convert bounding box to mag1

CHANGELOG.unreleased.md

@@ -15,7 +15,7 @@ For upgrade instructions, please check the [migration guide](MIGRATIONS.released
 ### Changed
 
 ### Fixed
-- Fixed that segment statistics were requested in the wrong resolution within the statistics modal. [#7355](https://github.com/scalableminds/webknossos/pull/7355)
+- Fixed that segment statistics were requested in the wrong resolution. [#7355](https://github.com/scalableminds/webknossos/pull/7355)
 
 ### Removed
 

frontend/javascripts/oxalis/model/sagas/volume/helpers.ts

@@ -23,7 +23,7 @@ import DataCube from "oxalis/model/bucket_data_handling/data_cube";
 import { Model } from "oxalis/singletons";
 import VolumeLayer, { VoxelBuffer2D } from "oxalis/model/volumetracing/volumelayer";
 import { enforceActiveVolumeTracing } from "oxalis/model/accessors/volumetracing_accessor";
-import { VolumeTracing } from "oxalis/store";
+import { BoundingBoxObject, VolumeTracing } from "oxalis/store";
 import { getFlooredPosition } from "oxalis/model/accessors/flycam_accessor";
 import { zoomedPositionToZoomedAddress } from "oxalis/model/helpers/position_converter";
 import { ResolutionInfo } from "oxalis/model/helpers/resolution_info";
@@ -58,6 +58,19 @@ export function* getBoundingBoxForViewport(
   return new BoundingBox(currentViewportBounding).intersectedWith(datasetBoundingBox);
 }
 
+export function getBoundingBoxInMag1(boudingBox: BoundingBoxObject, magOfBB: Vector3) {
+  return {
+    topLeft: [
+      boudingBox.topLeft[0] * magOfBB[0],
+      boudingBox.topLeft[1] * magOfBB[1],
+      boudingBox.topLeft[2] * magOfBB[2],
+    ] as Vector3,
+    width: boudingBox.width * magOfBB[0],
+    height: boudingBox.height * magOfBB[1],
+    depth: boudingBox.depth * magOfBB[2],
+  };
+}
+
 export function applyLabeledVoxelMapToAllMissingResolutions(
   inputLabeledVoxelMap: LabeledVoxelsMap,
   labeledZoomStep: number,

frontend/javascripts/oxalis/model/scaleinfo.ts

@@ -3,6 +3,13 @@ export function getBaseVoxel(dataSetScale: Vector3): number {
   // base voxel should be a cube with highest resolution
   return Math.min(...dataSetScale);
 }
+
+export function voxelToNm3(dataSetScale: Vector3, mag: Vector3, volumeInVx: number): number {
+  return (
+    mag[0] * mag[1] * mag[2] * dataSetScale[0] * dataSetScale[1] * dataSetScale[2] * volumeInVx
+  );
+}
+
 export function getBaseVoxelFactors(dataSetScale: Vector3): Vector3 {
   // base voxel should be a cube with highest resolution
   const baseVoxel = getBaseVoxel(dataSetScale);

frontend/javascripts/oxalis/view/context_menu.tsx

@@ -106,6 +106,8 @@ import { getSegmentBoundingBoxes, getSegmentVolumes } from "admin/admin_rest_api
 import { useFetch } from "libs/react_helpers";
 import { AsyncIconButton } from "components/async_clickables";
 import { type AdditionalCoordinate } from "types/api_flow_types";
+import { voxelToNm3 } from "oxalis/model/scaleinfo";
+import { getBoundingBoxInMag1 } from "oxalis/model/sagas/volume/helpers";
 
 type ContextMenuContextValue = React.MutableRefObject<HTMLElement | null> | null;
 export const ContextMenuContext = createContext<ContextMenuContextValue>(null);
@@ -1119,22 +1121,29 @@ function ContextMenuInner(propsWithInputRef: Props) {
         const tracingId = volumeTracing.tracingId;
         const tracingStoreUrl = Store.getState().tracing.tracingStore.url;
         const magInfo = getResolutionInfo(visibleSegmentationLayer.resolutions);
+        const layersFinestResolution = magInfo.getFinestResolution();
+        const dataSetScale = Store.getState().dataset.dataSource.scale;
         const [segmentSize] = await getSegmentVolumes(
           tracingStoreUrl,
           tracingId,
-          magInfo.getFinestResolution(),
+          layersFinestResolution,
           [segmentIdAtPosition],
         );
-        const [boundingBox] = await getSegmentBoundingBoxes(
+        const [boundingBoxInRequestedMag] = await getSegmentBoundingBoxes(
           tracingStoreUrl,
           tracingId,
-          magInfo.getFinestResolution(),
+          layersFinestResolution,
           [segmentIdAtPosition],
         );
-        const boundingBoxTopLeftString = `(${boundingBox.topLeft[0]}, ${boundingBox.topLeft[1]}, ${boundingBox.topLeft[2]})`;
-        const boundingBoxSizeString = `(${boundingBox.width}, ${boundingBox.height}, ${boundingBox.depth})`;
+        const boundingBoxInMag1 = getBoundingBoxInMag1(
+          boundingBoxInRequestedMag,
+          layersFinestResolution,
+        );
+        const boundingBoxTopLeftString = `(${boundingBoxInMag1.topLeft[0]}, ${boundingBoxInMag1.topLeft[1]}, ${boundingBoxInMag1.topLeft[2]})`;
+        const boundingBoxSizeString = `(${boundingBoxInMag1.width}, ${boundingBoxInMag1.height}, ${boundingBoxInMag1.depth})`;
+        const volumeInNm3 = voxelToNm3(dataSetScale, layersFinestResolution, segmentSize);
         return [
-          formatNumberToVolume(segmentSize),
+          formatNumberToVolume(volumeInNm3),
           `${boundingBoxTopLeftString}, ${boundingBoxSizeString}`,
         ];
       }

