isosurfaces for volume tracings

.prettierrc

@@ -5,7 +5,7 @@
     {
       "files": "effect-generators.js.flow",
       "options": {
-        "printWidth": 200
+        "printWidth": 240
       }
     }
   ]

CHANGELOG.unreleased.md

@@ -11,6 +11,7 @@ For upgrade instructions, please check the [migration guide](MIGRATIONS.released
 [Commits](https://github.com/scalableminds/webknossos/compare/20.07.0...HEAD)
 
 ### Added
+- Isosurface generation now also supports volume tracings without fallback layer. [#4567](https://github.com/scalableminds/webknossos/pull/4567)
 - Added a tool to initiate a flood fill in a volume tracing with the active cell id. [#4780](https://github.com/scalableminds/webknossos/pull/4780)
 - Added the possibility to merge volume tracings both via file upload (zip of zips) and when viewing projects/tasks as compound annotations. [#4709](https://github.com/scalableminds/webknossos/pull/4709)
 - Added the possibility to remove the fallback segmentation layer from a hybrid/volume tracing. Accessible by a minus button next to the layer's settings. [#4741](https://github.com/scalableminds/webknossos/pull/4766)

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,
@@ -821,6 +822,10 @@ class DataApi {
     return Store.getState().temporaryConfiguration.activeMapping.isMappingEnabled;
   }
 
+  refreshIsosurfaces() {
+    Store.dispatch(refreshIsosurfacesAction());
+  }
+
   /**
    * 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

@@ -51,6 +51,7 @@ import type { Edge, Tree, Node } 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";
 
@@ -88,7 +89,7 @@ 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) {
@@ -278,8 +279,9 @@ function onClick(
   ctrlPressed: boolean,
   plane: OrthoView,
   isTouch: boolean,
+  event?: MouseEvent,
 ): void {
-  if (!shiftPressed && !isTouch) {
+  if (!shiftPressed && !isTouch && !(ctrlPressed && event != null)) {
     // do nothing
     return;
   }
@@ -325,6 +327,8 @@ 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

@@ -37,6 +37,7 @@ 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;
@@ -169,6 +170,7 @@ export function getPlaneMouseControls(_planeId: OrthoView): * {
         );
         if (cellId > 0) {
           Store.dispatch(setActiveCellAction(cellId));
+          isosurfaceLeftClick(pos, plane, event);
         }
       } else if (event.shiftKey && event.ctrlKey) {
         Store.dispatch(floodFillAction(calculateGlobalPos(pos), plane));

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,
   is2d: boolean,

frontend/javascripts/oxalis/default_state.js

@@ -203,6 +203,7 @@ const defaultState: OxalisState = {
     isImportingMesh: false,
     isInAnnotationView: false,
     hasOrganizations: false,
+    isRefreshingIsosurfaces: 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", { isRefreshingIsosurfaces: true });
+    }
+
+    case "FINISHED_REFRESHING_ISOSURFACES": {
+      return updateKey(state, "uiInformation", { isRefreshingIsosurfaces: false });
+    }
+
     default:
       return state;
   }

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

@@ -29,6 +29,7 @@ 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 ------------------ */
 
@@ -59,7 +60,8 @@ declare type ContextCallFn = (<R, C: Context, Fn: Fn0<R>>(cfn: [C, Fn], ...rest:
   (<T1, T2, T3, R, C: Context, Fn: Fn3<T1, T2, T3, R>>(cfn: [C, Fn], t1: T1, t2: T2, t3: T3, ...rest: Array<void>) => Generator<*, R, *>) &
   (<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, 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 = ContextCallFn &
@@ -69,7 +71,8 @@ declare type CallFn = ContextCallFn &
   (<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 ------------------ */