Grid mode using vispy ViewBox and linked cameras by brisvag · Pull Request #7870 · napari/napari

brisvag · 2025-04-29T14:35:42Z

References and relevant issues

Multicanvas vs grid mode: Multicanvas viewer #5348
closes multicanvas grid display for layers in Napari #561
supersedes Backend multichannel #6902
~~Feature: Highlight currently selected layer in grid mode #2954~~ EDIT: postponed to a followup PR
depends on Refactor layer overlays visuals from VispyLayer to VispyCanvas #7835 (included in this PR)
closes Grid is not correctly calculated when dim order is not default (in 3D only?) #7825

Description

This PR replaces the current transform-based grid mode with a viewbox-based one using linked cameras.

Drag events will remain relative to the original viewbox, making annotation at the edges a breeze. Interacting with one viewbox, such as during annotation, will update the corresponding active layer, potentially in a different grid view.

Additionally, viewer canvas overlays (such as scale_bar) now have a gridded property which, when set to True, will make it so the overlay appears in every grid box instead that on the general canvas.

Grid mode spacing now works proportionally to the layer extensions (i.e. [0,1), as before this PR) or as a pixel value (1,1500]. If spacing amount exceeds a limit that will result in degenerate viewboxes, the spacing will automatically adjust and present a warning to the user. Stride continues to work as before. For discussion on changing the grid layout see #8044.

import napari
v = napari.Viewer(ndisplay=3)
l0, l1 = v.open_sample('napari', 'cells3d')
l1.bounding_box.visible = True

v.axes.visible = True
v.grid.enabled = True

v.scale_bar.visible = True
v.scale_bar.gridded = True

…odel

Co-authored-by: Wouter-Michiel Vierdag <w-mv@hotmail.com>

for more information, see https://pre-commit.ci

brisvag · 2025-05-06T14:16:26Z

Todo from pairing with @melonora:

fix camera getting stuck (and infinite event loops)
fix canvas overlays not being shown

…ag/7870-5

jni · 2025-06-24T06:22:13Z

-    center = tuple(np.round(np.divide(screenshot.shape[:2], 2)).astype(int))
-    np.testing.assert_almost_equal(screenshot[center], [0, 255, 255, 255])


maybe here and above, comment out the code and add a note, as you did with other tests above, so that we know to revive the test as soon as we can?

Will do, good catch! Didn't realize Lorenzo commented these out too ... another lead on how this issue is happening. 😬

or, why does it need commented out? the test passes?

ok actually I'm just confused on what I'm looking at. Is this the most recent commit? It's not what I see locally and I think it's the most recent commit. But this does look like a diff that has this code removed.

TimMonko · 2025-06-25T19:56:40Z

I am merging this PR because it has had many eyes from the team:

Lorenzo and Wouter-Michiel worked on this initial implementation, with Lorenzo following up for weeks to address issues.
Peter and I stress tested the PR, found many issues, which Lorenzo and I fixed over a period of days.
Juan has given excitement over these changes

We will open follow-up PRs to address a few things, and others revealed during the pre-release including

Figuring out why screenshot-related tests required some changes, despite non-test behavior seems similar.
Adding highlights to the active layer viewbox
Potentially adding borders to the viewboxes

imagesc-bot · 2025-06-26T05:04:04Z

This pull request has been mentioned on Image.sc Forum. There might be relevant details there:

https://forum.image.sc/t/test-out-the-upcoming-napari-0-6-2-release/114029/1

# References and and Description Follow up to #7870. After that PR, on main, stride results in layers stacking up in the wrong order, where lower indexed layers are on top of the stack. See #8053 and #8044 for original discussion ```python import napari from skimage import data viewer, layer = napari.imshow( data.lily(), name='lily', channel_axis=2, colormap=['red', 'green', 'blue', 'gray'], blending='translucent', opacity=1, ) viewer.grid.enabled = True viewer.grid.stride = 2 napari.run() ``` main: ![screenshot_XtB3XXSr@2x](https://github.com/user-attachments/assets/62725a9b-5409-405c-b0e4-b6cea548174e) this PR: ![screenshot_tsNdp7E1@2x](https://github.com/user-attachments/assets/1671a4a3-9955-4653-af41-74b6c6d2617c) --------- Co-authored-by: Peter Sobolewski <76622105+psobolewskiPhD@users.noreply.github.com>

