Evaluate segmentation in infer neurons task

CHANGELOG.unreleased.md

@@ -11,6 +11,7 @@ For upgrade instructions, please check the [migration guide](MIGRATIONS.released
 [Commits](https://github.com/scalableminds/webknossos/compare/24.11.1...HEAD)
 
 ### Added
+- It is now possible to start a split-merger evaluation when starting a neuron inference. [#8221](https://github.com/scalableminds/webknossos/pull/8221)
 - When exploring remote URIs pasted from Neuroglancer, the format prefixes like `precomputed://` are now ignored, so users don’t have to remove them. [#8195](https://github.com/scalableminds/webknossos/pull/8195)
 
 ### Changed

app/controllers/JobController.scala

@@ -223,7 +223,13 @@ class JobController @Inject()(
   def runInferNeuronsJob(datasetId: String,
                          layerName: String,
                          bbox: String,
-                         newDatasetName: String): Action[AnyContent] =
+                         newDatasetName: String,
+                         doSplitMergerEvaluation: Boolean,
+                         annotationId: Option[String],
+                         evalUseSparseTracing: Option[Boolean],
+                         evalMaxEdgeLength: Option[String],
+                         evalSparseTubeThresholdNm: Option[String],
+                         evalMinMergerPathLengthNm: Option[String]): Action[AnyContent] =
     sil.SecuredAction.async { implicit request =>
       log(Some(slackNotificationService.noticeFailedJobRequest)) {
         for {
@@ -245,6 +251,12 @@ class JobController @Inject()(
             "new_dataset_name" -> newDatasetName,
             "layer_name" -> layerName,
             "bbox" -> bbox,
+            "do_split_merger_evaluation" -> doSplitMergerEvaluation,
+            "annotation_id" -> annotationId,
+            "eval_use_sparse_tracing" -> evalUseSparseTracing,
+            "eval_max_edge_length" -> evalMaxEdgeLength,
+            "eval_sparse_tube_threshold_nm" -> evalSparseTubeThresholdNm,
+            "eval_min_merger_path_length_nm" -> evalMinMergerPathLengthNm,
           )
           job <- jobService.submitJob(command, commandArgs, request.identity, dataset._dataStore) ?~> "job.couldNotRunNeuronInferral"
           js <- jobService.publicWrites(job)

app/models/job/Job.scala

@@ -54,6 +54,7 @@ case class Job(
   def datasetId: Option[String] = argAsStringOpt("dataset_id")
 
   private def argAsStringOpt(key: String) = (commandArgs \ key).toOption.flatMap(_.asOpt[String])
+  private def argAsBooleanOpt(key: String) = (commandArgs \ key).toOption.flatMap(_.asOpt[Boolean])
 
   def resultLink(organizationId: String): Option[String] =
     if (effectiveState != JobState.SUCCESS) None
@@ -66,6 +67,8 @@ case class Job(
           }.getOrElse(datasetName.map(name => s"datasets/$organizationId/$name/view"))
         case JobCommand.export_tiff | JobCommand.render_animation =>
           Some(s"/api/jobs/${this._id}/export")
+        case JobCommand.infer_neurons if this.argAsBooleanOpt("do_evaluation").getOrElse(false) =>
+          returnValue.map { resultAnnotationLink => resultAnnotationLink}
         case JobCommand.infer_nuclei | JobCommand.infer_neurons | JobCommand.materialize_volume_annotation |
             JobCommand.infer_with_model | JobCommand.infer_mitochondria | JobCommand.align_sections =>
           // Old jobs before the dataset renaming changes returned the output dataset name.

