Fix flood fill tool for coarse mags (#8382)

* Fix flood fill tool for coarse mags.

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.

* update changelog

* Update frontend/javascripts/oxalis/model/sagas/volume/floodfill_saga.tsx

Co-authored-by: Philipp Otto <[email protected]>

* Apply naming feedback

* Add linting rule for unused imports and fix 10 occurrences

* Fix 3 new unused imports after master merge

---------

Co-authored-by: Philipp Otto <[email protected]>

Author: daniel-wer

CHANGELOG.unreleased.md

@@ -20,11 +20,13 @@ For upgrade instructions, please check the [migration guide](MIGRATIONS.released
 
 ### Changed
 - Improved the scrolling behaviour of sliders: Sliders must be focused to scroll them. Additionally, parent element scrolling is prevented when using the slider. [#8321](https://github.com/scalableminds/webknossos/pull/8321) [#8321](https://github.com/scalableminds/webknossos/pull/8321)
+- Increase the flood fill maximum bounding box size limits for segmentation layers restricted to coarser mags. [#8382](https://github.com/scalableminds/webknossos/pull/8382)
 
 ### Fixed
 - Fixed a bug that lead to trees being dropped when merging to trees together. [#8359](https://github.com/scalableminds/webknossos/pull/8359)
 - Fixed that the onboarding screen incorrectly appeared when a certain request failed. [#8356](https://github.com/scalableminds/webknossos/pull/8356)
 - Fixed the segment registering in coarser mags for non-mag-aligned bounding boxes. [#8364](https://github.com/scalableminds/webknossos/pull/8364)
+- Fixed using the flood fill tool in 2D mode for mags other than the finest one. [#8382](https://github.com/scalableminds/webknossos/pull/8382)
 
 ### Removed
  - Removed the feature to downsample existing volume annotations. All new volume annotations had a whole mag stack since [#4755](https://github.com/scalableminds/webknossos/pull/4755) (four years ago). [#7917](https://github.com/scalableminds/webknossos/pull/7917)

biome.json

@@ -64,6 +64,7 @@
       },
       "correctness": {
         "noUnusedVariables": "error",
+        "noUnusedImports": "error",
         "noRenderReturnValue": "off",
         "useHookAtTopLevel": "error"
       },

frontend/javascripts/components/slider.tsx

@@ -1,8 +1,7 @@
 import { Slider as AntdSlider, type SliderSingleProps } from "antd";
 import type { SliderRangeProps } from "antd/lib/slider";
 import { clamp } from "libs/utils";
-import _ from "lodash";
-import { useCallback, useEffect, useRef, useState } from "react";
+import { useCallback, useEffect, useRef } from "react";
 
 const DEFAULT_WHEEL_FACTOR = 0.02;
 const DEFAULT_STEP = 1;

frontend/javascripts/oxalis/model.ts

@@ -20,7 +20,6 @@ import Store from "oxalis/store";
 import type { APICompoundType } from "types/api_flow_types";
 
 import { globalToLayerTransformedPosition } from "./model/accessors/dataset_layer_transformation_accessor";
-import { invertTransform, transformPointUnscaled } from "./model/helpers/transformation_helpers";
 import { initialize } from "./model_initialization";
 
 // TODO: Non-reactive

frontend/javascripts/oxalis/model/bucket_data_handling/data_cube.ts

@@ -696,22 +696,27 @@ class DataCube {
               currentGlobalBucketPosition,
               V3.scale3(adjustedNeighbourVoxelXyz, currentMag),
             );
+            // When flood filling in a coarser mag, a voxel in the coarse mag is more than one voxel in mag 1
+            const voxelBoundingBoxInMag1 = new BoundingBox({
+              min: currentGlobalPosition,
+              max: V3.add(currentGlobalPosition, currentMag),
+            });
 
             if (bucketData[neighbourVoxelIndex] === sourceSegmentId) {
-              if (floodfillBoundingBox.containsPoint(currentGlobalPosition)) {
+              if (floodfillBoundingBox.intersectedWith(voxelBoundingBoxInMag1).getVolume() > 0) {
                 bucketData[neighbourVoxelIndex] = segmentId;
                 markUvwInSliceAsLabeled(neighbourVoxelUvw);
                 neighbourVoxelStackUvw.pushVoxel(neighbourVoxelUvw);
                 labeledVoxelCount++;
 
-                coveredBBoxMin[0] = Math.min(coveredBBoxMin[0], currentGlobalPosition[0]);
-                coveredBBoxMin[1] = Math.min(coveredBBoxMin[1], currentGlobalPosition[1]);
-                coveredBBoxMin[2] = Math.min(coveredBBoxMin[2], currentGlobalPosition[2]);
+                coveredBBoxMin[0] = Math.min(coveredBBoxMin[0], voxelBoundingBoxInMag1.min[0]);
+                coveredBBoxMin[1] = Math.min(coveredBBoxMin[1], voxelBoundingBoxInMag1.min[1]);
+                coveredBBoxMin[2] = Math.min(coveredBBoxMin[2], voxelBoundingBoxInMag1.min[2]);
 
