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
Sign data using symmetric-key algorithm encryption.

Sign data using symmetric-key algorithm encryption. Validate signed data and identify possible validation errors. Uses sha-(1, 224, 256, 385 and 512)/hmac for signature encryption. Custom hash algori

Artur Barseghyan 39 Jun 10, 2022
Genetic Algorithm for Robby Robot based on Complexity a Guided Tour by Melanie Mitchell

Robby Robot Genetic Algorithm A Genetic Algorithm based Robby the Robot in Chapter 9 of Melanie Mitchell's book Complexity: A Guided Tour Description

Matthew 2 Dec 01, 2022
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
Algorithmic virtual trading using the neostox platform

Documentation Neostox doesnt have an API Support, so this is a little selenium code to automate strategies How to use Clone this repository and then m

Abhishek Mittal 3 Jul 20, 2022
Genetic algorithms are heuristic search algorithms inspired by the process that supports the evolution of life.

Genetic algorithms are heuristic search algorithms inspired by the process that supports the evolution of life. The algorithm is designed to replicate the natural selection process to carry generatio

Mahdi Hassanzadeh 4 Dec 24, 2022
A simple python implementation of A* and bfs algorithm solving Eight-Puzzle

A simple python implementation of A* and bfs algorithm solving Eight-Puzzle

2 May 22, 2022
This repository is not maintained

This repository is no longer maintained, but is being kept around for educational purposes. If you want a more complete algorithms repo check out: htt

Nic Young 2.8k Dec 30, 2022
A minimal implementation of the IQRM interference flagging algorithm for radio pulsar and transient searches

A minimal implementation of the IQRM interference flagging algorithm for radio pulsar and transient searches. This module only provides the algorithm that infers a channel mask from some spectral sta

Vincent Morello 6 Nov 29, 2022
HashDB is a community-sourced library of hashing algorithms used in malware.

HashDB HashDB is a community-sourced library of hashing algorithms used in malware. How To Use HashDB HashDB can be used as a stand alone hashing libr

OALabs 216 Jan 06, 2023
Algorithms for calibrating power grid distribution system models

Distribution System Model Calibration Algorithms The code in this library was developed by Sandia National Laboratories under funding provided by the

Sandia National Laboratories 2 Oct 31, 2022
A pure Python implementation of a mixed effects random forest (MERF) algorithm

Mixed Effects Random Forest This repository contains a pure Python implementation of a mixed effects random forest (MERF) algorithm. It can be used, o

Manifold 199 Dec 06, 2022
Distributed algorithms, reimplemented for fun and practice

Distributed Algorithms Playground for reimplementing and experimenting with algorithms for distributed computing. Usage Running the code for Ring-AllR

Mahan Tourkaman 1 Oct 16, 2022
Benchmark for Robustness Tests of Control Alrogithms

A gym-like classical control benchmark for evaluating the robustnesses of control and reinforcement learning algorithms.

Kim Taekyung 4 Jan 18, 2022
Minimal pure Python library for working with little-endian list representation of bit strings.

bitlist Minimal Python library for working with bit vectors natively. Purpose This library allows programmers to work with a native representation of

Andrei Lapets 0 Jul 25, 2022
Cormen-Lib - An academic tool for data structures and algorithms courses

The Cormen-lib module is an insular data structures and algorithms library based on the Thomas H. Cormen's Introduction to Algorithms Third Edition. This library was made specifically for administeri

Cormen Lib 12 Aug 18, 2022
Gnat - GNAT is NOT Algorithmic Trading

GNAT GNAT is NOT Algorithmic Trading! GNAT is a financial tool with two goals in

Sher Shah 2 Jan 09, 2022
Python Package for Reflection Ultrasound Computed Tomography (RUCT) Delay And Sum (DAS) Algorithm

pyruct Python Package for Reflection Ultrasound Computed Tomography (RUCT) Delay And Sum (DAS) Algorithm The imaging setup is explained in these paper

Berkan Lafci 21 Dec 12, 2022
Nature-inspired algorithms are a very popular tool for solving optimization problems.

Nature-inspired algorithms are a very popular tool for solving optimization problems. Numerous variants of nature-inspired algorithms have been develo

NiaOrg 215 Dec 28, 2022
Evol is clear dsl for composable evolutionary algorithms that optimised for joy.

Evol is clear dsl for composable evolutionary algorithms that optimised for joy. Installation We currently support python3.6 and python3.7 and you can

GoDataDriven 178 Dec 27, 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