Allow rotating ortho view #8614

MichaelBuessemeyer · 2025-05-12T17:29:13Z

Documentation about rotation & 3d scene

https://www.notion.so/scalableminds/3D-Rotations-3D-Scene-210b51644c6380c2a4a6f5f3c069738a
This documentation explains the quirky of how rotations are handled in more details.

URL of deployed dev instance (used for testing):

https://___.webknossos.xyz

Steps to test:

Review the docs file above
UI
- Check in the navbar the position input. Right to the text input, there should be a new button.
- Hover that button. It is the new rotation pop over
- Play round with the pop over, slide the sliders. No value jumping should occur. When the rotation changes, the viewports should adjust accordingly
- Also use the manual number input
- Try the reset buttons individually. This should reset only the axis's value to 0.
- Try the reset all button. It should reset the whole rotation to 0,0,0
- Check the URL. When the rotation value changes, the rotation stored in the url hash should as well (deferred by 2 seconds or so)
Keyboard shortcuts:
- Use the shortcuts to rotate the cameras / planes: shift + up/down/left/right & alt + left/right. Holding should continue the rotation.
- Use the shortcuts to directly rotate by 90°. Same as above just with ctrl pressed additionally. Holding should !not! continue the rotation.
Tools
- In view mode check the line measurement tool & use it. The area measurement tool should not be available once the rotation is no longer 0,0,0.
- create an annotation of a dataset with anisotropic voxel scaling.
- once a rotation is configured, all tools except for the line measurement tool and the skeleton tool should no longer be available.
- test the line measurement tool again
- Skeleton tool testing
  - try creating some nodes while a rotation is active.
  - create multiple trees. Each tree should be traced with a different rotation active. Moreover, also trace some in different viewports.
  - try moving nodes around
  - in the layers tab - skeleton- disable "Auto-rotate to Nodes"
  - activate some previously traced nodes. The rotation should not change.
  - activate the "Auto-rotate to Nodes" setting. Again activate the trees / nodes. The rotation should now change to the rotation is was previously when the tree was traced.
    - This can easily be detected when the nodes are close to each other. All nodes of the tree should be visible as they were tracing in the same planar orientation. The viewports in which the "plane of nodes" should be visible should be the same as during the tracing.
  - Deactivate the "Auto-center nodes" setting. Now again active the trees / nodes. The cameras should still rotate towards the nodes but not move there to center the active node.
  - splitting trees and so on should also still work
  - Reset the orientation. Give the volume tools a try. They should work as expected.
  - Proofreading.
    - create an annotation with a hdf5 (or zarr) mapping and go into the proofreading tool.
    - Now do some proofreading actions. This should work
    - configure some rotation. Again do some proofreading actions. Everything should still work as expected.
- As the semantics of the getGlobalPosition from clicked position changed. Please give each other tracing tool a quick try whether it still works as expected.
3D viewport
- Please check the 3d viewport buttons.
- Configure a rotation
- Use the 4 orientation buttons of the 3d viewport. They should focus the clicked plane / look from the top-right corner down at the cross section. Just as when no rotaiton is configured.
- Reset the rotation. Check the buttons again. They should behave as on the master.
Tabs
- Give the segment, skeleton and so on tabs a quick little testing whether the basics still work. Just avoid unwanted easily catchable bugs.
Arbitrary view
- Check the tracing in arbitrary view. rotating there should still work as well as creating nodes and so on.
- Including flight & oblique mode
And of cause: Other things you thing might be broken by this PR
URL / Links
- Please check that links inlude the rotation in the hash and that it is applied on page load.
- Configure some rotation
- Copy the full URL into another tab and view it
- It should automatically show the configured rotation and the 3d viewport should still look like the 3d button of it was just clicked (-> looking at the planes correctly and not in wrong / weird way / angle)

TODOs:

Issues:

fixes Allow to rotate freely in orthogonal viewports #7569

(Please delete unneeded items, merge only when none are left open)

Updated changelog
Considered common edge cases

…lace :/)

coderabbitai · 2025-05-12T17:29:19Z

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📝 Walkthrough

Walkthrough

This update introduces free rotation in orthogonal viewports, refactoring core 3D transformation logic, UI, and state management to support arbitrary camera orientation in orthogonal mode. It adds rotation-aware shaders, disables incompatible tools when rotated, exposes rotation controls in the UI, and updates tests and reducers for consistent rotation handling throughout the application.

