genet / test_networkx.py

#!/usr/bin/env python
################################################################################
# $Id$
################################################################################
# Copyright (c) 2008 Santiago Paya Miralta <santiagopm::wanadoo.es>
#
# This file is part of mine.
#
# Mine is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
################################################################################

import pylab as P
import networkx as NX
from test_data import *

################################################################################
# Level 00
#
G00 = NX.XGraph(name='Level 00', multiedges=True, selfloops=True)

for r in db.query("SELECT * FROM gn_00_edges").dictresult():
    G00.add_edges_from([(r['idna'], r['idnb'], r['id'])])
    
# May be there are isolated nodes.
for r in db.query("SELECT * FROM gn_00_nodes").dictresult():
    G00.add_node(r['id'])

print 'G00 nodes:', G00.nodes()
print 'G00 edges:', G00.edges()

pos = NX.spring_layout(G00)
NX.draw_networkx(G00, pos)
P.show()

P.savefig("genet_L0.png")
print "Wrote genet_L0.png"

################################################################################
# Level 1
#
G101 = NX.XGraph(name='Infrastructure', multiedges=True, selfloops=True)

for e in genet.EL01:
    print e.idnA.id, e.idnB.id, e.id
    G101.add_edge(e.idnA.id, e.idnB.id, e.id)

# May be there are isolated nodes.
for n in genet.NL01:
    print n.id
    G101.add_node(n.id)

print 'G101 nodes:', G101.nodes()
print 'G101 edges:', G101.edges()

pos = NX.spring_layout(G101)
NX.draw_networkx(G101, pos)
P.show()

P.savefig("genet_L101.png")
print "Wrote genet_L101.png"

################################################################################
# Fancy draw & DOT
#
G102 = NX.XGraph(name='Infrastructure', multiedges=True, selfloops=True)

for e in genet.EL01:
    print e.idnA.id, e.idnB.id, e.id
    G102.add_edges_from([(e.idnA.id, e.idnB.id, e)])

# May be there are isolated nodes.
for n in genet.NL01:
    print n.id
    G102.add_node(n.id)

pos = NX.spring_layout(G102)
NX.draw_networkx_nodes(G102, pos, node_color='g', node_size=500)
NX.draw_networkx_edges(G102, pos, width=8.0, alpha=0.5, edge_color='g')
labels={}
labels[G102.nodes()[0]]='$\pi$'
labels[G102.nodes()[1]]='$\mu$'
labels[G102.nodes()[2]]='$\epsilon$'
NX.draw_networkx_labels(G102, pos, labels=labels, 
                        font_color='w', font_family='sans-serif', 
                        font_size=12)
P.show()

P.savefig("genet_L102.png")
print "Wrote genet_L102.png"

"""
With the dot file can do in the system:
$ neato -Tpng file.dot > file.png
$ eog file.png
"""
NX.write_dot(G102,"genet_L102.dot")
print "Wrote genet_L102.dot"

################################################################################
# Paths
#
"""
The Dijkstra algorithms seems not to support multiedge graphs, because
the NX._Graph.get_edge() function returns a list.

Line 438 in /var/lib/python-support/python2.5/networkx/path.py, function
single_source_dijkstra(G,source,target), should be:

...
if G.multiedges:
    vw_dist = dist[v] + reduce(min, G.get_edge(v,w))
else:
    vw_dist = dist[v] + G.get_edge(v,w)
...

or may be defining an appropiate function get_edge(v, w) depending on
the multiedges property before the loooop. 

Example:

>>> l = [0.23, 7, 0.1]
>>> print reduce(min, l)
0.1

"""
G103 = NX.XGraph(name='Infrastructure', multiedges=False, selfloops=True)

for e in genet.EL01:
    # When creating the graph with edges (dont worry about isolated nodes)
    # the information passed is the edges' weight. 
    print e.idnA.id, e.idnB.id, e.id
    G103.add_edge(e.idnA.id, e.idnB.id, e.iddown.len)

paths = NX.single_source_shortest_path_length(G103, G103.nodes()[0], 1000)
print paths

paths = NX.single_source_shortest_path(G103, G103.nodes()[0], 1000)
print paths

path = NX.shortest_path(G103, 
                        G103.nodes()[0], 
                        G103.nodes()[NX.number_of_nodes(G103)-1])
print path

paths = NX.single_source_dijkstra_path_length(G103, G103.nodes()[0])
print paths
print 'The', G103.edges()[0], 'weight is:', G103.edges()[0][2]

paths = NX.single_source_dijkstra_path(G103, G103.nodes()[0])
print paths
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