README.rst

pl-img2dcm

Table of Contents

• Abstract
• Description
• Usage
  • Arguments
  • Run
• Development
• Examples

Abstract

An app to convert an input image to a DICOM format

Description

img2dcm is a ChRIS ds-type is an app that simply converts an input image (jpg/png) to a DICOM format. It does require a base/reference DICOM image from which to import the tag header information.

Usage

docker run --rm fnndsc/pl-img2dcm img2dcm
    [-i|--inputImageFilter <imageFilter>]
    [-d|--inputDCMFilter <dicomFilter>]
    [-h|--help]
    [--json] [--man] [--meta]
    [--savejson <DIR>]
    [-v|--verbosity <level>]
    [--version]
    <inputDir> <outputDir>

Arguments

[-i|--inputImageFilter <imageFilter>]
A glob pattern string, default is "**/*.png", representing the input
file pattern to analyze.

[-d|--inputDCMFilter <dicomFilter>]
A glob pattern string, default is "**/*.dcm", representing the input
dicom files to fetch tags.

[-h] [--help]
If specified, show help message and exit.

[--json]
If specified, show json representation of app and exit.

[--man]
If specified, print (this) man page and exit.

[--meta]
If specified, print plugin meta data and exit.

[--savejson <DIR>]
If specified, save json representation file to DIR and exit.

[-v <level>] [--verbosity <level>]
Verbosity level for app. Not used currently.

[--version]
If specified, print version number and exit.

Getting inline help is:

docker run --rm fnndsc/pl-img2dcm img2dcm --man

Run

You need to specify input and output directories using the -v flag to docker run.

docker run --rm -u $(id -u)                             \
    -v $(pwd)/in:/incoming -v $(pwd)/out:/outgoing      \
    fnndsc/pl-img2dcm img2dcm                        \
    /incoming /outgoing

Development

Build the Docker container:

docker build -t local/pl-img2dcm .

Run unit tests:

docker run --rm local/pl-img2dcm nosetests

Examples

Put some examples here!