Metadata-Version: 2.1
Name: orientationpy
Version: 0.2.0.3
Summary: Package for greyscale orientation analysis on 2D and 3D images
Author-email: Edward Andò <edward.ando@epfl.ch>, Alexandru Vasile <vasilealexandrupetru@gmail.com>, Daniel Sage <daniel.sage@epfl.ch>
Maintainer-email: Edward Andò <edward.ando@epfl.ch>
License: The GNU General Public License, Version 3, 29 June 2007 (GPLv3)
        ===============================================================
        
        > Copyright &copy; 2007
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        ### 15. Disclaimer of Warranty.
        
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        ### 17. Interpretation of Sections 15 and 16.
        
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        END OF TERMS AND CONDITIONS
        
Project-URL: homepage, https://epfl-center-for-imaging.gitlab.io/orientationpy/index.html
Project-URL: documentation, https://readthedocs.org
Project-URL: repository, https://gitlab.com/epfl-center-for-imaging/orientationpy
Keywords: orientation,structure tensor,greylevel,image analysis
Classifier: Development Status :: 2 - Pre-Alpha
Classifier: Intended Audience :: Developers
Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
Classifier: Natural Language :: English
Classifier: Programming Language :: Python :: 3 :: Only
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Requires-Python: >=3.7
Description-Content-Type: text/x-rst
Provides-Extra: test
Provides-Extra: dev
License-File: LICENSE.md

========================================================================
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 greylevel-measuring software that we're aware of in python:

  - `skimage.feature.structure_tensor`_: Only using finite differences for gradient
  - `structure-tensor`_: Sobel filter for gradient
  - `pynamix.measure.orientation_map`_: FFT-based approach


Todo
=========

 - [X] 3D tests

 - [X] 3D coherency and energy

 - [X] integrate gradients and structure tensor into gradientStructureTensor

 - [X] Change 3D orientation system to z-top

 - [X] compare (and check compatibility) to skimage structure tensor

 - [X] write anglesToVectors()

 - [X] numba speedup?

 - [X] dict output to computeOrientations

 - [X] Write sphinx home page

 - [x] spam plots

 - [_] in Boxed functions, return box centres? AND/OR accept centres and sizes?

 - [_] factor for non-isotropic voxels

 - [_] asserts for input sanity (i.e., gradient shapes all the same)

 - [_] VTK out

 - [_] scripts with tiff in?

 - [_] rose plot

 - [_] rename plotOrientations → ZalignedStereoPlot?

 - [_] investigate smoothed 'pole plots'

 - [_] in `plotting.py` create an image synthesizer?

 - [_] mask greylevels

 - [_] dask


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


History
========

 - 0.2.0.2 (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)
