fix: correct merge anchor inconsistencies

src/datasource/catmaid/spatial_skeleton_commands.ts

@@ -921,7 +921,9 @@ async function commitAndApplyDeleteNode(
       resolvedNode.node.segmentId,
     ) ?? [];
   if (remainingNodes.length > 0) {
-    resolvedNode.skeletonLayer.retainOverlaySegment(resolvedNode.node.segmentId);
+    resolvedNode.skeletonLayer.retainOverlaySegment(
+      resolvedNode.node.segmentId,
+    );
   } else {
     resolvedNode.skeletonLayer.markSegmentEdited(resolvedNode.node.segmentId);
   }
@@ -2132,7 +2134,6 @@ class MergeCommand implements SpatialSkeletonCommand {
     if (deletedSkeletonId !== resultSkeletonId) {
       firstNode.skeletonLayer.markSegmentEdited(deletedSkeletonId);
     }
-    this.layer.clearSpatialSkeletonMergeAnchor();
     await refreshTopologySegments(
       this.layer,
       [resultSkeletonId, deletedSkeletonId],

src/layer/segmentation/index.ts

@@ -51,15 +51,6 @@ import {
   getSegmentIdFromLayerSelectionValue,
   SpatialSkeletonHoverState,
 } from "#src/layer/segmentation/selection.js";
-import {
-  executeSpatialSkeletonDeleteNode,
-  executeSpatialSkeletonNodeConfidenceUpdate,
-  executeSpatialSkeletonNodeDescriptionUpdate,
-  executeSpatialSkeletonNodeRadiusUpdate,
-  executeSpatialSkeletonReroot,
-  executeSpatialSkeletonNodeTrueEndUpdate,
-  showSpatialSkeletonActionError,
-} from "#src/layer/segmentation/spatial_skeleton_commands.js";
 import {
   MeshLayer,
   MeshSource,
@@ -138,6 +129,15 @@ import {
   SpatialSkeletonDisplayNodeType,
   SpatialSkeletonNodeFilterType,
 } from "#src/skeleton/node_types.js";
+import {
+  executeSpatialSkeletonDeleteNode,
+  executeSpatialSkeletonNodeConfidenceUpdate,
+  executeSpatialSkeletonNodeDescriptionUpdate,
+  executeSpatialSkeletonNodeRadiusUpdate,
+  executeSpatialSkeletonReroot,
+  executeSpatialSkeletonNodeTrueEndUpdate,
+  showSpatialSkeletonActionError,
+} from "#src/skeleton/spatial_skeleton_commands.js";
 import {
   editableSpatiallyIndexedSkeletonSourceSupportsAction,
   getEditableSpatiallyIndexedSkeletonSource,
@@ -2449,7 +2449,8 @@ export class SegmentationUserLayer extends Base {
       let committedTrueEnd = nodeHasTrueEnd;
       let leafTypeSavePending = false;
       const leafTypeEditor = document.createElement("div");
-      leafTypeEditor.className = "neuroglancer-selection-details-skeleton-leaf-type";
+      leafTypeEditor.className =
+        "neuroglancer-selection-details-skeleton-leaf-type";
       const leafTypeRadioName = `neuroglancer-selection-details-skeleton-leaf-type-${segmentId}-${fullNodeInfo.nodeId}`;
       const leafTypeOptionElements: HTMLLabelElement[] = [];
       const makeLeafTypeOption = (options: {
@@ -2458,15 +2459,17 @@ export class SegmentationUserLayer extends Base {
         trueEnd: boolean;
       }) => {
         const option = document.createElement("label");
-        option.className = "neuroglancer-selection-details-skeleton-leaf-type-option";
+        option.className =
+          "neuroglancer-selection-details-skeleton-leaf-type-option";
         const input = document.createElement("input");
         input.type = "radio";
         input.name = leafTypeRadioName;
         input.value = options.trueEnd ? "trueEnd" : "virtualEnd";
         input.className =
           "neuroglancer-selection-details-skeleton-leaf-type-option-input";
         const icon = document.createElement("span");
-        icon.className = "neuroglancer-selection-details-skeleton-leaf-type-option-icon";
+        icon.className =
+          "neuroglancer-selection-details-skeleton-leaf-type-option-icon";
         icon.appendChild(
           makeIcon({
             svg: options.svg,
@@ -2475,7 +2478,8 @@ export class SegmentationUserLayer extends Base {
           }),
         );
         const text = document.createElement("span");
-        text.className = "neuroglancer-selection-details-skeleton-leaf-type-option-text";
+        text.className =
+          "neuroglancer-selection-details-skeleton-leaf-type-option-text";
         text.textContent = options.label;
         option.appendChild(input);
         option.appendChild(icon);
@@ -2639,7 +2643,8 @@ export class SegmentationUserLayer extends Base {
     } else {
       let committedRadius = fullNodeInfo.radius ?? 0;
       const radiusInput = document.createElement("input");
-      radiusInput.className = "neuroglancer-selection-details-skeleton-properties-input";
+      radiusInput.className =
+        "neuroglancer-selection-details-skeleton-properties-input";
       radiusInput.type = "number";
       radiusInput.step = "any";
       radiusInput.value = formatSpatialSkeletonEditableNumber(

