@cornerstonejs/tools 0.56.2 → 0.56.4

package/src/tools/displayTools/Labelmap/labelmapDisplay.ts

@@ -0,0 +1,461 @@
+import vtkPiecewiseFunction from '@kitware/vtk.js/Common/DataModel/PiecewiseFunction';
+import vtkColorTransferFunction from '@kitware/vtk.js/Rendering/Core/ColorTransferFunction';
+
+import {
+  cache,
+  getEnabledElementByIds,
+  Types,
+  utilities,
+} from '@cornerstonejs/core';
+
+import Representations from '../../../enums/SegmentationRepresentations';
+import * as SegmentationConfig from '../../../stateManagement/segmentation/config/segmentationConfig';
+import * as SegmentationState from '../../../stateManagement/segmentation/segmentationState';
+import { getToolGroup } from '../../../store/ToolGroupManager';
+import type { LabelmapConfig } from '../../../types/LabelmapTypes';
+import {
+  RepresentationPublicInput,
+  SegmentationRepresentationConfig,
+  ToolGroupSpecificRepresentation,
+} from '../../../types/SegmentationStateTypes';
+
+import addLabelmapToElement from './addLabelmapToElement';
+
+import removeLabelmapFromElement from './removeLabelmapFromElement';
+
+const MAX_NUMBER_COLORS = 255;
+const labelMapConfigCache = new Map();
+
+/**
+ * For each viewport, in the toolGroup it adds the segmentation labelmap
+ * representation to its viewports.
+ * @param toolGroup - the tool group that contains the viewports
+ * @param representationInput - The segmentation representation input
+ * @param toolGroupSpecificConfig - The configuration object for toolGroup
+ *
+ * @returns The UID of the new segmentation representation
+ */
+async function addSegmentationRepresentation(
+  toolGroupId: string,
+  representationInput: RepresentationPublicInput,
+  toolGroupSpecificConfig?: SegmentationRepresentationConfig
+): Promise<string> {
+  const { segmentationId } = representationInput;
+  const segmentationRepresentationUID = utilities.uuidv4();
+
+  // Todo: make these configurable during representation input by user
+  const segmentsHidden = new Set() as Set<number>;
+  const colorLUTIndex = 0;
+  const active = true;
+  const cfun = vtkColorTransferFunction.newInstance();
+  const ofun = vtkPiecewiseFunction.newInstance();
+
+  ofun.addPoint(0, 0);
+
+  const toolGroupSpecificRepresentation: ToolGroupSpecificRepresentation = {
+    segmentationId,
+    segmentationRepresentationUID,
+    type: Representations.Labelmap,
+    segmentsHidden,
+    colorLUTIndex,
+    active,
+    segmentationRepresentationSpecificConfig: {},
+    segmentSpecificConfig: {},
+    config: {
+      cfun,
+      ofun,
+    },
+  };
+
+  // Update the toolGroup specific configuration
+  if (toolGroupSpecificConfig) {
+    // Since setting configuration on toolGroup will trigger a segmentationRepresentation
+    // update event, we don't want to trigger the event twice, so we suppress
+    // the first one
+    const currentToolGroupConfig =
+      SegmentationConfig.getToolGroupSpecificConfig(toolGroupId);
+
+    const mergedConfig = utilities.deepMerge(
+      currentToolGroupConfig,
+      toolGroupSpecificConfig
+    );
+
+    SegmentationConfig.setToolGroupSpecificConfig(toolGroupId, {
+      renderInactiveSegmentations:
+        mergedConfig.renderInactiveSegmentations || true,
+      representations: {
+        ...mergedConfig.representations,
+      },
+    });
+  }
+
+  SegmentationState.addSegmentationRepresentation(
+    toolGroupId,
+    toolGroupSpecificRepresentation
+  );
+
+  return segmentationRepresentationUID;
+}
+
+/**
+ * For each viewport, and for each segmentation, set the segmentation for the viewport's enabled element
+ * Initializes the global and viewport specific state for the segmentation in the
+ * SegmentationStateManager.
