Voxel data pipette tool

docs/ui/toolbar.md

@@ -125,6 +125,9 @@ And many other tools. For detailed information, see the [volume annotation guide
 ![Measurement Tool](./images/measure-tool.jpg){align=left width="60"}
 **Measurement Tool**: Allows you to calculate distances between points of interest, measure surface areas of segmented structures, and place waypoints for complex measurements. See also [statistics for volume annotations](../volume_annotation/segments_statistics.md). 
 
+![Voxel Pipette Tool](../ui/images/segment-picker-tool.jpg){align=left width="60"} 
+**Voxel Pipette**: Hover over your data to see the exact values at a specific voxel. A tooltip will be shown that shows the intensity values for color layers and the segment id for the visible segmentation layer. The tooltip can be pinned by clicking so that the values can be copied. Pressing shift while clicking will activate the hovered segment id. This is alternative to selecting the segment ID from the [Segments list](./segments_list.md) sidebar or context menu.
+
 ![AI Analysis Tools](./images/ai-analysis-tools.jpg){align=left width="60"}
 **AI Analysis**: Launch automated segmentation processes using various analysis workflows. The AI tools can significantly speed up your annotation work. Learn more about [AI-assisted analysis](../automation/ai_segmentation.md).
 
@@ -134,4 +137,4 @@ And many other tools. For detailed information, see the [volume annotation guide
 
 To create a bounding box, select the tool and then click and drag with the mouse on one of the 2D viewports. You can resize the bounding box by dragging its corners or edges.
 
-All created bounding boxes are listed in the **BBoxes** tab in the right-hand sidebar. From there, you can manage your bounding boxes, for example, by renaming, deleting, or jumping to them. Read more about the sidebar tabs in the [Object Info and Lists](./object_info.md) documentation.
+All created bounding boxes are listed in the **BBoxes** tab in the right-hand sidebar. From there, you can manage your bounding boxes, for example, by renaming, deleting, or jumping to them. Read more about the sidebar tabs in the [Object Info and Lists](./object_info.md) documentation.

docs/volume_annotation/tools.md

@@ -24,9 +24,6 @@ Volume annotation in WEBKNOSSOS allows you to label and segment 3D structures in
 - The fill behavior can be modified using the 2D/3D fill modifiers (see below).
 - This tool only takes existing labels into account and does not look at any other underlying (microscopy) layers. Have a look at the [quick-select-tool](#quick-select-tool) for quickly annotating new structures.
 
-![Segment Picker Tool](../ui/images/segment-picker-tool.jpg){align=left width="60"} 
-**Segment Picker**: Click any segment to use its label ID as the active segment ID and keep annotating with that ID. This is alternative to selecting the segment ID from the [Segments list](./segments_list.md) sidebar or context menu.
-
 ![Quick Select Tool](../ui/images/quickselect-tool.jpg){align=left width="60"} 
 **Quick Select**: Automatically annotate segments using either:
 

frontend/javascripts/test/reducers/volumetracing_reducer.spec.ts

@@ -192,7 +192,7 @@ describe("VolumeTracing", () => {
     newState = UiReducer(newState, cycleToolAction());
     expect(newState.uiInformation.activeTool).toBe(AnnotationTool.FILL_CELL);
     newState = UiReducer(newState, cycleToolAction());
-    expect(newState.uiInformation.activeTool).toBe(AnnotationTool.PICK_CELL);
+    expect(newState.uiInformation.activeTool).toBe(AnnotationTool.VOXEL_PIPETTE);
     newState = UiReducer(newState, cycleToolAction());
     expect(newState.uiInformation.activeTool).toBe(AnnotationTool.QUICK_SELECT);
     newState = UiReducer(newState, cycleToolAction());

frontend/javascripts/test/sagas/annotation_tool_disabled_info.spec.ts

@@ -6,7 +6,7 @@ import { AnnotationTool, VolumeTools } from "viewer/model/accessors/tool_accesso
 import type { CoordinateTransformation } from "types/api_types";
 
 const zoomSensitiveVolumeTools = VolumeTools.filter(
-  (name) => name !== AnnotationTool.PICK_CELL,
+  (name) => name !== AnnotationTool.VOXEL_PIPETTE,
 ) as AnnotationTool[];
 
 const zoomedInInitialState = update(initialState, {
@@ -152,6 +152,7 @@ describe("Annotation Tool Disabled Info", () => {
       AnnotationTool.MOVE,
       AnnotationTool.LINE_MEASUREMENT,
       AnnotationTool.AREA_MEASUREMENT,
+      AnnotationTool.VOXEL_PIPETTE,
     ] as AnnotationTool[];
     const disabledInfo = getDisabledInfoForTools(rotatedState);
     for (const tool of Object.values(AnnotationTool)) {

