Aneurysm-Detection

Setup

File structure

Add a data folder into your locally cloned repository so that the directory structure looks similar to this:

ANEURYSM-DETECTION
│   README.md
│   pyproject.toml
│   ...
│
└───data 
│   │
│   └───training
│   │   │   ...
│   │
│   └───3DUnet_training
│       │   ...
│   
└───externals
│   │
│   └───pytorch3dunet
│       │   ...
│   
└───src
    │   ...

The 3DUnet_training data for testing the external repository can be downloaded fom here (Cell boundary predictions for lightsheet images of Arabidopsis thaliana lateral root). Our aneurysm dataset was privately shared.

Poetry shell (virtual env)

Install poetry

Follow the poetry installation guide to install poetry if not already installed. The following should be sufficient:

curl -sSL https://raw.githubusercontent.com/python-poetry/poetry/master/get-poetry.py | python -

Verify by running

poetry --version

Setup env

In repository run following command to setup evnironment:

poetry install

To activate poetry shell run:

poetry shell

External repositories

To include the external repositories execute the following command:

git submodule update --init --recursive 

VSCode

To include the path for each external library (example path given) include this into your settings.json:

"python.analysis.extraPaths": [
        "/home/user/Aneurysm-Detection/externals/pytorch3dunet"
    ]