
        g.remove_edge(e)
    pprint.pprint(g)
    print "g is connected?", g.is_connected()

    # Isolate v and check is_connected() again


if __name__ == '__main__':
    import sys
    main(*sys.argv)