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

Last update: Dec 12, 2022

Related tags

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.

Path finding algorithm visualizer with python

path-finding-algorithm-visualizer ~ click on the grid to place the starting block and then click elsewhere to add the end block ~ click again to place

1 Oct 31, 2021

This python algorithm creates a simple house floor plan based on a user-provided CSV file.

This python algorithm creates a simple house floor plan based on a user-provided CSV file. The algorithm generates possible router placements and evaluates where a signal will be reached in every room of the floor plan.

1 Nov 12, 2021

This is a Python implementation of the HMRF algorithm on networks with categorial variables.

Salad Salad is an Open Source Python library to segment tissues into different biologically relevant regions based on Hidden Markov Random Fields. The

1 Nov 16, 2021

🌟 Python algorithm team note for programming competition or coding test

3 Feb 25, 2022

Exact algorithm for computing two-sided statistical tolerance intervals under a normal distribution assumption using Python.

norm-tol-int Exact algorithm for computing two-sided statistical tolerance intervals under a normal distribution assumption using Python. Methods The

1 Jan 6, 2022

A Python project for optimizing the 8 Queens Puzzle using the Genetic Algorithm implemented in PyGAD.

Comments

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)

v1.0.3(Nov 23, 2021)

Indexing in cpuReconUS and exampleCpuDAS is changed.
Source code(tar.gz)
Source code(zip)
v1.0.2(Nov 8, 2021)

Citation and readme information are updated
Source code(tar.gz)
Source code(zip)
v1.0.1(Nov 7, 2021)

Bugs with filtering axis and Hilbert transform axis are fixed
Source code(tar.gz)
Source code(zip)
v1.0.0(Oct 26, 2021)

First Release of Python Package for Reflection Ultrasound Computed Tomography (RUCT) Delay And Sum (DAS) Algorithm
Source code(tar.gz)
Source code(zip)

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

Related tags

Overview

pyruct

Installation

Usage

Data

Citation

Acknowledgements

References

License

You might also like...

Path finding algorithm visualizer with python

This python algorithm creates a simple house floor plan based on a user-provided CSV file.

This is a Python implementation of the HMRF algorithm on networks with categorial variables.

🌟 Python algorithm team note for programming competition or coding test

Exact algorithm for computing two-sided statistical tolerance intervals under a normal distribution assumption using Python.

A Python project for optimizing the 8 Queens Puzzle using the Genetic Algorithm implemented in PyGAD.

A Python program to easily solve the n-queens problem using min-conflicts algorithm

This is an implementation of the QuickHull algorithm in Python. I

Data Model built using Logistic Regression Algorithm on Python.

Comments

Bug with Hilbert transform and filtering

Releases(v1.0.3)

v1.0.3(Nov 23, 2021)

v1.0.2(Nov 8, 2021)

v1.0.1(Nov 7, 2021)

v1.0.0(Oct 26, 2021)

Owner

Berkan Lafci

Wordle-solver - A program that solves a Wordle using a simple algorithm

Path finding algorithm visualizer with python

ROS Basics and TurtleSim

Code for generating alloy / disordered structures through the special quasirandom structure (SQS) algorithm

Apriori - An algorithm for frequent item set mining and association rule learning over relational databases

A Python Package for Portfolio Optimization using the Critical Line Algorithm

Infomap is a network clustering algorithm based on the Map equation.

Algorithms and data structures for educational, demonstrational and experimental purposes.

Repository for Comparison based sorting algorithms in python

Algorithmic virtual trading using the neostox platform

Python-Strongest-Encrypter - Transform your text into encrypted symbols using their dictionary

Search algorithm implementations meant for teaching

A litle algorithm that i made for transform a picture in a spreadsheet.

Optimal skincare partition finder using graph theory

Provide player's names and mmr and generate mathematically balanced teams

Gnat - GNAT is NOT Algorithmic Trading

The DarkRift2 networking framework written in Python 3

Python algorithm to determine the optimal elevation threshold of a GNSS receiver, by using a statistical test known as the Brown-Forsynthe test.

Genetic Algorithm for Robby Robot based on Complexity a Guided Tour by Melanie Mitchell

Policy Gradient Algorithms (One Step Actor Critic & PPO) from scratch using Numpy