fix: move add cube tool to annotationlayer, todo: share

seung-lab · Feb 13, 2024 · db7b43d · db7b43d
1 parent a367893
commit db7b43d
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Showing 2 changed files with 50 additions and 17 deletions.
diff --git a/config/custom-keybinds.json b/config/custom-keybinds.json
@@ -10,7 +10,7 @@
     "provider": "graphene"
   },
   "keyt": {
-    "layer": "segmentation",
+    "layer": "annotation",
     "tool": "annotateCustomCube"
   }
 }
diff --git a/src/widgets/add_cube_annotation.ts b/src/widgets/add_cube_annotation.ts
@@ -1,9 +1,9 @@
 import {LayerTool, makeToolActivationStatusMessageWithHeader, registerTool, ToolActivation} from "neuroglancer/ui/tool";
-import {SegmentationUserLayer} from "neuroglancer/segmentation_user_layer";
+// import {SegmentationUserLayer} from "neuroglancer/segmentation_user_layer";
 import {makeIcon} from "neuroglancer/widget/icon";
 import {EventActionMap} from "neuroglancer/util/mouse_bindings";
 import {TextInputWidget} from "neuroglancer/widget/text_input";
-import {TrackableValue, WatchableValue} from "neuroglancer/trackable_value";
+import {TrackableValue} from "neuroglancer/trackable_value";
 import {
     Annotation,
     LocalAnnotationSource,
@@ -17,12 +17,16 @@ import {removeChildren} from "neuroglancer/util/dom";
 import {RenderLayerRole} from "neuroglancer/renderlayer";
 import {LoadedDataSubsource} from "neuroglancer/layer_data_source";
 import {vec3} from "neuroglancer/util/geom";
-import {TrackableBoolean} from "neuroglancer/trackable_boolean";
+// import {TrackableBoolean} from "neuroglancer/trackable_boolean";
 import {RefCounted} from "neuroglancer/util/disposable";
 import {Trackable} from "neuroglancer/util/trackable";
 import {verifyOptionalObjectProperty} from "neuroglancer/util/json";
 import {NullarySignal} from "neuroglancer/util/signal";
 import {StatusMessage} from "neuroglancer/status";
+import {AnnotationUserLayer} from "neuroglancer/annotation/user_layer";
+// import {SegmentationUserLayer} from "neuroglancer/segmentation_user_layer";
+// import {SegmentationUserLayer} from "neuroglancer/segmentation_user_layer";
+// import {makeAnnotationListElement} from 'neuroglancer/ui/annotations';
 
 const ADD_CUBE_TOOL_ID = "annotateCustomCube";
 const ADD_CUBE_EVENT_MAP = EventActionMap.fromObject({
@@ -64,19 +68,19 @@ const calculateBoundingBox = (mousePoint: Float32Array, cubeSize: Float32Array)
 }
 
 function makeColoredAnnotationState(
-    layer: SegmentationUserLayer, loadedSubsource: LoadedDataSubsource,
+    layer: AnnotationUserLayer, loadedSubsource: LoadedDataSubsource,
     subsubsourceId: string, color: vec3, readonly = false) {
     const {subsourceEntry} = loadedSubsource;
-    const source = new LocalAnnotationSource(loadedSubsource.loadedDataSource.transform, [], ['associated segments']);
+    const source = new LocalAnnotationSource(loadedSubsource.loadedDataSource.transform, [], []);
+    // const source = new AnnotationSource();
     source.readonly = readonly;
-
     const displayState = new AnnotationDisplayState();
     displayState.color.value.set(color);
-
-    displayState.relationshipStates.set('associated segments', {
-        segmentationState: new WatchableValue(layer.displayState),
-        showMatches: new TrackableBoolean(false),
-    });
+    console.log(loadedSubsource, source, displayState)
+    // displayState.relationshipStates.set('associated segments', {
+    //     segmentationState: new WatchableValue(layer.displayState),
+    //     showMatches: new TrackableBoolean(false),
+    // });
 
     const state = new AnnotationLayerState({
         localPosition: layer.localPosition,
@@ -89,17 +93,21 @@ function makeColoredAnnotationState(
         subsubsourceId,
         role: RenderLayerRole.ANNOTATION,
     });
+    console.log(layer)
     layer.addAnnotationLayerState(state, loadedSubsource);
+    console.log(state)
     return state;
 }
 
