pl-chrisproject-matplotlib

Table of Contents

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

Abstract

Create static, animated, and interactive visualizations with Matplotlib for ChRIS

Description

chrisproject_matplotlib is a ChRIS ds-type application that takes in data as text files and produces images.

Usage

docker run --rm fnndsc/pl-chrisproject-matplotlib chrisproject_matplotlib
    [-h|--help]
    [--json] [--man] [--meta]
    [--savejson <DIR>]
    [-v|--verbosity <level>]
    [--version]
    <inputDir> <outputDir>

Arguments

[-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-chrisproject-matplotlib chrisproject_matplotlib --man

Run

You need to specify input (containing NII files) and output directories (to which PNGs of the plots would be written to) using the -v flag to docker run.

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

Development

Build the Docker container:

docker build -t local/pl-chrisproject-matplotlib .

Run unit tests:

docker run --rm local/pl-chrisproject-matplotlib nosetests

Examples

Overview of many common plotting commands in Matplotlib: https://matplotlib.org/stable/plot_types/index.html

Example plots: https://matplotlib.org/stable/gallery/index.html