fnndsc/pl-dicom_filter repository overview

⁠pl-dicom_filter

pl-dicom_filter is a ChRIS⁠ ds plugin which takes in DICOM files in its input directory and filters DICOMs based on specified criteria into its output directory.

⁠Abstract

A ChRIS plugin to filter DICOM files using filters on DICOM tags, image count thresholds, and text similarity, with optional PHI handling.

⁠Installation

pl-dicom_filter is a ChRIS⁠ plugin, meaning it can run either within ChRIS or from the command line using container technologies such as Apptainer⁠.

⁠Local Usage

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

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

To print its available options, run:

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

⁠Examples

dicom_filter 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-dicom_filter:latest dicom_filter [--args] incoming/ outgoing/

⁠Development

Instructions for developers.

⁠Building

Build a local container image:

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

⁠Running

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

docker run --rm -it --userns=host -u $(id -u):$(id -g) \
    -v $PWD/dicom_filter.py:/usr/local/lib/python3.11/site-packages/dicom_filter.py:ro \
    -v $PWD/in:/incoming:ro -v $PWD/out:/outgoing:rw -w /outgoing \
    localhost/fnndsc/pl-dicom_filter dicom_filter /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_filter:dev --build-arg extras_require=dev .
docker run --rm -it localhost/fnndsc/pl-dicom_filter: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 dicom_filter.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_filter:1.2.3 .
docker push docker.io/fnndsc/pl-dicom_filter: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-dicom_filter:1.2.3 chris_plugin_info -d docker.io/fnndsc/pl-dicom_filter:1.2.3 > chris_plugin_info.json

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