scikit-surgeryutils
===============================
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:target: https://github.com/SciKit-Surgery/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
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