Communicate truncated 64 bit segmentation (#4598)

* add warning to user if 64-segmentation is active * not working as intended as the segmentation is 32 bit for the frontend * add optional originalElementClass field, which is filled for uint64 segmentation layer * use original element class to determine whether the segmentation is uint64 * add changelog entry * remove original element class and always send real element class to frontend * fix typo * add check so volumes can not be created for uint64 fallback layer * added manually saving of the originalElementClass in the frontend * update error message * Update frontend/javascripts/messages.js Co-authored-by: Daniel <[email protected]> * make comments more concise and remove unnecessary changes * Change "Show debug information" in toast to "Show more information" Co-authored-by: Michael Büßemeyer <[email protected]> Co-authored-by: MichaelBuessemeyer <[email protected]> Co-authored-by: Daniel <[email protected]>
scalableminds · May 27, 2020 · 9bb14a6 · 9bb14a6
1 parent b0e90f2
commit 9bb14a6
Show file tree

Hide file tree

Showing 10 changed files with 80 additions and 37 deletions.
diff --git a/CHANGELOG.released.md b/CHANGELOG.released.md
@@ -77,7 +77,7 @@ For upgrade instructions, please check the [migration guide](MIGRATIONS.released
 - Fixed a rendering error which could make some layers disappear in certain circumstances. [#4556](https://github.com/scalableminds/webknossos/pull/4556)
 - Fixed a rendering error which caused negative float data to be rendered white. [#4556](https://github.com/scalableminds/webknossos/pull/4571)
 - Fixed the histogram creation if some sampled positions don't contain data. [#4584](https://github.com/scalableminds/webknossos/pull/4584)
-- Fixed a rendering exception which could occur in rare circumstandes. [#4588](https://github.com/scalableminds/webknossos/pull/4588)
+- Fixed a rendering exception which could occur in rare circumstances. [#4588](https://github.com/scalableminds/webknossos/pull/4588)
 
 ## [20.04.0](https://github.com/scalableminds/webknossos/releases/tag/20.04.0) - 2020-03-23
 [Commits](https://github.com/scalableminds/webknossos/compare/20.03.0...20.04.0)

diff --git a/CHANGELOG.unreleased.md b/CHANGELOG.unreleased.md
@@ -12,9 +12,10 @@ For upgrade instructions, please check the [migration guide](MIGRATIONS.released
 
 ### Added
 
-- 
+- Added a warning to the segmentation tab when viewing `uint64` bit segmentation data. [#4598](https://github.com/scalableminds/webknossos/pull/4598)
 
 ### Changed
+
 - 
 
 ### Fixed

diff --git a/app/models/annotation/AnnotationService.scala b/app/models/annotation/AnnotationService.scala
@@ -14,6 +14,7 @@ import com.scalableminds.util.tools.{BoxImplicits, Fox, FoxImplicits, TextUtils}
 import com.scalableminds.webknossos.tracingstore.SkeletonTracing._
 import com.scalableminds.webknossos.tracingstore.VolumeTracing.{VolumeTracing, VolumeTracingOpt, VolumeTracings}
 import com.scalableminds.webknossos.datastore.models.datasource.{
+  ElementClass,
   DataSourceLike => DataSource,
   SegmentationLayerLike => SegmentationLayer
 }
@@ -102,18 +103,11 @@ class AnnotationService @Inject()(annotationInformationProvider: AnnotationInfor
 
   private def createVolumeTracing(
       dataSource: DataSource,
-      withFallback: Boolean,
+      fallbackLayer: Option[SegmentationLayer],
       boundingBox: Option[BoundingBox] = None,
       startPosition: Option[Point3D] = None,
       startRotation: Option[Vector3D] = None
-  ): VolumeTracing = {
-    val fallbackLayer: Option[SegmentationLayer] = if (withFallback) {
-      dataSource.dataLayers.flatMap {
-        case layer: SegmentationLayer => Some(layer)
-        case _                        => None
-      }.headOption
-    } else None
-
+  ): VolumeTracing =
     VolumeTracing(
       None,
       boundingBoxToProto(boundingBox.getOrElse(dataSource.boundingBox)),
@@ -127,14 +121,21 @@ class AnnotationService @Inject()(annotationInformationProvider: AnnotationInfor
       0,
       VolumeTracingDefaults.zoomLevel
     )
-  }
 
