neurobooth / neurobooth-os

Python package for digital phenotyping data synchronization and acquisition

Neurobooth-os

Neurobooth-os is a python package to initialize, synchronize and record behavioral and physiological data streams from wearables, D-/RGB cameras, eye tracker, ECG, mouse and microphone in a booth.

Installations

We recommend the Anaconda Python distribution. To install neurobooth-os, simply do:

$ pip install -e git+https://github.com/neurobooth/neurobooth-os.git#egg=neurobooth_os

and it will install neurobooth-os along with the dependencies which are not already installed.

To check if everything worked fine, you can do:

$ python -c 'import neurobooth_os'

and it should not give any error messages.

Install Pylink running on the STM:

$ pip install --index-url=https://pypi.sr-support.com sr-research-pylink

If pip install from sr-research doesn't work, please follow the following steps:

• Create an sr-research support account

* Download the EyeLink Developers Kit v2.1.1 (32 and 64 bit) installer from the SR Research Support forum. * Install the Eyelink Developers Kit * Run: $ cd C:'\Program Files (x86)\SR Research\EyeLink\SampleExperiments\Python\' * Run: $ python install_pylink.py

For pyspin FLIR installation on the ACQ: Download SDK from https://www.flir.com/products/spinnaker-sdk/?vertical=machine+vision&segment=iis direct link to wheel file: https://flir.app.boxcn.net/v/SpinnakerSDK/file/982785545712 then unzip the file, cd to the folder and run: $ pip install spinnaker_python-2.x.x.x-cp3x-cp3x-win_amd64.whl

Setup

It requires a postgreSQL database running on a server. Connection is established with the function neurobooth_os.iout.metadator.get_conn(). Currently, as specified in ~/.neurobooth_os_secrets the local IP is 192.168.100.1, and remotely it connects to neurodoor.nmr.mgh.harvard.edu using the private key in '~/.ssh/id_rsa'.

To setup a private key, first activate the VPN (partner's virtual private network), then run in the terminal:

$ ssh-keygen
$ ssh-copy-id [e-mail]

Next, set up the configuration data. Please see the instructions at: https://github.com/neurobooth/neurobooth-os/blob/master/docs/system_configuration.md

Run

The program runs on 3 different computers and the starting point is gui.py. The computers are:

* CTR (control) computer: This computer hosts the GUI and relays commands to the other computers to start recording from the Neurobooth devices and presenting stimuli. The lab recorder software is on this computer.

• STM (stimulus) computer: This computer runs the tasks using psychopy.
• ACQ (acquisition) computer: This computer acquires data.

Each computer has a server that listens for communication from the other computers in the form of string messages. CTR and STM computer communicate with the database.