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

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:

# Import:
from flexdata import data

# Read raw projections and flat field images:
proj = data.read_tiffs(path, file_name)
flat = data.read_tiffs(path, file_name)

# Read metadata:
geom = data.read_flexraylog(path)

# Generate an ASTRA-compatible projection geometry description:
proj_geom = geom.astra_proj_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.