-function getGraphLoadedSubsource(layer: SegmentationUserLayer) {
+function getDefaultLoadedSubsource(layer: AnnotationUserLayer) {
+
     for (const dataSource of layer.dataSources) {
+        console.log(dataSource)
         const {loadState} = dataSource;
         if (loadState === undefined || loadState.error !== undefined) continue;
         for (const subsource of loadState.subsources) {
             if (subsource.enabled) {
-                if (subsource.subsourceEntry.id === 'graph') {
+                if (subsource.subsourceEntry.id === 'default') {
                     return subsource;
                 }
             }
@@ -150,7 +158,8 @@ class AddCubeAnnotationState extends RefCounted implements Trackable {
     }
 }
 
-class AddCubeAnnotationTool extends LayerTool<SegmentationUserLayer> {
+// class AddCubeAnnotationTool extends LayerTool<SegmentationUserLayer> {
+class AddCubeAnnotationTool extends LayerTool<AnnotationUserLayer> {
     cubeAnnotationState: AnnotationLayerState;
     annotation: Annotation;
     addCubeAnnotationState = new AddCubeAnnotationState();
@@ -212,7 +221,12 @@ class AddCubeAnnotationTool extends LayerTool<SegmentationUserLayer> {
 
         const updateAnnotationElements = () => {
             removeChildren(annotationElements);
-            const loadedSubsource = getGraphLoadedSubsource(layer)!;
+            // const maxColumnWidths = [0, 0, 0];
+            // const globalDimensionIndices = [0, 1, 2];
+            // const localDimensionIndices: number[] = [0, 1, 2];
+            // const template = '[symbol] 2ch [dim] var(--neuroglancer-column-0-width) [dim] var(--neuroglancer-column-1-width) [dim] var(--neuroglancer-column-2-width) [delete] min-content';
+
+            const loadedSubsource =  getDefaultLoadedSubsource(layer)!;
             const YELLOW_COLOR = vec3.fromValues(1, 1, 0);
             const annotationGroup = makeColoredAnnotationState(layer, loadedSubsource, "addcustomcube", YELLOW_COLOR, false);
             this.cubeAnnotationState = annotationGroup;
@@ -229,6 +243,22 @@ class AddCubeAnnotationTool extends LayerTool<SegmentationUserLayer> {
                 properties: []
             };
             this.cubeAnnotationState.source.add(annotation);
+            // this.cubeAnnotationState.disposed();
+            // layer.updateAttachedAnnotationLayerStates();
+            // layer.addAnnotationLayerState(this.cubeAnnotationState, loadedSubsource)
+            // layer.annotations.add()
+            // console.log(this.cubeAnnotationState)
+
+            // const [element, elementColumnWidths] = makeAnnotationListElement(this.layer, annotation, this.cubeAnnotationState, template, globalDimensionIndices, localDimensionIndices);
+            // for (const [column, width] of elementColumnWidths.entries()) {
+            //     maxColumnWidths[column] = width;
+            // }
+            // console.log(element, elementColumnWidths)
+            // annotationElements.appendChild(element);
+            //
+            // for (const [column, width] of maxColumnWidths.entries()) {
+            //     annotationElements.style.setProperty(`--neuroglancer-column-${column}-width`, `${width + 2}ch`);
+            // }
         };
 
         activation.bindInputEventMap(ADD_CUBE_EVENT_MAP);
@@ -258,7 +288,10 @@ class AddCubeAnnotationTool extends LayerTool<SegmentationUserLayer> {
 }
 
 export function registerAnnotateCubeTool() {
-    registerTool(SegmentationUserLayer, ADD_CUBE_TOOL_ID, layer => {
+    // registerTool(SegmentationUserLayer, ADD_CUBE_TOOL_ID, layer => {
+    //     return new AddCubeAnnotationTool(layer, true)
+    // })
+    registerTool(AnnotationUserLayer, ADD_CUBE_TOOL_ID, layer => {
         return new AddCubeAnnotationTool(layer, true)
     })
 }