pl-covidnet

Table of Contents

• Abstract
• Synopsis
• Description
• Agruments
• Local Build
• Run
• Links

Abstract

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

Synopsis

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

[--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

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

Run

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