Function iamstk_and

Synopse

iamstk_and - Find a minimum spanning tree in a weighted graph.

  • g = iamstk_and(W, A)
    • Output
      • g: tuple, (T, weights). T, with shape=(n,2), is a list of the MST edges, and weights is an array of weights for each MST edge.
    • Input
      • W: ndarray, 2D, square. Weighted graph matrix. If A is not specified, W must have value :eq:+Infty where there are no relations.
      • A: ndarray, 2D, square, boolean (optional). Adjacency matrix with 1/True where there is an edge/arc, and 0/False where there is not.

Description

Function iamstk_and() find a minimum spanning tree in a weighted graph. This implementation is based on Kruskal's MST algorithm.

Function Code

 1 def iamstk_and(W, A=None):
 2     from numpy import triu, arange, logical_not, argsort, array, uint32
 3 
 4     if A is None:
 5         A = W!=float('inf')
 6 
 7     n,_ = A.shape
 8     A = triu(A)
 9     orig, dest = A.nonzero()
10     weights = W[orig,dest]
11     edgeSeq = argsort(weights)
12     labels = arange(n)
13     n -= 1
14     T = []
15     for i in edgeSeq:
16         u,v = (orig[i],dest[i])
17         if not labels[u]==labels[v]:
18             T.append([u,v,weights[i]])
19             labels[labels==labels[v]] = labels[u]
20             if len(T)==n:
21                 break
22     T = array(T)
23     return (T[:,:2].astype(uint32), T[:,2])

Examples

In a small weighted graph.

 1 from iamstk_and import iamstk_and
 2 from time import time
 3 from numpy import array, zeros
 4 
 5 A = array( [[0,1,1,0,0,0,0,0,0],
 6             [1,0,0,0,0,0,0,1,0],
 7             [1,0,0,1,1,0,0,1,0],
 8             [0,0,1,0,0,0,0,1,0],
 9             [0,0,1,0,0,1,1,0,0],
10             [0,0,0,0,1,0,1,0,1],
11             [0,0,0,0,1,1,0,0,1],
12             [0,1,1,1,0,0,0,0,0],
13             [0,0,0,0,0,1,1,0,0]], dtype=byte)
14 
15 W = array( [[0,1,2,0,0,0,0,0,0],
16             [1,0,0,0,0,0,0,3,0],
17             [2,0,0,4,5,0,0,6,0],
18             [0,0,4,0,0,0,0,7,0],
19             [0,0,5,0,0,8,9,0,0],
20             [0,0,0,0,8,0,1,0,2],
21             [0,0,0,0,9,1,0,0,3],
22             [0,3,6,7,0,0,0,0,0],
23             [0,0,0,0,0,2,3,0,0]], dtype=byte)
24 
25 t = time()
26 T, weights = iamstk_and(W,A)
27 print 'MST edges:\n', T
28 print 'MST weight: ', sum(weights)
29 print 'Computational time: ', time() - t
MST edges:
[[0 1]
 [5 6]
 [0 2]
 [5 8]
 [1 7]
 [2 3]
 [2 4]
 [4 5]]
MST weight:  26
Computational time:  0.00126886367798

Performance Tests

This function is tested by running the tests defined at the page MST Test.

/usr/local/lib/python2.6/dist-packages/scikits/__init__.py:1: UserWarning: Module dateutil was already imported from /usr/local/lib/python2.6/dist-packages/matplotlib-1.1.0-py2.6-linux-x86_64.egg/dateutil/__init__.pyc, but /usr/lib/pymodules/python2.6 is being added to sys.path
__import__('pkg_resources').declare_namespace(__name__)

System Message: WARNING/2 (<string>, line 114)

Definition list ends without a blank line; unexpected unindent.

<type 'numpy.float64'>

gravando arquivo: /home/rubens/www/media/Attachments/iaOPF/iamstk_and/testperf.pkl

Autor Funcao A simple   A: rand(6,6)   100 nodes, complete   100 nodes, 0.5   Grafo MST  
Andre iamstk_and 0.169 ms 9.0 0.156 ms 21.0 2.874 ms 318.055294457 2.446 ms 624.679654926 0.211 ms 139.0

References

[Feof2009]Paulo Feofiloff. Algoritmos para Grafos em C via Sedgewick. IME-USP. http://www.ime.usp.br/~pf/algoritmos_para_grafos

Contributions

  • André Costa, 1o semestre de 2012.