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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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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
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
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!
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:
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_.
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.
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
PyMedPhys is what it is today due to its maintainers and contributors, both past and present. Here is our team.
Maintainers
Simon Biggs_
Radiotherapy AI_, Australia.. _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_
University of New South Wales_, AustraliaIngham Institute_, Australia.. _Phillip Chlap: https://github.com/pchlap
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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_, ItalyHumanitas 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
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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>_.. |rai| image:: https://github.com/pymedphys/pymedphys/raw/286deacdea2b3af9322796d413d0da6e1d8935a9/logos/rai.png
:target: Radiotherapy AI_
.. |rah| image:: https://github.com/pymedphys/pymedphys/raw/3f8d82fc3b53eb636a75336477734e39fa406110/docs/logos/gosa_200x200.png
:target: Royal Adelaide Hospital_
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:target: UT Health San Antonio_
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:target: Swerdloff Family_
.. _Radiotherapy AI: https://radiotherapy.ai/
.. _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
.. _Ingham Institute: https://inghaminstitute.org.au/
.. _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/
.. END_OF_DOCS_IMPORT
.. _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/
FAQs
Medical Physics library
We found that pymedphys demonstrated a healthy version release cadence and project activity because the last version was released less than a year ago. It has 4 open source maintainers collaborating on the project.
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