@cornerstonejs/tools 2.0.0-beta.1 → 2.0.0-beta.10

package/dist/esm/utilities/segmentation/invalidateBrushCursor.js.map

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

@@ -0,0 +1,50 @@
+import { cache } from '@cornerstonejs/core';
+import { vec3 } from 'gl-matrix';
+export default function isLineInSegment(point1, point2, isInSegment) {
+    const ijk1 = isInSegment.toIJK(point1);
+    const ijk2 = isInSegment.toIJK(point2);
+    const testPoint = vec3.create();
+    const { testIJK } = isInSegment;
+    const delta = vec3.sub(vec3.create(), ijk1, ijk2);
+    const testSize = Math.round(Math.max(...delta.map(Math.abs)));
+    if (testSize < 2) {
+        return true;
+    }
+    const unitDelta = vec3.scale(vec3.create(), delta, 1 / testSize);
+    for (let i = 1; i < testSize; i++) {
+        vec3.scaleAndAdd(testPoint, ijk2, unitDelta, i);
+        if (!testIJK(testPoint)) {
+            return false;
+        }
+    }
+    return true;
+}
+function createIsInSegment(segVolumeId, segmentIndex, containedSegmentIndices) {
+    const vol = cache.getVolume(segVolumeId);
+    if (!vol) {
+        console.warn(`No volume found for ${segVolumeId}`);
+        return;
+    }
+    const segData = vol.imageData.getPointData().getScalars().getData();
+    const width = vol.dimensions[0];
+    const pixelsPerSlice = width * vol.dimensions[1];
+    return {
+        testCenter: (point1, point2) => {
+            const point = vec3.add(vec3.create(), point1, point2).map((it) => it / 2);
+            const ijk = vol.imageData.worldToIndex(point).map(Math.round);
+            const [i, j, k] = ijk;
+            const index = i + j * width + k * pixelsPerSlice;
+            const value = segData[index];
+            return value === segmentIndex || containedSegmentIndices?.has(value);
+        },
+        toIJK: (point) => vol.imageData.worldToIndex(point),
+        testIJK: (ijk) => {
+            const [i, j, k] = ijk;
+            const index = Math.round(i) + Math.round(j) * width + Math.round(k) * pixelsPerSlice;
+            const value = segData[index];
+            return value === segmentIndex || containedSegmentIndices?.has(value);
+        },
+    };
+}
+export { createIsInSegment, isLineInSegment };
+//# sourceMappingURL=isLineInSegment.js.map

package/dist/esm/utilities/segmentation/isLineInSegment.js.map

@@ -0,0 +1 @@
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package/dist/esm/utilities/segmentation/isValidRepresentationConfig.js.map

@@ -1 +1 @@
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+{"version":3,"file":"isValidRepresentationConfig.js","sourceRoot":"","sources":["../../../../src/utilities/segmentation/isValidRepresentationConfig.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,qBAAqB,EAAE,MAAM,kDAAkD,CAAC;AACzF,OAAO,0BAA0B,MAAM,yCAAyC,CAAC;AAUjF,MAAM,CAAC,OAAO,UAAU,2BAA2B,CACjD,kBAA0B,EAC1B,MAA4B;IAE5B,QAAQ,kBAAkB,EAAE,CAAC;QAC3B,KAAK,0BAA0B,CAAC,QAAQ;YACtC,OAAO,qBAAqB,CAAC,MAAM,CAAC,CAAC;QACvC;YACE,MAAM,IAAI,KAAK,CAAC,gCAAgC,kBAAkB,EAAE,CAAC,CAAC;IAC1E,CAAC;AACH,CAAC"}

package/dist/esm/utilities/segmentation/rectangleROIThresholdVolumeByRange.js

@@ -15,6 +15,7 @@ function rectangleROIThresholdVolumeByRange(annotationUIDs, segmentationVolume,
         }
     }
     const outputSegmentationVolume = thresholdVolumeByRange(segmentationVolume, thresholdVolumeInformation, { ...options, boundsIJK });
+    outputSegmentationVolume.modified();
     return outputSegmentationVolume;
 }
 function _validateAnnotations(annotations) {

package/dist/esm/utilities/segmentation/rectangleROIThresholdVolumeByRange.js.map

