Allow to restore older volume versions (#3349)

* collect all bucket on version restore and refresh view, add placeholder if no versions are available * fix lint, fix tests * add version when requesting segmentation layer buckets * allow version restore for volumes * add possibilty to specify a version in a dataRequest #3146 * fix tests * add changelog entry and change docs * reset to newest volume version when closing version view
scalableminds · Oct 16, 2018 · be56b0b · be56b0b
1 parent b2a9789
commit be56b0b
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -12,6 +12,7 @@ For upgrade instructions, please check the [migration guide](MIGRATIONS.md).
 ### Added
 
 - Added support for duplicate dataset names for different organizations [#3137](https://github.com/scalableminds/webknossos/pull/3137)
+- Extended the version restore view and added a view to restore older versions of a volume tracing. Access it through the dropdown next to the Save button. [#3349](https://github.com/scalableminds/webknossos/pull/3349)
 - Added support to watch additional dataset directories, automatically creating symbolic links to the main directory [#3330](https://github.com/scalableminds/webknossos/pull/3330)
 - A User can now have multiple layouts for tracing views. [#3299](https://github.com/scalableminds/webknossos/pull/3299)
 

diff --git a/app/assets/javascripts/oxalis/model/bucket_data_handling/data_cube.js b/app/assets/javascripts/oxalis/model/bucket_data_handling/data_cube.js
@@ -275,6 +275,18 @@ class DataCube {
     this.bucketIterator = ++this.bucketIterator % this.MAXIMUM_BUCKET_COUNT;
   }
 
+  collectAllBuckets(): void {
+    for (const bucket of this.buckets) {
+      if (bucket != null) {
+        this.collectBucket(bucket);
+        bucket.trigger("bucketCollected");
+      }
+    }
+    this.buckets = [];
+    this.bucketCount = 0;
+    this.bucketIterator = 0;
+  }
+
   collectBucket(bucket: DataBucket): void {
     const address = bucket.zoomedAddress;
     const bucketIndex = this.getBucketIndex(address);

diff --git a/app/assets/javascripts/oxalis/model/bucket_data_handling/layer_rendering_manager.js b/app/assets/javascripts/oxalis/model/bucket_data_handling/layer_rendering_manager.js
@@ -79,6 +79,7 @@ export default class LayerRenderingManager {
   };
   name: string;
   isSegmentation: boolean;
+  needsRefresh: boolean = false;
 
   constructor(
     name: string,
@@ -96,6 +97,10 @@ export default class LayerRenderingManager {
     this.isSegmentation = isSegmentation;
   }
 
+  refresh() {
+    this.needsRefresh = true;
+  }
+
   setupDataTextures(): void {
     const bytes = getByteCount(Store.getState().dataset, this.name);
 
@@ -164,14 +169,16 @@ export default class LayerRenderingManager {
       (isArbitrary && !_.isEqual(this.lastZoomedMatrix, matrix)) ||
       viewMode !== this.lastViewMode ||
       sphericalCapRadius !== this.lastSphericalCapRadius ||
-      isInvisible !== this.lastIsInvisible
+      isInvisible !== this.lastIsInvisible ||
+      this.needsRefresh
     ) {
       this.lastSubBucketLocality = subBucketLocality;
       this.lastAreas = areas;
       this.lastZoomedMatrix = matrix;
       this.lastViewMode = viewMode;
       this.lastSphericalCapRadius = sphericalCapRadius;
       this.lastIsInvisible = isInvisible;
+      this.needsRefresh = false;
 
       const bucketQueue = new PriorityQueue({
         // small priorities take precedence

diff --git a/app/assets/javascripts/oxalis/model/bucket_data_handling/wkstore_adapter.js b/app/assets/javascripts/oxalis/model/bucket_data_handling/wkstore_adapter.js
@@ -30,6 +30,7 @@ export type SendBucketInfo = {
 type RequestBucketInfo = {
   ...SendBucketInfo,
   fourBit: boolean,
+  version: ?number,
 };
 
