isosurfaces for volume tracings

CHANGELOG.unreleased.md

@@ -14,6 +14,7 @@ For upgrade instructions, please check the [migration guide](MIGRATIONS.released
 - Added the possibility to move nodes in skeleton tracings. This can be done either by pressing CTRL + arrow key or by dragging while holding CTRL. [#4743](https://github.com/scalableminds/webknossos/pull/4743)
 - Added the possibility to delete datasets on disk from webKnossos. Use with care. [#4696](https://github.com/scalableminds/webknossos/pull/4696)
 - Added error toasts for failing bucket requests. [#4740](https://github.com/scalableminds/webknossos/pull/4740)
+- Isosurface generation now also supports volume tracings without fallback layer. [#4567](https://github.com/scalableminds/webknossos/pull/4567)
 - Improved the distinguishability of segments by improving the color generation and also by rendering patterns within the segments. The pattern opacity can be adapted in the layer settings (next to the opacity of the segmentation layer). [#4730](https://github.com/scalableminds/webknossos/pull/4730)
 - Added a list of all projects containing tasks of a specific task type. It's accessible from the task types list view. [#4420](https://github.com/scalableminds/webknossos/pull/4745)
 

frontend/javascripts/admin/admin_rest_api.js

@@ -1251,20 +1251,18 @@ type IsosurfaceRequest = {
   segmentId: number,
   voxelDimensions: Vector3,
   cubeSize: Vector3,
+  scale: Vector3,
 };
 
 export function computeIsosurface(
-  datastoreUrl: string,
-  datasetId: APIDatasetId,
+  requestUrl: string,
   layer: DataLayer,
   isosurfaceRequest: IsosurfaceRequest,
 ): Promise<{ buffer: ArrayBuffer, neighbors: Array<number> }> {
-  const { position, zoomStep, segmentId, voxelDimensions, cubeSize } = isosurfaceRequest;
+  const { position, zoomStep, segmentId, voxelDimensions, cubeSize, scale } = isosurfaceRequest;
   return doWithToken(async token => {
     const { buffer, headers } = await Request.sendJSONReceiveArraybufferWithHeaders(
-      `${datastoreUrl}/data/datasets/${datasetId.owningOrganization}/${datasetId.name}/layers/${
-        layer.fallbackLayer != null ? layer.fallbackLayer : layer.name
-      }/isosurface?token=${token}`,
+      `${requestUrl}/isosurface?token=${token}`,
       {
         data: {
           // The back-end needs a small padding at the border of the
@@ -1280,6 +1278,7 @@ export function computeIsosurface(
           mappingType: layer.activeMappingType,
           // "size" of each voxel (i.e., only every nth voxel is considered in each dimension)
           voxelDimensions,
+          scale,
         },
       },
     );

frontend/javascripts/libs/ThreeDMap.js

@@ -44,6 +44,24 @@ export default class ThreeDMap<T> {
       .set(z, value);
   }
 
+  entries(): Array<[T, Vector3]> {
+    const entries: Array<[T, Vector3]> = [];
+    this.map.forEach((atX, x) => {
+      if (!atX) {
+        return;
+      }
+      atX.forEach((atY, y) => {
+        if (!atY) {
+          return;
+        }
+        atY.forEach((value, z) => {
+          entries.push([value, [x, y, z]]);
+        });
+      });
+    });
+    return entries;
+  }
+
   // This could be extended so the key is a Vector1 | Vector2
   // if needed in the future
   delete(key: number): boolean {

frontend/javascripts/oxalis/api/api_latest.js

@@ -71,6 +71,7 @@ import {
   setTreeGroupsAction,
 } from "oxalis/model/actions/skeletontracing_actions";
 import { setPositionAction, setRotationAction } from "oxalis/model/actions/flycam_actions";
+import { refreshIsosurfacesAction } from "oxalis/model/actions/annotation_actions";
 import {
   updateUserSettingAction,
   updateDatasetSettingAction,
@@ -102,6 +103,7 @@ import messages from "messages";
 import window, { location } from "libs/window";
 import { type ElementClass } from "admin/api_flow_types";
 import UserLocalStorage from "libs/user_local_storage";
+import { listenToStoreProperty } from "oxalis/model/helpers/listener_helpers";
 
 type OutdatedDatasetConfigurationKeys = "segmentationOpacity" | "isSegmentationDisabled";
 
@@ -821,6 +823,22 @@ class DataApi {
     return Store.getState().temporaryConfiguration.activeMapping.isMappingEnabled;
   }
 
+  refreshIsosurfaces(): Promise<void> {
+    Store.dispatch(refreshIsosurfacesAction());
+    const isRefreshingComplete = new Promise(resolve => {
+      const unsubscribe = listenToStoreProperty(
+        state => state.uiInformation.refreshingIsosurfaces,
+        refreshingIsosurfaces => {
+          if (!refreshingIsosurfaces) {
+            unsubscribe();
+            resolve();
+          }
+        },
+      );
+    });
+    return isRefreshingComplete;
+  }
+
   /**
    * Returns the bounding box for a given layer name.
    */

frontend/javascripts/oxalis/controller/combinations/segmentation_plane_controller.js

@@ -0,0 +1,33 @@
+// @flow
+import { type OrthoView, type Point2 } from "oxalis/constants";
+import Model from "oxalis/model";
+import { changeActiveIsosurfaceCellAction } from "oxalis/model/actions/segmentation_actions";
+import { calculateGlobalPos } from "oxalis/controller/viewmodes/plane_controller";
+import { getRequestLogZoomStep } from "oxalis/model/accessors/flycam_accessor";
+import Store from "oxalis/store";
+
+function isosurfaceLeftClick(pos: Point2, plane: OrthoView, event: MouseEvent) {
+  if (!event.shiftKey) {
+    return;
+  }
+  let cellId = 0;
+  const position = calculateGlobalPos(pos);
+  const volumeTracingMaybe = Store.getState().tracing.volume;
+  if (volumeTracingMaybe) {
+    cellId = volumeTracingMaybe.activeCellId;
+  } else {
+    const segmentation = Model.getSegmentationLayer();
+    if (!segmentation) {
+      return;
+    }
+    cellId = segmentation.cube.getMappedDataValue(
+      position,
+      getRequestLogZoomStep(Store.getState()),
+    );
+  }
+  if (cellId > 0) {
+    Store.dispatch(changeActiveIsosurfaceCellAction(cellId, position));
+  }
+}
+
+export default isosurfaceLeftClick;

frontend/javascripts/oxalis/controller/combinations/skeletontracing_plane_controller.js

@@ -48,6 +48,7 @@ import Store from "oxalis/store";
 import api from "oxalis/api/internal_api";
 import getSceneController from "oxalis/controller/scene_controller_provider";
 import { renderToTexture } from "oxalis/view/rendering_utils";
+import isosurfaceLeftClick from "oxalis/controller/combinations/segmentation_plane_controller";
 import { getBaseVoxelFactors } from "oxalis/model/scaleinfo";
 import Dimensions from "oxalis/model/dimensions";
 
@@ -85,7 +86,7 @@ export function getPlaneMouseControls(planeView: PlaneView) {
       }
     },
     leftClick: (pos: Point2, plane: OrthoView, event: MouseEvent, isTouch: boolean) =>
-      onClick(planeView, pos, event.shiftKey, event.altKey, event.ctrlKey, plane, isTouch),
+      onClick(planeView, pos, event.shiftKey, event.altKey, event.ctrlKey, plane, isTouch, event),
     rightClick: (pos: Point2, plane: OrthoView, event: MouseEvent) => {
       const { volume } = Store.getState().tracing;
       if (!volume || volume.activeTool !== VolumeToolEnum.BRUSH) {
@@ -183,8 +184,9 @@ function onClick(
   ctrlPressed: boolean,
   plane: OrthoView,
   isTouch: boolean,
+  event?: MouseEvent,
 ): void {
-  if (!shiftPressed && !isTouch) {
+  if (!shiftPressed && !isTouch && !(ctrlPressed && event != null)) {
     // do nothing
     return;
   }
@@ -230,6 +232,8 @@ function onClick(
     } else {
       Store.dispatch(setActiveNodeAction(nodeId));
     }
+  } else if (shiftPressed && event != null) {
+    isosurfaceLeftClick(position, plane, event);
   }
 }
 

frontend/javascripts/oxalis/controller/combinations/volumetracing_plane_controller.js

@@ -36,6 +36,7 @@ import { movePlaneFlycamOrthoAction, setPositionAction } from "oxalis/model/acti
 import Model from "oxalis/model";
 import Store from "oxalis/store";
 import * as Utils from "libs/utils";
+import isosurfaceLeftClick from "oxalis/controller/combinations/segmentation_plane_controller";
 
 // TODO: Build proper UI for this
 window.isAutomaticBrushEnabled = false;
@@ -168,6 +169,7 @@ export function getPlaneMouseControls(_planeId: OrthoView): * {
         );
         if (cellId > 0) {
           Store.dispatch(setActiveCellAction(cellId));
+          isosurfaceLeftClick(pos, plane, event);
         }
       } else if (event.ctrlKey) {
         if (isAutomaticBrushEnabled()) {

frontend/javascripts/oxalis/controller/scene_controller.js

@@ -186,6 +186,7 @@ class SceneController {
       .to({ opacity: 0.95 }, 500)
       .onUpdate(function onUpdate() {
         meshMaterial.opacity = this.opacity;
+        app.vent.trigger("rerender");
       })
       .start();
 

frontend/javascripts/oxalis/controller/viewmodes/plane_controller.js

@@ -10,7 +10,6 @@ import * as React from "react";
 import _ from "lodash";
 
 import { InputKeyboard, InputKeyboardNoLoop, InputMouse, type ModifierKeys } from "libs/input";
-import { changeActiveIsosurfaceCellAction } from "oxalis/model/actions/segmentation_actions";
 import { document } from "libs/window";
 import { getBaseVoxel, getBaseVoxelFactors } from "oxalis/model/scaleinfo";
 import { getViewportScale, getInputCatcherRect } from "oxalis/model/accessors/view_mode_accessor";
@@ -51,6 +50,7 @@ import getSceneController from "oxalis/controller/scene_controller_provider";
 import * as skeletonController from "oxalis/controller/combinations/skeletontracing_plane_controller";
 import * as volumeController from "oxalis/controller/combinations/volumetracing_plane_controller";
 import { downloadScreenshot } from "oxalis/view/rendering_utils";
+import isosurfaceLeftClick from "oxalis/controller/combinations/segmentation_plane_controller";
 
 const MAX_BRUSH_CHANGE_VALUE = 5;
 const BRUSH_CHANGING_CONSTANT = 0.02;
@@ -69,24 +69,6 @@ function ensureNonConflictingHandlers(skeletonControls: Object, volumeControls:
   }
 }
 
-const isosurfaceLeftClick = (pos: Point2, plane: OrthoView, event: MouseEvent) => {
-  if (!event.shiftKey) {
-    return;
-  }
-  const segmentation = Model.getSegmentationLayer();
-  if (!segmentation) {
-    return;
-  }
-  const position = calculateGlobalPos(pos);
-  const cellId = segmentation.cube.getMappedDataValue(
-    position,
-    getRequestLogZoomStep(Store.getState()),
-  );
-  if (cellId > 0) {
-    Store.dispatch(changeActiveIsosurfaceCellAction(cellId, position));
-  }
-};
-
 type StateProps = {|
   tracing: Tracing,
 |};

frontend/javascripts/oxalis/default_state.js

@@ -203,6 +203,7 @@ const defaultState: OxalisState = {
     isImportingMesh: false,
     isInAnnotationView: false,
     hasOrganizations: false,
+    refreshingIsosurfaces: false,
   },
 };
 

frontend/javascripts/oxalis/model/actions/annotation_actions.js

@@ -75,6 +75,14 @@ export type TriggerIsosurfaceDownloadAction = {
   type: "TRIGGER_ISOSURFACE_DOWNLOAD",
 };
 