conf/application.conf

@@ -151,8 +151,8 @@ features {
   taskReopenAllowedInSeconds = 30
   allowDeleteDatasets = true
   # to enable jobs for local development, use "yarn enable-jobs" to also activate it in the database
-  jobsEnabled = false
-  voxelyticsEnabled = false
+  jobsEnabled = true
+  voxelyticsEnabled = true
   # For new users, the dashboard will show a banner which encourages the user to check out the following dataset.
   # If isWkorgInstance == true, `/createExplorative/hybrid/true` is appended to the URL so that a new tracing is opened.
   # If isWkorgInstance == false, `/view` is appended to the URL so that it's opened in view mode (since the user might not

conf/webknossos.latest.routes

@@ -265,7 +265,7 @@ POST          /jobs/run/computeMeshFile/:datasetId
 POST          /jobs/run/computeSegmentIndexFile/:datasetId                                      controllers.JobController.runComputeSegmentIndexFileJob(datasetId: String, layerName: String)
 POST          /jobs/run/exportTiff/:datasetId                                                   controllers.JobController.runExportTiffJob(datasetId: String, bbox: String, additionalCoordinates: Option[String], layerName: Option[String], mag: Option[String], annotationLayerName: Option[String], annotationId: Option[String], asOmeTiff: Boolean)
 POST          /jobs/run/inferNuclei/:datasetId                                                  controllers.JobController.runInferNucleiJob(datasetId: String, layerName: String, newDatasetName: String)
-POST          /jobs/run/inferNeurons/:datasetId                                                 controllers.JobController.runInferNeuronsJob(datasetId: String, layerName: String, bbox: String, newDatasetName: String)
+POST          /jobs/run/inferNeurons/:datasetId                                                 controllers.JobController.runInferNeuronsJob(datasetId: String, layerName: String, bbox: String, newDatasetName: String, doSplitMergerEvaluation: Boolean, annotationId: Option[String], evalUseSparseTracing: Option[Boolean], evalMaxEdgeLength: Option[String], evalSparseTubeThresholdNm: Option[String], evalMinMergerPathLengthNm: Option[String])
 POST          /jobs/run/inferMitochondria/:datasetId                                            controllers.JobController.runInferMitochondriaJob(datasetId: String, layerName: String, bbox: String, newDatasetName: String)
 POST          /jobs/run/alignSections/:datasetId                                                controllers.JobController.runAlignSectionsJob(datasetId: String, layerName: String, newDatasetName: String, annotationId: Option[String])
 POST          /jobs/run/materializeVolumeAnnotation/:datasetId                                  controllers.JobController.runMaterializeVolumeAnnotationJob(datasetId: String, fallbackLayerName: String, annotationId: String, annotationType: String, newDatasetName: String, outputSegmentationLayerName: String, mergeSegments: Boolean, volumeLayerName: Option[String])

frontend/javascripts/admin/api/jobs.ts

@@ -179,12 +179,37 @@ export function startNeuronInferralJob(
   layerName: string,
   bbox: Vector6,
   newDatasetName: string,
+  doSplitMergerEvaluation: boolean,
+  annotationId?: string,
+  useSparseTracing?: boolean,
+  evalMaxEdgeLength?: string,
+  evalSparseTubeThresholdNm?: string,
+  evalMinMergerPathLengthNm?: string,
 ): Promise<APIJob> {
   const urlParams = new URLSearchParams({
     layerName,
     bbox: bbox.join(","),
     newDatasetName,
+    doSplitMergerEvaluation: doSplitMergerEvaluation.toString(),
   });
+  if (doSplitMergerEvaluation) {
+    if (!annotationId) {
+      throw new Error("annotationId is required when doEvaluation is true");
+    }
+    urlParams.append("annotationId", `${annotationId}`);
+    if (useSparseTracing != null) {
+      urlParams.append("evalUseSparseTracing", `${useSparseTracing}`);
+    }
+    if (evalMaxEdgeLength != null) {
+      urlParams.append("evalMaxEdgeLength", `${evalMaxEdgeLength}`);
+    }
+    if (evalSparseTubeThresholdNm != null) {
+      urlParams.append("evalSparseTubeThresholdNm", `${evalSparseTubeThresholdNm}`);
+    }
+    if (evalMinMergerPathLengthNm != null) {
+      urlParams.append("evalMinMergerPathLengthNm", `${evalMinMergerPathLengthNm}`);
+    }
+  }
   return Request.receiveJSON(`/api/jobs/run/inferNeurons/${datasetId}?${urlParams.toString()}`, {
     method: "POST",
   });

