Occipet is a python package I have built to have several customizable tools to work with medical images. It is a library that can be used as a building block in other python scripts. It also exposes several scripts that can be called from the command line thanks to Typer.

First, clone this repository:

git clone [email protected]:ValentinGautierCreatis/occipet.git

Then you have to install dependencies. I recommend doing it in a virtual environment (conda, virtualenv, pyenv, ...)

pip install -r requirements.txt

Finally, just install the library by running the following at the root of the repository:

pip install .

You can install it in development mode. Changes in the source files will be applied without having to install the package again. To do so, run the following :

pip install -e .

You can use the library in your python code. Example :

from occipet import reconstruction

reconstruction.MLEM

You can also run scripts from the command line. Get more info on the available commands with:

occipet --help