+ * @param toolGroup - the tool group that contains the viewports
+ * @param segmentationRepresentationUID - The uid of the segmentation representation
+ * @param renderImmediate - If true, there will be a render call after the labelmap is removed
+ */
+function removeSegmentationRepresentation(
+  toolGroupId: string,
+  segmentationRepresentationUID: string,
+  renderImmediate = false
+): void {
+  _removeLabelmapFromToolGroupViewports(
+    toolGroupId,
+    segmentationRepresentationUID
+  );
+  SegmentationState.removeSegmentationRepresentation(
+    toolGroupId,
+    segmentationRepresentationUID
+  );
+
+  if (renderImmediate) {
+    const viewportsInfo = getToolGroup(toolGroupId).getViewportsInfo();
+    viewportsInfo.forEach(({ viewportId, renderingEngineId }) => {
+      const enabledElement = getEnabledElementByIds(
+        viewportId,
+        renderingEngineId
+      );
+      enabledElement.viewport.render();
+    });
+  }
+}
+
+/**
+ * It takes the enabled element, the segmentation Id, and the configuration, and
+ * it sets the segmentation for the enabled element as a labelmap
+ * @param enabledElement - The cornerstone enabled element
+ * @param segmentationId - The id of the segmentation to be rendered.
+ * @param configuration - The configuration object for the labelmap.
+ */
+async function render(
+  viewport: Types.IVolumeViewport,
+  representation: ToolGroupSpecificRepresentation,
+  toolGroupConfig: SegmentationRepresentationConfig
+): Promise<void> {
+  const {
+    colorLUTIndex,
+    active,
+    segmentationId,
+    segmentationRepresentationUID,
+    segmentsHidden,
+    config: renderingConfig,
+  } = representation;
+
+  const segmentation = SegmentationState.getSegmentation(segmentationId);
+  const labelmapData =
+    segmentation.representationData[Representations.Labelmap];
+  const { volumeId: labelmapUID } = labelmapData;
+
+  const labelmap = cache.getVolume(labelmapUID);
+
+  if (!labelmap) {
+    throw new Error(`No Labelmap found for volumeId: ${labelmapUID}`);
+  }
+
+  let actorEntry = viewport.getActor(segmentationRepresentationUID);
+
+  if (!actorEntry) {
+    const segmentation = SegmentationState.getSegmentation(segmentationId);
+    const { volumeId } =
+      segmentation.representationData[Representations.Labelmap];
+    // only add the labelmap to ToolGroup viewports if it is not already added
+    await _addLabelmapToViewport(
+      viewport,
+      volumeId,
+      segmentationRepresentationUID
+    );
+
+    actorEntry = viewport.getActor(segmentationRepresentationUID);
+  }
+
+  const { cfun, ofun } = renderingConfig;
+
+  const renderInactiveSegmentations =
+    toolGroupConfig.renderInactiveSegmentations;
+
+  _setLabelmapColorAndOpacity(
+    viewport.id,
+    actorEntry,
+    cfun,
+    ofun,
+    colorLUTIndex,
+    toolGroupConfig.representations[Representations.Labelmap],
+    representation,
+    active,
+    renderInactiveSegmentations,
+    segmentsHidden
+  );
+}
+
+function _setLabelmapColorAndOpacity(
+  viewportId: string,
+  actorEntry: Types.ActorEntry,
+  cfun: vtkColorTransferFunction,
+  ofun: vtkPiecewiseFunction,
+  colorLUTIndex: number,
+  toolGroupLabelmapConfig: LabelmapConfig,
+  segmentationRepresentation: ToolGroupSpecificRepresentation,
+  isActiveLabelmap: boolean,
+  renderInactiveSegmentations: boolean,
+  segmentsHidden: Set<number>
+): void {
+  const { segmentSpecificConfig, segmentationRepresentationSpecificConfig } =
+    segmentationRepresentation;
+
+  const segmentationRepresentationLabelmapConfig =
+    segmentationRepresentationSpecificConfig[Representations.Labelmap];
+
+  // Note: MAX_NUMBER_COLORS = 256 is needed because the current method to generate
+  // the default color table uses RGB.
