Installation
We recommend using anaconda and pip. You can install anaconda by downloading and executing appropriate installers from the Anaconda website, pip often comes included with python otherwise check the following instructions. We support all Python version starting from 3.8.
You may need make for simplification. The following command will install all packages used by all datasets within FLamby. If you already know you will only need a fraction of the datasets inside the suite you can do a partial installation and update it along the way using the options described below.
Create and launch the environment using:
git clone https://github.com/owkin/FLamby.git
cd FLamby
make install
conda activate flamby
To limit the number of installed packages you can use the enable argument to specify which dataset(s)
you want to build required dependencies for and if you will need to execute the tests (tests) and build the documentation (docs):
git clone https://github.com/owkin/FLamby.git
cd FLamby
make enable=option_name install
conda activate flamby
where option_name can be one of the following:
cam16, heart, isic2019, ixi, kits19, lidc, tcga, docs, tests
if you want to use more than one option you can do it using comma
(WARNING: there should be no space after ,), eg:
git clone https://github.com/owkin/FLamby.git
cd FLamby
make enable=cam16,kits19,tests install
conda activate flamby
Be careful, each command tries to create a conda environment named flamby therefore make install will fail if executed numerous times as the flamby environment will already exist. Use make update as explained in the next section if you decide to use more datasets than intended originally.
Update environment
Use the following command if new dependencies have been added, and you want to update the environment for additional datasets:
make update
or you can use enable option:
make enable=cam16 update
In case you don’t have the make command (e.g. Windows users)
You can install the environment by running:
git clone https://github.com/owkin/FLamby.git
cd FLamby
conda env create -f environment.yml
conda activate flamby
pip install -e .[all_extra]
or if you wish to install the environment for only one or more datasets, tests or documentation:
git clone https://github.com/owkin/FLamby.git
cd FLamby
conda env create -f environment.yml
conda activate flamby
pip install -e .[option_name]
where option_name can be one of the following:
cam16, heart, isic2019, ixi, kits19, lidc, tcga, docs, tests. If you want to use more than one option you can do it
using comma (‘,’) (no space), eg:
pip install -e .[cam16,ixi]
Datasets
All datasets but one have to be downloaded and preprocessed to be accessible. Refer either to the Quickstart or directly to the datasets’ sections: