@cornerstonejs/tools 1.41.0 → 1.42.1

package/src/tools/segmentation/BrushTool.ts

@@ -171,7 +171,7 @@ class BrushTool extends BaseTool {
 
   createEditData(element) {
     const enabledElement = getEnabledElement(element);
-    const { viewport, renderingEngine } = enabledElement;
+    const { viewport } = enabledElement;
 
     const toolGroupId = this.toolGroupId;
 
@@ -198,8 +198,6 @@ class BrushTool extends BaseTool {
     const labelmapData =
       representationData[SegmentationRepresentations.Labelmap];
 
-    const viewportIdsToRender = [viewport.id];
-
     if (isVolumeSegmentation(labelmapData)) {
       const { volumeId } = representationData[
         type
@@ -235,11 +233,9 @@ class BrushTool extends BaseTool {
       // and should throw an error or maybe simply just allow circle manipulation
       // and not sphere manipulation
       if (this.configuration.activeStrategy.includes('SPHERE')) {
-        console.warn(
-          'Sphere manipulation is not supported for this stack of images yet'
+        throw new Error(
+          'Sphere manipulation is not supported for stacks of image segmentations yet'
         );
-        return;
-
         // Todo: add sphere (volumetric) manipulation support for stacks of images
         // we should basically check if the stack constructs a valid volume
         // meaning all the metadata is present and consistent
@@ -428,6 +424,10 @@ class BrushTool extends BaseTool {
 
     this._calculateCursor(element, centerCanvas);
 
+    if (!this._hoverData) {
+      return;
+    }
+
     triggerAnnotationRenderForViewportUIDs(
       getEnabledElement(element).renderingEngine,
       this._hoverData.viewportIdsToRender
@@ -549,6 +549,10 @@ class BrushTool extends BaseTool {
       rightCursorInWorld[i] = centerCursorInWorld[i] + viewRight[i] * brushSize;
     }
 
+    if (!this._hoverData) {
+      return;
+    }
+
     const { brushCursor } = this._hoverData;
     const { data } = brushCursor;
 

package/src/tools/segmentation/strategies/fillCircle.ts

@@ -14,10 +14,7 @@ import type { CanvasCoordinates } from '../../../types';
 import { StrategyCallbacks } from '../../../enums';
 import compositions from './compositions';
 
-const { transformWorldToIndex } = csUtils;
-const EPSILON = 1e-4;
-const nearOrZero = (testValue, nearValue) =>
-  Math.abs(testValue) < EPSILON || Math.abs(testValue - nearValue) < EPSILON;
+const { transformWorldToIndex, isEqual } = csUtils;
 
 const initializeCircle = {
   [StrategyCallbacks.Initialize]: (operationData: InitializedOperationData) => {
@@ -98,9 +95,9 @@ function createPointInEllipse(worldInfo: {
 
   const radius = Math.max(xRadius, yRadius, zRadius);
   if (
-    nearOrZero(xRadius, radius) &&
-    nearOrZero(yRadius, radius) &&
-    nearOrZero(zRadius, radius)
+    isEqual(xRadius, radius) &&
+    isEqual(yRadius, radius) &&
+    isEqual(zRadius, radius)
   ) {
     const sphereObj = {
       center,

package/src/tools/segmentation/strategies/utils/isWithinThreshold.ts

@@ -2,7 +2,7 @@ import { Types } from '@cornerstonejs/core';
 
 function isWithinThreshold(
   index: number,
-  imageScalarData: Types.VolumeScalarData,
+  imageScalarData: Types.PixelDataTypedArray,
   strategySpecificConfiguration: any
 ) {
   const { THRESHOLD, THRESHOLD_INSIDE_CIRCLE } = strategySpecificConfiguration;

package/src/types/LabelmapTypes.ts

@@ -42,11 +42,8 @@ export type LabelmapSegmentationDataVolume = {
 
 export type LabelmapSegmentationDataStack = {
   /**
-   * This is a Map from referenced imageId to the segmentation (Derived) imageId that
-   * has been used to create the derived labelmap.
-   * Todo: later I guess we can have it as Record<string, metadata> where metadata
-   * can contain a derived image arbitrary information, for use cases such that the labelmap is
-   * derived from another image that is irrelevant to the current viewport.
+   * This is a Map from referenced imageId to the segmentation (Derived) imageIds (can be
+   * multiple) that are associated with it.
    */
   imageIdReferenceMap: Map<string, string>;
 };

