@cornerstonejs/tools 2.0.0-beta.6 → 2.0.0-beta.8

package/dist/esm/stateManagement/segmentation/helpers/clipAndCacheSurfacesForViewport.js

@@ -0,0 +1,91 @@
+import { Enums, getWebWorkerManager, eventTarget, triggerEvent, } from '@cornerstonejs/core';
+import { WorkerTypes } from '../../../enums';
+import { pointToString } from '../../../utilities';
+import { registerPolySegWorker } from '../polySeg/registerPolySegWorker';
+const workerManager = getWebWorkerManager();
+const polyDataCache = new Map();
+const surfacesAABBCache = new Map();
+const triggerWorkerProgress = (eventTarget, progress) => {
+    triggerEvent(eventTarget, Enums.Events.WEB_WORKER_PROGRESS, {
+        progress,
+        type: WorkerTypes.SURFACE_CLIPPING,
+    });
+};
+export async function clipAndCacheSurfacesForViewport(surfacesInfo, viewport, segmentationRepresentationUID) {
+    registerPolySegWorker();
+    const planesInfo = viewport.getSlicesClippingPlanes?.();
+    if (!planesInfo) {
+        return;
+    }
+    const currentSliceIndex = viewport.getSliceIndex();
+    planesInfo.sort((a, b) => {
+        const diffA = Math.abs(a.sliceIndex - currentSliceIndex);
+        const diffB = Math.abs(b.sliceIndex - currentSliceIndex);
+        return diffA - diffB;
+    });
+    triggerWorkerProgress(eventTarget, 0);
+    await updateSurfacesAABBCache(surfacesInfo);
+    const surfacesAABB = new Map();
+    surfacesInfo.forEach((surface) => {
+        surfacesAABB.set(surface.id, surfacesAABBCache.get(surface.id));
+    });
+    const camera = viewport.getCamera();
+    await workerManager
+        .executeTask('polySeg', 'cutSurfacesIntoPlanes', {
+        surfacesInfo,
+        planesInfo,
+        surfacesAABB,
+    }, {
+        callbacks: [
+            ({ progress }) => {
+                triggerWorkerProgress(eventTarget, progress);
+            },
+            ({ sliceIndex, polyDataResults }) => {
+                polyDataResults.forEach((polyDataResult, surfaceId) => {
+                    const actorUID = `${segmentationRepresentationUID}_${surfaceId}`;
+                    const cacheId = generateCacheId(viewport, camera.viewPlaneNormal, sliceIndex);
+                    updatePolyDataCache(actorUID, cacheId, polyDataResult);
+                });
+            },
+        ],
+    })
+        .catch((error) => {
+        console.error(error);
+    });
+    triggerWorkerProgress(eventTarget, 1);
+    return polyDataCache;
+}
+async function updateSurfacesAABBCache(surfacesInfo) {
+    const surfacesWithoutAABB = surfacesInfo.filter((surface) => !surfacesAABBCache.has(surface.id));
+    if (!surfacesWithoutAABB.length) {
+        return;
+    }
+    const surfacesAABB = await workerManager.executeTask('polySeg', 'getSurfacesAABBs', {
+        surfacesInfo: surfacesWithoutAABB,
+    }, {
+        callbacks: [
+            ({ progress }) => {
+                triggerWorkerProgress(eventTarget, progress);
+            },
+        ],
+    });
+    surfacesAABB.forEach((aabb, id) => {
+        surfacesAABBCache.set(id, aabb);
+    });
+}
+export function getSurfaceActorUID(segmentationRepresentationUID, surfaceId) {
+    return `${segmentationRepresentationUID}_${surfaceId}`;
+}
+export function generateCacheId(viewport, viewPlaneNormal, sliceIndex) {
+    return `${viewport.id}-${pointToString(viewPlaneNormal)}-${sliceIndex}`;
+}
+export function updatePolyDataCache(actorUID, cacheId, polyDataResult) {
+    const { points, lines, numberOfCells } = polyDataResult;
+    let actorCache = polyDataCache.get(actorUID);
+    if (!actorCache) {
+        actorCache = new Map();
+        polyDataCache.set(actorUID, actorCache);
+    }
+    actorCache.set(cacheId, { points, lines, numberOfCells });
+}
+//# sourceMappingURL=clipAndCacheSurfacesForViewport.js.map

package/dist/esm/stateManagement/segmentation/helpers/clipAndCacheSurfacesForViewport.js.map

@@ -0,0 +1 @@
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package/dist/esm/stateManagement/segmentation/helpers/getRepresentationSpecificConfig.js

