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Bring HyperSpy 2 compatibility work into develop branch #696

Merged
merged 67 commits into from
Nov 7, 2024
Merged

Bring HyperSpy 2 compatibility work into develop branch #696

merged 67 commits into from
Nov 7, 2024

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hakonanes
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@hakonanes
Set minimal version of HyperSpy to v2
e045625 
Signed-off-by: Håkon Wiik Ånes <hwaanes@gmail.com>
@hakonanes
Set HyperSpy >= 2 as the minimal version also on CI
d69ff03 
Signed-off-by: Håkon Wiik Ånes <hwaanes@gmail.com>
@hakonanes
Fix PR link in changelog
a9d0f64 
Signed-off-by: Håkon Wiik Ånes <hwaanes@gmail.com>
@hakonanes
Add RosettaSciIO dependency
bcba247 
Signed-off-by: Håkon Wiik Ånes <hwaanes@gmail.com>
@hakonanes
Install unreleased HyperSpy 2.2 from GitHub
0f274a8 
Signed-off-by: Håkon Wiik Ånes <hwaanes@gmail.com>
@hakonanes
Allow import NumPy's VisibleDeprecationWarning before/after v1.25
28df169 
Signed-off-by: Håkon Wiik Ånes <hwaanes@gmail.com>
@hakonanes
Prepare IO module for updating to RosettaSciIO's design
978dcc8 
Signed-off-by: Håkon Wiik Ånes <hwaanes@gmail.com>
@hakonanes
Update NORDIF plugin to RosettaSciIO's design
f5fab17 
Signed-off-by: Håkon Wiik Ånes <hwaanes@gmail.com>
@hakonanes
Update NORDIF calibration patterns plugin to RosettaSciIO's design
1ec4744 
Signed-off-by: Håkon Wiik Ånes <hwaanes@gmail.com>
@hakonanes
Update Bruker h5ebsd reader to RosettaSciIO's design
ae90889 
Signed-off-by: Håkon Wiik Ånes <hwaanes@gmail.com>
@hakonanes
Update EBSD directory reader to RosettaSciIO's design
0e4e51a 
Signed-off-by: Håkon Wiik Ånes <hwaanes@gmail.com>
@hakonanes
Update EDAX binary patterns reader to RosettaSciIO's design
c667c12 
Signed-off-by: Håkon Wiik Ånes <hwaanes@gmail.com>
@hakonanes
Update EDAX h5ebsd reader to RosettaSciIO's design
e200de1 
Signed-off-by: Håkon Wiik Ånes <hwaanes@gmail.com>
@hakonanes
Update EMsoft EBSD reader to RosettaSciIO's design
6af9a80 
Signed-off-by: Håkon Wiik Ånes <hwaanes@gmail.com>
@hakonanes
Update EMsoft EBSD master pattern reader to RosettaSciIO's design
8ea5075 
Signed-off-by: Håkon Wiik Ånes <hwaanes@gmail.com>
@hakonanes
Update EMsoft ECP master pattern reader to RosettaSciIO's design
fbb488b 
Signed-off-by: Håkon Wiik Ånes <hwaanes@gmail.com>
@hakonanes
Update EMsoft TKD master pattern reader to RosettaSciIO's design
ee7ffad 
Signed-off-by: Håkon Wiik Ånes <hwaanes@gmail.com>
@hakonanes
Update our h5ebsd reader/writer to RosettaSciIO's design
917b2cc 
Signed-off-by: Håkon Wiik Ånes <hwaanes@gmail.com>
@hakonanes
Update Oxford binary EBSD pattern reader to RosettaSciIO's design
f060f73 
Signed-off-by: Håkon Wiik Ånes <hwaanes@gmail.com>
@hakonanes
Update Oxford's h5ebsd/H5OINA reader to RosettaSciIO's design
88641ea 
Signed-off-by: Håkon Wiik Ånes <hwaanes@gmail.com>
@hakonanes
Fix creation of IO plugin list and look-up
16b5ef7 
Signed-off-by: Håkon Wiik Ånes <hwaanes@gmail.com>
@hakonanes
Remove unused HyperSpy markers tools
8e8fdf7 
Signed-off-by: Håkon Wiik Ånes <hwaanes@gmail.com>
@hakonanes
Remove passing of parallel=True to HyperSpy's map function
ec9e7e0 
Signed-off-by: Håkon Wiik Ånes <hwaanes@gmail.com>
@hakonanes
Update IO plugin tests following updates to RosettaSciIO's design
bb2e2d3 
Signed-off-by: Håkon Wiik Ånes <hwaanes@gmail.com>
@hakonanes
Import RGB8 and RGB16 data types from RosettaSciIO
0f0d24d 
Signed-off-by: Håkon Wiik Ånes <hwaanes@gmail.com>
@hakonanes
Replace HyperSpy marker functionality so tests don't error (not meant…
4c94df9 
… to work!)

