pacsman: Picture Archiving and Communication System Manager And Numpifier

pacsman is a utility to manage interactions with a PACS in Python. It has a BaseDicomClient that provides abstract methods for a variety of DICOM-related interactions, and it supplies several backends that implement these methods using tools such as:

• DCMTK
• pynetdicom
• your local filesystem

It provides the ability to fetch images and render as thumbnail PNGs, or fetch raw DICOM files.

In addition to the supplied backends, you can write your own backend implementing the BaseDicomClient. This can be a useful interface layer for non-PACS systems such as a cloud storage system.

Development

Linting is done with flake8 and testing with pytest.

GitHub actions has automatic checks for both linting and tests, using tox as the runner (see ./tox.ini). To replicate this locally, install tox, then run tox . in the root of the project.

If you get an error about DCMDICTPATH or SCPCFGPATH not being found, change the tox.ini setenv values to your local path to the referenced files.

If you get an error about "InterpreterNotFound", make sure you have that version of Python installed and in the path (e.g., discoverable with which python{version}). Or use --skip-missing-interpreters to skip those.

Remote DICOM Testing - Using Orthanc

Tests marked remote rely on a live DICOM server. For GitHub actions, an instance of Orthanc will be used, and you can re-use this service locally as well.

docker-compose up -d orthanc

# If this is the first time, and test data files have not yet been loaded
python3 pacsman/upload_test.py remote

# If you have DCMTK installed, here is a quick test
echoscu localhost 4242

# Or, with pynetdicom
python -m pynetdicom echoscu localhost 4242