WIP calculate surface area of segments

app/controllers/DatasetController.scala

@@ -339,6 +339,34 @@ class DatasetController @Inject()(userService: UserService,
     } yield Ok(Json.toJson(usersJs))
   }
 
+  // Note that dataSource is also included in the full publicWrites. This
+  def readDataSource(datasetId: ObjectId,
+                     // Optional sharing token allowing access to datasets your team does not normally have access to.")
+                     sharingToken: Option[String]): Action[AnyContent] =
+    sil.UserAwareAction.async { implicit request =>
+      log() {
+        val ctx = URLSharing.fallbackTokenAccessContext(sharingToken)
+        for {
+          dataset <- datasetDAO.findOne(datasetId)(ctx) ?~> notFoundMessage(datasetId.toString) ~> NOT_FOUND
+          organization <- organizationDAO.findOne(dataset._organization)(GlobalAccessContext) ~> NOT_FOUND
+          _ <- Fox.runOptional(request.identity)(user =>
+            datasetLastUsedTimesDAO.updateForDatasetAndUser(dataset._id, user._id))
+          // Access checked above via dataset. In case of shared dataset/annotation, show datastore even if not otherwise accessible
+          dataStore <- datasetService.dataStoreFor(dataset)(GlobalAccessContext)
+          js <- datasetService.publicWrites(dataset, request.identity, Some(organization), Some(dataStore))
+          _ = request.identity.map { user =>
+            analyticsService.track(OpenDatasetEvent(user, dataset))
+            if (dataset.isPublic) {
+              mailchimpClient.tagUser(user, MailchimpTag.HasViewedPublishedDataset)
+            }
+            userDAO.updateLastActivity(user._id)
+          }
+        } yield {
+          Ok(Json.toJson(js))
+        }
+      }
+    }
+
   def read(datasetId: ObjectId,
            // Optional sharing token allowing access to datasets your team does not normally have access to.")
            sharingToken: Option[String]): Action[AnyContent] =

app/controllers/WKRemoteDataStoreController.scala

@@ -296,11 +296,10 @@ class WKRemoteDataStoreController @Inject()(
     Action.async { implicit request =>
       dataStoreService.validateAccess(name, key) { _ =>
         for {
-          dataset <- datasetDAO.findOne(datasetId)(GlobalAccessContext)
+          dataset <- datasetDAO.findOne(datasetId)(GlobalAccessContext) ?~> "dataset.notFound" ~> NOT_FOUND
           dataSource <- datasetService.dataSourceFor(dataset)
         } yield Ok(Json.toJson(dataSource))
       }
-
     }
 
   def updateDataSource(name: String, key: String, datasetId: ObjectId): Action[DataSource] =

app/controllers/WKRemoteTracingStoreController.scala

@@ -161,6 +161,16 @@ class WKRemoteTracingStoreController @Inject()(tracingStoreService: TracingStore
       }
     }
 
+  def getDataSource(name: String, key: String, datasetId: ObjectId): Action[AnyContent] =
+    Action.async { implicit request =>
+      tracingStoreService.validateAccess(name, key) { _ =>
+        for {
+          dataset <- datasetDAO.findOne(datasetId)(GlobalAccessContext) ?~> "dataset.notFound" ~> NOT_FOUND
+          dataSource <- datasetService.dataSourceFor(dataset)
+        } yield Ok(Json.toJson(dataSource))
+      }
+    }
+
   def createTracing(name: String,
                     key: String,
                     annotationId: ObjectId,

conf/messages

@@ -276,6 +276,7 @@ mesh.file.lookup.failed=Failed to look up mesh file “{0}”
 mesh.file.readVersion.failed=Failed to read format version from file “{0}”
 mesh.file.readMappingName.failed=Failed to read mapping name from mesh file “{0}”
 mesh.meshFileName.required=Trying to load mesh from mesh file, but mesh file name was not supplied.
+mesh.loadFull.failed=Failed to load full segment mesh.
 
