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Pymedphys

A community effort to develop an open standard library for Medical Physics in Python. Building quality transparent software together via peer review and open source distribution. Open code is better science.

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/learn @pymedphys/Pymedphys
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Quality Score

0/100

Supported Platforms

Universal

README

|logo|

.. |logo| image:: https://github.com/pymedphys/pymedphys/raw/ca501275227f190a77e641a75af925d9070952b6/lib/pymedphys/docs/_static/pymedphys_title.svg :target: https://docs.pymedphys.com/

.. START_OF_DOCS_IMPORT

A community effort to develop an open standard library for Medical Physics in Python. We build high quality, transparent software together via peer review and open source distribution. Open code is better science.

|build| |pypi| |python| |license|

.. |build| image:: https://img.shields.io/github/actions/workflow/status/pymedphys/pymedphys/library.yml?branch=main :target: https://github.com/pymedphys/pymedphys/actions?query=branch%3Amain

.. |pypi| image:: https://img.shields.io/pypi/v/pymedphys :target: https://pypi.org/project/pymedphys/

.. |python| image:: https://img.shields.io/pypi/pyversions/pymedphys :target: https://pypi.org/project/pymedphys/

.. |license| image:: https://img.shields.io/pypi/l/pymedphys :target: https://choosealicense.com/licenses/apache-2.0/

What is PyMedPhys?

PyMedPhys is an open-source Medical Physics Python library built by an open community that values code sharing, review, improvement, and learning from each other. It is inspired by the collaborative work of our physics peers in astronomy and the Astropy Project. PyMedPhys is available on PyPI and GitHub_.

PyMedPhys supports three main ways of working:

  • a Python library for notebooks, scripts, and clinic-specific tooling
  • a command line interface (CLI) for repeatable automation
  • a point-and-click app layer for selected workflows

Beta level of development

PyMedPhys is currently within the beta stage of its life-cycle. It will stay in this stage until the version number leaves 0.x.x and enters 1.x.x. While PyMedPhys is in beta stage, no API is guaranteed to be stable from one release to the next. Upgrading pymedphys can therefore break existing scripts or workflows. We try to stay ahead of that by documenting breaking changes in the Release Notes_.

Start here

If you are new to PyMedPhys, start with these four questions in order:

  1. What PyMedPhys can do_
  2. Choose your path_
  3. Installation options_
  4. Quick Start Guide_

Common task areas

PyMedPhys is often used to:

  • compare dose or fluence-like data with gamma, interpolation, and MetersetMap
  • work with DICOM and pseudonymisation workflows
  • work with delivery, logfile, and iCom data
  • query or integrate with Mosaiq
  • use point-and-click apps for selected workflows

Install PyMedPhys

PyMedPhys currently supports Python 3.10, 3.11, and 3.12.

For most users, we recommend using uv to create an environment and install PyMedPhys:

.. code:: bash

uv python install 3.12
uv venv --python 3.12
uv pip install "pymedphys[user]"

If you cannot use uv on your workstation, the Quick Start Guide_ also includes a standard Python + venv + pip fallback path.

Choose the right interface

Use the Python library when you want notebooks, analysis, plots, and clinic-specific workflows.

Use the CLI when you want repeatable commands, scheduled jobs, or shell automation.

Use the app layer when you want the least coding and a graphical workflow.

For a fuller comparison, read Choose your path_.

Documentation

The PyMedPhys documentation has two overarching guides:

  1. The Users Guide: where you can get started_ with the library, the CLI, and the app layer; read task-focused how-to guides; find background information on larger projects and concepts; and browse the Technical Reference_ when you already know the feature you need.

  2. The Contributors Guide: for those who want to contribute to PyMedPhys. This includes the Contributors Guide_ landing page, detailed workstation setup guides, important repository information, and some tips & tricks_ for common problems.

Community

PyMedPhys has a GitHub Discussions <https://github.com/pymedphys/pymedphys/discussions>_ page to help users find their feet and to support collaboration and general discussion.

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Citing PyMedPhys

PyMedPhys' first paper in the Journal of Open Source Software contains more background information, including the Statement of Need. You can access the paper here <https://joss.theoj.org/papers/10.21105/joss.04555>.

When referencing PyMedPhys, please cite this paper as follows:

Biggs, S., Jennings, M., Swerdloff, S., Chlap, P., Lane, D., Rembish, J., McAloney, J., King, P., Ayala, R., Guan, F., Lambri, N., Crewson, C., Sobolewski, M. (2022). PyMedPhys: A community effort to develop an open, Python-based standard library for medical physics applications. Journal of Open Source Software, 7(78), 4555, https://doi.org/10.21105/joss.04555

Development

PyMedPhys uses uv_ for package and project management.

After cloning the repository, install the PyMedPhys dependencies and set up pre-commit by running:

.. code:: bash

uv sync --extra all --group dev
uv run -- pre-commit install

Run automated tests with:

.. code:: bash

uv run -- pymedphys dev tests

Our Team

PyMedPhys is what it is today due to its maintainers and contributors, both past and present. Here is our team.

