arena-interface 3.0.0

Python interface to the Reiser lab ArenaController.

• About

• Example Usage

• Installation

• Development

About

- Python Package Name: arena_interface
- Description: Python interface to the Reiser lab ArenaController.
- Version: 3.0.0
- Python Version: 3.11
- Release Date: 2025-09-09
- Creation Date: 2023-10-17
- License: BSD-3-Clause
- URL: https://github.com/janelia-python/arena_interface_python
- Author: Peter Polidoro
- Email: [e-mail]
- Copyright: 2025 Howard Hughes Medical Institute
- References:
  - https://github.com/janelia-arduino/ArenaController
- Dependencies:
  - click
  - schedule
  - pyserial

Example Usage

Python

from arena_interface import ArenaInterface

ai = ArenaInterface(debug=True)
ai.set_ethernet_mode()
# or
ai.set_serial_mode(port='/dev/ttyACM0', baudrate=115200)
ai.all_on()
ai.all_off()
ai.stream_frame(path='./patterns/pat0004.pat', frame_index=0)
ai.stream_frames(path='./patterns/pat0004.pat', frame_rate=20, runtime_duration=50)
ai.trial_params(pattern_id=3, frame_rate=20, runtime_duration=50)
ai.trial_params(pattern_id=3, frame_rate=-20, runtime_duration=50)

Command Line

help

arena-interface --help
# Usage: arena-interface [OPTIONS] COMMAND [ARGS]...

Options:
  --help  Show this message and exit.

Commands:
  all-off
  all-on
  display-reset
  set-refresh-rate
  stream-frame
  trial-params

arena-interface stream-frame --help
# Usage: arena-interface [OPTIONS] PATH FRAME_INDEX

Options:
  --help  Show this message and exit.

1. example commands

   arena-interface all-on
   

   $FRAME_INDEX=0
   arena-interface stream-frame ./patterns/pat0004.pat $FRAME_INDEX
   arena-interface stream-frame ./patterns/pat0004.pat 0
   

   FRAME_RATE=2
   RUNTIME_DURATION=50 # 50 * 100ms = 5000ms = 5s
   arena-interface stream-frames ./patterns/pat0004.pat $FRAME_RATE $RUNTIME_DURATION
   arena-interface stream-frames ./patterns/pat0004.pat 2 50
   

   PATTERN_ID=3
   FRAME_RATE=20
   RUNTIME_DURATION=50 # 50 * 100ms = 5000ms = 5s
   arena-interface trial-params -- $PATTERN_ID $FRAME_RATE $RUNTIME_DURATION
   arena-interface trial-params -- 3 20 50
   

   PATTERN_ID=3
   FRAME_RATE=-20
   RUNTIME_DURATION=50 # 50 * 100ms = 5000ms = 5s
   arena-interface trial-params -- $PATTERN_ID $FRAME_RATE $RUNTIME_DURATION
   arena-interface trial-params -- 3 -20 50
   

   arena-interface all-off
   

2. advanced commands

   arena-interface set-refresh-rate 175
   

   arena-interface switch-grayscale 0 # 0=binary, 1=grayscale
   

Installation

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

GNU/Linux

Ethernet

C-x C-f /sudo::/etc/network/interfaces

auto eth1

iface eth1 inet static

    address 192.168.10.2

    netmask 255.255.255.0

    gateway 192.168.10.1

    dns-nameserver 8.8.8.8 8.8.4.4

nmap -sn 192.168.10.0/24
nmap -p 62222 192.168.10.62
nmap -sV -p 62222 192.168.10.0/24

sudo -E guix shell nmap
sudo -E guix shell wireshark -- wireshark

make guix-container

Serial

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/arena_interface
   source ~/venvs/arena_interface/bin/activate
   pip install arena_interface
   

2. guix

   Setup guix-janelia channel:

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

   guix install python-arena-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\arena_interface
   C:\venvs\arena_interface\Scripts\activate
   pip install arena_interface
   

Development

Clone Repository

git clone [e-mail]:janelia-python/arena_interface_python.git
cd arena_interface_python

Guix

Install Guix

Install Guix

Edit metadata.org

make metadata-edits

Tangle metadata.org

make metadata

Develop Python package

make guix-dev-container
exit

Test Python package using ipython shell

make guix-dev-container-ipython
import arena_interface
exit

Test Python package installation

make guix-container
exit

Upload Python package to pypi

make upload

Test direct device interaction using serial terminal

make guix-dev-container-port-serial # PORT=/dev/ttyACM0
# make 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 docker-dev-container
exit

Test Python package using ipython shell

make docker-dev-container-ipython
import arena_interface
exit

Test Python package installation

make docker-container
exit