                 // The maximum is exclusive which is why we add 1 to the position
-                coveredBBoxMax[0] = Math.max(coveredBBoxMax[0], currentGlobalPosition[0] + 1);
-                coveredBBoxMax[1] = Math.max(coveredBBoxMax[1], currentGlobalPosition[1] + 1);
-                coveredBBoxMax[2] = Math.max(coveredBBoxMax[2], currentGlobalPosition[2] + 1);
+                coveredBBoxMax[0] = Math.max(coveredBBoxMax[0], voxelBoundingBoxInMag1.max[0] + 1);
+                coveredBBoxMax[1] = Math.max(coveredBBoxMax[1], voxelBoundingBoxInMag1.max[1] + 1);
+                coveredBBoxMax[2] = Math.max(coveredBBoxMax[2], voxelBoundingBoxInMag1.max[2] + 1);
 
                 if (labeledVoxelCount % 1000000 === 0) {
                   console.log(`Labeled ${labeledVoxelCount} Vx. Continuing...`);

frontend/javascripts/oxalis/model/reducers/skeletontracing_reducer.ts

@@ -10,7 +10,6 @@ import {
   getNodeAndTree,
   getSkeletonTracing,
   getTree,
-  getTreesWithType,
   isSkeletonLayerTransformed,
 } from "oxalis/model/accessors/skeletontracing_accessor";
 import type { Action } from "oxalis/model/actions/actions";

frontend/javascripts/oxalis/model/reducers/ui_reducer.ts

@@ -1,4 +1,4 @@
-import { AnnotationToolEnum, AvailableToolsInViewMode, ControlModeEnum } from "oxalis/constants";
+import { AnnotationToolEnum, AvailableToolsInViewMode } from "oxalis/constants";
 import type { Action } from "oxalis/model/actions/actions";
 import { updateKey, updateKey2 } from "oxalis/model/helpers/deep_update";
 import {

frontend/javascripts/oxalis/model/sagas/proofread_saga.ts

@@ -66,7 +66,7 @@ import {
   updateSegmentAction,
 } from "oxalis/model/actions/volumetracing_actions";
 import type { Saga } from "oxalis/model/sagas/effect-generators";
-import { select, take } from "oxalis/model/sagas/effect-generators";
+import { select } from "oxalis/model/sagas/effect-generators";
 import {
   type UpdateActionWithoutIsolationRequirement,
   mergeAgglomerate,

frontend/javascripts/oxalis/model/sagas/saga_helpers.ts

@@ -1,4 +1,4 @@
-import type { ActionPattern, Predicate } from "@redux-saga/types";
+import type { ActionPattern } from "@redux-saga/types";
 import { Modal } from "antd";
 import Toast from "libs/toast";
 import messages from "messages";

frontend/javascripts/oxalis/model/sagas/volume/floodfill_saga.tsx

@@ -27,7 +27,7 @@ import {
 import BoundingBox from "oxalis/model/bucket_data_handling/bounding_box";
 import Dimensions from "oxalis/model/dimensions";
 import type { Saga } from "oxalis/model/sagas/effect-generators";
-import { select, take } from "oxalis/model/sagas/effect-generators";
+import { select } from "oxalis/model/sagas/effect-generators";
 import { requestBucketModificationInVolumeTracing } from "oxalis/model/sagas/saga_helpers";
 import { Model } from "oxalis/singletons";
 import { call, put, takeEvery } from "typed-redux-saga";
@@ -41,7 +41,24 @@ export function* floodFill(): Saga<void> {
   yield* takeEvery("FLOOD_FILL", handleFloodFill);
 }
 
-function* getBoundingBoxForFloodFillWhenRestricted(position: Vector3, currentViewport: OrthoView) {
+function getMaximumBoundingBoxSizeForFloodfill(
+  fillMode: FillMode,
+  finestSegmentationLayerMag: Vector3,
+): Vector3 {
+  const maximumBoundingBoxMag1 = Constants.FLOOD_FILL_EXTENTS[fillMode];
+  // If the finest mag of the segmentation layer is not Mag(1), the maximum bounding box needs to be scaled accordingly
+  const maximumBoundingBoxInFinestMag = V3.scale3(
+    maximumBoundingBoxMag1,
+    finestSegmentationLayerMag,
+  );
+  return maximumBoundingBoxInFinestMag;
+}
+
+function* getBoundingBoxForFloodFillWhenRestricted(
+  position: Vector3,
+  currentViewport: OrthoView,
+  finestSegmentationLayerMag: Vector3,
+) {
   const fillMode = yield* select((state) => state.userConfiguration.fillMode);
   const bboxes = yield* select((state) => getUserBoundingBoxesThatContainPosition(state, position));
   if (bboxes.length === 0) {
@@ -52,9 +69,12 @@ function* getBoundingBoxForFloodFillWhenRestricted(position: Vector3, currentVie
   }
   const smallestBbox = _.sortBy(bboxes, (bbox) => new BoundingBox(bbox.boundingBox).getVolume())[0];
 
