orientationpy 0.2.0.3

Package for greyscale orientation analysis on 2D and 3D images

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:

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

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)