README.rst

pl-lungct

Table of Contents

• Abstract
• Description
• Usage
  • Arguments
• Development
• Debug
• Examples
  • Copy the embedded lung CT data to the out directory
  • Copy a user specified directory to the out directory

Abstract

This plugin copies canned data to its output and is primarily of use in the COVID-NET workflow.

Description

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.

Usage

lungct                                                          \
    [--dir <dir>]                                               \
    [-h] [--help]                                               \
    [--json]                                                    \
    [--man]                                                     \
    [--meta]                                                    \
    [--savejson <DIR>]                                          \
    [-v <level>] [--verbosity <level>]                          \
    [--version]                                                 \
    <outputDir>

Arguments

[--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:

docker run --rm fnndsc/pl-lungct lungct --man

Development

Build the Docker container:

docker build --build-arg UID=$UID -t local/pl-lungct .

Debug

Assuming you are in the root dir of the source repo:

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.

# 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

# 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