pl-brainmri_preprocessed

Table of Contents

• Abstract
• Synopsis
• Description
• Arguments
• Run
  • Using PyPI
  • Using docker run
• Examples
  • Check available pre-processed data
  • Simulate a processing delay
  • Copy only specific folders

Abstract

A app to demonstrate the various results of GE pipeline

Synopsis

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

Description

brainmri_preprocessed.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.

[--copySpec]
If specified, copies only specific directories

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 brainmri_preprocessed

and run with

brainmri_preprocessed.py --man /tmp /tmp

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

brainmri_preprocessed.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-brainmri_preprocessed brainmri_preprocessed.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-brainmri_preprocessed brainmri_preprocessed.py                        \
        --man                                                       \
        /incoming /outgoing

Examples

Check available pre-processed data

To get a listing of the internal tree of already processed:

docker run --rm -v $(pwd)/in:/incoming -v $(pwd)/out:/outgoing      \
        fnndsc/pl-brainmri_preprocessed brainmri_preprocessed.py                    \
        -T ../preprocessed                                          \
        /incoming /outgoing

Simulate a processing delay

To simulate a processing delay, specify some time in seconds:

docker run --rm -v $(pwd)/in:/incoming -v $(pwd)/out:/outgoing      \
        fnndsc/pl-brainmri_preprocessed brainmri_preprocessed.py                    \
        -P 20                                                       \
        /incoming /outgoing

Copy only specific folders

To copy only 'input_data' & 'ground_truth_slices'

docker run --rm -v $(pwd)/in:/incoming -v $(pwd)/out:/outgoing      \
        fnndsc/pl-brainmri_preprocessed brainmri_preprocessed.py                    \
        -c input,truth                                     \
        /incoming /outgoing