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

@@ -15,6 +15,9 @@ import {
   Switch,
   type FormInstance,
   Checkbox,
+  Collapse,
+  Col,
+  InputNumber,
 } from "antd";
 import {
   startNucleiInferralJob,
@@ -98,6 +101,7 @@ type StartJobFormProps = Props & {
   jobApiCall: (arg0: JobApiCallArgsType, form: FormInstance<any>) => Promise<void | APIJob>;
   jobName: keyof typeof jobNameToImagePath;
   description: React.ReactNode;
+  jobSpecificInputFields?: React.ReactNode | undefined;
   isBoundingBoxConfigurable?: boolean;
   chooseSegmentationLayer?: boolean;
   suggestedDatasetSuffix: string;
@@ -523,11 +527,85 @@ function ShouldUseTreesFormItem() {
   );
 }
 
+function CollapsibleSplitMergersplitMergerEvaluationSettings({
+  isActive = false,
+  setActive,
+}: { isActive: boolean; setActive: (active: boolean) => void }) {
+  return (
+    <Collapse
+      style={{ marginBottom: 8 }}
+      onChange={() => setActive(!isActive)}
+      expandIcon={() => <Checkbox checked={isActive} />}
+      items={[
+        {
+          key: "evaluation",
+          label: "Evaluation Settings",
+          children: (
+            <Row>
+              <Col style={{ width: "100%" }}>
+                <Form.Item
+                  layout="horizontal"
+                  label="Use sparse ground truth tracing"
+                  name={["splitMergerEvaluationSettings", "useSparseTracing"]}
+                  valuePropName="checked"
+                  initialValue={true}
+                  tooltip="The evaluation mode can either be `dense`
+    in case all processes in the volume are annotated in the ground-truth.
+    If not, use the `sparse` mode."
+                >
+                  <Checkbox style={{ width: "100%" }} />
+                </Form.Item>
+                <Form.Item
+                  label="Max edge length in nm"
+                  name={["splitMergerEvaluationSettings", "maxEdgeLength"]}
+                  tooltip="Ground truth tracings can be densified so that
+    nodes are at most max_edge_length nm apart.
+    However, this can also introduce wrong nodes in curved processes."
+                >
+                  <InputNumber style={{ width: "100%" }} placeholder="None" />
+                </Form.Item>
+                <Form.Item
+                  label="Sparse tube threshold in nm"
+                  name={["splitMergerEvaluationSettings", "sparseTubeThresholdInNm"]}
+                  tooltip="Tube threshold for sparse evaluation,
+    determining if a process is too far from the ground-truth."
+                >
+                  <InputNumber style={{ width: "100%" }} placeholder="1000" />
+                </Form.Item>
+                <Form.Item
+                  label="Sparse minimum merger path length in nm"
+                  name={["splitMergerEvaluationSettings", "minimumMergerPathLengthInNm"]}
+                  tooltip="Minimum ground truth path length of a merger component
+    to be counted as a relevant merger (for sparse evaluation).
+    Note, the path length to neighboring nodes of a component is included for this comparison. This optimistic path length
+    estimation makes sure no relevant mergers are ignored."
+                >
+                  <InputNumber style={{ width: "100%" }} placeholder="800" />
+                </Form.Item>
+                <Form.Item name="useAnnotation" initialValue={true} hidden />
+              </Col>
+            </Row>
+          ),
+        },
+      ]}
+      activeKey={isActive ? "evaluation" : []}
+    />
+  );
+}
+
 function StartJobForm(props: StartJobFormProps) {
   const isBoundingBoxConfigurable = props.isBoundingBoxConfigurable || false;
   const isSkeletonSelectable = props.isSkeletonSelectable || false;
   const chooseSegmentationLayer = props.chooseSegmentationLayer || false;
-  const { handleClose, jobName, jobApiCall, fixedSelectedLayer, title, description } = props;
+  const {
+    handleClose,
+    jobName,
+    jobApiCall,
+    fixedSelectedLayer,
+    title,
+    description,
+    jobSpecificInputFields,
+  } = props;
   const [form] = Form.useForm();
   const rawUserBoundingBoxes = useSelector((state: OxalisState) =>
     getUserBoundingBoxesFromState(state),
@@ -650,6 +728,7 @@ function StartJobForm(props: StartJobFormProps) {
         onChangeSelectedBoundingBox={(bBoxId) => form.setFieldsValue({ boundingBoxId: bBoxId })}
         value={form.getFieldValue("boundingBoxId")}
       />
+      {jobSpecificInputFields}
       {isSkeletonSelectable && <ShouldUseTreesFormItem />}
       {props.showWorkflowYaml ? (
         <CollapsibleWorkflowYamlEditor
@@ -701,7 +780,9 @@ export function NucleiDetectionForm() {
 }
 export function NeuronSegmentationForm() {
   const dataset = useSelector((state: OxalisState) => state.dataset);
+  const hasSkeletonAnnotation = useSelector((state: OxalisState) => state.tracing.skeleton != null);
   const dispatch = useDispatch();
+  const [doSplitMergerEvaluation, setDoSplitMergerEvaluation] = React.useState(false);
   return (
     <StartJobForm
       handleClose={() => dispatch(setAIJobModalStateAction("invisible"))}
@@ -710,13 +791,40 @@ export function NeuronSegmentationForm() {
       title="AI Neuron Segmentation"
       suggestedDatasetSuffix="with_reconstructed_neurons"
       isBoundingBoxConfigurable
-      jobApiCall={async ({ newDatasetName, selectedLayer: colorLayer, selectedBoundingBox }) => {
-        if (!selectedBoundingBox) {
+      jobApiCall={async (
+        { newDatasetName, selectedLayer: colorLayer, selectedBoundingBox, annotationId },
+        form: FormInstance<any>,
+      ) => {
+        const splitMergerEvaluationSettings = form.getFieldValue("splitMergerEvaluationSettings");
+        if (
+          !selectedBoundingBox ||
+          (doSplitMergerEvaluation && splitMergerEvaluationSettings == null)
+        ) {
           return;
         }
 
