The state of our project is summarized here. The document is basically a progress report, including details on what we did, how, and why, and our results. It also includes information on planned analyses, and our general strategy. Since we also have too many figures to be reasonably putting on github and constantly remaking when we re-analyze things, you can see some of what we have plot-wise there too.
Plotted data and analyses are in:
'./figs/behavior' : Analysis of subjects behavioral data
'./figs/channels' : Channel locations and coverage for each subject
Behavioral data processing files are:
'./src/behavior/analysis.py' : Loads behavioral data and generates plots in /figs/behavior
'./src/behavior/behavior_overview.R' : Similar function as analysis.py
'./src/behavior/restructure_behavioral_data.m': Puts behavioral data from _A.mat and _B.mat files in more useful format
Pytorch model files for neural data prediction are:
'./src/models/loader.py' : Contains functions for getting data into proper format for model training/testing
'./src/models/models.py' : Contains pytorch network models
'./src/models/run.ipy' : Contains code for producing our analyses
'./src/tmp.py' : Snippets file for undeveloped and in-process code
Model-free neural data analysis code is:
'./src/neural/plots.py' : Plotting functions for plots under ./figs/neural
'./src/neural/run.py' : Script for generating said plots
Preprocessing code can be found in:
'./src/preproc/functions.py' : These are the main preprocessing functions (see file header for details)
'./src/preproc/params.py' : Preprocessing parameters (equivalent to a config.json)
'./src/preproc/run.ipy' : Script which keeps the full pipeline in order
'./src/preproc/utils.py' : Subsidiary utilities for the main functions in functions.py
Miscellaneous shared code:
'./src/shared/paths.py' : Path predefinitions for different computers. Again, basically a config.json.
'./src/shared/utils.py' : Data manipulation utilities that don't belong in any more specific place
Sharp-wave ripple and oscillatory event-detection code:
'./src/swrs/initial/extract_ca1_data.py' : Original file for getting CA1 data into matlab format
'./src/swrs/initial/vl-shared/' : Copy of Van der Meer lab SWR toolbox
'./src/swrs/initial/LFPeventDetection_SEEG.m/' : Matlab code for using Van der Meer toolbox on extract_ca1_data.py output
'./src/swrs/initial/riple_events.py/' : Computes ripple event statistics
'./src/swrs/initial/visualize_events.py/' : File for showing ripples
'./src/swrs/functions_ca1.py' : Aggregates LFP data from electrodes for processing
'./src/swrs/functions_swr.py' : Functions for computing oscillatory events
'./src/swrs/misc.py' : Code for printing SWR times, comparing pipelines, other miscellany.
'./src/swrs/run.py' : Script for running oscillatory event detection