Merge Zarrv3#165
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Jun 18, 2026
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- Depends on Multiview-Reconstruction 9.0.1-SNAPSHOT
- Adds on-the-fly BDV opening mode (for datasets with large number of tiles)
- Now builds using Java 21
- minor bug fixes
Bump multiview-reconstruction 8.1.2 -> 9.0.0-SNAPSHOT and mirror MVR's zarrv3 dependency overrides (n5 4.0.0-alpha-12 & friends, imglib2 8.0.1, imglib2-algorithm 0.18.3, imglib2-realtransform 4.0.5, imglib2-cache 1.0.0-beta-20, bigdataviewer-core 10.6.5, mpicbg 1.6.6) so the transitive n5/imglib2 versions match what MVR was compiled against. Without these the shared pom-scijava 43.0.0 BOM would force MVR's transitive n5 back to 3.x. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
MVR 9.0.0 (zarrv3) moved two things BigStitcher depends on: - ColorStream: net.preibisch.mvrecon.fiji.spimdata.explorer.util -> util - 5 static BDV helpers (getBDVSourceIndex, whiteSources, setFusedModeSimple, sameColorSources, resetBDVManualTransformations) from FilteredAndGroupedExplorerPanel -> util.BDVTools Update imports and the corresponding call sites. StitchingExplorerPanel keeps its own local setFusedModeSimple/whiteSources/getBDVSourceIndex copies, so only its inherited resetBDVManualTransformations call needed BDVTools. updateBDV and addListener remain on FilteredAndGroupedExplorerPanel (unchanged). Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Mirror MVR's Data_Explorer "Large dataset" flow in BigStitcher's opener and support an on-the-fly BDV mode for large/heavily-split datasets: - plugin/BigStitcher.java: add a "Show advanced options" checkbox and a "Large dataset" dialog (thresholds: warn >100 views, lazy recommended >=1000, BDV-at-startup default off >=10000) that sets BDVPopup.useLazyMode, the open-BDV-at-startup choice, and the alignment log-line caps. - StitchingExplorer: thread an openBDV flag through a new 4-arg constructor (3-arg delegates to true, preserving existing callers). - StitchingExplorerPanel.initPopups(): register LazyBDVPopupStitching when BDVPopup.useLazyMode is set, else the eager BDVPopupStitching; branch the constructor auto-open accordingly. - LazyBDVPopupStitching: a BDVPopup subclass (so the inherited bdvPopup() accessor and its many call sites keep working) that opens an empty BDV and adds/removes sources as views are selected (logic ported from MVR's LazyBDVPopup), rendered with MaximumProjectorARGB and the stitching LinkOverlay. Per-channel coloring is intentionally skipped in lazy mode. No multiview-reconstruction changes are required; lazy support is fully self-contained in BigStitcher. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
The install script hardcoded VERSION=2.1.1-SNAPSHOT, so the generated ./bigstitcher launcher loaded a stale BigStitcher jar on the classpath. Against multiview-reconstruction 9.0.0-SNAPSHOT this caused a NoSuchMethodError (FilteredAndGroupedExplorerPanel.setFusedModeSimple, which moved to util.BDVTools). Derive the version from the pom via 'mvn help:evaluate' so the launchers always point at the freshly built jar (now 2.6.2-SNAPSHOT). Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
After Global Optimization, ExecuteGlobalOpt only called bdvPopup().updateBDV() (reloads transforms / repaints) but never reset which BDV sources are visible. If the user had inspected links in preview mode, BDV was left showing only that tile pair even though all stitched views remained selected in the explorer (observed: 6 of 18 views visible). Re-apply visibility for the full current selection via the new StitchingExplorerPanel.showSelectedInBDV() so the complete stitched result is shown. Pre-existing behavior (identical in MVR 8.1.2); surfaced now that the opener defaults BigDataViewer-at-startup on. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
…peg to runtime so the release javadoc jar builds
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@cgoina @StephanPreibisch Thanks for the multiview-reconstruction 9.0.1 release supporting the new N5! I gather that this PR is necessary for BigStitcher to play nicely with those new releases? Is this PR almost ready to go? Or is there more to do? |
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@ctrueden you are correct - this is just to make BigStitcher work with the latest MVR and zarrv3. |
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@cgoina Thanks. Once this merges and a new BigStitcher is released containing the update, I will be able to update Fiji as a whole to ship the new N5 libraries. Exciting! ✨ |
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