scikit-surgeryutils

https://github.com/scikit-surgery/scikit-surgeryutils

Science Score: 36.0%

This score indicates how likely this project is to be science-related based on various indicators:

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CITATION.cff file
✓
codemeta.json file
Found codemeta.json file
✓
.zenodo.json file
Found .zenodo.json file
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DOI references
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Academic publication links
✓
Committers with academic emails
6 of 7 committers (85.7%) from academic institutions
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Institutional organization owner
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JOSS paper metadata
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Scientific vocabulary similarity
Low similarity (13.8%) to scientific vocabulary

Keywords

augmented-reality opencv scikit-surgery ucl vtk

Keywords from Contributors

surgery ultrasound

Last synced: 6 months ago · JSON representation

Repository

Basic Info

Host: GitHub
Owner: SciKit-Surgery
License: other
Language: Python
Default Branch: master
Homepage: https://github.com/SciKit-Surgery
Size: 123 MB

Statistics

Stars: 4
Watchers: 2
Forks: 2
Open Issues: 4
Releases: 3

Topics

augmented-reality opencv scikit-surgery ucl vtk

Created over 5 years ago · Last pushed about 1 year ago

Metadata Files

Readme Contributing License Code of conduct Citation

README.rst

scikit-surgeryutils 
===============================

.. image:: https://github.com/SciKit-Surgery/scikit-surgeryutils/raw/master/sksutils_logo.png
   :height: 128px
   :width: 128px
   :target: https://github.com/SciKit-Surgery/scikit-surgeryutils 
   :alt: Logo

|

.. image:: https://github.com/SciKit-Surgery/scikit-surgeryutils/workflows/.github/workflows/ci.yml/badge.svg
   :target: https://github.com/SciKit-Surgery/scikit-surgeryutils/actions
   :alt: GitHub Actions CI statuss

.. image:: https://coveralls.io/repos/github/SciKit-Surgery/scikit-surgeryutils/badge.svg?branch=master&service=github
    :target: https://coveralls.io/github/SciKit-Surgery/scikit-surgeryutils?branch=master
    :alt: Test coverage

.. image:: https://readthedocs.org/projects/scikit-surgeryutils /badge/?version=latest
    :target: http://scikit-surgeryutils .readthedocs.io/en/latest/?badge=latest
    :alt: Documentation Status

.. image:: https://img.shields.io/badge/Contributor%20Covenant-2.1-4baaaa.svg
   :target: CODE_OF_CONDUCT.md

.. image:: https://img.shields.io/twitter/follow/scikit_surgery?style=social
   :target: https://twitter.com/scikit_surgery?ref_src=twsrc%5Etfw
   :alt: Follow scikit_surgery on twitter

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 `_ - 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

Owner

Name: SciKit-Surgery
Login: SciKit-Surgery
Kind: organization
Email: s.thompson@ucl.ac.uk

Website: https://scikit-surgery.github.io/scikit-surgery/
Twitter: scikit_surgery
Repositories: 28
Profile: https://github.com/SciKit-Surgery

Compact Libraries for Surgical Navigation

GitHub Events

Total

Issues event: 1
Push event: 4
Create event: 2

Last Year

Issues event: 1
Push event: 4
Create event: 2

Committers

Last synced: over 1 year ago

All Time

Total Commits: 188
Total Committers: 7
Avg Commits per committer: 26.857
Development Distribution Score (DDS): 0.66

Past Year

Commits: 0
Committers: 0
Avg Commits per committer: 0.0
Development Distribution Score (DDS): 0.0

Top Committers

Name	Email	Commits
Miguel Xochicale	m**e@u**k	64
Matt Clarkson	m**n@u**k	56
Thomas Dowrick	t**k@g**m	35
Thomas Dowrick	t**k@u**k	16
Stephen Thompson	s**n@u**k	14
Joao_Ramalhinho_Dell	j**5@u**k	2
Mian Ahmad	m**d@u**k	1

