pyControl

Open source, Python based, behavioural experiment control.

run_task_GUI.jpg

Overview

pyControl is a system of open source hardware and software for controlling behavioural experiments, built around the Micropython microcontroller.

pyControl makes it easy to program complex behavioural tasks using a clean, intuitive, and flexible syntax for specifying tasks as state machines. User created task definition files, written in Python, run directly on the microcontroller, supported by pyControl framework code. This gives users the power and simplicity of Python for specifying task behaviour, while allowing advanced users low-level access to the microcontroller hardware. For more information see programming tasks.

Hardware overview

pyControl hardware consists of a breakout board and a set of devices such as nose-pokes, audio boards, LED drivers, rotary encoders and stepper motor controllers that are connected to the breakout board to create behavioural setups. Assembled pyControl hardware is available from the OpenEphys store.

pyControl has a Graphical User Interface for controlling experiments and visualing behaviour.

Tools for importing pyControl data into Python for analysis are provided in the data_import module.

The pyControl google group is a email list for pyControl users.


Getting started

Installation

Download the latest version of pyControl as a zip file from the repository's downloads page. Unzip the folder on your computer and you will have the following folder structure:

- pyControl
    - gui          # Graphical user interface
    - cli          # Command line interface
    - com          # Serial communication and data logging
    - config       # Configuration files edited by user
    - data         # Behavioural data.
    - experiments  # Experiment definition files.
    - devices      # pyControl hardware classes (uploaded to pyboard).
    - pyControl    # pyControl framework        (uploaded to pyboard).
    - tasks        # Task definition files
    - tools        # Tools for importing and visualising pycontrol data

Dependencies

pyControl has the following dependencies:

  • Python 3
  • pyserial
  • numpy
  • pyqtgraph

The simplest way to install the required dependencies is to download and install the Anaconda Python distribution, then use the conda package management utility to install the other packages using the following commands in the Anaconda Prompt:

conda update conda
conda install -c anaconda pyserial
conda install -c anaconda numpy
conda install -c anaconda pyqtgraph

pyControl has been tested primarily on Windows 7 and 10 but in principle should be cross platform and has been used on Mac and Linux. You may need to install the micropython USB drivers to ensure your operating system recognizes the board and can open a serial connection to it, see micropython windows setup and the micropython docs. The micropython drivers are unsigned so to install them on Windows 10, follow the instructions here under Install Unsigned Drivers from Advanced Boot Menu. You should only need to do this the first time you install the drivers on a computer.

Micropython boards (pyboards) need to be running a fairly recent version of the Micropython firmware to work with pyControl (version >= 1.9). When you connect to a pyboard with the GUI, the micropython version running on the board is displayed. Instructions for updating the micropython firmware can be found for windows here and for Linux/Mac here. You can use the GUI's board config menu to put the pyboard into device firmware upgrade (DFU) mode rather than physically connecting the DFU pin to 3.3V.

Updating

To update pyControl, download the latest version from the download page, unzip it, and copy across the config and tasks directories from your old installation to keep you configuration settings and tasks. After updating pyControl you should reload the pyControl framework onto your pyboards using the GUI's board config menu.

Alternatively you can use version control software to clone the repository rather than downloading it as a zip. You can then pull the latest version from the repository to update, but be careful not to overwrite your configuration files.

Running a task

Run the file pyControl_GUI.py in the folder pyControl/gui, you will see a GUI window like that shown above.

Plug in a pyboard and it will appear in the Select drop down menu in the Setup box. Select the board and press the Connect button. The GUI will connect to the board and upload the pyControl framework.

From the Tasks drop down menu, select the task blinker. Press the Upload button to upload the task to the pyboard.

Press the Start button. The task will run causing the blue LED on the pyboard to start blinking.

While the task is running, press the Variables button to open the dialog for setting and getting task variables. Set the variable LED_n to 1,2,3 or 4 to change the color of LED that is flashing.

Stop the task with the Stop button.

To save data generated by the task to disk, enter a subject ID in the Subject ID text box. The Start button will change to Record indicating that data from the run will be saved. Run the task with the Record button, a data file will be created in the pyControl/data folder.

See the GUI user guide for information on configuring and running experiments on multiple boxes in parrallel.

Developer's guide

Do you want to contribute for the pyControl project? You can find more information here.