[SciPy-Dev] scipy.signal.correlate2d extremely slow

[James Bergstra]

Your point is valid, but for your own use in the short term you might
try scipy.ndimage, it can be faster IIRC.

- James

On Fri, Mar 9, 2012 at 4:47 PM, Frédéric Bastien <nouiz at nouiz.org> wrote:
> Hi,
>
> >From memory, scipy.signal.correlate2d call the same c code as the
> convolution2d. As we have shown in a paper[1], this is not a fast
> version. In Theano, we have a much faster version, but don't support
> all option of the scipy version. If you go look at the c code of this
> function in scipy, you will see that it was done to be ultra
> generic(same c code for all dtype!, ...). It was not done for speed.
> The version in Theano allow to do in C batch and stack of image and
> filter as used in neural network. So this also save some overhead.
>
> So if my memory is right and that correlate2d call the same c code,
> you probably can use the Theano code for it by passing it the right
> parameter. It you do so, we would like to add it to Theano itself.
>
> [1] http://www.iro.umontreal.ca/~lisa/publications2/index.php/publications/show/461
>
> Otherwise, there is the opencv project that have a python binding and
> could implement what you want in a faster way.
>
> HTH
>
> Fred
>
> On Mon, Mar 5, 2012 at 11:57 AM, Malcolm Reynolds
> <malcolm.reynolds at gmail.com> wrote:
>> Hi,
>>
>> I've been compiling numpy and scipy from source for a while, and as
>> far as I was aware everything was configured correctly. However I
>> noticed today that scipy.signal.correlate2d is enormously slow,
>> several orders of magnitude slower in that it takes many minutes to
>> compute the correlation for two 216x384 matrices. For the same size
>> matrices, matlab's normxcorr2 (which I know is not entirely
>> equivalent, due to the added normalisation, but much of the
>> computation is analogous surely?) takes under half a second.
>>
>> Is this a known issue with the underlying algorithm, or does it
>> indicate that my scipy has not linked correctly with some optimised
>> routines from atlas / blas / etc, or that I have made some other
>> mistake in the compilation?
>>
>> Any help on this issue would be appreciated, I was relying on being
>> able to compute 2d cross correlations pretty fast.. Thanks!
>>
>> Malcolm
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