Process DICOM tags and performs substitutions -- part of the pf* family.


License
MIT
Install
pip install pfdicom-tagSub==1.4.22

Documentation

pfdicom_tagSub

https://travis-ci.org/FNNDSC/pfdicom_tagSub.svg?branch=master

Quick Overview

  • pfdicom_tagSub reads/edits/saves DICOM meta information. It can be used to anonymize DICOM header data.

Overview

pfdicom_tagSub replaces a set of <tag, value> pairs in a DICOM header with values passed in a JSON structure.

The script accepts an <inputDir>, and then from this point an os.walk() is performed to extract all the subdirs. Each subdir is examined for DICOM files (in the simplest sense by a file extension mapping) are passed to a processing method that reads and replaces specified DICOM tags, saving the result in a corresponding directory and filename in the output tree.

Installation

Dependencies

The following dependencies are installed on your host system/python3 virtual env (they will also be automatically installed if pulled from pypi):

  • pfmisc (various misc modules and classes for the pf* family of objects)
  • pftree (create a dictionary representation of a filesystem hierarchy)
  • pfdicom (handle underlying DICOM file reading)

Using PyPI

The best method of installing this script and all of its dependencies is by fetching it from PyPI

pip3 install pfdicom_tagSub

Command line arguments

-I|--inputDir <inputDir>
Input DICOM directory to examine. By default, the first file in this
directory is examined for its tag information. There is an implicit
assumption that each <inputDir> contains a single DICOM series.

-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 <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>
passed directly in the command line.

-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.

[-x|--man]
Show full help.

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

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

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

-v|--verbosity <level>
Set the app verbosity level.

    0: No internal output;
    1: Run start / stop output notification;
    2: As with level '1' but with simpleProgress bar in 'pftree';
    3: As with level '2' but with list of input dirs/files in 'pftree';
    5: As with level '3' but with explicit file logging for
            - read
            - analyze
            - write

Examples

Perform a DICOM anonymization by processing specific tags:

pfdicom_tagSub                                      \\
    -I /var/www/html/normsmall -e dcm               \\
    -O /var/www/html/anon                           \\
    --tagStruct '
    {
        "PatientName":              "%_name|patientID_PatientName",
        "PatientID":                "%_md5|7_PatientID",
        "AccessionNumber":          "%_md5|10_AccessionNumber",
        "PatientBirthDate":         "%_strmsk|******01_PatientBirthDate",
        "ReferringPhysicianName":   "ReferringPhysicianName",
        "PhysiciansOfRecord":       "PhysiciansOfRecord",
        "RequestingPhysician":      "RequestingPhysician",
        "InstitutionAddress":       "InstitutionAddress",
        "InstitutionName":          "InstitutionName"
    }
    ' --threads 0 --printElapsedTime

which will output only at script conclusion and will log a JSON formatted string.