PyMUST 0.1.9

Python port of the MUST toolbox for ultrasound signal processing and generation of simulated images

PyMUST

This is a Python reimplementation of the MUST ultrasound toolbox for synthetic image generation and reconstruction (https://www.biomecardio.com/MUST/).

Notice: this is still under development, and might have bugs and errors. Also, even if results should be the same with Matlab version, small numerical differences are expected. If you find any bug/unconsistency with the matlab version, please open a github issue, or send an email to ({[e-mail], [e-mail]}).

As a design decision, we have tried to keep syntax as close as possible with the matlab version, specially regarding the way functions are called. This has resulted in non-pythonic arguments (i.e., overuse of variable number of positional arguments). This allows to make use of Must documentation (https://www.biomecardio.com/MUST/documentation.html). Keep in mind that, since Python does not allow a changing number of returns, each function will output the maximum number of variables of the matlab version.

Installation

You can obtain the latest version from github, or alternatively install it using pip or conda. Please note that the github version might have bugs or other issues, since it is in development. Do not hesitate to create an issue in Pymust.

Install from pip

pip install pymust

Install from conda

conda install -c conda-forge pymut

Download from github

To install a local version of pymust with its dependencies (matplotlib, scipy, numpy), download it, go to the main folder and then run:

pip install -e .

The package works in OsX, Linux and Windows (but parallelism might not be available on Windows). We recommend installing it in a separate conda environment.

To install pymust with its dependencies (matplotlib, scipy, numpy), you can directly install from pip:

pip install git+https://github.com/creatis-ULTIM/PyMUST.git

Main functions

Please refer to the Matlab documentation or examples for a full description of the functions involved

• Transducer definition (getparam)
• Element delays (txdelay)
• Simulation (simus, pfield)
• Bmode and Doppler image beamforming from radiofrequencies (tgc, rf2iq, das, bmode, iq2doppler)

Examples

In the folder "examples", you have python notebooks ilustrating the main functionalities of PyMUST. They are the same as the ones available in the Matlab version. As a quickstart, please use this notebook. There are also more specific demos for some fetures:

• 3D acoustics
• Motion estimation

Tutorials

The tutorials folder are incomplete notebooks for a course at Universitat Pompeu Fabra on ultrasound image acquisition and reconstruction (Biomedical Imaging Systems), that students need to complete during the practical sessions.

Next steps

If there is a functionality that you would like to see, please open an issue.

• Update function documentation.
• Find computational bottlenecks, and optimise (possibly with C extensions).
• GPU acceleration (coming soon!)
• Harmonic imaging (coming soon!)
• Differentiable rendering.

Citation

If you use this library for your research, please cite:

• G. Bernardino, D. Garcia "PyMUST: an open-Source Python Library for the Simulation and Analysis of Ultrasound." 2024 IEEE Ultrasonics, Ferroelectrics, and Frequency Control Joint Symposium doi:10.1109/uffc-js60046.2024.10793881
• D. Garcia, "Make the most of MUST, an open-source MATLAB UltraSound Toolbox", 2021 IEEE International Ultrasonics Symposium (IUS), 2021, pp. 1-4, doi: 10.1109/IUS52206.2021.9593605
• D. Garcia, "SIMUS: an open-source simulator for medical ultrasound imaging. Part I: theory & examples", Computer Methods and Programs in Biomedicine, 218, 2022, p. 106726, doi: 10.1016/j.cmpb.2022.106726
• A. Cigier, F. Varray and D. Garcia "SIMUS: an open-source simulator for medical ultrasound imaging. Part II: comparison with four simulators," Computer Methods and Programs in Biomedicine, 218, 2022, p. 106726, doi: 10.1016/j.cmpb.2022.106726.

If you use the speckle tracking:

• V. Perrot and D. Garcia, "Back to basics in ultrasound velocimetry: tracking speckles by using a standard PIV algorithm", 2018 IEEE International Ultrasonics Symposium (IUS), 2018, pp. 206-212, doi: 10.1109/ULTSYM.2018.8579665

If you use beamforming:

• V. Perrot, M. Polichetti, F. Varray and D. Garcia, "So you think you can DAS? A viewpoint on delay-and-sum beamforming," 'Ultrasonics, 111, 2021, p. 106309, doi 10.1016/j.ultras.2020.106309

If you use vector flow:

• C. Madiena, J. Faurie, J. Porée and D. Garcia "Color and vector flow imaging in parallel ultrasound with sub-Nyquist sampling," IEEE Transactions on Ultrasonics, Ferroelectrics, and Frequency Control 65, 2018, pp. 795-802 10.1109/TUFFC.2018.2817885

Acknowledgements

This work has been patially funded by Grant #RYC2022-035960-I funded by MICIU/AEI/ 10.13039/501100011033 and by the FSE+