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.
1 maintainer
Metadata
1 maintainer
Release files for pyezzi 1.0.1.post1
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | Provenance | |
|---|---|---|---|---|
| pyezzi-1.0.1.post1.tar.gz | 9.2 MB | Without provenance | Details |
Built distributions (wheels)
Total release size: 52.6 MB
Release files / pyezzi-1.0.1.post1.tar.gz
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Release files / pyezzi-1.0.1.post1-cp315-cp315-win_amd64.whl
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Release files / pyezzi-1.0.1.post1-cp315-cp315-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_38_x86_64.whl
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Release files / pyezzi-1.0.1.post1-cp315-cp315-macosx_11_0_arm64.whl
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Release files / pyezzi-1.0.1.post1-cp314-cp314-win_amd64.whl
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Release files / pyezzi-1.0.1.post1-cp314-cp314-macosx_11_0_arm64.whl
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Release files / pyezzi-1.0.1.post1-cp313-cp313-win_amd64.whl
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Release files / pyezzi-1.0.1.post1-cp313-cp313-macosx_11_0_arm64.whl
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Release files / pyezzi-1.0.1.post1-cp312-cp312-win_amd64.whl
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uv/0.11.2 {"installer":{"name":"uv","version":"0.11.2","subcommand":["publish"]},"python":null,"implementation":{"name":null,"version":null},"distro":{"name":"Alpine Linux","version":"3.23.3","id":null,"libc":null},"system":{"name":null,"release":null},"cpu":null,"openssl_version":null,"setuptools_version":null,"rustc_version":null,"ci":true}
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Release files / pyezzi-1.0.1.post1-cp310-cp310-macosx_11_0_arm64.whl
| Download URL | pyezzi-1.0.1.post1-cp310-cp310-macosx_11_0_arm64.whl |
|---|---|
| Size | 1.4 MB |
| Tags | CPython 3.10 macOS 11.0+ ARM64 |
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SHA-256 checksum How to use checksums |
d0aa5b1bf475312a70bbbe42f8a9ca83f1e427a65e702a8ee65b63b37bf22ed7
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BLAKE2b-256 checksum How to use checksums |
6cbcf17cee65d83c4a01de7600660859773742bccfe1a634b62f4ce0fa52c1dc
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| Upload date | |
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Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
uv/0.11.2 {"installer":{"name":"uv","version":"0.11.2","subcommand":["publish"]},"python":null,"implementation":{"name":null,"version":null},"distro":{"name":"Alpine Linux","version":"3.23.3","id":null,"libc":null},"system":{"name":null,"release":null},"cpu":null,"openssl_version":null,"setuptools_version":null,"rustc_version":null,"ci":true}
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Security for pyezzi 1.0.1.post1
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