What is PyMedPhys?

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

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:

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 page to help users find their feet and to support collaboration and general discussion.

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