src/layer/segmentation/style.css

@@ -312,7 +312,8 @@
   justify-content: center;
 }
 
-.neuroglancer-selection-details-skeleton-leaf-type-option-icon .neuroglancer-icon {
+.neuroglancer-selection-details-skeleton-leaf-type-option-icon
+  .neuroglancer-icon {
   min-width: 14px;
   min-height: 14px;
 }

src/skeleton/frontend.ts

@@ -1824,7 +1824,9 @@ interface SelectedSkeletonNodeInfo {
 
 interface SpatiallyIndexedSkeletonLayerOptions {
   sources2d?: SpatiallyIndexedSkeletonSourceEntry[];
-  selectedNodeInfo?: WatchableValueInterface<SelectedSkeletonNodeInfo | undefined>;
+  selectedNodeInfo?: WatchableValueInterface<
+    SelectedSkeletonNodeInfo | undefined
+  >;
   pendingNodePositionVersion?: WatchableValueInterface<number>;
   getPendingNodePosition?: (nodeId: number) => ArrayLike<number> | undefined;
   getCachedNode?: (nodeId: number) => SpatiallyIndexedSkeletonNode | undefined;

src/layer/segmentation/spatial_skeleton_commands.spec.ts → src/skeleton/spatial_skeleton_commands.spec.ts

@@ -19,6 +19,14 @@ import { afterEach, describe, expect, it, vi } from "vitest";
 import { makeCatmaidNodeSourceState } from "#src/datasource/catmaid/api.js";
 import { buildCatmaidNeighborhoodEditContext } from "#src/datasource/catmaid/edit_state.js";
 import { CatmaidSpatialSkeletonEditCommands } from "#src/datasource/catmaid/spatial_skeleton_commands.js";
+import { SpatialSkeletonActions } from "#src/skeleton/actions.js";
+import type { SpatiallyIndexedSkeletonNode } from "#src/skeleton/api.js";
+import { SpatialSkeletonCommandHistory } from "#src/skeleton/command_history.js";
+import {
+  findSpatiallyIndexedSkeletonNode,
+  getSpatiallyIndexedSkeletonDirectChildren,
+  getSpatiallyIndexedSkeletonNodeParent,
+} from "#src/skeleton/node_traversal.js";
 import {
   executeSpatialSkeletonAddNode,
   executeSpatialSkeletonDeleteNode,
@@ -33,15 +41,7 @@ import {
   executeSpatialSkeletonSplit,
   redoSpatialSkeletonCommand,
   undoSpatialSkeletonCommand,
-} from "#src/layer/segmentation/spatial_skeleton_commands.js";
-import { SpatialSkeletonActions } from "#src/skeleton/actions.js";
-import type { SpatiallyIndexedSkeletonNode } from "#src/skeleton/api.js";
-import { SpatialSkeletonCommandHistory } from "#src/skeleton/command_history.js";
-import {
-  findSpatiallyIndexedSkeletonNode,
-  getSpatiallyIndexedSkeletonDirectChildren,
-  getSpatiallyIndexedSkeletonNodeParent,
-} from "#src/skeleton/node_traversal.js";
+} from "#src/skeleton/spatial_skeleton_commands.js";
 import { SpatialSkeletonState } from "#src/skeleton/spatial_skeleton_manager.js";
 import { StatusMessage } from "#src/status.js";
 

src/layer/segmentation/spatial_skeleton_commands.ts → src/skeleton/spatial_skeleton_commands.ts

@@ -14,7 +14,6 @@
  * limitations under the License.
  */
 
-import type { SegmentationUserLayer } from "#src/layer/segmentation/index.js";
 import {
   SpatialSkeletonActions,
   type SpatialSkeletonAction,
@@ -32,6 +31,7 @@ import { getSpatialSkeletonActionErrorMessage } from "#src/skeleton/edit_errors.
 import {
   getEditableSpatiallyIndexedSkeletonSource,
   getSpatialSkeletonEditCommandFactoryForAction,
+  type SpatialSkeletonLayerContext,
 } from "#src/skeleton/spatial_skeleton_manager.js";
 import { StatusMessage } from "#src/status.js";
 
