Add OME-Zarrs to an already open BigDataViewer by stefanhahmann · Pull Request #150 · BioImageTools/ome-zarr-fiji-java

stefanhahmann · 2026-10-08T16:24:46Z

Lets a second OME-Zarr, e.g. a segmentation, be added to a BigDataViewer window this plugin opened (part of #127):

Opener "BigDataViewer (add to active window)": adds to the BDV holding the active pyramidal, or opens a new one. The existing BDV opener is relabelled "BigDataViewer (new window)". A BDV window's active pyramidal now follows BDV's current source.
Drop onto a BDV window: files, folders and URLs dropped onto the image area are added to that window, regardless of the configured opener.
Several images at once (aka the "low-hanging fruit" of Open several currently open OME-Zarr images in BDV #108, no BigDataViewer change needed): "Open Current OME-Zarr Image in BigDataViewer" asks which of the open OME-Zarrs to show, like BDV's "Open Current Image", and shows the selected ones in one BDV window afterwards.
API: new OmeZarr.showInBdv(BdvHandle) and OmeZarrOpenActions.showInBdv(BdvHandle) (null = new window). BdvUtils' show/register methods are merged into show; showBdvAndRegisterWindow and the helpers are no longer public.
New Test data: bdv_testing/ with logo_spots (spots laid out like our logo, plus the Zarr wordmark) and their segmentation logo_labels (including OMERO colors and contrast limits).

BDV windows opened outside of this plugin are not covered by this PR; see the sketch in #127 and bigdataviewer/bigdataviewer-core#227.

🤖 Generated with Claude Code

It becomes the only focus listener, so PyramidalService and the BDV opener share one precedence rule (review of #150). Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>

PyramidalBdv.getBdvHandle() knew only the last of several BDVs, so a window could check the wrong viewer (review of #150). Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>

It is now the only AWT focus listener. PyramidalService follows it instead of listening itself, so it and the BDV opener share one rule for which viewer is active (review of #150). OmeZarr reports viewers it opens itself, since their focus events arrive late. Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>

PyramidalBdv.getBdvHandle() knew only the last of several BDVs, so a window could check the wrong viewer (review of #150). The opener now asks ActiveViewerService for the active viewer and BdvUtils.bdvHandleOf for its handle, a client property mirroring bigdataviewer-core#227. Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>

It is now the only AWT focus listener. PyramidalService follows it instead of listening itself (review of #150). Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>

PyramidalBdv.getBdvHandle() knew only the last of several BDVs, so a window could check the wrong viewer (review of #150). The opener now asks ActiveViewerService for the active viewer and BdvUtils.bdvHandleOf for its handle. Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>

BdvUtils had four similarly named show/register methods which become one show method with an optional BDVHandle param (null handle = new window, else add to that BDV). Some helpers are no longer public. The omeroChannels test moves to BdvUtilsTest. Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>

Adds the image to an already open BDV instead of opening a new one. null opens a new window, and showInBdv() now delegates to it. Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>

The label "BigDataViewer" becomes "BigDataViewer (new window)", so it stays distinguishable from an opener that adds to an open BDV. Its name bdv-multi-resolution stays, as it is persisted. Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>

Adds the image to the BDV holding the active pyramidal via OmeZarr.showInBdv(BdvHandle), or opens a new one if there is none. Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>

Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>

OmeZarrOpenActions gets showInBdv(BdvHandle), mirroring OmeZarr (null opens a new window), and showInBdv() delegates to it. Both BDV openers now go through the class OmeZarrOpenActions (like all other openers). This allows to add UI behaviour for BDV windows in one place (#127). Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>

Dropping files, folders or URLs onto the image area of a BDV windows that were opened through this plugin before adds them to that window, regardless of the configured opener (#127). OmeZarrDropListener parses them like pasted text, checks them with isZarr and reads them with the user's settings. The reading happens in a separate thread. Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>

OmeZarrDropListener had no test. This one opens logo_spots with the "add to active window" opener, drops logo_labels onto the window's real DropTarget (only the transferable is faked) and checks that BDV then shows both. droppedLocations is unit tested for file lists, text and unreadable drops. Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>

Opening logo_spots and then logo_labels: "add to active window" opens a new window only for the first and adds the second to it, while "new window" opens one window per image. Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>

Lists the OME-Zarrs that are open, once per PyramidContents Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>

A dialog to choose from a subset from a list of given OME-Zarrs based on PyramidContents Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>

Shows several OME-Zarrs in one new BDV window, one pyramidal each, so callers no longer thread the BdvHandle through a loop themselves. Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>

…OME-Zarr images at once. The command previously opened only the active OME-Zarr. With more than one open, in ImageJ or BDV, it now asks which to show, via OmeZarrImagesChooser, and shows them in one new BDV window, like BigDataViewer's own "Open Current Image" does. Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>

It is now the only AWT focus listener. PyramidalService follows it instead of listening itself (review of #150). Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>

PyramidalBdv.getBdvHandle() knew only the last of several BDVs, so a window could check the wrong viewer (review of #150). The opener now asks ActiveViewerService for the active viewer and BdvUtils.bdvHandleOf for its handle. Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>

Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>

Named like withDefaultBackend Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>

Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>

Not once per dropped location (review of #150). Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>

It reports the data transfer, not the opening (review of #150). Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>

It only works on BDV windows (review of #150). Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>

Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>

sonarqubecloud · 2026-10-26T14:29:37Z

Quality Gate passed

Issues
0 New issues
0 Accepted issues

Measures
0 Security Hotspots
88.1% Coverage on New Code
0.0% Duplication on New Code

