Implement option to export proofreading as segmentation

CHANGELOG.unreleased.md

@@ -13,6 +13,7 @@ For upgrade instructions, please check the [migration guide](MIGRATIONS.released
 ### Added
 - Added the total volume of a dataset to a tooltip in the dataset info tab. [#8229](https://github.com/scalableminds/webknossos/pull/8229)
 - Optimized performance of data loading with “fill value“ chunks. [#8271](https://github.com/scalableminds/webknossos/pull/8271)
+- Added the option to export a segmentation that was corrected with the proofreading tool to a new segmentation. [#8286](https://github.com/scalableminds/webknossos/pull/8286)
 - The fill tool can now be adapted so that it only acts within a specified bounding box. Use the new "Restrict Floodfill" mode for that in the toolbar. [#8267](https://github.com/scalableminds/webknossos/pull/8267)
 - Added the option for "Selective Segment Visibility" for segmentation layers. Select this option in the left sidebar to only show segments that are currently active or hovered.  [#8281](https://github.com/scalableminds/webknossos/pull/8281)
 - A segment can be activated with doubleclick now. [#8281](https://github.com/scalableminds/webknossos/pull/8281)

app/controllers/JobController.scala

@@ -379,7 +379,9 @@ class JobController @Inject()(
                                         newDatasetName: String,
                                         outputSegmentationLayerName: String,
                                         mergeSegments: Boolean,
-                                        volumeLayerName: Option[String]): Action[AnyContent] =
+                                        volumeLayerName: Option[String],
+                                        includesEditableMapping: Boolean,
+                                        boundingBox: Option[String]): Action[AnyContent] =
     sil.SecuredAction.async { implicit request =>
       log(Some(slackNotificationService.noticeFailedJobRequest)) {
         for {
@@ -393,6 +395,9 @@ class JobController @Inject()(
           command = JobCommand.materialize_volume_annotation
           _ <- datasetService.assertValidDatasetName(newDatasetName)
           _ <- datasetService.assertValidLayerNameLax(outputSegmentationLayerName)
+          multiUser <- multiUserDAO.findOne(request.identity._multiUser)
+          _ <- Fox.runIf(!multiUser.isSuperUser && includesEditableMapping)(Fox.runOptional(boundingBox)(bbox =>
+            jobService.assertBoundingBoxLimits(bbox, None)))
           commandArgs = Json.obj(
             "organization_id" -> organization._id,
             "dataset_name" -> dataset.name,
@@ -403,7 +408,9 @@ class JobController @Inject()(
             "annotation_type" -> annotationType,
             "new_dataset_name" -> newDatasetName,
             "merge_segments" -> mergeSegments,
-            "volume_layer_name" -> volumeLayerName
+            "volume_layer_name" -> volumeLayerName,
+            "use_zarr_streaming" -> includesEditableMapping,
+            "bounding_box" -> boundingBox
           )
           job <- jobService.submitJob(command, commandArgs, request.identity, dataset._dataStore) ?~> "job.couldNotRunApplyMergerMode"
           js <- jobService.publicWrites(job)

conf/webknossos.latest.routes

@@ -268,7 +268,7 @@ POST          /jobs/run/inferNuclei/:datasetId
 POST          /jobs/run/inferNeurons/:datasetId                                                 controllers.JobController.runInferNeuronsJob(datasetId: String, layerName: String, bbox: String, newDatasetName: 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])
+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], includesEditableMapping: Boolean, boundingBox: Option[String])
 POST          /jobs/run/findLargestSegmentId/:datasetId                                         controllers.JobController.runFindLargestSegmentIdJob(datasetId: String, layerName: String)
 POST          /jobs/run/renderAnimation/:datasetId                                              controllers.JobController.runRenderAnimationJob(datasetId: String)
 GET           /jobs/:id                                                                         controllers.JobController.get(id: String)

