pyezzi 1.0.1

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pYezzi

Compute the thickness of a solid using the method described by Yezzi and Prince (An Eulerian PDE Approach for Computing Tissue Thickness), extended by Cedilnik and Peyrat (Weighted Tissue Thickness).

Installation

Pyezzi is open-source and available on PyPI.org: pip install pyezzi. It uses cython extension modules, but portable binaries for recent python versions and major OSes are published as wheels, so it should just work in most cases.

If there is no binary available for your platform, pip will attempt to build the binaries from source. For this to work, you need a C compiler (eg, gcc on linux) and the OpenMP runtime (available in most linux distributions via the libgomp-something package). Beware, macOS's clang does not support OpenMP, so you need to install both OpenMP and llvm, eg, via brew. In case you are lost, you can have a look at the Containerfile and .gitlab-ci.yml files in the repository to see how the portable wheel are built.

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

Container

The command-line interface is also available as a container.

docker run \                                      # you can use podman too
    -v /path/to/endo.mha:/input/endo.mha \
    -v /path/to/epi.mha:/input/epi.mha \
    -v /path/to/weights.mha:/input/weights.mha \  # optional
    -v /path/to/output/:/output/ \                # thickness.mha will be created here
    registry.gitlab.inria.fr/ncedilni/pyezzi:latest

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 optionally be specified.

A weights parameter can be added to account for "holes" in the wall.

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