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Added bad channels for kilosort >= 4.0.14 #3316

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Added bad channels for kilosort >= 4.0.14 #3316

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14 changes: 13 additions & 1 deletion src/spikeinterface/sorters/external/kilosort4.py
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Original file line number Diff line number Diff line change
Expand Up @@ -57,6 +57,7 @@ class Kilosort4Sorter(BaseSorter):
"skip_kilosort_preprocessing": False,
"scaleproc": None,
"torch_device": "auto",
"bad_channels": None,
}

_params_description = {
Expand Down Expand Up @@ -99,6 +100,7 @@ class Kilosort4Sorter(BaseSorter):
"skip_kilosort_preprocessing": "Can optionally skip the internal kilosort preprocessing",
"scaleproc": "int16 scaling of whitened data, if None set to 200.",
"torch_device": "Select the torch device auto/cuda/cpu",
"bad_channels": "A list of channel indices (rows in the binary file) that should not be included in sorting. Listing channels here is equivalent to excluding them from the probe dictionary.",
}

sorter_description = """Kilosort4 is a Python package for spike sorting on GPUs with template matching.
Expand Down Expand Up @@ -205,7 +207,17 @@ def _run_from_folder(cls, sorter_output_folder, params, verbose):
# NOTE: Also modifies settings in-place
data_dir = ""
results_dir = sorter_output_folder
filename, data_dir, results_dir, probe = set_files(settings, filename, probe, probe_name, data_dir, results_dir)
bad_channels = params["bad_channels"]

if version.parse(cls.get_sorter_version()) >= version.parse("4.0.14"):
filename, data_dir, results_dir, probe = set_files(
settings, filename, probe, probe_name, data_dir, results_dir, bad_channels
)
else:
filename, data_dir, results_dir, probe = set_files(
settings, filename, probe, probe_name, data_dir, results_dir
)

if version.parse(cls.get_sorter_version()) >= version.parse("4.0.12"):
ops = initialize_ops(settings, probe, recording.get_dtype(), do_CAR, invert_sign, device, False)
n_chan_bin, fs, NT, nt, twav_min, chan_map, dtype, do_CAR, invert, _, _, tmin, tmax, artifact, _, _ = (
Expand Down