CEI_PacingSiteLocalization
This repo contains python code to localize pacing sites
To run this code, go to the covalic pacing site challenge: https://challenge.kitware.com/#challenge/573f26a5cad3a51cc63466ba
This code runs from a docker container here: https://hub.docker.com/r/ecgimaging/cei_pacingsitelocalization
Running code in covalic
To run this code in covalic, make sure the docker repository has a build with the recent changes. Note the repo and build tag name, eg, ecgimaging/cei_pacingsitelocalization:latest.
In the covalic phase, choose the 'Customize scoring behavior' options from the actions menu. Input the docker repo name in the 'Image identifier' field. You can leave the 'Container Arguments' as the default.
Next, choose 'Scoring metrics' from the action menu. Add a metric to match each metric name in the scoreCommon.py file.
A final note: It may be neccessary to make sure that the submissions do not need to match the ground truth files. Choose the 'Configure submission' option and uncheck the 'Require submission filenames to match ground truth filenames' option.
Testing the code locally
To run the code locally, Install docker and make sure that the docker container is up to date. Run the container with the call similar to the following:
docker run -v /path/to/data/folder:/mnt/girder_worker/data ecgimaging/cei_pacingsitelocalization:latest --groundtruth=/mnt/girder_worker/data/ground_truth --submission=/mnt/girder_worker/data/ground_truth