Release ibl-sort - Githubissues

int-brain-lab / ibl-sorter

GNU General Public License v2.0

1 stars 0 forks source link

Release ibl-sort #13

Open oliche opened 3 months ago

oliche commented 3 months ago

[x] fix #14
[ ] add generation of passingSpikes table to the computation of good units
[ ] release dependencies
- [x] ibllib, branch iblsort
- [x] iblscripts, branch iblsort
- [x] iblsort, branch develop
- [x] ibl-neuropixel >= 1.0.1
- [x] slidingRefractory 1.1.1
- [x] phylib 2.5.0
[ ] release as stand-alone
[ ] release on spike interface

Completion: the local servers are able to spike sort and register their data

chris-langfield commented 2 months ago

[x] Write a guide to setup pyks2 environment on linux server, update: https://docs.google.com/document/d/1CXjfEEtKkKw19xOnCjrqarLqdpyH4w4EmW-FzGFW8JM/edit
[x] saturation not output by decompress_destripe_cbin
[x] integration test on server

chris-langfield commented 2 months ago

Notes:

pyfftw install not covered by environment instructions
Have to change cupy to cupy-cuda11x in ibl-sorter requirements
Needs sudo to access integration data in /mnt/s0 Need to point to explicit venv python path i.e. sudo /home/ibladmin/Documents/PYTHON/SPIKE_SORTING/ibl-sorter/.venv/bin/python
https://github.com/int-brain-lab/ibl-sorter/blob/a6cbd4e33ad7e0bec708e72acc5d031cfb9d93f6/iblsorter/ibl.py#L18 change to __name__

chris-langfield commented 2 months ago

Error 1:

  File "/home/ibladmin/Documents/PYTHON/SPIKE_SORTING/ibl-sorter/.venv/lib/python3.10/site-packages/spikeinterface/core/binaryrecordingextractor.py", line 177, in __init__
    self.file = open(self.datfile, "r")
FileNotFoundError: [Errno 2] No such file or directory: '/home/ibladmin/scratch/pykilosort/.kilosort/imec_385_100s.ap/proc.dat'

chris-langfield commented 2 months ago

Tests have been cleaned up and all run (with GPU)