Fix segmentation opacity in recommended tasktype

CHANGELOG.md

@@ -30,6 +30,7 @@ For upgrade instructions, please check the [migration guide](MIGRATIONS.md).
 - Fixed the import of datasets which was temporarily broken. [#4497](https://github.com/scalableminds/webknossos/pull/4497)
 - Fixed the displayed segment ids in segmentation tab when "Render Missing Data Black" is turned off. [#4480](https://github.com/scalableminds/webknossos/pull/4480)
 - The datastore checks if a organization folder can be created before creating a new organization. [#4501](https://github.com/scalableminds/webknossos/pull/4501)
+- Fixed that `segmentationOpacity` could not be set anymore as part of the recommended settings for a task type. [#4545](https://github.com/scalableminds/webknossos/pull/4545)
 
 ### Removed
 

frontend/javascripts/admin/tasktype/recommended_configuration_view.js

@@ -31,6 +31,7 @@ const recommendedConfigByCategory = {
   dataset: {
     fourBit: false,
     interpolation: true,
+    segmentationOpacity: 80,
     highlightHoveredCellId: false,
     zoom: 0.8,
     renderMissingDataBlack: false,
@@ -51,6 +52,7 @@ const recommendedConfigByCategory = {
 export const DEFAULT_RECOMMENDED_CONFIGURATION: $Shape<{|
   ...UserConfiguration,
   ...DatasetConfiguration,
+  segmentationOpacity: number,
 |}> = {
   ...recommendedConfigByCategory.orthogonal,
   ...recommendedConfigByCategory.all,

frontend/javascripts/libs/user_settings.schema.js

@@ -28,6 +28,7 @@ export const userSettings = {
   fourBit: { type: "boolean" },
   interpolation: { type: "boolean" },
   loadingStrategy: { enum: ["BEST_QUALITY_FIRST", "PROGRESSIVE_QUALITY"] },
+  segmentationOpacity: { type: "number", minimum: 0, maximum: 100 },
   highlightHoveredCellId: { type: "boolean" },
   zoom: { type: "number", minimum: 0.005 },
   renderMissingDataBlack: { type: "boolean" },

frontend/javascripts/messages.js

@@ -18,6 +18,7 @@ export const settings = {
   fourBit: "4 Bit",
   interpolation: "Interpolation",
   quality: "Quality",
+  segmentationOpacity: "Segmentation Opacity",
   highlightHoveredCellId: "Highlight Hovered Cells",
   zoom: "Zoom",
   renderMissingDataBlack: "Render Missing Data Black",

frontend/javascripts/oxalis/geometries/plane.js

@@ -165,14 +165,6 @@ class Plane {
     this.crosshair[1].visible = visible && this.displayCrosshair;
   };
 
-  setSegmentationAlpha(alpha: number): void {
-    this.plane.material.setSegmentationAlpha(alpha);
-  }
-
-  setSegmentationVisibility(isVisible: boolean): void {
-    this.plane.material.setSegmentationVisibility(isVisible);
-  }
-
   getMeshes = () => [this.plane, this.TDViewBorders, this.crosshair[0], this.crosshair[1]];
 
   setLinearInterpolationEnabled = (enabled: boolean) => {

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

@@ -8,6 +8,7 @@ import { setZoomStepAction } from "oxalis/model/actions/flycam_actions";
 import {
   updateDatasetSettingAction,
   updateUserSettingAction,
+  updateLayerSettingAction,
 } from "oxalis/model/actions/settings_actions";
 import { setActiveUserAction } from "oxalis/model/actions/user_actions";
 import { setMergerModeEnabledAction } from "oxalis/model/actions/skeletontracing_actions";
@@ -17,6 +18,7 @@ import RecommendedConfigurationModal from "oxalis/view/recommended_configuration
 import Toast from "libs/toast";
 import messages from "messages";
 import renderIndependently from "libs/render_independently";
+import Model from "oxalis/model";
 
 function* maybeShowNewTaskTypeModal(taskType: APITaskType): Saga<void> {
   // Users can acquire new tasks directly in the tracing view. Occasionally,
@@ -41,11 +43,16 @@ function* maybeShowRecommendedConfiguration(taskType: APITaskType): Saga<void> {
   const userConfiguration = yield* select(state => state.userConfiguration);
   const datasetConfiguration = yield* select(state => state.datasetConfiguration);
   const zoomStep = yield* select(state => state.flycam.zoomStep);
+  const segmentationLayerName = yield* call([Model, Model.getSegmentationLayerName]);
+  const segmentationOpacity =
+    segmentationLayerName != null ? datasetConfiguration.layers[segmentationLayerName].alpha : 0;
 
   // $FlowFixMe Cannot call `_.find` because number [1] is incompatible with boolean [2] in property `brushSize` of type argument `T`.
   const configurationDifference = _.find(recommendedConfiguration, (value, key: string) => {
     if (key === "zoom" && zoomStep !== value) {
       return true;
+    } else if (key === "segmentationOpacity" && segmentationOpacity !== value) {
+      return true;
     } else if (key in userConfiguration && userConfiguration[key] !== value) {
       return true;
     } else if (key in datasetConfiguration && datasetConfiguration[key] !== value) {
@@ -72,12 +79,21 @@ function* maybeShowRecommendedConfiguration(taskType: APITaskType): Saga<void> {
     for (const key of Object.keys(recommendedConfiguration)) {
       if (key === "zoom") {
         yield* put(setZoomStepAction(recommendedConfiguration[key]));
+      } else if (key === "segmentationOpacity" && segmentationLayerName != null) {
+        yield* put(
+          updateLayerSettingAction(segmentationLayerName, "alpha", recommendedConfiguration[key]),
+        );
       } else if (key in userConfiguration) {
         // $FlowFixMe Cannot call updateUserSettingAction with key bound to propertyName because an indexer property is missing in UserConfiguration
         yield* put(updateUserSettingAction(key, recommendedConfiguration[key]));
       } else if (key in datasetConfiguration) {
         // $FlowFixMe Cannot call updateDatasetSettingAction with key bound to propertyName because an indexer property is missing in DatasetConfiguration
         yield* put(updateDatasetSettingAction(key, recommendedConfiguration[key]));
+      } else {
+        console.warn(
+          // $FlowIgnore
+          `Cannot apply recommended default for key/value: ${key}/${recommendedConfiguration[key]}`,
+        );
       }
     }
     Toast.success("You are using the recommended settings now.");

frontend/javascripts/oxalis/store.js

@@ -272,6 +272,7 @@ export type RecommendedConfiguration = $Shape<{
   ...UserConfiguration,
   ...DatasetConfiguration,
   zoom: number,
+  segmentationOpacity: number,
 }>;
 
 export type Mapping = { [key: number]: number };

frontend/javascripts/oxalis/view/new_task_description_modal.js

@@ -23,9 +23,12 @@ export default class NewTaskDescriptionModal extends React.Component<Props, Stat
   };
 
   componentDidMount() {
-    this.timeoutId = setTimeout(() => {
-      this.allowClose();
-    }, 10000);
+    this.timeoutId = setTimeout(
+      () => {
+        this.allowClose();
+      },
+      process.env.NODE_ENV === "production" ? 10000 : 2000,
+    );
   }
 
   componentWillUnmount() {