Kilosort4 Wrapper

[alejoe91]

Fixes #2527

Kilosort now has a SpikeInterface Wrapper (RecordingExtractorAsArray), so we don't need to save to bin!

I had to port subsections of the run_kilosort function to allow to:

• do/skip drift correction
• do/skip preprocessing

Added tests for all cases.

The parameters and descriptions were ported from their parameters definition.

One last comment:
The RecordingExtractorAsArray concatenates multiple segment. I think we should handle this externally to "unconcatenate" the sorting output, so I set handle_multi_segment to False.

[zm711]

One other point about the save to binary that might be interesting is that Mountaintsort5 had a speed up by switching to using the cached binary (see this). Kilosort also recommends using a binary file as well (but more so that you can use their gui and phy which are not really our concerns per se). I'm wondering if it might make sense to give the user an option to do this with write to binary to make this completely compatible with a Kilosort4 workflow for people or not. I could see arguments either way (and SI already has the export_to_phy so it doesn't really matter. Just curious what you think about this Alessio.

[alejoe91]

Thanks Zach, that's a good point especially regarding the phy output. In my view, we should be as agnostic as possible to the sorter and just use the spike times outputs, so we can better compare and unify pipelines regardless of the sorter. In this spirit, I would rather not add this option and "force" the user to postprocess and export in SI. What do you think?

[zm711]

I think that's completely fair for the library. :) I guess if there are a lot of issues requesting something like that then there would be an impetus to do it and it could be reconsidered, but I agree this is the better initial choice. I think keeping the library agnostic is a good guiding principle, so thanks for framing it that way. Makes a lot of sense.

(And I already do all my postprocessing here anyway :) ).

[mhhennig]

Looks like the docker image is private right now - but with a pip installed KS4 this works as intended.

[alejoe91]

Looks like the docker image is private right now - but with a pip installed KS4 this works as intended.

It's not pushed to docker hub yet, so it would need to be built locally ;) I'll test it a bit more and publish it

[samuelgarcia]

Well done camarade.
Did they keep the same ouput format ?

[alejoe91]

Well done camarade. Did they keep the same ouput format ?

Yes, same old ;)

[samuelgarcia]

Could you also add it in documentation and the installation sorter page ?

[alejoe91]

Right! Will do that on Friday @samuelgarcia

[alejoe91]

@samuelgarcia ready to merge on my side. Added installation docs

[samuelgarcia]

Not a great way!

[samuelgarcia]

I merge this now in the main.
We will improve this in futuir PR.
So the bug fix 0.100.1 release will be able to have this fisrt KS4.