BORIS ( BinOcular Retinal Image Statistics ) Code

code for analyzing the Berkeley dataset of visual movies

GETTING SET UP

linking up data:

Adding repositories from Github:

(1) CODE: Clone this repository (this one) https://github.com/Berkeley-BORIS/BORIS_Code

(2) CAMERA TO EYE REGISTRAION: Clone this respository into session_data/raw/cam2eye_registration https://github.com/Berkeley-BORIS/BORIS_Cam2EyeRegData

Adding other raw data not on github:

(1) STEREO CALIBRATION: place stereo calibration data (~5GB) directory in session_data/raw/stereocalibration/

(2) GAZE: place eyelink ASC (SUBJ_RECORDING.asc) into session_data/raw/gaze/

(3) SCENE IMAGES: place stereo camera images in session_data/raw/scene

notes on structure:

subj: a participant in the study

kre, sah, tki

session: a single recording session

cafe, inside, nearwork, outside1, outside2

task: a subset of time within a session during which a particular task was performed

setting up Python environment:

If you're using OSX, the code will work with a custom python environment

Download Anaconda Python distribution:

https://store.continuum.io/cshop/anaconda/

add open cv -- currently using 2.4.10, not compatible with 3.0

conda install -c https://conda.binstar.org/jjhelmus opencv

add boris conda command line tool

conda install -c https://conda.binstar.org/bwsprague boris

Set up boris python environment:

conda create -n boris --file=conda_requirements.txt: do from BORIS code directory to create boris anaconda environment

activate it

source activate boris

if you want to use ipython notebook, add this too

conda install ipython ipython-notebook ipython-qtconsole:

set up environment for command line interface

boris config --root path/to/session_data

boris config --root /users/emily/BORIS/session_data

(this creates a .borisrc file in your home directory)

DATA ANALYSIS

run set up for analysis (from code folder)

python setup.py install

if using python or ipython notebook rather than CLI, do:

run setup.py install

import boris

running standard session-level pre-processing:

parsing the Eyelink files - gets gaze information from Eyelink file format

boris parse subj session

boris parse kre cafe

or

boris parse_all

calibrating stereo cameras - estimates intrinsics/extrinsics of the stereo cameras

boris stereocalibrate subj session

boris stereocalibrate kre cafe

or

boris stereocalibrate_all

registering camera to eyes - estimates the translation/rotation between the the left camera and the cyclopean eye (world origin)

boris cam2eye subj session

or

boris cam2eye_all