scikit-surgeryutils

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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-start

Features

• Common overlay apps <https://scikit-surgeryutils.readthedocs.io/en/latest/module_ref.html#module-sksurgeryutils.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.

.. features-end

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

Running the tests ^^^^^^^^^^^^^^^^^

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

::

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

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_.

.. _Wellcome EPSRC Centre for Interventional and Surgical Sciences: http://www.ucl.ac.uk/weiss .. _source code repository: https://github.com/SciKit-Surgery/scikit-surgeryutils .. _Documentation: https://scikit-surgeryutils.readthedocs.io .. _SciKit-Surgery: https://github.com/SciKit-Surgery/ .. _University College London (UCL): http://www.ucl.ac.uk/ .. _Wellcome: https://wellcome.ac.uk/ .. _EPSRC: https://www.epsrc.ac.uk/ .. _contributing guidelines: https://github.com/SciKit-Surgery/scikit-surgeryutils/blob/master/CONTRIBUTING.rst .. _license file: https://github.com/SciKit-Surgery/scikit-surgeryutils/blob/master/LICENSE .. _issue: https://github.com/SciKit-Surgery/scikit-surgeryutils/issues/new