SnappySonic¶
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¶
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.
Requirements for snappysonic¶
This is the software requirements file for snappysonic, part of the SciKit-Surgery project. The requirements listed below should define what snappysonic does. Each requirement can be matched to a unit test that checks whether the requirement is met.
Requirements¶
| ID | Description | Test |
|---|---|---|
| 0000 | Module has a help page | pylint, see tests/pylint.rc and tox.ini |
| 0001 | Functions are documented | pylint, see tests/pylint.rc and tox.ini |
| 0002 | Package has a version number | No test yet, handled by git. |
stable¶
snappysonic package¶
Subpackages¶
snappysonic.algorithms package¶
Functions for snappysonic
-
snappysonic.algorithms.algorithms.check_us_buffer(usbuffer)[source]¶ Checks that all ultrasound buffer contains all required key values.
Parameters: usbuffer – the buffer to check Raises: KeyError Raises: ValueError
-
snappysonic.algorithms.algorithms.configure_tracker(config)[source]¶ Configures a scikit-surgery tracker based on the passed config
Parameters: config – a tracker configuration dictionary Returns: The tracker Raises: KeyError
-
snappysonic.algorithms.algorithms.get_bg_image_size(config)[source]¶ Reads the geometry from a configuration and returns the extents of the buffer
Parameters: config – a tracker configuration dictionary Returns: the extents of the buffer
-
snappysonic.algorithms.algorithms.lookupimage(usbuffer, pts)[source]¶ determines whether a coordinate (pts) lies with an area defined by a usbuffer, and returns an image from the buffer if appropriate
Parameters: usbuffer – a dictionary containing bounding box information (x0,y0, x1,y1) and image data Returns: True if point in bounding box. Image.
snappysonic.overlay_widget package¶
Main loop for tracking visualisation
-
class
snappysonic.overlay_widget.overlay.OverlayApp(config)[source]¶ Bases:
sksurgeryutils.common_overlay_apps.OverlayBaseWidgetInherits from OverlayBaseWidget, adding code to read in video buffers, and display a frame of data that depends on the position of an external tracking system, e.g. surgeryarucotracker
-
staticMetaObject= <PySide2.QtCore.QMetaObject object>¶
-
-
snappysonic.overlay_widget.overlay.circle(img, center, radius, color[, thickness[, lineType[, shift]]]) → img¶ . @brief Draws a circle. . . The function cv::circle draws a simple or filled circle with a given center and radius. . @param img Image where the circle is drawn. . @param center Center of the circle. . @param radius Radius of the circle. . @param color Circle color. . @param thickness Thickness of the circle outline, if positive. Negative values, like #FILLED, . mean that a filled circle is to be drawn. . @param lineType Type of the circle boundary. See #LineTypes . @param shift Number of fractional bits in the coordinates of the center and in the radius value.
-
snappysonic.overlay_widget.overlay.imread(filename[, flags]) → retval¶ . @brief Loads an image from a file. . . @anchor imread . . The function imread loads an image from the specified file and returns it. If the image cannot be . read (because of missing file, improper permissions, unsupported or invalid format), the function . returns an empty matrix ( Mat::data==NULL ). . . Currently, the following file formats are supported: . . - Windows bitmaps - *.bmp, *.dib (always supported) . - JPEG files - *.jpeg, *.jpg, *.jpe (see the Note section) . - JPEG 2000 files - *.jp2 (see the Note section) . - Portable Network Graphics - *.png (see the Note section) . - WebP - *.webp (see the Note section) . - Portable image format - *.pbm, *.pgm, *.ppm *.pxm, *.pnm (always supported) . - PFM files - *.pfm (see the Note section) . - Sun rasters - *.sr, *.ras (always supported) . - TIFF files - *.tiff, *.tif (see the Note section) . - OpenEXR Image files - *.exr (see the Note section) . - Radiance HDR - *.hdr, *.pic (always supported) . - Raster and Vector geospatial data supported by GDAL (see the Note section) . . @note . - The function determines the type of an image by the content, not by the file extension. . - In the case of color images, the decoded images will have the channels stored in B G R order. . - When using IMREAD_GRAYSCALE, the codec’s internal grayscale conversion will be used, if available. . Results may differ to the output of cvtColor() . - On Microsoft Windows* OS and MacOSX*, the codecs shipped with an OpenCV image (libjpeg, . libpng, libtiff, and libjasper) are used by default. So, OpenCV can always read JPEGs, PNGs, . and TIFFs. On MacOSX, there is also an option to use native MacOSX image readers. But beware . that currently these native image loaders give images with different pixel values because of . the color management embedded into MacOSX. . - On Linux*, BSD flavors and other Unix-like open-source operating systems, OpenCV looks for . codecs supplied with an OS image. Install the relevant packages (do not forget the development . files, for example, “libjpeg-dev”, in Debian* and Ubuntu*) to get the codec support or turn . on the OPENCV_BUILD_3RDPARTY_LIBS flag in CMake. . - In the case you set WITH_GDAL flag to true in CMake and @ref IMREAD_LOAD_GDAL to load the image, . then the [GDAL](http://www.gdal.org) driver will be used in order to decode the image, supporting . the following formats: [Raster](http://www.gdal.org/formats_list.html), . [Vector](http://www.gdal.org/ogr_formats.html). . - If EXIF information is embedded in the image file, the EXIF orientation will be taken into account . and thus the image will be rotated accordingly except if the flags @ref IMREAD_IGNORE_ORIENTATION . or @ref IMREAD_UNCHANGED are passed. . - Use the IMREAD_UNCHANGED flag to keep the floating point values from PFM image. . - By default number of pixels must be less than 2^30. Limit can be set using system . variable OPENCV_IO_MAX_IMAGE_PIXELS . . @param filename Name of file to be loaded. . @param flags Flag that can take values of cv::ImreadModes
-
snappysonic.overlay_widget.overlay.putText(img, text, org, fontFace, fontScale, color[, thickness[, lineType[, bottomLeftOrigin]]]) → img¶ . @brief Draws a text string. . . The function cv::putText renders the specified text string in the image. Symbols that cannot be rendered . using the specified font are replaced by question marks. See #getTextSize for a text rendering code . example. . . @param img Image. . @param text Text string to be drawn. . @param org Bottom-left corner of the text string in the image. . @param fontFace Font type, see #HersheyFonts. . @param fontScale Font scale factor that is multiplied by the font-specific base size. . @param color Text color. . @param thickness Thickness of the lines used to draw a text. . @param lineType Line type. See #LineTypes . @param bottomLeftOrigin When true, the image data origin is at the bottom-left corner. Otherwise, . it is at the top-left corner.
-
snappysonic.overlay_widget.overlay.rectangle(img, pt1, pt2, color[, thickness[, lineType[, shift]]]) → img¶ . @brief Draws a simple, thick, or filled up-right rectangle. . . The function cv::rectangle draws a rectangle outline or a filled rectangle whose two opposite corners . are pt1 and pt2. . . @param img Image. . @param pt1 Vertex of the rectangle. . @param pt2 Vertex of the rectangle opposite to pt1 . . @param color Rectangle color or brightness (grayscale image). . @param thickness Thickness of lines that make up the rectangle. Negative values, like #FILLED, . mean that the function has to draw a filled rectangle. . @param lineType Type of the line. See #LineTypes . @param shift Number of fractional bits in the point coordinates.
rectangle(img, rec, color[, thickness[, lineType[, shift]]]) -> img . @overload . . use rec parameter as alternative specification of the drawn rectangle: r.tl() and . r.br()-Point(1,1) are opposite corners
Module contents¶
snappysonic