NeuTomPy toolbox

NeuTomPy toolbox is a Python package for tomographic data processing and reconstruction. Such toolbox includes pre-processing algorithms, artifacts removal and a wide range of iterative reconstruction methods as well as the Filtered Back Projection algorithm. The NeuTomPy toolbox was conceived primarily for Neutron Tomography and developed to support the need of users and researchers to compare state-of-the-art reconstruction methods and choose the optimal data-processing workflow for their data.

Features

Readers and writers for TIFF and FITS files and stack of images
Data normalization with dose correction, correction of the rotation axis tilt, ring-filters, outlier removals, beam-hardening correction
A wide range of reconstruction algorithms powered by ASTRA toolbox: FBP, SIRT, SART, ART, CGLS, NN-FBP, MR-FBP
Image quality assessment with several metrics

Installation

NeuTomPy toolbox supports Linux, Windows and Mac OS 64-bit operating systems.

First of all, install a conda python environment with Python 3.6 and then activate it:

conda create -n ntp_env python=3.6 
conda activate ntp_env

Install some dependencies:

conda install -c simpleitk simpleitk
conda install scikit-image
conda install ipython numexpr astropy tifffile mkl_fft  tqdm
conda install -c astra-toolbox astra-toolbox
pip install opencv-python read-roi
pip install -U numpy

Finally, install NeuTomPy toolbox via pip:

pip install neutompy

NB: If a segmentation fault occurs when importing NeuTomPy, install PyQt5 via pip:

pip install PyQt5

Update

To update a NeuTomPy installation to the latest version run:

pip install neutompy --upgrade

Documentation

Complete documentation can be found on Read the Docs: https://neutompy-toolbox.readthedocs.io.

Tutorials and code examples of typical usage can be found in the folder examples.

A sample dataset for testing purpose can be found here. This dataset includes neutron radiographs of a phantom sample acquired at the IMAT beamline, ISIS neutron spallation source, UK.

Reference

If you use the NeuTomPy toolbox for your research, please cite the following paper:

D. Micieli, T. Minniti, G. Gorini, “NeuTomPy toolbox, a Python package for tomographic data processing and reconstruction”, SoftwareX, Volume 9 (2019), pp. 260-264, https://doi.org/10.1016/j.softx.2019.01.005.

License

The project is licensed under the GPLv3 license.

Contact

If you want to contact us for any reasons, please send an email to: neutompy@gmail.com

dmici / NeuTomPy-toolbox

readme