pl-lung_cnp

Table of Contents

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

Abstract

This application houses a set of images that can be used in Normal/COVID/Pneumonia testing of COVIDNET.

Description

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 <dir>

Usage

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

Arguments

[--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:

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.

docker run --rm -u $(id -u)                             \
     -v $(pwd)/out:/outgoing                            \
    fnndsc/pl-lung_cnp lung_cnp                         \
    /outgoing

Development

Build the Docker container:

docker build -t local/pl-lung_cnp .

Run unit tests:

docker run --rm local/pl-lung_cnp nosetests

Examples

Copy the embedded lung CT data to the out directory

# 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

# 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