Create Annotation From View Mode: Keep Activated Mapping (#6647)

* [WIP] Create Annotation From View Mode: Keep Activated Mapping * fix typing errors * pass active mapping name when creating explorational from dataset view mode * clean up * changelog * also use potentially active mapping when making a segmentation layer editable (i.e., adding a volume annotation layer) Co-authored-by: Philipp Otto <[email protected]> Co-authored-by: Philipp Otto <[email protected]>
scalableminds · Nov 23, 2022 · a40db75 · a40db75
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diff --git a/CHANGELOG.unreleased.md b/CHANGELOG.unreleased.md
@@ -19,6 +19,7 @@ For upgrade instructions, please check the [migration guide](MIGRATIONS.released
 - When adding remote Zarr datasets with multiple channels, channels are converted into layers. [#6609](https://github.com/scalableminds/webknossos/pull/6609)
 - When adding a remote OME-NGFF dataset with labels, these are added as segmentation layers. [#6638](https://github.com/scalableminds/webknossos/pull/6638)
 - The scale bar is now included in screenshots of the viewports made using the `Q` shortcut or the "Screenshot" menu entry. If the scale bar should not be included, disable it using "Settings - Viewport Options - Show Scalebars". [#6644](https://github.com/scalableminds/webknossos/pull/6644)
+- When creating an annotation from the dataset view, a previously selected mapping of the segmentation layer is now automatically selected in the volume annotation layer fallback segmentation as well. [#6647](https://github.com/scalableminds/webknossos/pull/6647)
 
 ### Changed
 - The log viewer in the Voxelytics workflow reporting now uses a virtualized list. [#6579](https://github.com/scalableminds/webknossos/pull/6579)

diff --git a/app/controllers/AnnotationController.scala b/app/controllers/AnnotationController.scala
@@ -33,6 +33,7 @@ import scala.concurrent.duration._
 
 case class AnnotationLayerParameters(typ: AnnotationLayerType,
                                      fallbackLayerName: Option[String],
+                                     mappingName: Option[String] = None,
                                      resolutionRestrictions: Option[ResolutionRestrictions],
                                      name: String)
 object AnnotationLayerParameters {

diff --git a/app/controllers/LegacyApiController.scala b/app/controllers/LegacyApiController.scala
@@ -427,6 +427,7 @@ class LegacyApiController @Inject()(annotationController: AnnotationController,
         Some(
           AnnotationLayerParameters(AnnotationLayerType.Skeleton,
                                     request.body.fallbackLayerName,
+                                    None,
                                     request.body.resolutionRestrictions,
                                     name = AnnotationLayer.defaultSkeletonLayerName))
     val volumeParameters =
@@ -435,6 +436,7 @@ class LegacyApiController @Inject()(annotationController: AnnotationController,
         Some(
           AnnotationLayerParameters(AnnotationLayerType.Volume,
                                     request.body.fallbackLayerName,
+                                    None,
                                     request.body.resolutionRestrictions,
                                     name = AnnotationLayer.defaultVolumeLayerName))
     List(skeletonParameters, volumeParameters).flatten

