Improvement sprint v0.4

CHANGELOG.md

@@ -1,5 +1,70 @@
 # Changelog
 
+## [0.4-snapshot]
+
+### Added
+
+#### Desktop UI
+
+- Add desktop UI spinner to adjust the strength of the auto-contrast calculation ([#30](https://github.com/scenerygraphics/manvr3d/pull/30))
+- Add LUT preview swatches and LUT inversion toggle in the manvr3d UI ([#30](https://github.com/scenerygraphics/manvr3d/pull/30))
+- Add a few new LUTS (notabily Viridis) ([#30](https://github.com/scenerygraphics/manvr3d/pull/30))
+- Add spinner for link scale adjustments to the desktop UI ([#30](https://github.com/scenerygraphics/manvr3d/pull/30))
+
+#### VR UI
+- Add +/- buttons to quickly adjust volume transparency inside VR ([#30](https://github.com/scenerygraphics/manvr3d/pull/30))
+- Add VR button labels for quest controllers ([#30](https://github.com/scenerygraphics/manvr3d/pull/30))
+- Add VR buttons to adjust spot and track scaling analogous to manvr3d UI panel and keyboard shortcuts ([#30](https://github.com/scenerygraphics/manvr3d/pull/30))
+- Add VR buttons to toggle volume auto-contrast calculation, plus individual adjustment of lower & upper bounds ([#30](https://github.com/scenerygraphics/manvr3d/pull/30))
+- Add dedicated pointer for interacting with the UI when getting close to the buttons. Having to scale the annotation cursor for UI interaction is no longer required. ([#30](https://github.com/scenerygraphics/manvr3d/pull/30), [#823](https://github.com/scenerygraphics/scenery/pull/823))
+
+#### VR tools
+- Unconnected spots can be linked continuously with the controller tracking tool: When clicking into an unconnected spot, the linking process simply continues until the user clicks into a spot that already has a connection. ([#30](https://github.com/scenerygraphics/manvr3d/pull/30))
+- Added volume lensing tool to aid dataset exploration and annotation in dense areas and reduce mental load for complex datasets. Works on volumes and annotations. ([#30](https://github.com/scenerygraphics/manvr3d/pull/30), [#823](https://github.com/scenerygraphics/scenery/pull/823))
+- Edges can be selected and deleted with the same behaviors as spots (single click selects/deselects; dragging paints selections; clicking "delete" only deletes the connection, not the connected spots; holding "delete" will delete the connected branch including spots) ([#30](https://github.com/scenerygraphics/manvr3d/pull/30))
+- Support for forward tracking: changing the playback direction now also changes the tracking direction ([#30](https://github.com/scenerygraphics/manvr3d/pull/30))
+
+#### ELEPHANT integration
+- When the graph is empty and Elephant is set to predict all timepoints, the view automatically updates to the most recently predicted timepoint ([#30](https://github.com/scenerygraphics/manvr3d/pull/30))
+- Add support for uncertainty data from ELEPHANT ([#30](https://github.com/scenerygraphics/manvr3d/pull/30), [#13](https://github.com/elephant-track/elephant-client/pull/13), [#39](https://github.com/elephant-track/elephant-server/pull/39)). This requires ELEPHANT server v0.7 or higher. Pull from the latest ELEPHANT-server `main` branch to get the changes.
+
+#### Other
+- Add file-based logging of session statistics. Can be enabled via VM option `-Dmanvr3d.enableLogFile`. Enabled per default in standalone package via args file. Logs session lengths, interaction event counting and ELEPHANT prediction statistics. ([#30](https://github.com/scenerygraphics/manvr3d/pull/30))
+
+### Removed
+
+- Disable Ctrl-Scroll behavior from sciview in manvr3d, as this would cause the volume to shift forward/backward without the 3D instances to inherit the transformation ([#30](https://github.com/scenerygraphics/manvr3d/pull/30))
+- Remove unneeded toggle at project launch that asked whether to open the manvr3d UI window; we always need that window ([#30](https://github.com/scenerygraphics/manvr3d/pull/30))
