@cornerstonejs/tools 1.41.0 → 1.42.1

package/dist/esm/tools/displayTools/Labelmap/labelmapDisplay.js.map

@@ -1 +1 @@
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package/dist/esm/tools/segmentation/BrushTool.js

@@ -189,7 +189,7 @@ class BrushTool extends BaseTool {
     }
     createEditData(element) {
         const enabledElement = getEnabledElement(element);
-        const { viewport, renderingEngine } = enabledElement;
+        const { viewport } = enabledElement;
         const toolGroupId = this.toolGroupId;
         const activeSegmentationRepresentation = activeSegmentation.getActiveSegmentationRepresentation(toolGroupId);
         if (!activeSegmentationRepresentation) {
@@ -202,7 +202,6 @@ class BrushTool extends BaseTool {
         const segmentsLocked = segmentLocking.getLockedSegments(segmentationId);
         const { representationData } = segmentationState.getSegmentation(segmentationId);
         const labelmapData = representationData[SegmentationRepresentations.Labelmap];
-        const viewportIdsToRender = [viewport.id];
         if (isVolumeSegmentation(labelmapData)) {
             const { volumeId } = representationData[type];
             const actors = viewport.getActors();
@@ -221,8 +220,7 @@ class BrushTool extends BaseTool {
                 return;
             }
             if (this.configuration.activeStrategy.includes('SPHERE')) {
-                console.warn('Sphere manipulation is not supported for this stack of images yet');
-                return;
+                throw new Error('Sphere manipulation is not supported for stacks of image segmentations yet');
             }
             return {
                 imageIdReferenceMap,
@@ -274,6 +272,9 @@ class BrushTool extends BaseTool {
         const centerCanvas = currentPoints.canvas;
         this._hoverData = this.createHoverData(element, centerCanvas);
         this._calculateCursor(element, centerCanvas);
+        if (!this._hoverData) {
+            return;
+        }
         triggerAnnotationRenderForViewportUIDs(getEnabledElement(element).renderingEngine, this._hoverData.viewportIdsToRender);
     }
     getOperationData(element) {
@@ -322,6 +323,9 @@ class BrushTool extends BaseTool {
             leftCursorInWorld[i] = centerCursorInWorld[i] - viewRight[i] * brushSize;
             rightCursorInWorld[i] = centerCursorInWorld[i] + viewRight[i] * brushSize;
         }
+        if (!this._hoverData) {
+            return;
+        }
         const { brushCursor } = this._hoverData;
         const { data } = brushCursor;
         if (data.handles === undefined) {

package/dist/esm/tools/segmentation/BrushTool.js.map

@@ -1 +1 @@
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package/dist/esm/tools/segmentation/strategies/fillCircle.js

@@ -6,9 +6,7 @@ import { getBoundingBoxAroundShape } from '../../../utilities/boundingBox';
 import BrushStrategy from './BrushStrategy';
 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) => {
         const { points, imageVoxelManager: imageVoxelManager, viewport, segmentationImageData, segmentationVoxelManager: segmentationVoxelManager, } = operationData;
@@ -44,9 +42,9 @@ function createPointInEllipse(worldInfo) {
     const yRadius = Math.abs(topLeftWorld[1] - bottomRightWorld[1]) / 2;
     const zRadius = Math.abs(topLeftWorld[2] - bottomRightWorld[2]) / 2;
     const radius = Math.max(xRadius, yRadius, zRadius);
-    if (nearOrZero(xRadius, radius) &&
-        nearOrZero(yRadius, radius) &&
-        nearOrZero(zRadius, radius)) {
+    if (isEqual(xRadius, radius) &&
+        isEqual(yRadius, radius) &&
+        isEqual(zRadius, radius)) {
         const sphereObj = {
             center,
             radius,

package/dist/esm/tools/segmentation/strategies/fillCircle.js.map

@@ -1 +1 @@
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package/dist/esm/tools/segmentation/strategies/utils/isWithinThreshold.js.map

@@ -1 +1 @@
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+{"version":3,"file":"isWithinThreshold.js","sourceRoot":"","sources":["../../../../../../src/tools/segmentation/strategies/utils/isWithinThreshold.ts"],"names":[],"mappings":"AAEA,SAAS,iBAAiB,CACxB,KAAa,EACb,eAA0C,EAC1C,6BAAkC;IAElC,MAAM,EAAE,SAAS,EAAE,uBAAuB,EAAE,GAAG,6BAA6B,CAAC;IAE7E,MAAM,UAAU,GAAG,eAAe,CAAC,KAAK,CAAC,CAAC;IAG1C,MAAM,EAAE,SAAS,EAAE,GAAG,SAAS,IAAI,uBAAuB,CAAC;IAC3D,OAAO,SAAS,CAAC,CAAC,CAAC,IAAI,UAAU,IAAI,UAAU,IAAI,SAAS,CAAC,CAAC,CAAC,CAAC;AAClE,CAAC;AAED,eAAe,iBAAiB,CAAC"}

package/dist/esm/utilities/contours/AnnotationToPointData.js

@@ -0,0 +1,39 @@
+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 {
+    constructor() {
+    }
+    static { this.TOOL_NAMES = {}; }
+    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`);
+        }
+        const ContourSequence = toolClass.getContourSequence(annotation, metadataProvider);
+        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;
+//# sourceMappingURL=AnnotationToPointData.js.map

package/dist/esm/utilities/contours/AnnotationToPointData.js.map

@@ -0,0 +1 @@
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package/dist/esm/utilities/contours/RectangleROIStartEndThreshold.js

