_____  _       _                               _
                     / __  \| |     | |                             | |
 _ __ ___   __ _ ____`' / /'| |_   _| |_   _ __ ___ _ __   ___  _ __| |_
| '_ ` _ \ / _` |_  /  / /  | | | | | __| | '__/ _ \ '_ \ / _ \| '__| __|
| | | | | | (_| |/ / ./ /___| | |_| | |_  | | |  __/ |_) | (_) | |  | |_
|_| |_| |_|\__, /___|\_____/|_|\__,_|\__| |_|  \___| .__/ \___/|_|   \__|
            __/ |                     ______       | |
           |___/                     |______|      |_|

pl-mgz2LUT_report

Table of Contents

• pl-mgz2LUT_report
  • Abstract
  • Description
  • Usage
  • Arguments
  • Development
  • Run

Abstract

An app to generate a report on volumes of various brain segments listed in a Look-up Table (Default = FreeSurferLUT.txt)

Description

mgz2lut_report is a ChRIS DS plugin to generate a report (text,pdf, html, json) based on user's choice when an input .mgz file is provided. The default look up table used is FreeSurferColorLUT.txt but the user can specify their own look up file using the arg <lookUpFile>

Usage

mgz2lut_report                                                  \
    [--file_name <fileName>]                                    \
    [--report_name <reportName>]                                \
    [--report_types <reportTypes>]                              \
    [--LUT <lookUpFile>]                                        \
    [-v <level>] [--verbosity <level>]                          \
    [--version]                                                 \
    [--man]                                                     \
    [--meta]                                                    \
    <inputDir>
    <outputDir>

Arguments

[--file_name <fileName>]
Specify the path of the input mgz file here

[--report_name <reportName>]
If specified, creates an o/p in reportName
Default report name is mgz2LUT_report

[--report_types <reportTypes>]
Specify comma separated file types to generate multiple reports
You can specify txt, json, pdf, html
Default is txt

[--LUT <lookUpFile>]
If specified, the lookUpFile is referred instead to default LUT
Default LUT is FreeSurferColorLUT.txt

[-v <level>] [--verbosity <level>]
Verbosity level for app. Not used currently.

[--version]
If specified, print version number.

[--man]
If specified, print (this) man page.

[--meta]
If specified, print plugin meta data.


Getting inline help is

.. code::

    docker run --rm fnndsc/pl-mgz2lut_report mgz2lut_report --man

Development

Build the Docker container

docker build -t local/pl-mgz2lut_report .

Python dependencies can be added to setup.py. After a successful build, track which dependencies you have installed by generating the requirements.txt file

docker run --rm local/pl-mgz2lut_report -m pip freeze > requirements.txt

For the sake of reproducible builds, ensure that requirements.txt is up-to-date before you publish your code.

git add requirements.txt && git commit -m "Bump requirements.txt" && git push

Run

Assuming that we have mgz files in the in directory named myFile.mgz

mkdir in out && chmod 777 out
docker run --rm -v $(pwd)/in:/incoming -v $(pwd)/out:/outgoing      \
        fnndsc/pl-mgz2lut_report mgz2lut_report.py                  \
        --file_name myFile.mgz                                      \
        /incoming /outgoing