Fix flood fill tool for coarse mags #8382
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The 2D flood fill tool did not work properly when flood filling in a mag other than the finest one if the "third-dimension" coordinate was not divisible by the respective mag. This resulted in early-out flood fills only filling a single voxel. Also, this commit adjusts the flood fill maximum bounding size limits if the segmentation layer's finest mag is not 1. This allows to use the flood fill tool in coarser mags if the segmentation layer is properly mag-restricted.
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📝 WalkthroughWalkthroughThe pull request updates the flood fill functionality by refining bounding box calculations. In the Changes
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🧹 Nitpick comments (1)
frontend/javascripts/oxalis/model/sagas/volume/floodfill_saga.tsx (1)
44-55: Add safety checks for the fillMode lookup.
If a fillMode key is missing inConstants.FLOOD_FILL_EXTENTS,maximumBoundingBoxMag1could beundefined. Consider adding a fallback or assertion.
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frontend/javascripts/oxalis/model/bucket_data_handling/data_cube.ts(1 hunks)frontend/javascripts/oxalis/model/sagas/volume/floodfill_saga.tsx(6 hunks)
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🔇 Additional comments (5)
frontend/javascripts/oxalis/model/sagas/volume/floodfill_saga.tsx (4)
57-93: Bounding box logic well-structured.
This updated approach correctly clamps the bounding box volume. Ensure the maximum bounding box calculation and volume check work as expected for large-scale data.
95-128: Verify plane slices for 2D bounding box.
When applyingnumberOfSlices, confirm that partial slices or offsets don’t require additional clipping, especially for min/max boundaries.
130-153: Unified bounding box parameter usage looks good.
PassingfinestSegmentationLayerMagstreamlines bounding box calculations across restricted/unrestricted modes.
212-218: Ensure existence of a valid finest magnification.
IfmagInfo.getFinestMag()should always return a valid vector, handle corner cases if no magnifications are loaded. Otherwise, this looks fine.frontend/javascripts/oxalis/model/bucket_data_handling/data_cube.ts (1)
700-719: Check alignment of per-voxel bounding box with global boundaries.
Creating a bounding box in mag1 space is a solid approach for correctly handling coarse-to-fine mapping. The off-by-one formaxis consistent with an exclusive boundary, but keep an eye on partial overlaps if any dimension is fractional or if the bounding box extends beyond dataset limits.
frontend/javascripts/oxalis/model/sagas/volume/floodfill_saga.tsx
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Co-authored-by: Philipp Otto <[email protected]>
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🧹 Nitpick comments (3)
frontend/javascripts/oxalis/model/sagas/volume/floodfill_saga.tsx (3)
44-55: Consider renaming the function to better reflect its return type.The function returns a Vector3 representing the maximum dimensions, not an actual bounding box. A more accurate name would be
getMaximumBoundingBoxDimensionsForFloodFill.-function getMaximumBoundingBoxForFloodFill( +function getMaximumBoundingBoxDimensionsForFloodFill( fillMode: FillMode, finestSegmentationLayerMag: Vector3, ): Vector3 {
72-77: Improve variable naming for clarity.The variable
maxBboxrepresents the maximum dimensions, not an actual bounding box. A more descriptive name would bemaxDimensions.- const maxBbox = yield* call( + const maxDimensions = yield* call( getMaximumBoundingBoxForFloodFill, fillMode, finestSegmentationLayerMag, ); - const maxBboxVolume = Constants.FLOOD_FILL_MULTIPLIER_FOR_BBOX_RESTRICTION * V3.prod(maxBbox); + const maxBboxVolume = Constants.FLOOD_FILL_MULTIPLIER_FOR_BBOX_RESTRICTION * V3.prod(maxDimensions);
101-106: Improve variable naming for consistency.For consistency with the previous suggestions and to better reflect its purpose, rename
maxBoundingBoxtomaxDimensions.- const maxBoundingBox = yield* call( + const maxDimensions = yield* call( getMaximumBoundingBoxForFloodFill, fillMode, finestSegmentationLayerMag, ); - const halfBoundingBoxSize = V3.scale(maxBoundingBox, 0.5); + const halfBoundingBoxSize = V3.scale(maxDimensions, 0.5);
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frontend/javascripts/oxalis/model/sagas/volume/floodfill_saga.tsx(6 hunks)
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🔇 Additional comments (1)
frontend/javascripts/oxalis/model/sagas/volume/floodfill_saga.tsx (1)
212-218: LGTM! The changes correctly handle coarse magnifications.The code now properly handles flood fill at different magnifications by:
- Getting the finest magnification from magInfo
- Using it to scale the bounding box appropriately
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I stumbled upon an unused import and wondered why biome doesn't fail. Turns out the rule was not explicitly enabled and seems to be turned off by default 🤷 Was automatically fixable, though :) |
yes, that rule got lost in a pr which enabled import sorting. i already readded it in my dtype pr. hopefully that one gets merged soon 🙈 |
The 2D flood fill tool did not work properly when flood filling in a mag other than the finest one if the "third-dimension" coordinate was not divisible by the respective mag. This resulted in early-out flood fills only filling a single or a few voxels.
Also, this commit adjusts the flood fill maximum bounding size limits if the segmentation layer's finest mag is not 1. This allows to use the flood fill tool in coarser mags if the segmentation layer is properly mag-restricted.
URL of deployed dev instance (used for testing):
Steps to test:
Issues:
(Please delete unneeded items, merge only when none are left open)