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Add tutorials demonstrating projection center calibration functionality #588

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merged 25 commits into from
Jan 8, 2023

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@hakonanes hakonanes commented Jan 7, 2023

Description of the change

This PR adds three new tutorials demonstrating various projection center (PC) calibration functionality:

  • Extrapolate PCs from a mean to obtain a map of PCs
  • Fit PCs from selected PCs to obtain a map of PCs
  • Reproduce Ni example from Pang et al. (2020) (https://doi.org/10.1016/j.ultramic.2019.112876) to show sloppy orientation/PC optimization landscape. Our results using the Nelder-Mead algorithm reproduces theirs using the SNOBFIT global optimization algorithm.

Other notebooks are updated to use the new functionality.

Docs and tests are attempted to be excluded from the source distribution in this PR. This was tested using manifix. If this is actually the case is still uncertain, so at least one release candidate, 0.8.0rc1, will be made to ensure that they are indeed excluded.

Progress of the PR

Minimal example of the bug fix or new feature

See documentation built from this PR.

For reviewers

  • The PR title is short, concise, and will make sense 1 year later.
  • New functions are imported in corresponding __init__.py.
  • New features, API changes, and deprecations are mentioned in the unreleased
    section in CHANGELOG.rst.
  • New contributors are added to release.py, .zenodo.json and
    .all-contributorsrc with the table regenerated.

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>
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>
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>
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>
Signed-off-by: Håkon Wiik Ånes <hwaanes@gmail.com>
@hakonanes hakonanes added the documentation This relates to the documentation label Jan 7, 2023
@hakonanes hakonanes added this to the v0.8.0 milestone Jan 7, 2023
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>
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>
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>
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 merged commit 0799151 into pyxem:develop Jan 8, 2023
@hakonanes hakonanes deleted the add-pc-tutorials branch January 8, 2023 12:38
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