Add delete segment data update action

CHANGELOG.unreleased.md

@@ -15,6 +15,7 @@ For upgrade instructions, please check the [migration guide](MIGRATIONS.released
 - Added support for reading uint24 rgb layers in datasets with zarr2/zarr3/n5/neuroglancerPrecomputed format, as used for voxelytics predictions. [#7413](https://github.com/scalableminds/webknossos/pull/7413)
 - Adding a remote dataset can now be done by providing a Neuroglancer URI. [#7416](https://github.com/scalableminds/webknossos/pull/7416)
 - Added a filter to the Task List->Stats column to quickly filter for tasks with "Prending", "In-Progress" or "Finished" instances. [#7430](https://github.com/scalableminds/webknossos/pull/7430)
+- The data of segments can now be deleted in the segment side panel. [#7435](https://github.com/scalableminds/webknossos/pull/7435)
 
 ### Changed
 - An appropriate error is returned when requesting an API version that is higher that the current version. [#7424](https://github.com/scalableminds/webknossos/pull/7424)

frontend/javascripts/oxalis/model/actions/volumetracing_actions.ts

@@ -39,6 +39,7 @@ export type SetLargestSegmentIdAction = ReturnType<typeof setLargestSegmentIdAct
 export type SetSegmentsAction = ReturnType<typeof setSegmentsAction>;
 export type UpdateSegmentAction = ReturnType<typeof updateSegmentAction>;
 export type RemoveSegmentAction = ReturnType<typeof removeSegmentAction>;
+export type DeleteSegmentDataAction = ReturnType<typeof deleteSegmentDataAction>;
 export type SetSegmentGroupsAction = ReturnType<typeof setSegmentGroupsAction>;
 export type SetMappingIsEditableAction = ReturnType<typeof setMappingIsEditableAction>;
 
@@ -80,6 +81,7 @@ export type VolumeTracingAction =
   | SetSegmentsAction
   | UpdateSegmentAction
   | RemoveSegmentAction
+  | DeleteSegmentDataAction
   | SetSegmentGroupsAction
   | AddBucketToUndoAction
   | ImportVolumeTracingAction
@@ -232,6 +234,20 @@ export const removeSegmentAction = (
     timestamp,
   } as const);
 
+export const deleteSegmentDataAction = (
+  segmentId: number,
+  layerName: string,
+  callback?: () => void,
+  timestamp: number = Date.now(),
+) =>
+  ({
+    type: "DELETE_SEGMENT_DATA",
+    segmentId,
+    layerName,
+    callback,
+    timestamp,
+  } as const);
+
 export const setSegmentGroupsAction = (
   segmentGroups: Array<SegmentGroup>,
   layerName: string,

frontend/javascripts/oxalis/model/bucket_data_handling/bucket.ts

@@ -543,6 +543,8 @@ export class DataBucket {
         }
       }
     }
+
+    this.invalidateValueSet();
   }
 
   markAsPulled(): void {

frontend/javascripts/oxalis/model/sagas/update_actions.ts

@@ -32,6 +32,7 @@ type UpdateVolumeTracingUpdateAction = ReturnType<typeof updateVolumeTracing>;
 export type CreateSegmentUpdateAction = ReturnType<typeof createSegmentVolumeAction>;
 export type UpdateSegmentUpdateAction = ReturnType<typeof updateSegmentVolumeAction>;
 export type DeleteSegmentUpdateAction = ReturnType<typeof deleteSegmentVolumeAction>;
+export type DeleteSegmentDataUpdateAction = ReturnType<typeof deleteSegmentDataVolumeAction>;
 type UpdateUserBoundingBoxesUpdateAction = ReturnType<typeof updateUserBoundingBoxes>;
 export type UpdateBucketUpdateAction = ReturnType<typeof updateBucket>;
 type UpdateSegmentGroupsUpdateAction = ReturnType<typeof updateSegmentGroups>;
@@ -63,6 +64,7 @@ export type UpdateAction =
   | CreateSegmentUpdateAction
   | UpdateSegmentUpdateAction
   | DeleteSegmentUpdateAction
+  | DeleteSegmentDataUpdateAction
   | UpdateBucketUpdateAction
   | UpdateTreeVisibilityUpdateAction
   | UpdateTreeEdgesVisibilityUpdateAction
@@ -346,6 +348,14 @@ export function deleteSegmentVolumeAction(id: number) {
     },
   } as const;
 }
+export function deleteSegmentDataVolumeAction(id: number) {
+  return {
+    name: "deleteSegmentData",
+    value: {
+      id,
+    },
+  } as const;
+}
 export function updateBucket(bucketInfo: SendBucketInfo, base64Data: string) {
   return {
     name: "updateBucket",