frontend/javascripts/admin/api/jobs.ts

@@ -208,6 +208,8 @@ function startSegmentationAnnotationDependentJob(
   annotationId: string,
   annotationType: APIAnnotationType,
   mergeSegments?: boolean,
+  includesEditableMapping?: boolean,
+  boundingBox?: Vector6,
 ): Promise<APIJob> {
   const requestURL = new URL(`/api/jobs/run/${jobURLPath}/${datasetId}`, location.origin);
   if (volumeLayerName != null) {
@@ -222,6 +224,12 @@ function startSegmentationAnnotationDependentJob(
   if (mergeSegments != null) {
     requestURL.searchParams.append("mergeSegments", mergeSegments.toString());
   }
+  if (includesEditableMapping != null) {
+    requestURL.searchParams.append("includesEditableMapping", includesEditableMapping.toString());
+  }
+  if (boundingBox) {
+    requestURL.searchParams.append("boundingBox", boundingBox.join(","));
+  }
   return Request.receiveJSON(requestURL.href, {
     method: "POST",
   });
@@ -235,6 +243,8 @@ export function startMaterializingVolumeAnnotationJob(
   annotationId: string,
   annotationType: APIAnnotationType,
   mergeSegments: boolean,
+  includesEditableMapping: boolean,
+  boundingBox?: Vector6,
 ): Promise<APIJob> {
   return startSegmentationAnnotationDependentJob(
     "materializeVolumeAnnotation",
@@ -245,6 +255,8 @@ export function startMaterializingVolumeAnnotationJob(
     annotationId,
     annotationType,
     mergeSegments,
+    includesEditableMapping,
+    boundingBox,
   );
 }
 

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

@@ -891,6 +891,7 @@ export function MaterializeVolumeAnnotationModal({
 }: MaterializeVolumeAnnotationModalProps) {
   const dataset = useSelector((state: OxalisState) => state.dataset);
   const tracing = useSelector((state: OxalisState) => state.tracing);
+  let includesEditableMapping = false;
   const activeSegmentationTracingLayer = useSelector(getActiveSegmentationTracingLayer);
   const fixedSelectedLayer = selectedVolumeLayer || activeSegmentationTracingLayer;
   const readableVolumeLayerName =
@@ -925,6 +926,10 @@ export function MaterializeVolumeAnnotationModal({
         output dataset and the output segmentation layer.
       </p>
     );
+  } else if (fixedSelectedLayer && "tracingId" in fixedSelectedLayer) {
+    includesEditableMapping =
+      tracing.volumes.find((volume) => volume.tracingId === fixedSelectedLayer.tracingId)
+        ?.hasEditableMapping === true;
   }
   const jobImage =
     jobNameToImagePath[jobName] != null ? (
@@ -954,8 +959,13 @@ export function MaterializeVolumeAnnotationModal({
         jobName={"materialize_volume_annotation"}
         suggestedDatasetSuffix="with_merged_segmentation"
         chooseSegmentationLayer
+        isBoundingBoxConfigurable={includesEditableMapping}
         fixedSelectedLayer={fixedSelectedLayer}
-        jobApiCall={async ({ newDatasetName, selectedLayer: segmentationLayer }) => {
+        jobApiCall={async ({
+          newDatasetName,
+          selectedLayer: segmentationLayer,
+          selectedBoundingBox,
+        }) => {
           // There are 3 cases for the value assignments to volumeLayerName and baseSegmentationName for the job:
           // 1. There is a volume annotation with a fallback layer. volumeLayerName will reference the volume layer
           // and baseSegmentationName will reference the fallback layer. The job will merge those layers.
@@ -968,6 +978,9 @@ export function MaterializeVolumeAnnotationModal({
               ? getReadableNameOfVolumeLayer(segmentationLayer, tracing)
               : null;
           const baseSegmentationName = getBaseSegmentationName(segmentationLayer);
+          const bbox = selectedBoundingBox?.boundingBox
+            ? computeArrayFromBoundingBox(selectedBoundingBox.boundingBox)
+            : undefined;
           return startMaterializingVolumeAnnotationJob(
             dataset.id,
             baseSegmentationName,
@@ -976,6 +989,8 @@ export function MaterializeVolumeAnnotationModal({
             tracing.annotationId,
             tracing.annotationType,
             isMergerModeEnabled,
+            includesEditableMapping,
+            bbox,
           );
         }}
         description={