Changes

File(s) / Group	Change Summary
viewer/model/accessors/flycam_accessor.ts, viewer/model/helpers/rotation_helpers.ts	Refactored flycam rotation accessors to use radians, matrices, and add helpers for conversion between Euler angles and matrices; added new rotation helpers module.
viewer/model/reducers/flycam_reducer.ts	Unified rotation/movement logic with THREE.js Euler/Matrix4, storing normalized rotation in state, and updating movement to apply flycam rotation.
viewer/constants.ts, viewer/controller/camera_controller.ts	Added mappings and base rotations for orthogonal views; updated camera controller to apply flycam rotation to orthogonal cameras.
viewer/controller/scene_controller.ts, viewer/geometries/plane.ts	Refactored plane positioning and rotation to use flycam rotation and dataset scale factor, with reactive updates and improved matrix handling.
viewer/model/accessors/view_mode_accessor.ts	Replaced planar offset calculations with full 3D transformations using flycam rotation/translation; global position now includes both rounded and floating coordinates.
viewer/controller/combinations/*, viewer/controller/url_manager.ts, viewer/model/actions/skeletontracing_actions.ts	Updated all position and node creation handlers to use rounded/floating positions and pass rotation consistently; updated setActiveNodeAction to accept suppressRotation.
viewer/model/sagas/skeletontracing_saga.ts, volumetracing_saga.tsx, prefetch_saga.ts	Made tracing and prefetching rotation-aware; added logic to apply node rotation on activation and to disable prefetching and tracing when rotated.
viewer/model/accessors/disabled_tool_accessor.ts, view/action-bar/tools/toolbar_view.tsx, view/context_menu.tsx	Disabled volume, area, and bounding box tools and context menu items when rotated, providing user explanations.
viewer/view/action-bar/dataset_position_view.tsx, dataset_rotation_popover_view.tsx, action_bar_view.tsx	Refactored position view to functional component, added rotation popover with sliders and reset; updated action bar to use new component.
viewer/view/components/setting_input_views.tsx, left-border-tabs/layer_settings_tab.tsx, messages.tsx	Added UI for rotation setting and new setting key/messages; updated slider component for rotation controls.
viewer/model_initialization.ts, default_state.ts, store.ts	Added rotation to default flycam state and user config; always initializes rotation from dataset.
viewer/api/api_latest.ts, controller/viewmodes/arbitrary_controller.tsx, plane_controller.tsx	Updated API and controllers to support new rotation logic, keyboard controls, and passing suppress flags for rotation/centering.
viewer/geometries/materials/plane_material_factory.ts, shaders/*.glsl.ts	Added uniforms for flycam rotation and inverted voxel size, updated shader logic for rotation, coordinate transformation, and filtering; added getUnrotatedWorldCoordUVW.
viewer/view/distance_measurement_tooltip.tsx, statusbar.tsx, right-border-tabs/abstract_tree_tab.tsx, comment_tab/comment.tsx	Updated tooltip and tab logic to use new rotation and position handling; refactored components to functional/hooks.
test/*	Updated and extended tests to cover new rotation logic, node creation under rotation, and updated expectations for position/rotation.
viewer/model/helpers/nml_helpers.ts, model/sagas/volumetracing_saga.tsx	Updated serialization and tracing to use degrees for rotation.
viewer/types/schemas/url_state.types.ts	Removed obsolete type definition file.
viewer/geometries/arbitrary_plane.ts	Removed unused setPosition method.
viewer/geometries/helper_geometries.ts	Prevented duplicate edge points in contour geometry.
viewer/view/plane_view.ts	Renamed local variables for consistency.

