WIP: Option to invert color layer when starting neuron inferral

app/controllers/AiModelController.scala

@@ -48,7 +48,8 @@ case class RunInferenceParameters(annotationId: Option[ObjectId],
                                   boundingBox: String,
                                   newDatasetName: String,
                                   maskAnnotationLayerName: Option[String],
-                                  workflowYaml: Option[String])
+                                  workflowYaml: Option[String],
+                                  invertColorLayer: Option[Boolean])
 
 object RunInferenceParameters {
   implicit val jsonFormat: OFormat[RunInferenceParameters] = Json.format[RunInferenceParameters]
@@ -196,7 +197,8 @@ class AiModelController @Inject()(
           "model_id" -> request.body.aiModelId,
           "dataset_directory_name" -> request.body.datasetDirectoryName,
           "new_dataset_name" -> request.body.newDatasetName,
-          "custom_workflow_provided_by_user" -> request.body.workflowYaml
+          "custom_workflow_provided_by_user" -> request.body.workflowYaml,
+          "invert_color_layer" -> request.body.invertColorLayer
         )
         newInferenceJob <- jobService.submitJob(jobCommand, commandArgs, request.identity, dataStore.name) ?~> "job.couldNotRunInferWithModel"
         newAiInference = AiInference(

app/controllers/JobController.scala

@@ -202,7 +202,10 @@ class JobController @Inject()(jobDAO: JobDAO,
       } yield Ok(js)
     }
 
-  def runInferNucleiJob(datasetId: ObjectId, layerName: String, newDatasetName: String): Action[AnyContent] =
+  def runInferNucleiJob(datasetId: ObjectId,
+                        layerName: String,
+                        newDatasetName: String,
+                        invertColorLayer: Option[Boolean]): Action[AnyContent] =
     sil.SecuredAction.async { implicit request =>
       log(Some(slackNotificationService.noticeFailedJobRequest)) {
         for {
@@ -220,7 +223,8 @@ class JobController @Inject()(jobDAO: JobDAO,
             "dataset_name" -> dataset.name,
             "dataset_directory_name" -> dataset.directoryName,
             "layer_name" -> layerName,
-            "new_dataset_name" -> newDatasetName
+            "new_dataset_name" -> newDatasetName,
+            "invert_color_layer" -> invertColorLayer
           )
           job <- jobService.submitJob(command, commandArgs, request.identity, dataset._dataStore) ?~> "job.couldNotRunNucleiInferral"
           js <- jobService.publicWrites(job)
@@ -237,7 +241,8 @@ class JobController @Inject()(jobDAO: JobDAO,
                          evalUseSparseTracing: Option[Boolean],
                          evalMaxEdgeLength: Option[Double],
                          evalSparseTubeThresholdNm: Option[Double],
-                         evalMinMergerPathLengthNm: Option[Double]): Action[AnyContent] =
+                         evalMinMergerPathLengthNm: Option[Double],
+                         invertColorLayer: Option[Boolean]): Action[AnyContent] =
     sil.SecuredAction.async { implicit request =>
       log(Some(slackNotificationService.noticeFailedJobRequest)) {
         for {
@@ -267,6 +272,7 @@ class JobController @Inject()(jobDAO: JobDAO,
             "eval_max_edge_length" -> evalMaxEdgeLength,
             "eval_sparse_tube_threshold_nm" -> evalSparseTubeThresholdNm,
             "eval_min_merger_path_length_nm" -> evalMinMergerPathLengthNm,
+            "invert_color_layer" -> invertColorLayer
           )
           creditTransactionComment = s"AI neuron segmentation for dataset ${dataset.name}"
           jobAsJs <- jobService.submitPaidJob(command,

