orientationpy 0.2.0.3

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)