 segmentIndexFile.notFound=Could not find requested segment index file
 

conf/webknossos.latest.routes

@@ -103,12 +103,12 @@ GET           /datasets/:datasetId/layers/:layer/thumbnail
 POST          /datasets/:datasetId/layers/:layer/segmentAnythingMask                            controllers.DatasetController.segmentAnythingMask(datasetId: ObjectId, layer: String, intensityMin: Option[Float], intensityMax: Option[Float])
 PUT           /datasets/:datasetId/clearThumbnailCache                                          controllers.DatasetController.removeFromThumbnailCache(datasetId: ObjectId)
 GET           /datasets/:datasetName/isValidNewName                                             controllers.DatasetController.isValidNewName(datasetName: String)
-GET           /datasets/:datasetId                                                              controllers.DatasetController.read(datasetId: ObjectId, sharingToken: Option[String])
 DELETE        /datasets/:datasetId/deleteOnDisk                                                 controllers.DatasetController.deleteOnDisk(datasetId: ObjectId)
 POST          /datasets/:datasetId/reserveAttachmentUploadToPath                                controllers.DatasetController.reserveAttachmentUploadToPath(datasetId: ObjectId)
 POST          /datasets/:datasetId/finishAttachmentUploadToPath                                 controllers.DatasetController.finishAttachmentUploadToPath(datasetId: ObjectId)
 POST          /datasets/:datasetId/reserveUploadToPathsForPreliminary                           controllers.DatasetController.reserveUploadToPathsForPreliminary(datasetId: ObjectId)
 POST          /datasets/:datasetId/finishUploadToPaths                                          controllers.DatasetController.finishUploadToPaths(datasetId: ObjectId)
+GET           /datasets/:datasetId                                                              controllers.DatasetController.read(datasetId: ObjectId, sharingToken: Option[String])
 POST          /datasets/compose                                                                 controllers.DatasetController.compose()
 POST          /datasets/reserveUploadToPaths                                                    controllers.DatasetController.reserveUploadToPaths()
 
@@ -152,6 +152,7 @@ GET           /tracingstores/:name/datasetId
 GET           /tracingstores/:name/annotationId                                                 controllers.WKRemoteTracingStoreController.annotationIdForTracing(name: String, key: String, tracingId: String)
 GET           /tracingstores/:name/dataStoreUri/:datasetId                                      controllers.WKRemoteTracingStoreController.dataStoreUriForDataset(name: String, key: String, datasetId: ObjectId)
 POST          /tracingstores/:name/createTracing                                                controllers.WKRemoteTracingStoreController.createTracing(name: String, key: String, annotationId: ObjectId, previousVersion: Long)
+GET           /tracingstores/:name/datasources/:datasetId                                       controllers.WKRemoteTracingStoreController.getDataSource(name: String, key: String, datasetId: ObjectId)
 
 # User access tokens for datastore authentication
 POST          /userToken/generate                                                               controllers.UserTokenController.generateTokenForDataStore()

frontend/javascripts/admin/rest_api.ts

@@ -870,6 +870,48 @@ export function getSegmentVolumes(
   );
 }
 
+type SegmentStatisticsParametersMeshBased = {
+  mag: Vector3;
+  segmentIds: number[];
+  mappingName?: string | null;
+  additionalCoordinates?: AdditionalCoordinate[] | null;
+  meshFileName?: string | null;
+  lod?: number;
+  seedPosition?: Vector3 | null;
+};
+
+export function getSegmentSurfaceArea(
+  //                     tracings/volume/:tracingId/...
+  // data/datasets/:datasetId/layers/:dataLayerName/...
+  requestUrl: string,
+  mag: Vector3,
+  lod: number | undefined,
+  seedPosition: Vector3 | undefined | null,
+  meshFileName: string | undefined | null,
+  segmentIds: Array<number>,
+  additionalCoordinates: AdditionalCoordinate[] | undefined | null,
+  mappingName: string | null | undefined,
+): Promise<number[]> {
+  return doWithToken((token) => {
+    const data: SegmentStatisticsParametersMeshBased = {
+      mag,
+      segmentIds,
+      mappingName,
+      additionalCoordinates,
+      lod,
+      meshFileName,
+      seedPosition,
+    };
+    return Request.sendJSONReceiveJSON(
+      `${requestUrl}/segmentStatistics/surfaceArea?token=${token}`,
+      {
+        data,
+        method: "POST",
+      },
+    );
+  });
+}
+
 export function getSegmentBoundingBoxes(
   requestUrl: string,
   mag: Vector3,

