Extend JS API with createNode functionality and refactor (#7998)

* rename setWaypoint to handleCreateNode in arbitrary controller * rename setWaypoint to handleNodeCreation * refactor * implement createNode in api_latest; refactor to allow better parameteriziation; fix that centering node did not work when new node was not activated * refactor getActiveNode accessor to not use a Maybe * refactor getActiveTree accessor to not use a Maybe * update changelog * remove unused import * allow to pass additionalCoordinates when creating nodes via API * set skipCenteringAnimationInThirdDimension to false when using api
scalableminds · Sep 2, 2024 · bc5f278 · bc5f278
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diff --git a/CHANGELOG.unreleased.md b/CHANGELOG.unreleased.md
@@ -29,6 +29,7 @@ For upgrade instructions, please check the [migration guide](MIGRATIONS.released
 - To improve performance, only the visible bounding boxes are rendered in the bounding box tab (so-called virtualization). [#7974](https://github.com/scalableminds/webknossos/pull/7974)
 - Added support for reading zstd-compressed zarr2 datasets [#7964](https://github.com/scalableminds/webknossos/pull/7964)
 - The alignment job is in a separate tab of the "AI Tools" now. The "Align Sections" AI job now supports including manually created matches between adjacent section given as skeletons. [#7967](https://github.com/scalableminds/webknossos/pull/7967)  
+- Added `api.tracing.createNode(position, options)`` to the front-end API. [#7998](https://github.com/scalableminds/webknossos/pull/7998)
 - Added a feature to register all segments for a given bounding box at once via the context menu of the bounding box. [#7979](https://github.com/scalableminds/webknossos/pull/7979)
 
 ### Changed

diff --git a/frontend/javascripts/libs/utils.ts b/frontend/javascripts/libs/utils.ts
@@ -669,10 +669,6 @@ export function withoutValues<T>(arr: Array<T>, elements: Array<T>): Array<T> {
   return arr.filter((x) => !auxSet.has(x));
 }
 
-export function zipMaybe<T, U>(maybeA: Maybe<T>, maybeB: Maybe<U>): Maybe<[T, U]> {
-  return maybeA.chain((valueA) => maybeB.map((valueB) => [valueA, valueB]));
-}
-
 // Maybes getOrElse is defined as getOrElse(defaultValue: T): T, which is why
 // you can't do getOrElse(null) without flow complaining
 export function toNullable<T>(_maybe: Maybe<T>): T | null | undefined {

diff --git a/frontend/javascripts/oxalis/api/api_latest.ts b/frontend/javascripts/oxalis/api/api_latest.ts
@@ -178,6 +178,10 @@ import { setLayerTransformsAction } from "oxalis/model/actions/dataset_actions";
 import { ResolutionInfo } from "oxalis/model/helpers/resolution_info";
 import { type AdditionalCoordinate } from "types/api_flow_types";
 import { getMaximumGroupId } from "oxalis/model/reducers/skeletontracing_reducer_helpers";
+import {
+  createSkeletonNode,
+  getOptionsForCreateSkeletonNode,
+} from "oxalis/controller/combinations/skeleton_handlers";
 
 type TransformSpec =
   | { type: "scale"; args: [Vector3, Vector3] }
@@ -248,19 +252,15 @@ class TracingApi {
    */
   getActiveNodeId(): number | null | undefined {
     const tracing = assertSkeleton(Store.getState().tracing);
-    return getActiveNode(tracing)
-      .map((node) => node.id)
-      .getOrElse(null);
+    return getActiveNode(tracing)?.id ?? null;
   }
 
   /**
    * Returns the id of the current active tree.
    */
   getActiveTreeId(): number | null | undefined {
     const tracing = assertSkeleton(Store.getState().tracing);
-    return getActiveTree(tracing)
-      .map((tree) => tree.treeId)
-      .getOrElse(null);
+    return getActiveTree(tracing)?.treeId ?? null;
   }
 
   /**
@@ -322,11 +322,21 @@ class TracingApi {
   }
 
   /**
-   * Creates a new and empty tree
+   * Creates a new and empty tree. Returns the
+   * id of that tree.
    */
   createTree() {
     assertSkeleton(Store.getState().tracing);
-    Store.dispatch(createTreeAction());
+    let treeId = null;
+    Store.dispatch(
+      createTreeAction((id) => {
+        treeId = id;
+      }),
+    );
+    if (treeId == null) {
+      throw new Error("Could not create tree.");
+    }
+    return treeId;
   }
 