@@ -0,0 +1,12 @@
+import SegmentationRepresentations from '../../../enums/SegmentationRepresentations';
+import { getRepresentationRenderingConfig as getLabelmapRenderingConfig } from '../../../tools/displayTools/Labelmap/labelmapDisplay';
+export function getRepresentationSpecificConfig(representationInput) {
+    const { type } = representationInput;
+    if (type === SegmentationRepresentations.Labelmap) {
+        return getLabelmapRenderingConfig();
+    }
+    else {
+        return {};
+    }
+}
+//# sourceMappingURL=getRepresentationSpecificConfig.js.map

package/dist/esm/stateManagement/segmentation/helpers/getRepresentationSpecificConfig.js.map

@@ -0,0 +1 @@
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package/dist/esm/stateManagement/segmentation/helpers/normalizeSegmentationInput.js

@@ -1,5 +1,17 @@
+import { SegmentationRepresentations } from '../../../enums';
 function normalizeSegmentationInput(segmentationInput) {
     const { segmentationId, representation } = segmentationInput;
+    const isContourRepresentation = representation.type === SegmentationRepresentations.Contour;
+    let data = representation.data ? { ...representation.data } : null;
+    data = !data && isContourRepresentation ? {} : data;
+    if (!data) {
+        throw new Error('Segmentation representation data may not be undefined');
+    }
+    if (isContourRepresentation) {
+        const contourData = data;
+        contourData.geometryIds = contourData.geometryIds ?? [];
+        contourData.annotationUIDsMap = contourData.annotationUIDsMap ?? new Map();
+    }
     return {
         segmentationId,
         cachedStats: {},
@@ -10,7 +22,7 @@ function normalizeSegmentationInput(segmentationInput) {
         activeSegmentIndex: 1,
         representationData: {
             [representation.type]: {
-                ...representation.data,
+                ...data,
             },
         },
     };

package/dist/esm/stateManagement/segmentation/helpers/normalizeSegmentationInput.js.map

@@ -1 +1 @@
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package/dist/esm/stateManagement/segmentation/helpers/validateSegmentationInput.js

@@ -1,19 +1,19 @@
 import * as Enums from '../../../enums';
-import validateLabelmap from '../../../tools/displayTools/Labelmap/validateRepresentationData';
+import { validatePublic as validatePublicLabelmap } from '../../../tools/displayTools/Labelmap/validateLabelmap';
 function validateSegmentationInput(segmentationInputArray) {
-    if (!segmentationInputArray || !segmentationInputArray.length) {
-        throw new Error('The segmentationInputArray is undefined or empty array');
+    if (!segmentationInputArray || segmentationInputArray.length === 0) {
+        throw new Error('The segmentationInputArray is undefined or an empty array');
     }
     segmentationInputArray.forEach((segmentationInput) => {
         if (segmentationInput.segmentationId === undefined) {
-            throw new Error('The segmentationInput.segmentationId is undefined, please provide a valid segmentationId');
+            throw new Error('Undefined segmentationInput.segmentationId. Please provide a valid segmentationId');
         }
         if (segmentationInput.representation === undefined) {
-            throw new Error('The segmentationInput.representation is undefined, please provide a valid representation');
+            throw new Error('Undefined segmentationInput.representation. Please provide a valid representation');
         }
         if (segmentationInput.representation.type ===
             Enums.SegmentationRepresentations.Labelmap) {
-            validateLabelmap(segmentationInput);
+            validatePublicLabelmap(segmentationInput);
         }
     });
 }

package/dist/esm/stateManagement/segmentation/helpers/validateSegmentationInput.js.map

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package/dist/esm/stateManagement/segmentation/index.js

@@ -1,11 +1,15 @@
 import removeSegmentationsFromToolGroup from './removeSegmentationsFromToolGroup';
 import addSegmentations from './addSegmentations';
 import addSegmentationRepresentations from './addSegmentationRepresentations';
+import addRepresentationData from './addRepresentationData';
+import { convertStackToVolumeSegmentation } from './convertStackToVolumeSegmentation';
+import { convertVolumeToStackSegmentation } from './convertVolumeToStackSegmentation';
 import * as activeSegmentation from './activeSegmentation';
 import * as segmentLocking from './segmentLocking';
 import * as state from './segmentationState';
 import * as config from './config';
 import * as segmentIndex from './segmentIndex';
 import * as triggerSegmentationEvents from './triggerSegmentationEvents';
-export { state, addSegmentations, activeSegmentation, addSegmentationRepresentations, removeSegmentationsFromToolGroup, segmentLocking, config, segmentIndex, triggerSegmentationEvents, };
+import * as polySegManager from './polySeg';
+export { addSegmentations, addSegmentationRepresentations, removeSegmentationsFromToolGroup, addRepresentationData, state, activeSegmentation, segmentLocking, config, segmentIndex, triggerSegmentationEvents, convertStackToVolumeSegmentation, convertVolumeToStackSegmentation, polySegManager as polySeg, };
 //# sourceMappingURL=index.js.map

