pyoat

Python Package for Optoacoustic Tomography (OAT)

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/pyoat.git

Usage

After installing package, the functions can be called using python scripts.

Example scripts to use pyoat package can be found in _examples folder.

For example, backprojection reconstruction example on cpu is called with following commands in terminal.

python exampleCpuBP.py

The example scripts can be written by users.

pyoat package can be imported in python scripts using following line.

import pyoat as pt

After importing the package, the functions can be called with following lines in python script.

oaData      = pt.oaReader(filePath=filePath) 	# read data
bp          = pt.cpuBP()                      	# create reconstruction object
imageRecon  = bp.recon(oaData.sigMat)         	# reconstruct image

Data

Test data will be made publicly available.

After the download, place the data in "data/rawData/" folder that shares the same root directory with "exampleCpuBP.py" script that can be run for testing "pyoat".

Citation

If you use this package in your research, please cite it as follows

Lafci, B., Ozbek, A., Ozdemir, F., Klimovskaia, A., Perez-Cruz, F., Dean-Ben, X.L., & Razansky, D. (2022). pyoat (Version 1.0.0) [Computer software].

Acknowledgements

This project is supported by Swiss Data Science Center (SDSC) grant C19-04.

License

This project is licensed under MIT License.