peppocola / ct-covid

Screening CT 3d images for interpretable COVID19 detection.

CT-COVID

Screening CT 3d images for interpretable COVID19 detection.

Usage

API Endpoints

The API is accessible at the following endpoints:

• / which gives a welcome message
• /docs which provides a documentation of the API
• /models which provides a list of available models
• /predict used to receive prediction for a given image and his bounding box

Request of prediction

The request is made by passing:

• the image to be processed
• the bounding box of the image

An example of request with curl:

curl -X 'POST' \
  'http://localhost:5000/predict?xmin=0&ymin=0&xmax=224&ymax=224' \
  -H 'accept: application/json' \
  -H 'Content-Type: multipart/form-data' \
  -F 'file=filename.png;type=image/png'

Container

Pull docker container

Our container is hosted on dockerhub:

docker pull peppocola/ct-covid:v1

Run container

It is preferable to run the container with a GPU, but if you don't have one, you can run it with a CPU without problems.

Run on CPU

docker run -p 5000:5000 --rm -it --name=ct-covid peppocola/ct-covid:v1

Run on GPU

docker run -p 5000:5000 --rm -it --gpus 1 --name=ct-covid peppocola/ct-covid:v1

Run locally

Requirements

If you just want to run the api:

pip install -r requirements.txt

If you want to use tools like locust, pytest and great_expectations:

pip install -r requirements_dev.txt

Run api

python src/api.py

Those commands will run the api, which will accept requests on port 5000.

Frontend

cd src/frontend
npm install
npm start

Prometheus

docker run -d -p 9090:9090 --add-host host.docker.internal:host-gateway \
    -v "$PWD/prometheus.yml":/etc/prometheus/prometheus.yml \
    --name=prometheus prom/prometheus

Grafana

docker run -d -p 3000:3000 --add-host host.docker.internal:host-gateway \
    --name=grafana grafana/grafana-enterprise

Locust

locust -f tests/locust.py --host http://localhost:5000

PyTest

To run pytest without gpu:

PYTHONPATH=src pytest -m "not gpu" --cov src/covidx tests/

To run pytest with gpu:

PYTHONPATH=src pytest --cov src/covidx tests/

Great Expectations

cd tests
for checkpoint in ct-train ct-valid ct-test
do
  great_expectations --v3-api checkpoint run $checkpoint
done