Find data for volumes (#4847)

* first version of frontend and backend * update changelog * Merge branch 'master' of github.com:scalableminds/webknossos into find-volume-data * extract find methods into new trait * apply pr feedback
scalableminds · Oct 7, 2020 · bb73244 · bb73244
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diff --git a/CHANGELOG.unreleased.md b/CHANGELOG.unreleased.md
@@ -12,6 +12,7 @@ For upgrade instructions, please check the [migration guide](MIGRATIONS.released
 
 ### Added
 - Hybrid tracings can now be imported directly in the tracing view via drag'n'drop. [#4837](https://github.com/scalableminds/webknossos/pull/4837)
+- The find data function now works for volume tracings, too. [#4847](https://github.com/scalableminds/webknossos/pull/4847)
 
 ### Changed
 - Brush circles are now connected with rectangles to provide a continuous stroke even if the brush is moved quickly. [#4785](https://github.com/scalableminds/webknossos/pull/4822)

diff --git a/frontend/javascripts/admin/admin_rest_api.js b/frontend/javascripts/admin/admin_rest_api.js
@@ -1015,6 +1015,16 @@ export async function findDataPositionForLayer(
   return { position, resolution };
 }
 
+export async function findDataPositionForVolumeTracing(
+  tracingstoreUrl: string,
+  tracingId: string,
+): Promise<{ position: ?Vector3, resolution: ?Vector3 }> {
+  const { position, resolution } = await doWithToken(token =>
+    Request.receiveJSON(`${tracingstoreUrl}/tracings/volume/${tracingId}/findData?token=${token}`),
+  );
+  return { position, resolution };
+}
+
 export async function getHistogramForLayer(
   datastoreUrl: string,
   datasetId: APIDatasetId,

diff --git a/frontend/javascripts/oxalis/view/settings/dataset_settings_view.js b/frontend/javascripts/oxalis/view/settings/dataset_settings_view.js
@@ -20,7 +20,11 @@ import {
   DropdownSetting,
   ColorSetting,
 } from "oxalis/view/settings/setting_input_views";
-import { findDataPositionForLayer, clearCache } from "admin/admin_rest_api";
+import {
+  clearCache,
+  findDataPositionForLayer,
+  findDataPositionForVolumeTracing,
+} from "admin/admin_rest_api";
 import { getGpuFactorsWithLabels } from "oxalis/model/bucket_data_handling/data_rendering_logic";
 import { getMaxZoomValueForResolution } from "oxalis/model/accessors/flycam_accessor";
 import {
@@ -77,18 +81,11 @@ class DatasetSettings extends React.PureComponent<DatasetSettingsProps> {
     let tooltipText = isDisabled
       ? "You cannot search for data when the layer is disabled."
       : "If you are having trouble finding your data, webKnossos can try to find a position which contains data.";
-    // If the tracing contains a volume tracing, the backend can only
-    // search in the fallback layer of the segmentation layer for data.
-    let layerNameToSearchDataIn = layerName;
-    if (!isColorLayer) {
-      const { volume } = Store.getState().tracing;
-      if (volume && volume.fallbackLayer) {
-        layerNameToSearchDataIn = volume.fallbackLayer;
-      } else if (volume && !volume.fallbackLayer && !isDisabled) {
-        isDisabled = true;
-        tooltipText =
-          "You do not have a fallback layer for this segmentation layer. It is only possible to search in fallback layers.";
-      }
+
+    const { volume } = Store.getState().tracing;
+    if (!isColorLayer && volume && volume.fallbackLayer) {
+      tooltipText =
+        "webKnossos will try to find data in your volume tracing first and in the fallback layer afterwards.";
     }
 
     return (
@@ -97,7 +94,7 @@ class DatasetSettings extends React.PureComponent<DatasetSettingsProps> {
           type="scan"
           onClick={
             !isDisabled
-              ? () => this.handleFindData(layerNameToSearchDataIn)
+              ? () => this.handleFindData(layerName, isColorLayer)
               : () => Promise.resolve()
           }
           style={{
@@ -405,14 +402,34 @@ class DatasetSettings extends React.PureComponent<DatasetSettingsProps> {
     this.props.onChangeUser("gpuMemoryFactor", gpuFactor);
   };
 
