========================================================================
OrientationPy - greylevel orientation computation for 2D and 3D images
========================================================================
.. image:: https://badge.fury.io/py/orientationpy.png
:target: http://badge.fury.io/py/orientationpy
.. image:: https://gitlab.com/epfl-center-for-imaging/orientationpy/badges/main/pipeline.svg
:target: https://gitlab.com/epfl-center-for-imaging/orientationpy/-/commits/main
.. image:: https://gitlab.com/epfl-center-for-imaging/orientationpy/badges/main/coverage.svg
:target: https://epfl-center-for-imaging.gitlab.io/orientationpy/coverage/
OrientationPy is the pythonic successor to the well-loved `OrientationJ`_ Fiji Plugin (`github`_) from the BIG (`Biomedical Imaging Group`_) in EPFL.
It is a library that takes in 2D images or 3D volumes and computes the orientation of the greylevels.
A key step is the computation of image gradients, for which we offer a number of different techniques.
Please visit the `OrientationPy online docs`_.
Highlights
===========
Please see the `Example Gallery`_ for some small examples of the use of the code, allowing the computation of orientations maps like this:
.. figure:: https://epfl-center-for-imaging.gitlab.io/orientationpy/_images/sphx_glr_plot_fibres_2d_005.png
:width: 400
:align: center
Other noteworthy python projects
=================================
Other orientation or structure tensor software that we're aware of in python:
- `skimage.feature.structure_tensor`_: Sobel filter for gradient
- `structure-tensor`_: Only using finite differences for gradient
- `pynamix.measure.orientation_map`_: FFT-based approach
- `PyTextureAnalysis`_: 2D orientation package with overlay rendering
Acknowledgements
=================
- The initial prototype was coded by Alexandru Vasile during a 6-week visit to the EPFL Center for Imaging, supported by Mariana Verezhak from PSI
- We used some of this data for testing: https://zenodo.org/record/5483719#.Yyra4vFBy2A
- We initialised this repository from a cookie-cutter: https://github.com/Nekroze/cookiecutter-pypackage
.. _OrientationJ: http://bigwww.epfl.ch/demo/orientation/
.. _github: https://github.com/Biomedical-Imaging-Group/OrientationJ
.. _Biomedical Imaging Group: https://github.com/Biomedical-Imaging-Group/OrientationJ
.. _OrientationPy online docs: https://epfl-center-for-imaging.gitlab.io/orientationpy/index.html
.. _Example Gallery: https://epfl-center-for-imaging.gitlab.io/orientationpy/orientationpy_examples/index.html
.. _skimage.feature.structure_tensor: https://scikit-image.org/docs/stable/api/skimage.feature.html#skimage.feature.structure_tensor
.. _structure-tensor: https://pypi.org/project/structure-tensor/
.. _pynamix.measure.orientation_map: https://scigem.github.io/PynamiX/build/html/notebooks/Fibres.html
.. _PyTextureAnalysis: https://github.com/ajinkya-kulkarni/PyTextureAnalysis
History
========
- 0.3.0.0 (2023-08-07) Closed form solution for eigenvalue decomposition
- 0.2.0.4 (2023-01-20) Anisotropy of voxel sizes implemented
- 0.2.0.3 (2023-01-13) Moved code to `/src/orientationpy` so it gets packaged?
- 0.2.0.2 (2023-01-13) Moved code to `/src` so it gets packaged?
- 0.2.0.1 (2023-01-13) Moved to `pyproject.toml`
- 0.2.0.0 (2023-01-13) First version on pip (non-working due to requirements.txt)
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"description": "========================================================================\nOrientationPy - greylevel orientation computation for 2D and 3D images\n========================================================================\n\n.. image:: https://badge.fury.io/py/orientationpy.png\n :target: http://badge.fury.io/py/orientationpy\n\n.. image:: https://gitlab.com/epfl-center-for-imaging/orientationpy/badges/main/pipeline.svg\n :target: https://gitlab.com/epfl-center-for-imaging/orientationpy/-/commits/main\n\n.. image:: https://gitlab.com/epfl-center-for-imaging/orientationpy/badges/main/coverage.svg\n :target: https://epfl-center-for-imaging.gitlab.io/orientationpy/coverage/\n\nOrientationPy is the pythonic successor to the well-loved `OrientationJ`_ Fiji Plugin (`github`_) from the BIG (`Biomedical Imaging Group`_) in EPFL.\nIt is a library that takes in 2D images or 3D volumes and computes the orientation of the greylevels.\nA key step is the computation of image gradients, for which we offer a number of different techniques.\n\nPlease visit the `OrientationPy online docs`_.\n\n\nHighlights\n===========\n\nPlease see the `Example Gallery`_ for some small examples of the use of the code, allowing the computation of orientations maps like this:\n\n\n.. figure:: https://epfl-center-for-imaging.gitlab.io/orientationpy/_images/sphx_glr_plot_fibres_2d_005.png\n :width: 400\n :align: center\n\n\n\nOther noteworthy python projects\n=================================\n\nOther orientation or structure tensor software that we're aware of in python:\n\n - `skimage.feature.structure_tensor`_: Sobel filter for gradient\n - `structure-tensor`_: Only using finite differences for gradient\n - `pynamix.measure.orientation_map`_: FFT-based approach\n - `PyTextureAnalysis`_: 2D orientation package with overlay rendering\n\n\nAcknowledgements\n=================\n\n - The initial prototype was coded by Alexandru Vasile during a 6-week visit to the EPFL Center for Imaging, supported by Mariana Verezhak from PSI\n\n - We used some of this data for testing: https://zenodo.org/record/5483719#.Yyra4vFBy2A\n\n - We initialised this repository from a cookie-cutter: https://github.com/Nekroze/cookiecutter-pypackage\n\n.. _OrientationJ: http://bigwww.epfl.ch/demo/orientation/\n.. _github: https://github.com/Biomedical-Imaging-Group/OrientationJ\n.. _Biomedical Imaging Group: https://github.com/Biomedical-Imaging-Group/OrientationJ\n\n.. _OrientationPy online docs: https://epfl-center-for-imaging.gitlab.io/orientationpy/index.html\n.. _Example Gallery: https://epfl-center-for-imaging.gitlab.io/orientationpy/orientationpy_examples/index.html\n\n\n.. _skimage.feature.structure_tensor: https://scikit-image.org/docs/stable/api/skimage.feature.html#skimage.feature.structure_tensor\n.. _structure-tensor: https://pypi.org/project/structure-tensor/\n.. _pynamix.measure.orientation_map: https://scigem.github.io/PynamiX/build/html/notebooks/Fibres.html\n.. _PyTextureAnalysis: https://github.com/ajinkya-kulkarni/PyTextureAnalysis\n\n\nHistory\n========\n\n - 0.3.0.0 (2023-08-07) Closed form solution for eigenvalue decomposition\n\n - 0.2.0.4 (2023-01-20) Anisotropy of voxel sizes implemented\n\n - 0.2.0.3 (2023-01-13) Moved code to `/src/orientationpy` so it gets packaged?\n\n - 0.2.0.2 (2023-01-13) Moved code to `/src` so it gets packaged?\n\n - 0.2.0.1 (2023-01-13) Moved to `pyproject.toml`\n\n - 0.2.0.0 (2023-01-13) First version on pip (non-working due to requirements.txt)\n",
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