TimMonko · 2025-06-29T21:55:00Z

for release notes. this includes #8053

2025-06-29.16-52-45.mp4

# References and relevant issues - depends on napari/napari#7870 # Description Updated the descripion of grid mode to better reflect the new version, and added a small video to showcase it. --------- Co-authored-by: Peter Sobolewski <76622105+psobolewskiPhD@users.noreply.github.com> Co-authored-by: TimMonko <47310455+TimMonko@users.noreply.github.com>

Alternative to #8044 Depends on #8057 More context #8044 (comment) and #7870 (comment) Test with this script: ```python import napari from skimage import data viewer, layer = napari.imshow( data.lily(), name='lily', channel_axis=2, colormap=['red', 'green', 'blue', 'gray'], blending='translucent', opacity=1, ) viewer.grid.enabled = True viewer.grid.stride = 2 napari.run() ``` This PR reverses the default order of the panels with a default stride, so that later layers end up to the bottom-right of earlier layers. To enable the earlier behaviour, set a stride of -1, which can be set as default in the viewer preferences. ![screenshot_4nFePQ5C@2x](https://github.com/user-attachments/assets/528aebca-d623-4f9a-97f4-691329d2a2a7) ## Script output: main: ![screenshot_ikFxA97W@2x](https://github.com/user-attachments/assets/6d961f78-17ac-4ef7-aa8c-5fd66bc91dca) this PR: ![screenshot_dlFFazIh@2x](https://github.com/user-attachments/assets/4516932d-0b2b-4e61-b378-6ff221d8c9be) this PR with negative grid stride: ![screenshot_yQwsLxv6@2x](https://github.com/user-attachments/assets/4f791a10-9f00-4309-b029-50b6842f728d) Co-authored-by: TimMonko <47310455+TimMonko@users.noreply.github.com>

# References and relevant issues Discussed, in part, in #8053 and at napari community meeting Follow-up to #7870 # Description Improves tooltips for Grid stride to clarify how stride works. Improves layout of strings in the GUI

# References and relevant issues - #7870 # Description We use grid mode in a few examples, but there's no explicit example just to showcase it, especially now that we have extra related features such as the `Overlay.gridded` attributes.

# References and relevant issues - closes #7956 - closes (kinda?) #6055 # Description 1. This issue has been bothering me for a long time and I finally figured it out. On main, if you have the scalebar enabled and zoom out beyond 1000, it will suddenly collapse to a single pixel. Turns out, when the scalebar is dimensionless we need to ensure to keep the world pixel length to the *real* lenght, because we don't have unit multiples. Funny thing is, we already had this check in place, but for some reason only applied to high zooms, and not low zooms. Anyways, AFAICT this works. 2. The second issue is ultimately caused by our camera reporting a zoom of `1` when it reaches a low enough scale factor. This code points to #2875, but I can't figure out why. EDIT: it seems to be #2958. I tried to remove this guard completely and I don't actually see that issue anymore... I think it might be solved, either by the fact that we moved a lot of camera updates to `on_draw` in #7870 specifically because the viewbox was degenerate, or for some other reason. Maybe we can just remove this? --------- Co-authored-by: Tim Monko <timmonko@gmail.com>