diff --git a/app/models/annotation/AnnotationService.scala b/app/models/annotation/AnnotationService.scala
@@ -139,7 +139,8 @@ class AnnotationService @Inject()(
       boundingBox: Option[BoundingBox] = None,
       startPosition: Option[Vec3Int] = None,
       startRotation: Option[Vec3Double] = None,
-      resolutionRestrictions: ResolutionRestrictions
+      resolutionRestrictions: ResolutionRestrictions,
+      mappingName: Option[String]
   ): Fox[VolumeTracing] = {
     val resolutions = VolumeTracingDownsampling.resolutionsForVolumeTracing(dataSource, fallbackLayer)
     val resolutionsRestricted = resolutionRestrictions.filterAllowed(resolutions)
@@ -160,6 +161,7 @@ class AnnotationService @Inject()(
         0,
         VolumeTracingDefaults.zoomLevel,
         organizationName = Some(datasetOrganizationName),
+        mappingName = mappingName,
         resolutions = resolutionsRestricted.map(vec3IntToProto)
       )
   }
@@ -249,7 +251,8 @@ class AnnotationService @Inject()(
                 datasetOrganizationName,
                 fallbackLayer,
                 resolutionRestrictions =
-                  annotationLayerParameters.resolutionRestrictions.getOrElse(ResolutionRestrictions.empty)
+                  annotationLayerParameters.resolutionRestrictions.getOrElse(ResolutionRestrictions.empty),
+                mappingName = annotationLayerParameters.mappingName
               )
               volumeTracingAdapted = oldPrecedenceLayerProperties.map { p =>
                 volumeTracing.copy(
@@ -361,6 +364,7 @@ class AnnotationService @Inject()(
       newAnnotationLayerParameters = AnnotationLayerParameters(
         newAnnotationLayerType,
         usedFallbackLayerName,
+        None,
         Some(ResolutionRestrictions.empty),
         AnnotationLayer.defaultNameForType(newAnnotationLayerType))
       _ <- addAnnotationLayer(annotation, organizationName, newAnnotationLayerParameters) ?~> "makeHybrid.createTracings.failed"
@@ -524,7 +528,8 @@ class AnnotationService @Inject()(
         },
         startPosition = Some(startPosition),
         startRotation = Some(startRotation),
-        resolutionRestrictions = resolutionRestrictions
+        resolutionRestrictions = resolutionRestrictions,
+        mappingName = None
       )
     } yield volumeTracing
 

diff --git a/frontend/javascripts/admin/admin_rest_api.ts b/frontend/javascripts/admin/admin_rest_api.ts
@@ -661,6 +661,7 @@ type AnnotationLayerCreateDescriptor = {
   typ: "Skeleton" | "Volume";
   name: string;
   fallbackLayerName?: string | null | undefined;
+  mappingName?: string | null | undefined;
   resolutionRestrictions?: APIResolutionRestrictions | null | undefined;
 };
 
@@ -789,6 +790,7 @@ export function createExplorational(
   datasetId: APIDatasetId,
   typ: TracingType,
   fallbackLayerName?: string | null | undefined,
+  mappingName?: string | null | undefined,
   resolutionRestrictions?: APIResolutionRestrictions | null | undefined,
   options: RequestOptions = {},
 ): Promise<APIAnnotation> {
@@ -808,6 +810,7 @@ export function createExplorational(
         typ: "Volume",
         name: fallbackLayerName || "Volume",
         fallbackLayerName,
+        mappingName,
         resolutionRestrictions,
       },
     ];
@@ -821,6 +824,7 @@ export function createExplorational(
         typ: "Volume",
         name: fallbackLayerName || "Volume",
         fallbackLayerName,
+        mappingName,
         resolutionRestrictions,
       },
     ];

diff --git a/frontend/javascripts/oxalis/view/action_bar_view.tsx b/frontend/javascripts/oxalis/view/action_bar_view.tsx
@@ -12,7 +12,7 @@ import {
 import { trackAction } from "oxalis/model/helpers/analytics";
 import AddNewLayoutModal from "oxalis/view/action-bar/add_new_layout_modal";
 import { withAuthentication } from "admin/auth/authentication_modal";
-import type { ViewMode, ControlMode } from "oxalis/constants";
+import { ViewMode, ControlMode, MappingStatusEnum } from "oxalis/constants";
 import constants, { ControlModeEnum } from "oxalis/constants";
 import DatasetPositionView from "oxalis/view/action-bar/dataset_position_view";
 import type { OxalisState } from "oxalis/store";
@@ -26,6 +26,7 @@ import {
   is2dDataset,
   doesSupportVolumeWithFallback,
   getVisibleSegmentationLayer,
+  getMappingInfoForSupportedLayer,
 } from "oxalis/model/accessors/dataset_accessor";
 import { AsyncButton } from "components/async_clickables";
 
