pl-mpcs

Table of Contents

• Abstract
• Synopsis
• Run
  • Using PyPI
  • Using docker run
• Arguments
• Examples
  • Create a z-file with values between -3.0 and +3.0

Abstract

This app simulates a call to a remote Multi-Party Compute (MPC) in the context of a FreeSurfer workflow.

This particular application simply returns a z-score file to be consumed by a downstream plugin, typciall pl-z2labelmap.

NOTE: The <inputDir> is largely ignored by this plugin.

Synopsis

python mpcs.py                                                  \
    [--random] [--seed <seed>]                                  \
    [-p <f_posRange>] [--posRange <f_posRange>]                 \
    [-n <f_negRange>] [--negRange <f_negRange>]                 \
    [-z <zFile>] [--zFile <zFile>]                              \
    [-v <level>] [--verbosity <level>]                          \
    [--version]                                                 \
    [--man]                                                     \
    [--meta]                                                    \
    <inputDir>
    <outputDir>

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 mpcs

and run with

mpcs.py --man /tmp /tmp

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

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

Arguments

[--random] [--seed <seed>]
If specified, generate a z-score file based on <posRange> and
<negRange>. In addition, if a further optional <seed> is passed,
then initialize the random generator with that seed, otherwise
system time is used.

[-p <f_posRange>] [--posRange <f_posRange>]
Positive range for random max deviation generation.

[-n <f_negRange>] [--negRange <f_negRange>]
Negative range for random max deviation generation.

[-z <zFile>] [--zFile <zFile>]
z-score file to save in output directory. Defaults to 'zfile.csv'.

[-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.

Examples

Create a z-file with values between -3.0 and +3.0

mkdir in out && chmod 777 out
docker run --rm -v $(pwd)/in:/incoming -v $(pwd)/out:/outgoing      \
        fnndsc/pl-mpcs mpcs.py                                      \
        -random --seed 1                                            \
        --posRange 3.0 --negRange -3.0                              \
        in out