Fix flood fill tool for coarse mags

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,

frontend/javascripts/oxalis/view/action-bar/toolbar_view.tsx

@@ -26,7 +26,6 @@ import { document } from "libs/window";
 import {
   type AnnotationTool,
   AnnotationToolEnum,
-  ControlModeEnum,
   FillModeEnum,
   type InterpolationMode,
   InterpolationModeEnum,

frontend/javascripts/types/schemas/dataset_view_configuration_defaults.ts

@@ -1,6 +1,6 @@
 import _ from "lodash";
 import { getDefaultValueRangeOfLayer, isColorLayer } from "oxalis/model/accessors/dataset_accessor";
-import type { APIDataLayer, APIDataset, APIMaybeUnimportedDataset } from "types/api_flow_types";
+import type { APIDataset, APIMaybeUnimportedDataset } from "types/api_flow_types";
 import {
   defaultDatasetViewConfiguration,
   getDefaultLayerViewConfiguration,