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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.

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What is PyMedPhys?

PyMedPhys is an open-source Medical Physics python library built by an open community that values and prioritises 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 first paper in the Journal of Open Source Software contains more background information, including a 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

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

Beta level of development

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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. In fact, it is very likely that the entire API will change multiple times before a 1.0.0 release. In practice, this means that upgrading pymedphys to a new version will possibly break any code that was using the old version of pymedphys. We try to be abreast of this by providing details of any breaking changes from one release to the next within the Release Notes_.

Community

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PyMedPhys has a Discourse community <https://pymedphys.discourse.group/>_ to both help you find your feet using PyMedPhys and to facilitate collaboration and general discussion. Please reach out over there and we'd love to get to know you!

Documentation

PyMedPhys can be installed with:

.. code:: bash

pip install pymedphys[user]

Further user installation instructions can be found in the Quick Start Guide_.

The PyMedPhys documentation contains two overarching guides:

1. The Users Guide: where you can find instructions to get started_ with the library and the CLI, in-depth how-to guides_ (examples for users) on PyMedPhys' various tools, some background information_ on individual PyMedPhys projects as well as the Technical Reference_.

2. The Contributors Guide: for those who wish to make new contributions to the PyMedPhys library, CLI or app. Here you'll find detailed workstation setup guides_ to enable contributions, important repository information, and some tips & tricks to overcome common issues.

Development

The PyMedPhys project is managed using Poetry_.

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

.. code:: bash

poetry install -E all
poetry run pre-commit install

Run automated tests with:

.. code:: bash

poetry 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

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• Simon Biggs_
  • Anthropic PBC_

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

• Stuart Swerdloff_
  • ELEKTA Pty Ltd_: New Zealand

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

• Matthew Jennings_
  • Royal Adelaide Hospital_, 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

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Active contributors

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• 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

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Past contributors

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• 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>_

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

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

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

.. _Royal Adelaide Hospital: https://www.rah.sa.gov.au/

.. _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

.. _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/

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.. _Release Notes: ./CHANGELOG.md

.. _Statement of Need: https://docs.pymedphys.com/en/latest/statement-of-need.html .. _Quick Start Guide: https://docs.pymedphys.com/en/latest/users/get-started/quick-start.html .. _get started: https://docs.pymedphys.com/en/latest/users/get-started/index.html .. _how-to guides: https://docs.pymedphys.com/en/latest/users/howto/index.html .. _background information: https://docs.pymedphys.com/en/latest/users/background/index.html .. _Technical Reference: https://docs.pymedphys.com/en/latest/users/ref/index.html .. _workstation setup guides: https://docs.pymedphys.com/en/latest/contrib/setups/index.html .. _repository information: https://docs.pymedphys.com/en/latest/contrib/info/index.html .. _tips & tricks: https://docs.pymedphys.com/en/latest/contrib/tips/index.html .. _Poetry: https://python-poetry.org/