pyezzi 0.2.0

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, especially the anisotropic part.

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.

A spacing parameter specifying the spacing between voxels along the axes can optionnaly be specified.

Check out the included jupyter notebooks in the example for more details.

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.