fnndsc/pl-covidnet

By fnndsc

Updated over 2 years ago

COVID-Net inference for chest x-ray

Image
Data Science
Integration & Delivery
Machine Learning & AI

10K+

pl-covidnet

.. 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

Abstract

A ChRIS plugin to do predictive analysis on chest x-ray for COVID-19 diagnostics.

Synopsis

.. code::

python covidnet.py                                              \
    [--imagefile <imagefile>]                                   \
    [-v <level>] [--verbosity <level>]                          \
    [--version]                                                 \
    [--man]                                                     \
    [--meta]                                                    \
    <inputDir>                                                  \
    <outputDir>                                                 

Description

covidnet.py is a ChRIS-based application that integrates the COVID-Net inference engine in a ChRIS plugin.

Agruments

.. 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.

Local Build

.. code:: bash

DOCKER_BUILDKIT=1 docker build -t local/pl-covidnet .

Run

.. 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

Links

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 Command

docker pull fnndsc/pl-covidnet