+  const colorLUT = SegmentationState.getColorLUT(colorLUTIndex);
+  const numColors = Math.min(256, colorLUT.length);
+  const volumeActor = actorEntry.actor as Types.VolumeActor;
+  const { uid: actorUID } = actorEntry;
+
+  // Note: right now outlineWidth and renderOutline are not configurable
+  // at the segment level, so we don't need to check for segment specific
+  // configuration in the loop, Todo: make them configurable at the segment level
+  const { outlineWidth, renderOutline, outlineOpacity } = _getLabelmapConfig(
+    toolGroupLabelmapConfig,
+    segmentationRepresentationLabelmapConfig,
+    isActiveLabelmap
+  );
+
+  for (let i = 0; i < numColors; i++) {
+    const segmentIndex = i;
+    const segmentColor = colorLUT[segmentIndex];
+
+    const segmentSpecificLabelmapConfig =
+      segmentSpecificConfig[segmentIndex]?.[Representations.Labelmap];
+
+    const { fillAlpha, outlineWidth, renderFill, renderOutline } =
+      _getLabelmapConfig(
+        toolGroupLabelmapConfig,
+        segmentationRepresentationLabelmapConfig,
+        isActiveLabelmap,
+        segmentSpecificLabelmapConfig
+      );
+
+    const { forceOpacityUpdate, forceColorUpdate } =
+      _needsTransferFunctionUpdate(viewportId, actorUID, segmentIndex, {
+        fillAlpha,
+        renderFill,
+        renderOutline,
+        segmentColor,
+        outlineWidth,
+        segmentsHidden,
+      });
+
+    if (forceColorUpdate) {
+      cfun.addRGBPoint(
+        segmentIndex,
+        segmentColor[0] / MAX_NUMBER_COLORS,
+        segmentColor[1] / MAX_NUMBER_COLORS,
+        segmentColor[2] / MAX_NUMBER_COLORS
+      );
+    }
+
+    if (forceOpacityUpdate) {
+      if (renderFill) {
+        const segmentOpacity = segmentsHidden.has(segmentIndex)
+          ? 0
+          : (segmentColor[3] / 255) * fillAlpha;
+
+        ofun.removePoint(segmentIndex);
+        ofun.addPointLong(segmentIndex, segmentOpacity, 0.5, 1.0);
+      } else {
+        ofun.addPointLong(segmentIndex, 0.01, 0.5, 1.0);
+      }
+    }
+  }
+
+  volumeActor.getProperty().setRGBTransferFunction(0, cfun);
+
+  ofun.setClamping(false);
+  volumeActor.getProperty().setScalarOpacity(0, ofun);
+
+  volumeActor.getProperty().setInterpolationTypeToNearest();
+
+  volumeActor.getProperty().setUseLabelOutline(renderOutline);
+
+  // @ts-ignore: setLabelOutlineWidth is not in the vtk.d.ts apparently
+  volumeActor.getProperty().setLabelOutlineOpacity(outlineOpacity);
+  volumeActor.getProperty().setLabelOutlineThickness(outlineWidth);
+
+  // Set visibility based on whether actor visibility is specifically asked
+  // to be turned on/off (on by default) AND whether is is in active but
+  // we are rendering inactive labelmap
+  const visible = isActiveLabelmap || renderInactiveSegmentations;
+  volumeActor.setVisibility(visible);
+}
+
+function _getLabelmapConfig(
+  toolGroupLabelmapConfig: LabelmapConfig,
+  segmentationRepresentationLabelmapConfig: LabelmapConfig,
+  isActiveLabelmap: boolean,
+  segmentsLabelmapConfig?: LabelmapConfig
+) {
+  const segmentLabelmapConfig = segmentsLabelmapConfig || {};
+
+  const configToUse = {
+    ...toolGroupLabelmapConfig,
+    ...segmentationRepresentationLabelmapConfig,
+    ...segmentLabelmapConfig,
+  };
+
+  const fillAlpha = isActiveLabelmap
+    ? configToUse.fillAlpha
+    : configToUse.fillAlphaInactive;
+  const outlineWidth = isActiveLabelmap
+    ? configToUse.outlineWidthActive
+    : configToUse.outlineWidthInactive;
+
+  const renderFill = isActiveLabelmap
+    ? configToUse.renderFill
+    : configToUse.renderFillInactive;
+
+  const renderOutline = configToUse.renderOutline;
+
+  const outlineOpacity = isActiveLabelmap
