Implemented RT-Sort as an external sorter

[max-c-lim]

No description provided.

[chrishalcrow]

Hello, this looks great! A few things:

• It'd be great to add some details to the docs. You can add the sorter to the list of supported sorters in doc/modules/sorters.rst and add the reference to your paper in doc/references.rst.
• Could you add the basic sorter test suite please? This does some very basic testing for sorters. It should be straightforward. For an example, see src/spikeinterface/sorters/external/tests/test_herdingspikes.py
• I've had an issue running the sorter on my data (rt-sort doesn't allow for channel_ids with non-integer-convertible names braingeneers/braindance#2). This isn't really related to the implementation of the sorter in spikeinterface, but I'll be able to test the PR a bit better if I can run it on a dataset I know well :)

Thanks!

[samuelgarcia]

Hi.
This is a super good news to have a new sorter here.
Welcome to RT-sort. Welcome in the game.
Thanks for the work.
I will have look also.

[max-c-lim]

Thank you for your fast review!

In the first commit, RT-Sort was added to the "Supported Spike Sorters" section. Is there another section where I should add it?

In the most recent commit, I added a reference to my paper in doc/references.rst and created src/spikeinterface/sorters/external/tests/test_rtsort.py.

I'll resolve the error with your data next. Thanks for documenting the issue so well and providing example data.

[alejoe91]

@max-c-lim

I think it would be great if you published RT-sort as a python package with all its dependencies. That would make installation instructions and the is_installed method much easier

[samuelgarcia]

Does it means that rt-sort is making a full copy of the traces ?
is it necessary ?
The main idea of the spikeinterface recording API is to avoid copy.

[max-c-lim]

Yes, RT-Sort writes a full copy of the traces on disk. While not technically necessary, because RT-Sort needs to repeatedly access the traces, testing has shown that this makes RT-Sort extremely faster. I can have the detect_sequences method delete the copy if that would be useful.

RT-Sort utilizes the other main idea of the spikeinterface recording API well by being able to sort traces from any acquisition device with at least 50 micrometer pitch.

[max-c-lim]

Thank you for all your comments! I simplified the installation process and implemented braindance.__version__.

[max-c-lim]

My branch (before merging main) failed the tests Complete tests / windows-latest Python 3.9, Complete tests / windows-latest Python 3.12, and Complete tests / windows-latest Python 3.12.

I may be mistaken, but I believe that all three failed because of the same reason: the command git clone --filter=blob:none --quiet https://github.com/SpikeInterface/probeinterface.git raised the error invalid path 'resources/wiring_references/ASSY-116>RHD2132.pdf'. My branch does not use or change probeinterface or RHD2132.pdf.

Could someone please advise me on how I could resolve this error?

Thanks!

[alejoe91]

@max-c-lim that has been fixed! Can you try again?

@samuelgarcia tests fail for tdc1. Do you plan to update it to support numpy 2.0?