package/dist/esm/stateManagement/segmentation/index.js.map

@@ -1 +1 @@
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package/dist/esm/stateManagement/segmentation/polySeg/Contour/computeAndAddContourRepresentation.js

@@ -0,0 +1,7 @@
+import { SegmentationRepresentations } from '../../../../enums';
+import { computeAndAddRepresentation } from '../computeAndAddRepresentation';
+import { computeContourData } from './contourComputationStrategies';
+export function computeAndAddContourRepresentation(segmentationId, options = {}) {
+    return computeAndAddRepresentation(segmentationId, SegmentationRepresentations.Contour, () => computeContourData(segmentationId, options), () => undefined);
+}
+//# sourceMappingURL=computeAndAddContourRepresentation.js.map

package/dist/esm/stateManagement/segmentation/polySeg/Contour/computeAndAddContourRepresentation.js.map

@@ -0,0 +1 @@
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package/dist/esm/stateManagement/segmentation/polySeg/Contour/contourComputationStrategies.js

@@ -0,0 +1,105 @@
+import { cache } from '@cornerstonejs/core';
+import { getUniqueSegmentIndices } from '../../../../utilities/segmentation';
+import { getSegmentation, setSegmentationRepresentationSpecificConfig, } from '../../segmentationState';
+import { computeSurfaceFromLabelmapSegmentation } from '../Surface/surfaceComputationStrategies';
+import { clipAndCacheSurfacesForViewport, } from '../../helpers/clipAndCacheSurfacesForViewport';
+import { extractContourData } from './utils/extractContourData';
+import { createAndAddContourSegmentationsFromClippedSurfaces } from './utils/createAndAddContourSegmentationsFromClippedSurfaces';
+import { getToolGroupForViewport } from '../../../../store/ToolGroupManager';
+export async function computeContourData(segmentationId, options = {}) {
+    const segmentIndices = options.segmentIndices?.length
+        ? options.segmentIndices
+        : getUniqueSegmentIndices(segmentationId);
+    let rawContourData;
+    const segmentation = getSegmentation(segmentationId);
+    const representationData = segmentation.representationData;
+    try {
+        if (representationData.SURFACE) {
+            rawContourData = await computeContourFromSurfaceSegmentation(segmentationId, {
+                segmentIndices,
+                ...options,
+            });
+        }
+        else if (representationData.LABELMAP) {
+            rawContourData = await computeContourFromLabelmapSegmentation(segmentationId, {
+                segmentIndices,
+                ...options,
+            });
+        }
+    }
+    catch (error) {
+        console.error(error);
+        throw error;
+    }
+    if (!rawContourData) {
+        throw new Error('Not enough data to convert to contour, currently only support converting volume labelmap to contour if available');
+    }
+    const { viewport, segmentationRepresentationUID } = options;
+    const annotationUIDsMap = createAndAddContourSegmentationsFromClippedSurfaces(rawContourData, viewport, segmentationId);
+    const toolGroupId = getToolGroupForViewport(viewport.id)?.id;
+    setSegmentationRepresentationSpecificConfig(toolGroupId, segmentationRepresentationUID, {
+        CONTOUR: {
+            fillAlpha: 0,
+        },
+    });
+    return {
+        annotationUIDsMap,
+    };
+}
+async function computeContourFromLabelmapSegmentation(segmentationId, options = {}) {
+    if (!options.viewport) {
+        throw new Error('Viewport is required to compute contour from labelmap');
+    }
+    const results = await computeSurfaceFromLabelmapSegmentation(segmentationId, options);
+    if (!results?.length) {
+        console.error('Failed to convert labelmap to surface or labelmap is empty');
+        return;
+    }
+    const { viewport, segmentationRepresentationUID } = options;
+    const pointsAndPolys = results.map((surface) => {
+        return {
+            id: surface.segmentIndex.toString(),
+            points: surface.data.points,
+            polys: surface.data.polys,
+            segmentIndex: surface.segmentIndex,
+        };
+    });
+    const polyDataCache = await clipAndCacheSurfacesForViewport(pointsAndPolys, viewport, segmentationRepresentationUID);
+    const rawResults = extractContourData(polyDataCache);
+    return rawResults;
+}
+async function computeContourFromSurfaceSegmentation(segmentationId, options = {}) {
+    if (!options.viewport) {
+        throw new Error('Viewport is required to compute contour from surface');
+    }
+    const { viewport, segmentationRepresentationUID } = options;
+    const segmentIndices = options.segmentIndices?.length
+        ? options.segmentIndices
+        : getUniqueSegmentIndices(segmentationId);
+    const segmentIndexToSurfaceId = new Map();
+    const surfaceIdToSegmentIndex = new Map();
+    const segmentation = getSegmentation(segmentationId);
+    const representationData = segmentation.representationData.SURFACE;
+    const surfacesInfo = [];
+    representationData.geometryIds.forEach((geometryId, segmentIndex) => {
+        if (segmentIndices.includes(segmentIndex)) {
+            segmentIndexToSurfaceId.set(segmentIndex, geometryId);
+            const surface = cache.getGeometry(geometryId)?.data;
+            if (surface) {
+                surfacesInfo.push({
+                    id: geometryId,
+                    points: surface.getPoints(),
+                    polys: surface.getPolys(),
+                });
+            }
+        }
+    });
+    segmentIndexToSurfaceId.forEach((surfaceId, segmentIndex) => {
+        surfaceIdToSegmentIndex.set(surfaceId, segmentIndex);
+    });
+    const polyDataCache = await clipAndCacheSurfacesForViewport(surfacesInfo, viewport, segmentationRepresentationUID);
+    const rawResults = extractContourData(polyDataCache, surfaceIdToSegmentIndex);
+    return rawResults;
+}
+export { computeContourFromLabelmapSegmentation };
+//# sourceMappingURL=contourComputationStrategies.js.map

