https://github.com/pymedphys/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.
https://github.com/pymedphys/pymedphys

dicom medical-physics radiation-oncology radiation-physics radiation-therapy radiotherapy

Last synced: 12 days ago
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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.

• Host: GitHub
• URL: https://github.com/pymedphys/pymedphys
• Owner: pymedphys
• License: apache-2.0
• Created: 2019-01-29T22:20:04.000Z (over 5 years ago)
• Default Branch: main
• Last Pushed: 2024-05-21T04:35:07.000Z (about 1 month ago)
• Last Synced: 2024-06-18T18:51:57.163Z (12 days ago)
• Topics: dicom, medical-physics, radiation-oncology, radiation-physics, radiation-therapy, radiotherapy
• Language: Python
• Homepage: https://docs.pymedphys.com
• Size: 53.1 MB
• Stars: 293
• Watchers: 29
• Forks: 71
• Open Issues: 113
• Metadata Files:
  • Readme: README.rst
  • Changelog: CHANGELOG.md
  • Contributing: CONTRIBUTING.md
  • License: LICENSE
  • Code of conduct: CODE_OF_CONDUCT.md

Lists

• awesome-medphys - 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.  (Libraries)

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 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 `_. 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 `_

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

***********

* `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

|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 `_

* `Pedro Martinez `_

* `Rafael Ayala `_

* `Matthew Sobolewski `_

* `Paul King `_

* `Jacob McAloney `_

..

   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/

.. _`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/

.. 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/