QuantImage v2 - Backend

Context

This repository is part of the QuantImage v2 platform, which includes the following repositories:

• https://github.com/medgift/quantimage2-setup - Setup script for the platform
• https://github.com/medgift/quantimage2-frontend - Frontend in React
• https://github.com/medgift/quantimage2_backend - Backend in Python
• https://github.com/medgift/quantimage2-kheops - Custom configuration for the Kheops platform

Deployment on ehealth server at HEVS

When deploying this project on the ehealth server one needs to ensure that another instance of keycloak has not been started by another project. This repo is supposed to only start keycloak if another one is already running. If this process does not work and you end up with two instances of keycloak running we end up with authentification problems.

After starting quantimage - please check:

docker ps | grep keycloak. If you find two - then grab the id of the container named quantimagev2-keycloak and finally remove the running keycloak container and associated postgres database container by doing docker rm -f <id_container>. Possibly `docker compose rm <docker_compose_service_name> is working as well.

Project Structure

Docker

The project uses Docker for easy build & deployment, using the following files :

• webapp/Dockerfile : Installs the Python backend dependencies and starts the Flask server
• workers/Dockerfile : Installs the Celery worker dependencies and starts the worker
• flower/Dockerfile : Installs & starts the Flower monitoring interface for the Celery workers
• docker-compose.yml : Base Docker Compose file
• docker-compose.override.yml : Override file for local development, exposing ports & mapping source directories to containers.
• docker-compose.local.yml : Exports ports but does not map the source code directly
• docker-compose.vm.yml : File for the QuantImage v2 VM, restarting containers automatically on reboot or crash
• docker-compose.zrad.yml : File to include the ZRad feature extraction library (currently not publicly available)
• docker-compose.prod.yml : Production file for use with Traefik

Below is an overview of the various containers that constitute the backend:

Local development

The .env file defines the QUANTIMAGE2_DATA_MOUNT_DIRECTORY environment variable to specify which directory will be used to mount the different docker volumes. This is not part of git - please set the mounting directory at setup and create a .env file at the root of this repo when setting up the repo for the first time.

The content of the file could be the following:

# Docker volumes mount directory
QUANTIMAGE2_DATA_MOUNT_DIRECTORY=/Users/thomasvetterli/quantimage2-data

Note: On macOS you cannot mount on / as it's not writeable on the newest versions of macOS.

To run the python code locally without being in the web app use the following steps:

• install homebrew and pyenv to install python version
• install python 3.8 pyenv install 3.8.15 (it's what is used in the webapp dockerfile and workers dockerfile)
• install uv to manage python virtual environments plus install requirements
• create a virutal environment in the sub folder that you want to work on: uv venv (you may need one for the webapp and one for the worker)
• install dependencies with uv pip install -r requirements.txt
• for jupyter notebook development - run (after having activated the environment with ßource .venv/bin/activate) - python -m ipykernel install --user --name webapp --display-name "Webapp python environment"
• in the notebook subfolder we provide example scrips on how to interact with the db via pandas or a local flask context.

Code Structure

See the Documentation for more information on the code structure.