@@ -1 +1 @@
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package/dist/esm/utilities/segmentation/segmentContourAction.js

@@ -0,0 +1,97 @@
+import { getEnabledElement } from '@cornerstonejs/core';
+import * as segmentation from '../../stateManagement/segmentation';
+import { state as annotationState, config as annotationConfig, } from '../../stateManagement/annotation';
+import { jumpToSlice } from '../viewport';
+import contourAndFindLargestBidirectional from './contourAndFindLargestBidirectional';
+import createBidirectionalToolData from './createBidirectionalToolData';
+import BidirectionalTool from '../../tools/annotation/BidirectionalTool';
+export default function segmentContourAction(element, configuration) {
+    const { data: configurationData } = configuration;
+    const enabledElement = getEnabledElement(element);
+    const segment = (configurationData.getSegment || defaultGetSegment)(enabledElement, configurationData);
+    if (!segment) {
+        return;
+    }
+    const FrameOfReferenceUID = enabledElement.viewport.getFrameOfReferenceUID();
+    const segmentationsList = segmentation.state.getSegmentations();
+    const { segmentIndex, segmentationId } = segment;
+    const bidirectionals = annotationState.getAnnotations(this.toolName || BidirectionalTool.toolName, FrameOfReferenceUID);
+    let hasExistingActiveSegment = false;
+    const existingLargestBidirectionals = bidirectionals.filter((existingBidirectionalItem) => {
+        const { segment } = existingBidirectionalItem.data;
+        if (!segment) {
+            return;
+        }
+        if (segment.segmentationId === segmentationId &&
+            segment.segmentIndex === segmentIndex) {
+            hasExistingActiveSegment = true;
+            existingBidirectionalItem.data.segment = segment;
+        }
+        return !!segment;
+    });
+    if (!hasExistingActiveSegment) {
+        existingLargestBidirectionals.push({
+            data: { segment },
+        });
+    }
+    let newBidirectional;
+    existingLargestBidirectionals.forEach((existingLargestBidirectional) => {
+        const segments = [];
+        const { segment: updateSegment } = existingLargestBidirectional.data;
+        const { segmentIndex, segmentationId } = updateSegment;
+        segments[segmentIndex] = updateSegment;
+        annotationState.removeAnnotation(existingLargestBidirectional.annotationUID);
+        const bidirectionalData = contourAndFindLargestBidirectional({
+            ...segmentationsList.find((segmentation) => segmentation.segmentationId === segmentationId),
+            segments,
+        });
+        if (!bidirectionalData) {
+            return;
+        }
+        const bidirectionalToolData = createBidirectionalToolData(bidirectionalData, enabledElement.viewport);
+        bidirectionalToolData.annotationUID =
+            existingLargestBidirectional.annotationUID;
+        bidirectionalToolData.data.segment = updateSegment;
+        const annotationUID = annotationState.addAnnotation(bidirectionalToolData, FrameOfReferenceUID);
+        if (updateSegment.segmentIndex === segment.segmentIndex &&
+            updateSegment.segmentationId === segment.segmentationId) {
+            newBidirectional = bidirectionalData;
+            const { style } = segment;
+            if (style) {
+                annotationConfig.style.setAnnotationStyles(annotationUID, style);
+            }
+        }
+    });
+    if (newBidirectional) {
+        const { sliceIndex } = newBidirectional;
+        const imageIds = enabledElement.viewport.getImageIds();
+        jumpToSlice(element, {
+            imageIndex: imageIds.length - 1 - sliceIndex,
+        });
+        enabledElement.viewport.render();
+    }
+    else {
+        console.warn('No bidirectional found');
+    }
+    return newBidirectional;
+}
+export function defaultGetSegment(enabledElement, configuration) {
+    const segmentationsList = segmentation.state.getSegmentations();
+    if (!segmentationsList.length) {
+        return;
+    }
+    const segmentationId = configuration.segmentationId || segmentationsList[0].segmentationId;
+    const segmentIndex = configuration.segmentIndex ??
+        segmentation.segmentIndex.getActiveSegmentIndex(segmentationId);
+    if (!segmentIndex) {
+        return;
+    }
+    const segmentData = configuration.segmentData?.get(segmentIndex);
+    return {
+        label: `Segment ${segmentIndex}`,
+        segmentIndex,
+        segmentationId,
+        ...segmentData,
+    };
+}
+//# sourceMappingURL=segmentContourAction.js.map

