This repository contains a Python implementation of the Fishsense lite pipeline. It contains tools for camera calibration, laser calibration, and fish length calculation. This pipeline assumes that you already have access to all the data necessary to run this pipeline. As this code is meant to be a temporary measure, the user may need to edit some file paths, so apologies in advance.
- Install the
poetrypackages.poetry install. - Install
git annex. On Ubuntu, executesudo apt install git-annex. - Install
git-annex-remote-synologyfrom git-annex-remote-synology. - Run
git-annex-remote-synology setup --hostname e4e-nas.ucsd.edu - Run
git annex enableremote synology. - Download data
git annex copy --from=synology.
We provide a docker container which has the dependencies pre-installed. In order to use this, please ensure you have docker installed on your system. When running Visual Studio Code, ensure that you use the option to reopen in the container. This step will time for the intial setup.
poetry run pytest