Edit DICOM header fields

pl-dicom_headerEdit is a ChRIS ds plugin which accepts as input a filesystem tree containing nested DICOM files, and edits each DICOM header consistently. Output DICOMs are saved in a concordant location in the output directory.

Abstract

This page briefly describes a ChRIS plugin that is built around pfdicom_tagSub and exposes all of its functionality. Please refer to the referenced link for detailed information about the usage flags. The most common use case of this plugin is to anonymize DICOM files by editing their headers; however any potential use case that requires header changes is supported. Note that this is largely a rewrite of the pl-pfdicom_tagSub plugin using the chris_plugin_template to allow for the new design pattern of "percolating" arg_parsers up from ancestor apps.

Installation

pl-dicom_headerEdit is a ChRIS plugin, meaning it can run from either within ChRIS or the command-line.

Local Usage

To get started with local command-line usage, use Apptainer (a.k.a. Singularity) to run pl-dicom_headerEdit as a container:

singularity exec docker://fnndsc/pl-dicom_headeredit dicom_headerEdit [--args values...] input/ output/

To print its available options, run:

singularity exec docker://fnndsc/pl-dicom_headeredit dicom_headerEdit --help

Take care that the plugin image is all small letters (pl-dicom_headeredit), but the actual script name has some Camel case (dicom_headerEdit)!

Examples

You can run dicom_headerEdit with a --man flag to get in-line help (including some examples):

singularity exec --cleanenv docker://fnndsc/pl-dicom_headeredit dicom_headerEdit --man in out   

Note that being a ChRIS DS plugin, dicom_headerEdit requires two positional arguments: a directory containing input data, and a directory where to create output data. The order of these positional arguments in largely irrelevant. We suggest positioning them either at the very front or very end of the CLI.

In this example, assume that you have a directory called in that contains DICOM data. This data can be nested into any arbitrary tree.

singularity exec --cleanenv docker://fnndsc/pl-dicom_headeredit dicom_headerEdit  \
            in out                                                                \
            --fileFilter 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

Here, the script will create for each directory in the input that contains files with dcm a corresponding directory in the output tree. In each output location, the corresponding input DICOM files will have headers edited as in the --tagInfo.

• the PatientName value will be replaced with a Fake Name, seeded on the PatientID;

• the PatientID value will be replaced with the first 7 characters of an md5 hash of the PatientID;

• the AccessionNumber value will be replaced with the first 8 characters of an md5 hash of the AccessionNumber

• the PatientBirthDate value will set the final two characters, i.e. the day of birth, to 01 and preserve the other birthdate values

• any tags with the substring hysician will have their values replaced with the first 4 characters of the corresponding tag value md5 hash

• any tags with stitution and ddress substrings in the tag contents will have the corresponding value simply set to the tag name.

Development

Instructions for developers.

Building

Build a local container image:

docker build -t localhost/fnndsc/pl-dicom_headerEdit .

Running

Mount the source code dicom_headerEdit.py into a container to try out changes without rebuild.

docker run --rm -it --userns=host -u $(id -u):$(id -g) \
    -v $PWD/dicom_headerEdit.py:/usr/local/lib/python3.10/site-packages/dicom_headerEdit.py:ro \
    -v $PWD/in:/incoming:ro -v $PWD/out:/outgoing:rw -w /outgoing \
    localhost/fnndsc/pl-dicom_headerEdit dicom_headerEdit /incoming /outgoing

Testing

Run unit tests using pytest. It's recommended to rebuild the image to ensure that sources are up-to-date. Use the option --build-arg extras_require=dev to install extra dependencies for testing.

docker build -t localhost/fnndsc/pl-dicom_headerEdit:dev --build-arg extras_require=dev .
docker run --rm -it localhost/fnndsc/pl-dicom_headerEdit:dev pytest

Release

Steps for release can be automated by Github Actions. This section is about how to do those steps manually.

Increase Version Number

Increase the version number in setup.py and commit this file.

Push Container Image

Build and push an image tagged by the version. For example, for version 1.2.3:

docker build -t docker.io/fnndsc/pl-dicom_headerEdit:1.2.3 .
docker push docker.io/fnndsc/pl-dicom_headerEdit:1.2.3

Get JSON Representation

Run chris_plugin_info to produce a JSON description of this plugin, which can be uploaded to a ChRIS Store.

docker run --rm localhost/fnndsc/pl-dicom_headerEdit:dev chris_plugin_info > chris_plugin_info.json

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