Python Package for Reflection Ultrasound Computed Tomography (RUCT) Delay And Sum (DAS) Algorithm

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Algorithmspyruct
Overview

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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Comments
  • Bug with Hilbert transform and filtering

    Bug with Hilbert transform and filtering

    There is a bug in the Hilbert transform and filtering of the rf-signals due to differences between corresponding packages in Matlab and Python. In python, axis=0 should be included. Correction:

    In /pyruct/reconstruction/cpuReconUS.py --> analyticalSigMat = hilbert(sigMatN, axis=0)

    In /pyruct/preprocessing/filterBandPass.py --> sigMatF = filtfilt(lowF, highF, sigMat, padlen=0, axis=0)

    In /pyruct/reconstruction/cpuReconUS.py --> sigMatN = sigMatNormalizeUS(sigMatF) [This is not needed anymore once the filtering is done correctly]

    opened by naiarako 1
Releases(v1.0.3)
Owner
Berkan Lafci
🔬 PhD Candidate at ETH Zürich 🔬 🩺 Medical Imaging, AI Researcher 🩺 🎓 Boğaziçi University ‘15, TU München ‘18 🎓 (he/him/his)
Berkan Lafci
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