This project is a part of the larger X-ray tomographic reconstruction toolbox comprised of [flexDATA], [flexTOMO] and [flexCALC]. flexCALC contains various routines useful with tomographic reconstructions but not directly reconstruction algorithms. These routines include data pre- and post-processing tools, simulation of spectral data, and batch-processing of large number of datasets.
Before installing flexCALC, please download and install flexDATA and flexTOMO. Once installation of flexTOMO is complete, one can install flexCALC from the source code or using Anaconda.
Simply install with:
conda create -n <your-environment> python=3.7
conda install -c cicwi -c astra-toolbox/label/dev -c conda-forge -c simpleitk flexcalc
To install flexCALC, clone this GitHub project. Go to the cloned directory and run PIP installer:
git clone https://github.com/cicwi/flexcalc.git
cd flexcalc
pip install -e .
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.
flexCALC is comprised of several modules:
- process: pre- and post-processing routines. For instance: volume registration, rings removal etc.
- analyze: utilities for data analysis.
- batch: define a batch processing pipeline and push multiple datasets through it.
Typical code:
# Import:
from flextomo import project
from flexcalc import process
# Read data and apply beam-hardening:
proj, geom = process.process_flex(path)
proj = process.equivalent_density(proj, geom, energy, spec, compound = 'Al', density = 2.7)
# Align the rotation centre:
process.optimize_rotation_center(proj, geom, subscale = 2)
# Reconstruct:
vol = project.init_volume(proj)
project.FDK(proj, vol, meta['geometry'])
- Alexander Kostenko - Initial work
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.
This project is licensed under the GNU GENERAL PUBLIC License - see the LICENSE.md file for details