Editable Mappings aka Supervoxel Proofreading

CHANGELOG.unreleased.md

@@ -16,6 +16,7 @@ For upgrade instructions, please check the [migration guide](MIGRATIONS.released
 - Added a warning for when the resolution in the XY viewport on z=1-downsampled datasets becomes too low, explaining the problem and how to mitigate it. [#6255](https://github.com/scalableminds/webknossos/pull/6255)
 - Provide a UI to download/export a dataset in view-mode. The UI explains how to access the data with the python library. [#6283](https://github.com/scalableminds/webknossos/pull/6283)
 - Added the possibility to view and download older versions of read-only annotations. [#6274](https://github.com/scalableminds/webknossos/pull/6274)
+- Added a proofreading tool which can be used to edit agglomerate mappings. After activating an agglomerate mapping the proofreading tool can be selected. While the tool is active, agglomerates can be clicked to load their agglomerate skeletons. Use the context menu to delete or create edges for those agglomerate skeletons to split or merge agglomerates. The changes will immediately reflect in the segmentation and meshes. [#6195](https://github.com/scalableminds/webknossos/pull/6195)
 
 ### Changed
 

MIGRATIONS.unreleased.md

@@ -8,4 +8,6 @@ User-facing changes are documented in the [changelog](CHANGELOG.released.md).
 ## Unreleased
 [Commits](https://github.com/scalableminds/webknossos/compare/22.06.1...HEAD)
 
+ - FossilDB now has to be started with two new additional column families: editableMappings,editableMappingUpdates. Note that this upgrade can not be trivially rolled back, since new rocksDB column families are added and it is not easy to remove them again from an existing database. In case webKnossos needs to be rolled back, it is recommended to still keep the new column families in FossilDB. [#6195](https://github.com/scalableminds/webknossos/pull/6195)
+
 ### Postgres Evolutions:

app/controllers/AnnotationIOController.scala

@@ -403,9 +403,9 @@ Expects:
 
     def exportMimeTypeForAnnotation(annotation: Annotation): String =
       if (annotation.tracingType == TracingType.skeleton)
-        "application/xml"
+        xmlMimeType
       else
-        "application/zip"
+        zipMimeType
 
     for {
       annotation <- provider.provideAnnotation(typ, annotationId, issuingUser) ~> NOT_FOUND

app/controllers/DataSetController.scala

@@ -116,7 +116,7 @@ class DataSetController @Inject()(userService: UserService,
           dataLayerName) ~> NOT_FOUND
         image <- imageFromCacheIfPossible(dataSet)
       } yield {
-        addRemoteOriginHeaders(Ok(image)).as("image/jpeg").withHeaders(CACHE_CONTROL -> "public, max-age=86400")
+        addRemoteOriginHeaders(Ok(image)).as(jpegMimeType).withHeaders(CACHE_CONTROL -> "public, max-age=86400")
       }
     }
 

app/controllers/SitemapController.scala

@@ -15,7 +15,7 @@ class SitemapController @Inject()(sitemapWriter: SitemapWriter, sil: Silhouette[
     val downloadStream = sitemapWriter.toSitemapStream(prefix)
 
     Ok.chunked(Source.fromPublisher(IterateeStreams.enumeratorToPublisher(downloadStream)))
-      .as("application/xml")
+      .as(xmlMimeType)
       .withHeaders(CONTENT_DISPOSITION ->
         """sitemap.xml""")
   }

app/models/annotation/AnnotationService.scala

@@ -833,7 +833,7 @@ class AnnotationService @Inject()(
     }
 
   //for Explorative Annotations list
-  def compactWrites(annotation: Annotation)(implicit ctx: DBAccessContext): Fox[JsObject] =
+  def compactWrites(annotation: Annotation): Fox[JsObject] =
     for {
       dataSet <- dataSetDAO.findOne(annotation._dataSet)(GlobalAccessContext) ?~> "dataSet.notFoundForAnnotation"
       organization <- organizationDAO.findOne(dataSet._organization)(GlobalAccessContext) ?~> "organization.notFound"

conf/application.conf

@@ -145,7 +145,7 @@ datastore {
     address = "localhost"
     port = 6379
   }
-  agglomerateSkeleton.maxEdges = 10000
+  agglomerateSkeleton.maxEdges = 100000
 }
 
