This app simulates an MPC compute call and creates a z-score file.
Project description
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 mpcsand run with
mpcs.py --man /tmp /tmpto get inline help. The app should also understand being called with only two positional arguments
mpcs.py /some/input/directory /destination/directoryUsing 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 /outgoingArguments
[--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