package/dist/esm/utilities/segmentation/segmentContourAction.js.map

@@ -0,0 +1 @@
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package/dist/esm/utilities/segmentation/thresholdSegmentationByRange.js.map

@@ -1 +1 @@
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package/dist/esm/utilities/segmentation/thresholdVolumeByRange.js

@@ -59,8 +59,9 @@ function thresholdVolumeByRange(segmentationVolume, thresholdVolumeInformation,
                 break;
             }
         }
-        if (insert)
-            scalarData[index] = 1;
+        if (insert) {
+            scalarData[index] = options.segmentIndex || 1;
+        }
     };
     pointInShapeCallback(segmentationImageData, () => true, callback, boundsIJK);
     triggerSegmentationDataModified(segmentationVolume.volumeId);

package/dist/esm/utilities/segmentation/thresholdVolumeByRange.js.map

@@ -1 +1 @@
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package/dist/esm/utilities/segmentation/triggerSegmentationRender.js

@@ -1,7 +1,7 @@
 import { triggerEvent, eventTarget, getRenderingEngine, Enums, } from '@cornerstonejs/core';
 import { Events as csToolsEvents } from '../../enums';
 import { getToolGroup, getToolGroupForViewport, } from '../../store/ToolGroupManager';
-import SegmentationDisplayTool from '../../tools/displayTools/SegmentationDisplayTool';
+import { SegmentationDisplayTool } from '../../tools';
 class SegmentationRenderingEngine {
     constructor() {
         this._needsRender = new Set();
@@ -54,15 +54,19 @@ class SegmentationRenderingEngine {
             return;
         }
         const { viewportsInfo } = toolGroup;
-        const viewports = [];
-        viewportsInfo.forEach(({ viewportId, renderingEngineId }) => {
+        const viewports = viewportsInfo
+            .map(({ viewportId, renderingEngineId }) => {
             const renderingEngine = getRenderingEngine(renderingEngineId);
             if (!renderingEngine) {
                 console.warn('rendering Engine has been destroyed');
                 return;
             }
-            viewports.push(renderingEngine.getViewport(viewportId));
-        });
+            const viewport = renderingEngine.getViewport(viewportId);
+            if (viewport) {
+                return viewport;
+            }
+        })
+            .filter(Boolean);
         const segmentationDisplayToolInstance = toolGroup.getToolInstance(SegmentationDisplayTool.toolName);
         if (!segmentationDisplayToolInstance) {
             console.warn('No segmentation tool found inside', toolGroupId);

package/dist/esm/utilities/segmentation/triggerSegmentationRender.js.map

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package/dist/esm/utilities/segmentation/utilities.js

