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__Documents__ https://bhallalab.github.io/MouseBehaviour

A `cmake` based C++/Python pipeline to run behavioural experiment.
A C++/Python pipeline to run behavioural experiment.

# Protocols

A protocols must be listed in `./Protocols/BehaviourProtocols.csv`. You must specify the right
protocol code duging configuration. See section __How to run the pipeline__ below.
protocol code duging cmake configuration. See section __How to run the pipeline__ below.

# How to run the pipeline

Both the arduino and the camera should be connected to the computer before starting the
The Arduino uno board and the camera should be connected to the computer before starting the
session.

## Download and setup (done once)

This code will __only__ work on Ubuntu-16.04. Install arduino, c++ compiler
(gcc), cmake, and boost libraries.
This application works __only__ on Ubuntu-18.04 because of the camera firmware available in this repository
from PointGrey Inc works only with Ubuntu 18.04.

Install arduino, c++ compiler (gcc), cmake, and boost libraries.

Script `bootstrap.sh` will try to install all dependencies. Required
libraries for PointGrey camera is in the source.

$ git clone https://github.com/BhallaLab/MouseBehaviour.git
$ cd MouseBehaviour
$ sudo -E ./bootstrap.sh # on first time post login. If it fails, manual configuration is needed.

The script `bootstap.sh` will try to configure your system. You must have `sudo`
permissions because we need to add to various groups (`pgrimaging` and `dialout`)
before you can access camera and serial port. __In case, something odd happens,
raise an issue on github__.
$ sudo -E ./bootstrap.sh # If it fails, manual configuration is needed.

Once bootstrap is successful, logout and login. Changes made to your groups comes
into effect only after a fresh login. To verify that you are in appropriate groups, type `groups`
command in terminal. Make sure that `pgrimaging` and `dialout` appears in the
group list. If not, things have not gone properly.
command in terminal. Make sure that `flirimaging` and `dialout` appears in the
group list.

To build and upload to arduino:

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