Install the dependencies
sudo apt-get install -y build-essential git libssl-dev zlib1g-dev libbz2-dev libreadline-dev libsqlite3-dev wget curl llvm libncurses5-dev libncursesw5-dev xz-utils tk-dev libffi-dev liblzma-dev python3-openssl
Then, make sure you have pyenv installed.
curl https://pyenv.run | bash
Then, add the following to your ~/.bashrc
export PYENV_ROOT="$HOME/.pyenv"
[[ -d $PYENV_ROOT/bin ]] && export PATH="$PYENV_ROOT/bin:$PATH"
eval "$(pyenv init -)"
eval "$(pyenv virtualenv-init -)"
Source your ~/.bashrc, install Python 3.11, and poetry
source ~/.bashrc
pyenv install 3.11
Install rustup
curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh
In the root of this project, run the following. If you do not have x86 with CUDA, you may need to delete poetry.lock.
pip install poetry
pip install --upgrade pip
poetry install
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.
Open the notebook in demo/pipeline.ipynb
To run the CLI to process data. Note that this will not rerun files previously stored in ./output/results.db.
poetry run python -m fishsense_lite process ~/data/**/*.ORF --lens-calibration ~/data/fsl-01d-lens-raw.pkg --laser-calibration ~/data/laser-calibration.pkg --output ./output/results.db