 # Proxy some routes to prefix + route (only if features.isDemoInstance, route "/" only if logged out)

conf/messages

@@ -277,6 +277,8 @@ annotation.reopen.failed=Failed to reopen the annotation.
 annotation.sandbox.skeletonOnly=Sandbox annotations are currently available as skeleton only.
 annotation.multiLayers.skeleton.notImplemented=This feature is not implemented for annotations with more than one skeleton layer
 annotation.multiLayers.volume.notImplemented=This feature is not implemented for annotations with more than one volume layer
+annotation.noMappingSet=No mapping is pinned for this annotation, cannot generate agglomerate skeleton.
+annotation.volumeBucketsNotEmpty=Cannot make mapping editable in an annotation with mutated volume data
 
 mesh.notFound=Mesh couldn’t be found
 mesh.write.failed=Failed to convert mesh info to json

docker-compose.yml

@@ -265,7 +265,7 @@ services:
     command:
       - fossildb
       - -c
-      - skeletons,skeletonUpdates,volumes,volumeData,volumeUpdates
+      - skeletons,skeletonUpdates,volumes,volumeData,volumeUpdates,editableMappings,editableMappingUpdates
     user: ${USER_UID:-fossildb}:${USER_GID:-fossildb}
 
   fossildb-persisted:

fossildb/run.sh

@@ -14,6 +14,6 @@ if [ ! -f "$JAR" ] || [ ! "$CURRENT_VERSION" == "$VERSION" ]; then
   wget -q --show-progress -O "$JAR" "$URL"
 fi
 
-COLLECTIONS="skeletons,skeletonUpdates,volumes,volumeData,volumeUpdates"
+COLLECTIONS="skeletons,skeletonUpdates,volumes,volumeData,volumeUpdates,editableMappings,editableMappingUpdates"
 
 exec java -jar "$JAR" -c "$COLLECTIONS" -d "$FOSSILDB_HOME/data" -b "$FOSSILDB_HOME/backup"

frontend/javascripts/admin/admin_rest_api.ts

@@ -54,6 +54,7 @@ import type {
   ServerTracing,
   TracingType,
   WkConnectDatasetConfig,
+  ServerEditableMapping,
   APICompoundType,
 } from "types/api_flow_types";
 import { APIAnnotationTypeEnum } from "types/api_flow_types";
@@ -81,6 +82,7 @@ import Toast from "libs/toast";
 import * as Utils from "libs/utils";
 import messages from "messages";
 import window, { location } from "libs/window";
+import { SaveQueueType } from "oxalis/model/actions/save_actions";
 
 const MAX_SERVER_ITEMS_PER_RESPONSE = 1000;
 
@@ -854,11 +856,11 @@ export async function getTracingForAnnotationType(
 export function getUpdateActionLog(
   tracingStoreUrl: string,
   tracingId: string,
-  tracingType: "skeleton" | "volume",
+  versionedObjectType: SaveQueueType,
 ): Promise<Array<APIUpdateActionBatch>> {
   return doWithToken((token) =>
     Request.receiveJSON(
-      `${tracingStoreUrl}/tracings/${tracingType}/${tracingId}/updateActionLog?token=${token}`,
+      `${tracingStoreUrl}/tracings/${versionedObjectType}/${tracingId}/updateActionLog?token=${token}`,
     ),
   );
 }
@@ -1584,6 +1586,29 @@ export function fetchMapping(
   );
 }
 
+export function makeMappingEditable(
+  tracingStoreUrl: string,
+  tracingId: string,
+): Promise<ServerEditableMapping> {
+  return doWithToken((token) =>
+    Request.receiveJSON(
+      `${tracingStoreUrl}/tracings/volume/${tracingId}/makeMappingEditable?token=${token}`,
+      {
+        method: "POST",
+      },
+    ),
+  );
+}
+
+export function getEditableMapping(
+  tracingStoreUrl: string,
+  tracingId: string,
+): Promise<ServerEditableMapping> {
+  return doWithToken((token) =>
+    Request.receiveJSON(`${tracingStoreUrl}/tracings/mapping/${tracingId}?token=${token}`),
+  );
+}
+
 export async function getAgglomeratesForDatasetLayer(
   datastoreUrl: string,
   datasetId: APIDatasetId,
@@ -1871,10 +1896,12 @@ export function getMeshData(id: string): Promise<ArrayBuffer> {
 // These parameters are bundled into an object to avoid that the computeIsosurface function
 // receives too many parameters, since this doesn't play well with the saga typings.
 type IsosurfaceRequest = {
+  // The position is in voxels in mag 1
   position: Vector3;
   mag: Vector3;
   segmentId: number;
   subsamplingStrides: Vector3;
+  // The cubeSize is in voxels in mag <mag>
   cubeSize: Vector3;
   scale: Vector3;
   mappingName: string | null | undefined;
@@ -1938,7 +1965,26 @@ export function getAgglomerateSkeleton(
   return doWithToken((token) =>
     Request.receiveArraybuffer(
       `${dataStoreUrl}/data/datasets/${datasetId.owningOrganization}/${datasetId.name}/layers/${layerName}/agglomerates/${mappingId}/skeleton/${agglomerateId}?token=${token}`, // The webworker code cannot do proper error handling and always expects an array buffer from the server.
-      // In this case, the server sends an error json instead of an array buffer sometimes. Therefore, don't use the webworker code.
+      // The webworker code cannot do proper error handling and always expects an array buffer from the server.
+      // However, the server might send an error json instead of an array buffer. Therefore, don't use the webworker code.
+      {
+        useWebworkerForArrayBuffer: false,
+        showErrorToast: false,
+      },
+    ),
+  );
+}
+
+export function getEditableAgglomerateSkeleton(
+  tracingStoreUrl: string,
+  tracingId: string,
+  agglomerateId: number,
+): Promise<ArrayBuffer> {
+  return doWithToken((token) =>
+    Request.receiveArraybuffer(
+      `${tracingStoreUrl}/tracings/volume/${tracingId}/agglomerateSkeleton/${agglomerateId}?token=${token}`,
+      // The webworker code cannot do proper error handling and always expects an array buffer from the server.
+      // However, the server might send an error json instead of an array buffer. Therefore, don't use the webworker code.
       {
         useWebworkerForArrayBuffer: false,
         showErrorToast: false,

