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

Related tags

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.

You might also like...
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

izumi 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.

Joshua Miller 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

null 1 Nov 16, 2021
🌟 Python algorithm team note for programming competition or coding test

🌟 Python algorithm team note for programming competition or coding test

Seung Hoon Lee 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

Jed Ludlow 1 Jan 6, 2022
A Python project for optimizing the 8 Queens Puzzle using the Genetic Algorithm implemented in PyGAD.
A Python project for optimizing the 8 Queens Puzzle using the Genetic Algorithm implemented in PyGAD.

8QueensGenetic A Python project for optimizing the 8 Queens Puzzle using the Genetic Algorithm implemented in PyGAD. The project uses the Kivy cross-p

Ahmed Gad 16 Nov 13, 2022
A Python program to easily solve the n-queens problem using min-conflicts algorithm

QueensProblem A program to easily solve the n-queens problem using min-conflicts algorithm Performances estimated with a sample of 1000 different rand

null 0 Oct 21, 2022
This is an implementation of the QuickHull algorithm in Python. I

QuickHull This is an implementation of the QuickHull algorithm in Python. It randomly generates a set of points and finds the convex hull of this set

Anant Joshi 4 Dec 4, 2022
Data Model built using Logistic Regression Algorithm on Python.

Logistic-Regression Problem Statement: Your client is a retail banking institution. Term deposits are a major source of income for a bank. A term depo

Hemanth Babu Muthineni 0 Dec 25, 2021
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
GitHub Repository
This project consists of a collaborative filtering algorithm to predict movie reviews ratings from a dataset of Netflix ratings.

Collaborative Filtering - Netflix movie reviews Description This project consists of a collaborative filtering algorithm to predict movie reviews rati

Shashank Kumar 1 Dec 21, 2021
PathPlanning - Common used path planning algorithms with animations.

Overview This repository implements some common path planning algorithms used in robotics, including Search-based algorithms and Sampling-based algori

Huiming Zhou 5.1k Jan 08, 2023
Better control of your asyncio tasks

quattro: task control for asyncio quattro is an Apache 2 licensed library, written in Python, for task control in asyncio applications. quattro is inf

Tin Tvrtković 37 Dec 28, 2022
PickMush - A mini study/project on boosting algorithm

PickMush A mini project implementing Boosting Author Shashwat Vaibhav What does it do? Classifies whether Mushroom is edible or is non-edible (binary

Shashwat Vaibahav 3 Nov 08, 2022
N Queen Problem using Genetic Algorithm

The N Queen is the problem of placing N chess queens on an N×N chessboard so that no two queens attack each other.

Mahdi Hassanzadeh 2 Nov 11, 2022
A custom prime algorithm, implementation, and performance code & review

Colander A custom prime algorithm, implementation, and performance code & review Pseudocode Algorithm 1. given a number of primes to find, the followi

Finn Lancaster 3 Dec 17, 2021
Genetic algorithm which evolves aoe2 DE ai scripts

AlphaScripter Use the power of genetic algorithms to evolve AI scripts for Age of Empires II : Definitive Edition. For now this package runs in AOC Us

6 Nov 04, 2022
Python based framework providing a simple and intuitive framework for algorithmic trading

Harvest is a Python based framework providing a simple and intuitive framework for algorithmic trading. Visit Harvest's website for details, tutorials

100 Jan 03, 2023
All algorithms implemented in Python for education

The Algorithms - Python All algorithms implemented in Python - for education Implementations are for learning purposes only. As they may be less effic

1 Oct 20, 2021
A tictactoe where you never win, implemented using minimax algorithm

Unbeatable_TicTacToe A tictactoe where you never win, implemented using minimax algorithm Requirements Make sure you have the pygame module along with

Jessica Jolly 3 Jul 28, 2022
Implements (high-dimenstional) clustering algorithm

Description Implements (high-dimenstional) clustering algorithm described in https://arxiv.org/pdf/1804.02624.pdf Dependencies python3 pytorch (=0.4)

Eric Elmoznino 5 Dec 27, 2022
Dynamic Programming-Join Optimization Algorithm

DP-JOA Join optimization is the process of optimizing the joining, or combining, of two or more tables in a database. Here is a simple join optimizati

Haoze Zhou 3 Feb 03, 2022
A Python project for optimizing the 8 Queens Puzzle using the Genetic Algorithm implemented in PyGAD.

8QueensGenetic A Python project for optimizing the 8 Queens Puzzle using the Genetic Algorithm implemented in PyGAD. The project uses the Kivy cross-p

Ahmed Gad 16 Nov 13, 2022
FLIght SCheduling OPTimization - a simple optimization library for flight scheduling and related problems in the discrete domain

Fliscopt FLIght SCheduling OPTimization 🛫 or fliscopt is a simple optimization library for flight scheduling and related problems in the discrete dom

33 Dec 17, 2022
It is a platform that implements some path planning algorithms.

PathPlanningAlgorithms It is a platform that implements some path planning algorithms. Main dependence: python3.7, opencv4.1.1.26 (for image show) Tip

5 Feb 24, 2022
Search algorithm implementations meant for teaching

Search-py A collection of search algorithms for teaching and experimenting. Non-adversarial Search There’s a heavy separation of concerns which leads

Dietrich Daroch 5 Mar 07, 2022
Sorting-Algorithms - All information about sorting algorithm you need and you can visualize the code tracer

Sorting-Algorithms - All information about sorting algorithm you need and you can visualize the code tracer

Ahmed Hossam 15 Oct 16, 2022
Algorithms implemented in Python

Python Algorithms Library Laurent Luce Description The purpose of this library is to help you with common algorithms like: A* path finding. String Mat

Laurent Luce 264 Dec 06, 2022
Algorithmic trading backtest and optimization examples using order book imbalances. (bitcoin, cryptocurrency, bitmex)

Algorithmic trading backtest and optimization examples using order book imbalances. (bitcoin, cryptocurrency, bitmex)

172 Dec 21, 2022
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 roo

Joshua Miller 1 Nov 12, 2021