@@ -40,7 +40,7 @@ interface SpatialSkeletonSourceAccess {
 }
 
 function getEditSource(
-  layer: SegmentationUserLayer,
+  layer: SpatialSkeletonLayerContext,
 ): EditableSpatiallyIndexedSkeletonSource {
   const source = getEditableSpatiallyIndexedSkeletonSource(
     layer.getSpatiallyIndexedSkeletonLayer(),
@@ -63,7 +63,7 @@ export function getSpatialSkeletonEditCommandFactory(
 }
 
 function executeCommand(
-  layer: SegmentationUserLayer,
+  layer: SpatialSkeletonLayerContext,
   command: SpatialSkeletonCommand,
 ) {
   return layer.spatialSkeletonState.commandHistory.execute(command);
@@ -88,7 +88,7 @@ export function showSpatialSkeletonActionError(action: string, error: unknown) {
 }
 
 function createSpatialSkeletonCommand(
-  layer: SegmentationUserLayer,
+  layer: SpatialSkeletonLayerContext,
   action: SpatialSkeletonAction,
   payload: SpatialSkeletonCommandPayload,
   unsupportedMessage: string,
@@ -101,7 +101,10 @@ function createSpatialSkeletonCommand(
   if (commandFactory === undefined) {
     throw new Error(unsupportedMessage);
   }
-  return commandFactory.createCommand(layer, payload);
+  // The concrete createCommand implementations expect the full layer type; the
+  // cast is safe because in practice layer always satisfies those requirements.
+
+  return commandFactory.createCommand(layer as any, payload);
 }
 
 interface SpatialSkeletonExecutionMetadata {
@@ -198,7 +201,7 @@ const spatialSkeletonExecutionMetadata = new Map<
 ]);
 
 function executeSpatialSkeletonAction(
-  layer: SegmentationUserLayer,
+  layer: SpatialSkeletonLayerContext,
   action: SpatialSkeletonAction,
   payload: SpatialSkeletonCommandPayload,
 ) {
@@ -219,7 +222,7 @@ function executeSpatialSkeletonAction(
 }
 
 export function executeSpatialSkeletonAddNode(
-  layer: SegmentationUserLayer,
+  layer: SpatialSkeletonLayerContext,
   options: SpatialSkeletonCommandPayload,
 ) {
   return executeSpatialSkeletonAction(
@@ -230,7 +233,7 @@ export function executeSpatialSkeletonAddNode(
 }
 
 export function executeSpatialSkeletonInsertNode(
-  layer: SegmentationUserLayer,
+  layer: SpatialSkeletonLayerContext,
   options: SpatialSkeletonCommandPayload,
 ) {
   return executeSpatialSkeletonAction(
@@ -241,7 +244,7 @@ export function executeSpatialSkeletonInsertNode(
 }
 
 export function executeSpatialSkeletonMoveNode(
-  layer: SegmentationUserLayer,
+  layer: SpatialSkeletonLayerContext,
   options: SpatialSkeletonCommandPayload,
 ) {
   return executeSpatialSkeletonAction(
@@ -252,7 +255,7 @@ export function executeSpatialSkeletonMoveNode(
 }
 
 export function executeSpatialSkeletonDeleteNode(
-  layer: SegmentationUserLayer,
+  layer: SpatialSkeletonLayerContext,
   node: SpatiallyIndexedSkeletonNode,
 ) {
   return executeSpatialSkeletonAction(
@@ -263,7 +266,7 @@ export function executeSpatialSkeletonDeleteNode(
 }
 
 export function executeSpatialSkeletonNodeDescriptionUpdate(
-  layer: SegmentationUserLayer,
+  layer: SpatialSkeletonLayerContext,
   options: SpatialSkeletonCommandPayload,
 ) {
   return executeSpatialSkeletonAction(
@@ -274,7 +277,7 @@ export function executeSpatialSkeletonNodeDescriptionUpdate(
 }
 
 export function executeSpatialSkeletonNodeTrueEndUpdate(
-  layer: SegmentationUserLayer,
+  layer: SpatialSkeletonLayerContext,
   options: SpatialSkeletonCommandPayload,
 ) {
   return executeSpatialSkeletonAction(
@@ -285,7 +288,7 @@ export function executeSpatialSkeletonNodeTrueEndUpdate(
 }
 
