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 in out && chmod 777 out
docker run --rm -v $(pwd)/in:/incoming -v $(pwd)/out:/outgoing \
fnndsc/pl-mri10yr06mo01da_normal mri10yr06mo01da_normal.py \
--man \
/incoming /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 $(pwd)/out:/outgoing \
fnndsc/pl-mri10yr06mo01da_normal mri10yr06mo01da_normal.py \
--dir /usr/src
/outgoing
================================
.. image:: https://badge.fury.io/py/mri10yr06mo01da_normal.svg
:target: https://badge.fury.io/py/mri10yr06mo01da_normal
.. image:: https://travis-ci.org/FNNDSC/mri10yr06mo01da_normal.svg?branch=master
:target: https://travis-ci.org/FNNDSC/mri10yr06mo01da_normal
.. image:: https://img.shields.io/badge/python-3.5%2B-blue.svg
:target: https://badge.fury.io/py/pl-mri10yr06mo01da_normal
.. contents:: Table of Contents
Abstract
--------
This application simply copies from embedded data a reference normal anonymized MRI of a subject aged 10 years, 06 months, 01 days.
Synopsis
--------
.. code:: bash
mri10yr06mo01da_normal.python \
[-v <level>] [--verbosity <level>] \
[--version] \
[--man] \
[--meta] \
[--dir <dir>] \
<outputDir>
Run
----
This ``plugin`` can be run in two modes: natively as a python package or as a containerized docker image.
Using PyPI
~~~~~~~~~~
To run from PyPI, simply do a
.. code:: bash
pip install mri10yr06mo01da_normal
and run with
.. code:: bash
mri10yr06mo01da_normal.py --man /tmp
to get inline help. The app should also understand being called with only one positional argument
.. code:: bash
mri10yr06mo01da_normal.py /destination/directory
Using ``docker run``
~~~~~~~~~~~~~~~~~~~~
To run using ``docker``, be sure to assign an "input" directory to ``/incoming`` and an output directory to ``/outgoing``. *Make sure that the* ``$(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 in out && chmod 777 out
docker run --rm -v $(pwd)/in:/incoming -v $(pwd)/out:/outgoing \
fnndsc/pl-mri10yr06mo01da_normal mri10yr06mo01da_normal.py \
--man \
/incoming /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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