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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 Anaconda package manager for Python 3.

Installing with conda

Simply install with:

conda create -n <your-environment> python=3.7
conda install -c cicwi -c astra-toolbox/label/dev -c conda-forge -c owlas flexdata

NOTE: currently, the latest version of flexDATA is only available for python version 3.7.

Installing from source

To install flexDATA you will need the latest version of the ASTRA toobox (preferably development version). It can be installed via command line with Anaconda:

conda install -c astra-toolbox/label/dev astra-toolbox

To install flexDATA, simply clone this GitHub project. Go to the cloned directory and run PIP installer:

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 Spyder environment step-by-step.

Modules

flexDATA is comprised of the following modules:

  • data: read / write raw projection stacks (tiffs), parse settings file of the scanner to produce meta data.
  • geometry: geometry classes (circular, helical and linear).
  • display: simple display routines for 3D arrays

Typical code:

# 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

See also the list of contributors who participated in this project.

How to contribute

Contributions are always welcome. Please submit pull requests against the develop branch.

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 endles advices regarding the use of ASTRA toolbox.