• About
• Example Usage
• Example Set CSV Input File
• Example Trials CSV Ouput File
• Installation

• Development

About

markdown - 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-python/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

   ```python from mousejoystickinterface 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.startassay(setpath='~/set_example.csv') ```

2. Linux Specific

   ```python from mousejoystickinterface 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.startassay(setpath='~/set_example.csv') ```

3. Windows Specific

   ```python from mousejoystickinterface 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.startassay(setpath='~/set_example.csv') ```

4. MacOS Specific

   ```python from mousejoystickinterface 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.startassay(setpath='~/set_example.csv') ```

Optional methods

python 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

python 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-python/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

   sh 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

   sh sudo service udev restart

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

   sh 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

   sh 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

   sh 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

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

Conda/Spyder

sh 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

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

Guix

Install Guix

Install Guix

Edit metadata.org

sh make -f .metadata/Makefile metadata-edits

Tangle metadata.org

sh make -f .metadata/Makefile metadata

Develop Python package

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

Test Python package using ipython shell

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

Test Python package installation

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

Upload Python package to pypi

sh make -f .metadata/Makefile upload

Test direct device interaction using serial terminal

```sh 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

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

Test Python package using ipython shell

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

Test Python package installation

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