package/dist/esm/stateManagement/segmentation/polySeg/Contour/contourComputationStrategies.js.map

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package/dist/esm/stateManagement/segmentation/polySeg/Contour/utils/createAndAddContourSegmentationsFromClippedSurfaces.js

@@ -0,0 +1,72 @@
+import { PlanarFreehandContourSegmentationTool } from '../../../../../tools';
+import { addAnnotation } from '../../../../annotation/annotationState';
+import { utilities } from '@cornerstonejs/core';
+export function createAndAddContourSegmentationsFromClippedSurfaces(rawContourData, viewport, segmentationId) {
+    const annotationUIDsMap = new Map();
+    for (const [segmentIndex, contoursData] of rawContourData) {
+        for (const contourData of contoursData) {
+            const { points } = contourData;
+            const { lineSegments, linesNumberOfPoints } = _extractLineSegments(contourData);
+            for (let i = 0; i < lineSegments.length; i++) {
+                const line = lineSegments[i];
+                const polyline = [];
+                for (let j = 0; j < linesNumberOfPoints[i]; j++) {
+                    const pointIndex = line[j];
+                    polyline.push([
+                        points[3 * pointIndex],
+                        points[3 * pointIndex + 1],
+                        points[3 * pointIndex + 2],
+                    ]);
+                }
+                if (polyline.length < 3) {
+                    continue;
+                }
+                const contourSegmentationAnnotation = {
+                    annotationUID: utilities.uuidv4(),
+                    data: {
+                        contour: {
+                            closed: true,
+                            polyline,
+                        },
+                        segmentation: {
+                            segmentationId,
+                            segmentIndex,
+                        },
+                        handles: {},
+                    },
+                    handles: {},
+                    highlighted: false,
+                    autoGenerated: false,
+                    invalidated: false,
+                    isLocked: false,
+                    isVisible: true,
+                    metadata: {
+                        toolName: PlanarFreehandContourSegmentationTool.toolName,
+                        ...viewport.getViewReference(),
+                    },
+                };
+                addAnnotation(contourSegmentationAnnotation, viewport.element);
+                const currentSet = annotationUIDsMap.get(segmentIndex) || new Set();
+                currentSet.add(contourSegmentationAnnotation.annotationUID);
+                annotationUIDsMap.set(segmentIndex, currentSet);
+            }
+        }
+    }
+    return annotationUIDsMap;
+}
+const _extractLineSegments = (contourData) => {
+    const { numberOfCells, lines } = contourData;
+    const lineSegments = [];
+    const linesNumberOfPoints = [];
+    for (let i = 0; i < lines.length;) {
+        const pointsInLine = lines[i];
+        linesNumberOfPoints.push(pointsInLine);
+        lineSegments.push(lines.slice(i + 1, i + pointsInLine + 1));
+        i += pointsInLine + 1;
+        if (lineSegments.length === numberOfCells) {
+            break;
+        }
+    }
+    return { lineSegments, linesNumberOfPoints };
+};
+//# sourceMappingURL=createAndAddContourSegmentationsFromClippedSurfaces.js.map

package/dist/esm/stateManagement/segmentation/polySeg/Contour/utils/createAndAddContourSegmentationsFromClippedSurfaces.js.map

