sleap-io 0.0.1

Standalone utilities for working with SLEAP pose data.

sleap-io

Standalone utilities for working with animal pose tracking data.

This is intended to be a complement to the core SLEAP package that aims to provide functionality for interacting with pose tracking-related data structures and file formats with minimal dependencies. This package does not have any functionality related to labeling, training, or inference.

Installation

pip install sleap-io

For development, use one of the following syntaxes:

conda env create -f environment.yml

pip install -e .[dev]

See CONTRIBUTING.md for more information on development.

Usage

import sleap_io as sio
import numpy as np

skeleton = sio.Skeleton(
    nodes=["head", "thorax", "abdomen"],
    edges=[("head", "thorax"), ("thorax", "abdomen")]
)

instance = sio.Instance.from_numpy(
    points=np.array([
        [10.2, 20.4],
        [5.8, 15.1],
        [0.3, 10.6],
    ]),
    skeleton=skeleton
)

Support

For technical inquiries specific to this package, please open an Issue with a description of your problem or request.

For general SLEAP usage, see the main website.

Other questions? Reach out to [e-mail].

License

This package is distributed under a BSD 3-Clause License and can be used without restrictions. See LICENSE for details. BSD 3-Clause License

Copyright (c) 2022, Talmo Lab All rights reserved.

Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:

1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.

2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.

3. Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.