@@ -1,8 +1,8 @@
 import { utilities as csUtils } from '@cornerstonejs/core';
 import { getToolGroup } from '../../store/ToolGroupManager';
 import BrushTool from '../../tools/segmentation/BrushTool';
-import getBoundingBoxAroundShape from '../boundingBox/getBoundingBoxAroundShape';
-export default function getBrushToolInstances(toolGroupId) {
+import { getBoundingBoxAroundShapeIJK } from '../boundingBox/getBoundingBoxAroundShape';
+export function getBrushToolInstances(toolGroupId, toolName) {
     const toolGroup = getToolGroup(toolGroupId);
     if (toolGroup === undefined) {
         return;
@@ -11,6 +11,9 @@ export default function getBrushToolInstances(toolGroupId) {
     if (!Object.keys(toolInstances).length) {
         return;
     }
+    if (toolName && toolInstances[toolName]) {
+        return [toolInstances[toolName]];
+    }
     const brushBasedToolInstances = Object.values(toolInstances).filter((toolInstance) => toolInstance instanceof BrushTool);
     return brushBasedToolInstances;
 }
@@ -22,7 +25,7 @@ export function getVoxelOverlap(imageData, dimensions, voxelSpacing, voxelCenter
     for (let i = 0; i < 2; i++) {
         for (let j = 0; j < 2; j++) {
             for (let k = 0; k < 2; k++) {
-                const point = voxelCenter;
+                const point = [...voxelCenter];
                 point[0] = point[0] + ((i * 2 - 1) * voxelSpacing[0]) / 2;
                 point[1] = point[1] + ((j * 2 - 1) * voxelSpacing[1]) / 2;
                 point[2] = point[2] + ((k * 2 - 1) * voxelSpacing[2]) / 2;
@@ -31,11 +34,11 @@ export function getVoxelOverlap(imageData, dimensions, voxelSpacing, voxelCenter
         }
     }
     const voxelCornersIJK = voxelCornersWorld.map((world) => csUtils.transformWorldToIndex(imageData, world));
-    const overlapBounds = getBoundingBoxAroundShape(voxelCornersIJK, dimensions);
+    const overlapBounds = getBoundingBoxAroundShapeIJK(voxelCornersIJK, dimensions);
     return overlapBounds;
 }
 export function processVolumes(segmentationVolume, thresholdVolumeInformation) {
-    const { spacing: segmentationSpacing, imageData: segmentationImageData } = segmentationVolume;
+    const { spacing: segmentationSpacing } = segmentationVolume;
     const scalarData = segmentationVolume.getScalarData();
     const volumeInfoList = [];
     let baseVolumeIdx = 0;

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

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

@@ -1,3 +1,4 @@
-import { enable, disable, setConfiguration, getConfiguration, } from './stackPrefetch';
-export { enable, disable, setConfiguration, getConfiguration };
+import stackPrefetch from './stackPrefetch';
+import stackContextPrefetch from './stackContextPrefetch';
+export { stackPrefetch, stackContextPrefetch };
 //# sourceMappingURL=index.js.map

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

@@ -1 +1 @@
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+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../../../src/utilities/stackPrefetch/index.ts"],"names":[],"mappings":"AAAA,OAAO,aAAa,MAAM,iBAAiB,CAAC;AAC5C,OAAO,oBAAoB,MAAM,wBAAwB,CAAC;AAE1D,OAAO,EAAE,aAAa,EAAE,oBAAoB,EAAE,CAAC"}

