[graph-tool] Performance question
guillaume at mitotic-machine.org
Fri Mar 21 10:10:37 CET 2014
There is a propertymap that contains the out degrees of each vertex, it
might be much faster to access it, i.e.:
`i_degree = graph.degree_property_map('out')[i]`
I guess I would also iterate over the edges rather than the indices of
the adjacency matrix...
Le 21/03/2014 09:44, Hang Mang a écrit :
> Maybe graph.vertex(i).out_degree() is slow itself? If so, should I
> store all the degrees in a matrix then?
> On Friday, March 21, 2014 9:09:23 AM UTC+1, Hang Mang wrote:
> I have a graph with 1034 vertices and 53498 edges. I'm manually
> computing the preferential attachement index for the vertices, and
> other indices. I'm aware that graph-tool has that implemented but
> I'm doing it for personal stuff. However I noticed that my
> computations are very slow. It took 2.7 minutes to compute that
> for the mentioned graph. I'm not sure if it's my algorithm that is
> slow or the something is wrong with graph-tool. I would be very
> thankful if someone could have a little look into my code.
> def pa(graph):
> Calculates Preferential Attachment index.
> Returns S the similarity matrix.
> A = gts.adjacency(graph)
> S = np.zeros(A.shape)
> for i in xrange(S.shape):
> for j in xrange(S.shape):
> i_degree = graph.vertex(i).out_degree()
> j_degree = graph.vertex(j).out_degree()
> factor = i_degree * j_degree
> S[i,j] = factor
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