   def createTracings(
       dataSet: DataSet,
       dataSource: DataSource,
       tracingType: TracingType.Value,
       withFallback: Boolean,
-      oldTracingId: Option[String] = None)(implicit ctx: DBAccessContext): Fox[(Option[String], Option[String])] =
+      oldTracingId: Option[String] = None)(implicit ctx: DBAccessContext): Fox[(Option[String], Option[String])] = {
+    def getFallbackLayer(): Option[SegmentationLayer] =
+      if (withFallback) {
+        dataSource.dataLayers.flatMap {
+          case layer: SegmentationLayer => Some(layer)
+          case _                        => None
+        }.headOption
+      } else None
+
     tracingType match {
       case TracingType.skeleton =>
         for {
@@ -148,23 +149,29 @@ class AnnotationService @Inject()(annotationInformationProvider: AnnotationInfor
       case TracingType.volume =>
         for {
           client <- tracingStoreService.clientFor(dataSet)
-          volumeTracingId <- client.saveVolumeTracing(createVolumeTracing(dataSource, withFallback))
+          fallbackLayer = getFallbackLayer()
+          _ <- bool2Fox(fallbackLayer.forall(_.elementClass != ElementClass.uint64)) ?~> "annotation.volume.uint64"
+          volumeTracingId <- client.saveVolumeTracing(createVolumeTracing(dataSource, fallbackLayer))
         } yield (None, Some(volumeTracingId))
       case TracingType.hybrid =>
         for {
           client <- tracingStoreService.clientFor(dataSet)
+          fallbackLayer = getFallbackLayer()
+          _ <- bool2Fox(fallbackLayer.forall(_.elementClass != ElementClass.uint64)) ?~> "annotation.volume.uint64"
           skeletonTracingId <- client.saveSkeletonTracing(
             SkeletonTracingDefaults.createInstance.copy(dataSetName = dataSet.name, editPosition = dataSource.center))
-          volumeTracingId <- client.saveVolumeTracing(createVolumeTracing(dataSource, withFallback))
+          volumeTracingId <- client.saveVolumeTracing(createVolumeTracing(dataSource, fallbackLayer))
         } yield (Some(skeletonTracingId), Some(volumeTracingId))
     }
+  }
 
   def createExplorationalFor(user: User, _dataSet: ObjectId, tracingType: TracingType.Value, withFallback: Boolean)(
-      implicit ctx: DBAccessContext): Fox[Annotation] =
+      implicit ctx: DBAccessContext,
+      m: MessagesProvider): Fox[Annotation] =
     for {
-      dataSet <- dataSetDAO.findOne(_dataSet)
+      dataSet <- dataSetDAO.findOne(_dataSet) ?~> "dataSet.noAccessById"
       dataSource <- dataSetService.dataSourceFor(dataSet)
-      usableDataSource <- dataSource.toUsable ?~> "DataSet is not imported."
+      usableDataSource <- dataSource.toUsable ?~> Messages("dataSet.notImported", dataSource.id.name)
       tracingIds <- createTracings(dataSet, usableDataSource, tracingType, withFallback)
       teamId <- selectSuitableTeam(user, dataSet)
       annotation = Annotation(
@@ -338,9 +345,18 @@ class AnnotationService @Inject()(annotationInformationProvider: AnnotationInfor
       dataSet <- dataSetDAO.findOneByNameAndOrganization(dataSetName, organizationId) ?~> Messages("dataset.notFound",
                                                                                                    dataSetName)
       dataSource <- dataSetService.dataSourceFor(dataSet).flatMap(_.toUsable)
+
+      fallbackLayer = if (volumeShowFallbackLayer) {
+        dataSource.dataLayers.flatMap {
+          case layer: SegmentationLayer => Some(layer)
+          case _                        => None
+        }.headOption
+      } else None
+      _ <- bool2Fox(fallbackLayer.forall(_.elementClass != ElementClass.uint64)) ?~> "annotation.volume.uint64"
+
       volumeTracing = createVolumeTracing(
         dataSource,
-        withFallback = volumeShowFallbackLayer,
+        fallbackLayer = fallbackLayer,
         boundingBox = boundingBox.flatMap { box =>
           if (box.isEmpty) None else Some(box)
         },

