Kitware TechTip 04-03-2013 Part 1: Graph construction from a binary adjacency matrix and a vertex label file.

kw-techtip-04-03-2013-p1.py

"""kw-techtip-04-03-2013-p1.py
 
Simple example of how to construct a graph from a {0,1} adjacency matrix and a
file with vertex labels.
 
Usage
-----
 
$ python kw-techtip-04-03-2013-p1.py <AdjacencyFile> <LabelFile>
 
Example 
-------
Adjacency file (3 vertices):
 
0 1 0 
1 0 0
0 1 0
 
Corresponding label file:
2
1
2
"""
 
 
import sys
import pickle
import numpy as np
import networkx as nx
import matplotlib.pyplot as plt
 
 
# Load adjacency information into numpy ndarray
adj_info = np.genfromtxt(sys.argv[1], skip_header=0)
 
# Build graph from adjacency matrix ... 
G = nx.Graph(adj_info)
 
# Load label information
labels = np.genfromtxt(sys.argv[2], skip_header=0)
        
# Set vertex labels
for idx, l in enumerate(labels):
    G.node[idx]['type'] = int(l)
 
# Iterate through nodes and show vertex labels
for n in G.nodes():
    print "Node : %d [type=%d]" % (n, int(G.node[n]['type']))
 
# Iterate through edges ...
for e in G.edges():
    print e
 
# Visualize with matplotlib
plt.title("mutag_001")
nx.draw(G,node_color=range(len(G)))
plt.savefig("/tmp/mutag_001.png")
#plt.show()

pickle.dump(G,open("/tmp/graph.txt","w"))