package/dist/esm/utilities/stackPrefetch/stackContextPrefetch.js

@@ -0,0 +1,222 @@
+import { imageLoader, Enums, eventTarget, imageLoadPoolManager, cache, getConfiguration as getCoreConfiguration, } from '@cornerstonejs/core';
+import { addToolState, getToolState } from './state';
+import { getStackData, requestType, priority, clearFromImageIds, getPromiseRemovedHandler, } from './stackPrefetchUtils';
+import { roundNumber } from '../../utilities';
+let configuration = {
+    maxImagesToPrefetch: Infinity,
+    minBefore: 2,
+    maxAfter: 2,
+    directionExtraImages: 10,
+    preserveExistingPool: false,
+};
+let resetPrefetchTimeout;
+const resetPrefetchDelay = 5;
+const enable = (element) => {
+    const stack = getStackData(element);
+    if (!stack || !stack.imageIds || stack.imageIds.length === 0) {
+        console.warn('CornerstoneTools.stackPrefetch: No images in stack.');
+        return;
+    }
+    updateToolState(element);
+    prefetch(element);
+    element.removeEventListener(Enums.Events.STACK_NEW_IMAGE, onImageUpdated);
+    element.addEventListener(Enums.Events.STACK_NEW_IMAGE, onImageUpdated);
+    const promiseRemovedHandler = getPromiseRemovedHandler(element);
+    eventTarget.removeEventListener(Enums.Events.IMAGE_CACHE_IMAGE_REMOVED, promiseRemovedHandler);
+    eventTarget.addEventListener(Enums.Events.IMAGE_CACHE_IMAGE_REMOVED, promiseRemovedHandler);
+};
+function prefetch(element) {
+    const stack = getStackData(element);
+    if (!stack?.imageIds?.length) {
+        console.warn('CornerstoneTools.stackPrefetch: No images in stack.');
+        return;
+    }
+    const stackPrefetchData = getToolState(element);
+    if (!stackPrefetchData) {
+        return;
+    }
+    const stackPrefetch = stackPrefetchData || {};
+    stackPrefetch.enabled &&= stackPrefetch.indicesToRequest?.length;
+    if (stackPrefetch.enabled === false) {
+        return;
+    }
+    function removeFromList(imageIdIndex) {
+        const index = stackPrefetch.indicesToRequest.indexOf(imageIdIndex);
+        if (index > -1) {
+            stackPrefetch.indicesToRequest.splice(index, 1);
+        }
+    }
+    const indicesToRequestCopy = stackPrefetch.indicesToRequest.slice();
+    const { currentImageIdIndex } = stack;
+    indicesToRequestCopy.forEach((imageIdIndex) => {
+        const imageId = stack.imageIds[imageIdIndex];
+        if (!imageId) {
+            return;
+        }
+        const distance = Math.abs(currentImageIdIndex - imageIdIndex);
+        const imageCached = distance < 6
+            ? cache.getImageLoadObject(imageId)
+            : cache.isLoaded(imageId);
+        if (imageCached) {
+            removeFromList(imageIdIndex);
+        }
+    });
+    if (!stackPrefetch.indicesToRequest.length) {
+        return;
+    }
+    if (!configuration.preserveExistingPool) {
+        imageLoadPoolManager.filterRequests(clearFromImageIds(stack));
+    }
+    function doneCallback(imageId) {
+        const imageIdIndex = stack.imageIds.indexOf(imageId);
+        removeFromList(imageIdIndex);
+        const image = cache.getCachedImageBasedOnImageURI(imageId);
+        const { stats } = stackPrefetch;
+        const decodeTimeInMS = image?.image?.decodeTimeInMS || 0;
+        if (decodeTimeInMS) {
+            stats.imageIds.set(imageId, decodeTimeInMS);
+            stats.decodeTimeInMS += decodeTimeInMS;
+            const loadTimeInMS = image?.image?.loadTimeInMS || 0;
+            stats.loadTimeInMS += loadTimeInMS;
+        }
+        if (!stackPrefetch.indicesToRequest.length) {
+            if (image?.sizeInBytes) {
+                const { sizeInBytes } = image;
+                const usage = cache.getMaxCacheSize() / 4 / sizeInBytes;
+                if (!stackPrefetch.cacheFill) {
+                    stats.initialTime = Date.now() - stats.start;
+                    stats.initialSize = stats.imageIds.size;
+                    updateToolState(element, usage);
+                    prefetch(element);
+                }
+                else if (stats.imageIds.size) {
+                    stats.fillTime = Date.now() - stats.start;
+                    const { size } = stats.imageIds;
+                    stats.fillSize = size;
+                    console.log('Done cache fill', stats.fillTime, 'ms', size, 'items', 'average total time', roundNumber(stats.fillTime / size), 'ms', 'average load', roundNumber(stats.loadTimeInMS / size), 'ms', 'average decode', roundNumber(stats.decodeTimeInMS / size), 'ms');
+                }
+            }
