@cornerstonejs/tools 2.0.0-beta.5 → 2.0.0-beta.7

package/dist/esm/utilities/dynamicVolume/getDataInTime.js

@@ -1,26 +1,21 @@
 import { utilities, cache } from '@cornerstonejs/core';
+import { getVoxelOverlap } from '../segmentation/utilities';
+import pointInShapeCallback from '../pointInShapeCallback';
 function getDataInTime(dynamicVolume, options) {
     let dataInTime;
     const frames = options.frameNumbers || [
         ...Array(dynamicVolume.numTimePoints).keys(),
     ];
     if (!options.maskVolumeId && !options.imageCoordinate) {
-        throw new Error('No ROI provided');
+        throw new Error('You should provide either maskVolumeId or imageCoordinate');
     }
     if (options.maskVolumeId && options.imageCoordinate) {
-        throw new Error('Please provide only one ROI');
+        throw new Error('You can only use one of maskVolumeId or imageCoordinate');
     }
     if (options.maskVolumeId) {
         const segmentationVolume = cache.getVolume(options.maskVolumeId);
-        const segScalarData = segmentationVolume.getScalarData();
-        const indexArray = [];
-        for (let i = 0, len = segScalarData.length; i < len; i++) {
-            if (segScalarData[i] !== 0) {
-                indexArray.push(i);
-            }
-        }
-        const dataInTime = _getTimePointDataMask(frames, indexArray, dynamicVolume);
-        return dataInTime;
+        const [dataInTime, ijkCoords] = _getTimePointDataMask(frames, dynamicVolume, segmentationVolume);
+        return [dataInTime, ijkCoords];
     }
     if (options.imageCoordinate) {
         const dataInTime = _getTimePointDataCoordinate(frames, options.imageCoordinate, dynamicVolume);
@@ -48,18 +43,68 @@ function _getTimePointDataCoordinate(frames, coordinate, volume) {
     });
     return value;
 }
-function _getTimePointDataMask(frames, indexArray, volume) {
-    const allScalarData = volume.getScalarDataArrays();
-    const value = [];
-    for (let i = 0; i < indexArray.length; i++) {
-        const indexValues = [];
-        frames.forEach((frame) => {
-            const activeScalarData = allScalarData[frame];
-            indexValues.push(activeScalarData[indexArray[i]]);
-        });
-        value.push(indexValues);
+function _getTimePointDataMask(frames, dynamicVolume, segmentationVolume) {
+    const { imageData: maskImageData } = segmentationVolume;
+    const segScalarData = segmentationVolume.getScalarData();
+    const len = segScalarData.length;
+    const nonZeroVoxelIndices = [];
+    nonZeroVoxelIndices.length = len;
+    const ijkCoords = [];
+    const dimensions = segmentationVolume.dimensions;
+    let actualLen = 0;
+    for (let i = 0, len = segScalarData.length; i < len; i++) {
+        if (segScalarData[i] !== 0) {
+            ijkCoords.push([
+                i % dimensions[0],
+                Math.floor((i / dimensions[0]) % dimensions[1]),
+                Math.floor(i / (dimensions[0] * dimensions[1])),
+            ]);
+            nonZeroVoxelIndices[actualLen++] = i;
+        }
     }
-    return value;
+    nonZeroVoxelIndices.length = actualLen;
+    const dynamicVolumeScalarDataArray = dynamicVolume.getScalarDataArrays();
+    const values = [];
+    const isSameVolume = dynamicVolumeScalarDataArray[0].length === len &&
+        JSON.stringify(dynamicVolume.spacing) ===
+            JSON.stringify(segmentationVolume.spacing);
+    if (isSameVolume) {
+        for (let i = 0; i < nonZeroVoxelIndices.length; i++) {
+            const indexValues = [];
+            frames.forEach((frame) => {
+                const activeScalarData = dynamicVolumeScalarDataArray[frame];
+                indexValues.push(activeScalarData[nonZeroVoxelIndices[i]]);
+            });
+            values.push(indexValues);
+        }
+        return [values, ijkCoords];
+    }
+    const callback = ({ pointLPS: segPointLPS, value: segValue, pointIJK: segPointIJK, }) => {
+        if (segValue === 0) {
+            return;
+        }
+        const overlapIJKMinMax = getVoxelOverlap(dynamicVolume.imageData, dynamicVolume.dimensions, dynamicVolume.spacing, segPointLPS);
+        let count = 0;
+        const perFrameSum = new Map();
+        frames.forEach((frame) => perFrameSum.set(frame, 0));
+        const averageCallback = ({ index }) => {
+            for (let i = 0; i < frames.length; i++) {
+                const value = dynamicVolumeScalarDataArray[i][index];
+                const frame = frames[i];
+                perFrameSum.set(frame, perFrameSum.get(frame) + value);
+            }
+            count++;
+        };
+        pointInShapeCallback(dynamicVolume.imageData, () => true, averageCallback, overlapIJKMinMax);
+        const averageValues = [];
+        perFrameSum.forEach((sum) => {
+            averageValues.push(sum / count);
+        });
+        ijkCoords.push(segPointIJK);
+        values.push(averageValues);
+    };
+    pointInShapeCallback(maskImageData, () => true, callback);
+    return [values, ijkCoords];
 }
 export default getDataInTime;
 //# sourceMappingURL=getDataInTime.js.map