frontend/javascripts/libs/format_utils.ts

@@ -293,7 +293,7 @@ export const nmFactorToUnit3D = new Map([
   [1e99, "Ym³"],
 ]);
 
-// Accepts an volume that is interpreted in the given unit and returns a string
+// Accepts a volume that is interpreted in the given unit and returns a string
 // that uses a readable unit to represent the volume.
 // E.g. formatNumberToVolume(0.003, Unit.m) == "3000.0 cm³"
 export function formatNumberToVolume(

frontend/javascripts/viewer/model/accessors/volumetracing_accessor.ts

@@ -947,3 +947,14 @@ export function getReadableNameOfVolumeLayer(
     ? getReadableNameByVolumeTracingId(tracing, layer.tracingId)
     : null;
 }
+
+export function getCurrentMappingName(state: WebknossosState) {
+  const visibleSegmentationLayer = getVisibleSegmentationLayer(state);
+  const volumeTracing = getActiveSegmentationTracing(state);
+  if (volumeTracing?.mappingName != null) return volumeTracing?.mappingName;
+  const mappingInfo = getMappingInfo(
+    state.temporaryConfiguration.activeMappingByLayer,
+    visibleSegmentationLayer?.name,
+  );
+  return mappingInfo.mappingName;
+}

frontend/javascripts/viewer/view/context_menu.tsx

@@ -1,5 +1,5 @@
 import { CopyOutlined, PushpinOutlined, ReloadOutlined, WarningOutlined } from "@ant-design/icons";
-import { getSegmentBoundingBoxes, getSegmentVolumes } from "admin/rest_api";
+import { getSegmentBoundingBoxes, getSegmentSurfaceArea, getSegmentVolumes } from "admin/rest_api";
 import {
   ConfigProvider,
   Dropdown,
@@ -18,7 +18,12 @@ import type {
 } from "antd/es/menu/interface";
 import { AsyncIconButton } from "components/async_clickables";
 import FastTooltip from "components/fast_tooltip";
-import { formatLengthAsVx, formatNumberToLength, formatNumberToVolume } from "libs/format_utils";
+import {
+  formatLengthAsVx,
+  formatNumberToArea,
+  formatNumberToLength,
+  formatNumberToVolume,
+} from "libs/format_utils";
 import { V3 } from "libs/mjs";
 import { useFetch } from "libs/react_helpers";
 import { useWkSelector } from "libs/react_hooks";
@@ -75,6 +80,7 @@ import { maybeGetSomeTracing } from "viewer/model/accessors/tracing_accessor";
 import {
   getActiveCellId,
   getActiveSegmentationTracing,
+  getCurrentMappingName,
   getSegmentsForLayer,
   hasAgglomerateMapping,
   hasConnectomeFile,
@@ -1396,7 +1402,7 @@ function getNoNodeContextMenuOptions(props: NoNodeContextMenuProps): ItemType[]
       ? [
           // Segment 0 cannot/shouldn't be made active (as this
           // would be an eraser effectively).
-          segmentIdAtPosition > 0 && !disabledVolumeInfo.PICK_CELL.isDisabled
+          segmentIdAtPosition !== 0 && !disabledVolumeInfo.PICK_CELL.isDisabled
             ? {
                 key: "select-cell",
                 onClick: () => {
@@ -1415,9 +1421,9 @@ function getNoNodeContextMenuOptions(props: NoNodeContextMenuProps): ItemType[]
                 ),
               }
             : null,
-          segmentIdAtPosition > 0 ? onlyShowThisSegmentItem : null,
-          segmentIdAtPosition > 0 ? toggleSegmentVisibilityItem : null,
-          segmentIdAtPosition > 0 ? showAllSegmentsItem : null,
+          segmentIdAtPosition !== 0 ? onlyShowThisSegmentItem : null,
+          segmentIdAtPosition !== 0 ? toggleSegmentVisibilityItem : null,
+          segmentIdAtPosition !== 0 ? showAllSegmentsItem : null,
