glowgreen

A Python package for calculating radiation dose from close contact patterns with radioactive patients.

Requires

• Python >= 3.9

Installation

Install the package from the Python Package Index (PyPI) using pip:

python -m pip install --upgrade glowgreen

Alternatively, if you have a clone of the repository on your local computer, you can install it via the pyproject.toml file. First update your pip:

python -m pip install --upgrade pip

Then enter e.g.:

python -m pip install -e \path\to\glowgreen\

These are the preferred methods as they handle the dependencies for you. Another way is to add the src directory to the PYTHONPATH environment variable. For example, for Windows:

set PYTHONPATH=%PYTHONPATH%;\path\to\glowgreen\src\

Dependencies

Python packages:

• numpy >= 1.21.4
• scipy >= 1.7.3
• matplotlib >= 3.5.0
• pandas >= 1.3.4

It has not been tested with earlier versions of these packages.

Test suite

You can run the test suite if you have a clone of this repository and glowgreen is installed or in PYTHONPATH. Install pytest:

python -m pip install pytest

Then in the root directory run:

python -m pytest

Documentation

Documentation including API reference can be found here: https://glowgreen.readthedocs.io.

Building the documentation

Documentation is generated using sphinx. See this tutorial.

If the docs/source/ directory does not exist, see howto_documentation.md to bootstrap the documentation. Otherwise, do the following:

Ensure the hand-crafted elements of the documentation in the docs directory are up-to-date:

• project information in docs/source/conf.py
• src/glowgreen_sample.py is used to generate the figures in docs/source and some of the text in docs/source/overview.rst

Install sphinx:

python -m pip install sphinx

Note the empty directories docs/source/_static and docs/source/_templates are not under version control; optionally create these empty directories to avoid a warning in the next step.

In docs directory, run:

make html

This last step is how the documentation hosted on Read the Docs is built (see also the configuration file .readthedocs.yaml).

Source

https://github.com/SAMI-Medical-Physics/glowgreen

Bug tracker

https://github.com/SAMI-Medical-Physics/glowgreen/issues

Authors

• Jake Forster (Jake.Forster@sa.gov.au)
• Erin Lukas (Erin.Lukas@sa.gov.au)

Copyright

glowgreen is Copyright (C) 2022, 2023, 2025 South Australia Medical Imaging.

License

MIT license. See LICENSE file.

Publishing

glowgreen is published on PyPI:

https://pypi.org/project/glowgreen/

See this tutorial.

Publications

Papers that use glowgreen:

• Forster JC et al. "Close contact restriction periods for patients who have received iodine-131 therapy for differentiated thyroid cancer." J Radiol Prot. 2023;43(2):021501. doi: 10.1088/1361-6498/acc4d0.