@@ -0,0 +1 @@
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package/dist/esm/stateManagement/segmentation/polySeg/Contour/utils/extractContourData.js

@@ -0,0 +1,21 @@
+export function extractContourData(polyDataCache, segmentIndexMap) {
+    const rawResults = new Map();
+    for (const [cacheId, intersectionInfo] of polyDataCache) {
+        const surfaceId = cacheId.split('_')[1];
+        for (const [_, result] of intersectionInfo) {
+            if (!result) {
+                continue;
+            }
+            const segmentIndex = Number(surfaceId) || segmentIndexMap?.get(surfaceId);
+            if (!segmentIndex) {
+                continue;
+            }
+            if (!rawResults.has(segmentIndex)) {
+                rawResults.set(segmentIndex, []);
+            }
+            rawResults.get(segmentIndex).push(result);
+        }
+    }
+    return rawResults;
+}
+//# sourceMappingURL=extractContourData.js.map

package/dist/esm/stateManagement/segmentation/polySeg/Contour/utils/extractContourData.js.map

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package/dist/esm/stateManagement/segmentation/polySeg/Contour/utils/updateContoursOnCameraModified.js

@@ -0,0 +1,26 @@
+import { utilities, Enums } from '@cornerstonejs/core';
+import { extractContourData } from './extractContourData';
+import { clipAndCacheSurfacesForViewport } from '../../../helpers/clipAndCacheSurfacesForViewport';
+import { createAndAddContourSegmentationsFromClippedSurfaces } from './createAndAddContourSegmentationsFromClippedSurfaces';
+const currentViewportNormal = new Map();
+export function updateContoursOnCameraModified(surfacesInfo, viewport, segmentationRepresentationUID) {
+    async function cameraModifiedCallback(evt) {
+        const { camera } = evt.detail;
+        const { viewPlaneNormal } = camera;
+        const surface1 = surfacesInfo[0];
+        const currentNormal = currentViewportNormal.get(surface1.id);
+        if (utilities.isEqual(viewPlaneNormal, currentNormal)) {
+            return;
+        }
+        currentViewportNormal.set(surface1.id, viewPlaneNormal);
+        const polyDataCache = await clipAndCacheSurfacesForViewport(surfacesInfo, viewport, segmentationRepresentationUID);
+        const results = extractContourData(polyDataCache);
+        createAndAddContourSegmentationsFromClippedSurfaces(results, viewport, segmentationRepresentationUID);
+        viewport.render();
+    }
+    const camera = viewport.getCamera();
+    currentViewportNormal.set(surfacesInfo[0].id, camera.viewPlaneNormal);
+    viewport.element.removeEventListener(Enums.Events.CAMERA_MODIFIED, cameraModifiedCallback);
+    viewport.element.addEventListener(Enums.Events.CAMERA_MODIFIED);
+}
+//# sourceMappingURL=updateContoursOnCameraModified.js.map

package/dist/esm/stateManagement/segmentation/polySeg/Contour/utils/updateContoursOnCameraModified.js.map

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package/dist/esm/stateManagement/segmentation/polySeg/Labelmap/computeAndAddLabelmapRepresentation.js

@@ -0,0 +1,7 @@
+import { SegmentationRepresentations } from '../../../../enums';
+import { computeAndAddRepresentation } from '../computeAndAddRepresentation';
+import { computeLabelmapData } from './labelmapComputationStrategies';
+export function computeAndAddLabelmapRepresentation(segmentationId, options = {}) {
+    return computeAndAddRepresentation(segmentationId, SegmentationRepresentations.Labelmap, () => computeLabelmapData(segmentationId, options), () => undefined);
+}
+//# sourceMappingURL=computeAndAddLabelmapRepresentation.js.map

package/dist/esm/stateManagement/segmentation/polySeg/Labelmap/computeAndAddLabelmapRepresentation.js.map

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