Allow permanent dataset layer rotation in dataset settings

[MichaelBuessemeyer]

This PR adds new settings to the dataset settings for each layer. A interface (still in design process) enables the user to set a affine transformation matrix by letting the user define angles for each axis around which the dataset should be rotated.

• https://___.webknossos.xyz

Steps to test:

• abc

TODOs / Problems:

• [ ] Design a visualization of the result. For some first ideas look at the issue #7334
• [ ] The rotation should be done around the center of the dataset. For this, a translation by the dataset center is needed
• [ ] The interface works by defining Euler angles. The problem is that Euler angles are not deterministic / there are multiple ways to express a certain rotation with different Euler angle values. See: https://stackoverflow.com/questions/32235395/does-euler-angles-quaternion-euler-angles-always-result-in-an-equivalent-r
  • This makes it hard to update the settings correctly -> a 180 degree rotation around y is equivalent to 180 on x and 180 on z axis :/
  • A solution for this is needed as the interface currently is pretty quirky.
• [ ]

Issues:

• fixes #7334

---

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

• [ ] Updated changelog
• [ ] Updated migration guide if applicable
• [ ] Updated documentation if applicable
• [ ] Adapted wk-libs python client if relevant API parts change
• [ ] Removed dev-only changes like prints and application.conf edits
• [ ] Considered common edge cases
• [ ] Needs datastore update after deployment

[coderabbitai[bot]]

📝 Walkthrough

Walkthrough

This pull request introduces comprehensive changes to dataset layer transformations across multiple frontend files. The modifications focus on enhancing dataset rotation capabilities, reorganizing transformation-related functions, and improving the user interface for layer transformations. Key changes include creating a new dataset_layer_transformation_accessor.ts module, updating type definitions, and implementing rotation controls for dataset layers.

Changes

File	Change Summary
frontend/javascripts/oxalis/model/accessors/dataset_layer_transformation_accessor.ts	New module created with comprehensive transformation handling functions.
frontend/javascripts/dashboard/dataset/dataset_rotation_form_item.tsx	Added components for managing dataset rotation along x, y, z axes.
frontend/javascripts/dashboard/dataset/dataset_settings_data_tab.tsx	Integrated axis rotation settings component.
frontend/javascripts/oxalis/model/accessors/dataset_accessor.ts	Removed functions related to coordinate transformations.
Multiple files	Relocated transformation-related imports from dataset_accessor to new transformation accessor module.

Assessment against linked issues

Objective	Addressed	Explanation
Rotate dataset layers (7334)	✅
Persist rotation (7334)	✅
Handle skeleton layer transformations (7334)	✅

Possibly related PRs

• #8176: The main PR modifies the import of flatToNestedMatrix from dataset_accessor to dataset_layer_transformation_accessor, which is also addressed in this PR that fixes a performance bottleneck related to tree deletions, indicating a shared focus on the dataset layer transformation functionality.
• #8231: This PR includes fixes for performance issues when deleting multiple trees, which relates to the overall dataset management and transformation processes, similar to the changes made in the main PR regarding dataset handling.
• #8311: The main PR's changes to dataset transformations align with this PR's focus on supporting translations in OME-NGFF Zarr datasets, indicating a broader context of enhancing dataset transformation capabilities across multiple PRs.

Suggested labels

usability, bug, documentation

Poem

🐰 Rotation's dance, a matrix's grace,
Layers twirl in digital space
Transforms align with pixel's might
Bringing datasets to new height!
Code rabbits spin their magic wheel 🌀

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[philippotto]

@philippotto This PR is ready for the first review round. To you have time to take on this task or should I ask daniel?

Yes, I can review it :)

[MichaelBuessemeyer]

@philippotto my newest changes should implement discussed changes and also fix the new position calculation after toggling which layer is rendered natively. Please have another look at my changes :pray:

[MichaelBuessemeyer]

From slack: https://scm.slack.com/archives/C5AKLAV0B/p1736434462796459

i just tested the rotation feature a bit and i noticed that e.g. the hovering of segment ids does not work if the segmentation layer is rotated. this was probably already broken independently of your PR (but i didn't notice it because the previous feature was not used in this context). you would probably have to consider the rotation matrix when looking up from mouse position to voxel position

Should be fixed now with commit 3f1bdb9e03063274f06824126c4a0f313e7c9bf9

[philippotto]

From slack: https://scm.slack.com/archives/C5AKLAV0B/p1736434462796459

i just tested the rotation feature a bit and i noticed that e.g. the hovering of segment ids does not work if the segmentation layer is rotated. this was probably already broken independently of your PR (but i didn't notice it because the previous feature was not used in this context). you would probably have to consider the rotation matrix when looking up from mouse position to voxel position

Should be fixed now with commit 3f1bdb9

Hmm, still doesn't work for me? I tested it here: https://allowpermadatasetrotation.webknossos.xyz/datasets/l4_sample-677e47bc010000b800249ffc/view#3584,3584,1024,0,1.3

[MichaelBuessemeyer]

Hmm, still doesn't work for me? I tested it here: https://allowpermadatasetrotation.webknossos.xyz/datasets/l4_sample-677e47bc010000b800249ffc/view#3584,3584,1024,0,1.3

Oh well. Thanks for finding this. I still had a little logic bug (I applied the segmentation layer's transform instead of the inverse of the transform). The newest commit 3c06db5 should fix this. :tm:

Testing for me worked because I only had a 180 degree rotation for x configured and in that case applying the same rotation again instead of the inverse seems to result in the correct behaviour. As your test case was more complex and it worked for me locally with these settings, this should hopefully be fixed now :)

[philippotto]

Great! Unfortunately, the context menu uses the wrong position apparently (e.g., load mesh or the segment id in the context menu footer is wrong). Can you have another look? :see_no_evil:

[MichaelBuessemeyer]

While working on this I also noticed that bounding boxes are not rotated :see_no_evil:? Should this be included here as well or in a follow up pr?

[MichaelBuessemeyer]

Same for meshes :see_no_evil:

[philippotto]

Bummer! The layer bboxes are able to transform according to the active layer transform. user bounding boxes probably need to use the same transforms as the skeleton layer. meshes should use the same transforms as their segmentation layer. however, I would suggest to do this later as a follow-up pr, as you have other stuff on our plate, too. can you open an issue? :)

[MichaelBuessemeyer]

The issue is here: https://github.com/scalableminds/webknossos/issues/8340

And I found a but that toggling the skeleton layer crashed wk. I fixed this by disabling toggling skeleton layer / letting the user configure them as the active native layer. The mini discussion about this can be found here: https://scm.slack.com/archives/C083DBRCFC6/p1737378159151899

[MichaelBuessemeyer]

Moreover, the newest commits should hopefully fix all code locations that try to get the segmentation information based on a global position.

Please give this another PR testing try and check my newest changes :pray:

I am sorry, that this PR takes so many iterations.