package/src/types/index.ts

@@ -73,11 +73,13 @@ import type { ISpline } from './ISpline';
 import type { SplineCurveSegment } from './SplineCurveSegment';
 import type { SplineLineSegment } from './SplineLineSegment';
 import type { SplineProps } from './SplineProps';
+import type { BidirectionalData } from '../utilities/segmentation/createBidirectionalToolData';
 
 export type {
   // AnnotationState
   Annotation,
   Annotations,
+  BidirectionalData,
   CanvasCoordinates,
   IAnnotationManager,
   GroupSpecificAnnotations,

package/src/utilities/contours/AnnotationToPointData.ts

@@ -0,0 +1,61 @@
+import RectangleROIStartEndThreshold from './RectangleROIStartEndThreshold';
+
+function validateAnnotation(annotation) {
+  if (!annotation?.data) {
+    throw new Error('Tool data is empty');
+  }
+
+  if (!annotation.metadata || annotation.metadata.referenceImageId) {
+    throw new Error('Tool data is not associated with any imageId');
+  }
+}
+
+class AnnotationToPointData {
+  static TOOL_NAMES: Record<string, any> = {};
+
+  constructor() {
+    // empty
+  }
+
+  static convert(annotation, index, metadataProvider) {
+    validateAnnotation(annotation);
+
+    const { toolName } = annotation.metadata;
+    const toolClass = AnnotationToPointData.TOOL_NAMES[toolName];
+
+    if (!toolClass) {
+      throw new Error(
+        `Unknown tool type: ${toolName}, cannot convert to RTSSReport`
+      );
+    }
+
+    // Each toolData should become a list of contours, ContourSequence
+    // contains a list of contours with their pointData, their geometry
+    // type and their length.
+    const ContourSequence = toolClass.getContourSequence(
+      annotation,
+      metadataProvider
+    );
+
+    // Todo: random rgb color for now, options should be passed in
+    const color = [
+      Math.floor(Math.random() * 255),
+      Math.floor(Math.random() * 255),
+      Math.floor(Math.random() * 255),
+    ];
+
+    return {
+      ReferencedROINumber: index + 1,
+      ROIDisplayColor: color,
+      ContourSequence,
+    };
+  }
+
+  static register(toolClass) {
+    AnnotationToPointData.TOOL_NAMES[toolClass.toolName] = toolClass;
+  }
+}
+
+AnnotationToPointData.register(RectangleROIStartEndThreshold);
+
+export default AnnotationToPointData;

package/src/utilities/contours/RectangleROIStartEndThreshold.ts

@@ -0,0 +1,60 @@
+// comment
+class RectangleROIStartEndThreshold {
+  static toolName: string;
+
+  constructor() {
+    // empty
+  }
+
+  static getContourSequence(toolData, metadataProvider) {
+    const { data } = toolData;
+    const { projectionPoints, projectionPointsImageIds } = data.cachedStats;
+
+    return projectionPoints.map((point, index) => {
+      const ContourData = getPointData(point);
+      const ContourImageSequence = getContourImageSequence(
+        projectionPointsImageIds[index],
+        metadataProvider
+      );
+
+      return {
+        NumberOfContourPoints: ContourData.length / 3,
+        ContourImageSequence,
+        ContourGeometricType: 'CLOSED_PLANAR',
+        ContourData,
+      };
+    });
+  }
+}
+
+RectangleROIStartEndThreshold.toolName = 'RectangleROIStartEndThreshold';
+
+function getPointData(points) {
+  // Since this is a closed contour, the order of the points is important.
+  // re-order the points to be in the correct order clockwise
+  // Spread to make sure Float32Arrays are converted to arrays
+  const orderedPoints = [
+    ...points[0],
+    ...points[1],
+    ...points[3],
+    ...points[2],
+  ];
+  const pointsArray = orderedPoints.flat();
+
+  // reduce the precision of the points to 2 decimal places
+  const pointsArrayWithPrecision = pointsArray.map((point) => {
+    return point.toFixed(2);
+  });
+
+  return pointsArrayWithPrecision;
+}
+
+function getContourImageSequence(imageId, metadataProvider) {
+  const sopCommon = metadataProvider.get('sopCommonModule', imageId);
+
+  return {
+    ReferencedSOPClassUID: sopCommon.sopClassUID,
+    ReferencedSOPInstanceUID: sopCommon.sopInstanceUID,
+  };
+}
+export default RectangleROIStartEndThreshold;