package/dist/esm/utilities/dynamicVolume/getDataInTime.js.map

@@ -1 +1 @@
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package/dist/esm/utilities/getCalibratedUnits.js

@@ -1,34 +1,134 @@
-import { Enums } from '@cornerstonejs/core';
+import { Enums, utilities } from '@cornerstonejs/core';
 const { CalibrationTypes } = Enums;
 const PIXEL_UNITS = 'px';
-const getCalibratedLengthUnits = (handles, image) => {
+const SUPPORTED_REGION_DATA_TYPES = [
+    1,
+];
+const SUPPORTED_LENGTH_VARIANT = [
+    '3,3',
+];
+const SUPPORTED_PROBE_VARIANT = [
+    '4,3',
+];
+const UNIT_MAPPING = {
+    3: 'cm',
+    4: 'seconds',
+};
+const EPS = 1e-3;
+const SQUARE = '\xb2';
+const getCalibratedLengthUnitsAndScale = (image, handles) => {
     const { calibration, hasPixelSpacing } = image;
-    const units = hasPixelSpacing ? 'mm' : PIXEL_UNITS;
-    if (!calibration || !calibration.type) {
-        return units;
+    let units = hasPixelSpacing ? 'mm' : PIXEL_UNITS;
+    let areaUnits = units + SQUARE;
+    let scale = 1;
+    let calibrationType = '';
+    if (!calibration ||
+        (!calibration.type && !calibration.sequenceOfUltrasoundRegions)) {
+        return { units, areaUnits, scale };
     }
     if (calibration.type === CalibrationTypes.UNCALIBRATED) {
-        return PIXEL_UNITS;
+        return { units: PIXEL_UNITS, areaUnits: PIXEL_UNITS + SQUARE, scale };
+    }
+    if (calibration.sequenceOfUltrasoundRegions) {
+        let imageIndex1, imageIndex2;
+        if (Array.isArray(handles) && handles.length === 2) {
+            [imageIndex1, imageIndex2] = handles;
+        }
+        else if (typeof handles === 'function') {
+            const points = handles();
+            imageIndex1 = points[0];
+            imageIndex2 = points[1];
+        }
+        let regions = calibration.sequenceOfUltrasoundRegions.filter((region) => imageIndex1[0] >= region.regionLocationMinX0 &&
+            imageIndex1[0] <= region.regionLocationMaxX1 &&
+            imageIndex1[1] >= region.regionLocationMinY0 &&
+            imageIndex1[1] <= region.regionLocationMaxY1 &&
+            imageIndex2[0] >= region.regionLocationMinX0 &&
+            imageIndex2[0] <= region.regionLocationMaxX1 &&
+            imageIndex2[1] >= region.regionLocationMinY0 &&
+            imageIndex2[1] <= region.regionLocationMaxY1);
+        if (!regions?.length) {
+            return { units, areaUnits, scale };
+        }
+        regions = regions.filter((region) => SUPPORTED_REGION_DATA_TYPES.includes(region.regionDataType) &&
+            SUPPORTED_LENGTH_VARIANT.includes(`${region.physicalUnitsXDirection},${region.physicalUnitsYDirection}`));
+        if (!regions.length) {
+            return { units: PIXEL_UNITS, areaUnits: PIXEL_UNITS + SQUARE, scale };
+        }
+        const region = regions[0];
+        const physicalDeltaX = Math.abs(region.physicalDeltaX);
+        const physicalDeltaY = Math.abs(region.physicalDeltaY);
+        const isSamePhysicalDelta = utilities.isEqual(physicalDeltaX, physicalDeltaY, EPS);
+        if (isSamePhysicalDelta) {
+            scale = 1 / (physicalDeltaX * 10);
+            calibrationType = 'US Region';
+            units = 'mm';
+            areaUnits = 'mm' + SQUARE;
+        }
+        else {
+            return { units: PIXEL_UNITS, areaUnits: PIXEL_UNITS + SQUARE, scale };
+        }
     }
-    if (calibration.SequenceOfUltrasoundRegions) {
