fnndsc/pl-dyanon repository overview

⁠A dynamic anonymization ChRIS plugin

pl-dyanon is a ChRIS⁠ ds plugin which takes CSV-based DICOM selection and rule definition files as input and produces dynamically anonymized DICOM studies as output. The plugin can optionally push results to Orthanc, a remote PACS, or downstream ChRIS workflows.

⁠Abstract

Medical imaging workflows frequently require flexible, rule-driven anonymization that can adapt dynamically to different studies, projects, or data-sharing requirements. pl-dyanon enables scalable, bulk DICOM anonymization driven by external metadata, CSV inputs, and configurable tag-preservation rules.

The plugin integrates with the ChRIS ecosystem, Orthanc servers, and optional PACS endpoints. It supports parallel execution, selective DICOM filtering, image-count–based rules, and optional email notifications upon completion.

⁠Installation

pl-dyanon 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-dyanon as a container:

apptainer exec docker://fnndsc/pl-dyanon dyanon [--args values...] input/ output/

To print its available options, run:

apptainer exec docker://fnndsc/pl-dyanon dyanon --help

⁠Examples

dyanon requires two positional arguments: a directory containing input data, and a directory where to create output data. First, create the input directory and move input data into it.

mkdir incoming/ outgoing/
mv some.dat other.dat incoming/
apptainer exec docker://fnndsc/pl-dyanon:latest dyanon [--args] incoming/ outgoing/

⁠Development

Instructions for developers.

⁠Building

Build a local container image:

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

⁠Running

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

docker run --rm -it --userns=host -u $(id -u):$(id -g) \
    -v $PWD/dyanon.py:/usr/local/lib/python3.12/site-packages/dyanon.py:ro \
    -v $PWD/in:/incoming:ro -v $PWD/out:/outgoing:rw -w /outgoing \
    localhost/fnndsc/pl-dyanon dyanon /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-dyanon:dev --build-arg extras_require=dev .
docker run --rm -it localhost/fnndsc/pl-dyanon: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-dyanon:1.2.3 .
docker push docker.io/fnndsc/pl-dyanon:1.2.3

⁠Get JSON Representation

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

docker run --rm docker.io/fnndsc/pl-dyanon:1.2.3 chris_plugin_info -d docker.io/fnndsc/pl-dyanon:1.2.3 > chris_plugin_info.json

Intructions on how to upload the plugin to ChRIS can be found here: https://chrisproject.org/docs/tutorials/upload_plugin⁠