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Add zone axes to geometrical EBSD simulations, improve plotting of simulation features #232

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merged 14 commits into from
Oct 21, 2020

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@hakonanes hakonanes commented Oct 15, 2020

Description of the change

This PR concludes the basic functionality of simulations of geometrical EBSD patterns.

  • Add zone axes attribute to the GeometricalEBSDSimulation class. These are calculated from the cross product of the present Kikuchi bands, and can be plotted along with the bands.
  • Default Kikuchi band coloring using the color palette from EDAX TSL. The user can provide custom colors if desired.
  • PC plotting is fixed, ensuring that only one PC is plotted per pattern
  • Which zone axes to plot can be set in two ways: (1) on the detector, and (2) within a gnomonic radius (of course centered on the PC). Default is to exclude zone axis outside the detector
  • Plotting of zone axes labels is updated, however, a warning is raised before plotting, see this pending HyperSpy PR for details: Add visibility boolean for all markers, only used by text markers hyperspy/hyperspy#2558
  • Some routines for getting which HKL family a certain HKL belongs to are added as private functions in the geometrical simulation script. The extra functionality in these functions should be added to the already existing diffsims.crystallography.ReciprocalLatticePoint.unique() method.
  • KikuchiBand and ZoneAxis __getitem__() methods are added. These should also, I think, be moved to ReciprocalLatticePoint.__getitem__().

Progress of the PR

  • Docstrings for all functions
  • Unit tests with pytest for all lines
  • Clean style in as per black
  • Test it all for signal navigation dimensions 0, 1 and 2 (coverage should be 100% after this PR)
  • Jupyter Notebook showing how to simulate geometrical EBSD patterns and plot them as markers. This notebook should be placed in doc/notebook.ipynb and included in the user guide with nbsphinx (https://nbsphinx.readthedocs.io/en/0.7.1/index.html) will do this in a later PR.

For reviewers

  • Check that the PR title is short, concise, and will make sense 1 year
    later.
  • Check that new functions are imported in corresponding __init__.py.
  • Check that new features, API changes, and deprecations are mentioned in
    the unreleased section in doc/changelog.rst.

Signed-off-by: Håkon Wiik Ånes <hwaanes@gmail.com>
Signed-off-by: Håkon Wiik Ånes <hwaanes@gmail.com>
Signed-off-by: Håkon Wiik Ånes <hwaanes@gmail.com>
@hakonanes hakonanes added the enhancement New feature or request label Oct 15, 2020
@hakonanes hakonanes added this to the v0.3.0 milestone Oct 15, 2020
@hakonanes hakonanes self-assigned this Oct 15, 2020
@hakonanes hakonanes marked this pull request as draft October 15, 2020 16:02
Signed-off-by: Håkon Wiik Ånes <hwaanes@gmail.com>
…or uvw from hkl

Signed-off-by: Håkon Wiik Ånes <hwaanes@gmail.com>
Signed-off-by: Håkon Wiik Ånes <hwaanes@gmail.com>
Signed-off-by: Håkon Wiik Ånes <hwaanes@gmail.com>
…ing)

Signed-off-by: Håkon Wiik Ånes <hwaanes@gmail.com>
Signed-off-by: Håkon Wiik Ånes <hwaanes@gmail.com>
Signed-off-by: Håkon Wiik Ånes <hwaanes@gmail.com>
… sim.

Signed-off-by: Håkon Wiik Ånes <hwaanes@gmail.com>
Signed-off-by: Håkon Wiik Ånes <hwaanes@gmail.com>
@hakonanes hakonanes changed the title Add zone axes to geometrical EBSD simulations, improve other simulation features Add zone axes to geometrical EBSD simulations, improve plotting of simulation features Oct 21, 2020
Signed-off-by: Håkon Wiik Ånes <hwaanes@gmail.com>
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