+export type RefreshIsosurfacesAction = {
+  type: "REFRESH_ISOSURFACES",
+};
+
+export type FinishedRefreshingIsosurfacesAction = {
+  type: "FINISHED_REFRESHING_ISOSURFACES",
+};
+
 export type ImportIsosurfaceFromStlAction = {
   type: "IMPORT_ISOSURFACE_FROM_STL",
   buffer: ArrayBuffer,
@@ -99,6 +107,8 @@ export type AnnotationActionTypes =
   | CreateMeshFromBufferAction
   | UpdateLocalMeshMetaDataAction
   | TriggerIsosurfaceDownloadAction
+  | RefreshIsosurfacesAction
+  | FinishedRefreshingIsosurfacesAction
   | ImportIsosurfaceFromStlAction
   | RemoveIsosurfaceAction;
 
@@ -192,6 +202,14 @@ export const triggerIsosurfaceDownloadAction = (): TriggerIsosurfaceDownloadActi
   type: "TRIGGER_ISOSURFACE_DOWNLOAD",
 });
 
+export const refreshIsosurfacesAction = (): RefreshIsosurfacesAction => ({
+  type: "REFRESH_ISOSURFACES",
+});
+
+export const finishedRefreshingIsosurfacesAction = (): FinishedRefreshingIsosurfacesAction => ({
+  type: "FINISHED_REFRESHING_ISOSURFACES",
+});
+
 export const importIsosurfaceFromStlAction = (
   buffer: ArrayBuffer,
 ): ImportIsosurfaceFromStlAction => ({

frontend/javascripts/oxalis/model/reducers/ui_reducer.js

@@ -31,6 +31,14 @@ function UiReducer(state: OxalisState, action: Action): OxalisState {
       return updateKey(state, "uiInformation", { hasOrganizations: action.value });
     }
 
+    case "REFRESH_ISOSURFACES": {
+      return updateKey(state, "uiInformation", { refreshingIsosurfaces: true });
+    }
+
+    case "FINISHED_REFRESHING_ISOSURFACES": {
+      return updateKey(state, "uiInformation", { refreshingIsosurfaces: false });
+    }
+
     default:
       return state;
   }

frontend/javascripts/oxalis/model/sagas/effect-generators.js.flow

@@ -8,7 +8,7 @@ import {
   type Saga as _Saga,
   channel,
   effects
-} from 'redux-saga';
+} from "redux-saga";
 import {
   all as typedAll,
   race as typedRace,
@@ -19,7 +19,7 @@ import {
   takeLeading as typedTakeLeading,
   throttle as typedThrottle,
   cancel as typedCancel,
-} from 'redux-saga/effects';
+} from "redux-saga/effects";
 
 import type { Action } from "oxalis/model/actions/actions";
 import type { OxalisState } from "oxalis/store";
@@ -37,6 +37,7 @@ declare type Fn3<T1, T2, T3, R> = (t1: T1, t2: T2, t3: T3) => Promise<R> | Gener
 declare type Fn4<T1, T2, T3, T4, R> = (t1: T1, t2: T2, t3: T3, t4: T4) => Promise<R> | Generator<*,R,*> | R;
 declare type Fn5<T1, T2, T3, T4, T5, R> = (t1: T1, t2: T2, t3: T3, t4: T4, t5: T5) => Promise<R> | Generator<*,R,*> | R;
 declare type Fn6<T1, T2, T3, T4, T5, T6, R> = (t1: T1, t2: T2, t3: T3, t4: T4, t5: T5, t6: T6) => Promise<R> | Generator<*,R,*> | R;
+declare type Fn7<T1, T2, T3, T4, T5, T6, T7, R> = (t1: T1, t2: T2, t3: T3, t4: T4, t5: T5, t6: T6, t7: T7) => Promise<R> | Generator<*,R,*> | R;
 
