feature request: irc version 1

[WeissShahaf]

Dear Devs,

please add a wrapper for ironclust running the irc *** instead of the irc2 **** commands.
several labs in our institute use ironclust from the irc command and irc2 is buggy and doesn't actually allow manual curation.

thanks,
Shahaf

[alejoe91]

Hi @WeissShahaf

It might be as easy as #2809

Can you try to run from that PR and try:

sorting_irc1 = ss.run_sorter("ironclust", recording, ..., version=1)

[WeissShahaf]

i'm afraid not:
Cell In[17], line 1
sorting_irc1 = ss.run_sorter("ironclust", recording=rec,output_folder=savefolder,remove_existing_folder=True, version=1)

File G:\mambaroot\envs\spkiPR\lib\site-packages\spikeinterface\sorters\runsorter.py:175 in run_sorter
return run_sorter_local(**common_kwargs)

File G:\mambaroot\envs\spkiPR\lib\site-packages\spikeinterface\sorters\runsorter.py:223 in run_sorter_local
SorterClass.set_params_to_folder(recording, output_folder, sorter_params, verbose)

File G:\mambaroot\envs\spkiPR\lib\site-packages\spikeinterface\sorters\basesorter.py:180 in set_params_to_folder
raise AttributeError("Bad parameters: " + str(bad_params))

AttributeError: Bad parameters: ['version']

[alejoe91]

@WeissShahaf did you install from source using the PR branch?

Here's what you should do:

pip uninstall -y spikeinterface
git clone https://github.com/SpikeInterface/spikeinterface.git
cd spikeinterface
git checkout -b alejoe91-irc1 main
git pull https://github.com/alejoe91/spikeinterface.git irc1
pip install -e .

[alejoe91]

@WeissShahaf did you get the chance to try my suggestion?

[WeissShahaf]

yes. i'm kinda struggling with my IDE. (spyder). it insists on using the main spikeinterface definition of the spikeinterface modules instead of the pre-release one.

i also tried directly from mamba's command line. same thing.

[WeissShahaf]

##i finally managed to make it run.

#sorting_irc1 = ss.run_sorter("ironclust", recording, ..., version=1) did not work, but this did:
other_params=ss.get_default_sorter_params('ironclust')
other_params['version']=1

sorting_irc1 = ss.run_sorter("ironclust", recording=rec,output_folder=savefolder,remove_existing_folder=True,**other_params)

however, i crashed:

Traceback (most recent call last):

Cell In[12], line 1
sorting_irc1 = ss.run_sorter("ironclust", recording=rec,output_folder=savefolder,remove_existing_folder=True,**other_params)

File D:\GitHub\NewGit\spkpre_release\spikeinterface\src\spikeinterface\sorters\runsorter.py:175 in run_sorter
return run_sorter_local(**common_kwargs)

File D:\GitHub\NewGit\spkpre_release\spikeinterface\src\spikeinterface\sorters\runsorter.py:225 in run_sorter_local
SorterClass.run_from_folder(output_folder, raise_error, verbose)

File D:\GitHub\NewGit\spkpre_release\spikeinterface\src\spikeinterface\sorters\basesorter.py:293 in run_from_folder
raise SpikeSortingError(

SpikeSortingError: Spike sorting error trace:
Traceback (most recent call last):
File "D:\GitHub\NewGit\spkpre_release\spikeinterface\src\spikeinterface\sorters\basesorter.py", line 258, in run_from_folder
SorterClass._run_from_folder(sorter_output_folder, sorter_params, verbose)
File "D:\GitHub\NewGit\spkpre_release\spikeinterface\src\spikeinterface\sorters\external\ironclust.py", line 268, in _run_from_folder
raise Exception("ironclust returned a non-zero exit code")
Exception: ironclust returned a non-zero exit code

Spike sorting failed. You can inspect the runtime trace in E:\afm16505\231213\231213_neuropixels\231212_test4_g0_imec0\SI_out_test/spikeinterface_log.json.

the json file shows that matlab did run. but then there was an error:

"File 1/1 took 1627.9s (81114.4 MB, 49.8 MB/s, x2.6 realtime)",
"----------------------------------------Index in position 1 exceeds array bounds.ERROR: MATLAB error Exit Status: 0x00000001"
],
"error": true,
"error_trace": "Traceback (most recent call last):\n File "D:\GitHub\NewGit\spkpre_release\spikeinterface\src\spikeinterface\sorters\basesorter.py", line 258, in run_from_folder\n SorterClass._run_from_folder(sorter_output_folder, sorter_params, verbose)\n File "D:\GitHub\NewGit\spkpre_release\spikeinterface\src\spikeinterface\sorters\external\ironclust.py", line 268, in _run_from_folder\n raise Exception("ironclust returned a non-zero exit code")\nException: ironclust returned a non-zero exit code\n",
"run_time": null
}

[alejoe91]

I see..unfortunately that's an IronClust error, so not sure how we can help!