+    ? configToUse.outlineOpacity
+    : configToUse.outlineOpacityInactive;
+
+  return {
+    fillAlpha,
+    outlineWidth,
+    renderFill,
+    renderOutline,
+    outlineOpacity,
+  };
+}
+
+function _needsTransferFunctionUpdate(
+  viewportId: string,
+  actorUID: string,
+  segmentIndex: number,
+  {
+    fillAlpha,
+    renderFill,
+    renderOutline,
+    segmentColor,
+    outlineWidth,
+    segmentsHidden,
+  }: {
+    fillAlpha: number;
+    renderFill: boolean;
+    renderOutline: boolean;
+    outlineWidth: number;
+    segmentColor: number[];
+    segmentsHidden: Set<number>;
+  }
+) {
+  const cacheUID = `${viewportId}-${actorUID}-${segmentIndex}`;
+  const oldConfig = labelMapConfigCache.get(cacheUID);
+
+  if (!oldConfig) {
+    labelMapConfigCache.set(cacheUID, {
+      fillAlpha,
+      renderFill,
+      renderOutline,
+      outlineWidth,
+      segmentColor,
+      segmentsHidden: new Set(segmentsHidden), // Create a copy
+    });
+
+    return {
+      forceOpacityUpdate: true,
+      forceColorUpdate: true,
+    };
+  }
+
+  const {
+    fillAlpha: oldFillAlpha,
+    renderFill: oldRenderFill,
+    renderOutline: oldRenderOutline,
+    outlineWidth: oldOutlineWidth,
+    segmentColor: oldSegmentColor,
+    segmentsHidden: oldSegmentsHidden,
+  } = oldConfig;
+
+  const forceColorUpdate =
+    oldSegmentColor[0] !== segmentColor[0] ||
+    oldSegmentColor[1] !== segmentColor[1] ||
+    oldSegmentColor[2] !== segmentColor[2];
+
+  const forceOpacityUpdate =
+    oldSegmentColor[3] !== segmentColor[3] ||
+    oldFillAlpha !== fillAlpha ||
+    oldRenderFill !== renderFill ||
+    oldRenderOutline !== renderOutline ||
+    oldOutlineWidth !== outlineWidth ||
+    oldSegmentsHidden.has(segmentIndex) !== segmentsHidden.has(segmentIndex);
+
+  // update the cache
+  labelMapConfigCache.set(cacheUID, {
+    fillAlpha,
+    renderFill,
+    renderOutline,
+    outlineWidth,
+    segmentColor,
+    segmentsHidden: new Set(segmentsHidden), // Create a copy
+  });
+
+  return {
+    forceOpacityUpdate,
+    forceColorUpdate,
+  };
+}
+
+function _removeLabelmapFromToolGroupViewports(
+  toolGroupId: string,
+  segmentationRepresentationUID: string
+): void {
+  const toolGroup = getToolGroup(toolGroupId);
+
+  if (toolGroup === undefined) {
+    throw new Error(`ToolGroup with ToolGroupId ${toolGroupId} does not exist`);
+  }
+
+  const { viewportsInfo } = toolGroup;
+
+  for (const viewportInfo of viewportsInfo) {
+    const { viewportId, renderingEngineId } = viewportInfo;
+    const enabledElement = getEnabledElementByIds(
+      viewportId,
+      renderingEngineId
+    );
+    removeLabelmapFromElement(
+      enabledElement.viewport.element,
+      segmentationRepresentationUID
+    );
+  }
+}
+
+async function _addLabelmapToViewport(
+  viewport: Types.IVolumeViewport,
+  volumeId: string,
+  segmentationRepresentationUID: string
+): Promise<void> {
+  await addLabelmapToElement(
+    viewport.element,
+    volumeId,
+    segmentationRepresentationUID
+  );
+}
+
+export default {
+  render,
+  addSegmentationRepresentation,
+  removeSegmentationRepresentation,
+};

package/src/tools/displayTools/Labelmap/removeLabelmapFromElement.ts

@@ -0,0 +1,27 @@
+import { getEnabledElement } from '@cornerstonejs/core';
+import type { Types } from '@cornerstonejs/core';
+
+/**
+ * Remove the labelmap segmentation representation from the viewport's HTML Element.
+ * NOTE: This function should not be called directly.
+ *
+ * @param element - The element that the segmentation is being added to.
+ * @param segmentationRepresentationUID - The UID of the labelmap representation to remove.