diff --git a/app/models/binary/DataSetService.scala b/app/models/binary/DataSetService.scala
@@ -321,13 +321,12 @@ class DataSetService @Inject()(organizationDAO: OrganizationDAO,
       lastUsedByUser <- lastUsedTimeFor(dataSet._id, requestingUserOpt)
       dataStoreJs <- dataStoreService.publicWrites(dataStore)
       dataSource <- dataSourceFor(dataSet, Some(organization), skipResolutions)
-      dataSourceWith64BitSupport = dataSource.toUsable.map(replaceUint64Layers).getOrElse(dataSource)
       publicationOpt <- Fox.runOptional(dataSet._publication)(publicationDAO.findOne(_))
       publicationJson <- Fox.runOptional(publicationOpt)(publicationService.publicWrites)
     } yield {
       Json.obj(
         "name" -> dataSet.name,
-        "dataSource" -> dataSourceWith64BitSupport,
+        "dataSource" -> dataSource,
         "dataStore" -> dataStoreJs,
         "owningOrganization" -> organization.name,
         "allowedTeams" -> teamsJs,
@@ -346,16 +345,4 @@ class DataSetService @Inject()(organizationDAO: OrganizationDAO,
         "isForeign" -> dataStore.isForeign
       )
     }
-
-  private def replaceUint64Layers(dataSource: GenericDataSource[DataLayer]) = {
-    val newLayers = dataSource.dataLayers.map {
-      case l: WKWSegmentationLayer if l.elementClass == ElementClass.uint64 =>
-        l.copy(elementClass = ElementClass.uint32)
-      case l: AbstractSegmentationLayer if l.elementClass == ElementClass.uint64 =>
-        l.copy(elementClass = ElementClass.uint32)
-      case l => l
-    }
-
-    dataSource.copy(dataLayers = newLayers)
-  }
 }
diff --git a/conf/messages b/conf/messages
@@ -85,6 +85,7 @@ dataSet.notFound=Dataset {0} does not exist or could not be accessed
 dataSet.notFoundConsiderLogin=Dataset {0} does not exist or could not be accessed. You may need to log in.
 dataSet.notFoundForAnnotation=The Dataset for this annotation does not exist or could not be accessed.
 dataSet.noAccess=Could not access DataSet {0}. Does your team have access?
+dataSet.noAccessById=Could not access the corresponding DataSet. This is likely because you are not a member of a team that has access to it.
 dataSet.notImported=Dataset {0} is not imported
 dataSet.name.invalid=A dataset name can only contain letters, digits and underscores
 dataSet.import.impossible.name=Import impossible. Dataset name can only consist of a-Z, 0-9, "-" and "_".
@@ -183,7 +184,8 @@ role.added=Added role to {0}
 tracing=Annotation
 tracing.notFound=Tracing couldn’t be found
 
-annotation.create.failed=Failed to create annotation. This is likely because you are not a member of a team that has access to the dataset.
+annotation.create.failed=Failed to create annotation.
+annotation.volume.uint64=Creating volume tracings on a uint64 fallback layer is not allowed.
 annotation.notFound=Annotation couldn’t be found
 annotation.notFound.considerLoggingIn=Annotation couldn’t be found. If the annotation is not public, you need to log in to see it.
 annotation.invalid=Invalid annotation

diff --git a/frontend/javascripts/admin/api_flow_types.js b/frontend/javascripts/admin/api_flow_types.js
@@ -54,6 +54,7 @@ export type APISegmentationLayer = {|
   ...APIDataLayerBase,
   +category: "segmentation",
   +largestSegmentId: number,
+  +originalElementClass?: ElementClass,
   +mappings?: Array<string>,
   +agglomerates?: Array<string>,
   +fallbackLayer?: ?string,