frontend/javascripts/test/sagas/annotation_tool_saga.spec.ts

@@ -38,7 +38,7 @@ import {
   DrawToolController,
   EraseToolController,
   FillCellToolController,
-  PickCellToolController,
+  VoxelPipetteToolController,
   QuickSelectToolController,
   ProofreadToolController,
   LineMeasurementToolController,
@@ -56,7 +56,7 @@ describe("Annotation Tool Saga", () => {
     DrawToolController,
     EraseToolController,
     FillCellToolController,
-    PickCellToolController,
+    VoxelPipetteToolController,
     QuickSelectToolController,
     ProofreadToolController,
     LineMeasurementToolController,
@@ -98,7 +98,7 @@ describe("Annotation Tool Saga", () => {
     cycleTool();
     expect(FillCellToolController.onToolDeselected).toHaveBeenCalledTimes(1);
     cycleTool();
-    expect(PickCellToolController.onToolDeselected).toHaveBeenCalledTimes(1);
+    expect(VoxelPipetteToolController.onToolDeselected).toHaveBeenCalledTimes(1);
     cycleTool();
     expect(QuickSelectToolController.onToolDeselected).toHaveBeenCalledTimes(1);
     cycleTool();
@@ -139,10 +139,10 @@ describe("Annotation Tool Saga", () => {
     expect(DrawToolController.onToolDeselected).toHaveBeenCalledTimes(2);
     cycleTool(AnnotationTool.FILL_CELL);
     expect(EraseToolController.onToolDeselected).toHaveBeenCalledTimes(2);
-    cycleTool(AnnotationTool.PICK_CELL);
+    cycleTool(AnnotationTool.VOXEL_PIPETTE);
     expect(FillCellToolController.onToolDeselected).toHaveBeenCalledTimes(1);
     cycleTool(AnnotationTool.BOUNDING_BOX);
-    expect(PickCellToolController.onToolDeselected).toHaveBeenCalledTimes(1);
+    expect(VoxelPipetteToolController.onToolDeselected).toHaveBeenCalledTimes(1);
     cycleTool(AnnotationTool.PROOFREAD);
     expect(BoundingBoxToolController.onToolDeselected).toHaveBeenCalledTimes(1);
     cycleTool(AnnotationTool.LINE_MEASUREMENT);

frontend/javascripts/viewer/api/api_latest.ts

@@ -52,6 +52,7 @@ import {
   getLayerByName,
   getMagInfo,
   getMappingInfo,
+  getMappingInfoOrNull,
   getVisibleSegmentationLayer,
 } from "viewer/model/accessors/dataset_accessor";
 import { flatToNestedMatrix } from "viewer/model/accessors/dataset_layer_transformation_accessor";
@@ -1516,15 +1517,15 @@ class TracingApi {
 
   /**
    * Returns the active tool which is either
-   * "MOVE", "SKELETON", "TRACE", "BRUSH", "FILL_CELL" or "PICK_CELL"
+   * "MOVE", "SKELETON", "TRACE", "BRUSH", "FILL_CELL" or "VOXEL_PIPETTE"
    */
   getAnnotationTool(): AnnotationToolId {
     return Store.getState().uiInformation.activeTool.id;
   }
 
   /**
    * Sets the active tool which should be either
-   * "MOVE", "SKELETON", "TRACE", "BRUSH", "FILL_CELL" or "PICK_CELL"
+   * "MOVE", "SKELETON", "TRACE", "BRUSH", "FILL_CELL" or "VOXEL_PIPETTE"
    * _Volume tracing only!_
    */
   setAnnotationTool(toolId: AnnotationToolId) {
@@ -1863,42 +1864,63 @@ class DataApi {
    */
   async getDataValue(
     layerName: string,
-    position: Vector3,
+    position: Vector3, // in layer space
     _zoomStep: number | null | undefined = null,
     additionalCoordinates: AdditionalCoordinate[] | null = null,
+    respectMapping: boolean = false,
   ): Promise<number> {
     let zoomStep;
+    const state = Store.getState();
 
     if (_zoomStep != null) {
       zoomStep = _zoomStep;
     } else {
-      const layer = getLayerByName(Store.getState().dataset, layerName);
+      const layer = getLayerByName(state.dataset, layerName);
       const magInfo = getMagInfo(layer.mags);
       zoomStep = magInfo.getFinestMagIndex();
     }
 
