Check bounding boxes and trees before starting neuron segmentation (#8678)

### Steps to test:
- enable long-running jobs
- create an annotation and open the `AI jobs` modal. select neuron
segmentation. enable `Evaluation settings`. Either of the following
conditions should yield a corresponding error toasts and prevent you
from starting the job:
    - having no skeleton trees
    - having an empty skeleton (any trees without nodes)
    - having no user bounding boxes
    - having multiple user bounding boxes
    - having exactly one user bounding box and a task bounding box.
- all this should be independent of the selected bounding box.
- open the annotation of a finished task. if a bounding box appears in
the bounding box tab, this bounding box should be selectable in the
bounding box dropdown of the modal. after selecting it (given that there
are skeletons with nodes), you should be able to start the job.

- the scene controller was adjusted in the place where the task bounding
boxes are updated. thus you should create some tasks with different
bounding boxes and check after clicking `Finish and get next task` the
lime green task bounding box is updated within the view port.
 
### context
questions/feedback:
https://scm.slack.com/archives/C5AKLAV0B/p1749201952606739

### TODOs:
- [x] maybe incorporate feedback from slack

### Issues:
- fixes #8537 

------
(Please delete unneeded items, merge only when none are left open)
- [x] Updated
[changelog](../blob/master/CHANGELOG.unreleased.md#unreleased)
- [ ] Updated [migration
guide](../blob/master/MIGRATIONS.unreleased.md#unreleased) if applicable
- [x] ❓ Updated [documentation](../blob/master/docs) if
applicable [not much in the docs anyway, description was added to modal]
- [ ] Adapted [wk-libs python
client](https://github.com/scalableminds/webknossos-libs/tree/master/webknossos/webknossos/client)
if relevant API parts change
- [ ] Removed dev-only changes like prints and application.conf edits
- [x] Considered [common edge
cases](../blob/master/.github/common_edge_cases.md)
- [ ] Needs datastore update after deployment

---------

Co-authored-by: Florian M <fm3@users.noreply.github.com>
Co-authored-by: Philipp Otto <philipp.4096@gmail.com>

Author: 3 people

frontend/javascripts/messages.tsx

@@ -503,4 +503,6 @@ instead. Only enable this option if you understand its effect. All layers will n
     `This feature is not available in your organization's plan. Ask the owner of your organization ${organizationOwnerName} to upgrade to a ${requiredPlan} plan or higher.`,
   "organization.plan.feature_not_available.owner": (requiredPlan: string) =>
     `This feature is not available in your organization's plan. Consider upgrading to a ${requiredPlan} plan or higher.`,
+  "jobs.wrongNumberOfBoundingBoxes":
+    "To use the split/merger evaluation, make sure to have exactly one bounding box, either user-defined or from a task.",
 };

frontend/javascripts/viewer/controller/scene_controller.ts

@@ -329,13 +329,18 @@ class SceneController {
      adding a new one. Since this function is executed very rarely,
      this is not a performance problem.
      */
-    for (const [tracingId, boundingBox] of Object.entries(taskCubeByTracingId)) {
+
+    // Clean up old entries
+    for (const [tracingId, _boundingBox] of Object.entries(this.taskCubeByTracingId)) {
       let taskCube = this.taskCubeByTracingId[tracingId];
-      // Remove the old box if it exists
       if (taskCube != null) {
         taskCube.getMeshes().forEach((mesh) => this.rootNode.remove(mesh));
       }
       this.taskCubeByTracingId[tracingId] = null;
+    }
+    // Add new entries
+    for (const [tracingId, boundingBox] of Object.entries(taskCubeByTracingId)) {
+      let taskCube = this.taskCubeByTracingId[tracingId];
       if (boundingBox == null || Store.getState().task == null) {
         continue;
       }
@@ -728,7 +733,7 @@ class SceneController {
         this.updateMeshesAccordingToLayerVisibility(),
       ),
       listenToStoreProperty(
-        (storeState) => getTaskBoundingBoxes(storeState.annotation),
+        (storeState) => getTaskBoundingBoxes(storeState),
         (boundingBoxesByTracingId) => this.updateTaskBoundingBoxes(boundingBoxesByTracingId),
         true,
       ),

frontend/javascripts/viewer/model/accessors/skeletontracing_accessor.ts

@@ -117,6 +117,10 @@ export function findTreeByNodeId(trees: TreeMap, nodeId: number): Tree | undefin
   return trees.values().find((tree) => tree.nodes.has(nodeId));
 }
 