Committer Domains (Top 20 + Academic)

ucl.ac.uk: 6

Issues and Pull Requests

Last synced: 6 months ago

All Time

Total issues: 53
Total pull requests: 9
Average time to close issues: about 1 month
Average time to close pull requests: about 16 hours
Total issue authors: 7
Total pull request authors: 3
Average comments per issue: 5.02
Average comments per pull request: 0.11
Merged pull requests: 9
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 1
Pull requests: 0
Average time to close issues: N/A
Average time to close pull requests: N/A
Issue authors: 1
Pull request authors: 0
Average comments per issue: 0.0
Average comments per pull request: 0
Merged pull requests: 0
Bot issues: 0
Bot pull requests: 0

View more stats

Top Authors

Issue Authors

tdowrick (34)
thompson318 (6)
MattClarkson (5)
mxochicale (4)
hacker0121 (1)
liushuya7 (1)
mianasbat (1)

Pull Request Authors

tdowrick (3)
thompson318 (3)
mxochicale (3)

Top Labels

Issue Labels

gitlab merge request (10) p1-high (3) p2-medium (2) has attachment (2) p0-critical (1) p3-low (1)

Pull Request Labels

Packages

Total packages: 1
Total downloads:
- pypi 232 last-month

Total dependent packages: 1
Total dependent repositories: 5
Total versions: 24
Total maintainers: 2

pypi.org: scikit-surgeryutils

scikit-surgeryutils - Tests/demos utilities, based around opencv-contrib-python-headless and PySide6

Homepage: https://github.com/SciKit-Surgery/scikit-surgeryutils
Documentation: https://scikit-surgeryutils.readthedocs.io/
License: BSD-3 license
Latest release: 2.0.1
published about 1 year ago

Versions: 24
Dependent Packages: 1
Dependent Repositories: 5
Downloads: 232 Last month

Rankings

Dependent packages count: 4.7%

Dependent repos count: 6.6%

Downloads: 12.7%

Average: 14.3%

Forks count: 22.6%

Stargazers count: 25.0%

Maintainers (2)

MattClarkson weiss_ucl

Last synced: 6 months ago

Dependencies

requirements-dev.txt pypi

coverage * development
coveralls * development
mock * development
parameterized * development
pyfakefs * development
pyinstaller * development
pylint <2.14 development
pytest * development
pytest-qt * development
pyyaml * development
sphinx * development
sphinx_rtd_theme * development
tox * development

requirements.txt pypi

PySide2 >=5.12.0
numpy >=1.11
opencv-contrib-python-headless >=4.1.1.26,<4.6
scikit-surgeryarucotracker >=0.2.7
scikit-surgerycalibration >=0.2.1
scikit-surgerycore >=0.1.7
scikit-surgeryimage >=0.10.1
scikit-surgeryvtk >=1.0.6
six >=1.10

setup.py pypi

PySide2 <5.15.0
numpy >=1.11
opencv-contrib-python-headless >=4.1.1.26
scikit-surgeryarucotracker >=0.2.7
scikit-surgerycalibration >=0.2.1
scikit-surgerycore >=0.1.7
scikit-surgeryimage >=0.10.1
scikit-surgeryvtk >=1.0.6
six >=1.10

.github/workflows/ci.yml actions

actions/checkout v2 composite
actions/checkout master composite
actions/setup-python v1 composite
pypa/gh-action-pypi-publish master composite

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Open Source Science

scikit-surgeryutils

Science Score: 36.0%

Keywords

Keywords from Contributors

Repository

Basic Info

Statistics

Topics

Metadata Files

README.rst

Owner

GitHub Events

Total

Last Year

Committers

All Time

Past Year

Top Committers

Committer Domains (Top 20 + Academic)

Issues and Pull Requests

All Time

Past Year

Top Authors

Issue Authors

Pull Request Authors

Top Labels

Issue Labels

Pull Request Labels

Packages

pypi.org: scikit-surgeryutils

Rankings

Maintainers (2)

Dependencies