This is the main analysis pipeline for physiology data collected in the coxlab.

The pipeline (as seen from 1000m) looks like this:

raw data -> (processing) -> hdf5 session file -> (statistics & visualization) -> results

Most options are configured by creating and editing a .physio file in the users home directory. This is an ini type file with default settings found in the physio/cfg.py.

Analyzing a session is as simple as:

import physio

physio.analysis.analyze.analyze(session)

where session is in the form of <animal>_<date:yearmonthday> example: K4_110720

This will produce a hdf5 file within the results repository (specified in ~/.physio).

Opening session file:

import physio

mysession = physio.session.Session(sessionfile)

where sessionfile is the path to the hdf5 session file

See physio/session.py for more info.