+ * @param removeFromCache - boolean
+ *
+ * @internal
+ */
+function removeLabelmapFromElement(
+  element: HTMLDivElement,
+  segmentationRepresentationUID: string,
+  removeFromCache = false // Todo
+): void {
+  const enabledElement = getEnabledElement(element);
+  const { viewport } = enabledElement;
+
+  (viewport as Types.IVolumeViewport).removeVolumeActors([
+    segmentationRepresentationUID,
+  ]);
+}
+
+export default removeLabelmapFromElement;

package/src/tools/displayTools/Labelmap/validateRepresentationData.ts

@@ -0,0 +1,30 @@
+import { SegmentationPublicInput } from '../../../types/SegmentationStateTypes';
+import { cache } from '@cornerstonejs/core';
+import { LabelmapSegmentationData } from '../../../types/LabelmapTypes';
+
+function validate(segmentationInput: SegmentationPublicInput): void {
+  if (!segmentationInput.representation.data) {
+    throw new Error(
+      'The segmentationInput.representationData.data is undefined, please provide a valid representationData.data'
+    );
+  }
+
+  const representationData = segmentationInput.representation
+    .data as LabelmapSegmentationData;
+
+  if (!representationData.volumeId) {
+    throw new Error(
+      'The segmentationInput.representationData.volumeId is undefined, please provide a valid representationData.volumeId'
+    );
+  }
+
+  const cachedVolume = cache.getVolume(representationData.volumeId);
+
+  if (!cachedVolume) {
+    throw new Error(
+      `volumeId of ${representationData.volumeId} not found in cache, you should load and cache volume before adding segmentation`
+    );
+  }
+}
+
+export default validate;

package/src/tools/displayTools/SegmentationDisplayTool.ts

@@ -0,0 +1,198 @@
+import {
+  getEnabledElementByIds,
+  Types,
+  utilities as csUtils,
+} from '@cornerstonejs/core';
+import Representations from '../../enums/SegmentationRepresentations';
+import { config as segmentationConfig } from '../../stateManagement/segmentation';
+import { setSegmentationVisibility } from '../../stateManagement/segmentation/config/segmentationVisibility';
+import { getSegmentationRepresentations } from '../../stateManagement/segmentation/segmentationState';
+import { getToolGroup } from '../../store/ToolGroupManager';
+import { PublicToolProps, ToolProps } from '../../types';
+import { BaseTool } from '../base';
+
+import {
+  SegmentationRepresentationConfig,
+  ToolGroupSpecificRepresentation,
+} from '../../types/SegmentationStateTypes';
+import { contourDisplay } from './Contour';
+import { labelmapDisplay } from './Labelmap';
+
+/**
+ * In Cornerstone3DTools, displaying of segmentations are handled by the SegmentationDisplayTool.
+ * Generally, any Segmentation can be viewed in various representations such as
+ * labelmap (3d), contours, surface etc. As of now, Cornerstone3DTools only implements
+ * Labelmap representation.
+ *
+ * SegmentationDisplayTool works at ToolGroup level, and is responsible for displaying the
+ * segmentation representation for ALL viewports of a toolGroup, this way we can support complex
+ * scenarios for displaying segmentations.
+ *
+ * Current Limitations:
+ * - Only supports rendering of the volumetric segmentations in 3D space. (StackViewport segmentations are not supported yet)
+ * - Labelmap representation is the only supported representation for now.
+ *
+ * Similar to other tools in Cornerstone3DTools, the SegmentationDisplayTool should
+ * be added to the CornerstoneTools by calling cornerstoneTools.addTool(SegmentationDisplayTool)
+ * and a toolGroup should be created for it using the ToolGroupManager API, finally
+ * viewports information such as viewportId and renderingEngineId should be provided
+ * to the toolGroup and the SegmentationDisplayTool should be set to be activated.
