Add neuron reconstruction job backend and frontend part

app/controllers/JobsController.scala

@@ -149,6 +149,33 @@ class JobsController @Inject()(jobDAO: JobDAO,
       }
     }
 
+  def runInferNeuronsJob(organizationName: String,
+                         dataSetName: String,
+                         layerName: String,
+                         bbox: String): Action[AnyContent] =
+    sil.SecuredAction.async { implicit request =>
+      log(Some(slackNotificationService.noticeFailedJobRequest)) {
+        for {
+          organization <- organizationDAO.findOneByName(organizationName) ?~> Messages("organization.notFound",
+                                                                                       organizationName)
+          _ <- bool2Fox(request.identity._organization == organization._id) ?~> "job.inferNeurons.notAllowed.organization" ~> FORBIDDEN
+          dataSet <- dataSetDAO.findOneByNameAndOrganization(dataSetName, organization._id) ?~> Messages(
+            "dataSet.notFound",
+            dataSetName) ~> NOT_FOUND
+          command = "infer_neurons"
+          commandArgs = Json.obj(
+            "organization_name" -> organizationName,
+            "dataset_name" -> dataSetName,
+            "layer_name" -> layerName,
+            "webknossos_token" -> RpcTokenHolder.webKnossosToken,
+            "bbox" -> bbox,
+          )
+          job <- jobService.submitJob(command, commandArgs, request.identity, dataSet._dataStore) ?~> "job.couldNotRunNeuronInferral"
+          js <- jobService.publicWrites(job)
+        } yield Ok(js)
+      }
+    }
+
   def runExportTiffJob(organizationName: String,
                        dataSetName: String,
                        bbox: String,

conf/messages

@@ -337,6 +337,7 @@ job.couldNotRunCubing = Failed to start WKW conversion job.
 job.couldNotRunTiffExport = Failed to start Tiff export job.
 job.couldNotRunComputeMeshFile = Failed to start mesh file computation job.
 job.couldNotRunNucleiInferral = Failed to start nuclei inferral job.
+job.couldNotRunNeuronInferral = Failed to start neuron inferral job.
 job.disabled = Long-running jobs are not enabled for this webKnossos instance.
 jobs.worker.notFound = Could not find this worker in the database.
 job.export.fileNotFound = Exported file not found. The link may be expired.
@@ -345,6 +346,7 @@ job.export.tiff.volumeExceeded = The volume of the selected bounding box is too
 job.export.tiff.edgeLengthExceeded = An edge length of the selected bounding box is too large.
 job.export.notAllowed.organization = Currently tiff export is only allowed for datasets of your own organization.
 job.inferNuclei.notAllowed.organization = Currently nuclei inferral is only allowed for datasets of your own organization.
+job.inferNeurons.notAllowed.organization = Currently neuron inferral is only allowed for datasets of your own organization.
 job.meshFile.notAllowed.organization = Calculating mesh files is only allowed for datasets of your own organization.
 
 agglomerateSkeleton.failed=Could not generate agglomerate skeleton.

conf/webknossos.latest.routes

@@ -206,6 +206,7 @@ GET           /jobs/run/convertToWkw/:organizationName/:dataSetName            c
 GET           /jobs/run/computeMeshFile/:organizationName/:dataSetName         controllers.JobsController.runComputeMeshFileJob(organizationName: String, dataSetName: String, layerName: String, mag: String, agglomerateView: Option[String])
 GET           /jobs/run/exportTiff/:organizationName/:dataSetName              controllers.JobsController.runExportTiffJob(organizationName: String, dataSetName: String, bbox: String, layerName: Option[String], tracingId: Option[String], tracingVersion: Option[String], annotationId: Option[String], annotationType: Option[String], hideUnmappedIds: Option[Boolean], mappingName: Option[String], mappingType: Option[String])
 GET           /jobs/run/inferNuclei/:organizationName/:dataSetName             controllers.JobsController.runInferNucleiJob(organizationName: String, dataSetName: String, layerName: Option[String])
+GET           /jobs/run/inferNeurons/:organizationName/:dataSetName            controllers.JobsController.runInferNeuronsJob(organizationName: String, dataSetName: String, layerName: String, bbox: String)
 GET           /jobs/:id                                                        controllers.JobsController.get(id: String)
 PATCH         /jobs/:id/cancel                                                 controllers.JobsController.cancel(id: String)
 POST          /jobs/:id/status                                                 controllers.WKRemoteWorkerController.updateJobStatus(key: String, id: String)

