Moved KiloSort's template_features to _additional_kilosort_files#222
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ttngu207 merged 2 commits intodatajoint:mainfrom Jun 4, 2025
Merged
Moved KiloSort's template_features to _additional_kilosort_files#222ttngu207 merged 2 commits intodatajoint:mainfrom
ttngu207 merged 2 commits intodatajoint:mainfrom
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ttngu207
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Jun 4, 2025
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Hello there,
Our fork of the ephys pipeline current errors out on the ingestion of Kilosort files as part of the element-array-ephys. The error originates specifically in validate , in which certain required files are part of the _kilosort_core_files (DJ's current repo) but not part of the Kilosort output anymore (Kilosort4 repo), specifically
template_features.npyandtemplate_features_ind.npyAfter chatting with @ttngu207, I believe the solution is to move
template_features.npyandtemplate_features_ind.npyfrom core Kilosort files to the additional files.File "/home/u19prod@pu.win.princeton.edu/miniconda3/envs/U19-pipeline_python_env3/lib/python3.12/site-packages/element_array_ephys/readers/kilosort.py", line 78, in validate
raise FileNotFoundError(
FileNotFoundError: Kilosort files missing in (/mnt/cup/braininit/Data/Processed/electrophysiology/jk8386/jk8386_jk71/20250530_g2/jk71_05302025_g0/jk71_05302025_g0_imec0/job_id_837/kilosort4_output): ['template_features.npy', 'template_feature_ind.npy']