Welcome to the AIND Dynamic Foraging project documentation!¶

aind-dynamic-foraging¶

A repository for the Dynamic Foraging task and its associated curricula.

📋 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 Dynamic Foraging 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 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>

However, for a better experiment management user experience, it is recommended to use the provided experiment launcher below.

[> ] CLI tools¶

Task CLI¶

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

uv run dynamic-foraging <subcommand>

for a list of all sub commands available:

uv run dynamic-foraging -h

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

Curriculum CLI¶

Curricula are available via the curriculum CLI entry point. For a full list of commands:

uv run curriculum -h

`list` - List Available Curricula¶

uv run curriculum list

`init` - Initialize a Curriculum¶

Creates an initial trainer state for enrolling a subject in a curriculum.

# Start at the first stage
uv run curriculum init --curriculum coupled_baiting --output initial_state.json

# Start at a specific stage
uv run curriculum init --curriculum coupled_baiting --stage s_stage_1 --output initial_state.json

`run` - Run a Curriculum¶

Evaluates a curriculum based on session data and current trainer state.

uv run curriculum run \
  --data-directory /path/to/session/data \
  --input-trainer-state current_state.json \
  --output-suggestion /path/to/output

Force a specific curriculum:

uv run curriculum run \
  --data-directory /path/to/session/data \
  --input-trainer-state current_state.json \
  --curriculum coupled_baiting \
  --output-suggestion /path/to/output

`version` / `dsl-version` - Show Versions¶

uv run curriculum version      # Package version
uv run curriculum dsl-version  # Underlying DSL library version

Typical curriculum workflow¶

List available curricula:
```
uv run curriculum list
```

Initialize a subject:

uv run curriculum init --curriculum coupled_baiting --output trainer_state.json

After a session, evaluate progress:

uv run curriculum run \
  --data-directory /path/to/session/data \
  --input-trainer-state trainer_state.json \
  --output-suggestion /path/to/output

Use the suggestion for the next session: The suggestion.json output can be passed as --input-trainer-state for the next session.

Style guide¶

To keep things clear, the following naming conventions are recommended:

Policies should start with p_ (e.g., p_identity_policy)
Policy transitions should start with pt_
Stages should start with s_ (e.g., s_stage1)
Stage transitions should start with st_ and be named after the stages they transition between (e.g., st_s_stage1_s_stage2)

Define the following modules within a curriculum:

metrics: Defines (or imports) metrics classes and how to calculate them from data
stages: Defines the different stages of the task, including task settings and optionally policies
curriculum: Defines transitions between stages and generates the entry point to the application

🎮 Experiment launcher (temporarily CLABE)¶

To manage experiments and input files, this repository contains a launcher script that can be used to run the Dynamic Foraging task. A default script is located at ./scripts/aind-launcher.py. It can be run from the command line as follows:

uv run clabe run ./scripts/aind-launcher.py
# or uv run ./scripts/main.py

Additional arguments can be passed to the script as needed. For instance to allow the script to run with uncommitted changes in the repository, the --allow-dirty flag can be used:

uv run clabe run ./scripts/aind-launcher.py --allow-dirty

or via a ./local/clabe.yml file. Additional custom launcher scripts can be created and used as needed. See documentation in the clabe repository for more details.

🔍 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 launcher using:

uv run dynamic-foraging data-qc <path-to-data-dir>

🔄 Regenerating schemas¶

DSL schemas can be modified in ./src/aind_behavior_dynamic_foraging/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 dynamic-foraging regenerate

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