frontend/javascripts/admin/admin_rest_api.js

@@ -1039,6 +1039,19 @@ export function startNucleiInferralJob(
   );
 }
 
+export function startNeuronInferralJob(
+  organizationName: string,
+  datasetName: string,
+  layerName: string,
+  bbox: Vector6,
+): Promise<APIJob> {
+  return Request.receiveJSON(
+    `/api/jobs/run/inferNeurons/${organizationName}/${datasetName}?layerName=${layerName}&bbox=${bbox.join(
+      ",",
+    )}`,
+  );
+}
+
 export function getDatasetDatasource(
   dataset: APIMaybeUnimportedDataset,
 ): Promise<APIDataSourceWithMessages> {

frontend/javascripts/admin/job/job_list_view.js

@@ -230,6 +230,20 @@ class JobListView extends React.PureComponent<Props, State> {
           )}
         </span>
       );
+    } else if (job.type === "reconstruct_neurons") {
+      return (
+        <span>
+          {job.state === "SUCCESS" && job.result && job.organizationName && (
+            <Link
+              to={`/datasets/${job.organizationName}/${job.result}/view`}
+              title="View Segmentation"
+            >
+              <EyeOutlined />
+              View
+            </Link>
+          )}
+        </span>
+      );
     } else return null;
   };
 

frontend/javascripts/libs/utils.js

@@ -163,6 +163,13 @@ export function capitalize(str: string): string {
   return str[0].toUpperCase() + str.slice(1);
 }
 
+export function capitalizeWords(str: string): string {
+  return str
+    .split(" ")
+    .map(capitalize)
+    .join(" ");
+}
+
 function intToHex(int: number, digits: number = 6): string {
   return (_.repeat("0", digits) + int.toString(16)).slice(-digits);
 }

frontend/javascripts/oxalis/model/accessors/tracing_accessor.js

@@ -5,6 +5,7 @@ import type {
   ReadOnlyTracing,
   SkeletonTracing,
   Tracing,
+  UserBoundingBox,
   VolumeTracing,
 } from "oxalis/store";
 import { type ServerTracing, type TracingType, TracingTypeEnum } from "types/api_flow_types";
@@ -69,3 +70,8 @@ export function selectTracing(
 
   return volumeTracing;
 }
+
+export const getUserBoundingBoxesFromState = (state: OxalisState): Array<UserBoundingBox> => {
+  const maybeSomeTracing = maybeGetSomeTracing(state.tracing);
+  return maybeSomeTracing != null ? maybeSomeTracing.userBoundingBoxes : [];
+};

frontend/javascripts/oxalis/model/sagas/save_saga.js

@@ -83,7 +83,10 @@ import {
 } from "oxalis/model/accessors/volumetracing_accessor";
 import { getResolutionInfo } from "oxalis/model/accessors/dataset_accessor";
 import { globalPositionToBucketPosition } from "oxalis/model/helpers/position_converter";
-import { maybeGetSomeTracing, selectTracing } from "oxalis/model/accessors/tracing_accessor";
+import {
+  getUserBoundingBoxesFromState,
+  selectTracing,
+} from "oxalis/model/accessors/tracing_accessor";
 import { selectQueue } from "oxalis/model/accessors/save_accessor";
 import { setBusyBlockingInfoAction } from "oxalis/model/actions/ui_actions";
 import Date from "libs/date";
@@ -171,11 +174,6 @@ function unpackRelevantActionForUndo(action): RelevantActionsForUndoRedo {
   throw new Error("Could not unpack redux action from channel");
 }
 
-const getUserBoundingBoxesFromState = state => {
-  const maybeSomeTracing = maybeGetSomeTracing(state.tracing);
-  return maybeSomeTracing != null ? maybeSomeTracing.userBoundingBoxes : [];
-};
-
 export function* collectUndoStates(): Saga<void> {
   const undoStack: Array<UndoState> = [];
   const redoStack: Array<UndoState> = [];

frontend/javascripts/oxalis/view/components/setting_input_views.js

@@ -507,15 +507,9 @@ export class ColorSetting extends React.PureComponent<ColorSettingPropTypes> {
     style = style || {};
     return (
       <div
-        id="color-picker-wrapper"
+        className="color-display-wrapper"
         style={{
           backgroundColor: value,
-          display: "inline-block",
-          width: 16,
-          height: 16,
-          borderRadius: 3,
-          boxShadow: "0px 0px 3px #cacaca",
-          verticalAlign: "middle",
           ...style,
         }}
       >