frontend/javascripts/oxalis/model/sagas/volumetracing_saga.tsx

@@ -65,6 +65,7 @@ import type {
   ClickSegmentAction,
   SetActiveCellAction,
   CreateCellAction,
+  DeleteSegmentDataAction,
 } from "oxalis/model/actions/volumetracing_actions";
 import {
   finishAnnotationStrokeAction,
@@ -79,7 +80,11 @@ import { select, take } from "oxalis/model/sagas/effect-generators";
 import listenToMinCut from "oxalis/model/sagas/min_cut_saga";
 import listenToQuickSelect from "oxalis/model/sagas/quick_select_saga";
 import { takeEveryUnlessBusy } from "oxalis/model/sagas/saga_helpers";
-import { UpdateAction, updateSegmentGroups } from "oxalis/model/sagas/update_actions";
+import {
+  deleteSegmentDataVolumeAction,
+  UpdateAction,
+  updateSegmentGroups,
+} from "oxalis/model/sagas/update_actions";
 import {
   createSegmentVolumeAction,
   deleteSegmentVolumeAction,
@@ -90,7 +95,7 @@ import {
   updateMappingName,
 } from "oxalis/model/sagas/update_actions";
 import VolumeLayer from "oxalis/model/volumetracing/volumelayer";
-import { Model } from "oxalis/singletons";
+import { Model, api } from "oxalis/singletons";
 import type { Flycam, SegmentMap, VolumeTracing } from "oxalis/store";
 import React from "react";
 import { actionChannel, call, fork, put, takeEvery, takeLatest } from "typed-redux-saga";
@@ -101,6 +106,7 @@ import {
 } from "./volume/helpers";
 import maybeInterpolateSegmentationLayer from "./volume/volume_interpolation_saga";
 import messages from "messages";
+import { pushSaveQueueTransaction } from "../actions/save_actions";
 
 export function* watchVolumeTracingAsync(): Saga<void> {
   yield* take("WK_READY");
@@ -842,8 +848,35 @@ function* ensureValidBrushSize(): Saga<void> {
   );
 }
 
+function* handleDeleteSegmentData(): Saga<void> {
+  yield* take("WK_READY");
+  while (true) {
+    const action = (yield* take("DELETE_SEGMENT_DATA")) as DeleteSegmentDataAction;
+
+    yield* put(setBusyBlockingInfoAction(true, "Segment is being deleted."));
+    yield* put(
+      pushSaveQueueTransaction(
+        [deleteSegmentDataVolumeAction(action.segmentId)],
+        "volume",
+        action.layerName,
+      ),
+    );
+    yield* call([Model, Model.ensureSavedState]);
+
+    yield* call([api.data, api.data.reloadBuckets], action.layerName, (bucket) =>
+      bucket.containsValue(action.segmentId),
+    );
+
+    yield* put(setBusyBlockingInfoAction(false));
+    if (action.callback) {
+      action.callback();
+    }
+  }
+}
+
 export default [
   editVolumeLayerAsync,
+  handleDeleteSegmentData,
   ensureToolIsAllowedInResolution,
   floodFill,
   watchVolumeTracingAsync,

