Update Ksort'ers

[alexmorley]

Note this may also require the following changes to kilosort2 itself which can be found in my fork here: alexmorley/Kilosort2@43cbbff

Todo (here)

• Expose more of the kilosort2 parameters to spikeforest
• Allow no clusters to be found and (if there were no other errors) write the null result to a file
• Write mda files in blocks to avoid reading entire recordings into memory [matlab]
• Write mda files in blocks to avoid reading entire recordings into memory [sfmdarecordingextractors]
• Don't copy the mda file from recording day to kilosort_dir (we are just going to convert it anyway)
• Write the mda file as and 64bit integer to avoid loss of precision (currently it is a 32bit float, I have changed to 32bit integer for now just because the matlab mda implementation doesn't have a int64 option) This one is really important (hotfix in Kilosort(2) firings.mda dtype increase #47)
• Re-base and test with new master

To do (kilosort2 fork)

• Fix various assumptions that channel count will be high (> 32)
• Fix (or warn) double detection of same spike by different templates

[magland]

@alexmorley , just getting to this now. What's the state of this, should we still try to merge?

[alexmorley]

I've added a todo list for what I'd like to do before merging. I think we should because there are a couple of things that I think are quite important.

Most of the things on the list are implemented I just haven't pushed the changes yet.

[samuelgarcia]

Alex,
@alexmorley : if you change some parameters here could you also change parameters in spiketoolkit.
https://github.com/SpikeInterface/spiketoolkit

Normally @magland should rebase spikeforest wrapper one by one on top on spiketoolkit wrappers.
The idea is to have a unique place for mofying parameters at wrappers level.

So if chnages occurs in between this rebase you could have differents parameters at the end.

best

Samuel

[alexmorley]

Yeah I'll make sure everything matches before we merge this no worries. Submitting my thesis in a couple weeks so just waiting till that's out of the way.

[samuelgarcia]

Good luck to you.

[alejoe91]

@alexmorley update on spikeforest/spiketoolkit sorter wrappers.

From the next release, they will both depend on spikesorters, so all the changes should be done there!