Science Score: 13.0%
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○CITATION.cff file
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✓codemeta.json file
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○.zenodo.json file
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○Scientific vocabulary similarity
Low similarity (15.6%) to scientific vocabulary
Keywords
Repository
I/O routines for CT data
Basic Info
- Host: GitHub
- Owner: cicwi
- License: gpl-3.0
- Language: Python
- Default Branch: master
- Homepage: https://cicwi.github.io/flexDATA/
- Size: 6.35 MB
Statistics
- Stars: 6
- Watchers: 7
- Forks: 5
- Open Issues: 2
- Releases: 1
Topics
Metadata Files
README.md
flexDATA
This project is a part of the larger X-ray tomographic reconstruction toolbox comprised of flexDATA, flexTOMO and flexCALC. flexDATA contains IO routines that were originally developed for the Flex-Ray X-ray CT scanner but can be used for reading and writing data from other types of CT scanners. It provides an interface between a scanner and a GPU-based CT reconstruction ASTRA Toolbox. It can be especially helpful when the scanner has many degrees of freedom and the geometry of each scan is defined by a large number of parameters.
Getting Started
It takes a few steps to setup flexDATA on your machine. We recommend that the user installs conda package manager for Python 3.
Installing with conda
conda install flexdata -c cicwi -c astra-toolbox -c nvidia
Installing with pip
pip install flexdata
Installing from source
bash
git clone https://github.com/cicwi/flexdata.git
cd flexdata
pip install -e .
Running the examples
To learn about the functionality of the package check out our examples/ folder. Examples are separated into blocks that are best to run in VS Code / Spyder environment step-by-step.
Modules
flexDATA is comprised of the following modules:
flexdata.data: Read / write raw projection stacks (tiffs), parse settings file of the scanner to produce meta data.flexdata.geometry: Geometry classes (circular, helical and linear).flexdata.display: Simple display routines for 3D arrays
Typical usage: ```python
Import:
from flexdata import data
Read raw projections and flat field images:
proj = data.readtiffs(path, filename) flat = data.readtiffs(path, filename)
Read metadata:
geom = data.read_flexraylog(path)
Generate an ASTRA-compatible projection geometry description:
projgeom = geom.astraproj_geom(proj.shape) ```
Authors and contributors
- Alexander Kostenko - Initial work
- Allard Hendriksen - Packaging and installation
- Jan-Willem Buurlage - Packaging and installation
- Willem Jan Palenstijn - Packaging, installation and maintenance
- Alexander Skorikov - Packaging, installation and maintenance
See also the list of contributors who participated in this project.
How to contribute
Contributions are always welcome. If you have any issues, questions, or remarks, then please open an issue on GitHub.
License
This project is licensed under the GNU GENERAL PUBLIC License - see the LICENSE.md file for details
Acknowledgments
- To Willem Jan Palenstijn for endless advices regarding the use of ASTRA toolbox.
Owner
- Name: Computational Imaging, CWI
- Login: cicwi
- Kind: organization
- Repositories: 14
- Profile: https://github.com/cicwi
GitHub Events
Total
Last Year
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 5
- Total pull requests: 8
- Average time to close issues: 8 months
- Average time to close pull requests: 8 months
- Total issue authors: 5
- Total pull request authors: 4
- Average comments per issue: 0.4
- Average comments per pull request: 1.13
- Merged pull requests: 6
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 0
- Pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Issue authors: 0
- Pull request authors: 0
- Average comments per issue: 0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- ahendriksen (1)
- D1rk123 (1)
- RaghuSh (1)
- wjp (1)
- jwbuurlage (1)
Pull Request Authors
- ahendriksen (4)
- fgbossema (2)
- wjp (1)
- vandriiashen (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
-
Total downloads:
- pypi 60 last-month
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 2
- Total maintainers: 1
pypi.org: flexdata
IO routines for CT data
- Homepage: https://github.com/cicwi/flexdata
- Documentation: https://flexdata.readthedocs.io/
- License: gpl-3.0
-
Latest release: 1.0.1
published over 1 year ago
Rankings
Maintainers (1)
Dependencies
- astra-toolbox *
- imageio *
- matplotlib *
- numpy *
- psutil *
- pyqtgraph *
- scipy *
- toml *
- tqdm *