Make isosurfaces more robust (#5102)

* don't crash front-end if isosurface request fails; retry isosurface requests; indicate loading state of isosurfaces also on initial request
* use exponential back off
* improve seed position when importing isosurface via STL file
* update changelog
* ensure the same isosurface is not added twice to the store
* Merge branch 'master' of github.com:scalableminds/webknossos into robust-isosurfaces
* fix CI

Author: philippotto

CHANGELOG.unreleased.md

@@ -11,14 +11,16 @@ For upgrade instructions, please check the [migration guide](MIGRATIONS.released
 [Commits](https://github.com/scalableminds/webknossos/compare/21.02.0...HEAD)
 
 ### Added
+- The "Meshes" tab was overhauled, so that it displays generated isosurfaces and imported meshes. Generated isosurfaces can be jumped to, reloaded, downloaded and removed. [#4917](https://github.com/scalableminds/webknossos/pull/4917)
 - Added an explicit `/signup` (or `/auth/signup`) route. [#5091](https://github.com/scalableminds/webknossos/pull/5091/files)
 
 ### Changed
+- Make the isosurface feature in the meshes tab more robust. If a request fails, a retry is initiated. [#5102](https://github.com/scalableminds/webknossos/pull/5102)
 - Support for the old invite links was removed. These contained the organization name in the URL. The new links contain a token (can be generated in the users view). For instances with a single organization the old invite links should still work. [#5091](https://github.com/scalableminds/webknossos/pull/5091/files)
 - Users are no longer allowed to deactivate their own accounts.  [#5070](https://github.com/scalableminds/webknossos/pull/5070)
 
 ### Fixed
 -
 
 ### Removed
--
+- The isosurface setting was removed. Instead, isosurfaces can be generated via the "Meshes" tab. Also note that the Shift+Click binding for generating an isosurface was removed (for now). Please refer to the "Meshes" tab, too. [#4917](https://github.com/scalableminds/webknossos/pull/4917)

frontend/javascripts/oxalis/model/reducers/annotation_reducer.js

@@ -116,22 +116,26 @@ function AnnotationReducer(state: OxalisState, action: Action): OxalisState {
 
     case "ADD_ISOSURFACE": {
       const { cellId, seedPosition } = action;
-      return updateKey2(state, "isosurfaces", cellId.toString(), {
+      // $FlowIgnore[incompatible-call] updateKey has problems with updating Objects as Dictionaries
+      return updateKey2(state, "isosurfaces", cellId, {
         segmentId: cellId,
         seedPosition,
+        isLoading: false,
       });
     }
 
     case "START_REFRESHING_ISOSURFACE": {
       const { cellId } = action;
-      return updateKey2(state, "isosurfaces", cellId.toString(), {
+      // $FlowIgnore[incompatible-call] updateKey has problems with updating Objects as Dictionaries
+      return updateKey2(state, "isosurfaces", cellId, {
         isLoading: true,
       });
     }
 
     case "FINISHED_REFRESHING_ISOSURFACE": {
       const { cellId } = action;
-      return updateKey2(state, "isosurfaces", cellId.toString(), {
+      // $FlowIgnore[incompatible-call] updateKey has problems with updating Objects as Dictionaries
+      return updateKey2(state, "isosurfaces", cellId, {
         isLoading: false,
       });
     }

frontend/javascripts/oxalis/model/sagas/isosurface_saga.js

@@ -1,6 +1,8 @@
 // @flow
 import { saveAs } from "file-saver";
 
+import { sleep } from "libs/utils";
+import ErrorHandling from "libs/error_handling";
 import type { APIDataset } from "types/api_flow_types";
 import { ResolutionInfo, getResolutionInfo } from "oxalis/model/accessors/dataset_accessor";
 import {
@@ -46,6 +48,9 @@ import { saveNowAction } from "oxalis/model/actions/save_actions";
 import Toast from "libs/toast";
 import messages from "messages";
 
+const MAX_RETRY_COUNT = 5;
+const RETRY_WAIT_TIME = 5000;
+
 const isosurfacesMap: Map<number, ThreeDMap<boolean>> = new Map();
 const cubeSize = [256, 256, 256];
 const modifiedCells: Set<number> = new Set();
@@ -207,9 +212,13 @@ function* loadIsosurfaceWithNeighbors(
     seedPosition != null ? seedPosition : yield* select(state => getFlooredPosition(state.flycam));
   const clippedPosition = clipPositionToCubeBoundary(position, zoomStep, resolutionInfo);
   let positionsToRequest = [clippedPosition];
-  if (seedPosition) {
-    yield* put(addIsosurfaceAction(segmentId, seedPosition));
+
+  const hasIsosurface = yield* select(state => state.isosurfaces[segmentId] != null);
+  if (!hasIsosurface) {
+    yield* put(addIsosurfaceAction(segmentId, position));
   }
+  yield* put(startRefreshingIsosurfaceAction(segmentId));
+
   while (positionsToRequest.length > 0) {
     const currentPosition = positionsToRequest.shift();
     const neighbors = yield* call(
@@ -225,6 +234,8 @@ function* loadIsosurfaceWithNeighbors(
     isInitialRequest = false;
     positionsToRequest = positionsToRequest.concat(neighbors);
   }
+
+  yield* put(finishedRefreshingIsosurfaceAction(segmentId));
 }
 
 function hasBatchCounterExceededLimit(segmentId: number): boolean {
@@ -267,34 +278,46 @@ function* maybeLoadIsosurface(
   const volumeTracing = yield* select(state => state.tracing.volume);
   // Fetch from datastore if no volumetracing exists or if the tracing has a fallback layer.
   const useDataStore = volumeTracing == null || volumeTracing.fallbackLayer != null;
-  const { buffer: responseBuffer, neighbors } = yield* call(
-    computeIsosurface,
-    useDataStore ? dataStoreUrl : tracingStoreUrl,
-    layer,
-    {
-      position: clippedPosition,
-      zoomStep,
-      segmentId,
-      voxelDimensions,
-      cubeSize,
-      scale,
-    },
-  );
 