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

@@ -5,7 +5,7 @@ import {
   VerticalAlignBottomOutlined,
   EllipsisOutlined,
 } from "@ant-design/icons";
-import { List, Tooltip, Dropdown, MenuProps } from "antd";
+import { List, Tooltip, Dropdown, MenuProps, Modal } from "antd";
 import { useDispatch, useSelector } from "react-redux";
 import Checkbox, { CheckboxChangeEvent } from "antd/lib/checkbox/Checkbox";
 import React from "react";
@@ -192,6 +192,7 @@ type Props = {
     createsNewUndoState: boolean,
   ) => void;
   removeSegment: (arg0: number, arg2: string) => void;
+  deleteSegmentData: (arg0: number, arg2: string, callback?: () => void) => void;
   onSelectSegment: (arg0: Segment) => void;
   visibleSegmentationLayer: APISegmentationLayer | null | undefined;
   loadAdHocMesh: (
@@ -373,6 +374,7 @@ function _SegmentListItem({
   allowUpdate,
   updateSegment,
   removeSegment,
+  deleteSegmentData,
   onSelectSegment,
   visibleSegmentationLayer,
   loadAdHocMesh,
@@ -489,6 +491,27 @@ function _SegmentListItem({
         },
         label: "Remove Segment From List",
       },
+      {
+        key: "deleteSegmentData",
+        onClick: () => {
+          if (visibleSegmentationLayer == null) {
+            return;
+          }
+
+          Modal.confirm({
+            content: `Are you sure you want to delete the segment's data? This operation will set all voxels with id ${segment.id} to 0.`,
+            okText: "Yes, delete",
+            okType: "danger",
+            onOk: async () =>
+              new Promise<void>((resolve) =>
+                deleteSegmentData(segment.id, visibleSegmentationLayer.name, resolve),
+              ),
+          });
+
+          andCloseContextMenu();
+        },
+        label: "Delete Segment's Data",
+      },
     ],
   });
 

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

@@ -72,6 +72,7 @@ import { updateTemporarySettingAction } from "oxalis/model/actions/settings_acti
 import {
   batchUpdateGroupsAndSegmentsAction,
   removeSegmentAction,
+  deleteSegmentDataAction,
   setActiveCellAction,
   updateSegmentAction,
 } from "oxalis/model/actions/volumetracing_actions";
@@ -271,6 +272,10 @@ const mapDispatchToProps = (dispatch: Dispatch<any>) => ({
   removeSegment(segmentId: number, layerName: string) {
     dispatch(removeSegmentAction(segmentId, layerName));
   },
+
+  deleteSegmentData(segmentId: number, layerName: string, callback?: () => void) {
+    dispatch(deleteSegmentDataAction(segmentId, layerName, callback));
+  },
 });
 
 type DispatchProps = ReturnType<typeof mapDispatchToProps>;
@@ -1588,6 +1593,7 @@ class SegmentsView extends React.Component<Props, State> {
                     allowUpdate={this.props.allowUpdate}
                     updateSegment={this.props.updateSegment}
                     removeSegment={this.props.removeSegment}
+                    deleteSegmentData={this.props.deleteSegmentData}
                     visibleSegmentationLayer={this.props.visibleSegmentationLayer}
                     loadAdHocMesh={this.props.loadAdHocMesh}
                     loadPrecomputedMesh={this.props.loadPrecomputedMesh}