     const cube = this.model.getCubeByLayerName(layerName);
-    additionalCoordinates = additionalCoordinates || Store.getState().flycam.additionalCoordinates;
+    additionalCoordinates = additionalCoordinates || state.flycam.additionalCoordinates;
     const bucketAddress = cube.positionToZoomedAddress(position, additionalCoordinates, zoomStep);
     await this.getLoadedBucket(layerName, bucketAddress);
+
+    let mapping = null;
+    if (respectMapping) {
+      const activeMappingInfo = getMappingInfoOrNull(
+        state.temporaryConfiguration.activeMappingByLayer,
+        layerName,
+      );
+      mapping =
+        activeMappingInfo?.mappingStatus === MappingStatusEnum.ENABLED
+          ? activeMappingInfo.mapping
+          : null;
+    }
+
     // Bucket has been loaded by now or was loaded already
-    const dataValue = cube.getDataValue(position, additionalCoordinates, null, zoomStep);
+    const dataValue = cube.getDataValue(position, additionalCoordinates, mapping, zoomStep);
     return dataValue;
   }
 
   /**
    * Returns the magnification that is _currently_ rendered at the given position.
    */
-  getRenderedZoomStepAtPosition(layerName: string, position: Vector3 | null | undefined): number {
-    return this.model.getCurrentlyRenderedZoomStepAtPosition(layerName, position);
+  getRenderedZoomStepAtPosition(
+    layerName: string,
+    positionInLayerSpace: Vector3 | null | undefined,
+  ): number {
+    return this.model.getCurrentlyRenderedZoomStepAtPosition(layerName, positionInLayerSpace);
   }
 
   /**
    * Returns the maginfication that will _ultimately_ be rendered at the given position, once
    * all respective buckets are loaded.
    */
-  getUltimatelyRenderedZoomStepAtPosition(layerName: string, position: Vector3): Promise<number> {
-    return this.model.getUltimatelyRenderedZoomStepAtPosition(layerName, position);
+  getUltimatelyRenderedZoomStepAtPosition(
+    layerName: string,
+    positionInLayerSpace: Vector3,
+  ): Promise<number> {
+    return this.model.getUltimatelyRenderedZoomStepAtPosition(layerName, positionInLayerSpace);
   }
 
   async getLoadedBucket(layerName: string, bucketAddress: BucketAddress): Promise<Bucket> {

frontend/javascripts/viewer/controller/combinations/tool_controls.ts

@@ -208,6 +208,7 @@ export class MoveToolController {
     _ctrlOrMetaKey: boolean,
     altKey: boolean,
     _isTDViewportActive: boolean,
+    _activeToolWithoutModifiers: AnnotationTool,
   ): ActionDescriptor {
     const { useLegacyBindings } = userConfiguration;
     // In legacy mode, don't display a hint for
@@ -377,6 +378,7 @@ export class SkeletonToolController {
     ctrlOrMetaKey: boolean,
     altKey: boolean,
     _isTDViewportActive: boolean,
+    _activeToolWithoutModifiers: AnnotationTool,
   ): ActionDescriptor {
     const { continuousNodeCreation } = Store.getState().userConfiguration;
     const { useLegacyBindings } = userConfiguration;
@@ -514,6 +516,7 @@ export class DrawToolController {
     _ctrlOrMetaKey: boolean,
     _altKey: boolean,
     _isTDViewportActive: boolean,
+    _activeToolWithoutModifiers: AnnotationTool,
   ): ActionDescriptor {
     let rightClick;
     const { useLegacyBindings } = userConfiguration;
@@ -574,6 +577,7 @@ export class EraseToolController {
     _ctrlOrMetaKey: boolean,
     _altKey: boolean,
     _isTDViewportActive: boolean,
+    _activeToolWithoutModifiers: AnnotationTool,
   ): ActionDescriptor {
     return {
       leftDrag: `Erase (${activeTool === AnnotationTool.ERASE_BRUSH ? "Brush" : "Trace"})`,
@@ -583,30 +587,59 @@ export class EraseToolController {
 