-        return 'US Region';
+    else if (calibration.scale) {
+        scale = calibration.scale;
     }
-    return `${units} ${calibration.type}`;
+    const types = [
+        CalibrationTypes.ERMF,
+        CalibrationTypes.USER,
+        CalibrationTypes.ERROR,
+        CalibrationTypes.PROJECTION,
+    ];
+    if (types.includes(calibration?.type)) {
+        calibrationType = calibration.type;
+    }
+    return {
+        units: units + (calibrationType ? ` ${calibrationType}` : ''),
+        areaUnits: areaUnits + (calibrationType ? ` ${calibrationType}` : ''),
+        scale,
+    };
 };
-const SQUARE = '\xb2';
-const getCalibratedAreaUnits = (handles, image) => {
-    const { calibration, hasPixelSpacing } = image;
-    const units = (hasPixelSpacing ? 'mm' : PIXEL_UNITS) + SQUARE;
-    if (!calibration || !calibration.type) {
-        return units;
+const getCalibratedProbeUnitsAndValue = (image, handles) => {
+    const [imageIndex] = handles;
+    const { calibration } = image;
+    let units = ['raw'];
+    let values = [null];
+    let calibrationType = '';
+    if (!calibration ||
+        (!calibration.type && !calibration.sequenceOfUltrasoundRegions)) {
+        return { units, values };
     }
-    if (calibration.SequenceOfUltrasoundRegions) {
-        return 'US Region';
+    if (calibration.sequenceOfUltrasoundRegions) {
+        const supportedRegionsMetadata = calibration.sequenceOfUltrasoundRegions.filter((region) => SUPPORTED_REGION_DATA_TYPES.includes(region.regionDataType) &&
+            SUPPORTED_PROBE_VARIANT.includes(`${region.physicalUnitsXDirection},${region.physicalUnitsYDirection}`));
+        if (!supportedRegionsMetadata?.length) {
+            return { units, values };
+        }
+        const region = supportedRegionsMetadata.find((region) => imageIndex[0] >= region.regionLocationMinX0 &&
+            imageIndex[0] <= region.regionLocationMaxX1 &&
+            imageIndex[1] >= region.regionLocationMinY0 &&
+            imageIndex[1] <= region.regionLocationMaxY1);
+        if (!region) {
+            return { units, values };
+        }
+        const { referencePixelX0 = 0, referencePixelY0 = 0 } = region;
+        const { physicalDeltaX, physicalDeltaY } = region;
+        const yValue = (imageIndex[1] - region.regionLocationMinY0 - referencePixelY0) *
+            physicalDeltaY;
+        const xValue = (imageIndex[0] - region.regionLocationMinX0 - referencePixelX0) *
+            physicalDeltaX;
+        calibrationType = 'US Region';
+        values = [xValue, yValue];
+        units = [
+            UNIT_MAPPING[region.physicalUnitsXDirection],
+            UNIT_MAPPING[region.physicalUnitsYDirection],
+        ];
     }
-    return `${units} ${calibration.type}`;
+    return {
+        units,
+        values,
+        calibrationType,
+    };
 };
-const getCalibratedScale = (image) => image.calibration?.scale || 1;
 const getCalibratedAspect = (image) => image.calibration?.aspect || 1;
-export default getCalibratedLengthUnits;
-export { getCalibratedAreaUnits, getCalibratedLengthUnits, getCalibratedScale, getCalibratedAspect, };
+export { getCalibratedLengthUnitsAndScale, getCalibratedAspect, getCalibratedProbeUnitsAndValue, };
 //# sourceMappingURL=getCalibratedUnits.js.map

package/dist/esm/utilities/getCalibratedUnits.js.map

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package/dist/esm/utilities/getSphereBoundsInfo.js