+export function hasEmptyTrees(trees: TreeMap): boolean {
+  return trees.values().some((tree: Tree) => tree.nodes.size() === 0);
+}
+
 export function findTreeByName(trees: TreeMap, treeName: string): Tree | undefined {
   return trees.values().find((tree: Tree) => tree.name === treeName);
 }

frontend/javascripts/viewer/model/accessors/tracing_accessor.ts

@@ -86,9 +86,10 @@ export function selectTracing(
   return tracing;
 }
 
-function _getTaskBoundingBoxes(annotation: StoreAnnotation) {
-  const layers = _.compact([annotation.skeleton, ...annotation.volumes, annotation.readOnly]);
-
+function _getTaskBoundingBoxes(state: WebknossosState) {
+  const { annotation, task } = state;
+  if (task == null) return {};
+  const layers = _.compact([annotation.skeleton, ...annotation.volumes]);
   return Object.fromEntries(layers.map((l) => [l.tracingId, l.boundingBox]));
 }
 

frontend/javascripts/viewer/view/action-bar/starting_job_modals.tsx

@@ -47,6 +47,7 @@ import {
   rgbToHex,
 } from "libs/utils";
 import _ from "lodash";
+import messages from "messages";
 import React, { useEffect, useState, useMemo } from "react";
 import { useDispatch } from "react-redux";
 import { type APIDataLayer, type APIJob, APIJobType, type VoxelSize } from "types/api_types";
@@ -56,7 +57,11 @@ import {
   getMagInfo,
   getSegmentationLayers,
 } from "viewer/model/accessors/dataset_accessor";
-import { getUserBoundingBoxesFromState } from "viewer/model/accessors/tracing_accessor";
+import { hasEmptyTrees } from "viewer/model/accessors/skeletontracing_accessor";
+import {
+  getTaskBoundingBoxes,
+  getUserBoundingBoxesFromState,
+} from "viewer/model/accessors/tracing_accessor";
 import {
   getActiveSegmentationTracingLayer,
   getReadableNameOfVolumeLayer,
@@ -636,6 +641,19 @@ function CollapsibleSplitMergerEvaluationSettings({
           children: (
             <Row>
               <Col style={{ width: "100%" }}>
+                <div style={{ marginBottom: 24 }}>
+                  You can evaluate splits/mergers on a given bounding box. <br />
+                  By default this is the user defined bounding box or the bounding box of a task.{" "}
+                  <br />
+                  Thus your annotation should contain
+                  <ul>
+                    <li> either one user defined bounding box or the bounding box of a task</li>
+                    <li>
+                      with at least one neuron (sparse) or all neurons (dense) annotated as
+                      skeletons.
+                    </li>
+                  </ul>
+                </div>
                 <Form.Item
                   layout="horizontal"
                   label="Use sparse ground truth tracing"
@@ -1054,9 +1072,10 @@ export function NucleiDetectionForm() {
 export function NeuronSegmentationForm() {
   const dataset = useWkSelector((state) => state.dataset);
   const { neuronInferralCostPerGVx } = features();
-  const hasSkeletonAnnotation = useWkSelector((state) => state.annotation.skeleton != null);
+  const skeletonAnnotation = useWkSelector((state) => state.annotation.skeleton);
   const dispatch = useDispatch();
   const [doSplitMergerEvaluation, setDoSplitMergerEvaluation] = React.useState(false);
+
   return (
     <StartJobForm
       handleClose={() => dispatch(setAIJobModalStateAction("invisible"))}
@@ -1099,6 +1118,31 @@ export function NeuronSegmentationForm() {
             doSplitMergerEvaluation,
           );
         }
+
+        const state = Store.getState();
+        const userBoundingBoxCount = getUserBoundingBoxesFromState(state).length;
+
+        if (userBoundingBoxCount > 1) {
+          Toast.error(messages["jobs.wrongNumberOfBoundingBoxes"]);
+          return;
+        }
+
+        const taskBoundingBoxes = getTaskBoundingBoxes(state);
+        if (Object.values(taskBoundingBoxes).length + userBoundingBoxCount !== 1) {
+          Toast.error(messages["jobs.wrongNumberOfBoundingBoxes"]);
+          return;
+        }
+
+        if (skeletonAnnotation == null || skeletonAnnotation.trees.size() === 0) {
+          Toast.error(
+            "Please ensure that a skeleton tree exists within the selected bounding box.",
+          );
+          return;
+        }
+        if (hasEmptyTrees(skeletonAnnotation.trees)) {
+          Toast.error("Please ensure that all skeleton trees in this annotation have some nodes.");
+          return;
+        }
         return startNeuronInferralJob(
           dataset.id,
           colorLayer.name,
@@ -1126,7 +1170,7 @@ export function NeuronSegmentationForm() {
         </>
       }
       jobSpecificInputFields={
-        hasSkeletonAnnotation && (
+        skeletonAnnotation != null && (
           <CollapsibleSplitMergerEvaluationSettings
             isActive={doSplitMergerEvaluation}
             setActive={setDoSplitMergerEvaluation}

unreleased_changes/8678.md

@@ -0,0 +1,2 @@
+### Changed
+- Before starting a neuron segmentation with `Evaluation Settings` enabled, it is checked that a useful bounding box was selected and that some skeletons exist within the annotation, preventing the job from failing.