frontend/javascripts/oxalis/view/right-border-tabs/segments_tab/segment_statistics_modal.tsx

@@ -10,7 +10,8 @@ import React from "react";
 import { SegmentHierarchyNode, SegmentHierarchyGroup } from "./segments_view_helper";
 import { Store, api } from "oxalis/singletons";
 import { APISegmentationLayer } from "types/api_flow_types";
-import { getBaseVoxel } from "oxalis/model/scaleinfo";
+import { voxelToNm3 } from "oxalis/model/scaleinfo";
+import { getBoundingBoxInMag1 } from "oxalis/model/sagas/volume/helpers";
 
 const SEGMENT_STATISTICS_CSV_HEADER =
   "segmendId,segmentName,groupId,groupName,volumeInVoxel,volumeInNm3,boundingBoxTopLeftPositionX,boundingBoxTopLeftPositionY,boundingBoxTopLeftPositionZ,boundingBoxSizeX,boundingBoxSizeY,boundingBoxSizeZ";
@@ -84,22 +85,23 @@ export function SegmentStatisticsModal({
   parentGroup,
   groupTree,
 }: Props) {
-  const mag = getResolutionInfo(visibleSegmentationLayer.resolutions);
-  const scaleFactor = getBaseVoxel(Store.getState().dataset.dataSource.scale);
+  const magInfo = getResolutionInfo(visibleSegmentationLayer.resolutions);
+  const layersFinestResolution = magInfo.getFinestResolution();
+  const dataSetScale = Store.getState().dataset.dataSource.scale;
   const dataSource = useFetch(
     async () => {
       await api.tracing.save();
       const segmentStatisticsObjects = await Promise.all([
         getSegmentVolumes(
           tracingStoreUrl,
           tracingId,
-          mag.getFinestResolution(),
+          layersFinestResolution,
           segments.map((segment) => segment.id),
         ),
         getSegmentBoundingBoxes(
           tracingStoreUrl,
           tracingId,
-          mag.getFinestResolution(),
+          layersFinestResolution,
           segments.map((segment) => segment.id),
         ),
       ]).then((response) => {
@@ -110,10 +112,18 @@ export function SegmentStatisticsModal({
           // segments in request and their statistics in the response are in the same order
           const currentSegment = segments[i];
           const currentBoundingBox = boundingBoxes[i];
+          const boundingBoxInMag1 = getBoundingBoxInMag1(
+            currentBoundingBox,
+            layersFinestResolution,
+          );
           const currentSegmentSizeInVx = segmentSizes[i];
-          const volumeInNm3 = currentSegmentSizeInVx * scaleFactor;
+          const volumeInNm3 = voxelToNm3(
+            dataSetScale,
+            layersFinestResolution,
+            currentSegmentSizeInVx,
+          );
           const currentGroupId = getGroupIdForSegment(currentSegment);
-          const segmentStatObject = {
+          const segmentStateObject = {
             key: currentSegment.id,
             segmentId: currentSegment.id,
             segmentName:
@@ -123,16 +133,16 @@ export function SegmentStatisticsModal({
             volumeInVoxel: currentSegmentSizeInVx,
             volumeInNm3,
             formattedSize: formatNumberToVolume(volumeInNm3),
-            boundingBoxTopLeft: currentBoundingBox.topLeft,
-            boundingBoxTopLeftAsString: `(${currentBoundingBox.topLeft.join(", ")})`,
+            boundingBoxTopLeft: boundingBoxInMag1.topLeft,
+            boundingBoxTopLeftAsString: `(${boundingBoxInMag1.topLeft.join(", ")})`,
             boundingBoxPosition: [
-              currentBoundingBox.width,
-              currentBoundingBox.height,
-              currentBoundingBox.depth,
+              boundingBoxInMag1.width,
+              boundingBoxInMag1.height,
+              boundingBoxInMag1.depth,
             ] as Vector3,
-            boundingBoxPositionAsString: `(${currentBoundingBox.width}, ${currentBoundingBox.height}, ${currentBoundingBox.depth})`,
+            boundingBoxPositionAsString: `(${boundingBoxInMag1.width}, ${boundingBoxInMag1.height}, ${boundingBoxInMag1.depth})`,
           };
-          statisticsObjects.push(segmentStatObject);
+          statisticsObjects.push(segmentStateObject);
         }
         return statisticsObjects;
       });