 // Converts a zoomed address ([x, y, z, zoomStep] array) into a bucket JSON
@@ -38,9 +39,11 @@ const createRequestBucketInfo = (
   zoomedAddress: Vector4,
   resolutions: Array<Vector3>,
   fourBit: boolean,
+  version: ?number,
 ): RequestBucketInfo => ({
   ...createSendBucketInfo(zoomedAddress, resolutions),
   fourBit,
+  ...(version != null ? { version } : {}),
 });
 
 function createSendBucketInfo(zoomedAddress: Vector4, resolutions: Array<Vector3>): SendBucketInfo {
@@ -55,12 +58,14 @@ export async function requestFromStore(
   layerInfo: DataLayerType,
   batch: Array<Vector4>,
 ): Promise<{ buffer: Uint8Array, missingBuckets: number[] }> {
-  const fourBit =
-    Store.getState().datasetConfiguration.fourBit &&
-    !isSegmentationLayer(Store.getState().dataset, layerInfo.name);
-  const resolutions = getResolutions(Store.getState().dataset);
+  const state = Store.getState();
+  const isSegmentation = isSegmentationLayer(state.dataset, layerInfo.name);
+  const fourBit = state.datasetConfiguration.fourBit && !isSegmentation;
+  const resolutions = getResolutions(state.dataset);
+  const version =
+    isSegmentation && state.tracing.volume != null ? state.tracing.volume.version : null;
   const bucketInfo = batch.map(zoomedAddress =>
-    createRequestBucketInfo(zoomedAddress, resolutions, fourBit),
+    createRequestBucketInfo(zoomedAddress, resolutions, fourBit, version),
   );
 
   return doWithToken(async token => {

diff --git a/app/assets/javascripts/oxalis/model/sagas/save_saga.js b/app/assets/javascripts/oxalis/model/sagas/save_saga.js
@@ -418,17 +418,23 @@ export function* saveTracingTypeAsync(tracingType: "skeleton" | "volume"): Saga<
     }
   }
   yield* take("WK_READY");
-  const allowUpdate = yield* select(
+  const initialAllowUpdate = yield* select(
     state => state.tracing[tracingType] && state.tracing.restrictions.allowUpdate,
   );
-  if (!allowUpdate) return;
+  if (!initialAllowUpdate) return;
 
   while (true) {
     if (tracingType === "skeleton") {
       yield* take([...SkeletonTracingSaveRelevantActions, ...FlycamActions, "UNDO", "REDO"]);
     } else {
       yield* take([...VolumeTracingSaveRelevantActions, ...FlycamActions]);
     }
+    // The allowUpdate setting could have changed in the meantime
+    const allowUpdate = yield* select(
+      state => state.tracing[tracingType] && state.tracing.restrictions.allowUpdate,
+    );
+    if (!allowUpdate) return;
+
     const tracing = yield* select(state => state.tracing);
     const flycam = yield* select(state => state.flycam);
     const items = compactUpdateActions(

diff --git a/app/assets/javascripts/oxalis/model/sagas/volumetracing_saga.js b/app/assets/javascripts/oxalis/model/sagas/volumetracing_saga.js
@@ -146,6 +146,9 @@ function* createVolumeLayer(planeId: OrthoView): Saga<VolumeLayer> {
 }
 
 function* labelWithIterator(iterator, contourTracingMode): Saga<void> {
+  const allowUpdate = yield* select(state => state.tracing.restrictions.allowUpdate);
+  if (!allowUpdate) return;
+
   const activeCellId = yield* select(state => enforceVolumeTracing(state.tracing).activeCellId);
   const segmentationLayer = yield* call([Model, Model.getSegmentationLayer]);
   const { cube } = segmentationLayer;
@@ -168,6 +171,9 @@ function* labelWithIterator(iterator, contourTracingMode): Saga<void> {
 }
 
 function* copySegmentationLayer(action: CopySegmentationLayerAction): Saga<void> {
+  const allowUpdate = yield* select(state => state.tracing.restrictions.allowUpdate);
+  if (!allowUpdate) return;
+
   const activeViewport = yield* select(state => state.viewModeData.plane.activeViewport);
   if (activeViewport === "TDView") {
     // Cannot copy labels from 3D view

diff --git a/app/assets/javascripts/oxalis/view/action-bar/tracing_actions_view.js b/app/assets/javascripts/oxalis/view/action-bar/tracing_actions_view.js
@@ -350,7 +350,7 @@ class TracingActionsView extends PureComponent<Props, State> {
       );
     }
 