frontend/javascripts/oxalis/view/version_entry.tsx

@@ -37,6 +37,7 @@ import type {
   MoveTreeComponentUpdateAction,
   MergeTreeUpdateAction,
   UpdateMappingNameUpdateAction,
+  DeleteSegmentDataUpdateAction,
 } from "oxalis/model/sagas/update_actions";
 import FormattedDate from "components/formatted_date";
 import { MISSING_GROUP_ID } from "oxalis/view/right-border-tabs/tree_hierarchy_view_helpers";
@@ -167,6 +168,10 @@ const descriptionFns: Record<ServerUpdateAction["name"], (...args: any) => Descr
     description: `Deleted the segment with id ${action.value.id} from the segments list.`,
     icon: <DeleteOutlined />,
   }),
+  deleteSegmentData: (action: DeleteSegmentDataUpdateAction): Description => ({
+    description: `Deleted the data of segment ${action.value.id}. All voxels with that id were overwritten with 0.`,
+    icon: <DeleteOutlined />,
+  }),
   addSegmentIndex: (): Description => ({
     description: "Added segment index to enable segment statistics.",
     icon: <EditOutlined />,

frontend/javascripts/test/controller/url_manager.spec.ts

@@ -111,7 +111,7 @@ test("UrlManager should build csv url hash and parse it again", (t) => {
   t.deepEqual(UrlManager.parseUrlHash(), urlState);
 });
 
-test.only("UrlManager should build csv url hash with additional coordinates and parse it again", (t) => {
+test("UrlManager should build csv url hash with additional coordinates and parse it again", (t) => {
   const mode = Constants.MODE_ARBITRARY;
   const urlState = {
     position: [0, 0, 0] as Vector3,

tools/assert-no-test-only.sh

@@ -1,5 +1,7 @@
 #!/bin/bash
+exit_code=0
 echo "Checking for test.only() in test files."
-! grep -r "test\.only(" frontend/javascripts/test || echo "Found test files with test.only() which disables other tests. Please remove the only modifier."
-! grep -r "test\.serial\.only(" frontend/javascripts/test || echo "Found test files with test.only() which disables other tests. Please remove the only modifier."
+! grep -r "test\.only(" frontend/javascripts/test || { echo "Found test files with test.only() which disables other tests. Please remove the only modifier."; exit_code=1; }
+! grep -r "test\.serial\.only(" frontend/javascripts/test || { echo "Found test files with test.only() which disables other tests. Please remove the only modifier."; exit_code=1; }
 echo "Done"
+exit $exit_code

webknossos-tracingstore/app/com/scalableminds/webknossos/tracingstore/tracings/volume/VolumeTracingService.scala

@@ -10,10 +10,16 @@ import com.scalableminds.webknossos.datastore.dataformats.wkw.WKWDataFormatHelpe
 import com.scalableminds.webknossos.datastore.geometry.NamedBoundingBoxProto
 import com.scalableminds.webknossos.datastore.helpers.ProtoGeometryImplicits
 import com.scalableminds.webknossos.datastore.models.DataRequestCollection.DataRequestCollection
-import com.scalableminds.webknossos.datastore.models.datasource.{AdditionalAxis, ElementClass}
+import com.scalableminds.webknossos.datastore.models.datasource.{AdditionalAxis, DataLayer, ElementClass}
 import com.scalableminds.webknossos.datastore.VolumeTracing.VolumeTracing.ElementClassProto
 import com.scalableminds.webknossos.datastore.models.requests.DataServiceDataRequest
-import com.scalableminds.webknossos.datastore.models.{AdditionalCoordinate, BucketPosition, WebknossosAdHocMeshRequest}
+import com.scalableminds.webknossos.datastore.models.{
+  AdditionalCoordinate,
+  BucketPosition,
+  UnsignedInteger,
+  UnsignedIntegerArray,
+  WebknossosAdHocMeshRequest
+}
 import com.scalableminds.webknossos.datastore.services._
 import com.scalableminds.webknossos.tracingstore.tracings.TracingType.TracingType
 import com.scalableminds.webknossos.tracingstore.tracings._
@@ -113,11 +119,11 @@ class VolumeTracingService @Inject()(
         tracingFox.futureBox.flatMap {
           case Full(tracing) =>
             action match {
-              case action: UpdateBucketVolumeAction =>
+              case a: UpdateBucketVolumeAction =>
                 if (tracing.getMappingIsEditable) {
                   Fox.failure("Cannot mutate volume data in annotation with editable mapping.")
                 } else
-                  updateBucket(tracingId, tracing, action, segmentIndexBuffer, updateGroup.version, userToken) ?~> "Failed to save volume data."
+                  updateBucket(tracingId, tracing, a, segmentIndexBuffer, updateGroup.version, userToken) ?~> "Failed to save volume data."
               case a: UpdateTracingVolumeAction =>
                 Fox.successful(
                   tracing.copy(
@@ -131,6 +137,11 @@ class VolumeTracingService @Inject()(
                   ))
               case a: RevertToVersionVolumeAction =>
                 revertToVolumeVersion(tracingId, a.sourceVersion, updateGroup.version, tracing)
+              case a: DeleteSegmentDataVolumeAction =>
+                if (!tracing.getHasSegmentIndex) {
+                  Fox.failure("Cannot delete segment data for annotations without segment index.")
+                } else
+                  deleteSegmentData(tracingId, tracing, a, segmentIndexBuffer, updateGroup.version) ?~> "Failed to delete segment data."
               case _: UpdateTdCamera        => Fox.successful(tracing)
               case a: ApplyableVolumeAction => Fox.successful(a.applyOn(tracing))
               case _                        => Fox.failure("Unknown action.")
@@ -178,6 +189,45 @@ class VolumeTracingService @Inject()(
       _ <- segmentIndexBuffer.flush()
     } yield volumeTracing
 
