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<!-- README.me is generated automatically from .single-source-of-truth.org
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About

- Name: <<name>>
- Version: <<version>>
- Description: <<description>>
- License: <<license>>
- URL: <<url>>
- Author: <<author>>
- Email: <<email>>
- Copyright: <<copyright>>
- Dependencies:
  - <<dependencies>>

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

SymbolMeaning
“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-python/python_setup

Linux and Mac OS X

python3 -m venv ~/venvs/<<name>>
source ~/venvs/<<name>>/bin/activate
pip install <<name>>

Windows

python3 -m venv C:\venvs\<<name>>
C:\venvs\<<name>>\Scripts\activate
pip install <<name>>

Guix

Setup guix-janelia channel:

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

guix install <<guix-name>>

Development

Guix

git clone <<url>>
cd <<repository_name>>
make shell
make edits
make all
exit

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