aind-behavior-core-analysis

A repository with core primitives for analysis shared across all Aind.Behavior tasks

This repository is part of a bigger infrastructure that is summarized here.

Getting started and API usage

The current goal of the API is to provide users with a way to instantiate "data contracts" and corresponding data ingestion logic. For instance, loading the data from different streams and converting them into a common format (e.g. pandas.DataFrame) can be done by:

from dataclasses import dataclass
from pathlib import Path
from typing import Dict, Union

from aind_behavior_core_analysis.io._core import DataStreamCollection
from aind_behavior_core_analysis.io.data_stream import (
    CsvStream,
    DataStreamCollectionFromFilePattern,
    HarpDataStreamCollectionFactory,
    SoftwareEventStream,
)

NodeType = Union[Dict[str, DataStreamCollection], DataStreamCollection]

@dataclass
class DataContract:
    behavior: Dict[str, NodeType]

root_path = Path(r"test_2024-11-05T190325Z")

dataset = DataContract(
    behavior={
        "Behavior": HarpDataStreamCollectionFactory(
            path=root_path / "behavior" / "Behavior.harp", default_inference_mode="register_0"
        ).build(),
        "LoadCells": HarpDataStreamCollectionFactory(
            path=root_path / "behavior" / "LoadCells.harp", default_inference_mode="register_0"
        ).build(),
        "RendererSynchState": DataStreamCollectionFromFilePattern(
            path=root_path / "behavior" / "Renderer", pattern="RendererSynchState.csv", stream_type=CsvStream
        ).build(),
        "SoftwareEvents": DataStreamCollectionFromFilePattern(
            path=root_path / "behavior" / "SoftwareEvents", pattern="*.json", stream_type=SoftwareEventStream
        ).build(),
    },
)

load_cell_data = dataset.behavior["LoadCells"]["LoadCellData"].load()
load_cell_data.plot()

Installing and Upgrading

if you choose to clone the repository, you can install the package by running the following command from the root directory of the repository:

pip install .

Otherwise, you can use pip:

pip install aind-behavior-core-analysis@https://github.com/AllenNeuralDynamics/Aind.Behavior.CoreAnalysis

Contributing

If you would like to contribute to this repository, open an Issue and/or Pull Request on this repository.

Linters and testing

• Install the provided linting and testing tools in the project.toml.

Tests

To run tests locally, run the following command from the root directory of the repository:

python -m unittest

Linters

• Use flake8 to check that code is up to standards (no unused imports, etc.):

flake8 .

• Use black to automatically format the code into PEP standards:

black .

• Use isort to automatically sort import statements:

isort .