scikit-surgerycore

SciKit-SurgeryCore implements algorithms and tools that are common to all SciKit-Surgery packages

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

Science Score: 67.0%

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

✓
CITATION.cff file
Found CITATION.cff file
✓
codemeta.json file
Found codemeta.json file
✓
.zenodo.json file
Found .zenodo.json file
✓
DOI references
Found 4 DOI reference(s) in README
○
Academic publication links
✓
Committers with academic emails
7 of 10 committers (70.0%) from academic institutions
○
Institutional organization owner
○
JOSS paper metadata
○
Scientific vocabulary similarity
Low similarity (13.4%) to scientific vocabulary

Keywords

python scikit-surgery surgery ucl

Last synced: 6 months ago · JSON representation ·

Repository

SciKit-SurgeryCore implements algorithms and tools that are common to all SciKit-Surgery packages

Basic Info

Host: GitHub
Owner: SciKit-Surgery
License: other
Language: Python
Default Branch: master
Homepage: https://github.com/SciKit-Surgery
Size: 33.3 MB

Statistics

Stars: 7
Watchers: 2
Forks: 1
Open Issues: 0
Releases: 1

Topics

python scikit-surgery surgery ucl

Created almost 6 years ago · Last pushed about 1 year ago

Metadata Files

Readme Contributing License Citation

README.rst

scikit-surgerycore
===============================

.. image:: https://github.com/SciKit-Surgery/scikit-surgerycore/raw/master/skscore_logo.png
   :height: 200px
   :target: https://github.com/SciKit-Surgery/scikit-surgerycore
   :alt: Logo

| 

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

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

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

.. image:: https://img.shields.io/badge/Cite-SciKit--Surgery-informational
   :target: https://doi.org/10.1007/s11548-020-02180-5
   :alt: The SciKit-Surgery paper

.. 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

Description
-----------

SciKit-SurgeryCore implements algorithms and tools that are common to all SciKit-Surgery packages.

SciKit-SurgeryCore 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)`_.

.. features-start

Features
--------

* A `Configuration Manager `_ to load parameters from a .json file
* A `Transform Manager `_ to manage combinations of 4x4 transformation matrices
* `Corresponding point `_ (i.e Landmark) based registration, based on `Arun et al., 1987`_.
* `Rotaiton/translation Matrix construction `_ and `validation functions `_, 
  checking a numpy array is a camera matrix, rotation matrix, rigid transform etc.

.. features-end

Citing
------
If you make use of SciKit-Surgery libraries in your work, please cite the following paper:


    | Thompson S, Dowrick T, Ahmad M, et al.
    | SciKit-Surgery: compact libraries for surgical navigation.
    | International Journal of Computer Assisted Radiology and Surgery. May 2020. 
    | DOI: 10.1007/s11548-020-02180-5


Installing
----------

You can pip install as follows:

::

    pip install scikit-surgerycore


Developing
----------

Cloning
^^^^^^^

You can clone the repository using the following command:

::

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


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

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

::

    pip install tox
     tox


Contributing
^^^^^^^^^^^^

Please see the `contributing guidelines`_.

Useful links
^^^^^^^^^^^^

* `Source code repository`_
* `Documentation`_


Licensing and copyright
-----------------------

Copyright 2018 University College London.
scikit-surgerycore 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-surgerycore
.. _`Documentation`: https://scikit-surgerycore.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-surgerycore/blob/master/CONTRIBUTING.rst
.. _`license file`: https://github.com/SciKit-Surgery/scikit-surgerycore/blob/master/LICENSE
.. _`Arun et al., 1987`: http://doi.ieeecomputersociety.org/10.1109/TPAMI.1987.4767965

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

Citation (CITATION.cff)