-    if (isSkeletonMode && restrictions.allowUpdate) {
+    if (restrictions.allowUpdate) {
       elements.push(
         <Menu.Item key="restore-button" onClick={this.handleRestore}>
           <Icon type="bars" theme="outlined" />

diff --git a/app/assets/javascripts/oxalis/view/version_list.js b/app/assets/javascripts/oxalis/view/version_list.js
@@ -1,7 +1,7 @@
 // @flow
 import * as React from "react";
 import _ from "lodash";
-import { Spin, List } from "antd";
+import { List } from "antd";
 import Store from "oxalis/store";
 import { ControlModeEnum } from "oxalis/constants";
 import Model from "oxalis/model";
@@ -27,10 +27,20 @@ type State = {
   versions: Array<APIUpdateActionBatch>,
 };
 
+const VERSION_LIST_PLACEHOLDER = { emptyText: "No versions created yet." };
+
 export async function previewVersion(versions?: Versions) {
   const { tracingType, annotationId } = Store.getState().tracing;
   await api.tracing.restart(tracingType, annotationId, ControlModeEnum.TRACE, versions);
   Store.dispatch(setAnnotationAllowUpdateAction(false));
+
+  const segmentationLayer = Model.getSegmentationLayer();
+  const shouldPreviewVolumeVersion = versions != null && versions.volume != null;
+  const shouldPreviewNewestVersion = versions == null;
+  if (segmentationLayer != null && (shouldPreviewVolumeVersion || shouldPreviewNewestVersion)) {
+    segmentationLayer.cube.collectAllBuckets();
+    segmentationLayer.layerRenderingManager.refresh();
+  }
 }
 
 class VersionList extends React.Component<Props, State> {
@@ -80,21 +90,22 @@ class VersionList extends React.Component<Props, State> {
     );
 
     return (
-      <Spin spinning={this.state.isLoading}>
-        <List>
-          {filteredVersions.map((batch, index) => (
-            <VersionEntry
-              actions={batch.value}
-              version={batch.version}
-              isNewest={index === 0}
-              isActive={this.props.tracing.version === batch.version}
-              onRestoreVersion={this.restoreVersion}
-              onPreviewVersion={version => previewVersion({ [this.props.tracingType]: version })}
-              key={batch.version}
-            />
-          ))}
-        </List>
-      </Spin>
+      <List
+        dataSource={filteredVersions}
+        loading={this.state.isLoading}
+        locale={VERSION_LIST_PLACEHOLDER}
+        renderItem={(batch, index) => (
+          <VersionEntry
+            actions={batch.value}
+            version={batch.version}
+            isNewest={index === 0}
+            isActive={this.props.tracing.version === batch.version}
+            onRestoreVersion={this.restoreVersion}
+            onPreviewVersion={version => previewVersion({ [this.props.tracingType]: version })}
+            key={batch.version}
+          />
+        )}
+      />
     );
   }
 }

diff --git a/app/assets/javascripts/oxalis/view/version_view.js b/app/assets/javascripts/oxalis/view/version_view.js
@@ -74,8 +74,7 @@ class VersionView extends React.Component<Props, State> {
                 <VersionList tracingType="skeleton" tracing={this.props.tracing.skeleton} />
               </TabPane>
             ) : null}
-            {/* "TODO: Enable after volume version restore was implemented" */}
-            {this.props.tracing.volume != null && false ? (
+            {this.props.tracing.volume != null ? (
               <TabPane tab="Volume" key="volume">
                 <VersionList tracingType="volume" tracing={this.props.tracing.volume} />
               </TabPane>

diff --git a/app/assets/javascripts/test/model/binary/layers/wkstore_adapter.spec.js b/app/assets/javascripts/test/model/binary/layers/wkstore_adapter.spec.js
@@ -33,6 +33,7 @@ const StoreMock = {
       dataSource,
     },
     datasetConfiguration: { fourBit: _fourBit },
+    tracing: {},
   }),
   dispatch: sinon.stub(),
 };

