README.rst

pl-dcm2mha_cnvtr

Table of Contents

• Abstract
• Description
• Usage
  • Arguments
  • Run
• Development
• Examples

Abstract

An app that converts between DICOM and mha format files.

Description

dcm2mha_cnvtr is a ChRIS ds-type application that consumes image files of one type as input and converts these files to a reciprocal type as output. The reciprocating types of files are DICOM (dcm) and MetaImage Medical Format (mha).

Usage

docker run --rm fnndsc/pl-dcm2mha_cnvtr dcm2mha_cnvtr
    [-f|--inputFileFilter <inputFileFilter>]
    [-s|--saveAsPng]
    [-n|--imageName <pngFileName>]
    [-p|--filterPerc <filterPercentage>]
    [-r| --rotate <rotateAngle>]
    [--pftelDB <DBURLpath>]
    [-h|--help]
    [--json] [--man] [--meta]
    [--savejson <DIR>]
    [-v|--verbosity <level>]
    [--version]
    <inputDir> <outputDir>

Arguments

[-f|--inputFileFilter <inputFileFilter>]
A glob pattern string, default is "**/*.mha", representing the
input file pattern to convert. Specify either "**/*mha" or
"**/*dcm".

[-s|--saveAsPng]
If specified, generate a resultant PNG image along with dicoms.

[-n|--imageName <pngFileName>]
The name of the resultant PNG file. Default is "composite.png"

[-p|--filterPerc <filterPercentage>]
An integer value that represents the threshold for a high-pass
filter on the image space. Image values less than this percentage
are set to 0. This field is particularly important if image is
noisy. Note that valid image data at intensities less than this
cutoff are of course also filtered out! Default is 30.

[-r| --rotate <rotateAngle>]
An integer value in multiples of 90 that represents a rotation
angle. The input image will be rotated anticlockwise for the
provide angle.

[--pftelDB <DBURLpath>]
If specified, send telemetry logging to the pftel server and the
specfied DBpath:

    --pftelDB   <URLpath>/<logObject>/<logCollection>/<logEvent>

for example

    --pftelDB http://localhost:22223/api/v1/weather/massachusetts/boston

Indirect parsing of each of the object, collection, event strings is
available through `pftag` so any embedded pftag SGML is supported. So

    http://localhost:22223/api/vi/%platform/%timestamp_strmsk|**********_/%name

would be parsed to, for example:

    http://localhost:22223/api/vi/Linux/2023-03-11/posix

[-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-dcm2mha_cnvtr dcm2mha_cnvtr --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)/in:/incoming -v $(pwd)/out:/outgoing      \
    fnndsc/pl-dcm2mha_cnvtr dcm2mha_cnvtr               \
    /incoming /outgoing

Development

Build the Docker container:

docker build -t local/pl-dcm2mha_cnvtr .

Run unit tests:

docker run --rm local/pl-dcm2mha_cnvtr nosetests

Debug container using live-mount:

Examples

Convert a set of DICOM files in a directory called dicom to MHA files in a directory called mha:

docker run -v $PWD/dicom:/incoming -v $PWD/mha:/outgoing    \
            fnndsc/pl-dcm2mha_cnvtr dcm2mha_cnvtr           \
            --inputFileFilter "**/*.dcm"                    \
            /incoming /outgoing

and convert these back to DICOM again

docker run -v $PWD/mha:/incoming -v $PWD/dicom:/outgoing    \
            fnndsc/pl-dcm2mha_cnvtr dcm2mha_cnvtr           \
            --inputFileFilter "**/*.mha"                    \
            /incoming /outgoing