cff-version: 1.2.0
message: "If you use SciKit-SurgeryCore in your research, please cite it as below."
authors:
- family-names: "Thompson"
  given-names: "Stephen"
  orcid: "https://orcid.org/0000-0001-7286-1326"
- family-names: "Dowrick"
  given-names: "Thomas"
  orcid: "https://orcid.org/0000-0002-2712-4447"
- family-names: "Ahmad"
  given-names: "Mian"
  orcid: "https://orcid.org/0000-0002-4706-4146"
- family-names: "Clarkson"
  given-names: "Matthew"
  orcid: "https://orcid.org/0000-0002-5565-1252"
title: "SciKit-SurgeryCore"
url: "https://github.com/SciKit-Surgery/scikit-surgerycore"
doi: "10.5281/zenodo.3965731"
preferred-citation:
  type: article
  authors:
  - family-names: "Thompson"
    given-names: "Stephen"
    orcid: "https://orcid.org/0000-0001-7286-1326"
  - family-names: "Dowrick"
    given-names: "Thomas"
    orcid: "https://orcid.org/0000-0002-2712-4447"
  - family-names: "Ahmad"
    given-names: "Mian"
    orcid: "https://orcid.org/0000-0002-4706-4146"
  - family-names: "Xiao"
    given-names: "Guofang"
  - family-names: "Koo"
    given-names: "Bongjin"
    orcid: "https://orcid.org/0000-0002-3611-4988"
  - family-names: "Bonmati"
    given-names: "Ester"
    orcid: "https://orcid.org/0000-0001-9217-5438"
  - family-names: "Kahl"
    given-names: "Kim"
  - family-names: "Clarkson"
    given-names: "Matthew"
    orcid: "https://orcid.org/0000-0002-5565-1252"
  doi: "10.1007/s11548-020-02180-5"
  journal: "International journal of computer assisted radiology and surgery"
  start: 1075
  end: 1084
  title: "SciKit-Surgery: Compact Libraries for Surgical Navigation"
  volume: 15
  issue: 7
  year: 2020

GitHub Events

Total

Issues event: 3
Delete event: 1
Issue comment event: 1
Push event: 4
Create event: 3

Last Year

Issues event: 3
Delete event: 1
Issue comment event: 1
Push event: 4
Create event: 3

Committers

Last synced: over 2 years ago

All Time

Total Commits: 190
Total Committers: 10
Avg Commits per committer: 19.0
Development Distribution Score (DDS): 0.705

Past Year

Commits: 6
Committers: 1
Avg Commits per committer: 6.0
Development Distribution Score (DDS): 0.0

Top Committers

Name	Email	Commits
Stephen Thompson	s**n@u**k	56
Matt Clarkson	m**n@u**k	40
Thomas Dowrick	t**k@g**m	37
rmapaah	r**h@u**k	21
Mian Asbat ahmad	m**d@e**k	8
Thomas Dowrick	t**k@u**k	7
Mian Ahmad	m**d@u**k	7
Guofang Xiao	g**o@u**k	5
bongjinkoo	d**a@g**m	5
Mian Asbat Ahmad	m**t@g**m	4

Committer Domains (Top 20 + Academic)

ucl.ac.uk: 6 eduroam-int-dhcp-97-228-159.ucl.ac.uk: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time

Total issues: 58
Total pull requests: 15
Average time to close issues: 25 days
Average time to close pull requests: about 23 hours
Total issue authors: 4
Total pull request authors: 5
Average comments per issue: 5.72
Average comments per pull request: 0.27
Merged pull requests: 14
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 1
Pull requests: 0
Average time to close issues: about 1 month
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

thompson318 (53)
MattClarkson (2)
tdowrick (1)
mianasbat (1)

Pull Request Authors

thompson318 (10)
tdowrick (2)
MattClarkson (2)
mianasbat (1)
Enzo-Kerkhof (1)

Top Labels

Issue Labels

gitlab merge request (14)

Pull Request Labels

Packages

Total packages: 1
Total downloads:
- pypi 2,879 last-month

Total dependent packages: 4
Total dependent repositories: 16
Total versions: 31
Total maintainers: 2

pypi.org: scikit-surgerycore

scikit-surgerycore contains commonly used Image Guided Surgery algorithms and tools

Homepage: https://github.com/SciKit-Surgery/scikit-surgerycore
Documentation: https://scikit-surgerycore.readthedocs.io/
License: BSD-3 license
Latest release: 0.8.0
published about 1 year ago

Versions: 31
Dependent Packages: 4
Dependent Repositories: 16
Downloads: 2,879 Last month

Rankings

Dependent packages count: 1.9%

Dependent repos count: 3.6%

Downloads: 5.6%

Average: 12.5%

Stargazers count: 21.5%

Forks count: 29.8%

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 * development
pytest * development
pyyaml * development
sphinx * development
sphinx_rtd_theme * development
tox * development

requirements.txt pypi

numpy *

setup.py pypi

numpy *

ecosyste.ms

Data

Tools

Indexes

Applications

Experiments

Open Source Science

scikit-surgerycore

Science Score: 67.0%

Keywords

Repository

Basic Info

Statistics

Topics

Metadata Files

README.rst

Owner

Citation (CITATION.cff)

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

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Top Labels

Issue Labels

Pull Request Labels

Packages

pypi.org: scikit-surgerycore

Rankings

Maintainers (2)

Dependencies