lungct
5.0K
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.. contents:: Table of Contents
This plugin copies canned data to its output and is primarily of use in the COVID-NET workflow.
lungct simply copies internal lungCT DICOM data dir to the <outputDir>. If an optional [--dir <dir>] is passed, then contents of <dir> are copied instead.
.. code::
lungct \
[--dir <dir>] \
[-h] [--help] \
[--json] \
[--man] \
[--meta] \
[--savejson <DIR>] \
[-v <level>] [--verbosity <level>] \
[--version] \
<outputDir>
Arguments
.. code::
[--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-lungct lungct --man
Development
-----------
Build the Docker container:
.. code:: bash
docker build --build-arg UID=$UID -t local/pl-lungct .
Debug
-----
Assuming you are in the root dir of the source repo:
.. code:: bash
docker run -ti \
-v $(pwd)/lungct:/usr/local/lib/python3.8/dist-packages/lungct \
-v $(pwd)/out:/outgoing \
local/pl-lungct lungct /outgoing
Examples
--------
Copy the embedded lung CT data to the ``out`` directory
You need you need to specify input and output directories using the -v flag to docker run.
.. 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-lungct lungct \
/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-lungct lungct \
--dir /etc \
/outgoing
.. image:: https://raw.githubusercontent.com/FNNDSC/cookiecutter-chrisapp/master/doc/assets/badge/light.png
:target: https://chrisstore.co
Content type
Image
Digest
Size
49.5 MB
Last updated
almost 5 years ago
docker pull fnndsc/pl-lungct:1.0.3