Welcome to the AIND Behavior Device Olfactometer project documentation!¶

aind-behavior-device-olfactometer¶

A library with a SDK for the Olfactometer behavior task

📋 General instructions¶

This repository follows the project structure laid out in the Aind.Behavior.Services repository.

🔧 Prerequisites¶

Pre-requisites for running the project can be found here.

🚀 Deployment¶

For convenience, once third-party dependencies are installed, Bonsai and python virtual environments can be bootstrapped by running:

./scripts/deploy.ps1

from the root of the repository.

⚙️ Generating settings files¶

The task is instantiated by a set of three settings files that strictly follow a DSL schema. These files are:

task_logic.json
rig.json
session.json

Examples on how to generate these files can be found in the ./examples directory of the repository. Once generated, these are the only required inputs to run the Bonsai workflow in ./src/main.bonsai.

The workflow can thus be executed using the Bonsai CLI:

"./.bonsai/Bonsai.exe" "./src/main.bonsai" -p SessionPath=<path-to-session.json> -p RigPath=<path-to-rig.json> -p TaskLogicPath=<path-to-task_logic.json>

[> ] CLI tools¶

Task CLI¶

The platform exposes a few CLI tools to facilitate various tasks. Tools are available via:

uv run device-olfactometer <subcommand>

for a list of all sub commands available:

uv run device-olfactometer -h

You may need to install optional dependencies depending on the sub-commands you run.

🔍 Primary data quality-control¶

Once an experiment is collected, the primary data quality-control script can be run to check the data for issues. This script can be launched using:

uv run device-olfactometer data-qc <path-to-data-dir>

🗂️ AIND metadata mapping¶

After a calibration session is collected, acquisition.json, instrument.json and subject.json (following aind-data-schema) can be generated from Python:

from aind_behavior_device_olfactometer.data_mappers import map_dataset

mapped = map_dataset(
    session_directory,  # where the Bonsai workflow wrote its data
    repository_path,  # this repository's checkout
    session_end_time=utcnow(),
)
mapped.write_standard_files(session_directory)

🔄 Regenerating schemas¶

DSL schemas can be modified in ./src/aind_behavior_device_olfactometer/rig.py (or (...)/task_logic.py).

Once modified, changes to the DSL must be propagated to json-schema and csharp API. This can be done by running:

uv run device-olfactometer regenerate

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