@@ -0,0 +1,42 @@
+import { utilities as csUtils } from '@cornerstonejs/core';
+import { vec3 } from 'gl-matrix';
+import { getBoundingBoxAroundShapeIJK } from './boundingBox';
+const { transformWorldToIndex } = csUtils;
+function getSphereBoundsInfo(circlePoints, imageData, viewport) {
+    const [bottom, top] = circlePoints;
+    const centerWorld = vec3.fromValues((bottom[0] + top[0]) / 2, (bottom[1] + top[1]) / 2, (bottom[2] + top[2]) / 2);
+    const radiusWorld = vec3.distance(bottom, top) / 2;
+    if (!viewport) {
+        throw new Error('viewport is required in order to calculate the sphere bounds');
+    }
+    const { boundsIJK, topLeftWorld, bottomRightWorld } = _computeBoundsIJKWithCamera(imageData, viewport, circlePoints, centerWorld, radiusWorld);
+    return {
+        boundsIJK,
+        centerWorld: centerWorld,
+        radiusWorld,
+        topLeftWorld: topLeftWorld,
+        bottomRightWorld: bottomRightWorld,
+    };
+}
+function _computeBoundsIJKWithCamera(imageData, viewport, circlePoints, centerWorld, radiusWorld) {
+    const [bottom, top] = circlePoints;
+    const dimensions = imageData.getDimensions();
+    const camera = viewport.getCamera();
+    const viewUp = vec3.fromValues(camera.viewUp[0], camera.viewUp[1], camera.viewUp[2]);
+    const viewPlaneNormal = vec3.fromValues(camera.viewPlaneNormal[0], camera.viewPlaneNormal[1], camera.viewPlaneNormal[2]);
+    const viewRight = vec3.create();
+    vec3.cross(viewRight, viewUp, viewPlaneNormal);
+    const topLeftWorld = vec3.create();
+    const bottomRightWorld = vec3.create();
+    vec3.scaleAndAdd(topLeftWorld, top, viewPlaneNormal, radiusWorld);
+    vec3.scaleAndAdd(bottomRightWorld, bottom, viewPlaneNormal, -radiusWorld);
+    vec3.scaleAndAdd(topLeftWorld, topLeftWorld, viewRight, -radiusWorld);
+    vec3.scaleAndAdd(bottomRightWorld, bottomRightWorld, viewRight, radiusWorld);
+    const topLeftIJK = transformWorldToIndex(imageData, topLeftWorld);
+    const bottomRightIJK = transformWorldToIndex(imageData, bottomRightWorld);
+    const pointsIJK = circlePoints.map((p) => transformWorldToIndex(imageData, p));
+    const boundsIJK = getBoundingBoxAroundShapeIJK([topLeftIJK, bottomRightIJK, ...pointsIJK], dimensions);
+    return { boundsIJK, topLeftWorld, bottomRightWorld };
+}
+export { getSphereBoundsInfo };
+//# sourceMappingURL=getSphereBoundsInfo.js.map

package/dist/esm/utilities/getSphereBoundsInfo.js.map

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package/dist/esm/utilities/getVOIMultipliers.js

@@ -0,0 +1,19 @@
+import { utilities as csUtils } from '@cornerstonejs/core';
+import { isViewportPreScaled } from './viewport';
+const DEFAULT_MULTIPLIER = 4;
+function getVOIMultipliers(viewport, volumeId, options) {
+    const modality = csUtils.getViewportModality(viewport, volumeId);
+    if (modality === 'PT') {
+        const { clientWidth, clientHeight } = viewport.element;
+        const ptMultiplier = 5 / Math.max(clientWidth, clientHeight);
+        const isPreScaled = isViewportPreScaled(viewport, volumeId);
+        const { fixedPTWindowWidth = true } = options ?? {};
+        const xMultiplier = fixedPTWindowWidth ? 0 : ptMultiplier;
+        return isPreScaled
+            ? [xMultiplier, ptMultiplier]
+            : [xMultiplier, DEFAULT_MULTIPLIER];
+    }
+    return [DEFAULT_MULTIPLIER, DEFAULT_MULTIPLIER];
+}
+export { getVOIMultipliers as default, getVOIMultipliers };
+//# sourceMappingURL=getVOIMultipliers.js.map

