graphTest.py

#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Tue Nov  1 00:01:20 2016

@author: jpdjere
"""

from networkx import *

G = lollipop_graph(4,6)

pathlengths=[]

print("source vertex {target:length, }")
for v in G.nodes():
    spl=single_source_shortest_path_length(G,v)
    print('%s %s' % (v,spl))
    for p in spl.values():
        pathlengths.append(p)

print('')
print("average shortest path length %s" % (sum(pathlengths)/len(pathlengths)))

# histogram of path lengths
dist={}
for p in pathlengths:
    if p in dist:
        dist[p]+=1
    else:
        dist[p]=1

print('')
print("length #paths")
verts=dist.keys()
for d in sorted(verts):
    print('%s %d' % (d,dist[d]))

print("radius: %d" % radius(G))
print("diameter: %d" % diameter(G))
print("eccentricity: %s" % eccentricity(G))
print("center: %s" % center(G))
print("periphery: %s" % periphery(G))
print("density: %s" % density(G))

import sys
G=grid_2d_graph(5,5)  # 5x5 grid
try: # Python 2.6+
    write_adjlist(G,sys.stdout) # write adjacency list to screen
except TypeError: # Python 3.x
    write_adjlist(G,sys.stdout.buffer) # write adjacency list to screen
# write edgelist to grid.edgelist
write_edgelist(G,path="grid.edgelist",delimiter=":")
# read edgelist from grid.edgelist
H=read_edgelist(path="grid.edgelist",delimiter=":")


def atlas6():
    """ Return the atlas of all connected graphs of 6 nodes or less.
        Attempt to check for isomorphisms and remove.
    """

    Atlas = graph_atlas_g()[0:208] # 208
    # remove isolated nodes, only connected graphs are left
    U = nx.Graph() # graph for union of all graphs in atlas
    for G in Atlas:
        zerodegree = [n for n in G if G.degree(n)==0]
        for n in zerodegree:
            G.remove_node(n)
        U = nx.disjoint_union(U, G)

    # list of graphs of all connected components
    C = nx.connected_component_subgraphs(U)

    UU = nx.Graph()
    # do quick isomorphic-like check, not a true isomorphism checker
    nlist = [] # list of nonisomorphic graphs
    for G in C:
        # check against all nonisomorphic graphs so far
        if not iso(G, nlist):
            nlist.append(G)
            UU = nx.disjoint_union(UU, G) # union the nonisomorphic graphs
    return UU

def iso(G1, glist):
    """Quick and dirty nonisomorphism checker used to check isomorphisms."""
    for G2 in glist:
        if isomorphic(G1, G2):
            return True
    return False


if __name__ == '__main__':
    G=atlas6()

    print("graph has %d nodes with %d edges"\
          %(nx.number_of_nodes(G), nx.number_of_edges(G)))
    print(nx.number_connected_components(G), "connected components")

    try:
        import pygraphviz
        from networkx.drawing.nx_agraph import graphviz_layout
    except ImportError:
        try:
            import pydotplus
            from networkx.drawing.nx_pydot import graphviz_layout
        except ImportError:
            raise ImportError("This example needs Graphviz and either "
                              "PyGraphviz or PyDotPlus")

    import matplotlib.pyplot as plt
    plt.figure(1, figsize=(8, 8))
    # layout graphs with positions using graphviz neato
    pos = graphviz_layout(G, prog="neato")
    # color nodes the same in each connected subgraph
    C = nx.connected_component_subgraphs(G)
    for g in C:
        c = [random.random()] * nx.number_of_nodes(g) # random color...
        nx.draw(g,
             pos,
             node_size=40,
             node_color=c,
             vmin=0.0,
             vmax=1.0,
             with_labels=False
             )
    plt.savefig("atlas.png", dpi=75)