           focusInSegmentListItem,
           loadPrecomputedMeshItem,
           computeMeshAdHocItem,
@@ -1672,17 +1678,10 @@ function ContextMenuInner() {
     dataset,
     visibleSegmentationLayer?.name,
   );
-  const mappingName: string | null | undefined = useWkSelector((state) => {
-    if (volumeTracing?.mappingName != null) return volumeTracing?.mappingName;
-    const mappingInfo = getMappingInfo(
-      state.temporaryConfiguration.activeMappingByLayer,
-      visibleSegmentationLayer?.name,
-    );
-    return mappingInfo.mappingName;
-  });
+  const mappingName: string | null | undefined = useWkSelector(getCurrentMappingName);
   const isLoadingMessage = "loading";
   const isLoadingVolumeAndBB = [isLoadingMessage, isLoadingMessage];
-  const [segmentVolumeLabel, boundingBoxInfoLabel] = useFetch(
+  const [segmentVolumeLabel, boundingBoxInfoLabel, segmentSurfaceAreaLabel] = useFetch(
     async () => {
       const { annotation, flycam } = Store.getState();
       // The value that is returned if the context menu is closed is shown if it's still loading
@@ -1715,13 +1714,25 @@ function ContextMenuInner() {
           additionalCoordinates,
           mappingName,
         );
+        const lod = 0; // todop
+        const [surfaceArea] = await getSegmentSurfaceArea(
+          requestUrl,
+          layersFinestMag,
+          lod,
+          globalPosition,
+          currentMeshFile?.name,
+          [clickedSegmentOrMeshId],
+          additionalCoordinates,
+          mappingName,
+        );
         const boundingBoxInMag1 = getBoundingBoxInMag1(boundingBoxInRequestedMag, layersFinestMag);
         const boundingBoxTopLeftString = `(${boundingBoxInMag1.topLeft[0]}, ${boundingBoxInMag1.topLeft[1]}, ${boundingBoxInMag1.topLeft[2]})`;
         const boundingBoxSizeString = `(${boundingBoxInMag1.width}, ${boundingBoxInMag1.height}, ${boundingBoxInMag1.depth})`;
         const volumeInUnit3 = voxelToVolumeInUnit(voxelSize, layersFinestMag, segmentSize);
         return [
           formatNumberToVolume(volumeInUnit3, LongUnitToShortUnitMap[voxelSize.unit]),
           `${boundingBoxTopLeftString}, ${boundingBoxSizeString}`,
+          formatNumberToArea(surfaceArea, LongUnitToShortUnitMap[voxelSize.unit]),
         ];
       } catch (_error) {
         const notFetchedMessage = "could not be fetched";
@@ -1797,7 +1808,7 @@ function ContextMenuInner() {
       getInfoMenuItem(
         "positionInfo",
         <>
-          <PushpinOutlined style={{ transform: "rotate(-45deg)" }} /> Position:{" "}
+          <PushpinOutlined style={{ transform: "rotate(-45deg)", marginInlineEnd: 5 }} /> Position:{" "}
           {nodePositionAsString}
           {copyIconWithTooltip(nodePositionAsString, "Copy node position")}
         </>,
@@ -1810,7 +1821,8 @@ function ContextMenuInner() {
       getInfoMenuItem(
         "positionInfo",
         <>
-          <PushpinOutlined style={{ transform: "rotate(-45deg)" }} /> Position: {positionAsString}
+          <PushpinOutlined style={{ transform: "rotate(-45deg)", marginInlineEnd: 5 }} /> Position:{" "}
+          {positionAsString}
           {copyIconWithTooltip(positionAsString, "Copy position")}
         </>,
       ),
@@ -1847,9 +1859,19 @@ function ContextMenuInner() {
         </>,
       ),
     );
-  }
 
