Science Score: 44.0%
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✓CITATION.cff file
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✓codemeta.json file
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○Scientific vocabulary similarity
Low similarity (11.3%) to scientific vocabulary
Keywords
Repository
Python Package for Optoacoustic Tomography (OAT)
Basic Info
Statistics
- Stars: 24
- Watchers: 2
- Forks: 5
- Open Issues: 1
- Releases: 0
Topics
Metadata Files
README.md
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.
bash
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.
bash
python exampleCpuBP.py
The example scripts can be written by users.
pyoat package can be imported in python scripts using following line.
python
import pyoat as pt
After importing the package, the functions can be called with following lines in python script.
python
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.
Owner
- Name: Berkan Lafci
- Login: berkanlafci
- Kind: user
- Location: Zurich, Switzerland
- Company: University of Zurich
- Website: https://berkanlafci.github.io/
- Repositories: 5
- Profile: https://github.com/berkanlafci
🔬 Postdoctoral Researcher at UZH 🔬 🎓 Boğaziçi University ‘15, TU München ‘18, ETH Zurich '23 🎓 (he/him/his)
Citation (CITATION.cff)
cff-version: 1.0.0 message: "If you use this package, please include citation." authors: - family-names: "Lafci" given-names: "Berkan" orcid: "https://orcid.org/0000-0001-5387-1748" - family-names: "Ozbek" given-names: "Ali" orcid: "https://orcid.org/0000-0001-8389-4924" - family-names: "Ozdemir" given-names: "Firat" orcid: "https://orcid.org/0000-0001-6643-7318" - family-names: "Klimovskaia" given-names: "Anna" orcid: "https://orcid.org/0000-0002-1057-6690" - family-names: "Perez-Cruz" given-names: "Fernando" orcid: "https://orcid.org/0000-0001-8996-5076" - family-names: "Dean-Ben" given-names: "Xose Luis" orcid: "https://orcid.org/0000-0002-8557-7778" - family-names: "Razansky" given-names: "Daniel" orcid: "https://orcid.org/0000-0001-8676-0964" title: "pyruct" version: 1.0.0 doi: date-released: 2022-03-07 url: "https://github.com/berkanlafci/pyoat"
GitHub Events
Total
- Watch event: 3
- Fork event: 1
Last Year
- Watch event: 3
- Fork event: 1
Dependencies
- Pillow *
- h5py *
- matplotlib *
- numpy *
- scipy *