JingfeiPeng / pl-pdfgeneration

pl-pdfgeneration

Table of Contents

• Abstract
• Synopsis
• Description
• Agruments
• Run
  • Using docker run
• Examples

Abstract

An app that takes in prediction results and generates PDF

Synopsis

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

Description

pdfgeneration.py is a ChRIS-based application that...

Agruments

[-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.

[--imagefile]
required field, the name of the patient chest X-Ray image

[--patientId]
patient's id

Run

This plugin can be run in two modes: natively as a python package or as a containerized docker image.

Using docker run

To run using docker, be sure to assign an "input" directory to /incoming and an output directory to /outgoing. Make sure that the $(pwd)/out directory is world writable!

Now, prefix all calls with

docker run --rm -v $(pwd)/in:/incoming -v $(pwd)/out:/outgoing            \
  local/pl-pdfgeneration pdfgeneration.py --imagefile ex-covid.jpeg             \
  --patientId 1234567  /incoming /outgoing               \

Examples

docker build -t local/pl-pdfgeneration .

docker run --rm -v $(pwd)/in:/incoming -v $(pwd)/out:/outgoing local/pl-pdfgeneration pdfgeneration.py --imagefile ex-covid.jpeg --patientId 1234567 /incoming /outgoing

docker run --rm local/pl-pdfgeneration pdfgeneration.py --json