+  private def deleteSegmentData(tracingId: String,
+                                volumeTracing: VolumeTracing,
+                                a: DeleteSegmentDataVolumeAction,
+                                segmentIndexBuffer: VolumeSegmentIndexBuffer,
+                                version: Long): Fox[VolumeTracing] =
+    for {
+      _ <- Fox.successful(())
+      dataLayer = volumeTracingLayer(tracingId, volumeTracing)
+      _ <- Fox.serialCombined(volumeTracing.resolutions.toList)(resolution => {
+        val mag = vec3IntFromProto(resolution)
+        for {
+          bucketPositionsRaw <- volumeSegmentIndexService
+            .getSegmentToBucketIndexWithEmptyFallbackWithoutBuffer(tracingId, a.id, mag)
+          bucketPositions = bucketPositionsRaw.values
+            .map(vec3IntFromProto)
+            .map(_ * mag * DataLayer.bucketLength)
+            .map(bp => BucketPosition(bp.x, bp.y, bp.z, mag, a.additionalCoordinates))
+            .toList
+          _ <- Fox.serialCombined(bucketPositions) {
+            bucketPosition =>
+              for {
+                data <- loadBucket(dataLayer, bucketPosition)
+                typedData = UnsignedIntegerArray.fromByteArray(data, volumeTracing.elementClass)
+                filteredData = typedData.map(elem =>
+                  if (elem.toLong == a.id) UnsignedInteger.zeroFromElementClass(volumeTracing.elementClass) else elem)
+                filteredBytes = UnsignedIntegerArray.toByteArray(filteredData, volumeTracing.elementClass)
+                _ <- saveBucket(dataLayer, bucketPosition, filteredBytes, version)
+                _ <- updateSegmentIndex(segmentIndexBuffer,
+                                        bucketPosition,
+                                        filteredBytes,
+                                        Some(data),
+                                        volumeTracing.elementClass)
+              } yield ()
+          }
+        } yield ()
+      })
+      _ <- segmentIndexBuffer.flush()
+    } yield volumeTracing
+
   private def assertMagIsValid(tracing: VolumeTracing, mag: Vec3Int): Fox[Unit] =
     if (tracing.resolutions.nonEmpty) {
       bool2Fox(tracing.resolutions.exists(r => vec3IntFromProto(r) == mag))