MLEBE (Machine Learning Enabled Brain Extraction) is a python package for both the training of a 3D Unet for segmentation and its integration into the SAMRI workflow.
Python's setuptools allows you to install Python packages independently of your distribution (or operating system, even).
This approach cannot manage any of our numerous non-Python dependencies (by design) and at the moment will not even manage Python dependencies;
as such, given any other alternative, we do not recommend this approach:
git clone https://github.com/Jimmy2027/MLEBE.git
cd MLEBE
python setup.py install --user
If you are getting a Permission denied (publickey) error upon trying to clone, you can either:
- Add an SSH key to your GitHub account.
- Pull via the HTTPS link
git clone https://github.com/Jimmy2027/MLEBE.git.
git clone https://github.com/Jimmy2027/MLEBE.git
cd MLEBE
path/to/conda/environment/bin/python -m pip install .
Python's setuptools allows you to install Python packages independently of your distribution (or operating system, even);
it also allows you to install a "live" version of the package - dynamically linking back to the source code.
This permits you to test code (with real module functionality) as you develop it.
This method is sub-par for dependency management (see above notice), but - as a developer - you should be able to manually ensure that your package manager provides the needed packages.
git clone git@github.com:Jimmy2027/MLEBE.git
cd MLEBE
echo "export PATH=\$HOME/.local/bin/:\$PATH" >> ~/.bashrc
source ~/.bashrc
python setup.py develop --user
If you are getting a Permission denied (publickey) error upon trying to clone, you can either:
- Add an SSH key to your GitHub account.
- Pull via the HTTPS link
git clone https://github.com/Jimmy2027/MLEBE.git.
git clone https://github.com/Jimmy2027/MLEBE.git
cd MLEBE
path/to/conda/environment/bin/python -m pip install -e .