diff --git a/app/assets/javascripts/test/sagas/skeletontracing_saga.spec.js b/app/assets/javascripts/test/sagas/skeletontracing_saga.spec.js
@@ -113,20 +113,21 @@ const createBranchPointAction = SkeletonTracingActions.createBranchPointAction(
 test("SkeletonTracingSaga should create a tree if there is none (saga test)", t => {
   const saga = saveTracingTypeAsync("skeleton");
   expectValueDeepEqual(t, saga.next(), take("INITIALIZE_SKELETONTRACING"));
-  saga.next({ initSkeleton: true });
+  saga.next();
   saga.next({ tracing: { trees: {} } });
   t.is(saga.next(true).value.PUT.action.type, "CREATE_TREE");
 });
 
 test("SkeletonTracingSaga shouldn't do anything if unchanged (saga test)", t => {
   const saga = saveTracingTypeAsync("skeleton");
   expectValueDeepEqual(t, saga.next(), take("INITIALIZE_SKELETONTRACING"));
-  saga.next({ initSkeleton: true });
+  saga.next();
   saga.next(initialState.tracing);
   saga.next(false);
   saga.next();
   saga.next(true);
   saga.next();
+  saga.next(true);
   saga.next(initialState.tracing);
   // only updateTracing
   const items = execCall(t, saga.next(initialState.flycam));
@@ -138,12 +139,13 @@ test("SkeletonTracingSaga should do something if changed (saga test)", t => {
 
   const saga = saveTracingTypeAsync("skeleton");
   expectValueDeepEqual(t, saga.next(), take("INITIALIZE_SKELETONTRACING"));
-  saga.next({ initSkeleton: true });
+  saga.next();
   saga.next(initialState.tracing);
   saga.next(false);
   saga.next();
   saga.next(true);
   saga.next();
+  saga.next(true);
   saga.next(newState.tracing);
   const items = execCall(t, saga.next(newState.flycam));
   t.true(withoutUpdateTracing(items).length > 0);

diff --git a/app/assets/javascripts/test/sagas/volumetracing_saga.spec.js b/app/assets/javascripts/test/sagas/volumetracing_saga.spec.js
@@ -69,11 +69,12 @@ const resetContourAction = VolumeTracingActions.resetContourAction();
 test("VolumeTracingSaga shouldn't do anything if unchanged (saga test)", t => {
   const saga = saveTracingTypeAsync("volume");
   expectValueDeepEqual(t, saga.next(), take("INITIALIZE_VOLUMETRACING"));
-  saga.next({ initVolume: true });
+  saga.next();
   saga.next(initialState.tracing);
   saga.next();
   saga.next(true);
   saga.next();
+  saga.next(true);
   saga.next(initialState.tracing);
   // only updateTracing
   const items = execCall(t, saga.next(initialState.flycam));
@@ -85,11 +86,12 @@ test("VolumeTracingSaga should do something if changed (saga test)", t => {
 
   const saga = saveTracingTypeAsync("volume");
   expectValueDeepEqual(t, saga.next(), take("INITIALIZE_VOLUMETRACING"));
-  saga.next({ initVolume: true });
+  saga.next();
   saga.next(initialState.tracing);
   saga.next();
   saga.next(true);
   saga.next();
+  saga.next(true);
   saga.next(newState.tracing);
   const items = execCall(t, saga.next(newState.flycam));
   t.is(withoutUpdateTracing(items).length, 0);

diff --git a/docs/tracing_ui.md b/docs/tracing_ui.md
@@ -20,7 +20,7 @@ The most common buttons are:
 - `Download`: Starts the download of the current annotation. Skeleton annotations are downloaded as [NML](./data_formats.md#nml) files. Volume annotation downloads contain the raw segmentation data as [WKW](./data_formats.md#wkw) files.
 - `Share`: Create a shareable link to your dataset containing the current position, rotation, zoom level etc. Use this to collaboratively work with colleagues. Read more about this feature in the [Sharing guide](./sharing.md).  
 - `Add Script`: Using the [webKnossos frontend API](https://demo.webknossos.org/assets/docs/frontend-api/index.html) users can interact with webKnossos programmatically. User scripts can be executed from here. Admins can add often used scripts to webKnossos to make them available to all users for easy access.
-- `Restore Older Version`: Only available for skeleton tracings. Opens a view that shows all previous versions of a skeleton tracing. From this view, any older version can be selected, previewed, and restored.
+- `Restore Older Version`: Opens a view that shows all previous versions of a tracing. From this view, any older version can be selected, previewed, and restored.
 - `Import STL Mesh`: 3D Meshes can be imported into the current tracing view by uploading corresponding STL files. Read more information in [Mesh Visualization](#mesh-visualization).
 
