Spelunker rebase stop layer

.github/workflows/build.yml

@@ -17,17 +17,17 @@ jobs:
     strategy:
       matrix:
         node-version:
-          - "16.x"
+          - "20.x"
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
         with:
           fetch-depth: 0
       - name: Use Node.js ${{ matrix.node-version }}
-        uses: actions/setup-node@v1
+        uses: actions/setup-node@v4
         with:
           node-version: ${{ matrix.node-version }}
-      - uses: actions/cache@v3
+      - uses: actions/cache@v4
         with:
           path: "**/node_modules"
           key: ${{ runner.os }}-${{ matrix.node-version }}-node_modules-${{ hashFiles('**/package-lock.json') }}
@@ -50,7 +50,7 @@ jobs:
         run: echo ${{ env.BUILD_INFO }} >> src/version.json
         shell: bash
       - name: Build client bundles
-        run: node ./config/esbuild-cli.js --config=min --no-typecheck --define STATE_SERVERS=$(cat config/state_servers.json | tr -d " \t\n\r") --define NEUROGLANCER_BUILD_INFO='${{ env.BUILD_INFO }}' --define CUSTOM_BINDINGS=$(cat config/custom-keybinds.json | tr -d " \t\n\r")
+        run: npm run build -- --no-typecheck --no-lint
       - run: cp -r ./dist/min appengine/frontend/static/
       - name: start deployment
         uses: bobheadxi/deployments@v1
@@ -61,12 +61,12 @@ jobs:
           env: ${{ env.BRANCH_NAME }}
           desc: Setting up staging deployment for ${{ env.BRANCH_NAME }}
       - id: "auth"
-        uses: "google-github-actions/auth@v1"
+        uses: "google-github-actions/auth@v2"
         with:
           workload_identity_provider: "projects/483670036293/locations/global/workloadIdentityPools/neuroglancer-github/providers/github"
           service_account: "[email protected]"
       - id: deploy
-        uses: google-github-actions/deploy-appengine@main
+        uses: google-github-actions/deploy-appengine@v2
         with:
           version: ${{ env.GITHUB_SHA }}
           deliverables: appengine/frontend/app.yaml

.github/workflows/build_preview.yml

@@ -14,7 +14,7 @@ jobs:
     steps:
       - uses: actions/checkout@v4
       - name: Use Node.js ${{ matrix.node-version }}
-        uses: actions/setup-node@v1
+        uses: actions/setup-node@v4
         with:
           node-version: ${{ matrix.node-version }}
       - run: npm install

src/credentials_provider/index.ts

@@ -17,14 +17,15 @@
 /**
  * @file Generic facility for providing authentication/authorization credentials.
  */
-
+import { type OAuth2Credentials } from "#src/credentials_provider/oauth2.js";
 import type { CancellationToken } from "#src/util/cancellation.js";
 import { MultipleConsumerCancellationTokenSource } from "#src/util/cancellation.js";
 import type { Owned } from "#src/util/disposable.js";
 import { RefCounted } from "#src/util/disposable.js";
+import { type HttpError } from "#src/util/http_request.js";
 import { StringMemoize } from "#src/util/memoize.js";
-import { HttpError } from "#src/util/http_request";
-import { OAuth2Credentials } from "#src/credentials_provider/oauth2";
+
+
 
 /**
  * Wraps an arbitrary JSON credentials object with a generation number.

