pl-pfdicom_tagExtract

Table of Contents

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

Abstract

This app performs a recursive walk down an input tree, and for each location with a DICOM file, will generate a report in the corresponding location in the output tree.

Description

dcm_tagExtract is a ChRIS-based application that generates reports in various formats (txt, html, etc) based on parsing DICOM meta data (i.e. DICOM tags).

Usage

python dcm_tagExtract.py
    [-h|--help]
    [--json] [--man] [--meta]
    [--savejson <DIR>]
    [-v|--verbosity <level>]
    [-i|--inputFile <inputFile>]
    [-e|--extension <extension>]
    [-F|--tagFile <tags>]
    [-T|--tagList <list_of_tags>]
    [-r]
    [-m|--imageFile <imageFile>]
    [-s|--imageScale <imageScale>]
    [-o|--outputFileStem <outputFileStem>]
    [-t|--outputFileType <list_of_output_types>]
    [--printElapsedTime]
    [--useIndexhtml]
    [-p|--printToScreen]
    [-y|--synopsis]
    [--threads]
    [--outputLeafDir]
    [--followLinks]
    [--jsonReturn]
    [--version]
    <inputDir> <outputDir>

Arguments

[-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.

[-i|--inputFile <inputFile>]
An optional <inputFile> specified relative to the <inputDir>. If
specified, then do not perform a directory walk, but convert only
this file.

[-e|--extension <extension>]
An optional extension to filter the DICOM files of interest from the
<inputDir>.

[-F|--tagFile <tags>]
Read the tags, one-per-line in <tagFile>, and print the
corresponding tag information in the DICOM <inputFile>.

[-T|--tagList <list_of_tags>]
Read the list of comma-separated tags in <tagList>, and print the
corresponding tag information parsed from the DICOM <inputFile>.

[-r]
If specified, display raw tags

[-m|--imageFile <imageFile>]
If specified, also convert the <inputFile> to <imageFile>. If the
name is preceded by an index and colon, then convert this indexed
file in the particular <inputDir>.

[-s|--imageScale <imageScale>]
If an image conversion is specified, this flag will scale the image
by <factor> and use an interpolation <order>. This is useful in
increasing the size of images for the html output.

Note that certain interpolation choices can result in a significant
slowdown!

    interpolation order:

    'none', 'nearest', 'bilinear', 'bicubic', 'spline16',
    'spline36', 'hanning', 'hamming', 'hermite', 'kaiser', 'quadric',
    'catrom', 'gaussian', 'bessel', 'mitchell', 'sinc', 'lanczos'

[-o|--outputFileStem <outputFileStem>]
The output file stem to store data. This should *not* have a file
extension, or rather, any "." in the name are considered part of
the stem and are *not* considered extensions.

[-t|--outputFileType <list_of_output_types>]
A comma specified list of output types. These can be:

    o <type>    <ext>       <desc>
    o raw       -raw.txt    the raw internal dcm structure to string
    o json      .json       a json representation
    o html      .html       an html representation with optional image
    o dict      -dict.txt   a python dictionary
    o col       -col.txt    a two-column text representation (tab sep)
    o csv       .csv        a csv representation

    Note that if not specified, a default type of 'raw' is assigned.

[--printElapsedTime]
If specified, print run time

[--useIndexhtml]
If specified, force html file to be called index.html

[-p|--printToScreen]
If specified, will print tags to screen.

[-y|--synopsis]
Show brief help.

[--threads]

[--outputLeafDir]
If specified, will apply the <outputLeafDirFormat> to the output
directories containing data. This is useful to blanket describe
final output directories with some descriptive text, such as
'anon' or 'preview'.

This is a formatting spec, so

    --outputLeafDir 'preview-%s'

where %s is the original leaf directory node, will prefix each
final directory containing output with the text 'preview-' which
can be useful in describing some features of the output set.

[--followLinks]
If specified, follow symbolic links.

[--jsonReturn]
If specified, output a JSON dump of final return.

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

Getting inline help is:

docker run --rm fnndsc/pl-pfdicom_tagExtract dcm_tagExtract --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-pfdicom_tagExtract dcm_tagExtract                        \
    /incoming /outgoing

Development

Build the Docker container:

docker build -t local/pl-pfdicom_tagExtract .

Run unit tests:

docker run --rm local/pl-pfdicom_tagExtract nosetests

Examples

Put some examples here!

docker run -it --rm -v $(pwd)/in:/incoming -v $(pwd)/out:/outgoing      \
        -v $(pwd)/dcm_tagExtract/dcm_tagExtract.py:/usr/src/dcm_tagExtract/dcm_tagExtract.py  \
        -v $(pwd)/dcm_tagExtract/pfdicom_tagExtract.py:/usr/local/lib/python3.5/dist-packages/pfdicom_tagExtract/pfdicom_tagExtract.py \
        fnndsc/pl-pfdicom_tagextract dcm_tagExtract.py                  \
        -o '%_md5|6_PatientID-%PatientAge'                              \
        -m 'm:%_nospc|-_ProtocolName.jpg'                               \
        -s 3:none --useIndexhtml                                        \
        -t raw,json,html,dict,col,csv                                   \
        --threads 0 -v 2 -e .dcm                                        \
        /incoming /outgoing