         const bbox = computeArrayFromBoundingBox(selectedBoundingBox.boundingBox);
-        return startNeuronInferralJob(dataset.id, colorLayer.name, bbox, newDatasetName);
+        if (!doSplitMergerEvaluation) {
+          return startNeuronInferralJob(
+            dataset.id,
+            colorLayer.name,
+            bbox,
+            newDatasetName,
+            doSplitMergerEvaluation,
+          );
+        }
+        return startNeuronInferralJob(
+          dataset.id,
+          colorLayer.name,
+          bbox,
+          newDatasetName,
+          doSplitMergerEvaluation,
+          annotationId,
+          splitMergerEvaluationSettings.useSparseTracing,
+          splitMergerEvaluationSettings.maxEdgeLength,
+          splitMergerEvaluationSettings.sparseTubeThresholdInNm,
+          splitMergerEvaluationSettings.minimumMergerPathLengthInNm,
+        );
       }}
       description={
         <>
@@ -731,6 +839,14 @@ export function NeuronSegmentationForm() {
           </Space>
         </>
       }
+      jobSpecificInputFields={
+        hasSkeletonAnnotation && (
+          <CollapsibleSplitMergersplitMergerEvaluationSettings
+            isActive={doSplitMergerEvaluation}
+            setActive={setDoSplitMergerEvaluation}
+          />
+        )
+      }
     />
   );
 }

package.json

@@ -141,7 +141,7 @@
     "@tanstack/react-query-persist-client": "4.36.1",
     "@zip.js/zip.js": "^2.7.32",
     "ansi-to-react": "^6.1.6",
-    "antd": "5.17.4",
+    "antd": "5.18",
     "ball-morphology": "^0.1.0",
     "base64-js": "^1.2.1",
     "beautiful-react-hooks": "^3.11.1",