pyoat
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Python Package for Optoacoustic Tomography (OAT)
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.