pl-generate_hdf5

Table of Contents

• Abstract
• Synopsis
• Description
• Arguments
• Run
  • Using PyPI
  • Using docker run
• Examples

Abstract

An app to convert original and segmented brain images in mgz format to .hdf5 format in axial, sagittall, and coronal plane

Synopsis

python generate_hdf5.py                                           \
    [-v <level>] [--verbosity <level>]                          \
    [--version]                                                 \
    [--man]                                                     \
    [--meta]                                                    \
    <inputDir>
    <outputDir>

Description

generate_hdf5.py is a ChRIS-based application that...

Arguments

[-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.

Run

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

Using PyPI

To run from PyPI, simply do a

pip install generate_hdf5

and run with

generate_hdf5.py --man /tmp /tmp

to get inline help. The app should also understand being called with only two positional arguments

generate_hdf5.py /some/input/directory /destination/directory

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)/out:/outgoing                             \
        fnndsc/pl-generate_hdf5 generate_hdf5.py                        \

Thus, getting inline help is:

mkdir in out && chmod 777 out
docker run --rm -v $(pwd)/in:/incoming -v $(pwd)/out:/outgoing      \
        fnndsc/pl-generate_hdf5 generate_hdf5.py                        \
        --man                                                       \
        /incoming /outgoing

Examples