frontend/javascripts/messages.ts

@@ -113,6 +113,9 @@ In order to restore the current window, a reload is necessary.`,
   "undo.no_undo":
     "There is no action that could be undone. However, if you want to restore an earlier version of this annotation, use the 'Restore Older Version' functionality in the dropdown next to the 'Save' button.",
   "undo.no_redo": "There is no action that could be redone.",
+  "undo.no_undo_during_proofread":
+    "Undo is not supported during proofreading yet. Please manually revert the last action you took.",
+  "undo.no_redo_during_proofread": "Redo is not supported during proofreading yet.",
   "undo.import_volume_tracing":
     "Importing a volume annotation cannot be undone. However, if you want to restore an earlier version of this annotation, use the 'Restore Older Version' functionality in the dropdown next to the 'Save' button.",
   "download.wait": "Please wait...",

frontend/javascripts/oxalis/api/api_latest.ts

@@ -1528,7 +1528,11 @@ class DataApi {
     });
   }
 
-  getRawDataCuboid(layerName: string, topLeft: Vector3, bottomRight: Vector3): Promise<void> {
+  getRawDataCuboid(
+    layerName: string,
+    topLeft: Vector3,
+    bottomRight: Vector3,
+  ): Promise<ArrayBuffer> {
     return doWithToken((token) => {
       const downloadUrl = this._getDownloadUrlForRawDataCuboid(
         layerName,

frontend/javascripts/oxalis/constants.ts

@@ -180,6 +180,7 @@ export enum AnnotationToolEnum {
   FILL_CELL = "FILL_CELL",
   PICK_CELL = "PICK_CELL",
   BOUNDING_BOX = "BOUNDING_BOX",
+  PROOFREAD = "PROOFREAD",
 }
 export const VolumeTools: Array<keyof typeof AnnotationToolEnum> = [
   AnnotationToolEnum.BRUSH,
@@ -257,7 +258,7 @@ export type ShowContextMenuFunction = (
   arg1: number,
   arg2: number | null | undefined,
   arg3: number | null | undefined,
-  arg4: Vector3,
+  arg4: Vector3 | null | undefined,
   arg5: OrthoView,
 ) => void;
 const Constants = {
@@ -294,6 +295,8 @@ const Constants = {
   DEFAULT_NODE_RADIUS: 1.0,
   RESIZE_THROTTLE_TIME: 50,
   MIN_TREE_ID: 1,
+  // TreeIds > 1024^2 break webKnossos, see https://github.com/scalableminds/webknossos/issues/5009
+  MAX_TREE_ID: 1048576,
   MIN_NODE_ID: 1,
   // Maximum of how many buckets will be held in RAM (per layer)
   MAXIMUM_BUCKET_COUNT_PER_LAYER: 5000,