   /**
@@ -337,6 +347,37 @@ class TracingApi {
     Store.dispatch(deleteTreeAction(treeId));
   }
 
+  /**
+   * Creates a new node in the current tree. If the active tree
+   * is not empty, the node will be connected with an edge to
+   * the currently active node.
+   */
+  createNode(
+    position: Vector3,
+    options?: {
+      additionalCoordinates?: AdditionalCoordinate[];
+      rotation?: Vector3;
+      center?: boolean;
+      branchpoint?: boolean;
+      activate?: boolean;
+      skipCenteringAnimationInThirdDimension?: boolean;
+    },
+  ) {
+    assertSkeleton(Store.getState().tracing);
+    const defaultOptions = getOptionsForCreateSkeletonNode();
+    createSkeletonNode(
+      position,
+      options?.additionalCoordinates ?? defaultOptions.additionalCoordinates,
+      options?.rotation ?? defaultOptions.rotation,
+      options?.center ?? defaultOptions.center,
+      options?.branchpoint ?? defaultOptions.branchpoint,
+      options?.activate ?? defaultOptions.activate,
+      // This is the only parameter where we don't fall back to the default option,
+      // as the parameter mostly makes sense when the user creates a node *manually*.
+      options?.skipCenteringAnimationInThirdDimension ?? false,
+    );
+  }
+
   /**
    * Completely resets the skeleton tracing.
    */
@@ -1296,20 +1337,23 @@ class TracingApi {
    * Starts an animation to center the given position. See setCameraPosition for a non-animated version of this function.
    *
    * @param position - Vector3
-   * @param skipDimensions - Boolean which decides whether the third dimension shall also be animated (defaults to true)
+   * @param skipCenteringAnimationInThirdDimension -
+   *        Boolean which decides whether the third dimension shall also be animated (defaults to true)
+   *        When true, this lets the user still manipulate the "third dimension"
+   *        during the animation (important because otherwise the user cannot continue to trace until
+   *        the animation is over).
    * @param rotation - Vector3 (optional) - Will only be noticeable in flight or oblique mode.
    * @example
    * api.tracing.centerPositionAnimated([0, 0, 0])
    */
   centerPositionAnimated(
     position: Vector3,
-    skipDimensions: boolean = true,
+    skipCenteringAnimationInThirdDimension: boolean = true,
     rotation?: Vector3,
   ): void {
-    // Let the user still manipulate the "third dimension" during animation
     const { activeViewport } = Store.getState().viewModeData.plane;
     const dimensionToSkip =
-      skipDimensions && activeViewport !== OrthoViews.TDView
+      skipCenteringAnimationInThirdDimension && activeViewport !== OrthoViews.TDView
         ? dimensions.thirdDimensionForPlane(activeViewport)
         : null;
     const curPosition = getPosition(Store.getState().flycam);

diff --git a/frontend/javascripts/oxalis/api/api_v2.ts b/frontend/javascripts/oxalis/api/api_v2.ts
@@ -92,19 +92,15 @@ class TracingApi {
    */
   getActiveNodeId(): number | null | undefined {
     const tracing = assertSkeleton(Store.getState().tracing);
-    return getActiveNode(tracing)
-      .map((node) => node.id)
-      .getOrElse(null);
+    return getActiveNode(tracing)?.id ?? null;
   }
 
   /**
    * Returns the id of the current active tree.
    */
   getActiveTreeId(): number | null | undefined {
     const tracing = assertSkeleton(Store.getState().tracing);
-    return getActiveTree(tracing)
-      .map((tree) => tree.treeId)
-      .getOrElse(null);
+    return getActiveTree(tracing)?.treeId ?? null;
   }
 
   /**

diff --git a/frontend/javascripts/oxalis/controller/combinations/skeleton_handlers.ts b/frontend/javascripts/oxalis/controller/combinations/skeleton_handlers.ts
@@ -3,7 +3,7 @@ import type { OrthoView, OrthoViewMap, Point2, Vector3, Viewport } from "oxalis/
 import { OrthoViews } from "oxalis/constants";
 import { V3 } from "libs/mjs";
 import _ from "lodash";
-import { enforce, values } from "libs/utils";
+import { values } from "libs/utils";
 import {
   enforceSkeletonTracing,
   getSkeletonTracing,
@@ -47,6 +47,7 @@ import { getClosestHoveredBoundingBox } from "oxalis/controller/combinations/bou
 import { getEnabledColorLayers } from "oxalis/model/accessors/dataset_accessor";
 import ArbitraryView from "oxalis/view/arbitrary_view";
 import { showContextMenuAction } from "oxalis/model/actions/ui_actions";
+import { AdditionalCoordinate } from "types/api_flow_types";
 const OrthoViewToNumber: OrthoViewMap<number> = {
   [OrthoViews.PLANE_XY]: 0,
   [OrthoViews.PLANE_YZ]: 1,
@@ -64,9 +65,10 @@ export function handleMergeTrees(
 