package/dist/esm/utilities/getVOIMultipliers.js.map

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

@@ -0,0 +1,6 @@
+import getViewportsForAnnotation from './getViewportsForAnnotation';
+export default function getViewportForAnnotation(annotation) {
+    const viewports = getViewportsForAnnotation(annotation);
+    return viewports.length ? viewports[0] : undefined;
+}
+//# sourceMappingURL=getViewportForAnnotation.js.map

package/dist/esm/utilities/getViewportForAnnotation.js.map

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

@@ -0,0 +1,17 @@
+import { getEnabledElements, utilities as csUtils } from '@cornerstonejs/core';
+const { isEqual } = csUtils;
+export default function getViewportsForAnnotation(annotation) {
+    const { metadata } = annotation;
+    return getEnabledElements()
+        .filter((enabledElement) => {
+        if (enabledElement.FrameOfReferenceUID === metadata.FrameOfReferenceUID) {
+            const viewport = enabledElement.viewport;
+            const { viewPlaneNormal, viewUp } = viewport.getCamera();
+            return (isEqual(viewPlaneNormal, metadata.viewPlaneNormal) &&
+                (!metadata.viewUp || isEqual(viewUp, metadata.viewUp)));
+        }
+        return;
+    })
+        .map((enabledElement) => enabledElement.viewport);
+}
+//# sourceMappingURL=getViewportsForAnnotation.js.map

package/dist/esm/utilities/getViewportsForAnnotation.js.map

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

@@ -1,16 +1,24 @@
+import { utilities } from '@cornerstonejs/core';
 import { getAnnotationNearPoint, getAnnotationNearPointOnEnabledElement, } from './getAnnotationNearPoint';
 import debounce from './debounce';
 import throttle from './throttle';
 import isObject from './isObject';
 import clip from './clip';
 import calibrateImageSpacing from './calibrateImageSpacing';
+import { getCalibratedLengthUnitsAndScale, getCalibratedProbeUnitsAndValue, getCalibratedAspect, } from './getCalibratedUnits';
 import triggerAnnotationRenderForViewportIds from './triggerAnnotationRenderForViewportIds';
+import triggerAnnotationRenderForToolGroupIds from './triggerAnnotationRenderForToolGroupIds';
 import triggerAnnotationRender from './triggerAnnotationRender';
 import jumpToSlice from './viewport/jumpToSlice';
 import pointInShapeCallback from './pointInShapeCallback';
-import pointInSurroundingSphereCallback from './pointInSurroundingSphereCallback';
+import { getSphereBoundsInfo } from './getSphereBoundsInfo';
 import scroll from './scroll';
-import roundNumber from './roundNumber';
+import { pointToString } from './pointToString';
+import annotationFrameRange from './annotationFrameRange';
+import pointInSurroundingSphereCallback from './pointInSurroundingSphereCallback';
+import getViewportForAnnotation from './getViewportForAnnotation';
+import { annotationHydration, getClosestImageIdForStackViewport, } from './annotationHydration';
+import * as contours from './contours';
 import * as segmentation from './segmentation';
 import * as drawing from './drawing';
 import * as math from './math';
@@ -25,6 +33,10 @@ import { stackPrefetch, stackContextPrefetch } from './stackPrefetch';
 import * as viewport from './viewport';
 import * as touch from './touch';
 import * as dynamicVolume from './dynamicVolume';
+import * as polyDataUtils from './polyData/utils';
+import * as voi from './voi';
+import * as contourSegmentation from './contourSegmentation';
+const roundNumber = utilities.roundNumber;
 import { triggerEvent } from '@cornerstonejs/core';
-export { math, planar, viewportFilters, drawing, debounce, dynamicVolume, throttle, orientation, isObject, touch, triggerEvent, calibrateImageSpacing, segmentation, triggerAnnotationRenderForViewportIds, triggerAnnotationRender, pointInShapeCallback, pointInSurroundingSphereCallback, getAnnotationNearPoint, getAnnotationNearPointOnEnabledElement, jumpToSlice, viewport, cine, clip, boundingBox, rectangleROITool, planarFreehandROITool, stackPrefetch, stackContextPrefetch, scroll, roundNumber, };
+export { math, planar, viewportFilters, drawing, debounce, dynamicVolume, throttle, orientation, isObject, touch, triggerEvent, calibrateImageSpacing, getCalibratedLengthUnitsAndScale, getCalibratedProbeUnitsAndValue, getCalibratedAspect, segmentation, contours, triggerAnnotationRenderForViewportIds, triggerAnnotationRenderForToolGroupIds, triggerAnnotationRender, pointInShapeCallback, getSphereBoundsInfo, getAnnotationNearPoint, getViewportForAnnotation, getAnnotationNearPointOnEnabledElement, jumpToSlice, pointInSurroundingSphereCallback, viewport, cine, clip, boundingBox, rectangleROITool, planarFreehandROITool, stackPrefetch, stackContextPrefetch, scroll, roundNumber, pointToString, polyDataUtils, voi, annotationFrameRange, contourSegmentation, annotationHydration, getClosestImageIdForStackViewport, };
 //# sourceMappingURL=index.js.map