frontend/javascripts/oxalis/controller/combinations/bounding_box_handlers.ts

@@ -1,4 +1,7 @@
-import { calculateGlobalPos } from "oxalis/model/accessors/view_mode_accessor";
+import {
+  calculateGlobalPos,
+  calculateMaybeGlobalPos,
+} from "oxalis/model/accessors/view_mode_accessor";
 import _ from "lodash";
 import type { OrthoView, Point2, Vector3, BoundingBoxType } from "oxalis/constants";
 import Store from "oxalis/store";
@@ -140,7 +143,10 @@ export function getClosestHoveredBoundingBox(
   plane: OrthoView,
 ): [SelectedEdge, SelectedEdge | null | undefined] | null {
   const state = Store.getState();
-  const globalPosition = calculateGlobalPos(state, pos, plane);
+  const globalPosition = calculateMaybeGlobalPos(state, pos, plane);
+
+  if (globalPosition == null) return null;
+
   const { userBoundingBoxes } = getSomeTracing(state.tracing);
   const indices = Dimension.getIndices(plane);
   const planeRatio = getBaseVoxelFactors(state.dataset.dataSource.scale);

frontend/javascripts/oxalis/controller/combinations/segmentation_handlers.ts

@@ -17,6 +17,7 @@ import {
   getSegmentIdForPositionAsync,
 } from "oxalis/controller/combinations/volume_handlers";
 import { setActiveConnectomeAgglomerateIdsAction } from "oxalis/model/actions/connectome_actions";
+import { getTreeNameForAgglomerateSkeleton } from "oxalis/model/accessors/skeletontracing_accessor";
 export function hasAgglomerateMapping(state: OxalisState) {
   const segmentation = Model.getVisibleSegmentationLayer();
 
@@ -81,22 +82,22 @@ export async function handleAgglomerateSkeletonAtClick(clickPosition: Point2) {
   const globalPosition = calculateGlobalPos(state, clickPosition);
   loadAgglomerateSkeletonAtPosition(globalPosition);
 }
-export async function loadAgglomerateSkeletonAtPosition(position: Vector3): Promise<void> {
+export async function loadAgglomerateSkeletonAtPosition(position: Vector3): Promise<string | null> {
   const segmentation = Model.getVisibleSegmentationLayer();
 
   if (!segmentation) {
-    return;
+    return null;
   }
 
   const segmentId = await getSegmentIdForPositionAsync(position);
-  loadAgglomerateSkeletonForSegmentId(segmentId);
+  return loadAgglomerateSkeletonForSegmentId(segmentId);
 }
-export function loadAgglomerateSkeletonForSegmentId(segmentId: number): void {
+export function loadAgglomerateSkeletonForSegmentId(segmentId: number): string | null {
   const state = Store.getState();
   const segmentation = Model.getVisibleSegmentationLayer();
 
   if (!segmentation) {
-    return;
+    return null;
   }
 
   const { mappingName } = getMappingInfo(
@@ -107,9 +108,11 @@ export function loadAgglomerateSkeletonForSegmentId(segmentId: number): void {
 
   if (mappingName && isAgglomerateMappingEnabled.value) {
     Store.dispatch(loadAgglomerateSkeletonAction(segmentation.name, mappingName, segmentId));
+    return getTreeNameForAgglomerateSkeleton(segmentId, mappingName);
   } else {
     Toast.error(isAgglomerateMappingEnabled.reason);
   }
+  return null;
 }
 export async function loadSynapsesOfAgglomerateAtPosition(position: Vector3) {
   const state = Store.getState();

frontend/javascripts/oxalis/controller/combinations/skeleton_handlers.ts

@@ -17,7 +17,11 @@ import {
   getNodeAndTree,
   getNodeAndTreeOrNull,
 } from "oxalis/model/accessors/skeletontracing_accessor";
-import { getInputCatcherRect, calculateGlobalPos } from "oxalis/model/accessors/view_mode_accessor";
+import {
+  getInputCatcherRect,
+  calculateGlobalPos,
+  calculateMaybeGlobalPos,
+} from "oxalis/model/accessors/view_mode_accessor";
 import {
   getPosition,
   getRotationOrtho,
@@ -132,13 +136,11 @@ export function handleOpenContextMenu(
 ) {
   const { activeViewport } = Store.getState().viewModeData.plane;
 
-  if (activeViewport === OrthoViews.TDView) {
-    return;
-  }
-
   const nodeId = maybeGetNodeIdFromPosition(planeView, position, plane, isTouch);
   const state = Store.getState();
-  const globalPosition = calculateGlobalPos(state, position);
+  // Use calculateMaybeGlobalPos instead of calculateGlobalPos, since calculateGlobalPos
+  // only works for the data viewports, but this function is also called for the 3d viewport.
+  const globalPosition = calculateMaybeGlobalPos(state, position);
   const hoveredEdgesInfo = getClosestHoveredBoundingBox(position, plane);
   const clickedBoundingBoxId = hoveredEdgesInfo != null ? hoveredEdgesInfo[0].boxId : null;
   showNodeContextMenuAt(