   static onToolDeselected() {}
 }
-export class PickCellToolController {
+export class VoxelPipetteToolController {
   static getPlaneMouseControls(_planeId: OrthoView): any {
     return {
-      leftClick: (pos: Point2, _plane: OrthoView, _event: MouseEvent) => {
-        VolumeHandlers.handlePickCell(pos);
+      mouseMove: (
+        _delta: Point2,
+        position: Point2,
+        plane: OrthoView | null | undefined,
+        event: MouseEvent,
+      ) => {
+        MoveHandlers.moveWhenAltIsPressed(_delta, position, plane, event);
+      },
+      leftClick: (position: Point2, plane: OrthoView, event: MouseEvent) => {
+        if (event.shiftKey) {
+          VolumeHandlers.handlePickCell(position);
+          return;
+        }
+
+        const state = Store.getState();
+        const lastMeasuredGlobalPosition =
+          state.uiInformation.measurementToolInfo.lastMeasuredPosition;
+
+        if (lastMeasuredGlobalPosition == null) {
+          const globalPosition = calculateGlobalPos(state, position, plane).floating;
+          Store.dispatch(setLastMeasuredPositionAction(globalPosition));
+        } else {
+          Store.dispatch(hideMeasurementTooltipAction());
+        }
+        Store.dispatch(setIsMeasuringAction(true));
       },
     };
   }
 
+  static onToolDeselected() {
+    Store.dispatch(hideMeasurementTooltipAction());
+  }
+
   static getActionDescriptors(
     _activeTool: AnnotationTool,
     _userConfiguration: UserConfiguration,
-    _shiftKey: boolean,
+    shiftKey: boolean,
     _ctrlOrMetaKey: boolean,
     _altKey: boolean,
     _isTDViewportActive: boolean,
+    _activeToolWithoutModifiers: AnnotationTool,
   ): ActionDescriptor {
     return {
-      leftClick: "Pick Segment",
+      leftClick:
+        _activeToolWithoutModifiers === AnnotationTool.VOXEL_PIPETTE && !shiftKey
+          ? "Pin Tooltip"
+          : "Activate Segment ID",
       rightClick: "Context Menu",
     };
   }
-
-  static onToolDeselected() {}
 }
 export class FillCellToolController {
   static getPlaneMouseControls(_planeId: OrthoView): any {
@@ -630,6 +663,7 @@ export class FillCellToolController {
     _ctrlOrMetaKey: boolean,
     _altKey: boolean,
     _isTDViewportActive: boolean,
+    _activeToolWithoutModifiers: AnnotationTool,
   ): ActionDescriptor {
     return {
       leftClick: "Fill Segment",
@@ -709,6 +743,7 @@ export class BoundingBoxToolController {
     ctrlOrMetaKey: boolean,
     _altKey: boolean,
     _isTDViewportActive: boolean,
+    _activeToolWithoutModifiers: AnnotationTool,
   ): ActionDescriptor {
     return {
       leftDrag: ctrlOrMetaKey ? "Move Bounding Boxes" : "Create/Resize Bounding Boxes",
@@ -838,6 +873,7 @@ export class QuickSelectToolController {
     _ctrlOrMetaKey: boolean,
     _altKey: boolean,
     _isTDViewportActive: boolean,
+    _activeToolWithoutModifiers: AnnotationTool,
   ): ActionDescriptor {
     return {
       leftDrag: shiftKey ? "Resize Rectangle symmetrically" : "Draw Rectangle around Segment",
@@ -962,6 +998,7 @@ export class LineMeasurementToolController {
     _ctrlOrMetaKey: boolean,
     _altKey: boolean,
     _isTDViewportActive: boolean,
+    _activeToolWithoutModifiers: AnnotationTool,
   ): ActionDescriptor {
     return {
       leftClick: "Left Click to measure distance",
@@ -1041,6 +1078,7 @@ export class AreaMeasurementToolController {
     _ctrlOrMetaKey: boolean,
     _altKey: boolean,
     _isTDViewportActive: boolean,
+    _activeToolWithoutModifiers: AnnotationTool,
   ): ActionDescriptor {
     return {
       leftDrag: "Drag to measure area",
@@ -1114,6 +1152,7 @@ export class ProofreadToolController {
     ctrlOrMetaKey: boolean,
     _altKey: boolean,
     isTDViewportActive: boolean,
+    _activeToolWithoutModifiers: AnnotationTool,
   ): ActionDescriptor {
     const { isMultiSplitActive } = userConfiguration;
 
@@ -1172,7 +1211,7 @@ const toolToToolController = {
   [AnnotationTool.ERASE_TRACE.id]: EraseToolController,
   [AnnotationTool.ERASE_BRUSH.id]: EraseToolController,
   [AnnotationTool.FILL_CELL.id]: FillCellToolController,
-  [AnnotationTool.PICK_CELL.id]: PickCellToolController,
+  [AnnotationTool.VOXEL_PIPETTE.id]: VoxelPipetteToolController,
   [AnnotationTool.LINE_MEASUREMENT.id]: LineMeasurementToolController,
   [AnnotationTool.AREA_MEASUREMENT.id]: AreaMeasurementToolController,
 };