AllenInstitute / ecephys_etl_pipelines

Pipelines and modules for processing extracellular electrophysiology data
Other
1 stars 2 forks source link

Update ecephys align timestamps to allow barcode_ephys line label variant #12

Closed wbwakeman closed 3 years ago

wbwakeman commented 3 years ago

The get_barcode_line of the align_timestamps module searches for barcode in several variations of sync file line labels that have been encountered. There is a new variation used by Visual Behavior Neuropixels: ephys_barcode

As defined in the excel file linked in the "Sync: PCIe 6612 DAQ" section of this confluence page.

Need to enable processing using this new line label. (Add another elif?)

Probably worth checking if there are other places in the code where the new line labels break old implementations.

njmei commented 3 years ago

More details:

Simple fix would be to add new elif clause to:

https://github.com/AllenInstitute/AllenSDK/blob/b29058f4c136f906123b3f93cd184edb9158b4e4/allensdk/brain_observatory/ecephys/align_timestamps/barcode_sync_dataset.py#L13

We may want to consider this an opportunity to move the whole align_timestamps module over to the ecephys_etl_pipelines repo though:

https://github.com/AllenInstitute/AllenSDK/tree/master/allensdk/brain_observatory/ecephys/align_timestamps

Validation:

Estimate of 1-2 if just putting in the fast fix. Estimate of 3-5 if moving the whole module over from AllenSDK + putting in fast fix