+
+
+### Changed
+- Faster link coloring through dual hash maps ([#30](https://github.com/scenerygraphics/manvr3d/pull/30))
+- Change default LUTs: links use "plasma" now, volume uses "viridis" ([#30](https://github.com/scenerygraphics/manvr3d/pull/30))
+- Rename "NN Linking" button to "Link All", since this action automatically utilizes flow-based linking when enabled in the ELEPHANT settings ([#30](https://github.com/scenerygraphics/manvr3d/pull/30))
+- Slow down the observer movement behavior with the left joystick ([#30](https://github.com/scenerygraphics/manvr3d/pull/30))
+- Block timepoint scrolling behavior when cell tracking is currently active ([#30](https://github.com/scenerygraphics/manvr3d/pull/30))
+- Block accidental controller tracking and editing/selection behaviors during menu interaction ([#30](https://github.com/scenerygraphics/manvr3d/pull/30)) 
+- Change default scenery log level to warn. Can be changed in args file ([#30](https://github.com/scenerygraphics/manvr3d/pull/30))
+- Adjust auto-contrast calculation to also include the volume's min values ([#30](https://github.com/scenerygraphics/manvr3d/pull/30))
+- VR buttons are now click-based to prevent accidental triggering ([#30](https://github.com/scenerygraphics/manvr3d/pull/30))
+
+### Fixed
+- Moving the dataset is now possible when the volume is invisible (it will be turned visible for the duration of the transformation) ([#30](https://github.com/scenerygraphics/manvr3d/pull/30))
+- Using cosmetic spot scaling now also influences the apparent size of the cursor, making it consistent ([#30](https://github.com/scenerygraphics/manvr3d/pull/30), [#823](https://github.com/scenerygraphics/scenery/pull/823)) 
+- Link colors update immediately on color mode changes ([#30](https://github.com/scenerygraphics/manvr3d/pull/30))
+- Link colors now properly reflect the assigned tag sets ([#30](https://github.com/scenerygraphics/manvr3d/pull/30))
+- Moving the dataset now respects the user-defined track visibility window ([#30](https://github.com/scenerygraphics/manvr3d/pull/30)
+- Fix focus & timepoint syncing when using arrow keys in trackscheme together with manvr3d in a group lock ([#30](https://github.com/scenerygraphics/manvr3d/pull/30))
+- Fix crash when eye tracking was selected in the UI, not ET hardware was found and the user stops the VR session ([#30](https://github.com/scenerygraphics/manvr3d/pull/30))
+- Fix debug hedgehog visualization when eye tracking is active ([#30](https://github.com/scenerygraphics/manvr3d/pull/30))
+- Fix occasional Vulkan crashes that happened when activating a VR session ([#823](https://github.com/scenerygraphics/scenery/pull/823))
+- Volume mipmap level chosen at launch is now honored by the UI and the volume ([#30](https://github.com/scenerygraphics/manvr3d/pull/30))
+- Fix out of stack space errors with Blackwell Nvidia GPUs on recent drivers by increasing stack space size in the args file ([#30](https://github.com/scenerygraphics/manvr3d/pull/30))
+- Fix potential link/spot color flickering during tracking, caused by duplicate instance buffer updates ([#30](https://github.com/scenerygraphics/manvr3d/pull/30))
+- Fix hidden full geometry redraws when moving the dataset with left grab, and during tracking ([#30](https://github.com/scenerygraphics/manvr3d/pull/30))
+- Fix hidden double link/spot redraws when changing their respective scaling through keyboard commands (L/shift+L and O/shift+O) ([#30](https://github.com/scenerygraphics/manvr3d/pull/30))
+- Fix closing behavior of the UI panel "Close" button (closes itself, sciview and linked BDV window now), and add identical behavior to the sciview window close button ([#30](https://github.com/scenerygraphics/manvr3d/pull/30))
+
 ## [0.3.1] - 2026-03-19
 
 ### Changed