src/datasource/graphene/frontend.ts

@@ -15,29 +15,32 @@
  */
 
 import "#src/datasource/graphene/graphene.css";
+import { debounce } from "lodash-es";
 import {
   AnnotationDisplayState,
   AnnotationLayerState,
 } from "#src/annotation/annotation_layer_state.js";
-import type {
-  AnnotationReference,
-  Annotation,
-  AnnotationSource,
-  AnnotationType,
-  Line,
-  Point,
+import { type MultiscaleAnnotationSource } from "#src/annotation/frontend_source.js";
+import {
+  type AnnotationReference,
+  type Annotation,
+  type AnnotationSource, AnnotationType,
+  type Line,
+  type Point,
+  LocalAnnotationSource,
+  makeDataBoundsBoundingBoxAnnotationSet,
 } from "#src/annotation/index.js";
 import { LayerChunkProgressInfo } from "#src/chunk_manager/base.js";
-import type { ChunkManager, WithParameters } from "#src/chunk_manager/frontend.js";
+import { type ChunkManager, WithParameters } from "#src/chunk_manager/frontend.js";
 import { makeIdentityTransform } from "#src/coordinate_transform.js";
 import { WithCredentialsProvider } from "#src/credentials_provider/chunk_source_frontend.js";
 import type { CredentialsManager } from "#src/credentials_provider/index.js";
+
 import type {
   ChunkedGraphChunkSource as ChunkedGraphChunkSourceInterface,
   ChunkedGraphChunkSpecification,
   MultiscaleMeshMetadata,
 } from "#src/datasource/graphene/base.js";
-import { MultiscaleAnnotationSource } from "#src/annotation/frontend_source";
 import {
   CHUNKED_GRAPH_LAYER_RPC_ID,
   CHUNKED_GRAPH_RENDER_LAYER_UPDATE_SOURCES_RPC_ID,
@@ -78,6 +81,7 @@ import type {
 import type { LoadedDataSubsource } from "#src/layer/layer_data_source.js";
 import { LoadedLayerDataSource } from "#src/layer/layer_data_source.js";
 import { SegmentationUserLayer } from "#src/layer/segmentation/index.js";
+import * as json_keys from "#src/layer/segmentation/json_keys.js";
 import { MeshSource } from "#src/mesh/frontend.js";
 import type { DisplayDimensionRenderInfo } from "#src/navigation_state.js";
 import type {
@@ -143,27 +147,32 @@ import {
   MergedAnnotationStates,
   PlaceLineTool,
 } from "#src/ui/annotations.js";
-import { getDefaultAnnotationListBindings } from "#src/ui/default_input_event_bindings";
+import { getDefaultAnnotationListBindings } from "#src/ui/default_input_event_bindings.js";
 import {
   LayerTool,
   makeToolActivationStatusMessageWithHeader,
   makeToolButton,
   registerLegacyTool,
   registerTool,
-  ToolActivation
+  type ToolActivation
 } from "#src/ui/tool.js";
-import type { Uint64Set } from "#src/uint64_set.js";
+import { Uint64Set } from "#src/uint64_set.js";
+import {
+  type CancellationToken,
+  CancellationTokenSource,
+} from "#src/util/cancellation.js";
 import { packColor } from "#src/util/color.js";
-import type { Owned, RefCounted } from "#src/util/disposable.js";
-import { ValueOrError, makeValueOrError, valueOrThrow } from "#src/util/error.js";
+import { type Owned, RefCounted } from "#src/util/disposable.js";
+import { removeChildren } from "#src/util/dom.js";
+import { type ValueOrError, makeValueOrError, valueOrThrow } from "#src/util/error.js";
 import { EventActionMap } from "#src/util/event_action_map.js";
 import { mat4, vec3, vec4 } from "#src/util/geom.js";
 import {
   HttpError,
   isNotFoundError,
   responseJson,
 } from "#src/util/http_request.js";
-import { removeChildren } from "#src/util/dom";
+
 import {
   parseArray,
   parseFixedLengthArray,
@@ -184,13 +193,13 @@ import {
   verifyString,
   verifyStringArray
 } from "#src/util/json.js";
+import { MouseEventBinder } from "#src/util/mouse_bindings.js";
 import { getObjectId } from "#src/util/object_id.js";
 import { NullarySignal } from "#src/util/signal.js";
 import type {
   SpecialProtocolCredentials,
   SpecialProtocolCredentialsProvider,
 } from "#src/util/special_protocol_request.js";
-import { MouseEventBinder } from "#src/util/mouse_bindings";
 import {
   cancellableFetchSpecialOk,
   parseSpecialUrl,
@@ -200,11 +209,11 @@ import { Uint64 } from "#src/util/uint64.js";
 import { makeDeleteButton } from "#src/widget/delete_button.js";
 import type { DependentViewContext } from "#src/widget/dependent_view_widget.js";
 import { makeIcon } from "#src/widget/icon.js";
-import {
-  CancellationToken,
-  CancellationTokenSource,
-} from "#src/util/cancellation";
-import { debounce } from "lodash";
+
+import type { LayerControlDefinition } from "#src/widget/layer_control.js";
+import { addLayerControlToOptionsTab } from "#src/widget/layer_control.js";
+import { rangeLayerControl } from "#src/widget/layer_control_range.js";
+
 