 /* ------------------ SELECT Stuff ------------------ */
 
@@ -69,6 +70,7 @@ declare type ContextCallFn =
   & (<T1, T2, T3, T4, R, C: Context, Fn: Fn4<T1, T2, T3, T4, R>>(cfn: [C, Fn], t1: T1, t2: T2, t3: T3, t4: T4, ...rest: Array<void>) => Generator<*, R, *>)
   & (<T1, T2, T3, T4, T5, R, C: Context, Fn: Fn5<T1, T2, T3, T4, T5, R>>(cfn: [C, Fn], t1: T1, t2: T2, t3: T3, t4: T4, t5: T5, ...rest: Array<void>) => Generator<*, R, *>)
   & (<T1, T2, T3, T4, T5, T6, R, C: Context, Fn: Fn6<T1, T2, T3, T4, T5, T6, R>>(cfn: [C, Fn], t1: T1, t2: T2, t3: T3, t4: T4, t5: T5, t6: T6, ...rest: Array<void>) => Generator<*, R, *>)
+  & (<T1, T2, T3, T4, T5, T6, T7, R, C: Context, Fn: Fn7<T1, T2, T3, T4, T5, T6, T7, R>>(cfn: [C, Fn], t1: T1, t2: T2, t3: T3, t4: T4, t5: T5, t6: T6, t7: T7, ...rest: Array<void>) => Generator<*, R, *>)
   // & (<T, R, C: Context, Fn: FnSpread<T, R>>(cfn: [C, Fn], t1: T, t2: T, t3: T, t4: T, t5: T, t6: T, ...args: Array<T>) => Generator<*, R, *>);
 
 declare type CallFn =
@@ -79,7 +81,8 @@ declare type CallFn =
   & (<T1, T2, T3, R, Fn: Fn3<T1, T2, T3, R>>(fn: Fn, t1: T1, t2: T2, t3: T3) => Generator<*, R, *>)
   & (<T1, T2, T3, T4, R, Fn: Fn4<T1, T2, T3, T4, R>>(fn: Fn, t1: T1, t2: T2, t3: T3, t4: T4) => Generator<*, R, *>)
   & (<T1, T2, T3, T4, T5, R, Fn: Fn5<T1, T2, T3, T4, T5, R>>(fn: Fn, t1: T1, t2: T2, t3: T3, t4: T4, t5: T5) => Generator<*, R, *>)
-  & (<T1, T2, T3, T4, T5, T6, R, Fn: Fn6<T1, T2, T3, T4, T5, T6, R>>(fn: Fn, t1: T1, t2: T2, t3: T3, t4: T4, t5: T5, t6: T6) => Generator<*, R, *>);
+  & (<T1, T2, T3, T4, T5, T6, R, Fn: Fn6<T1, T2, T3, T4, T5, T6, R>>(fn: Fn, t1: T1, t2: T2, t3: T3, t4: T4, t5: T5, t6: T6) => Generator<*, R, *>)
+  & (<T1, T2, T3, T4, T5, T6, T7, R, Fn: Fn7<T1, T2, T3, T4, T5, T6, T7, R>>(fn: Fn, t1: T1, t2: T2, t3: T3, t4: T4, t5: T5, t6: T6, t7: T7) => Generator<*, R, *>);
   // & (<T, R, Fn: FnSpread<T, R>>(fn: Fn, ...args: Array<T>) => Generator<*, R, *>);
 
   /* ------------------ CPS Stuff ------------------ */