[Numpy-discussion] nonuniform scatter operations

Nathan Bell wnbell@gmail....
Sun Sep 28 00:01:27 CDT 2008


On Sun, Sep 28, 2008 at 12:34 AM, Geoffrey Irving <irving@naml.us> wrote:
>
> Is there an efficient way to implement a nonuniform gather operation
> in numpy?  Specifically, I want to do something like
>
> n,m = 100,1000
> X = random.uniform(size=n)
> K = random.randint(n, size=m)
> Y = random.uniform(size=m)
>
> for k,y in zip(K,Y):
>    X[k] += y
>
> but I want it to be fast.  The naive attempt "X[K] += Y" does not
> work, since the slice assumes the indices don't repeat.
>

I don't know of  numpy solution, but in scipy you could use a sparse
matrix to perform the operation.  I think the following does what you
want.

from scipy.sparse import coo_matrix
X += coo_matrix( (Y, (K,zeros(m,dtype=int)), shape=(n,1)).sum(axis=1)

This reduces to a simple C++ loop, so speed should be good:
http://projects.scipy.org/scipy/scipy/browser/trunk/scipy/sparse/sparsetools/coo.h#L139

-- 
Nathan Bell wnbell@gmail.com
http://graphics.cs.uiuc.edu/~wnbell/


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