@@ -96,7 +97,22 @@ class ActionBarView extends React.PureComponent<Props, State> {
       maybeSegmentationLayer && doesSupportVolumeWithFallback(dataset, maybeSegmentationLayer)
         ? maybeSegmentationLayer.name
         : null;
-    const annotation = await createExplorational(dataset, "hybrid", fallbackLayerName);
+
+    const mappingInfo = getMappingInfoForSupportedLayer(Store.getState());
+    let maybeMappingName = null;
+    if (
+      mappingInfo.mappingStatus !== MappingStatusEnum.DISABLED &&
+      mappingInfo.mappingType === "HDF5"
+    ) {
+      maybeMappingName = mappingInfo.mappingName;
+    }
+
+    const annotation = await createExplorational(
+      dataset,
+      "hybrid",
+      fallbackLayerName,
+      maybeMappingName,
+    );
     trackAction("Create hybrid tracing (from view mode)");
     location.href = `${location.origin}/annotations/${annotation.typ}/${annotation.id}${location.hash}`;
   };

diff --git a/frontend/javascripts/oxalis/view/left-border-tabs/modals/add_volume_layer_modal.tsx b/frontend/javascripts/oxalis/view/left-border-tabs/modals/add_volume_layer_modal.tsx
@@ -8,11 +8,12 @@ import {
   NewVolumeLayerSelection,
   RestrictResolutionSlider,
 } from "dashboard/advanced_dataset/create_explorative_modal";
-import type { Tracing } from "oxalis/store";
+import Store, { type Tracing } from "oxalis/store";
 import { addAnnotationLayer } from "admin/admin_rest_api";
 import {
   getDatasetResolutionInfo,
   getLayerByName,
+  getMappingInfo,
   getSegmentationLayers,
 } from "oxalis/model/accessors/dataset_accessor";
 import {
@@ -23,6 +24,7 @@ import messages from "messages";
 import InputComponent from "oxalis/view/components/input_component";
 import api from "oxalis/api/internal_api";
 import Toast from "libs/toast";
+import { MappingStatusEnum } from "oxalis/constants";
 
 export type ValidationResult = { isValid: boolean; message: string };
 export function checkForLayerNameDuplication(
@@ -162,6 +164,19 @@ export default function AddVolumeLayerModal({
     } else {
       selectedSegmentationLayer = getLayerByName(dataset, selectedSegmentationLayerName);
       const fallbackLayerName = selectedSegmentationLayer.name;
+
+      const mappingInfo = getMappingInfo(
+        Store.getState().temporaryConfiguration.activeMappingByLayer,
+        selectedSegmentationLayerName,
+      );
+      let maybeMappingName = null;
+      if (
+        mappingInfo.mappingStatus !== MappingStatusEnum.DISABLED &&
+        mappingInfo.mappingType === "HDF5"
+      ) {
+        maybeMappingName = mappingInfo.mappingName;
+      }
+
       await addAnnotationLayer(tracing.annotationId, tracing.annotationType, {
         typ: "Volume",
         name: newLayerName,
@@ -170,6 +185,7 @@ export default function AddVolumeLayerModal({
           min: minResolutionAllowed,
           max: maxResolutionAllowed,
         },
+        mappingName: maybeMappingName,
       });
     }
 

diff --git a/frontend/javascripts/router.tsx b/frontend/javascripts/router.tsx
@@ -584,6 +584,7 @@ class ReactRouter extends React.Component<Props> {
                         dataset,
                         type,
                         fallbackLayerName,
+                        null,
                         resolutionRestrictions,
                       );
                       trackAction(`Create ${type} tracing`);

diff --git a/frontend/javascripts/test/puppeteer/dataset_rendering_helpers.ts b/frontend/javascripts/test/puppeteer/dataset_rendering_helpers.ts
@@ -84,6 +84,7 @@ async function _screenshotAnnotationHelper(
     typ,
     fallbackLayerName,
     null,
+    null,
     options,
   );
 
@@ -107,6 +108,7 @@ export async function screenshotDatasetWithMapping(
     "skeleton",
     null,
     null,
+    null,
     options,
   );
   await openTracingView(page, baseUrl, createdExplorational.id);
@@ -128,6 +130,7 @@ export async function screenshotDatasetWithMappingLink(
     "skeleton",
     null,
     null,
+    null,
     options,
   );
   await openTracingView(page, baseUrl, createdExplorational.id, optionalViewOverride);