Installation

Create an Anaconda Virtual Environment

conda create -n moseq-detectron python=3.8
conda activate moseq-detectron

Install PyTorch ≥ 1.7

Install using https://pytorch.org/ to insure you get the correct versions. Something along the lines of:

conda install pytorch torchvision torchaudio cudatoolkit=11.3 -c pytorch

Install Detectron2

python -m pip install git+https://github.com/facebookresearch/detectron2.git

Install FFMPEG

conda install -c conda-forge ffmpeg

Install this repo

git clone https://github.com/tischfieldlab/moseq2-detectron-extract.git
pip install -e moseq2-detectron-extract

Usage

Generate a training dataset

moseq2-detectron-extract generate-dataset /path/to/session.tar.gz

Train a model

moseq2-detectron-extract train /path/to/annotations.json /path/to/model-output

Run inference on data using a pre-trained model

moseq2-detectron-extract infer /path/to/model/directory/ /path/to/session.tar.gz

compile model into torchscript

moseq2-detectron-extract compile /path/to/model-output /path/to/annotations.json --evaluate

You can check the COCO evaluation statistics afterward to ensure the model was exported successfully

For production, extract moseq sessions:

moseq2-detectron-extract extract /path/to/model/directory/ /path/to/session.tar.gz