-  // Check again whether the limit was exceeded, since this variable could have been
-  // set in the mean time by ctrl-clicking the segment to remove it
-  if (hasBatchCounterExceededLimit(segmentId)) {
-    return [];
-  }
-  const vertices = new Float32Array(responseBuffer);
-  if (removeExistingIsosurface) {
-    getSceneController().removeIsosurfaceById(segmentId);
+  let retryCount = 0;
+  while (retryCount < MAX_RETRY_COUNT) {
+    try {
+      const { buffer: responseBuffer, neighbors } = yield* call(
+        computeIsosurface,
+        useDataStore ? dataStoreUrl : tracingStoreUrl,
+        layer,
+        {
+          position: clippedPosition,
+          zoomStep,
+          segmentId,
+          voxelDimensions,
+          cubeSize,
+          scale,
+        },
+      );
+
+      // Check again whether the limit was exceeded, since this variable could have been
+      // set in the mean time by ctrl-clicking the segment to remove it
+      if (hasBatchCounterExceededLimit(segmentId)) {
+        return [];
+      }
+      const vertices = new Float32Array(responseBuffer);
+      if (removeExistingIsosurface) {
+        getSceneController().removeIsosurfaceById(segmentId);
+      }
+      getSceneController().addIsosurfaceFromVertices(vertices, segmentId);
+
+      return neighbors.map(neighbor =>
+        getNeighborPosition(clippedPosition, neighbor, zoomStep, resolutionInfo),
+      );
+    } catch (exception) {
+      retryCount++;
+      ErrorHandling.notify(exception);
+      console.warn("Retrying isosurface generation...");
+      yield* call(sleep, RETRY_WAIT_TIME * 2 ** retryCount);
+    }
   }
-  getSceneController().addIsosurfaceFromVertices(vertices, segmentId);
-
-  return neighbors.map(neighbor =>
-    getNeighborPosition(clippedPosition, neighbor, zoomStep, resolutionInfo),
-  );
+  return [];
 }
 
 function* downloadIsosurfaceCellById(cellId: number): Saga<void> {
@@ -334,7 +357,11 @@ function* importIsosurfaceFromStl(action: ImportIsosurfaceFromStlAction): Saga<v
   const geometry = yield* call(parseStlBuffer, buffer);
   getSceneController().addIsosurfaceFromGeometry(geometry, segmentId);
   yield* put(setImportingMeshStateAction(false));
-  yield* put(addIsosurfaceAction(segmentId, [0, 0, 0])); // TODO: use good position as seed
+
+  // TODO: Ideally, persist the seed position in the STL file. As a workaround,
+  // we simply use the current position as a seed position.
+  const seedPosition = yield* select(state => getFlooredPosition(state.flycam));
+  yield* put(addIsosurfaceAction(segmentId, seedPosition));
 }
 
 function* removeIsosurface(

frontend/javascripts/oxalis/store.js

@@ -453,11 +453,11 @@ type UiInformation = {
   +isRefreshingIsosurfaces: boolean,
 };
 
-type IsosurfaceInformation = {
+export type IsosurfaceInformation = {|
   +segmentId: number,
   +seedPosition: Vector3,
   +isLoading: boolean,
-};
+|};
 
 export type OxalisState = {|
   +datasetConfiguration: DatasetConfiguration,
@@ -471,7 +471,7 @@ export type OxalisState = {|
   +viewModeData: ViewModeData,
   +activeUser: ?APIUser,
   +uiInformation: UiInformation,
-  +isosurfaces: { [segmentId: string]: IsosurfaceInformation },
+  +isosurfaces: { [segmentId: number]: IsosurfaceInformation },
 |};
 
 const sagaMiddleware = createSagaMiddleware();

frontend/javascripts/oxalis/view/right-menu/meshes_view.js

@@ -8,7 +8,7 @@ import _ from "lodash";
 
 import type { ExtractReturn } from "libs/type_helpers";
 import type { MeshMetaData, RemoteMeshMetaData } from "types/api_flow_types";
-import type { OxalisState } from "oxalis/store";
+import type { OxalisState, IsosurfaceInformation } from "oxalis/store";
 import Store from "oxalis/store";
 import Model from "oxalis/model";
 import type { Vector3 } from "oxalis/constants";
@@ -137,7 +137,7 @@ type StateProps = {|
 |};
 type DispatchProps = ExtractReturn<typeof mapDispatchToProps>;
 
-type Props = { ...OwnProps, ...DispatchProps, ...StateProps };
+type Props = {| ...OwnProps, ...DispatchProps, ...StateProps |};
 
 const getCheckboxStyle = isLoaded =>
   isLoaded
@@ -263,10 +263,11 @@ class MeshesView extends React.Component<
       </div>
     );
 
-    const renderIsosurfaceListItem = (isosurface: Object) => {
+    const renderIsosurfaceListItem = (isosurface: IsosurfaceInformation) => {
       const { segmentId, seedPosition, isLoading } = isosurface;
       const centeredCell = getIdForPos(getPosition(this.props.flycam));
-      const actionVisibility = segmentId === this.state.hoveredListItem ? "visible" : "hidden";
+      const actionVisibility =
+        isLoading || segmentId === this.state.hoveredListItem ? "visible" : "hidden";
       return (
         <List.Item
           style={{