[Neuroimaging] parallel computation of bundle_distances_mam/mdf ?

[Eleftherios Garyfallidis]

Hi Emanuele,

Here is an example of how we calculated the distance matrix in parallel
(for the MDF) using OpenMP
https://github.com/nipy/dipy/blob/master/dipy/align/bundlemin.pyx

You can just add another function that does the same using mam. It should
be really easy to implement as we have
already done it for the MDF for speeding up SLR.

Then we need to update the bundle_distances* functions to use the parallel
versions.

I'll be happy to help you with this. Let's try to schedule some time to
look at this together.

Best regards,
Eleftherios


On Mon, Dec 12, 2016 at 11:16 AM Emanuele Olivetti <olivetti at fbk.eu> wrote:

> Hi,
>
> I usually compute the distance matrix between two lists of streamlines
> using bundle_distances_mam() or bundle_distances_mdf(). When the lists are
> large, it is convenient and easy to exploit the multiple cores of the CPU
> because such computation is intrinsically (embarassingly) parallel. At the
> moment I'm doing it through the multiprocessing or the joblib modules,
> because I cannot find a way directly from DiPy, at least according to what
> I see in dipy/tracking/distances.pyx . But consider that I am not
> proficient in cython.parallel.
>
> Is there a preferable way to perform such parallel computation? I plan to
> prepare a pull request in future and I'd like to be on the right track.
>
> Best,
>
> Emanuele
>
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