-  handleFindData = async (layerName: string) => {
+  handleFindData = async (layerName: string, isDataLayer: boolean) => {
+    const { volume, tracingStore } = Store.getState().tracing;
     const { dataset } = this.props;
-    const { position, resolution } = await findDataPositionForLayer(
-      dataset.dataStore.url,
-      dataset,
-      layerName,
-    );
-    if (!position || !resolution) {
+    let foundPosition;
+    let foundResolution;
+
+    if (volume && !isDataLayer) {
+      const { position, resolution } = await findDataPositionForVolumeTracing(
+        tracingStore.url,
+        volume.tracingId,
+      );
+      if ((!position || !resolution) && volume.fallbackLayer) {
+        await this.handleFindData(volume.fallbackLayer, true);
+        return;
+      }
+      foundPosition = position;
+      foundResolution = resolution;
+    } else {
+      const { position, resolution } = await findDataPositionForLayer(
+        dataset.dataStore.url,
+        dataset,
+        layerName,
+      );
+      foundPosition = position;
+      foundResolution = resolution;
+    }
+
+    if (!foundPosition || !foundResolution) {
       const { upperBoundary, lowerBoundary } = getLayerBoundaries(dataset, layerName);
       const centerPosition = V3.add(lowerBoundary, upperBoundary).map(el => el / 2);
 
@@ -423,10 +440,10 @@ class DatasetSettings extends React.PureComponent<DatasetSettingsProps> {
       return;
     }
 
-    this.props.onSetPosition(position);
-    const zoomValue = this.props.onZoomToResolution(resolution);
+    this.props.onSetPosition(foundPosition);
+    const zoomValue = this.props.onZoomToResolution(foundResolution);
     Toast.success(
-      `Jumping to position ${position.join(", ")} and zooming to ${zoomValue.toFixed(2)}`,
+      `Jumping to position ${foundPosition.join(", ")} and zooming to ${zoomValue.toFixed(2)}`,
     );
   };
 

diff --git a/webknossos-datastore/app/com/scalableminds/webknossos/datastore/services/DataFinder.scala b/webknossos-datastore/app/com/scalableminds/webknossos/datastore/services/DataFinder.scala
@@ -0,0 +1,28 @@
+package com.scalableminds.webknossos.datastore.services
+
+import com.scalableminds.util.geometry.Point3D
+import com.scalableminds.webknossos.datastore.models.datasource.DataLayer
+
+trait DataFinder {
+  private def getExactDataOffset(data: Array[Byte], bytesPerElement: Int): Point3D = {
+    val bucketLength = DataLayer.bucketLength
+    for {
+      z <- 0 until bucketLength
+      y <- 0 until bucketLength
+      x <- 0 until bucketLength
+      scaledX = x * bytesPerElement
+      scaledY = y * bytesPerElement * bucketLength
+      scaledZ = z * bytesPerElement * bucketLength * bucketLength
+    } {
+      val voxelOffset = scaledX + scaledY + scaledZ
+      if (data.slice(voxelOffset, voxelOffset + bytesPerElement).exists(_ != 0)) return Point3D(x, y, z)
+    }
+    Point3D(0, 0, 0)
+  }
+
+  def getPositionOfNonZeroData(data: Array[Byte],
+                               globalPositionOffset: Point3D,
+                               bytesPerElement: Int): Option[Point3D] =
+    if (data.nonEmpty && data.exists(_ != 0)) Some(globalPositionOffset.move(getExactDataOffset(data, bytesPerElement)))
+    else None
+}
diff --git a/...ossos-datastore/app/com/scalableminds/webknossos/datastore/services/FindDataService.scala b/...ossos-datastore/app/com/scalableminds/webknossos/datastore/services/FindDataService.scala
@@ -19,6 +19,7 @@ object Histogram { implicit val jsonFormat = Json.format[Histogram] }
 
 class FindDataService @Inject()(dataServicesHolder: BinaryDataServiceHolder)(implicit ec: ExecutionContext)
     extends DataConverter
+    with DataFinder
     with FoxImplicits {
   val binaryDataService: BinaryDataService = dataServicesHolder.binaryDataService
 
@@ -98,23 +99,6 @@ class FindDataService @Inject()(dataServicesHolder: BinaryDataServiceHolder)(imp
   private def checkAllPositionsForData(dataSource: DataSource,
                                        dataLayer: DataLayer): Fox[Option[(Point3D, Point3D)]] = {
 
