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An anonymized MRI exemplar

Project description

pl-mri10yr06mo01da_normal
================================

.. image:: https://badge.fury.io/py/mri10yr06mo01da_normal.svg
:target: https://badge.fury.io/py/mri10yr06mo01da_normal

.. image:: https://travis-ci.org/FNNDSC/mri10yr06mo01da_normal.svg?branch=master
:target: https://travis-ci.org/FNNDSC/mri10yr06mo01da_normal

.. image:: https://img.shields.io/badge/python-3.5%2B-blue.svg
:target: https://badge.fury.io/py/pl-mri10yr06mo01da_normal

.. contents:: Table of Contents


Abstract
--------

This application simply copies from embedded data a reference normal anonymized MRI of a subject aged 10 years, 06 months, 01 days.

Synopsis
--------

.. code:: bash

mri10yr06mo01da_normal.python \
[-v <level>] [--verbosity <level>] \
[--version] \
[--man] \
[--meta] \
[--dir <dir>] \
<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

.. code:: bash

pip install mri10yr06mo01da_normal

and run with

.. code:: bash

mri10yr06mo01da_normal.py --man /tmp

to get inline help. The app should also understand being called with only one positional argument

.. code:: bash

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

.. code:: bash

docker run --rm -v $(pwd)/out:/outgoing \
fnndsc/pl-mri10yr06mo01da_normal mri10yr06mo01da_normal.py \

Thus, getting inline help is:

.. code:: bash

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
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

.. code:: bash

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
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

.. code:: bash

mkdir out && chmod 777 out
docker run --rm -v $(pwd)/out:/outgoing \
fnndsc/pl-mri10yr06mo01da_normal mri10yr06mo01da_normal.py \
--dir /usr/src
/outgoing

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