package/src/utilities/contours/contourFinder.ts

@@ -0,0 +1,78 @@
+function findNextLink(line, lines, contourPoints) {
+  let index = -1;
+  lines.forEach((cell, i) => {
+    if (index >= 0) {
+      return;
+    }
+
+    if (cell.a == line.b) {
+      index = i;
+    }
+  });
+
+  if (index >= 0) {
+    const nextLine = lines[index];
+    lines.splice(index, 1);
+
+    contourPoints.push(nextLine.b);
+
+    if (contourPoints[0] == nextLine.b) {
+      return {
+        remainingLines: lines,
+        contourPoints,
+        type: 'CLOSED_PLANAR',
+        //type: 'CLOSEDPLANAR_XOR',
+      };
+    }
+
+    return findNextLink(nextLine, lines, contourPoints);
+  }
+
+  return {
+    remainingLines: lines,
+    contourPoints,
+    type: 'OPEN_PLANAR',
+  };
+}
+
+/**
+ *
+ * @param {*} lines
+ */
+export function findContours(lines) {
+  if (lines.length == 0) {
+    return [];
+  }
+
+  const contourPoints = [];
+
+  const firstCell = lines.shift();
+  contourPoints.push(firstCell.a);
+  contourPoints.push(firstCell.b);
+  const result = findNextLink(firstCell, lines, contourPoints);
+
+  if (result.remainingLines.length == 0) {
+    return [
+      {
+        type: result.type,
+        contourPoints: result.contourPoints,
+      },
+    ];
+  } else {
+    const extraContours = findContours(result.remainingLines);
+    extraContours.push({
+      type: result.type,
+      contourPoints: result.contourPoints,
+    });
+    return extraContours;
+  }
+}
+
+export function findContoursFromReducedSet(lines) {
+  return findContours(lines);
+}
+
+export default {
+  findContours,
+  findContoursFromReducedSet,
+};

