snappysonic

SnappySonic is an Ultrasound Simulator for use in research and public engagement.

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

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SnappySonic is an Ultrasound Simulator for use in research and public engagement.

README.rst

SnappySonic
===============================

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Author: Stephen Thompson

SnappySonic can be used as an ultrasound acquisition simulator. The output from a tracking system (NDI or AruCo tags) is to select a frame of pre-recorded video to show. A suitable video of ultrasound data is included in the data directory, however the user can select a video of their choosing. The software and its use is described in the `SnappySonic paper`_.

SnappySonic 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)`_.

SnappySonic supports Python 3.6.

::

    pip install snappysonic
    python snappysonic.py --config config.json

The config file defines the tracking parameters and image buffer, e.g.

::

  {
   "ultrasound buffer": "data/usbuffer.mp4",
	 "buffer descriptions": [
		{
		 "name": "glove",
		 "start frame": 0,
		 "end frame": 284,
		 "x0": 20, "x1": 200,
		 "y0": 200, "y1": 260,
		 "scan direction": "x"
		},
    ]
    ....
    "tracker config": {
		"tracker type": "aruco",
		"video source": 2,
		"debug": true,
		"capture properties": {
			"CAP_PROP_FRAME_WIDTH": 640,
			"CAP_PROP_FRAME_HEIGHT": 480
		
   }
  }

An example configuration file can be downloaded from `here`_ and an image buffer from `source code repository data directory`_

Developing
----------

Cloning
^^^^^^^

You can clone the repository using the following command:

::

    git clone https://github.com/SciKit-Surgery/snappysonic


Running tests
^^^^^^^^^^^^^
Unit tests are performed in stand alone environments using tox, which also checks coding style.
::

    tox


Installing
----------

You can pip install from pypi with
::

  pip install snappysonic

or You can pip install directly from the repository as follows:
::

    pip install git+https://github.com/SciKit-Surgery/snappysonic

How to Cite
-----------
If you use this software in your research or teaching, please cite:

Thompson, S., Dowrick, T., Xiao, G., Ramalhinho, J., Robu, M., Ahmad, M., Taylor, D. and Clarkson, M.J., 2020. SnappySonic: An Ultrasound Acquisition Replay Simulator. Journal of Open Research Software, 8(1), p.8. DOI: http://doi.org/10.5334/jors.289

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

Please see the `contributing guidelines`_.


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

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


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

Copyright 2019 University College London.
snappysonic 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/snappysonic
.. _`here`: https://github.com/SciKit-Surgery/snappysonic/blob/master/config.json
.. _`source code repository data directory`: https://github.com/SciKit-Surgery/snappysonic/blob/master/data
.. _`Documentation`: https://snappysonic.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/snappysonic/blob/master/CONTRIBUTING.rst
.. _`license file`: https://github.com/SciKit-Surgery/snappysonic/blob/master/LICENSE
.. _`SnappySonic paper`: http://doi.org/10.5334/jors.289

Owner

Citation (CITATION.cff)

cff-version: 1.2.0
message: "If you use SnappySonic, 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: "SnappySonic"
doi: 10.5281/zenodo.3491054
url: "https://github.com/SciKit-Surgery/snappysonic"
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: "Xiao"
    given-names: "Guofang"
  - family-names: "Ramalhinho"
    given-names: "Jo{\~a}o"
  - family-names: "Robu"
    given-names: "Maria"
  - family-names: "Ahmad"
    given-names: "Mian"
    orcid: "https://orcid.org/0000-0002-4706-4146"
  - family-names: "Taylor"
    given-names: "Dan"
  - family-names: "Clarkson"
    given-names: "Matthew"
    orcid: "https://orcid.org/0000-0002-5565-1252"
  doi: 10.5334/jors.289
  journal: "Journal of Open Research Software"
  title: "SnappySonic: An Ultrasound Acquisition Replay Simulator"
  volume: 8
  issue: 1
  year: 2020

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