pyruct
Python Package for Reflection Ultrasound Computed Tomography (RUCT) Delay And Sum (DAS) Algorithm
The imaging setup is explained in these papers Lafci, B. et al., Merčep, E. et al. Synthetic Transmit Aperture (STA) method for pulse-echo ultrasound was used in data acquistion. All images were reconstructed using Delay And Sum (DAS) algorithm and compounded to create final high contrast images.
Installation
This project uses pip package manager. Please run the following command in your terminal to install the package.
pip install git+https://github.com/berkanlafci/pyruct.git
Usage
After installing package, the functions can be called using python scripts.
Example scripts to use pyruct package can be found in _examples folder.
For example, delay and sum example on cpu is called with following commands in terminal.
python exampleCpuDAS.py
The example scripts can be written by users.
pyruct package can be imported in python scripts using following line.
import pyruct as pt
After importing the package, the functions can be called with following lines in python script.
usData = pt.usReader(filePath=filePath) # read data
das = pt.cpuDAS() # create reconstruction object
imageRecon = das.recon(usData.sigMat) # reconstruct image
Data
Test data will be made publically available.
After the download, place the data in "data/rawData/" folder that shares the same root directory with "exampleCpuDAS.py" script that can be run for testing "pyruct".
Citation
If you use this package in your research, please cite it as follows
Lafci, B., Robin, J., Dean-Ben, X. L., & Razansky, D. (2021). pyruct (Version 1.0.0) [Computer software]. https://github.com/berkanlafci/pyruct
Acknowledgements
This project is supported by Swiss Data Science Center (SDSC).
References
[1] Lafci, B., Merčep, E., Herraiz, J.L., Deán-Ben, X.L., Razansky, D. Noninvasive multiparametric characterization of mammary tumors with transmission-reflection optoacoustic ultrasound, Neoplasia, Volume 22, Issue 12, 2020, Pages 770-777, ISSN 1476-5586, https://doi.org/10.1016/j.neo.2020.10.008.
[2] Merčep, E., Herraiz, J.L., Deán-Ben, X.L., Razansky, D. Transmission–reflection optoacoustic ultrasound (TROPUS) computed tomography of small animals. Light Sci Appl 8, 18 (2019). https://doi.org/10.1038/s41377-019-0130-5
License
This project is licensed under MIT License.
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