 A user can directly jump to positions within their datasets by entering them in the position input field.

diff --git a/webknossos-datastore/app/com/scalableminds/webknossos/datastore/models/DataRequests.scala b/webknossos-datastore/app/com/scalableminds/webknossos/datastore/models/DataRequests.scala
@@ -27,7 +27,8 @@ case class WebKnossosDataRequest(
                                   position: Point3D,
                                   zoomStep: Int,
                                   cubeSize: Int,
-                                  fourBit: Option[Boolean]
+                                  fourBit: Option[Boolean],
+                                  version: Option[Long]
                                 ) extends AbstractDataRequest {
 
   def cuboid(dataLayer: DataLayer) = Cuboid(
@@ -36,7 +37,7 @@ case class WebKnossosDataRequest(
     cubeSize,
     cubeSize)
 
-  def settings = DataServiceRequestSettings(halfByte = fourBit.getOrElse(false))
+  def settings = DataServiceRequestSettings(halfByte = fourBit.getOrElse(false), version)
 }
 
 object WebKnossosDataRequest {

diff --git a/...tore/app/com/scalableminds/webknossos/datastore/models/requests/DataServiceRequests.scala b/...tore/app/com/scalableminds/webknossos/datastore/models/requests/DataServiceRequests.scala
@@ -5,7 +5,7 @@ import java.nio.file.Path
 import com.scalableminds.webknossos.datastore.models.BucketPosition
 import com.scalableminds.webknossos.datastore.models.datasource.{DataLayer, DataSource, SegmentationLayer}
 
-case class DataServiceRequestSettings(halfByte: Boolean)
+case class DataServiceRequestSettings(halfByte: Boolean, version: Option[Long] = None)
 
 object DataServiceRequestSettings {
   val default = DataServiceRequestSettings(halfByte = false)
@@ -22,7 +22,8 @@ case class DataReadInstruction(
                             baseDir: Path,
                             dataSource: DataSource,
                             dataLayer: DataLayer,
-                            bucket: BucketPosition
+                            bucket: BucketPosition,
+                            version: Option[Long] = None
                           ) {
   val cube = bucket.toCube(dataLayer.lengthOfUnderlyingCubes(bucket.resolution))
 }

diff --git a/...sos-datastore/app/com/scalableminds/webknossos/datastore/services/BinaryDataService.scala b/...sos-datastore/app/com/scalableminds/webknossos/datastore/services/BinaryDataService.scala
@@ -86,7 +86,8 @@ class BinaryDataService @Inject()(config: DataStoreConfig) extends FoxImplicits
         dataBaseDir,
         request.dataSource,
         request.dataLayer,
-        bucket)
+        bucket,
+        request.settings.version)
 
       request.dataLayer.bucketProvider.load(readInstruction, cache, loadTimeout)
     } else {

diff --git a/...store/app/com/scalableminds/webknossos/datastore/tracings/volume/VolumeTracingLayer.scala b/...store/app/com/scalableminds/webknossos/datastore/tracings/volume/VolumeTracingLayer.scala
@@ -20,7 +20,7 @@ class VolumeTracingBucketProvider(layer: VolumeTracingLayer)
   val volumeDataStore: FossilDBClient = layer.volumeDataStore
 
   override def load(readInstruction: DataReadInstruction, cache: DataCubeCache, timeout: FiniteDuration)(implicit ec: ExecutionContext): Fox[Array[Byte]] = {
-    loadBucket(layer, readInstruction.bucket)
+    loadBucket(layer, readInstruction.bucket, readInstruction.version)
   }
 
   override def bucketStream(resolution: Int, version: Option[Long] = None): Iterator[(BucketPosition, Array[Byte])] = {