scikit-surgerynditracker

Easy communication with NDI trackers (Polaris Vicra, Spectra, Vega, and Aurora)

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

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 2 DOI reference(s) in README
○
Academic publication links
✓
Committers with academic emails
7 of 10 committers (70.0%) from academic institutions
○
Institutional organization owner
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JOSS paper metadata
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Scientific vocabulary similarity
Low similarity (13.0%) to scientific vocabulary

Keywords

ndi scikit-surgery ucl

Keywords from Contributors

augmented-reality opencv vtk surgery ultrasound

Last synced: 6 months ago · JSON representation ·

Repository

Easy communication with NDI trackers (Polaris Vicra, Spectra, Vega, and Aurora)

Basic Info

Host: GitHub
Owner: SciKit-Surgery
License: other
Language: Python
Default Branch: master
Homepage: https://github.com/SciKit-Surgery
Size: 1.63 MB

Statistics

Stars: 48
Watchers: 3
Forks: 14
Open Issues: 8
Releases: 0

Topics

ndi scikit-surgery ucl

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

Metadata Files

Readme Contributing License Code of conduct Citation

README.rst

scikit-surgerynditracker
===============================

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

|

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

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

.. image:: https://readthedocs.org/projects/scikit-surgerynditracker/badge/?version=latest
    :target: http://scikit-surgerynditracker.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

scikit-surgerynditracker is a python interface for Northern Digital (NDI) trackers. It should work with Polaris Vicra, Spectra, and Vega optical trackers and Aurora electromagnetic trackers. Tracking data is output as NumPy arrays.

Author: Stephen Thompson

scikit-surgerynditracker 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)`_.


Installing
----------

::

    pip install scikit-surgerynditracker

Using
-----
Configuration is done using Python libraries at instantiation. Invalid
configuration should raise exceptions. Tracking data is returned in a set of
lists, containing the port handles, timestamps, framenumbers, the tracking data
and a tracking quality metric. By default tracking data is returned as a 4x4 NumPy array,
though can be returned as a quaternion by changing the configuration.

::

    from sksurgerynditracker.nditracker import NDITracker
    SETTINGS = {
        "tracker type": "polaris",
        "romfiles" : ["../data/8700339.rom"]
            }
    TRACKER = NDITracker(SETTINGS)

    TRACKER.start_tracking()
    port_handles, timestamps, framenumbers, tracking, quality = TRACKER.get_frame()
    for t in tracking:
      print (t)
    TRACKER.stop_tracking()
    TRACKER.close()

See demo.py for a full example

Developing
----------

Cloning
^^^^^^^

You can clone the repository using the following command:

::

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


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-surgerynditracker 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-surgerynditracker
.. _`Documentation`: https://scikit-surgerynditracker.readthedocs.io
.. _`SciKit-Surgery`: https://www.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-surgerynditracker/blob/master/CONTRIBUTING.rst
.. _`license file`: https://github.com/SciKit-Surgery/scikit-surgerynditracker/blob/master/LICENSE

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-SurgeryNDITracker packages 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-Surgery"
url: "https://github.com/SciKit-Surgery/scikit-surgerynditracker"
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: 2
Watch event: 5
Issue comment event: 3
Fork event: 2

Last Year

Issues event: 2
Watch event: 5
Issue comment event: 3
Fork event: 2

Committers

Last synced: over 2 years ago

All Time

Total Commits: 208
Total Committers: 10
Avg Commits per committer: 20.8
Development Distribution Score (DDS): 0.192

Past Year

Commits: 47
Committers: 4
Avg Commits per committer: 11.75
Development Distribution Score (DDS): 0.532

Top Committers

Name	Email	Commits
Stephen Thompson	s**n@u**k	168
mxochicale	m**e@.**k	16
Miguel Xochicale	m**e@u**k	8
Thomas Dowrick	t**k@g**m	7
Guofang Xiao	g**o@u**k	3
Thomas Dowrick	t**k@u**k	2
Mian Ahmad	m**d@u**k	1
Matt Clarkson	m**n@u**k	1
Raj Kundu	r**8@g**m	1
Janis Börsig	3****9	1

Committer Domains (Top 20 + Academic)

ucl.ac.uk: 6 .ac.uk: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time

Total issues: 60
Total pull requests: 26
Average time to close issues: 3 months
Average time to close pull requests: 1 day
Total issue authors: 19
Total pull request authors: 6
Average comments per issue: 4.53
Average comments per pull request: 0.31
Merged pull requests: 25
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: 3.0
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 (38)
rajkundu (3)
mianasbat (2)
jsbyysheng (2)
tdowrick (2)
Mixmorks (2)
unbun (1)
emmeduz (1)
JKvet (1)
ckolluru (1)
marcinbalicki (1)
ekmungi (1)
ja99 (1)
Enzo-Kerkhof (1)
xlzhu0317 (1)

Pull Request Authors

thompson318 (22)
rajkundu (2)
Larbino1 (2)
ja99 (1)
tdowrick (1)
mxochicale (1)

Top Labels

Issue Labels

gitlab merge request (4)

Pull Request Labels

Packages

Total packages: 1
Total downloads:
- pypi 456 last-month

Total dependent packages: 1
Total dependent repositories: 4
Total versions: 30
Total maintainers: 2

pypi.org: scikit-surgerynditracker

Interface for Northern Digital (NDI) Trackers with data to NumPy arrays

Homepage: https://github.com/SciKit-Surgery/scikit-surgerynditracker
Documentation: https://scikit-surgerynditracker.readthedocs.io/
License: BSD-3 license
Latest release: 1.0.1
published almost 2 years ago

Versions: 30
Dependent Packages: 1
Dependent Repositories: 4
Downloads: 456 Last month

Rankings

Dependent packages count: 4.8%

Dependent repos count: 7.5%

Average: 9.3%

Forks count: 10.9%

Stargazers count: 11.1%

Downloads: 12.1%

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
pytest-mock * development
sphinx * development
sphinx_rtd_theme * development
tox * development

.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