package/src/utilities/contours/detectContourHoles.ts

@@ -0,0 +1,147 @@
+/**
+ * Functions for detecting and dealing with holes within contours.
+ * Expected Contour format:
+ * {
+ *   type,
+ *   contourPoints
+ * }
+ */
+
+/**
+ * Checks if point is inside polygon defined by vertices array
+ * Code from
+ * https://stackoverflow.com/questions/22521982/check-if-point-is-inside-a-polygon
+ * most original version based on:
+ * https://wrf.ecse.rpi.edu/Research/Short_Notes/pnpoly.html/pnpoly.html
+ * @param {*} point
+ * @param {*} vertices
+ * @returns
+ */
+const getIsPointInsidePolygon = (point, vertices) => {
+  const x = point[0];
+  const y = point[1];
+
+  let inside = false;
+  for (let i = 0, j = vertices.length - 1; i < vertices.length; j = i++) {
+    const xi = vertices[i][0],
+      yi = vertices[i][1];
+    const xj = vertices[j][0],
+      yj = vertices[j][1];
+
+    const intersect =
+      yi > y != yj > y && x < ((xj - xi) * (y - yi)) / (yj - yi) + xi;
+    if (intersect) {
+      inside = !inside;
+    }
+  }
+
+  return inside;
+};
+
+/**
+ * Check if inner contour is completely surrounded by outer contour.
+ * @param {*} outerContour
+ * @param {*} innerContour
+ * @returns
+ */
+function checkEnclosed(outerContour, innerContour, points) {
+  const vertices = [];
+  outerContour.contourPoints.forEach((point) => {
+    vertices.push([points[point][0], points[point][1]]);
+  });
+
+  let pointsNotEnclosed = 0;
+  innerContour.contourPoints.forEach((point) => {
+    const result = getIsPointInsidePolygon(
+      [points[point][0], points[point][1]],
+      vertices
+    );
+    //console.log(result);
+
+    if (!result) {
+      pointsNotEnclosed++;
+    }
+  });
+
+  return pointsNotEnclosed === 0;
+}
+
+/**
+ * Check if contours have holes, if so update contour accordingly
+ * @param {*} polyData
+ * @param {*} bypass
+ */
+export function processContourHoles(contours, points, useXOR = true) {
+  //console.log(points);
+
+  // Add non-closed planars to contour list
+  const retContours = contours.filter(
+    (contour) => contour.type !== 'CLOSED_PLANAR'
+  );
+
+  // Find closed planar contours
+  const closedContours = contours.filter(
+    (contour) => contour.type === 'CLOSED_PLANAR'
+  );
+
+  // Iterate through each contour in list check for contours that have holes
+  const contourWithHoles = [];
+  let contourWithoutHoles = [];
+  closedContours.forEach((contour, index) => {
+    const holes = [];
+
+    // Check if any other contour is a hole surrounded by current contour
+    closedContours.forEach((hContour, hIndex) => {
+      if (index != hIndex) {
+        // Check if inner loop contour is a hole of outer loop contour
+        if (checkEnclosed(contour, hContour, points)) {
+          holes.push(hIndex);
+        }
+      }
+    });
+
+    // Check if holes were found
+    if (holes.length > 0) {
+      // Note current contour and reference of its holes
+      contourWithHoles.push({
+        contour,
+        holes,
+      });
+    } else {
+      // Note contour index without holes
+      contourWithoutHoles.push(index);
+    }
+  });
+
+  if (useXOR) {
+    // XOR method
+    contourWithHoles.forEach((contourHoleSet) => {
+      // Modify contour with hole to type CLOSEDPLANAR_XOR
+      contourHoleSet.contour.type = 'CLOSEDPLANAR_XOR';
+      retContours.push(contourHoleSet.contour);
+
+      contourHoleSet.holes.forEach((holeIndex) => {
+        // Modify hole type to CLOSEDPLANAR_XOR
+        // and add to contour list to be returned
+        closedContours[holeIndex].type = 'CLOSEDPLANAR_XOR';
+        retContours.push(closedContours[holeIndex]);
+
+        // Remove hole from list of contours without holes
+        contourWithoutHoles = contourWithoutHoles.filter((contourIndex) => {
+          return contourIndex !== holeIndex;
+        });
+      });
+    });
+
+    // Add remaining contours to list (neither hole nor have holes)
+    contourWithoutHoles.forEach((contourIndex) => {
+      retContours.push(closedContours[contourIndex]);
+    });
+  } else {
+    // Keyhole method, not implemented
+  }
+
+  return retContours;
+}
+
+export default { processContourHoles };