-    def getExactDataOffset(data: Array[Byte]): Point3D = {
-      val bytesPerElement = dataLayer.bytesPerElement
-      val cubeLength = DataLayer.bucketLength / bytesPerElement
-      for {
-        z <- 0 until cubeLength
-        y <- 0 until cubeLength
-        x <- 0 until cubeLength
-        scaledX = x * bytesPerElement
-        scaledY = y * bytesPerElement
-        scaledZ = z * bytesPerElement
-      } {
-        val voxelOffset = scaledX + scaledY * cubeLength + scaledZ * cubeLength * cubeLength
-        if (data.slice(voxelOffset, voxelOffset + bytesPerElement).exists(_ != 0)) return Point3D(x, y, z)
-      }
-      Point3D(0, 0, 0)
-    }
-
     def searchPositionIter(positions: List[Point3D], resolution: Point3D): Fox[Option[Point3D]] =
       positions match {
         case List() => Fox.successful(None)
@@ -128,8 +112,8 @@ class FindDataService @Inject()(dataServicesHolder: BinaryDataServiceHolder)(imp
     def checkIfPositionHasData(position: Point3D, resolution: Point3D) =
       for {
         data <- getDataFor(dataSource, dataLayer, position, resolution)
-        if data.nonEmpty && data.exists(_ != 0)
-      } yield position.move(getExactDataOffset(data))
+        position <- getPositionOfNonZeroData(data, position, dataLayer.bytesPerElement)
+      } yield position
 
     def resolutionIter(positions: List[Point3D], remainingResolutions: List[Point3D]): Fox[Option[(Point3D, Point3D)]] =
       remainingResolutions match {

diff --git a/...e/app/com/scalableminds/webknossos/tracingstore/controllers/VolumeTracingController.scala b/...e/app/com/scalableminds/webknossos/tracingstore/controllers/VolumeTracingController.scala
@@ -5,7 +5,7 @@ import java.nio.{ByteBuffer, ByteOrder}
 
 import akka.stream.scaladsl.Source
 import com.google.inject.Inject
-import com.scalableminds.util.geometry.BoundingBox
+import com.scalableminds.util.geometry.{BoundingBox, Point3D}
 import com.scalableminds.util.tools.ExtendedTypes.ExtendedString
 import com.scalableminds.webknossos.tracingstore.VolumeTracing.{VolumeTracing, VolumeTracingOpt, VolumeTracings}
 import com.scalableminds.webknossos.datastore.models.{WebKnossosDataRequest, WebKnossosIsosurfaceRequest}
@@ -155,6 +155,22 @@ class VolumeTracingController @Inject()(val tracingService: VolumeTracingService
     }
   }
 
+  def importVolumeData(tracingId: String): Action[MultipartFormData[TemporaryFile]] =
+    Action.async(parse.multipartFormData) { implicit request =>
+      log {
+        accessTokenService.validateAccess(UserAccessRequest.writeTracing(tracingId)) {
+          AllowRemoteOrigin {
+            for {
+              tracing <- tracingService.find(tracingId)
+              currentVersion <- request.body.dataParts("currentVersion").headOption.flatMap(_.toIntOpt).toFox
+              zipFile <- request.body.files.headOption.map(f => new File(f.ref.path.toString)).toFox
+              largestSegmentId <- tracingService.importVolumeData(tracingId, tracing, zipFile, currentVersion)
+            } yield Ok(Json.toJson(largestSegmentId))
+          }
+        }
+      }
+    }
+
   def updateActionLog(tracingId: String) = Action.async { implicit request =>
     log {
       accessTokenService.validateAccess(UserAccessRequest.readTracing(tracingId)) {
@@ -194,19 +210,16 @@ class VolumeTracingController @Inject()(val tracingService: VolumeTracingService
   private def formatNeighborList(neighbors: List[Int]): String =
     "[" + neighbors.mkString(", ") + "]"
 
