README.rst

pl-csv2json

Table of Contents

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

Abstract

An app to convert CSV predition file generated from pl-lld_inference into a more meaningful JSON representation.

Description

csv2json is a ChRIS ds-type application processes an upstream CSV formatted predition file and generates a more friendly JSON representation. This JSON output is used in many downstream plugins and is interpreted to determine where to place drawing and measurement markers on an image.

Usage

docker run --rm fnndsc/pl-csv2json csv2json

    [-f| --inputFileFilter <inputFileFilter>]
    [-t|--tagFileFilter <tagFileFilter>]
    [-o| --outputFileStem <outputFileStem>]
    [-a|--addTags <commaSeparatedTags>]
    [-h|--help]
    [--json] [--man] [--meta]
    [--savejson <DIR>]
    [-v|--verbosity <level>]
    [--version]
    <inputDir> <outputDir>

Arguments

[-f| --inputFileFilter <inputFileFilter>]
A glob pattern string, default is "**/*.csv", representing the input
file pattern to analyze.

[-t|--tagFileFilter <tagFileFilter>]
A glob pattern string, default is "**/*.dcm", representing the input tag
file pattern to analyze.

[-t|--tagFileFilter <tagFileFilter>]
A glob pattern string, default is "**/*.dcm", representing the input
dicom file pattern to analyze.

[-o| --outputFileStem <outputFileStem>]
The name of the output JSON file to be created (without the extension).

[-a|--addTags <commaSeparatedTags>]
A comma separated string conatining the list of tags to add in the info section
of the output JSON. The default included tag is 'PatientID'.

[-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-csv2json csv2json --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-csv2json csv2json                         \
    /incoming /outgoing

Development

Build the Docker container:

docker build -t local/pl-csv2json .

Run unit tests:

docker run --rm local/pl-csv2json nosetests

Examples

Put some examples here!