BeEPy

Behavioral + electrophysiology analyses in python

Data structure

The main datastructures are:

beepy.Unit: Holds spike times, and indexes into Lfp and Session to get variables at spike times
- Unit.data: A dynamic dictionary of variables (from LFP and behavior) at spike time
beepy.Lfp: Holds LFP data
- Lfp.data: A dynamic dictionary of time-varying variables
beepy.Session: Holds behavioral data, session metadata, a dictionary of Units, and a dictionary of LFPs.
- Session.data: Dynamic dictionary of behavioral variables
- Session.active_unit: Key (eg: [0,0]) telling which unit to parse
- Session.active_lfp: Key (eg: [0]) telling which LFP channel to parse
- Session.epoch: List of time periods, in seconds, telling what behavioral periods to look at (eg: trials)
- Session.mode: When running with multiple epochs, should an analysis concatenate into one large epoch (session.mode = 'cat'), or evaluate seperately for each (session.mode = 'map')
The primary functionality of the datastructures is the introduction of dynamic dictionaries. These fields take some underlying time-varying signal, and index into it based on the active LFP, active Unit, and epoch.

LFP and Session come with a small number of predefined variables at load time:
- LFP
  - ts: Time stamp (seconds)
  - signal: Raw trace (mV?)
- Session
  - x: X position of animal (cm)
  - y: Y position of animal (cm)
  - hd: Head direction (radians)
Methods exist for adding certain variables:
- LFP
  - add_band: Adds the filtered signal and instantaneous frequency+phase+magnitude of a specific frequency band
- Session
  - vel: Calculates the Kalman filtered velocity, angular velocity, acceleration, and angular acceleration
For any other variable Lfp.add_custom and Session.add_custom allow you to pass a variable with the same length as the underlying timestamps (along with a name for the key). These will be added to the dynamic dictionaries and calculated just as the built-in variables are.

Analyses should accept a Session, respecting any states within it (eg: Session.epoch, Session.active_unit, Session.active_lfp)
Broken up into submodules based on the nature of the analysis:
- Analyses.fields: Receptive fields (# spikes / occupancy)
  - Analyses.fields.ratemap: 2D ratemap (default: x & y coordinates)
  - Analyses.fields.headdir: 1D polar ratemap (default: headdir)
- Analyses.lfp: Phase locking, phase coding, and phase-coupling measures here ...