adding code to compute and cache behavior performance for all sessions

AllenInstitute / visual_behavior_analysis

Python package for analyzing behavioral data for Brain Observatory: Visual Behavior

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adding code to compute and cache behavior performance for all sessions #772

Closed dougollerenshaw closed 3 years ago

dougollerenshaw commented 3 years ago

To summarize behavior data across sessions, I needed a more convenient/fast method for getting access to behavior data for all sessions. I opted to add some infrastructure to pre-compute behavior performance for all sessions using the cluster, which is included in this PR. We will then be able to quickly open the cached data for sessions of interest and compute meta-summary data

This PR:

adds function to utilities to compute behavior performance on a behavior session
adds function to utilities to cache behavior performance for a session as an h5 file
adds a script that will call the caching function for one session
adds a script that will call the caching function for all sessions

alexpiet commented 3 years ago

@dougollerenshaw This is useful thing to cache.

I have a similar table already computed at /nc-ophys/visual_behavior/behavior_model_output/_summary_table.pkl It might be good to think about whether we should combine these tables. My summary table as behavioral model outputs, but also model-free statistics like when the mouse was engaged, the lick rate, the reward rate, number of hits, number of engaged hits, etc.

dougollerenshaw commented 3 years ago

Thanks @alexpiet. Your table is only for ophys sessions, correct? When I load it, it's only 346 entries long: As paper figure 1 is currently outlined, it calls for summarizing behavior performance across all behavior sessions. While I'm not sure it makes sense to show all stages, I think it might make sense to at least show the last training day and/or the last pre-imaging habituation day. So we'll need the outputs of my method to get those sessions.

alexpiet commented 3 years ago

Thats correct that it is only for ophys sessions. There is a second table that has a subset of columns for all behavioral sessions _training_summary_table.csv. I've been meaning to update that table to include all the same values as the ophys table, but haven't updated it yet

If its too much work to think about how to combine these tables, its fine. I just wanted you to be aware that my tables existed.