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Merged
merged 125 commits into from
Mar 17, 2025
Merged

Pull from upstream/main #12

merged 125 commits into from
Mar 17, 2025

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@ttngu207
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@ttngu207 ttngu207 commented Feb 26, 2025

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pgunn and others added 30 commits May 31, 2024 15:26
@pgunn
VERSION to 1.11.2 after release
398c64f
@ethanbb
Add is3D setting to summary_images functions
e401f75
@ethanbb
Make movie.removeBL work with 3D movies
af09876
@ethanbb
Revert "Add is3D setting to summary_images functions"
d139588 
This reverts commit e401f75.
@ethanbb
Add tests for to2D and to3D
0857d7a
@ethanbb
Make cpp exclusion more specific
7e372b3
@salehtahini
added bokeh implementation of view_quilt
860e8d8
@salehtahini
updated documentation
827c541
@pgunn
Fix naming of Slider()
54b2fb7
@pgunn
Merge pull request #1365 from salehtahini/bokeh_view_quilt
90904b3 
Added bokeh implementation of view_quilt
@pgunn
pin peakutils >=1.3.5 (see #1369)
9c4646e
@ethanbb
Fix CoM calculation when swap_dim is true
522d456
@ethanbb
Fix plot_contours to use CoMs from updated get_contours
1f88e49
@pgunn
de-emoji the readme
8f359bb
@ethanbb
Add rewritten com function with C/F order and add test
b38f0fa
@pgunn
caiman_gui: if the user doesn't provide a filename, bail out with a g…
f6d30aa 
…ood message rather than crashing
@ethanbb
Restore individual dimension arguments for com
467c591
@ethanbb
Add slice_dim option for get_contours and 3D test for swap_dim
d883598
@ethanbb
Minor changes to make contours more consistent/predictable
830967c
@ethanbb
Use None instead of 'auto'
04d1ca2
@pgunn
Merge pull request #1370 from proektlab/contours-com-fix
d219783 
Get correct centers of mass from rois.com even when swap_dim is True in get_contours
@pgunn
demo_online_cnmfE: Fix a text cell that was mistakenly marked as code
d0732cb
@pgunn
Finish the fix started in #1326 (thanks to @EmeEmu and @marberi for b…
2a9d2c8 
…ringing it to my attention)
@pgunn
mmapping: fix a path goof where a double-correction caused a problem,…
2d0108e 
… thanks t o @nick-youngblut #1373
@pgunn
Merge pull request #1375 from flatironinstitute/dev-fix_path_goof
bf7e8de 
mmapping: fix a path goof where a double-correction caused a problem
@pgunn
Merge pull request #1363 from proektlab/summary-images-3d
0dac913 
Fix removeBL for 3D movies
@pgunn
Move (almost) all caiman logging under a named logger called "caiman"
c82e768
@pgunn
caiman-logger: Further cleanups, fix problems CI revealed
9bdbacb
@pgunn
caiman logging change: had to partly back off on import cleanup, fix …
b3fafb5 
…some goofs
@pgunn
Initial go at updating notebooks to use the logger we're calling caiman
d3a89fc
ethanbb and others added 27 commits January 6, 2025 11:49
@ethanbb
Refactor sliding_window and add get_patch_centers
254954d
@ethanbb
Add interp_shifts_precisely option for tile_and_correct
776c736
@ethanbb
Implement interp_shifts_precisely for non-opencv and for tile_and_cor…
70c6480 
…rect_3d
@ethanbb
Fix apparent bugs in register_ROIs
56c15fc
@ethanbb
Fix incorrectly handling dest indices when interpolating shifts and t…
4498856 
…ype of input to cv.remap
@ethanbb
Allow inputting parameters to override tile_and_correct defaults in r…
4cf09fd 
…egister_ROIs
@ethanbb
Make register_ROIs work with rigid correction
901a505
@ethanbb
Put align_options at the end to avoid messing up positional args
2e257c4
@ethanbb
Clarify exception to strides/overlaps for last patch
5c50e9f
@ethanbb
Add 'interp_shifts_precisely' motion parameter
2c214b4
@ethanbb
Use new option in apply_shifts_movie and fix apparent inconsistencies
8a6d62f
@ethanbb
Change interp_shifts_precisely to shifts_interpolate
a479909
@pgunn
Merge pull request #1444 from proektlab/register_ROIs-improvements
857ae12 
Fix and add more options for non-optical flow register_ROIs; add feature to interpolate shifts based on patch locations in tile_and_correct
@fdeguire03
Add npy support to load_memmap
2a14837
@fdeguire03
Add data consistency checks to mmapping.py
67787fe
@pgunn
Merge pull request #1446 from fdeguire03/dev
beb0f9b 
Add npy support to load_memmap
@pgunn
README: fewer inconsistencies in capitalisation of caiman
d8b7cb6
@pgunn
Add Darcy to dataset thanks, install instructions mention pip now
3ed5256
@pgunn
l1_ratio in cnmf.paras.init for call to NMF()
6cf6c27
@pgunn
Redo l1_ratio because we use splat operator
9403836
@pgunn
l1_ratio: fix debug message
56ffa62
@pgunn
Rename l1_ratio parameter for clarity
52dfd57
@pgunn
Notebooks: set default logging level to logging.WARNING, add a blurb.
4e0437f
@pgunn
Merge pull request #1448 from flatironinstitute/dev-l1_ratio_threadth…
f62debe 
…rough

l1_ratio in cnmf.paras.init for call to NMF()
@pgunn
motion_correction: move some noisy and not too useful messages from i…
919fa67 
…nfo to debug
@pgunn
Merge pull request #1449 from flatironinstitute/dev
02cbba6 
Merge dev for release 1.11.4
@pgunn
VERSION to 1.11.5 after release
0b5a9e1
ttngu207
ttngu207 commented Feb 26, 2025
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Reviewed, no major risks (except for dropping cuda support, but we know that).
Good to go

@kushalbakshi kushalbakshi merged commit ae7a6a5 into datajoint:main Mar 17, 2025
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10 participants

@ttngu207 @pgunn @kushalbakshi @ethanbb @salehtahini @deMalmazet @hmaarrfk @kushalkolar @darikoneil @fdeguire03