   // otherwise we have hit the background and do nothing
   if (nodeId != null && nodeId > 0) {
-    getActiveNode(skeletonTracing).map((activeNode) =>
-      Store.dispatch(mergeTreesAction(activeNode.id, nodeId)),
-    );
+    const activeNode = getActiveNode(skeletonTracing);
+    if (activeNode) {
+      Store.dispatch(mergeTreesAction(activeNode.id, nodeId));
+    }
   }
 }
 export function handleDeleteEdge(
@@ -80,9 +82,10 @@ export function handleDeleteEdge(
 
   // otherwise we have hit the background and do nothing
   if (nodeId != null && nodeId > 0) {
-    getActiveNode(skeletonTracing).map((activeNode) =>
-      Store.dispatch(deleteEdgeAction(activeNode.id, nodeId)),
-    );
+    const activeNode = getActiveNode(skeletonTracing);
+    if (activeNode) {
+      Store.dispatch(deleteEdgeAction(activeNode.id, nodeId));
+    }
   }
 }
 export function handleSelectNode(
@@ -101,7 +104,7 @@ export function handleSelectNode(
 
   return false;
 }
-export function handleCreateNode(position: Point2, ctrlPressed: boolean) {
+export function handleCreateNodeFromEvent(position: Point2, ctrlPressed: boolean) {
   const state = Store.getState();
 
   if (isMagRestrictionViolated(state)) {
@@ -123,7 +126,7 @@ export function handleCreateNode(position: Point2, ctrlPressed: boolean) {
   }
 
   const globalPosition = calculateGlobalPos(state, position);
-  setWaypoint(globalPosition, activeViewport, ctrlPressed);
+  handleCreateNodeFromGlobalPosition(globalPosition, activeViewport, ctrlPressed);
 }
 export function handleOpenContextMenu(
   planeView: PlaneView,
@@ -233,53 +236,83 @@ export function finishNodeMovement(nodeId: number) {
   );
 }
 
-export function setWaypoint(
+export function handleCreateNodeFromGlobalPosition(
   position: Vector3,
   activeViewport: OrthoView,
   ctrlIsPressed: boolean,
 ): void {
-  const skeletonTracing = enforceSkeletonTracing(Store.getState().tracing);
-  const activeNodeMaybe = getActiveNode(skeletonTracing);
-  const rotation = getRotationOrtho(activeViewport);
-  // set the new trace direction
-  activeNodeMaybe.map((activeNode) => {
-    const activeNodePosition = getNodePosition(activeNode, Store.getState());
-    return Store.dispatch(
-      setDirectionAction([
-        position[0] - activeNodePosition[0],
-        position[1] - activeNodePosition[1],
-        position[2] - activeNodePosition[2],
-      ]),
-    );
-  });
   const state = Store.getState();
   // Create a new tree automatically if the corresponding setting is true and allowed
   const createNewTree =
     state.tracing.restrictions.somaClickingAllowed && state.userConfiguration.newNodeNewTree;
+  if (createNewTree) {
+    Store.dispatch(createTreeAction());
+  }
+
+  const {
+    additionalCoordinates,
+    rotation,
+    center,
+    branchpoint,
+    activate,
+    skipCenteringAnimationInThirdDimension,
+  } = getOptionsForCreateSkeletonNode(activeViewport, ctrlIsPressed);
+  createSkeletonNode(
+    position,
+    additionalCoordinates,
+    rotation,
+    center,
+    branchpoint,
+    activate,
+    skipCenteringAnimationInThirdDimension,
+  );
+}
+
+export function getOptionsForCreateSkeletonNode(
+  activeViewport: OrthoView | null = null,
+  ctrlIsPressed: boolean = false,
+) {
+  const state = Store.getState();
+  const additionalCoordinates = state.flycam.additionalCoordinates;
+  const skeletonTracing = enforceSkeletonTracing(state.tracing);
+  const activeNode = getActiveNode(skeletonTracing);
+  const rotation = getRotationOrtho(activeViewport || state.viewModeData.plane.activeViewport);
+
   // Center node if the corresponding setting is true. Only pressing CTRL can override this.
   const center = state.userConfiguration.centerNewNode && !ctrlIsPressed;
+
   // Only create a branchpoint if CTRL is pressed. Unless newNodeNewTree is activated (branchpoints make no sense then)
   const branchpoint = ctrlIsPressed && !state.userConfiguration.newNodeNewTree;
+
   // Always activate the new node unless CTRL is pressed. If there is no current node,
   // the new one is still activated regardless of CTRL (otherwise, using CTRL+click in an empty tree multiple times would
   // not create any edges; see https://github.com/scalableminds/webknossos/issues/5303).
-  const activate = !ctrlIsPressed || activeNodeMaybe.isNothing;
-  addNode(position, rotation, createNewTree, center, branchpoint, activate);
+  const activate = !ctrlIsPressed || activeNode == null;
+
+  const skipCenteringAnimationInThirdDimension = true;
+
+  return {
+    additionalCoordinates,
+    rotation,
+    center,
+    branchpoint,
+    activate,
+    skipCenteringAnimationInThirdDimension,
+  };
 }
 