 function vec4FromVec3(vec: vec3, alpha = 0) {
   const res = vec4.clone([...vec]);
@@ -1626,7 +1635,7 @@ class GraphConnection extends SegmentationGraphSourceConnection {
       );
       const segmentConst = segmentId.clone();
       if (added && isBaseSegment) {
-        this.graph.getRoot(segmentConst).then((rootId) => {
+        this.graph.getRoot(segmentConst, this.layer.displayState.stopLayer.value).then((rootId) => {
           if (segmentsState.visibleSegments.has(segmentConst)) {
             segmentsState.visibleSegments.add(rootId);
           }
@@ -1952,11 +1961,14 @@ class GrapheneGraphServerInterface {
     private credentialsProvider: SpecialProtocolCredentialsProvider,
   ) { }
 
-  async getRoot(segment: Uint64, timestamp = "") {
+  async getRoot(segment: Uint64, timestamp = "", stop_layer: number | undefined = undefined) {
     const timestampEpoch = new Date(timestamp).valueOf() / 1000;
 
-    const url = `${this.url}/node/${String(segment)}/root?int64_as_str=1${Number.isNaN(timestampEpoch) ? "" : `&timestamp=${timestampEpoch}`
+    let url = `${this.url}/node/${String(segment)}/root?int64_as_str=1${Number.isNaN(timestampEpoch) ? "" : `&timestamp=${timestampEpoch}`
       }`;
+    if (stop_layer !== undefined) {
+      url += "&stop_layer=" + stop_layer;
+    }
 
     const promise = cancellableFetchSpecialOk(
       this.credentialsProvider,
@@ -2125,6 +2137,17 @@ class GrapheneGraphServerInterface {
   }
 }
 
+export const LAYER_CONTROLS: LayerControlDefinition<SegmentationUserLayer>[] = [
+  {
+    label: "Stop Layer", // Adjust the label as needed
+    toolJson: json_keys.STOP_LAYER,
+    // ... other properties (toolJson, isValid, title) based on your requirements
+    ...rangeLayerControl((layer) => ({
+      value: layer.displayState.stopLayer,
+      options: { min: 0.0, max: 10, step: 1.0 }
+    })), // Integrate your getter function
+  }]
+
 class GrapheneGraphSource extends SegmentationGraphSource {
   private connections = new Set<GraphConnection>();
   public graphServer: GrapheneGraphServerInterface;
@@ -2188,8 +2211,14 @@ class GrapheneGraphSource extends SegmentationGraphSource {
     }
   }
 
-  getRoot(segment: Uint64) {
-    return this.graphServer.getRoot(segment);
+
+  getRoot(segment: Uint64, stop_layer: number) {
+    if (stop_layer > 0) {
+      return this.graphServer.getRoot(segment, "", stop_layer);
+    }
+    else {
+      return this.graphServer.getRoot(segment);
+    }
   }
 
   async findPath(
@@ -2276,7 +2305,15 @@ class GrapheneGraphSource extends SegmentationGraphSource {
         title: "Find Path",
       }),
     );
+    for (const control of LAYER_CONTROLS) {
+      toolbox.appendChild(
+        addLayerControlToOptionsTab(tab, layer, tab.visibility, control),
+      );
+    }
+
+
     parent.appendChild(toolbox);
+
     parent.appendChild(
       context.registerDisposer(
         new MulticutAnnotationLayerView(layer, layer.annotationDisplayState),
@@ -2310,6 +2347,7 @@ class GrapheneGraphSource extends SegmentationGraphSource {
   }
 }
 