package/src/utilities/contours/generateContourSetsFromLabelmap.ts

@@ -0,0 +1,160 @@
+import { cache as cornerstoneCache } from '@cornerstonejs/core';
+import vtkImageMarchingSquares from '@kitware/vtk.js/Filters/General/ImageMarchingSquares';
+import vtkDataArray from '@kitware/vtk.js/Common/Core/DataArray';
+import vtkImageData from '@kitware/vtk.js/Common/DataModel/ImageData';
+
+import { removeDuplicatePoints } from './mergePoints';
+import { findContoursFromReducedSet } from './contourFinder';
+import SegmentationRepresentations from '../../enums/SegmentationRepresentations';
+
+const { Labelmap } = SegmentationRepresentations;
+
+function generateContourSetsFromLabelmap({ segmentations }) {
+  const { representationData, segments = [0, 1] } = segmentations;
+  const { volumeId: segVolumeId } = representationData[Labelmap];
+
+  // Get segmentation volume
+  const vol = cornerstoneCache.getVolume(segVolumeId);
+  if (!vol) {
+    console.warn(`No volume found for ${segVolumeId}`);
+    return;
+  }
+
+  const numSlices = vol.dimensions[2];
+
+  // Get image volume segmentation references
+  const imageVol = cornerstoneCache.getVolume(vol.referencedVolumeId);
+  if (!imageVol) {
+    console.warn(`No volume found for ${vol.referencedVolumeId}`);
+    return;
+  }
+
+  // NOTE: Workaround for marching squares not finding closed contours at
+  // boundary of image volume, clear pixels along x-y border of volume
+  const segData = vol.imageData.getPointData().getScalars().getData();
+  const pixelsPerSlice = vol.dimensions[0] * vol.dimensions[1];
+
+  for (let z = 0; z < numSlices; z++) {
+    for (let y = 0; y < vol.dimensions[1]; y++) {
+      const index = y * vol.dimensions[0] + z * pixelsPerSlice;
+      segData[index] = 0;
+      segData[index + vol.dimensions[0] - 1] = 0;
+    }
+  }
+
+  // end workaround
+  //
+  //
+  const ContourSets = [];
+
+  const { FrameOfReferenceUID } = imageVol.metadata;
+  // Iterate through all segments in current segmentation set
+  const numSegments = segments.length;
+  for (let segIndex = 0; segIndex < numSegments; segIndex++) {
+    const segment = segments[segIndex];
+
+    // Skip empty segments
+    if (!segment) {
+      continue;
+    }
+
+    const sliceContours = [];
+    const scalars = vtkDataArray.newInstance({
+      name: 'Scalars',
+      numberOfComponents: 1,
+      size: pixelsPerSlice * numSlices,
+      dataType: 'Uint8Array',
+    });
+    const { containedSegmentIndices } = segment;
+    for (let sliceIndex = 0; sliceIndex < numSlices; sliceIndex++) {
+      // Check if the slice is empty before running marching cube
+      if (
+        isSliceEmptyForSegment(sliceIndex, segData, pixelsPerSlice, segIndex)
+      ) {
+        continue;
+      }
+      const frameStart = sliceIndex * pixelsPerSlice;
+
+      try {
+        // Modify segData for this specific segment directly
+        for (let i = 0; i < pixelsPerSlice; i++) {
+          const value = segData[i + frameStart];
+          if (value === segIndex || containedSegmentIndices?.has(value)) {
+            (scalars as any).setValue(i + frameStart, 1);
+          } else {
+            (scalars as any).setValue(i, 0);
+          }
+        }
+
+        const mSquares = vtkImageMarchingSquares.newInstance({
+          slice: sliceIndex,
+        });
+
+        // filter out the scalar data so that only it has background and
+        // the current segment index
+        const imageDataCopy = vtkImageData.newInstance();
+
+        imageDataCopy.shallowCopy(vol.imageData);
+        imageDataCopy.getPointData().setScalars(scalars);
+
+        // Connect pipeline
+        mSquares.setInputData(imageDataCopy);
+        const cValues = [1];
+        mSquares.setContourValues(cValues);
+        mSquares.setMergePoints(false);
+
+        // Perform marching squares
+        const msOutput = mSquares.getOutputData();
+
+        // Clean up output from marching squares
+        const reducedSet = removeDuplicatePoints(msOutput);
+        if (reducedSet.points?.length) {
+          const contours = findContoursFromReducedSet(reducedSet.lines);
+
+          sliceContours.push({
+            referencedImageId: imageVol.imageIds[sliceIndex],
+            contours,
+            polyData: reducedSet,
+            FrameNumber: sliceIndex + 1,
+            sliceIndex,
+            FrameOfReferenceUID,
+          });
+        }
+      } catch (e) {
+        console.warn(sliceIndex);
+        console.warn(e);
+      }
+    }
+
+    const metadata = {
+      referencedImageId: imageVol.imageIds[0], // just use 0 for overall
+      FrameOfReferenceUID,
+    };
+
+    const ContourSet = {
+      label: segment.label,
+      color: segment.color,
+      metadata,
+      sliceContours,
+    };
+
+    ContourSets.push(ContourSet);
+  }
+
+  return ContourSets;
+}
+
+function isSliceEmptyForSegment(sliceIndex, segData, pixelsPerSlice, segIndex) {
+  const startIdx = sliceIndex * pixelsPerSlice;
+  const endIdx = startIdx + pixelsPerSlice;
+
+  for (let i = startIdx; i < endIdx; i++) {
+    if (segData[i] === segIndex) {
+      return false;
+    }
+  }
+
+  return true;
+}
+
+export { generateContourSetsFromLabelmap };

package/src/utilities/contours/index.ts

@@ -0,0 +1,14 @@
+import contourFinder from './contourFinder';
+import mergePoints from './mergePoints';
+import detectContourHoles from './detectContourHoles';
+import { generateContourSetsFromLabelmap } from './generateContourSetsFromLabelmap';
+
+import AnnotationToPointData from './AnnotationToPointData';
+
+export {
+  contourFinder,
+  mergePoints,
+  detectContourHoles,
+  generateContourSetsFromLabelmap,
+  AnnotationToPointData,
+};