pyezzi 0.1.1

Thickness calculation on binary 3D images

Compute the thickness of a solid using Anthony J. Yezzi’s method described in the article “An Eulerian PDE Approach for Computing Tissue Thickness, IEEE TRANSACTIONS ON MEDICAL IMAGING, VOL. 22, NO. 10, OCTOBER 2003”: http://dx.doi.org/10.1109/tmi.2003.817775

A C implementation by Rubén Cárdenes can be found at http://www.dtic.upf.edu/~rcardenes/Ruben_Cardenes/Software.html and helped me write this.

Requirements

numpy, cython, scikit-image. Tested with Debian Jessie, miniconda-python 3.5.2, cython 0.24, numpy 1.11.2, scikit image 0.12.3

Installation instruction

Available on pypi: https://pypi.python.org/pypi/pyezzi . Use pip: pip install pyezzi

Alternatively, clone the repository and build cython modules with python setup.py build_ext --inplace.

Usage

from pyezzi.thickness import compute_thickness
thickness = compute_thickness(labeled_image, debug=True)

labeled_image is a 3 dimensional numpy array where the wall is labeled 2 and the interior is labeled 1.

Check out the included jupyter notebooks for more detail and examples.

Contributions

Feel free to submit pull requests. I know the code is nowhere near optimal as it is.

License

You’re free to use and modify the code, but please cite me and the original paper.