+
 class ChunkedGraphChunkSource
   extends SliceViewChunkSource
   implements ChunkedGraphChunkSourceInterface {

src/datasource/middleauth/credentials_provider.ts

@@ -22,15 +22,16 @@ import {
   CredentialsProvider,
   makeCredentialsGetter,
 } from "#src/credentials_provider/index.js";
+import { type OAuth2Credentials } from "#src/credentials_provider/oauth2.js";
 import { StatusMessage } from "#src/status.js";
+import { type HttpError } from "#src/util/http_request.js";
 import {
   verifyObject,
   verifyObjectProperty,
   verifyString,
   verifyStringArray,
 } from "#src/util/json.js";
-import { HttpError } from "#src/util/http_request";
-import { OAuth2Credentials } from "#src/credentials_provider/oauth2";
+
 
 export type MiddleAuthToken = {
   tokenType: string;

src/layer/segmentation/index.ts

@@ -107,6 +107,7 @@ import { DisplayOptionsTab } from "#src/ui/segmentation_display_options_tab.js";
 import { Uint64Map } from "#src/uint64_map.js";
 import { Uint64OrderedSet } from "#src/uint64_ordered_set.js";
 import { Uint64Set } from "#src/uint64_set.js";
+import { gatherUpdate } from "#src/util/array.js";
 import {
   packColor,
   parseRGBColorSpecification,
@@ -122,14 +123,14 @@ import {
   verifyFiniteNonNegativeFloat,
   verifyObjectAsMap,
   verifyOptionalObjectProperty,
+  verifyPositiveInt,
   verifyString,
 } from "#src/util/json.js";
 import { Signal } from "#src/util/signal.js";
 import { Uint64 } from "#src/util/uint64.js";
 import { makeWatchableShaderError } from "#src/webgl/dynamic_shader.js";
 import type { DependentViewContext } from "#src/widget/dependent_view_widget.js";
 import { registerLayerShaderControlsTool } from "#src/widget/shader_controls.js";
-import { gatherUpdate } from "#src/util/array";
 
 export const SKELETON_RENDERING_SHADER_CONTROL_TOOL_ID =
   "skeletonShaderControl";
@@ -485,6 +486,7 @@ class SegmentationUserLayerDisplayState implements SegmentationDisplayState {
   );
   objectAlpha = trackableAlphaValue(1.0);
   ignoreNullVisibleSet = new TrackableBoolean(true, true);
+  stopLayer = new TrackableValue<number>(0, verifyPositiveInt);
   skeletonRenderingOptions = new SkeletonRenderingOptions();
   shaderError = makeWatchableShaderError();
   renderScaleHistogram = new RenderScaleHistogram();
@@ -595,7 +597,11 @@ export class SegmentationUserLayer extends Base {
   };
 
   displayState = new SegmentationUserLayerDisplayState(this);
-
+  stopLayer = new TrackableValue<number>(
+    0,
+    verifyFiniteNonNegativeFloat,
+    0,
+  );
   anchorSegment = new TrackableValue<Uint64 | undefined>(undefined, (x) =>
     x === undefined ? undefined : Uint64.parseString(x),
   );

src/layer/segmentation/json_keys.ts

@@ -9,6 +9,7 @@ export const IGNORE_NULL_VISIBLE_SET_JSON_KEY = "ignoreNullVisibleSet";
 export const MESH_JSON_KEY = "mesh";
 export const SKELETONS_JSON_KEY = "skeletons";
 export const SEGMENTS_JSON_KEY = "segments";
+export const STOP_LAYER = 'stop_layer';
 export const EQUIVALENCES_JSON_KEY = "equivalences";
 export const COLOR_SEED_JSON_KEY = "colorSeed";
 export const SEGMENT_STATED_COLORS_JSON_KEY = "segmentColors";

src/segmentation_display_state/frontend.ts

@@ -55,16 +55,16 @@ import {
 } from "#src/util/color.js";
 import { RefCounted } from "#src/util/disposable.js";
 import { measureElementClone } from "#src/util/dom.js";
-import type { vec3 } from "#src/util/geom.js";
-import { kOneVec, vec4 } from "#src/util/geom.js";
+import { vec3, kOneVec, vec4 } from "#src/util/geom.js";
 import { NullarySignal } from "#src/util/signal.js";
 import { Uint64 } from "#src/util/uint64.js";
 import { withSharedVisibility } from "#src/visibility_priority/frontend.js";
+import { ColorWidget } from "#src/widget/color.js";
 import { makeCopyButton } from "#src/widget/copy_button.js";
 import { makeEyeButton } from "#src/widget/eye_button.js";
 import { makeFilterButton } from "#src/widget/filter_button.js";
 import { makeStarButton } from "#src/widget/star_button.js";
-import { ColorWidget } from "#src/widget/color";
+
 
 export class Uint64MapEntry {
   constructor(