Maintainers

  • Simon Biggs_
    • Anthropic PBC_

.. _Simon Biggs: https://github.com/SimonBiggs

  • Stuart Swerdloff_
    • SJS Targeted Solutions, LLP_, New Zealand

.. _Stuart Swerdloff: https://github.com/sjswerdloff

  • Matthew Jennings_
    • Icon Group_, Australia

.. _Matthew Jennings: https://github.com/Matthew-Jennings

  • Phillip Chlap_
    • Radformation Inc._, USA
    • University of New South Wales_, Australia

.. _Phillip Chlap: https://github.com/pchlap

|sjs| |rah|

Active contributors

  • Derek Lane_
    • ELEKTA AB_, Houston TX

.. _Derek Lane: https://github.com/dg1an3

  • Marcelo Jordao_
    • ELEKTA AB_, Hong Kong SAR

.. _Marcelo Jordao: https://github.com/mguerrajordao

  • Jake Rembish_
    • UT Health San Antonio_, USA

.. _Jake Rembish: https://github.com/rembishj

  • Nicola Lambri_
    • IRCCS Humanitas Research Hospital_, Italy
    • Humanitas University_, Italy

.. _Nicola Lambri: https://github.com/nlambriICH

  • Cody Crewson_
    • Saskatchewan Cancer Agency_, Canada

.. _Cody Crewson: https://github.com/crcrewso

  • Fada Guan_
    • Yale University School of Medicine_, USA

.. _Fada Guan: https://github.com/guanfada

  • Marcus Fisk_
    • Cancer Care Riverina_, Australia

.. _Marcus Fisk: https://github.com/laser47-hue

|uth| |ccr|

Past contributors

  • Matthew Cooper <https://github.com/matthewdeancooper>_
  • Pedro Martinez <https://github.com/peterg1t>_
  • Rafael Ayala <https://github.com/ayalalazaro>_
  • Matthew Sobolewski <https://github.com/msobolewski>_
  • Paul King <https://github.com/kingrpaul>_
  • Jacob McAloney <https://github.com/JacobMcAloney>_

.. Unfortunately :target: being a variable name is no longer supported by GitHub within README.rst files. So... unfortunately we have some duplication below.

.. |rah| image:: https://github.com/pymedphys/pymedphys/raw/3f8d82fc3b53eb636a75336477734e39fa406110/docs/logos/gosa_200x200.png :target: https://www.rah.sa.gov.au/

.. |uth| image:: https://github.com/pymedphys/pymedphys/raw/3f8d82fc3b53eb636a75336477734e39fa406110/docs/logos/UTHSA_logo.png :target: https://www.uthscsa.edu/academics/biomedical-sciences/programs/radiological-sciences-phd

.. |sjs| image:: https://github.com/pymedphys/pymedphys/raw/7e9204656e0468b0843533472553a03a99387386/logos/swerdloff.png :target: https://github.com/sjswerdloff

.. |ccr| image:: https://github.com/pymedphys/pymedphys/raw/ec61e4e63a8624f4df44a8e90931bd0bca748e20/logos/cancercareriverina_200x200.png :target: https://cancercare.com.au/clinics/cancer-care-riverina/

.. _Anthropic PBC: https://www.anthropic.com/

.. _ELEKTA Pty Ltd: https://www.elekta.com/

.. _ELEKTA AB: https://www.elekta.com/

.. _Icon Group: https://icongroup.global/

.. _University of New South Wales: https://www.unsw.edu.au/

.. _South Western Sydney Local Health District: https://www.swslhd.health.nsw.gov.au/

.. _Anderson Regional Cancer Center: https://www.andersonregional.org/services/cancer-care/

.. _Northern Beaches Cancer Care: https://www.northernbeachescancercare.com.au/

.. _University of Calgary: https://www.ucalgary.ca/

.. _Tom Baker Cancer Centre: https://www.ahs.ca/tbcc

.. _UT Health San Antonio: https://www.uthscsa.edu/academics/biomedical-sciences/programs/radiological-sciences-phd

.. _Hospital General Universitario Gregorio Marañón: https://www.comunidad.madrid/hospital/gregoriomaranon/

.. _Swerdloff Family: https://github.com/sjswerdloff

.. _SJS Targeted Solutions, LLP: https://github.com/sjswerdloff

.. _Radformation Inc.: https://radformation.com/

.. _IRCCS Humanitas Research Hospital: https://www.humanitas.net/

.. _Saskatchewan Cancer Agency: http://www.saskcancer.ca/

.. _Humanitas University: https://www.hunimed.eu/

.. _Yale University School of Medicine: https://medicine.yale.edu/

.. _Cancer Care Riverina: https://cancercare.com.au/clinics/cancer-care-riverina/

.. _Astropy Project: https://www.astropy.org/ .. _PyPI: https://pypi.org/project/pymedphys/ .. _GitHub: https://github.com/pymedphys/pymedphys

.. _Release Notes: ./CHANGELOG.md

.. _Statement of Need: https://docs.pymedphys.com/en/latest/statement-of-need.html .. _What PyMedPhys can do: https://docs.pymedphys.com/en/latest/users/get-started/what-pymedphys-can-do.html .. _Choose your path: https://docs.pymedphys.com/en/latest/users/get-started/choose-your-path.html .. _`Installat

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pymedphys/pymedphys

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Python

Security Score

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