set_files requires bad_channels positional argument for kilosort v4.0.16

[jbowler06]

The 'set_files' method in kilosort4 version 4.0.16 now requires a 'bad_channels' positional argument which seems to call an error on line 208 in src/spikeinterface/sorters/external/kilosort4.py (..the issue can be easily mitigated by downgrading kilosort to 4.0.13)

e.g.:

Error running kilosort4                                                                                                                
Traceback (most recent call last):                                                                                                     
  File "/home/jack/code/ephys_tools/run_si_pipeline.py", line 303, in <module>                                                         
    main(sys.argv[1:])                                                                                                                 
  File "/home/jack/code/ephys_tools/run_si_pipeline.py", line 295, in main                                                             
    sorting = run_spike_sorting(recording_corrected, ks_path, sorter)                                                                  
              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^                                                                  
  File "/home/jack/code/ephys_tools/run_si_pipeline.py", line 175, in run_spike_sorting                                                
    sorting = si.run_sorter(                                                                                                           
              ^^^^^^^^^^^^^^                                                                                                           
  File "/home/jack/.miniconda3/envs/si/lib/python3.11/site-packages/spikeinterface/sorters/runsorter.py", line 216, in run_sorter      
    return run_sorter_local(**common_kwargs)                                                                                           
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^                                                                                           
  File "/home/jack/.miniconda3/envs/si/lib/python3.11/site-packages/spikeinterface/sorters/runsorter.py", line 276, in run_sorter_local
    SorterClass.run_from_folder(folder, raise_error, verbose)
  File "/home/jack/.miniconda3/envs/si/lib/python3.11/site-packages/spikeinterface/sorters/basesorter.py", line 301, in run_from_folder
    raise SpikeSortingError(                                       
spikeinterface.sorters.utils.misc.SpikeSortingError: Spike sorting error trace:                                                        
Traceback (most recent call last):                                  
  File "/home/jack/.miniconda3/envs/si/lib/python3.11/site-packages/spikeinterface/sorters/basesorter.py", line 261, in run_from_folder
    SorterClass._run_from_folder(sorter_output_folder, sorter_params, verbose)                                                          
  File "/home/jack/.miniconda3/envs/si/lib/python3.11/site-packages/spikeinterface/sorters/external/kilosort4.py", line 208, in _run_from_folder
    filename, data_dir, results_dir, probe = set_files(settings, filename, probe, probe_name, data_dir, results_dir)
                                             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^                   
TypeError: set_files() missing 1 required positional argument: 'bad_channels'                                                           

Spike sorting failed

[zm711]

Thanks! We will put it on our list to fix for newer versions!

[Hobart10]

Hi Zach, Is there a possibility of fixing this issue with a PR before the next version release? Kilosort versions prior to 4.0.15 have a problem with CUDA memory cache cleaning, so downgrading isn't a viable solution. Thank you!! https://github.com/MouseLand/Kilosort/issues/746

[chrishalcrow]

Hello, I made a PR (https://github.com/SpikeInterface/spikeinterface/pull/3316). If @jbowler06 or @Hobart10 could give it a try, that'd be great!

[Hobart10]

Thank you! @chrishalcrow It works for my case and the parameter bad_channels is well passed to kilosort.

[JoeZiminski]

@alejoe91 @chrishalcrow I think this has been added now in #3339 and can be closed?