Mercurial > public > think_complexity
view Graph.py @ 35:10db8c3a6b83
Chapter 5.5, exercise 6, #2: plot P(k) vs. k for a WS graph.
author | Brian Neal <bgneal@gmail.com> |
---|---|
date | Wed, 09 Jan 2013 20:51:16 -0600 |
parents | 84e183b40c63 |
children | 305cc03c2750 |
line wrap: on
line source
""" 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, Counter 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 get_p(self): """This method returns a dictionary of probabilities where each key is the connectivity k and the value is the probability [0-1] for this graph. """ # First, for each vertex, count up how many neighbors it has vs = self.vertices() c = Counter() for v in vs: n = len(self.out_vertices(v)) c[n] += 1 n = len(vs) if n > 0: for k in c: c[k] = float(c[k]) / n return c 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)