pl-pfdicom_tagSub
Table of Contents
Abstract
This app performs a recursive walk down an input tree, and for each DICOM file (as filtered with a -e .dcm), will perform an edit or substitution on a pattern of user specified DICOM tags. Resultant edited files are saved in the corresponding location in the output tree. This page is not the canonical reference for pfdicom_tagSub on which this plugin is based. Please see https://github.com/FNNDSC/pfdicom_tagSub for detail about the actual tag substitution process and the pattern of command line flags.
Note that the only different between this plugin and the reference pfdicom_tagSub is that the reference has explicit flags for inputDir and outputDir while this plugin uses positional arguments for the same.
Description
pl-pfdicom_tagsub is a ChRIS-based application that wraps around pfdicom_tagSub and is used to edit the contents of user-specified DICOM tags..
Usage
python dcm_tagSub.py
[-h|--help]
[--json] [--man] [--meta]
[--savejson <DIR>]
[-v|--verbosity <level>]
[--version]
[-e|--extension <DICOMextension>]
[-O|--outputDir <outputDir>]
[-F|--tagFile <JSONtagFile>]
[-T|--tagStruct <JSONtagStructure>]
[-n|--tagInfo <delimited_parameters>]
[-s|--splitToken <split_token>]
[-k|--splitKeyValue <keySplit>]
[-o|--outputFileStem <outputFileStem>]
[--outputLeafDir <outputLeafDirFormat>]
[--threads <numThreads>]
<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.
[--version]
If specified, print version number and exit.
[-e|--extension <DICOMextension>]
An optional extension to filter the DICOM files of interest from the
<inputDir>.
[-O|--outputDir <outputDir>]
The output root directory that will contain a tree structure identical
to the input directory, and each "leaf" node will contain the analysis
results.
[-F|--tagFile <JSONtagFile>]
Parse the tags and their "subs" from a JSON formatted <JSONtagFile>.
[-T|--tagStruct <JSONtagStructure>]
Parse the tags and their "subs" from a JSON formatted <JSONtagStucture>
string passed directly in the command line. Note that sometimes protecting
a JSON string can be tricky, especially when used in scripts or as variable
expansions. If the JSON string is problematic, use the [--tagInfo <string>]
instead.
[-n|--tagInfo <delimited_parameters>]
A token delimited string that is reconstructed into a JSON structure by the
script. This is often useful if the [--tagStruict] JSON string is hard to
parse in scripts and variable passing within scripts. The format of this
string is:
"<tag1><splitKeyValue><value1><split_token><tag2><splitKeyValue><value2>"
for example:
--splitToken ","
--splitKeyValue ':'
--tagInfo "PatientName:anon,PatientID:%_md5|7_PatientID"
or more complexly (esp if the ':' is part of the key):
--splitToken "++"
--splitKeyValue "="
--tagInfo "PatientBirthDate = %_strmsk|******01_PatientBirthDate ++
re:.*hysician" = %_md5|4_#tag"
[-s|--splitToken <split_token>]
The token on which to split the <delimited_parameters> string.
Default is '++'.
[-k|--splitKeyValue <keyValueSplit>]
The token on which to split the <key> <value> pair. Default is ':'
but this can be problematic if the <key> itself has a ':' (for example
in the regular expression expansion).
[-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.
[--outputLeafDir <outputLeafDirFormat>]
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.
[--threads <numThreads>]
If specified, break the innermost analysis loop into <numThreads>
threads.
Getting inline help is:
docker run --rm fnndsc/pl-pfdicom_tagSub dcm_tagSub --manRun
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_tagSub dcm_tagSub \
/incoming /outgoingDevelopment
Build the Docker container:
docker build -t local/pl-pfdicom_tagSub .Run unit tests:
docker run --rm local/pl-pfdicom_tagSub nosetestsExamples
docker run -it --rm -v $(pwd)/in:/incoming -v $(pwd)/out:/outgoing \
fnndsc/pl-pfdicom_tagsub dcm_tagSub \
--tagStruct '
{
"PatientName": "%_name|patientID_PatientName",
"PatientID": "%_md5|7_PatientID",
"AccessionNumber": "%_md5|8_AccessionNumber",
"PatientBirthDate": "%_strmsk|******01_PatientBirthDate",
"re:.*hysician": "%_md5|4_#tag",
"re:.*stitution": "#tag",
"re:.*ddress": "#tag"
}
' --threads 0 -v 2 -e .dcm \
/incoming /outgoing
-- OR equivalently --
docker run -it --rm -v $(pwd)/in:/incoming -v $(pwd)/out:/outgoing \
fnndsc/pl-pfdicom_tagsub dcm_tagSub \
-e dcm \
--splitToken "," \
--splitKeyValue "=" \
--tagInfo '
PatientName = %_name|patientID_PatientName,
PatientID = %_md5|7_PatientID,
AccessionNumber = %_md5|8_AccessionNumber,
PatientBirthDate = %_strmsk|******01_PatientBirthDate,
re:.*hysician = %_md5|4_#tag,
re:.*stitution = #tag,
re:.*ddress = #tag
' --threads 0 --printElapsedTime \
/incoming /outgoing