-function addNode(
+export function createSkeletonNode(
   position: Vector3,
+  additionalCoordinates: AdditionalCoordinate[] | null,
   rotation: Vector3,
-  createNewTree: boolean,
   center: boolean,
   branchpoint: boolean,
   activate: boolean,
+  skipCenteringAnimationInThirdDimension: boolean,
 ): void {
-  if (createNewTree) {
-    Store.dispatch(createTreeAction());
-  }
+  updateTraceDirection(position);
 
-  const state = Store.getState();
+  let state = Store.getState();
   const enabledColorLayers = getEnabledColorLayers(state.dataset, state.datasetConfiguration);
   const activeMagIndices = getActiveMagIndicesForLayers(state);
   const activeMagIndicesOfEnabledColorLayers = _.pick(
@@ -292,7 +325,7 @@ function addNode(
   Store.dispatch(
     createNodeAction(
       untransformNodePosition(position, state),
-      state.flycam.additionalCoordinates,
+      additionalCoordinates,
       rotation,
       OrthoViewToNumber[Store.getState().viewModeData.plane.activeViewport],
       // This is the magnification index at which the node was created. Since
@@ -305,21 +338,43 @@ function addNode(
     ),
   );
 
+  // We need a reference to the new store state, so that the new node exists in it.
+  state = Store.getState();
+
   if (center) {
-    // we created a new node, so get a new reference from the current store state
-    const newState = Store.getState();
-    enforce(getActiveNode)(newState.tracing.skeleton).map((newActiveNode) =>
-      // Center the position of the active node without modifying the "third" dimension (see centerPositionAnimated)
-      // This is important because otherwise the user cannot continue to trace until the animation is over
-      api.tracing.centerPositionAnimated(getNodePosition(newActiveNode, state), true),
-    );
+    const newSkeleton = enforceSkeletonTracing(state.tracing);
+    // Note that the new node isn't necessarily active
+    const newNodeId = newSkeleton.cachedMaxNodeId;
+
+    const { activeTreeId } = newSkeleton;
+    getNodeAndTree(newSkeleton, newNodeId, activeTreeId).map(([, newNode]) => {
+      api.tracing.centerPositionAnimated(
+        getNodePosition(newNode, state),
+        skipCenteringAnimationInThirdDimension,
+      );
+    });
   }
 
   if (branchpoint) {
     Store.dispatch(createBranchPointAction());
   }
 }
 
+function updateTraceDirection(position: Vector3) {
+  const skeletonTracing = enforceSkeletonTracing(Store.getState().tracing);
+  const activeNode = getActiveNode(skeletonTracing);
+  if (activeNode != null) {
+    const activeNodePosition = getNodePosition(activeNode, Store.getState());
+    return Store.dispatch(
+      setDirectionAction([
+        position[0] - activeNodePosition[0],
+        position[1] - activeNodePosition[1],
+        position[2] - activeNodePosition[2],
+      ]),
+    );
+  }
+}
+
 export function moveAlongDirection(reverse: boolean = false): void {
   const directionInverter = reverse ? -1 : 1;
   const { flycam } = Store.getState();