======
pYezzi
======
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. [#]_
A C implementation by Rubén Cárdenes [#]_ helped me a lot writing this,
especially the anisotropic part.
.. [#] http://dx.doi.org/10.1109/tmi.2003.817775
.. [#] 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. [#]_
Use pip: ``pip install pyezzi``
Alternatively, clone the repository and build cython modules with
``pip install .``.
.. [#] https://pypi.python.org/pypi/pyezzi
Usage
=====
Command line
------------
This package provides a basic CLI. Example usage:
.. code:: bash
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 <https://docs.astral.sh/uv/guides/tools/>`_, you can download and
launch it in a single command:
.. code:: bash
uvx pyezzi[cli] --help
Python API
----------
Full API documentation is available on
`gitlabpages.inria.fr <https://ncedilni.gitlabpages.inria.fr/pyezzi>`_.
.. code:: python
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". [#]_
Check out the included jupyter notebooks in the ``example`` folder for more
details.
.. [#] https://hal.science/hal-04111276/
Contributions
=============
We recommend using `uv <https://docs.astral.sh/uv/>`_ for project management
and `pre-commit <https://pre-commit.com/>`_ 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're free to use and modify the code, but please cite the original paper and
me.
.. [#] https://www.cecill.info/licences/Licence_CeCILL_V2.1-en.html
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