pyezzi 0.8.3.post1

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Compute the thickness of a solid using Yezzi and Prince method described in the article “An Eulerian PDE Approach for Computing Tissue Thickness”, IEEE TRANSACTIONS ON MEDICAL IMAGING, VOL. 22, NO. 10, OCTOBER 2003. [1]

A C implementation by Rubén Cárdenes [2] helped me a lot writing this, especially the anisotropic part.

[1]

http://dx.doi.org/10.1109/tmi.2003.817775

[2]

http://www.dtic.upf.edu/~rcardenes/Ruben_Cardenes/Software.html

Requirements

Runtime: numpy, OpenMP (e.g., the libgomp1 package on debian).

Build time: a C compiler (e.g., gcc + libc6-dev packages on debian). This is needed in case you are using a platform for which we do not provide binaries (“wheels”) on PyPI.

Test time: scikit-image, scipy.

Installation instruction

Available on pypi. [3] Use pip: pip install pyezzi

Alternatively, clone the repository and build cython modules with pip install ..

[3]

https://pypi.python.org/pypi/pyezzi

Usage

Command line

This package provides a basic CLI. Example usage:

pyezzi /path/to/endo.mha /path/to/epi.mha /path/to/output.mha [--weights /path/to/thickness_weights.mha]

If can use the excellent uvx, you can download and launch it in a single command:

uvx pyezzi[cli] --help

Python API

Full API documentation is available on gitlabpages.inria.fr.

from pyezzi import compute_thickness_cardiac

thickness = compute_thickness_cardiac(endo, epi)

endo and epi are numpy binary masks. endo represents the “inside” boundary of the domain, e.g., the cardiac ventricular blood pool. epi represents the “outside” boundary of the domain, e.g., the cardiac ventricular epicardium.

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

A weights parameter can be added to account for “holes” in the wall, cf “Cedilnik & Peyrat, Weighted tissue thickness, FIMH 2023”. [4]

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

[4]

https://hal.science/hal-04111276/

Contributions

We recommend using uv for project management and pre-commit to ensure code quality.

After cloning, use uv sync --frozen --all-groups --all-extras to install dev dependencies. This will set up a virtualenv in .venv that you can activate with source .venv/bin/activate. Tests can then be run with pytest test.

To build the cython extension modules in place, use python setup.py develop.

License

This work is licensed under the french CeCILL license. [5] You’re free to use and modify the code, but please cite the original paper and me.

[5]

https://www.cecill.info/licences/Licence_CeCILL_V2.1-en.html