serverkit-trackpy

Implementation of a web server for Trackpy (linking only).

Installing the algorithm server with pip

Install dependencies:

pip install -r requirements.txt

Run the server:

uvicorn main:app --host 0.0.0.0 --port 8000

or run python main.py. The server will be running on http://localhost:8000.

Endpoints

A documentation of the endpoints is automatically generated at http://localhost:8000/docs.

GET endpoints

• http://localhost:8000/ : Running algorithm message.
• http://localhost:8000/version : Version of the imaging-server-kit package.
• http://localhost:8000/trackpy/info : Web page displaying project metadata.
• http://localhost:8000/trackpy/demo : Plotly Dash web demo app.
• http://localhost:8000/trackpy/parameters : Json Schema representation of algorithm parameters.
• http://localhost:8000/trackpy/sample_images : Byte string representation of the sample images.

POST endpoints

• http://localhost:8000/trackpy/process : Endpoint to run the algorithm.

Running the server with docker-compose

To build the docker image and run a container for the algorithm server in a single command, use:

docker compose up

The server will be running on http://localhost:8000.

Running the server with docker

Build the docker image:

docker build --build-arg PYTHON_VERSION=3.9 -t serverkit-trackpy .

Run the server in a container:

docker run -it --rm -p 8000:8000 serverkit-trackpy:latest

The server will be running on http://localhost:8000.

Running unit tests

If you have implemented unit tests in the tests/ folder, you can run them using pytest:

pytest

if you are developing your server locally, or

docker run --rm serverkit-trackpy:latest pytest

to run the tests in a docker container.

Sample images provenance -->

• tracks.tif: Example image from the Trackmate getting started guide.