fnndsc/pl-lung_cnp
A ChRIS FS plugin that carries lung images of Normal/COVID/Pneumonia exemplars
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.. image:: https://img.shields.io/docker/v/fnndsc/pl-lung_cnp?sort=semver :target: https://hub.docker.com/r/fnndsc/pl-lung_cnp
.. image:: https://img.shields.io/github/license/fnndsc/pl-lung_cnp :target: https://github.com/FNNDSC/pl-lung_cnp/blob/master/LICENSE
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.. contents:: Table of Contents
This application houses a set of images that can be used in Normal/COVID/Pneumonia testing of COVIDNET.
lung_cnp
is a ChRIS-based application that simply copies a set of DICOM images to its output directory. The plugin is used as a convenient delivery vehicle containing images suitable for testing and further development.
The default behaviour is to copy all the files in the internal/default
.. code::
lung_cnp \
[--file <onlyCopyThisFile>] \
[--dir <dir>] \
[-h] [--help] \
[--json] \
[--man] \
[--meta] \
[--savejson <DIR>] \
[-v <level>] [--verbosity <level>] \
[--version] \
<outputDir>
Arguments
.. code::
[--file <onlyCopyThisFile>]
If specified, only copy this specific file to the output directory.
This course assumes that <onlyCopyThisFile> exists in the container
<dir>.
[--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.
[-h] [--help]
If specified, show help message and exit.
[--json]
If specified, show json representation of app and exit.
[--man]
If specified, print (this) man page and exit.
[--meta]
If specified, print plugin meta data and exit.
[--savejson <DIR>]
If specified, save json representation file to DIR and exit.
[-v <level>] [--verbosity <level>]
Verbosity level for app. Not used currently.
[--version]
If specified, print version number and exit.
Getting inline help is:
.. code:: bash
docker run --rm fnndsc/pl-lung_cnp lung_cnp --man
Run
~~~
You need to specify input and output directories using the `-v` flag to `docker run`.
.. code:: bash
docker run --rm -u $(id -u) \
-v $(pwd)/out:/outgoing \
fnndsc/pl-lung_cnp lung_cnp \
/outgoing
Development
-----------
Build the Docker container:
.. code:: bash
docker build -t local/pl-lung_cnp .
Run unit tests:
.. code:: bash
docker run --rm local/pl-lung_cnp nosetests
Examples
--------
Copy the embedded lung CT data to the ``out`` directory
.. code:: bash
# Here, files are copied as localuser
mkdir out && chmod 777 out
docker run --rm -u $(id -u) \
-v $(pwd)/out:/outgoing \
fnndsc/pl-lung_cnp lung_cnp \
/outgoing
Copy a user specified directory to the out
directory
.. code:: bash
# Here, files are copied as root
mkdir out && chmod 777 out
docker run --rm \
-v $(pwd)/out:/outgoing \
fnndsc/pl-lung_cnp lung_cnp \
--dir /etc \
/outgoing
.. image:: https://raw.githubusercontent.com/FNNDSC/cookiecutter-chrisapp/master/doc/assets/badge/light.png
:target: https://chrisstore.co
docker pull fnndsc/pl-lung_cnp