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

@@ -1 +1 @@
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package/dist/esm/utilities/livewire/LiveWirePath.js

@@ -0,0 +1,72 @@
+export class LivewirePath {
+    constructor(inputPointArray, inputControlPointIndexArray) {
+        this.pointArray = inputPointArray ? inputPointArray.slice() : [];
+        this._controlPointIndexes = inputControlPointIndexArray
+            ? inputControlPointIndexArray.slice()
+            : [];
+    }
+    getPoint(index) {
+        return this.pointArray[index];
+    }
+    getLastPoint() {
+        return this.pointArray[this.pointArray.length - 1];
+    }
+    isControlPoint(point) {
+        const index = this.pointArray.indexOf(point);
+        if (index !== -1) {
+            return this._controlPointIndexes.indexOf(index) !== -1;
+        }
+        else {
+            throw new Error('Error: isControlPoint called with not in list point.');
+        }
+    }
+    addPoint(point) {
+        this.pointArray.push(point);
+    }
+    addControlPoint(point) {
+        const index = this.pointArray.indexOf(point);
+        if (index !== -1) {
+            this._controlPointIndexes.push(index);
+        }
+        else {
+            throw new Error('Cannot mark a non registered point as control point.');
+        }
+    }
+    getControlPoints() {
+        return this._controlPointIndexes.map((i) => this.pointArray[i]);
+    }
+    getNumControlPoints() {
+        return this._controlPointIndexes.length;
+    }
+    removeLastControlPoint() {
+        if (this._controlPointIndexes.length) {
+            this._controlPointIndexes.pop();
+        }
+    }
+    getLastControlPoint() {
+        if (this._controlPointIndexes.length) {
+            return this.pointArray[this._controlPointIndexes[this._controlPointIndexes.length - 1]];
+        }
+    }
+    removeLastPoints(count) {
+        this.pointArray.splice(this.pointArray.length - count, count);
+    }
+    addPoints(newPointArray) {
+        this.pointArray = this.pointArray.concat(newPointArray);
+    }
+    prependPath(other) {
+        const otherSize = other.pointArray.length;
+        const shiftedIndexArray = [];
+        this.pointArray = other.pointArray.concat(this.pointArray);
+        for (let i = 0; i < this._controlPointIndexes.length; ++i) {
+            shiftedIndexArray[i] = this._controlPointIndexes[i] + otherSize;
+        }
+        this._controlPointIndexes =
+            other._controlPointIndexes.concat(shiftedIndexArray);
+    }
+    appendPath(other) {
+        this.addPoints(other.pointArray);
+        other._controlPointIndexes.forEach((point) => this._controlPointIndexes.push(point));
+    }
+}
+//# sourceMappingURL=LiveWirePath.js.map

package/dist/esm/utilities/livewire/LiveWirePath.js.map

@@ -0,0 +1 @@
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