Assessment against linked issues

Objective	Addressed	Explanation
Adapt bucket picking for rotated orthogonal viewports (#7569)	✅
Adapt shader logic for rotated orthogonal viewports (#7569)	✅
Adapt mouse interactions: mapping mouse position to voxel position (#7569)	✅
Disable or support segmentation/volume tools and rendering in rotated viewports; UI warnings/exposure (#7569)	✅
Expose rotation value and controls in UI for orthogonal viewports (#7569)	✅

Assessment against linked issues: Out-of-scope changes

Code Change	Explanation
Removal of `frontend/javascripts/types/schemas/url_state.types.ts`	This file was a workaround for schema generation and is not directly related to orthogonal viewport rotation features.
Refactor of `viewer/view/plane_view.ts` (variable renaming)	Variable renaming for camelCase consistency is unrelated to rotation or orthogonal viewport objectives.
Minor change in `geometries/helper_geometries.ts` (duplicate edge point prevention)	Preventing duplicate edge points in contour geometry is not directly related to orthogonal viewport rotation.
Removal of `setPosition` in `geometries/arbitrary_plane.ts`	Removing an unused method is unrelated to the objectives of orthogonal viewport rotation.

Possibly related PRs

Fix race condition when starting proofreading with a split action #8676: Both PRs address saga and save queue synchronization in tracing/proofreading, focusing on ensuring correct sequencing and state consistency.
Support rendering more dtypes #8325: Both PRs involve extensive changes to data handling and rendering logic for new data types, which may overlap with shader and geometry updates in this PR.

Suggested reviewers

philippotto

Poem

In orthogonal lands, the viewports now spin,
With shaders and matrices, let rotations begin!
The tools take a rest when the view is askew,
While sliders and popovers give angles their due.
The rabbit hops freely, with vectors in tow—
Orthogonal, arbitrary, all in a row!
🐇✨

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…ho-view-rotation-v2

…alculate correct global position in shader

MichaelBuessemeyer

Thanks for all the feedback. Here are my answers.

I'll ask for the next review hopefully soon. I just noticed that the line measurement tool does not work for datasets with anisotropic voxel scale. At least scale [1,1,1] works but the normal l4_sample voxel scale does not.

frontend/javascripts/viewer/constants.ts

frontend/javascripts/viewer/controller/viewmodes/plane_controller.tsx

frontend/javascripts/viewer/default_state.ts

frontend/javascripts/viewer/shaders/texture_access.glsl.ts

frontend/javascripts/viewer/shaders/main_data_shaders.glsl.ts

frontend/javascripts/viewer/geometries/materials/plane_material_factory.ts

frontend/javascripts/test/api/api_skeleton_latest.spec.ts

frontend/javascripts/viewer/shaders/main_data_shaders.glsl.ts

frontend/javascripts/viewer/view/action-bar/dataset_rotation_popover_view.tsx

frontend/javascripts/viewer/geometries/materials/plane_material_factory.ts

…led dataset

…lt back with calculateInViewportPos

…ho-view-rotation-v2

MichaelBuessemeyer

Ok, I fixed the line measurement tool for anisotropic datasets while they are viewed with rotation.

The bug was due to not correctly calcuating a global position back into the screen viewport space to check whether the user moved the viewport back / forth to hide the tooltip. Now the calculation is correct. I also added tests for the calculation of global positions which I used for debugging this. My initial understanding that the calculation of a global position from an event was wrong. I still kept the tests as they seemed useful to me.

Sooooo now that this is done, I'd say this ready for another review round and of cause a testing session :D

frontend/javascripts/viewer/model/accessors/view_mode_accessor.ts

frontend/javascripts/test/model/accessors/flycam_accessors.spec.ts

frontend/javascripts/test/model/accessors/view_mode_accessors.spec.ts

MichaelBuessemeyer · 2025-07-10T17:01:49Z

Oh and a frontend test seems to timeout consistently. I'll take a look at this but this should not block your review

MichaelBuessemeyer · 2025-07-11T11:09:08Z

@philippotto in my latest commit I "fixed" a test by removing a take statement. I am honestly confused why this is suddenly necessarry. Do you maybe have an idea?
Here are the logs from the test from the two branches. Each end enriched with some debug error loggings and logActions form wk_dev turned on. It shows that somehow on this branch the saga execution stops after the SET_VERSION_NUMBER.
Compared to the master, where additional actions are dispatched; inlcuding the expected FINISH_MAPPING_INITIALIZATION action.