-  const maximumVoxelSize =
-    Constants.FLOOD_FILL_MULTIPLIER_FOR_BBOX_RESTRICTION *
-    V3.prod(Constants.FLOOD_FILL_EXTENTS[fillMode]);
+  const maxBboxSize = yield* call(
+    getMaximumBoundingBoxSizeForFloodfill,
+    fillMode,
+    finestSegmentationLayerMag,
+  );
+  const maxBboxVolume = Constants.FLOOD_FILL_MULTIPLIER_FOR_BBOX_RESTRICTION * V3.prod(maxBboxSize);
   const bboxObj = new BoundingBox(smallestBbox.boundingBox);
 
   const bboxVolume =
@@ -64,9 +84,9 @@ function* getBoundingBoxForFloodFillWhenRestricted(position: Vector3, currentVie
         V2.prod(
           Dimensions.getIndices(currentViewport).map((idx) => bboxObj.getSize()[idx]) as Vector2,
         );
-  if (bboxVolume > maximumVoxelSize) {
+  if (bboxVolume > maxBboxVolume) {
     return {
-      failureReason: `The bounding box that encloses the clicked position is too large. Shrink its size so that it does not contain more than ${maximumVoxelSize} voxels.`,
+      failureReason: `The bounding box that encloses the clicked position is too large, containing ${bboxVolume} voxels. Shrink its size so that it does not contain more than ${maxBboxVolume} voxels.`,
     };
   }
   return smallestBbox.boundingBox;
@@ -75,18 +95,24 @@ function* getBoundingBoxForFloodFillWhenRestricted(position: Vector3, currentVie
 function* getBoundingBoxForFloodFillWhenUnrestricted(
   position: Vector3,
   currentViewport: OrthoView,
+  finestSegmentationLayerMag: Vector3,
 ) {
   const fillMode = yield* select((state) => state.userConfiguration.fillMode);
-  const halfBoundingBoxSizeUVW = V3.scale(Constants.FLOOD_FILL_EXTENTS[fillMode], 0.5);
+  const maxBoundingBoxSize = yield* call(
+    getMaximumBoundingBoxSizeForFloodfill,
+    fillMode,
+    finestSegmentationLayerMag,
+  );
+  const halfBoundingBoxSize = V3.scale(maxBoundingBoxSize, 0.5);
   const currentViewportBounding = {
-    min: V3.sub(position, halfBoundingBoxSizeUVW),
-    max: V3.add(position, halfBoundingBoxSizeUVW),
+    min: V3.sub(position, halfBoundingBoxSize),
+    max: V3.add(position, halfBoundingBoxSize),
   };
 
   if (fillMode === FillModeEnum._2D) {
     // Only use current plane
     const thirdDimension = Dimensions.thirdDimensionForPlane(currentViewport);
-    const numberOfSlices = 1;
+    const numberOfSlices = finestSegmentationLayerMag[thirdDimension];
     currentViewportBounding.min[thirdDimension] = position[thirdDimension];
     currentViewportBounding.max[thirdDimension] = position[thirdDimension] + numberOfSlices;
   }
@@ -104,14 +130,25 @@ function* getBoundingBoxForFloodFillWhenUnrestricted(
 function* getBoundingBoxForFloodFill(
   position: Vector3,
   currentViewport: OrthoView,
+  finestSegmentationLayerMag: Vector3,
 ): Saga<BoundingBoxType | { failureReason: string }> {
   const isRestrictedToBoundingBox = yield* select(
     (state) => state.userConfiguration.isFloodfillRestrictedToBoundingBox,
   );
   if (isRestrictedToBoundingBox) {
-    return yield* call(getBoundingBoxForFloodFillWhenRestricted, position, currentViewport);
+    return yield* call(
+      getBoundingBoxForFloodFillWhenRestricted,
+      position,
+      currentViewport,
+      finestSegmentationLayerMag,
+    );
   } else {
-    return yield* call(getBoundingBoxForFloodFillWhenUnrestricted, position, currentViewport);
+    return yield* call(
+      getBoundingBoxForFloodFillWhenUnrestricted,
+      position,
+      currentViewport,
+      finestSegmentationLayerMag,
+    );
   }
 }
 
@@ -172,7 +209,13 @@ function* handleFloodFill(floodFillAction: FloodFillAction): Saga<void> {
   if (!isModificationAllowed) {
     return;
   }
-  const boundingBoxForFloodFill = yield* call(getBoundingBoxForFloodFill, seedPosition, planeId);
+  const finestSegmentationLayerMag = magInfo.getFinestMag();
+  const boundingBoxForFloodFill = yield* call(
+    getBoundingBoxForFloodFill,
+    seedPosition,
+    planeId,
+    finestSegmentationLayerMag,
+  );
   if ("failureReason" in boundingBoxForFloodFill) {
     Toast.warning(boundingBoxForFloodFill.failureReason, {
       key: NO_FLOODFILL_BBOX_TOAST_KEY,