pymedphys 0.2.0

Medical Physics python modules

PyMedPhys

Description

A range of python modules encompased under the pymedphys package, designed to be built upon for Medical Physics applications.

This package is available on pypi at https://pypi.org/project/pymedphys/ and GitHub at https://github.com/CCA-Physics/pymedphys.

Alpha stage development

These libraries are currently under alpha level development. Be cautious with code in this library. Not only might code depending on it break, but the results given by this code likely may just be plain wrong.

This will be true throughout the alpha stage development of these libraries. This notice will be adjusted once this should no longer be the case.

Throughout the lifetime of this library however the following will always be true:

In no event and under no legal theory, whether in tort (including negligence), contract, or otherwise, unless required by applicable law (such as deliberate and grossly negligent acts) or agreed to in writing, shall any Contributor be liable to You for damages, including any direct, indirect, special, incidental, or consequential damages of any character arising as a result of this License or out of the use or inability to use the Work (including but not limited to damages for loss of goodwill, work stoppage, computer failure or malfunction, or any and all other commercial damages or losses), even if such Contributor has been advised of the possibility of such damages.

Installation

To install use the Anaconda Python distribution with the conda-forge channel:

conda config --add channels conda-forge
conda install pymedphys

You can of course also use pip to install, but you may have trouble with some of the dependencies without conda:

pip install pymedphys

To run a development install, which may often be required during the alpha development stage, clone this repository and then use pip:

git clone https://github.com/CCA-Physics/pymedphys.git
cd pymedphys
pip install -e .

Contributing

To contribute to pymedphys you will need a working knowledge of git processes. The contributing.md document provides links to some tutorials that may help get you up to speed.

Team and copyright

The aim of PyMedPhys is that it will be developed by an open community of contributors. We use a shared copyright model that enables all contributors to maintain the copyright on their contributions. All code is licensed under the AGPLv3+ with additional terms from the Apache-2.0 license.

PyMedPhys' current maintainers listed in alphabetical order, with affilliation, and main area of contribution:

• Anthony Bisulco, Northeastern University, USA (collapsed cone convolution)
• Matthew Sobolewski, Cancer Care Associates, Australia (oversight)
• Ramesh Boggula, Aurora St. Luke's Medical Center, USA (general development)
• Sangroh Kim, Baylor Scott & White Health, USA (collapsed cone convolution)
• Simon Biggs, Cancer Care Associates, Australia (general development)
• Theodore Mutanga, Trillium Health Partners, Canada (collapsed cone convolution)

License agreement

Copyright (C) 2018 PyMedPhys Contributors

This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version (the "AGPL-3.0+").

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License and the additional terms for more details.

You should have received a copy of the GNU Affero General Public License along with this program. If not, see http://www.gnu.org/licenses/.

ADDITIONAL TERMS are also included as allowed by Section 7 of the GNU Affrero General Public License. These aditional terms are Sections 1, 5, 6, 7, 8, and 9 from the Apache License, Version 2.0 (the "Apache-2.0") where all references to the definition "License" are instead defined to mean the AGPL-3.0+.

You should have received a copy of the Apache-2.0 along with this program. If not, see http://www.apache.org/licenses/LICENSE-2.0.

Benefits of using a copyleft license in Medical Physics

For more information on why you as a Medical Physicist might want to use the AGPL-3.0+ license read the benefits of AGPL-3.0+ for Medical Physics.

Justification for the inclusion of additional terms

A significant and justifiable fear within the Medical Physics community is that should code be shared the author of the code may be liable for negligence.

Within Australian courts if there is any ambiguity in liability exclusion clauses they will be interpreted narrowly. If liability for negligence is not expressly excluded it may not be read as excluded within an Australian court (https://eprints.qut.edu.au/7404/1/open_source_book.pdf page 80). The same is true for clauses which seek to exclude liability for consequential loss.

The AGPL-3.0+ (nor the MIT license) does not explicitly mention negligence anywhere within its license text. The Apache-2.0 does. The AGPL-3.0+ in Section 7 does define allowable additional terms. The negligence clauses within the Apache-2.0 fall under these allowable additional terms so, as such, they have been included.

There are also other desirable features of the Apache-2.0 license such as contribution, trademark, and warranty requirements. These were also included.

A note about the code sharing license requirement

If you only ever use this code internally within your company to create your own programs the only people who need to have access to the source code are those users whom you distribute the program to. Therefore you do not need to share your code outside of your company if your only users are within your company.

However there are significant benefits from sharing your code with the community. Please read the benefits of AGPL-3.0+ for Medical Physics.

Cyclic dependencies and the justification of file structure

If package A depends on package B, and package B depends on package C, it is important that package C does not then depend on package A. This is called a cyclic dependency. It causes issues in dependency logic and can be avoided by purposefully designing how the packages depend on one another.

Ideally library packages are split up module by module based upon single tasks that each library achieves. By having a very large number of small single purpose modules the dependency tree can become very complicated. Complicated dependency trees do not scale. As a result the inter dependencies between library packages is tightly regulated. The modules themselves need to be designed and programmed with these restrictions in mind.

The physical design of the module dependencies is inspired by John Lakos at Bloomberg, writer of Large-Scale C++ Software Design. He describes this methodology in a talk he gave which is available on YouTube:

https://youtu.be/QjFpKJ8Xx78?t=41m7s

Level 1

Level 1 packages are the foundation library packages.

These packages SHALL NOT depend on any internal package. They MAY however depend on external packages (Level 0).

Given that these Level 1 packages are foundation packages their external packages SHOULD only ever be those that are in wide use and are highly supported within the python community. Examples of reasonable external packages to be used are numpy, scipy, and pandas.

Level 2

Level 2 packages.

The internal packages that Level 2 packages depend on SHALL only be Level 1 packages or external packages as long as those external packages don't intern depend on one defined within this group.

Level 3

Level 3 packages.

The internal packages that these depend on SHALL only be Level 1 or Level 2. They MAY also depend external packages as long as those external packages don't intern depend on one defined within this group.