See analysis details on SonarQube Cloud

xulman

Clarified in a Zoom call. Now I'm happy :)

stefanhahmann mentioned this pull request Oct 8, 2026

Add OME-Zarr to an already open BigDataviewer #127

Closed

stefanhahmann self-assigned this Oct 9, 2026

stefanhahmann force-pushed the 127-add-to-open-bdv branch 8 times, most recently from 9211a8f to abe44ad Compare October 12, 2026 09:56

stefanhahmann mentioned this pull request Oct 12, 2026

Open several currently open OME-Zarr images in BDV #108

Closed

stefanhahmann force-pushed the 127-add-to-open-bdv branch from f698958 to f27d1ff Compare October 12, 2026 15:10

stefanhahmann requested a review from xulman October 12, 2026 15:13

stefanhahmann force-pushed the 127-add-to-open-bdv branch 6 times, most recently from 4ed8a1f to be870d1 Compare October 13, 2026 18:59

xulman reviewed Oct 21, 2026

View reviewed changes

stefanhahmann mentioned this pull request Oct 23, 2026

License headers and .editorconfig disagree on trailing whitespace #155

Closed

stefanhahmann force-pushed the 127-add-to-open-bdv branch from 134b84a to 06b5505 Compare October 23, 2026 11:24

stefanhahmann force-pushed the 127-add-to-open-bdv branch from 06b5505 to ce957be Compare October 23, 2026 11:25

stefanhahmann force-pushed the 127-add-to-open-bdv branch from ce957be to 1aa50a2 Compare October 23, 2026 11:29

stefanhahmann and others added 23 commits October 26, 2026 15:22

Add OmeZarr.showInBdv(BdvHandle)

1ec2431

Adds the image to an already open BDV instead of opening a new one. null opens a new window, and showInBdv() now delegates to it. Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>

Add "BigDataViewer (add to active window)" opener

a811e92

Adds the image to the BDV holding the active pyramidal via OmeZarr.showInBdv(BdvHandle), or opens a new one if there is none. Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>

Make stringToUri's error messages independent of the clipboard

495d1fd

Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>

Add PyramidalService.getPyramidContents()

187a49a

Lists the OME-Zarrs that are open, once per PyramidContents Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>

Add OmeZarrImagesChooser

78bc7d1

A dialog to choose from a subset from a list of given OME-Zarrs based on PyramidContents Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>

Add BdvUtils.showInOneWindow

90b1baa

Shows several OME-Zarrs in one new BDV window, one pyramidal each, so callers no longer thread the BdvHandle through a loop themselves. Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>

Track the active image viewer in ActiveViewerService

30ea26d

It is now the only AWT focus listener. PyramidalService follows it instead of listening itself (review of #150). Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>

Document the active-viewer tracking in CLAUDE.md

b6f236c

Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>

Make OmeZarrOpenActions.omeZarrFor public as withSettings

00ffadc

Named like withDefaultBackend Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>

Rename OmeZarrOpenerServiceTest.omeZarrFor to omeZarrWithoutBackend

eca31f1

Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>

Load the opening settings once per drop

d3546cf

Not once per dropped location (review of #150). Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>

Name the drop's success flag transferSucceeded

93af66a

It reports the data transfer, not the opening (review of #150). Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>

Rename OmeZarrDropListener to OmeZarrBdvDropListener

8396469

It only works on BDV windows (review of #150). Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>

Use array initializer shorthand in OmeZarrOpenActionsTest

be85dd3

Test ActiveViewerService.viewerOf

bc40c4d

Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>

stefanhahmann force-pushed the 127-add-to-open-bdv branch from d005bb4 to bc40c4d Compare October 26, 2026 14:25

xulman approved these changes Oct 27, 2026

View reviewed changes

Comment thread ome-zarr-fiji-ui/src/main/java/ome/zarr/fijiui/open/OmeZarrOpenActions.java

Comment thread ome-zarr-fiji/src/main/java/ome/zarr/fiji/PyramidalBdv.java Outdated

Comment thread ome-zarr-fiji/src/main/java/ome/zarr/fiji/PyramidalBdv.java Outdated

stefanhahmann merged commit f3340b5 into main Oct 27, 2026
6 checks passed

stefanhahmann deleted the 127-add-to-open-bdv branch October 27, 2026 10:34

This was referenced Oct 27, 2026

Add OME-Zarrs to BigDataViewer windows opened by other tools #160

Open

Let BigDataViewer's "Open Current Image" keep OME-Zarr pyramids and OMERO settings #161

Open

Navigation Menu

Repository navigation

Add OME-Zarrs to an already open BigDataViewer - #150

Add OME-Zarrs to an already open BigDataViewer#150
stefanhahmann merged 25 commits into
mainfrom
127-add-to-open-bdv

stefanhahmann commented Oct 8, 2026 •

edited

Loading

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Uh oh!

sonarqubecloud Bot commented Oct 26, 2026

Uh oh!

xulman left a comment

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Reviewers

Uh oh!

Assignees

Labels

Projects

Milestone

Development

Uh oh!

2 participants

Conversation

stefanhahmann commented Oct 8, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Uh oh!

sonarqubecloud Bot commented Oct 26, 2026

Quality Gate passed

Uh oh!

xulman left a comment

Choose a reason for hiding this comment

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Reviewers

Uh oh!

Assignees

Labels

Projects

Milestone

Development

Uh oh!

2 participants

stefanhahmann commented Oct 8, 2026 •

edited

Loading