frontend/javascripts/oxalis/view/right-border-tabs/dataset_info_tab_view.js

@@ -32,7 +32,15 @@ import EditableTextLabel from "oxalis/view/components/editable_text_label";
 import Model from "oxalis/model";
 import features from "features";
 import Store, { type OxalisState, type Task, type Tracing } from "oxalis/store";
-import NucleiInferralModal from "oxalis/view/right-border-tabs/nuclei_inferral_modal";
+import {
+  NucleiInferralModal,
+  NeuronInferralModal,
+} from "oxalis/view/right-border-tabs/starting_job_modals";
+
+const StartableJobsEnum = {
+  NUCLEI_INFERRAL: "nuclei inferral",
+  NEURON_INFERRAL: "neuron inferral",
+};
 
 type StateProps = {|
   tracing: Tracing,
@@ -49,7 +57,7 @@ type DispatchProps = {|
 type Props = {| ...StateProps, ...DispatchProps |};
 
 type State = {
-  showNucleiInferralModal: boolean,
+  showJobsDetailsModal: ?$Values<typeof StartableJobsEnum>,
 };
 
 const shortcuts = [
@@ -134,7 +142,7 @@ export function convertPixelsToNm(
 
 class DatasetInfoTabView extends React.PureComponent<Props, State> {
   state = {
-    showNucleiInferralModal: false,
+    showJobsDetailsModal: null,
   };
 
   setAnnotationName = (newName: string) => {
@@ -200,7 +208,8 @@ class DatasetInfoTabView extends React.PureComponent<Props, State> {
   }
 
   getProcessingJobsMenu = () => {
-    if (!this.props.dataset.jobsEnabled) {
+    const { dataset } = this.props;
+    if (!dataset.jobsEnabled) {
       return (
         <tr>
           <td style={{ paddingRight: 4, paddingTop: 10, verticalAlign: "top" }}>
@@ -216,21 +225,34 @@ class DatasetInfoTabView extends React.PureComponent<Props, State> {
         </tr>
       );
     }
-    const overlay = (
-      <Menu>
-        <Menu.Item onClick={() => this.setState({ showNucleiInferralModal: true })}>
-          <Tooltip title="Start a job that automatically detects nuclei for this dataset.">
-            Start Nuclei Inferral
+    const jobMenuItems = [
+      <Menu.Item
+        key="start_nuclei_inferal"
+        onClick={() => this.setState({ showJobsDetailsModal: StartableJobsEnum.NUCLEI_INFERRAL })}
+      >
+        <Tooltip title="Start a job that automatically detects nuclei for this dataset.">
+          Start Nuclei Inferral
+        </Tooltip>
+      </Menu.Item>,
+    ];
+    if (this.props.activeUser != null && this.props.activeUser.isAdmin) {
+      jobMenuItems.push(
+        <Menu.Item
+          key="start_neuron_inferral"
+          onClick={() => this.setState({ showJobsDetailsModal: StartableJobsEnum.NEURON_INFERRAL })}
+        >
+          <Tooltip title="Start a job that automatically reconstructs neurons for this dataset.">
+            Start Neuron Inferral
           </Tooltip>
-        </Menu.Item>
-      </Menu>
-    );
+        </Menu.Item>,
+      );
+    }
     return (
       <tr>
         <td style={{ paddingRight: 4, paddingTop: 10, verticalAlign: "top" }}>
           <StarOutlined className="info-tab-icon" style={{ fontSize: 18 }} />
         </td>
-        <Dropdown overlay={overlay} overlayStyle={{ minWidth: "unset" }}>
+        <Dropdown overlay={<Menu>{jobMenuItems}</Menu>} overlayStyle={{ minWidth: "unset" }}>
           <td>
             <Button type="link" style={{ padding: 0 }}>
               Process Dataset
@@ -434,6 +456,16 @@ class DatasetInfoTabView extends React.PureComponent<Props, State> {
     return null;
   }
 
+  renderSelectedStartingJobsModal() {
+    const handleClose = () => this.setState({ showJobsDetailsModal: null });
+    if (this.state.showJobsDetailsModal === StartableJobsEnum.NUCLEI_INFERRAL) {
+      return <NucleiInferralModal handleClose={handleClose} />;
+    } else if (this.state.showJobsDetailsModal === StartableJobsEnum.NEURON_INFERRAL) {
+      return <NeuronInferralModal handleClose={handleClose} />;
+    }
+    return null;
+  }
+
   render() {
     const { dataset, activeResolution, activeUser } = this.props;
     const isDatasetViewMode =
@@ -523,12 +555,7 @@ class DatasetInfoTabView extends React.PureComponent<Props, State> {
                 : null}
             </tbody>
           </table>
-          {this.state.showNucleiInferralModal ? (
-            <NucleiInferralModal
-              dataset={dataset}
-              handleClose={() => this.setState({ showNucleiInferralModal: false })}
-            />
-          ) : null}
+          {this.renderSelectedStartingJobsModal()}
         </div>
 
         <div className="info-tab-block">{this.getTracingStatistics()}</div>