-  def importVolumeData(tracingId: String): Action[MultipartFormData[TemporaryFile]] =
-    Action.async(parse.multipartFormData) { implicit request =>
-      log {
-        accessTokenService.validateAccess(UserAccessRequest.writeTracing(tracingId)) {
-          AllowRemoteOrigin {
-            for {
-              tracing <- tracingService.find(tracingId)
-              currentVersion <- request.body.dataParts("currentVersion").headOption.flatMap(_.toIntOpt).toFox
-              zipFile <- request.body.files.headOption.map(f => new File(f.ref.path.toString)).toFox
-              largestSegmentId <- tracingService.importVolumeData(tracingId, tracing, zipFile, currentVersion)
-            } yield Ok(Json.toJson(largestSegmentId))
-          }
+  def findData(tracingId: String) = Action.async { implicit request =>
+    accessTokenService.validateAccess(UserAccessRequest.readTracing(tracingId)) {
+      AllowRemoteOrigin {
+        for {
+          positionOpt <- tracingService.findData(tracingId)
+        } yield {
+          Ok(Json.obj("position" -> positionOpt, "resolution" -> positionOpt.map(_ => Point3D(1, 1, 1))))
         }
       }
     }
+  }
+
 }
diff --git a/.../app/com/scalableminds/webknossos/tracingstore/tracings/volume/VolumeTracingService.scala b/.../app/com/scalableminds/webknossos/tracingstore/tracings/volume/VolumeTracingService.scala
@@ -47,6 +47,7 @@ class VolumeTracingService @Inject()(
 ) extends TracingService[VolumeTracing]
     with VolumeTracingBucketHelper
     with WKWDataFormatHelper
+    with DataFinder
     with ProtoGeometryImplicits
     with FoxImplicits
     with LazyLogging {
@@ -415,6 +416,20 @@ class VolumeTracingService @Inject()(
       result <- isosurfaceService.requestIsosurfaceViaActor(isosurfaceRequest)
     } yield result
 
+  def findData(tracingId: String): Fox[Option[Point3D]] =
+    for {
+      tracing <- find(tracingId) ?~> "tracing.notFound"
+      volumeLayer = volumeTracingLayer(tracingId, tracing)
+      bucketStream = volumeLayer.bucketProvider.bucketStream(1, Some(tracing.version))
+      bucketPosOpt = if (bucketStream.hasNext) {
+        val bucket = bucketStream.next()
+        val bucketPos = bucket._1
+        getPositionOfNonZeroData(bucket._2,
+                                 Point3D(bucketPos.globalX, bucketPos.globalY, bucketPos.globalZ),
+                                 volumeLayer.bytesPerElement)
+      } else None
+    } yield bucketPosOpt
+
   def merge(tracings: Seq[VolumeTracing]): VolumeTracing = tracings.reduceLeft(mergeTwo)
 
   def mergeTwo(tracingA: VolumeTracing, tracingB: VolumeTracing): VolumeTracing = {

diff --git a/webknossos-tracingstore/conf/com.scalableminds.webknossos.tracingstore.routes b/webknossos-tracingstore/conf/com.scalableminds.webknossos.tracingstore.routes
@@ -3,7 +3,7 @@
 # ~~~~
 
 # Health endpoint
-GET         /health                                              @com.scalableminds.webknossos.tracingstore.controllers.Application.health
+GET         /health                                             @com.scalableminds.webknossos.tracingstore.controllers.Application.health
 
 # Volume tracings
 POST        /volume/save                                        @com.scalableminds.webknossos.tracingstore.controllers.VolumeTracingController.save
@@ -19,6 +19,7 @@ POST        /volume/:tracingId/duplicate                        @com.scalablemin
 GET         /volume/:tracingId/updateActionLog                  @com.scalableminds.webknossos.tracingstore.controllers.VolumeTracingController.updateActionLog(tracingId: String)
 POST        /volume/:tracingId/isosurface                       @com.scalableminds.webknossos.tracingstore.controllers.VolumeTracingController.requestIsosurface(tracingId: String)
 POST        /volume/:tracingId/importVolumeData                 @com.scalableminds.webknossos.tracingstore.controllers.VolumeTracingController.importVolumeData(tracingId: String)
+GET         /volume/:tracingId/findData                         @com.scalableminds.webknossos.tracingstore.controllers.VolumeTracingController.findData(tracingId: String)
 POST        /volume/getMultiple                                 @com.scalableminds.webknossos.tracingstore.controllers.VolumeTracingController.getMultiple
 POST        /volume/mergedFromIds                               @com.scalableminds.webknossos.tracingstore.controllers.VolumeTracingController.mergedFromIds(persist: Boolean)
 POST        /volume/mergedFromContents                          @com.scalableminds.webknossos.tracingstore.controllers.VolumeTracingController.mergedFromContents(persist: Boolean)