Signed-off-by: Håkon Wiik Ånes <hwaanes@gmail.com>
@hakonanes
Fix incorrect combining of desired projection/hemisphere labels
c33a3cc 
Signed-off-by: Håkon Wiik Ånes <hwaanes@gmail.com>
@hakonanes
Improve error handling for incompatible IO plugin and signal type
c68fe16 
Signed-off-by: Håkon Wiik Ånes <hwaanes@gmail.com>
@hakonanes
Set specification "_api" key using part of Path.parts list
7939f33 
Signed-off-by: Håkon Wiik Ånes <hwaanes@gmail.com>
@hakonanes
Add bounds to VirtualBSEImager.grid_shape based on signal shape
687e944 
Signed-off-by: Håkon Wiik Ånes <hwaanes@gmail.com>
@hakonanes
Fix IO API
58fbe20 
Signed-off-by: Håkon Wiik Ånes <hwaanes@gmail.com>
@hakonanes
Install ipykernel with pip on RTD using environments.yml
e7b9f2a 
Signed-off-by: Håkon Wiik Ånes <hwaanes@gmail.com>
@hakonanes
Add ipykernel in environment.yml file for RTD, not for binder...
7ae2057 
Signed-off-by: Håkon Wiik Ånes <hwaanes@gmail.com>
@hakonanes
Add convenience function to determine whether to overwrite file
34990db 
Signed-off-by: Håkon Wiik Ånes <hwaanes@gmail.com>
@hakonanes
Fall back to BaseSignal.save() if no matching write plugin found
8659c68 
Signed-off-by: Håkon Wiik Ånes <hwaanes@gmail.com>
@hakonanes
Add Path type option to EBSD.save() signature, improve docstring
51d9a80 
Signed-off-by: Håkon Wiik Ånes <hwaanes@gmail.com>
@hakonanes
Fix tests of internal IO convenience methods
1b75996 
Signed-off-by: Håkon Wiik Ånes <hwaanes@gmail.com>
@hakonanes
Remove explicit dependency on RosettaSciIO
b4fb343 
Signed-off-by: Håkon Wiik Ånes <hwaanes@gmail.com>
@hakonanes
Simplify path to saving to H/ZSPY from EBSD.save()
099349e 
Signed-off-by: Håkon Wiik Ånes <hwaanes@gmail.com>
@hakonanes
Merge pull request #694 from hakonanes/hs2-io-compat
b229aa8 
Adopt RosettaSciIO's plugin design
@hakonanes
Reintroduce dependency on RosettaSciIO, needed in kikuchipy h5ebsd pl…
50d6a7c 
…ugin

Signed-off-by: Håkon Wiik Ånes <hwaanes@gmail.com>
@hakonanes
Use HS2 markers when plotting VBSE grid on EBSD detector
dd6a979 
Signed-off-by: Håkon Wiik Ånes <hwaanes@gmail.com>
@hakonanes
Align tests of VBSE detector grid plots with HS2 markers
d7b531e 
Signed-off-by: Håkon Wiik Ånes <hwaanes@gmail.com>
@hakonanes
Make tests pass, albeit with temporary fix for line markers
ed0d373 
Signed-off-by: Håkon Wiik Ånes <hwaanes@gmail.com>
@hakonanes
Fix "PyVista not installed" error message
e04d261 
Signed-off-by: Håkon Wiik Ånes <hwaanes@gmail.com>
@hakonanes
Simplify VBSE imager tile labling, remove bug-as-feature
b3b3c24 
Signed-off-by: Håkon Wiik Ånes <hwaanes@gmail.com>
@hakonanes
Fix array indexing in VBSE imager
4796893 
Signed-off-by: Håkon Wiik Ånes <hwaanes@gmail.com>
@hakonanes
Fix (row, column) -> (x, y) inconsistency with HyperSpy
0d56e99 
Signed-off-by: Håkon Wiik Ånes <hwaanes@gmail.com>
@hakonanes
Remove incorrect enforcement of integer array for grid cols/rows
b1d4177 
Signed-off-by: Håkon Wiik Ånes <hwaanes@gmail.com>
@hakonanes
Exclude NaN entries when plotting Kikuchi pattern simulation features
dd8b2b9 
Signed-off-by: Håkon Wiik Ånes <hwaanes@gmail.com>
@hakonanes
Pass star polygon collection to HyperSpy for PC markers
f2cd03f 
Signed-off-by: Håkon Wiik Ånes <hwaanes@gmail.com>
@hakonanes
Test improved handling of PC markers
2884727 
Signed-off-by: Håkon Wiik Ånes <hwaanes@gmail.com>
@hakonanes
Remove unnecessary import for type checking
8b4f97b 
Signed-off-by: Håkon Wiik Ånes <hwaanes@gmail.com>
@hakonanes
Update notebooks with stored output following update to HyperSpy v2
e9a189d 
Signed-off-by: Håkon Wiik Ånes <hwaanes@gmail.com>
@hakonanes
Merge pull request #695 from hakonanes/hs2-markers-compat
b7f4dc8 
Update use of markers to HyperSpy v2
@hakonanes hakonanes added the maintenance This relates to package maintenance label Nov 7, 2024
@hakonanes hakonanes added this to the v0.11.0 milestone Nov 7, 2024
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@hakonanes hakonanes merged commit 82c3d99 into develop Nov 7, 2024
19 of 21 checks passed
@hakonanes hakonanes deleted the hyperspy2-support branch November 7, 2024 20:48
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