README.md

DL4MI

Workshop Deep Learning for Medical Imaging

To start

Notebooks are inside a folder named notebooks. Source file for the notebooks are inside the folder src_notebooks

Install the environment to transform the python scripts into notebooks. We recommend to create a conda environment and install inside the requirements:

conda create --name DL4MI  python=3.8
conda activate DL4MI
pip install -r requirements.txt

Contribute

Using jupytext

Jupytext is used to convert Python scripts into notebooks (and vice versa). When it is properly connected to Jupyter, the python files can be opened in Jupyter and directly displayed as notebooks.

Setting up jupytext

• If you use jupyter notebook use the following command jupyter serverextension enable jupytext
• If yoy use jupyter lab install nodejs (conda install nodejs), then in jupyter lab you have to right click "Open with -> notebook" to open the python scripts with the notebook interface.

Use jupytext to convert an existing notebook

If you have an existing notebook and you want to transform it pure Python, use the following command:

jupytext --to py notebook.ipynb

Update all the notebooks

Once your changes are done in the scripts (the src_notebooks files) run at the root folder:

make

This command will recreate automatically the notebooks and clean the outputs.