brisvag added 10 commits April 17, 2025 15:41

overlay base refactor

48551e3

fix proper initialization of overlays

eca2495

Merge branch 'main' of github.com:napari/napari into refactor/overlays

4a88c15

Merge branch 'main' into refactor/overlays

6ba5cdb

Merge branch 'main' into refactor/overlays

540f7ce

some progress

9146ed9

Merge branch 'main' of github.com:napari/napari into feature/canvas-m…

6b1d380

…odel

kinda works

7714d57

Merge branch 'refactor/overlays' into feature/canvas-model

8139702

include overlay refactor changes, but still broken

8b2ef3d

brisvag requested review from a team and melonora as code owners April 29, 2025 14:35

github-actions Bot added the tests Something related to our tests label Apr 29, 2025

brisvag marked this pull request as draft April 29, 2025 14:35

melonora reviewed May 5, 2025

View reviewed changes

Comment thread napari/_vispy/canvas.py Outdated

brisvag and others added 6 commits May 5, 2025 12:30

Update napari/_vispy/canvas.py

3c32009

Co-authored-by: Wouter-Michiel Vierdag <w-mv@hotmail.com>

Merge branch 'main' into feature/canvas-model

5240fee

[pre-commit.ci] auto fixes from pre-commit.com hooks

02e46b2

for more information, see https://pre-commit.ci

Merge branch 'main' into feature/canvas-model

59e80b1

Merge branch 'main' into refactor/overlays

e965d4a

Merge branch 'main' into refactor/overlays

c4d967f

github-actions Bot added the topic:qt Relates to qt label May 6, 2025

everything works???

da63dc6

brisvag force-pushed the feature/canvas-model branch from 443e246 to da63dc6 Compare May 6, 2025 12:58

Merge branch 'main' into feature/canvas-model

b9e53af

brisvag marked this pull request as ready for review May 6, 2025 13:56

brisvag requested review from Czaki, DragaDoncila and psobolewskiPhD as code owners May 6, 2025 13:56

TimMonko and others added 2 commits June 23, 2025 17:47

Merge branch 'main' into feature/canvas-model

623e033

Merge branch 'main' of https://github.com/napari/napari into pr/brisv…

3ab3149

…ag/7870-5

napari deleted a comment from github-actions Bot Jun 24, 2025

This was referenced Jun 24, 2025

Backend multichannel #6902

Closed

"Reverse" ordering of layers in grid mode, now matching LayerList index #8044

Closed

jni reviewed Jun 24, 2025

View reviewed changes

TimMonko added ready to merge Last chance for comments! Will be merged in ~24h feature New feature or request labels Jun 25, 2025

TimMonko merged commit 123d6b5 into napari:main Jun 25, 2025

github-actions Bot removed the ready to merge Last chance for comments! Will be merged in ~24h label Jun 25, 2025

jni mentioned this pull request Jun 26, 2025

Reverse canvas grid order #8053

Merged

This was referenced Jun 27, 2025

Fix grid stride layering #8057

Merged

Improve tooltips for Grid attributes #8058

Merged

brisvag mentioned this pull request Jul 1, 2025

Reenable failing multiscale test #8063

Open

This was referenced Jul 22, 2025

Add example for grid mode. #8131

Merged

Fix scalebar behaviour at high/low zoom #8144

Merged

psobolewskiPhD mentioned this pull request Nov 9, 2025

feature request: rotate multiple 3D volumes in gridded mode? #2070

Closed

TimMonko mentioned this pull request Nov 11, 2025

Progressively longer add_layer calls in recent versions #8421

Closed

TimMonko added topic:preferences Issues relating to the creation of new preference fields/panels and removed preferences labels Jun 8, 2026

TimMonko mentioned this pull request Jun 25, 2026

Separate tiling from nontiling overlays #9083

Open

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Grid mode using vispy ViewBox and linked cameras - #7870

Grid mode using vispy ViewBox and linked cameras#7870
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		center = tuple(np.round(np.divide(screenshot.shape[:2], 2)).astype(int))
		np.testing.assert_almost_equal(screenshot[center], [0, 255, 255, 255])

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brisvag commented Apr 29, 2025 •

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