scikit-surgeryutils

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

scikit-surgeryutils containing small demo apps and utilities.

scikit-surgeryutils 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-surgeryvtk is tested on Python 3.8. and may support other Python versions.

Features

• Common overlay apps - Examples of common uses of scikit-surgeryvtk's VTKOverlayWindow. Includes overlaying on a video feed, duplicating a feed.

Command line applications

Open a terminal, load your virtual environment and run the application as python sk*.py.

• sksurgeryvideolag.py - shows a millisecond timer and video image to crudely measure measure lag.
• sksurgerycharucotest.py - extracts charuco points and annotates video image with each id detected.
• sksurgeryrendermodelslikecamera.py - renders a VTK model, over background image, using OpenCV camera intrinsics.
• sksurgerymakecalibrationdots.py - Create a calibraiton dot pattern.
• sksurgeryreslice.py - DICOM reslice widget demo.
• sksurgerytextoverlay.py - VTK text overlay demo.
• sksurgerytransformpolydata.py - Read a surface mesh (.vtk,.vtp,.stl,.ply file), transform by 4x4 matrix and write as .vtk.
• sksurgerystereorenderer.py - Reads a set of meshes, overlays on stereo video. Documentation.

Installing

You can pip install directly from the repository as follows:

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

Developing

Cloning

You can clone the repository using the following command:

git clone https://github.com/SciKit-Surgery/scikit-surgeryutils

Installing the dependencies, running the tests

You can install dependencies and run the unit tests by installing and running tox:

pip install tox
tox
tox -e docs
tox -e lint

Tox will create a separate venv in .tox/test. See tox.ini for commands that tox runs.

Encountering Problems?

Please get in touch or raise an issue.

Contributing

Please see the contributing guidelines.

Useful links

• Source code repository
• `Documentation`_

Licensing and copyright

Copyright 2018 University College London. scikit-surgeryutils is released under the BSD-3 license. Please see the license file for details.

Acknowledgements

Supported by Wellcome and EPSRC.