An anonymized MRI exemplar
Project description
Abstract
This application simply copies from embedded data a reference normal anonymized MRI of a subject aged 10 years, 06 months, 01 days.
Synopsis
mri10yr06mo01da_normal.python \
[-v <level>] [--verbosity <level>] \
[--version] \
[--man] \
[--meta] \
[--dir <dir>] \
[--splash <splash>] \
<outputDir>
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.
[--splash <splash>]
An optional splash message to print on startup.
[--dir <dir>]
An optional override directory to copy to the <outputDir>.
Note, if run from a containerized version, this will copy
a directory from the *container* file system.
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 mri10yr06mo01da_normal
and run with
mri10yr06mo01da_normal.py --man /tmp
to get inline help. The app should also understand being called with only one positional argument
mri10yr06mo01da_normal.py /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-mri10yr06mo01da_normal mri10yr06mo01da_normal.py \
Thus, getting inline help is:
mkdir out && chmod 777 out
docker run --rm -v $(pwd)/in:/incoming -v $(pwd)/out:/outgoing \
fnndsc/pl-mri10yr06mo01da_normal mri10yr06mo01da_normal.py \
--man \
/outgoing
Examples
Copy the embedded MRI data to the out directory
mkdir out && chmod 777 out
docker run --rm -v $(pwd)/out:/outgoing \
fnndsc/pl-mri10yr06mo01da_normal mri10yr06mo01da_normal.py \
/outgoing
Copy a user specified directory to the out directory
mkdir out && chmod 777 out
docker run --rm -v $(pwd)/out:/outgoing \
fnndsc/pl-mri10yr06mo01da_normal mri10yr06mo01da_normal.py \
--dir /usr/src/data
/outgoing
Project details
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distribution
Close
Hashes for mri10yr06mo01da_normal-1.1.2.tar.gz
Algorithm | Hash digest | |
---|---|---|
SHA256 | 392eaaeb70192ab30deb8ce1a42cb0834600d5a62fd7e22c34f6e1b0a356d9bd |
|
MD5 | 97fd22044b323aa3298669f22e57db63 |
|
BLAKE2b-256 | f780a02a17e403c83d0e1d3c47acce6b5fb2a3e62bb1eb06970b74e27c264e9b |