lickport-array-interface 2.0.1

Python interface to the Janelia Dudman lab mouse lickport array.

About

- Name: lickport_array_interface
- Version: 2.0.1
- Description: Python interface to the Janelia Dudman lab mouse lickport array.
- License: BSD 3-Clause License
- URL: https://github.com/janelia-pypi/lickport_array_interface_python
- Author: Peter Polidoro
- Email: [e-mail]
- Copyright: 2022 Howard Hughes Medical Institute
- Dependencies:
  - modular_client

More Information

This library is an interface to the Lickport Array Module.

Example Usage

from lickport_array_interface import LickportArrayInterface, LickportArrayMetadata
dev = LickportArrayInterface() # Try to automatically detect port
dev = LickportArrayInterface(port='/dev/ttyACM0') # Linux specific port
dev = LickportArrayInterface(port='/dev/tty.usbmodem262471') # Mac OS X specific port
dev = LickportArrayInterface(port='COM3') # Windows specific port

data_path_str = '~/lickport_array_data/data_file'

metadata = LickportArrayMetadata()
metadata.experiment_name = 'mouse_library'
metadata.task_name = 'hex_foraging_V2'
metadata.subject_id = 'ML11_NAc'

dev.controller.activate_lickports([0,1])
dev.start_acquiring_data()
dev.start_saving_data(data_path_str,metadata)
dev.stop_saving_data()
dev.stop_acquiring_data()

dev.controller.dispense_lickport_for_duration(0,200)
dev.controller.dispense_lickports_for_duration([0,1],200)
dev.controller.dispense_all_lickports_for_duration(200)
dev.controller.get_activated_lickports()
dev.controller.activate_only_lickport(0)
dev.controller.activate_only_lickports([0,1])
dev.controller.activate_lickport(0)
dev.controller.activate_lickports([0,1])
dev.controller.deactivate_lickport(0)
dev.controller.deactivate_lickports([0,1])
dev.controller.activate_all_lickports()
dev.controller.deactivate_all_lickports()

Data

I Experiment name  : mouse_library
I Task name  : hex_foraging_V2
I Subject ID : ML11_NAc
I Start date : 2022/05/23 16:43:38
time,millis,lickport_0,lickport_1,lickport_2,lickport_3,lickport_4,lickport_5,lickport_6,lickport_7,lickport_8,lickport_9,lickport_10,lickport_11
1653338620,956503527,A,LA,,,,,,,,,,
1653338622,956505441,LA,A,,,,,,,,,,
1653338624,956507372,A,A,,,,,,,,,,L
1653338626,956509622,A,A,,,,,,L,,,,
1653338628,956511133,A,A,,L,,,,,,,,
1653338629,956512828,A,A,,,L,,,,,,,

time

time in seconds since the epoch

The epoch is the point where the time starts, and is platform dependent. For Unix, the epoch is January 1, 1970, 00:00:00 (UTC)

The term seconds since the epoch refers to the total number of elapsed seconds since the epoch, typically excluding leap seconds. Leap seconds are excluded from this total on all POSIX-compliant platforms.

millis

The number of milliseconds passed since the LickportArrayController board was powered. This number will overflow (go back to zero), after approximately 50 days.

lickport_n

Symbol	Meaning
"L"	lickport_n lick detected
"A"	lickport_n activated
"LA" or "AL"	lickport_n lick detected and activated
""	lickport_n neither lick detected nor activated

Installation

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

Linux and Mac OS X

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

Windows

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

Guix

Setup guix-janelia channel:

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

guix install python-lickport-array-interface