fnndsc/pl-pacs_retrieve repository overview

⁠A ChRIS plugin to retrieve from a remote PACS

pl-pacs_retrieve is a ChRIS⁠ ds plugin that retrieves DICOM images from a remote PACS using pfdcm⁠.
It consumes a JSON file describing DICOM studies or series and retrieves the corresponding DICOM files into the output directory.

⁠Abstract

Medical imaging workflows often require programmatic retrieval of DICOM data from a PACS.
pl-pacs_retrieve enables automated PACS retrieval within a ChRIS pipeline by consuming a JSON description of studies or series and fetching the associated DICOM files via pfdcm.

The plugin supports retrieving individual series defined in a JSON file or optionally retrieving an entire study.

⁠Installation

pl-pacs_retrieve 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-pacs_retrieve as a container:

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

To print its available options, run:

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

⁠Examples

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

⁠Development

Instructions for developers.

⁠Building

Build a local container image:

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

⁠Running

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

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