• About

• Example Usage

• Example Set CSV Input File

• Example Trials CSV Ouput File

• Installation

• Development

About

- Python Package Name: mouse_joystick_interface
- Description: Python interface to the Dudman lab Mouse Joystick Rig.
- Version: 5.0.1
- Python Version: 3.10
- Release Date: 2023-12-07
- Creation Date: 2023-10-17
- License: BSD-3-Clause
- URL: https://github.com/janelia-pypi/mouse_joystick_interface_python
- Author: Peter Polidoro
- Email: peter@polidoro.io
- Copyright: 2023 Howard Hughes Medical Institute
- References:
  - https://github.com/janelia-kicad/mouse_joystick_controller
- Dependencies:
  - modular_client
  - flatten_json

Example Usage

Python

Operation Systems

1. All

   from mouse_joystick_interface import MouseJoystickInterface
   dev = MouseJoystickInterface() # Automatically find device if available
   # abort_assay prematurely stops a running assay and leaves the rig ready to start a new assay
   dev.abort_assay()
   # start_assay is the main method that starts the assay, collects assay data, and saves data files
   dev.start_assay(set_path='~/set_example.csv')

2. Linux Specific

   from mouse_joystick_interface import MouseJoystickInterface
   dev = MouseJoystickInterface(use_ports=['/dev/ttyACM0']) # Linux specific port
   # abort_assay prematurely stops a running assay and leaves the rig ready to start a new assay
   dev.abort_assay()
   # start_assay is the main method that starts the assay, collects assay data, and saves data files
   dev.start_assay(set_path='~/set_example.csv')

3. Windows Specific

   from mouse_joystick_interface import MouseJoystickInterface
   dev = MouseJoystickInterface(use_ports=['COM3']) # Windows specific port
   # abort_assay prematurely stops a running assay and leaves the rig ready to start a new assay
   dev.abort_assay()
   # start_assay is the main method that starts the assay, collects assay data, and saves data files
   dev.start_assay(set_path='~/set_example.csv')

4. MacOS Specific

   from mouse_joystick_interface import MouseJoystickInterface
   dev = MouseJoystickInterface(use_ports=['/dev/tty.usbmodem262471']) # Mac OS X specific port
   # abort_assay prematurely stops a running assay and leaves the rig ready to start a new assay
   dev.abort_assay()
   # start_assay is the main method that starts the assay, collects assay data, and saves data files
   dev.start_assay(set_path='~/set_example.csv')

Optional methods

dev.mouse_joystick_controller.get_property_values(['ALL'])
dev.mouse_joystick_controller.repeat_aborted_trial('setValue',False)
dev.mouse_joystick_controller.get_assay_status()
dev.mouse_joystick_controller.move_joystick_to_base_position()
dev.mouse_joystick_controller.move_joystick_to_reach_position()
duration = 10
count = 1
dev.mouse_joystick_controller.activate_lickport(duration,count)
dev.mouse_joystick_controller.get_trial_timing_data()
dev.mouse_joystick_controller.abort_trial()

Before First Use

dev.mouse_joystick_controller.set_properties_to_defaults(['ALL'])

Example Set CSV Input File

repeat_trial_count	pull_torque	lickport_reward_duration	zero_torque_reward_delay	reach_position.0	reach_position.1
2	50	100	0	20	200
3	75	120	0	30	300
2	0	100	3	5	200

Example Trials CSV Ouput File

finished_trial_count	successful_trial_count	trial_aborted	assay_aborted	pull_threshold	set_in_assay	repeat_set_count	block_in_set	block_count	trial_in_block	block.repeat_trial_count	block.pull_torque	block.lickport_reward_duration	block.zero_torque_reward_delay	block.reach_position.0	block.reach_position.1	trial_start	mouse_ready	joystick_ready	pull	push	timeout	trial_abort

Installation

https://github.com/janelia-pypi/python_setup

GNU/Linux

1. Drivers

   GNU/Linux computers usually have all of the necessary drivers already installed, but users need the appropriate permissions to open the device and communicate with it.

   Udev is the GNU/Linux subsystem that detects when things are plugged into your computer.

   Udev may be used to detect when a device is plugged into the computer and automatically give permission to open that device.

   If you plug a sensor into your computer and attempt to open it and get an error such as: "FATAL: cannot open /dev/ttyACM0: Permission denied", then you need to install udev rules to give permission to open that device.

   Udev rules may be downloaded as a file and placed in the appropriate directory using these instructions:

   99-platformio-udev.rules

2. Download rules into the correct directory

   curl -fsSL https://raw.githubusercontent.com/platformio/platformio-core/master/scripts/99-platformio-udev.rules | sudo tee /etc/udev/rules.d/99-platformio-udev.rules

3. Restart udev management tool

   sudo service udev restart

4. Ubuntu/Debian users may need to add own “username” to the “dialout” group

   sudo usermod -a -G dialout $USER
   sudo usermod -a -G plugdev $USER

5. After setting up rules and groups

   You will need to log out and log back in again (or reboot) for the user group changes to take effect.

   After this file is installed, physically unplug and reconnect your board.

Python Code

The Python code in this library may be installed in any number of ways, chose one.

1. pip

   python3 -m venv ~/venvs/mouse_joystick_interface
   source ~/venvs/mouse_joystick_interface/bin/activate
   pip install mouse_joystick_interface

2. guix

   Setup guix-janelia channel:

   https://github.com/guix-janelia/guix-janelia

   guix install python-mouse-joystick-interface

Windows

Python Code

The Python code in this library may be installed in any number of ways, chose one.

1. pip

   python3 -m venv C:\venvs\mouse_joystick_interface
   C:\venvs\mouse_joystick_interface\Scripts\activate
   pip install mouse_joystick_interface

Conda/Spyder

conda update conda
conda create -n mouse_joystick_interface
conda activate mouse_joystick_interface
conda install pip
pip install mouse_joystick_interface
pip install spyder

Development

Clone Repository

git clone git@github.com:janelia-pypi/mouse_joystick_interface_python.git
cd mouse_joystick_interface_python

Guix

Install Guix

Install Guix

Edit metadata.org

make -f .metadata/Makefile metadata-edits

Tangle metadata.org

make -f .metadata/Makefile metadata

Develop Python package

make -f .metadata/Makefile guix-dev-container
exit

Test Python package using ipython shell

make -f .metadata/Makefile guix-dev-container-ipython
import mouse_joystick_interface
exit

Test Python package installation

make -f .metadata/Makefile guix-container
exit

Upload Python package to pypi

make -f .metadata/Makefile upload

Test direct device interaction using serial terminal

make -f .metadata/Makefile guix-dev-container-port-serial # PORT=/dev/ttyACM0
# make -f .metadata/Makefile PORT=/dev/ttyACM1 guix-dev-container-port-serial
? # help
[C-a][C-x] # to exit

Docker

Install Docker Engine

https://docs.docker.com/engine/

Develop Python package

make -f .metadata/Makefile docker-dev-container
exit

Test Python package using ipython shell

make -f .metadata/Makefile docker-dev-container-ipython
import mouse_joystick_interface
exit

Test Python package installation

make -f .metadata/Makefile docker-container
exit