conf/webknossos.latest.routes

@@ -255,8 +255,8 @@ POST          /jobs/run/convertToWkw/:datasetId
 POST          /jobs/run/computeMeshFile/:datasetId                                              controllers.JobController.runComputeMeshFileJob(datasetId: ObjectId, layerName: String, mag: String, agglomerateView: Option[String])
 POST          /jobs/run/computeSegmentIndexFile/:datasetId                                      controllers.JobController.runComputeSegmentIndexFileJob(datasetId: ObjectId, layerName: String)
 POST          /jobs/run/exportTiff/:datasetId                                                   controllers.JobController.runExportTiffJob(datasetId: ObjectId, bbox: String, additionalCoordinates: Option[String], layerName: Option[String], mag: Option[String], annotationLayerName: Option[String], annotationId: Option[ObjectId], asOmeTiff: Boolean)
-POST          /jobs/run/inferNuclei/:datasetId                                                  controllers.JobController.runInferNucleiJob(datasetId: ObjectId, layerName: String, newDatasetName: String)
-POST          /jobs/run/inferNeurons/:datasetId                                                 controllers.JobController.runInferNeuronsJob(datasetId: ObjectId, layerName: String, bbox: String, newDatasetName: String, doSplitMergerEvaluation: Boolean, annotationId: Option[String], evalUseSparseTracing: Option[Boolean], evalMaxEdgeLength: Option[Double], evalSparseTubeThresholdNm: Option[Double], evalMinMergerPathLengthNm: Option[Double])
+POST          /jobs/run/inferNuclei/:datasetId                                                  controllers.JobController.runInferNucleiJob(datasetId: ObjectId, layerName: String, newDatasetName: String, invertColorLayer: Option[Boolean])
+POST          /jobs/run/inferNeurons/:datasetId                                                 controllers.JobController.runInferNeuronsJob(datasetId: ObjectId, layerName: String, bbox: String, newDatasetName: String, doSplitMergerEvaluation: Boolean, annotationId: Option[String], evalUseSparseTracing: Option[Boolean], evalMaxEdgeLength: Option[Double], evalSparseTubeThresholdNm: Option[Double], evalMinMergerPathLengthNm: Option[Double], invertColorLayer: Option[Boolean])
 POST          /jobs/run/inferMitochondria/:datasetId                                            controllers.JobController.runInferMitochondriaJob(datasetId: ObjectId, layerName: String, bbox: String, newDatasetName: String)
 POST          /jobs/run/alignSections/:datasetId                                                controllers.JobController.runAlignSectionsJob(datasetId: ObjectId, layerName: String, newDatasetName: String, annotationId: Option[ObjectId])
 POST          /jobs/run/materializeVolumeAnnotation/:datasetId                                  controllers.JobController.runMaterializeVolumeAnnotationJob(datasetId: ObjectId, fallbackLayerName: String, annotationId: ObjectId, annotationType: String, newDatasetName: String, outputSegmentationLayerName: String, mergeSegments: Boolean, volumeLayerName: Option[String], includesEditableMapping: Boolean, boundingBox: Option[String])

frontend/javascripts/admin/api/jobs.ts

@@ -191,13 +191,18 @@ export function startNucleiInferralJob(
   datasetId: string,
   layerName: string,
   newDatasetName: string,
+  invertColorLayer?: boolean,
 ): Promise<APIJob> {
-  return Request.receiveJSON(
-    `/api/jobs/run/inferNuclei/${datasetId}?layerName=${layerName}&newDatasetName=${newDatasetName}`,
-    {
-      method: "POST",
-    },
-  );
+  const urlParams = new URLSearchParams({
+    layerName,
+    newDatasetName,
+  });
+  if (invertColorLayer != null) {
+    urlParams.append("invertColorLayer", `${invertColorLayer}`);
+  }
+  return Request.receiveJSON(`/api/jobs/run/inferNuclei/${datasetId}?${urlParams.toString()}`, {
+    method: "POST",
+  });
 }
 
 export function startNeuronInferralJob(
@@ -211,6 +216,7 @@ export function startNeuronInferralJob(
   evalMaxEdgeLength?: number,
   evalSparseTubeThresholdNm?: number,
   evalMinMergerPathLengthNm?: number,
+  invertColorLayer?: boolean,
 ): Promise<APIJob> {
   const urlParams = new URLSearchParams({
     layerName,
@@ -236,6 +242,9 @@ export function startNeuronInferralJob(
       urlParams.append("evalMinMergerPathLengthNm", `${evalMinMergerPathLengthNm}`);
     }
   }
+  if (invertColorLayer != null) {
+    urlParams.append("invertColorLayer", `${invertColorLayer}`);
+  }
   return Request.receiveJSON(`/api/jobs/run/inferNeurons/${datasetId}?${urlParams.toString()}`, {
     method: "POST",
   });
@@ -384,6 +393,7 @@ type RunInferenceParameters = {
   boundingBox: Vector6;
   newDatasetName: string;
   workflowYaml?: string;
+  invertColorLayer?: boolean;
   // maskAnnotationLayerName?: string | null
 };
 

unreleased_changes/8796.md

@@ -0,0 +1,2 @@
+### Added
+- When starting an inference job on a dataset with inverted intensity values, that inversion now also applies in the inference job.