-  if (areSegmentStatisticsAvailable) {
+    infoRows.push(
+      getInfoMenuItem(
+        "volumeInfo",
+        <>
+          <i className="fas fa-expand-alt segment-context-icon" />
+          Surface Area: {segmentSurfaceAreaLabel}
+          {copyIconWithTooltip(segmentSurfaceAreaLabel as string, "Copy surface area")}
+          {refreshButton}
+        </>,
+      ),
+    );
+
     infoRows.push(
       getInfoMenuItem(
         "boundingBoxPositionInfo",

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

@@ -1,4 +1,4 @@
-import { getSegmentBoundingBoxes, getSegmentVolumes } from "admin/rest_api";
+import { getSegmentBoundingBoxes, getSegmentSurfaceArea, getSegmentVolumes } from "admin/rest_api";
 import { Alert, Modal, Spin, Table } from "antd";
 import { formatNumberToVolume } from "libs/format_utils";
 import { useFetch } from "libs/react_helpers";
@@ -11,7 +11,10 @@ import {
   getAdditionalCoordinatesAsString,
   hasAdditionalCoordinates,
 } from "viewer/model/accessors/flycam_accessor";
-import { getVolumeTracingById } from "viewer/model/accessors/volumetracing_accessor";
+import {
+  getCurrentMappingName,
+  getVolumeTracingById,
+} from "viewer/model/accessors/volumetracing_accessor";
 import { saveAsCSV, transformToCSVRow } from "viewer/model/helpers/csv_helpers";
 import { getBoundingBoxInMag1 } from "viewer/model/sagas/volume/helpers";
 import { voxelToVolumeInUnit } from "viewer/model/scaleinfo";
@@ -116,6 +119,13 @@ export function SegmentStatisticsModal({
     additionalCoordinates,
     ", ",
   );
+  const currentMeshFile = useWkSelector((state) =>
+    visibleSegmentationLayer != null
+      ? state.localSegmentationData[visibleSegmentationLayer.name].currentMeshFile
+      : null,
+  );
+  const mappingName: string | null | undefined = useWkSelector(getCurrentMappingName);
+
   const segmentStatisticsObjects = useFetch(
     async () => {
       await api.tracing.save();
@@ -130,21 +140,33 @@ export function SegmentStatisticsModal({
         );
         return mappingInfo.mappingName;
       };
+      const lod = 0; // todop;
+      const segmentIds = segments.map((segment) => segment.id);
       const segmentStatisticsObjects = await Promise.all([
         getSegmentVolumes(
           requestUrl,
           layersFinestMag,
-          segments.map((segment) => segment.id),
+          segmentIds,
           additionalCoordinates,
           maybeGetMappingName(),
         ),
         getSegmentBoundingBoxes(
           requestUrl,
           layersFinestMag,
-          segments.map((segment) => segment.id),
+          segmentIds,
           additionalCoordinates,
           maybeGetMappingName(),
         ),
+        getSegmentSurfaceArea(
+          requestUrl,
+          layersFinestMag,
+          lod,
+          null,
+          currentMeshFile?.name,
+          segmentIds,
+          additionalCoordinates,
+          mappingName,
+        ),
       ]).then(
         (response) => {
           const segmentSizes = response[0];

webknossos-datastore/app/com/scalableminds/webknossos/datastore/controllers/DSMeshController.scala

@@ -95,4 +95,5 @@ class DSMeshController @Inject()(
         } yield Ok(data)
       }
     }
+
 }