+ *
+ *
+ */
+class SegmentationDisplayTool extends BaseTool {
+  static toolName;
+  constructor(
+    toolProps: PublicToolProps = {},
+    defaultToolProps: ToolProps = {
+      configuration: {},
+    }
+  ) {
+    super(toolProps, defaultToolProps);
+  }
+
+  onSetToolEnabled(): void {
+    const toolGroupId = this.toolGroupId;
+    const toolGroupSegmentationRepresentations =
+      getSegmentationRepresentations(toolGroupId);
+
+    if (
+      !toolGroupSegmentationRepresentations ||
+      toolGroupSegmentationRepresentations.length === 0
+    ) {
+      return;
+    }
+
+    // for each segmentationData, make the visibility true
+    toolGroupSegmentationRepresentations.forEach(
+      (segmentationRepresentation) => {
+        setSegmentationVisibility(
+          toolGroupId,
+          segmentationRepresentation.segmentationRepresentationUID,
+          true
+        );
+      }
+    );
+  }
+
+  onSetToolDisabled(): void {
+    const toolGroupId = this.toolGroupId;
+    const toolGroupSegmentationRepresentations =
+      getSegmentationRepresentations(toolGroupId);
+
+    if (
+      !toolGroupSegmentationRepresentations ||
+      toolGroupSegmentationRepresentations.length === 0
+    ) {
+      return;
+    }
+
+    // for each segmentationData, make the visibility false
+    toolGroupSegmentationRepresentations.forEach(
+      (segmentationRepresentation) => {
+        setSegmentationVisibility(
+          toolGroupId,
+          segmentationRepresentation.segmentationRepresentationUID,
+          false
+        );
+      }
+    );
+  }
+
+  /**
+   * It is used to trigger the render for each segmentations in the toolGroup.
+   * Based on the segmentation representation type, it will call the corresponding
+   * render function.
+   *
+   * @param toolGroupId - the toolGroupId
+   */
+  renderSegmentation = (toolGroupId: string): void => {
+    const toolGroup = getToolGroup(toolGroupId);
+
+    if (!toolGroup) {
+      return;
+    }
+
+    const toolGroupSegmentationRepresentations =
+      getSegmentationRepresentations(toolGroupId);
+
+    if (
+      !toolGroupSegmentationRepresentations ||
+      toolGroupSegmentationRepresentations.length === 0
+    ) {
+      return;
+    }
+
+    // toolGroup Viewports
+    const toolGroupViewports = toolGroup.viewportsInfo.map(
+      ({ renderingEngineId, viewportId }) => {
+        const enabledElement = getEnabledElementByIds(
+          viewportId,
+          renderingEngineId
+        );
+
+        if (enabledElement) {
+          return enabledElement.viewport;
+        }
+      }
+    );
+
+    // Render each segmentationData, in each viewport in the toolGroup
+    const segmentationRenderList = toolGroupSegmentationRepresentations.map(
+      (representation: ToolGroupSpecificRepresentation) => {
+        const config = this._getMergedRepresentationsConfig(toolGroupId);
+
+        const viewportsRenderList = [];
+        for (const viewport of toolGroupViewports) {
+          if (representation.type == Representations.Labelmap) {
+            viewportsRenderList.push(
+              labelmapDisplay.render(
+                viewport as Types.IVolumeViewport,
+                representation,
+                config
+              )
+            );
+          } else if (representation.type == Representations.Contour) {
+            viewportsRenderList.push(
+              contourDisplay.render(
+                viewport as Types.IVolumeViewport,
+                representation,
+                config
+              )
+            );
+          }
+        }
+
+        return viewportsRenderList;
+      }
+    );
+
+    Promise.allSettled(segmentationRenderList).then(() => {
+      // for all viewports in the toolGroup trigger a re-render
+      toolGroupViewports.forEach((viewport) => {
+        viewport.render();
+      });
+    });
+  };
+
+  /**
+   * Merge the toolGroup specific configuration with the default global configuration
+   * @param toolGroupId
+   * @returns
+   */
+  _getMergedRepresentationsConfig(
+    toolGroupId: string
+  ): SegmentationRepresentationConfig {
+    const toolGroupConfig =
+      segmentationConfig.getToolGroupSpecificConfig(toolGroupId);
+    const globalConfig = segmentationConfig.getGlobalConfig();
+
+    // merge two configurations and override the global config
+    const mergedConfig = csUtils.deepMerge(globalConfig, toolGroupConfig);
+
+    return mergedConfig;
+  }
+}
+
+SegmentationDisplayTool.toolName = 'SegmentationDisplay';
+export default SegmentationDisplayTool;