Re: Proposal: add axes argument to ndimage API

On Fri, Mar 3, 2023 at 3:37 PM Gregory Lee <[email protected]> wrote:

> Hi all,
>
> Most functions in scipy.ndimage can be applied to n-dimensional images,
> but applying the functions along a subset of axes is not as easy as it
> could be. For separable filters there tends to already be a 1D variant
> where a single axis can be specified, but the n-dimensional versions do not
> currently have a corresponding axes argument.
>
> I am proposing that we can expose an axes argument on functions to
> simplify the process of filtering along a subset of axes (e.g. a common
> scenario would be filtering along only the spatial axes of an array that
> may contain other axes corresponding to color channels, timepoints or an
> image batch). Users can technically apply filters to a subset of axes now
> by manipulating the input arguments. For a few concrete examples of this:
>
> For gaussian filter, set sigma=0 along any axis that should not be
> filtered. For rank filters set size 1 along the non-filtered axes. For
> convolution-based filters or morphology the weights array can have
> singleton axes inserted.
>
> None of these are particularly difficult to implement, but it may not
> always be apparent to library users and an axes argument would be more
> convenient. The proposed implementation would be purely at the Python API
> level and is straightforward to implement and maintain.
>
> I opened a proof of concept PR implementing only *gaussian_filter *here:
> https://github.com/scipy/scipy/pull/18016
>
> I am happy to extend this to the rest of the filtering module in a follow
> up PR if the general approach looks good. It can also potentially be
> extended to morphology or other submodules as well.
>
> Let me know what you think
>

+1 from me, this sounds like a useful feature to add. Thanks for working on
this Greg!

Cheers,
Ralf

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