on master, working:

stderr | frontend/javascripts/test/sagas/proofreading.spec.ts > Proofreading > should update the mapping when the server has a new update action with a merge operation
before tryToIncorporateActions
working on mergeAgglomerate with activeMapping:  {
  mappingName: 'sampleHdf5Mapping',
  mapping: Map(8) {
    1 => 10,
    2 => 10,
    3 => 10,
    4 => 11,
    5 => 11,
    6 => 12,
    7 => 12,
    1337 => 1337
  },
  mappingColors: undefined,
  hideUnmappedIds: false,
  mappingStatus: 'ENABLED',
  mappingType: 'HDF5',
  isMergerModeMapping: undefined
}
triggering setMappingAction
dispatching updating version action
dispatched updating action
after tryToIncorporateActions
before FINISH_MAPPING_INITIALIZATION

stdout | frontend/javascripts/test/sagas/proofreading.spec.ts > Proofreading > should update the mapping when the server has a new update action with a merge operation
SET_MAPPING
  dispatching {
    type: 'SET_MAPPING',
    layerName: 'volumeTracingId',
    mappingName: 'sampleHdf5Mapping',
    mappingType: 'HDF5',
    mapping: Map(8) {
      1 => 10,
      2 => 10,
      3 => 10,
      4 => 10,
      5 => 10,
      6 => 12,
      7 => 12,
      1337 => 1337
    },
    mappingColors: undefined,
    hideUnmappedIds: undefined,
    showLoadingIndicator: undefined,
    isMergerModeMapping: undefined
  }
SET_VERSION_NUMBER
  dispatching { type: 'SET_VERSION_NUMBER', version: 1 }

stdout | frontend/javascripts/test/sagas/proofreading.spec.ts > Proofreading > should update the mapping when the server has a new update action with a merge operation
SET_TOOL
  dispatching {
    type: 'SET_TOOL',
    tool: [class MoveTool extends AbstractAnnotationTool] {
      id: 'MOVE',
      readableName: 'Move Tool'
    }
  }
  Cancel old bucket watcher
  ENSURE_TRACINGS_WERE_DIFFED_TO_SAVE_QUEUE
    dispatching {
      type: 'ENSURE_TRACINGS_WERE_DIFFED_TO_SAVE_QUEUE',
      callback: [Function: callback]
    }

stdout | frontend/javascripts/test/sagas/proofreading.spec.ts > Proofreading > should update the mapping when the server has a new update action with a merge operation
FINISH_MAPPING_INITIALIZATION
  dispatching { type: 'FINISH_MAPPING_INITIALIZATION', layerName: 'volumeTracingId' }
  ENSURE_TRACINGS_WERE_DIFFED_TO_SAVE_QUEUE
    dispatching {
      type: 'ENSURE_TRACINGS_WERE_DIFFED_TO_SAVE_QUEUE',
      callback: [Function: callback]
    }
CLEAR_MAPPING
  dispatching { type: 'CLEAR_MAPPING', layerName: 'volumeTracingId' }

stderr | frontend/javascripts/test/sagas/proofreading.spec.ts > Proofreading > should update the mapping when the server has a new update action with a merge operation
  after FINISH_MAPPING_INITIALIZATION

on this branch

stderr | frontend/javascripts/test/sagas/proofreading.spec.ts > Proofreading > should update the mapping when the server has a new update action with a merge operation
before tryToIncorporateActions
working on mergeAgglomerate with activeMapping:  {
  mappingName: 'sampleHdf5Mapping',
  mapping: Map(8) {
    1 => 10,
    2 => 10,
    3 => 10,
    4 => 11,
    5 => 11,
    6 => 12,
    7 => 12,
    1337 => 1337
  },
  mappingColors: undefined,
  hideUnmappedIds: false,
  mappingStatus: 'ENABLED',
  mappingType: 'HDF5',
  isMergerModeMapping: undefined
}
triggering setMappingAction
dispatching updating version action
dispatched updating action
after tryToIncorporateActions
before FINISH_MAPPING_INITIALIZATION

stdout | frontend/javascripts/test/sagas/proofreading.spec.ts > Proofreading > should update the mapping when the server has a new update action with a merge operation
SET_MAPPING
  dispatching {
    type: 'SET_MAPPING',
    layerName: 'volumeTracingId',
    mappingName: 'sampleHdf5Mapping',
    mappingType: 'HDF5',
    mapping: Map(8) {
      1 => 10,
      2 => 10,
      3 => 10,
      4 => 10,
      5 => 10,
      6 => 12,
      7 => 12,
      1337 => 1337
    },
    mappingColors: undefined,
    hideUnmappedIds: undefined,
    showLoadingIndicator: undefined,
    isMergerModeMapping: undefined
  }
SET_VERSION_NUMBER
  dispatching { type: 'SET_VERSION_NUMBER', version: 1 }