@@ -0,0 +1,41 @@
+class RectangleROIStartEndThreshold {
+    constructor() {
+    }
+    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) {
+    const orderedPoints = [
+        ...points[0],
+        ...points[1],
+        ...points[3],
+        ...points[2],
+    ];
+    const pointsArray = orderedPoints.flat();
+    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;
+//# sourceMappingURL=RectangleROIStartEndThreshold.js.map

package/dist/esm/utilities/contours/RectangleROIStartEndThreshold.js.map

@@ -0,0 +1 @@
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package/dist/esm/utilities/contours/contourFinder.js

@@ -0,0 +1,63 @@
+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',
+            };
+        }
+        return findNextLink(nextLine, lines, contourPoints);
+    }
+    return {
+        remainingLines: lines,
+        contourPoints,
+        type: 'OPEN_PLANAR',
+    };
+}
+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,
+};
+//# sourceMappingURL=contourFinder.js.map

package/dist/esm/utilities/contours/contourFinder.js.map

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package/dist/esm/utilities/contours/detectContourHoles.js

@@ -0,0 +1,74 @@
+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;
+};
+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);
+        if (!result) {
+            pointsNotEnclosed++;
+        }
+    });
+    return pointsNotEnclosed === 0;
+}
+export function processContourHoles(contours, points, useXOR = true) {
+    const retContours = contours.filter((contour) => contour.type !== 'CLOSED_PLANAR');
+    const closedContours = contours.filter((contour) => contour.type === 'CLOSED_PLANAR');
+    const contourWithHoles = [];
+    let contourWithoutHoles = [];
+    closedContours.forEach((contour, index) => {
+        const holes = [];
+        closedContours.forEach((hContour, hIndex) => {
+            if (index != hIndex) {
+                if (checkEnclosed(contour, hContour, points)) {
+                    holes.push(hIndex);
+                }
+            }
+        });
+        if (holes.length > 0) {
+            contourWithHoles.push({
+                contour,
+                holes,
+            });
+        }
+        else {
+            contourWithoutHoles.push(index);
+        }
+    });
+    if (useXOR) {
+        contourWithHoles.forEach((contourHoleSet) => {
+            contourHoleSet.contour.type = 'CLOSEDPLANAR_XOR';
+            retContours.push(contourHoleSet.contour);
+            contourHoleSet.holes.forEach((holeIndex) => {
+                closedContours[holeIndex].type = 'CLOSEDPLANAR_XOR';
+                retContours.push(closedContours[holeIndex]);
+                contourWithoutHoles = contourWithoutHoles.filter((contourIndex) => {
+                    return contourIndex !== holeIndex;
+                });
+            });
+        });
+        contourWithoutHoles.forEach((contourIndex) => {
+            retContours.push(closedContours[contourIndex]);
+        });
+    }
+    else {
+    }
+    return retContours;
+}
+export default { processContourHoles };
+//# sourceMappingURL=detectContourHoles.js.map

package/dist/esm/utilities/contours/detectContourHoles.js.map

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package/dist/esm/utilities/contours/generateContourSetsFromLabelmap.js

@@ -0,0 +1,117 @@
+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];
+    const vol = cornerstoneCache.getVolume(segVolumeId);
+    if (!vol) {
+        console.warn(`No volume found for ${segVolumeId}`);
+        return;
+    }
+    const numSlices = vol.dimensions[2];
+    const imageVol = cornerstoneCache.getVolume(vol.referencedVolumeId);
+    if (!imageVol) {
+        console.warn(`No volume found for ${vol.referencedVolumeId}`);
+        return;
+    }
+    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;
+        }
+    }
+    const ContourSets = [];
+    const { FrameOfReferenceUID } = imageVol.metadata;
+    const numSegments = segments.length;
+    for (let segIndex = 0; segIndex < numSegments; segIndex++) {
+        const segment = segments[segIndex];
+        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++) {
+            if (isSliceEmptyForSegment(sliceIndex, segData, pixelsPerSlice, segIndex)) {
+                continue;
+            }
+            const frameStart = sliceIndex * pixelsPerSlice;
+            try {
+                for (let i = 0; i < pixelsPerSlice; i++) {
+                    const value = segData[i + frameStart];
+                    if (value === segIndex || containedSegmentIndices?.has(value)) {
+                        scalars.setValue(i + frameStart, 1);
+                    }
+                    else {
+                        scalars.setValue(i, 0);
+                    }
+                }
+                const mSquares = vtkImageMarchingSquares.newInstance({
+                    slice: sliceIndex,
+                });
+                const imageDataCopy = vtkImageData.newInstance();
+                imageDataCopy.shallowCopy(vol.imageData);
+                imageDataCopy.getPointData().setScalars(scalars);
+                mSquares.setInputData(imageDataCopy);
+                const cValues = [1];
+                mSquares.setContourValues(cValues);
+                mSquares.setMergePoints(false);
+                const msOutput = mSquares.getOutputData();
+                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],
+            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 };
+//# sourceMappingURL=generateContourSetsFromLabelmap.js.map

package/dist/esm/utilities/contours/generateContourSetsFromLabelmap.js.map

@@ -0,0 +1 @@
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package/dist/esm/utilities/contours/index.js

@@ -0,0 +1,7 @@
+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, };
+//# sourceMappingURL=index.js.map

package/dist/esm/utilities/contours/index.js.map

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