IBLLIB Matlab Installation Guide

Matlab-specific Dependencies

Matlab-specific dependency : Matlab R2016b or higher.

Install Matlab onto your machine

Download and install the latest Matlab version from here: https://www.mathworks.com/downloads/

Initialisation

Clone or download the repository here: https://github.com/int-brain-lab/ibllib-matlab

Launch Matlab. Set the Matlab path, add with subfolders the full .\ibllib-matlab directory.

Instantiate One class: Define connection settings

The first step is to instantiate the One class: behind the scenes, the constructor connects to the IBL cloud database and gets credentials.

The connections settings are defined in a JSON parameter file (named .one_params).

  • In Linux, the file is in ~/.one_params.
  • In Windows, the file is in the Roaming App directory C:\Users\olivier\AppData\Roaming\.one_params.
  • In Mac OS, the file is in the user directory /Users/olivier/.one_params.

In case of doubt, type the command io.getappdir in a Matlab prompt. It will return the directory of the JSON .one_params file.

There are two manners to define the connection settings.

1. The setup() static method in Matlab

In a Matlab prompt, write:

One.setup

You will be asked to enter the following information:

ALYX_LOGIN 				% Input your IBL user name
ALYX_PWD				% Input your IBL password
ALYX_URL:				% Should be automatically set as: https://alyx.internationalbrainlab.org - press ENTER
CACHE_DIR:				% Local repository, can ammend or press ENTER
FTP_DATA_SERVER: 		% Should be automatically set as: ftp://ibl.flatironinstitute.org - press ENTER
FTP_DATA_SERVER_LOGIN:	% Should be automatically set as: iblftp - press ENTER
FTP_DATA_SERVER_PWD		% Request Password for FTP from Olivier
HTTP_DATA_SERVER: 		% Should be automatically set as: http://ibl.flatironinstitute.org  - press ENTER 
HTTP_DATA_SERVER_LOGIN: % Should be automatically set as: iblmember  - press ENTER
HTTP_DATA_SERVER_PWD	% Request Password for HTTP from Olivier

The path to the .one_params file is displayed in the Matlab prompt as ans.

Note: using One.setup changes the JSON .one_params file. Also note that the file is shared across Python and Matlab platforms.

2. Edit the JSON .one_params

Note: In Mac OS or Linux, use the command nano in a terminal.

Once the connections settings are defined, there is no need to setup the class One again if willing to connect with the credentials saved in the JSON .one_params file.

The tutorial in the next section will show you how to change credentials without changing the JSON file (useful for a temporary connection with different credentials).

Run tests

Once the One class is instantiated with your IBL credentials, run the suite of Unit tests to check the installation:

RunTestsIBL('All')

If you see any Failure message, please report on GitHub or contact data admins (Olivier / Niccolo). If not, you are ready for the tutorial - go to next section !