 ❯ frontend/javascripts/test/sagas/proofreading.spec.ts (4 tests | 1 failed | 3 skipped) 20943ms
   ↓ Proofreading > should merge two agglomerates and update the mapping accordingly
   ↓ Proofreading > should split two agglomerates and update the mapping accordingly
   × Proofreading > should update the mapping when the server has a new update action with a merge operation 20941ms
     → Test timed out in 20000ms.
If this is a long-running test, pass a timeout value as the last argument or configure it globally with "testTimeout".
   ↓ Proofreading > should update the mapping when the server has a new update action with a split operation

MichaelBuessemeyer · 2025-07-11T13:01:41Z

@philippotto FYI: The new assertion that the active tool is still the proofreading tool after the test I fixed on this branch is working on this branch and failing on the master. On master the active tool indeed switches back to the the move tool.
Here is the assertion error from the master:

should update the mapping when the server has a new update action with a merge operation
AssertionError: expected [Function MoveTool] to be [Function ProofreadTool] // Object.is equality

- Expected
+ Received

- [Function ProofreadTool]
+ [Function MoveTool]

 ❯ frontend/javascripts/test/sagas/proofreading.spec.ts:309:26
    307| 
    308|       const activeTool = yield select((state) => state.uiInformation.activeTool);
    309|       expect(activeTool).toBe(AnnotationTool.PROOFREAD);
       |                          ^
    310|     });

So the fix of removing the take statement should indeed be correct

…ptimization code in the vertex shader are handled correctly

philippotto · 2025-07-11T14:36:03Z

testing went mostly well 🎉 however, I found one bug:

scrolling while keeping alt pressed should always zoom into the current mouse position. this only works when the rotation is 0,0,0 (or if the mouse is in the center of the viewport). if this is not the case, the zooming is weird because it does not keep the projection of the current viewport intact (the image data changes then because the current position changes, too).

- done by introducing new action translating the flycam absolute without any rotation / zoom etc. interference

…ho-view-rotation-v2

MichaelBuessemeyer

Thanks a lot for the thorough review @philippotto.
And thanks for finding this bug. I did know that alt + scroll is a feature.

Please give it another try. I just pushed the fix (see commit 01bbc9a). The fix includes a new flycam action for which I also added tests. I needed the new flycam action as the part of the zoom to mouse position was to modify the position of the flycam with an absolute translation that ignored the current rotation of the flycam and scaling / zoom value and so on. No action does this.

Of cause: I could also have used the setPosition action and handed it the flycamPos + offset. If you prefer this, please just tell me, but I don't really see the benefit for this except maybe no new action.

Once the CI is done, I'll redeploy for easier testing

MichaelBuessemeyer · 2025-07-14T13:16:50Z

frontend/javascripts/viewer/controller/combinations/move_handlers.ts

@@ -93,7 +95,7 @@ function getMousePosition() {
  return calculateGlobalPos(state, {
    x: mousePosition[0],
    y: mousePosition[1],
-  }).rounded;
+  }).floating;


I figured this might be a little better to have a bit more accuracy.

this is only used for the zoom to mouse position

frontend/javascripts/viewer/shaders/main_data_shaders.glsl.ts

philippotto

Awesome stuff! thanks for pulling this to the finish line 🥇

Co-authored-by: Philipp Otto <philippotto@users.noreply.github.com>

MichaelBuessemeyer added 18 commits May 6, 2025 15:36

wip: enable rotation for ortho views

0d4925c

fix shader

d53dfdc

WIP: make planes and cameras rotate accordingly

53fe573

fix base rotation of xy viewport

a0effba

fix rotation of xz and yz viewports (three js multiplys matrices in p…

4696242

…lace :/)

