SnappySonic
===============================
.. image:: https://github.com/SciKit-Surgery/snappysonic/raw/master/snappysonic.gif
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|
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:alt: The SnappySonic Paper
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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
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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`_.\n\nSnappySonic 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)`_.\n\nSnappySonic supports Python 3.6.\n\n::\n\n pip install snappysonic\n python snappysonic.py --config config.json\n\nThe config file defines the tracking parameters and image buffer, e.g.\n\n::\n\n {\n \"ultrasound buffer\": \"data/usbuffer.mp4\",\n\t \"buffer descriptions\": [\n\t\t{\n\t\t \"name\": \"glove\",\n\t\t \"start frame\": 0,\n\t\t \"end frame\": 284,\n\t\t \"x0\": 20, \"x1\": 200,\n\t\t \"y0\": 200, \"y1\": 260,\n\t\t \"scan direction\": \"x\"\n\t\t},\n ]\n ....\n \"tracker config\": {\n\t\t\"tracker type\": \"aruco\",\n\t\t\"video source\": 2,\n\t\t\"debug\": true,\n\t\t\"capture properties\": {\n\t\t\t\"CAP_PROP_FRAME_WIDTH\": 640,\n\t\t\t\"CAP_PROP_FRAME_HEIGHT\": 480\n\t\t\n }\n }\n\nAn example configuration file can be downloaded from `here`_ and an image buffer from `source code repository data directory`_\n\nDeveloping\n----------\n\nCloning\n^^^^^^^\n\nYou can clone the repository using the following command:\n\n::\n\n git clone https://github.com/SciKit-Surgery/snappysonic\n\n\nRunning tests\n^^^^^^^^^^^^^\nUnit tests are performed in stand alone environments using tox, which also checks coding style.\n::\n\n tox\n\n\nInstalling\n----------\n\nYou can pip install from pypi with\n::\n\n pip install snappysonic\n\nor You can pip install directly from the repository as follows:\n::\n\n pip install git+https://github.com/SciKit-Surgery/snappysonic\n\nHow to Cite\n-----------\nIf you use this software in your research or teaching, please cite:\n\nThompson, 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\n\nContributing\n^^^^^^^^^^^^\n\nPlease see the `contributing guidelines`_.\n\n\nUseful links\n^^^^^^^^^^^^\n\n* `Source code repository`_\n* `Documentation`_\n\n\nLicensing and copyright\n-----------------------\n\nCopyright 2019 University College London.\nsnappysonic is released under the BSD-3 license. Please see the `license file`_ for details.\n\n\nAcknowledgements\n----------------\n\nSupported by `Wellcome`_ and `EPSRC`_.\n\n\n.. _`Wellcome EPSRC Centre for Interventional and Surgical Sciences`: http://www.ucl.ac.uk/weiss\n.. _`source code repository`: https://github.com/SciKit-Surgery/snappysonic\n.. _`here`: https://github.com/SciKit-Surgery/snappysonic/blob/master/config.json\n.. _`source code repository data directory`: https://github.com/SciKit-Surgery/snappysonic/blob/master/data\n.. _`Documentation`: https://snappysonic.readthedocs.io\n.. _`SciKit-Surgery`: https://github.com/SciKit-Surgery\n.. _`University College London (UCL)`: http://www.ucl.ac.uk/\n.. _`Wellcome`: https://wellcome.ac.uk/\n.. _`EPSRC`: https://www.epsrc.ac.uk/\n.. _`contributing guidelines`: https://github.com/SciKit-Surgery/snappysonic/blob/master/CONTRIBUTING.rst\n.. _`license file`: https://github.com/SciKit-Surgery/snappysonic/blob/master/LICENSE\n.. _`SnappySonic paper`: http://doi.org/10.5334/jors.289\n\n\n",
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