diff --git a/frontend/javascripts/libs/toast.js b/frontend/javascripts/libs/toast.js
@@ -41,7 +41,7 @@ const Toast = {
           style={{ background: "transparent", marginLeft: -16 }}
         >
           <Panel
-            header="Show debug information"
+            header="Show more information"
             style={{ background: "transparent", border: 0, fontSize: 10 }}
           >
             {errorChain}

diff --git a/frontend/javascripts/messages.js b/frontend/javascripts/messages.js
@@ -96,6 +96,8 @@ instead. Only enable this option if you understand its effect. All layers will n
     "You didn't add a node after jumping to this branchpoint, do you really want to jump again?",
   "tracing.segmentation_zoom_warning":
     "Segmentation data and volume annotation is only fully supported at a smaller zoom level.",
+  "tracing.uint64_segmentation_warning":
+    "This is an unsigned 64-bit segmentation. The displayed ids are truncated to 32-bit. Thus, they might not match the ids on the server.",
   "tracing.segmentation_zoom_warning_agglomerate":
     "Segmentation data which is mapped using an agglomerate file cannot be rendered in this magnification. Please zoom in further.",
   "tracing.no_access": "You are not allowed to access this annotation.",

diff --git a/frontend/javascripts/oxalis/model_initialization.js b/frontend/javascripts/oxalis/model_initialization.js
@@ -295,6 +295,24 @@ function initializeDataset(
     dataSet: dataset.dataSource.id.name,
   });
 
+  // Add the originalElementClass property to the segmentation layer if it exists.
+  // Also set the elementClass to uint32 because uint64 segmentation data is truncated to uint32 by the backend.
+  const updatedDataLayers = dataset.dataSource.dataLayers.map(dataLayer => {
+    const { elementClass } = dataLayer;
+    if (dataLayer.category === "segmentation") {
+      const adjustedElementClass = elementClass === "uint64" ? "uint32" : elementClass;
+      return {
+        ...dataLayer,
+        originalElementClass: elementClass,
+        elementClass: adjustedElementClass,
+      };
+    } else {
+      return dataLayer;
+    }
+  });
+  // $FlowFixMe assigning the adjusted dataset layers, although this property is not writable.
+  dataset.dataSource.dataLayers = updatedDataLayers;
+
   serverTracingAsVolumeTracingMaybe(tracing).map(volumeTracing => {
     const newDataLayers = setupLayerForVolumeTracing(dataset, volumeTracing);
     // $FlowFixMe We mutate the dataset here to avoid that an outdated version is used somewhere else

diff --git a/frontend/javascripts/oxalis/view/right-menu/mapping_info_view.js b/frontend/javascripts/oxalis/view/right-menu/mapping_info_view.js
@@ -262,12 +262,28 @@ class MappingInfoView extends React.Component<Props, State> {
       title,
       dataIndex,
     });
+    const showSegmentation64bitWarning =
+      segmentationLayer && segmentationLayer.originalElementClass === "uint64";
+    const maybeWithTooltipWarningTitle = title =>
+      showSegmentation64bitWarning ? (
+        <React.Fragment>
+          {title}{" "}
+          <Tooltip title={message["tracing.uint64_segmentation_warning"]}>
+            <Icon type="warning" style={{ color: "rgb(255, 155, 85)" }} />
+          </Tooltip>
+        </React.Fragment>
+      ) : (
+        title
+      );
     const idColumns =
       hasMapping && this.props.isMappingEnabled
         ? // Show an unmapped and mapped id column if there's a mapping
-          [columnHelper("Unmapped", "unmapped"), columnHelper("Mapped", "mapped")]
+          [
+            columnHelper(maybeWithTooltipWarningTitle("Unmapped"), "unmapped"),
+            columnHelper(maybeWithTooltipWarningTitle("Mapped"), "mapped"),
+          ]
         : // Otherwise, only show an ID column
-          [columnHelper("ID", "unmapped")];
+          [columnHelper(maybeWithTooltipWarningTitle("ID"), "unmapped")];
     const columns = [
       columnHelper("", "name"),
       ...idColumns,