+        }
+    }
+    const requestFn = (imageId, options) => imageLoader
+        .loadAndCacheImage(imageId, options)
+        .then(() => doneCallback(imageId));
+    const { useNorm16Texture, preferSizeOverAccuracy } = getCoreConfiguration().rendering;
+    const useNativeDataType = useNorm16Texture || preferSizeOverAccuracy;
+    stackPrefetch.indicesToRequest.forEach((imageIdIndex) => {
+        const imageId = stack.imageIds[imageIdIndex];
+        const options = {
+            targetBuffer: {
+                type: useNativeDataType ? undefined : 'Float32Array',
+            },
+            preScale: {
+                enabled: true,
+            },
+            useNativeDataType,
+            requestType,
+        };
+        imageLoadPoolManager.addRequest(requestFn.bind(null, imageId, options), requestType, {
+            imageId,
+        }, priority);
+    });
+}
+function onImageUpdated(e) {
+    clearTimeout(resetPrefetchTimeout);
+    resetPrefetchTimeout = setTimeout(function () {
+        const element = e.target;
+        try {
+            updateToolState(element);
+            prefetch(element);
+        }
+        catch (error) {
+            return;
+        }
+    }, resetPrefetchDelay);
+}
+const signum = (x) => (x < 0 ? -1 : 1);
+const updateToolState = (element, usage) => {
+    const stack = getStackData(element);
+    if (!stack || !stack.imageIds || stack.imageIds.length === 0) {
+        console.warn('CornerstoneTools.stackPrefetch: No images in stack.');
+        return;
+    }
+    const { currentImageIdIndex } = stack;
+    let { maxAfter = 2, minBefore = 2 } = configuration;
+    const { directionExtraImages = 10 } = configuration;
+    const stackPrefetchData = getToolState(element) || {
+        indicesToRequest: [],
+        currentImageIdIndex,
+        stackCount: 0,
+        enabled: true,
+        direction: 1,
+        stats: {
+            start: Date.now(),
+            imageIds: new Map(),
+            decodeTimeInMS: 0,
+            loadTimeInMS: 0,
+            totalBytes: 0,
+        },
+    };
+    const delta = currentImageIdIndex - stackPrefetchData.currentImageIdIndex;
+    stackPrefetchData.direction = signum(delta);
+    stackPrefetchData.currentImageIdIndex = currentImageIdIndex;
+    stackPrefetchData.enabled = true;
+    if (stackPrefetchData.stackCount < 100) {
+        stackPrefetchData.stackCount += directionExtraImages;
+    }
+    if (Math.abs(delta) > maxAfter || !delta) {
+        stackPrefetchData.stackCount = 0;
+        if (usage) {
+            const positionFraction = currentImageIdIndex / stack.imageIds.length;
+            minBefore = Math.ceil(usage * positionFraction);
+            maxAfter = Math.ceil(usage * (1 - positionFraction));
+            stackPrefetchData.cacheFill = true;
+        }
+        else {
+            stackPrefetchData.cacheFill = false;
+        }
+    }
+    else if (delta < 0) {
+        minBefore += stackPrefetchData.stackCount;
+        maxAfter = 0;
+    }
+    else {
+        maxAfter += stackPrefetchData.stackCount;
+        minBefore = 0;
+    }
+    const minIndex = Math.max(0, currentImageIdIndex - minBefore);
+    const maxIndex = Math.min(stack.imageIds.length - 1, currentImageIdIndex + maxAfter);
+    const indicesToRequest = [];
+    for (let i = currentImageIdIndex + 1; i <= maxIndex; i++) {
+        indicesToRequest.push(i);
+    }
+    for (let i = currentImageIdIndex - 1; i >= minIndex; i--) {
+        indicesToRequest.push(i);
+    }
+    stackPrefetchData.indicesToRequest = indicesToRequest;
+    addToolState(element, stackPrefetchData);
+};
+function disable(element) {
+    clearTimeout(resetPrefetchTimeout);
+    element.removeEventListener(Enums.Events.STACK_NEW_IMAGE, onImageUpdated);
+    const promiseRemovedHandler = getPromiseRemovedHandler(element);
+    eventTarget.removeEventListener(Enums.Events.IMAGE_CACHE_IMAGE_REMOVED, promiseRemovedHandler);
+    const stackPrefetchData = getToolState(element);
+    if (stackPrefetchData) {
+        stackPrefetchData.enabled = false;
+    }
+}
+function getConfiguration() {
+    return configuration;
+}
+function setConfiguration(config) {
+    configuration = config;
+}
+const stackContextPrefetch = {
+    enable,
+    disable,
+    getConfiguration,
+    setConfiguration,
+};
+export default stackContextPrefetch;
+//# sourceMappingURL=stackContextPrefetch.js.map

package/dist/esm/utilities/stackPrefetch/stackContextPrefetch.js.map

@@ -0,0 +1 @@
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