Author(s): Stephen Thompson; Contributor(s): Matt Clarkson, Thomas Dowrick and Miguel Xochicale

scikit-surgerycalibration 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-surgerycalibration is tested on Python 3.7.

scikit-surgerycalibration contains algorithms to perform calibrations useful during surgery, for example pointer calibration, ultrasound calibration, and camera calibration.

Please explore the project structure, and request or implement your desired functionality.

• Pivot Calibration for pivot calibration.
• Calibration of mono or stereo tracked video data, calculating camera intrinsics and handeye transformation.

You can clone the repository using the following command: :

git clone https://github.com/SciKit-Surgery/scikit-surgerycalibration
git clone git@github.com:SciKit-Surgery/scikit-surgerycalibration.git # Alternatively, use password-protected SSH key.

We recommend using anaconda or miniconda to create a python 3.7 environment, then using tox to install all dependencies inside a dedicated venv. We then use github actions to run a matrix of builds for Windows, Linux and Mac and various python versions.

All library dependencies are specified via requirements-dev.txt which refers to requirements.txt.

So, assuming either anaconda or miniconda is installed, and your current working directory is the root directory of this project: :

conda create --name scikit-surgery python=3.7
conda activate scikit-surgery
pip install tox
tox

As the tox command runs, it will install all dependencies in a sub-directory .tox/py37 (Linux/Mac) or .tox\py37 (Windows). tox will also run pytest and linting for you.

To run commands inside the same environment as tox, you should: :

source .tox/py37/bin/activate

on Linux/Mac, or if you are Windows user: :

.tox\py37\Scripts\activate

Then you can run pytest, linting, or directly run python scripts, and know that the environment was created correctly by tox.

The simplest way is again using tox. :

tox -e docs

then open docs/build/html/index.html in your browser.

Pytest is used for running unit tests: :

python -m pytest
pytest -v -s tests/algorithms/test_triangulate.py #example for individual tests

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

pylint --rcfile=tests/pylintrc sksurgerycalibration

You can pip install directly from the repository as follows: :

pip install git+https://github.com/SciKit-Surgery/scikit-surgerycalibration 

Please see the contributing guidelines.

• Source code repository
• Documentation

Copyright 2020 University College London. scikit-surgerycalibration is released under the BSD-3 license. Please see the license file for details.

Supported by Wellcome and EPSRC.