little cleanup & WIP fixing rendering issues

1a98739

WIP fixing plane scaling

e9a91ca

try to fix plane scale

4d46f9c

remove plane wrapping group again

a645251

fix shearing & rotation for datasets with anisotropic scale

df0fdac

clean up scene graph hierarchy

9109d07

small potential speedup avoiding object creation

5eb8f24

remove doublesided material setting for plane as not needed

639e7e6

fix move tool in arbitrary orientation

1d5d499

fix line measurement tool location & rendering

d6557d8

fix f-ing through dataset

a3ffdba

disable unsupported tools when rotated in first version

4f5967c

fix new node rotation value calculation

9870d2e

MichaelBuessemeyer self-assigned this May 12, 2025

MichaelBuessemeyer added frontend new feature rendering labels May 12, 2025

MichaelBuessemeyer closed this May 12, 2025

MichaelBuessemeyer reopened this May 12, 2025

MichaelBuessemeyer mentioned this pull request May 12, 2025

WIP allowing rotating ortho views #8595

Closed

6 tasks

MichaelBuessemeyer added 4 commits May 13, 2025 18:32

Merge branch 'master' of github.com:scalableminds/webknossos into ort…

273a58c

…ho-view-rotation-v2

fix rendering correct data by passing position offset to shader and c…

dc5d301

…alculate correct global position in shader

remove unused method

813028f

make abstract tree tab a functional component

c51c6b4

MichaelBuessemeyer added 2 commits July 9, 2025 16:32

add keyboard shortcuts docs

c721989

remove unused import

18a9221

MichaelBuessemeyer commented Jul 9, 2025

View reviewed changes

MichaelBuessemeyer added 5 commits July 10, 2025 17:49

fix distance measurement tooltip to stay active in an anisotropic sca…

ef2b1c0

…led dataset

move flycam accessors spec

719d35f

add tests for calculateMaybeGlobalPos as well as calculating the resu…

06e6cc6

…lt back with calculateInViewportPos

fix imports

3f41568

Merge branch 'master' of github.com:scalableminds/webknossos into ort…

e5f0f91

…ho-view-rotation-v2

MichaelBuessemeyer commented Jul 10, 2025

View reviewed changes

fix proofreading test?

a1ea02c

MichaelBuessemeyer requested a review from philippotto July 11, 2025 10:44

MichaelBuessemeyer added 2 commits July 11, 2025 15:08

edit comment explaining why the outer vertices of the vertex moving o…

c405b65

…ptimization code in the vertex shader are handled correctly

add assertion to proofreading test that tool wasn't incorrectly switched

77c64c2

MichaelBuessemeyer added 5 commits July 11, 2025 16:38

add comment explaining default stored rotation of [0,0,180]

4121bc3

fix zoom to position

01bbc9a

- done by introducing new action translating the flycam absolute without any rotation / zoom etc. interference

Merge branch 'master' of github.com:scalableminds/webknossos into ort…

c0c8966

…ho-view-rotation-v2

remove debugging logging

704a111

add new flycam action to ignored list

5a7b341

MichaelBuessemeyer commented Jul 14, 2025

View reviewed changes

philippotto reviewed Jul 14, 2025

View reviewed changes

frontend/javascripts/viewer/shaders/main_data_shaders.glsl.ts Outdated Show resolved Hide resolved

philippotto approved these changes Jul 14, 2025

View reviewed changes

MichaelBuessemeyer and others added 2 commits July 15, 2025 08:22

Update frontend/javascripts/viewer/shaders/main_data_shaders.glsl.ts

3ecab95

Co-authored-by: Philipp Otto <philippotto@users.noreply.github.com>

Merge branch 'master' into ortho-view-rotation-v2

5682dbb

MichaelBuessemeyer enabled auto-merge (squash) July 15, 2025 07:17

MichaelBuessemeyer merged commit 254d094 into master Jul 15, 2025
5 checks passed

MichaelBuessemeyer deleted the ortho-view-rotation-v2 branch July 15, 2025 07:24

Allow rotating ortho view #8614

Allow rotating ortho view #8614

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MichaelBuessemeyer commented May 12, 2025 • edited Loading Uh oh! There was an error while loading. Please reload this page.

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Documentation about rotation & 3d scene

URL of deployed dev instance (used for testing):

Steps to test:

TODOs:

Issues:

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MichaelBuessemeyer commented Jul 10, 2025

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MichaelBuessemeyer commented Jul 11, 2025

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MichaelBuessemeyer commented Jul 11, 2025

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MichaelBuessemeyer Jul 14, 2025

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MichaelBuessemeyer commented May 12, 2025 •

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philippotto commented Jul 11, 2025 •

edited by MichaelBuessemeyer

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MichaelBuessemeyer Jul 14, 2025 •

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