 export function executeSpatialSkeletonNodeRadiusUpdate(
-  layer: SegmentationUserLayer,
+  layer: SpatialSkeletonLayerContext,
   options: SpatialSkeletonCommandPayload,
 ) {
   return executeSpatialSkeletonAction(
@@ -296,7 +299,7 @@ export function executeSpatialSkeletonNodeRadiusUpdate(
 }
 
 export function executeSpatialSkeletonNodeConfidenceUpdate(
-  layer: SegmentationUserLayer,
+  layer: SpatialSkeletonLayerContext,
   options: SpatialSkeletonCommandPayload,
 ) {
   return executeSpatialSkeletonAction(
@@ -307,7 +310,7 @@ export function executeSpatialSkeletonNodeConfidenceUpdate(
 }
 
 export function executeSpatialSkeletonReroot(
-  layer: SegmentationUserLayer,
+  layer: SpatialSkeletonLayerContext,
   node: SpatialSkeletonCommandPayload,
 ) {
   return executeSpatialSkeletonAction(
@@ -318,7 +321,7 @@ export function executeSpatialSkeletonReroot(
 }
 
 export function executeSpatialSkeletonSplit(
-  layer: SegmentationUserLayer,
+  layer: SpatialSkeletonLayerContext,
   node: SpatialSkeletonCommandPayload,
 ) {
   return executeSpatialSkeletonAction(
@@ -329,7 +332,7 @@ export function executeSpatialSkeletonSplit(
 }
 
 export function executeSpatialSkeletonMerge(
-  layer: SegmentationUserLayer,
+  layer: SpatialSkeletonLayerContext,
   firstNode: SpatialSkeletonCommandPayload,
   secondNode: SpatialSkeletonCommandPayload,
 ) {
@@ -340,15 +343,19 @@ export function executeSpatialSkeletonMerge(
   );
 }
 
-export async function undoSpatialSkeletonCommand(layer: SegmentationUserLayer) {
+export async function undoSpatialSkeletonCommand(
+  layer: SpatialSkeletonLayerContext,
+) {
   const changed = await layer.spatialSkeletonState.commandHistory.undo();
   if (!changed) {
     return false;
   }
   return true;
 }
 
-export async function redoSpatialSkeletonCommand(layer: SegmentationUserLayer) {
+export async function redoSpatialSkeletonCommand(
+  layer: SpatialSkeletonLayerContext,
+) {
   const changed = await layer.spatialSkeletonState.commandHistory.redo();
   if (!changed) {
     return false;

src/skeleton/spatial_skeleton_manager.ts

@@ -911,3 +911,8 @@ export class SpatialSkeletonState extends RefCounted {
     this.cachedNodesById.clear();
   }
 }
+
+export interface SpatialSkeletonLayerContext {
+  getSpatiallyIndexedSkeletonLayer(): SpatiallyIndexedSkeletonLayer | undefined;
+  readonly spatialSkeletonState: SpatialSkeletonState;
+}

src/ui/skeleton_edit_tools.spec.ts

@@ -18,16 +18,16 @@ import { afterEach, describe, expect, it, vi } from "vitest";
 
 import { makeCatmaidNodeSourceState } from "#src/datasource/catmaid/api.js";
 import { CatmaidSpatialSkeletonEditCommands } from "#src/datasource/catmaid/spatial_skeleton_commands.js";
-import {
-  executeSpatialSkeletonAddNode,
-  executeSpatialSkeletonMerge,
-} from "#src/layer/segmentation/spatial_skeleton_commands.js";
 import {
   SpatialSkeletonActions,
   type SpatialSkeletonAction,
 } from "#src/skeleton/actions.js";
 import type { SpatiallyIndexedSkeletonNode } from "#src/skeleton/api.js";
 import { SpatialSkeletonCommandHistory } from "#src/skeleton/command_history.js";
+import {
+  executeSpatialSkeletonAddNode,
+  executeSpatialSkeletonMerge,
+} from "#src/skeleton/spatial_skeleton_commands.js";
 import { StatusMessage } from "#src/status.js";
 
 if (!("WebGL2RenderingContext" in globalThis)) {
@@ -737,7 +737,10 @@ describe("spatial_skeleton_edit_tool", () => {
         },
       },
       spatialSkeletonMergeMode: makeModeWatchable(),
-      selectedSpatialSkeletonNodeInfo: { value: selectedNode, changed: makeChangedSignal() },
+      selectedSpatialSkeletonNodeInfo: {
+        value: selectedNode,
+        changed: makeChangedSignal(),
+      },
       spatialSkeletonState: {
         mergeAnchorNodeId,
         getCachedNode: vi.fn(),