fnndsc/pl-covidnet
COVID-Net inference for chest x-ray
10K+
.. image:: https://img.shields.io/github/license/FNNDSC/pl-covidnet :target: https://github.com/FNNDSC/pl-covidnet/blob/master/LICENSE :alt: License AGPL-3.0
.. image:: https://img.shields.io/docker/v/fnndsc/pl-covidnet?sort=semver :target: https://hub.docker.com/r/fnndsc/pl-covidnet
.. image:: https://github.com/FNNDSC/pl-covidnet/workflows/ci/badge.svg :target: https://github.com/FNNDSC/pl-covidnet/actions
.. contents:: Table of Contents
A ChRIS plugin to do predictive analysis on chest x-ray for COVID-19 diagnostics.
.. code::
python covidnet.py \
[--imagefile <imagefile>] \
[-v <level>] [--verbosity <level>] \
[--version] \
[--man] \
[--meta] \
<inputDir> \
<outputDir>
covidnet.py
is a ChRIS-based application that integrates the COVID-Net inference engine in a ChRIS plugin.
.. code::
[--imagefile <imageFile>]
The name of the input image in the input directory.
If not specified, the first ``png`` image file will be analyzed.
If no ``png`` images are found, the first ``jpg/jpeg`` image will
be analyzed.
[-v <level>] [--verbosity <level>]
Verbosity level for app. Not used currently.
[--version]
If specified, print version number.
[--man]
If specified, print (this) man page.
[--meta]
If specified, print plugin meta data.
.. code:: bash
DOCKER_BUILDKIT=1 docker build -t local/pl-covidnet .
.. code:: bash
docker run --rm -v $PWD/in:/incoming -v $PWD/out:/outgoing \
fnndsc/pl-covidnet:0.2.0 covidnet \
--imagefile ex-covid.jpeg /incoming /outgoing
Models are rehosted for the sake of convenience, opposed to using Google Drive as a CDN. They were originally sourced from https://github.com/lindawangg/COVID-Net/blob/master/docs/models.md
A custom UI was developed for a workflow which this plugin is a part of. https://github.com/FNNDSC/covidnet_ui
.. image:: https://raw.githubusercontent.com/FNNDSC/cookiecutter-chrisapp/master/doc/assets/badge/light.png :target: https://chrisstore.co/plugin/28
docker pull fnndsc/pl-covidnet