scikit-surgery-sphere-fitting 0.0.5

scikit-surgery-sphere-fitting implements a least squares sphere fitting algorithm, to read a vtk poly data file, a config file, and outputs the fitted sphere

Author: Stephen Thompson

scikit-surgery-sphere-fitting is part of the SciKit-Surgery software project, developed at the Wellcome EPSRC Centre for Interventional and Surgical Sciences, part of University College London (UCL).

scikit-surgery-sphere-fitting supports Python 3.6.

scikit-surgery-sphere-fitting fits a sphere to a set of 3D points. It includes a user interface that will read data from a vtk polydata file create an output polydata file showing the fitted sphere. Example usage:

python sksurgeryspherefitting.py polydata_in.vtp --output polydatata_out.vtp --config conf.json

It was created in part to provide a simple demonstration of algorithm development as part of a program of SNAPPY Tutorials, but also provides a useful service should you want to fit a sphere to some data.

Citing

If you use SciKit-Surgery-Sphere-Fitting in your research or teaching please cite it. Individual releases can be cited via the Zenodo tag above. SciKit-Surgery should be cited as:

Thompson S, Dowrick T, Ahmad M, et al. “SciKit-Surgery: compact libraries for surgical navigation.” International Journal of Computer Assisted Radiology and Surgery. 2020 May. DOI: 10.1007/s11548-020-02180-5.

Developing

Cloning

You can clone the repository using the following command:

git clone https://github.com/thompson318/scikit-surgery-sphere-fitting

Running tests

Pytest is used for running unit tests:

pip install pytest
python -m pytest

Linting

This code conforms to the PEP8 standard. Pylint can be used to analyse the code:

pip install pylint
pylint --rcfile=tests/pylintrc sksurgeryspherefitting

Installing

You can pip install directly from the repository as follows:

pip install git+https://github.com/thompson318/scikit-surgery-sphere-fitting

or directly from pypi

pip install scikit-surgery-sphere-fitting

Contributing

Please see the contributing guidelines.

Useful links

• Source code repository

• Documentation

Licensing and copyright

Copyright 2019 University College London. scikit-surgery-sphere-fitting is released under the BSD-3 license. Please see the license file for details.

Acknowledgements

Supported by Wellcome and EPSRC.