@cornerstonejs/tools 1.40.3 → 1.42.0

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

@@ -0,0 +1,44 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+const RectangleROIStartEndThreshold_1 = __importDefault(require("./RectangleROIStartEndThreshold"));
+function validateAnnotation(annotation) {
+    if (!(annotation === null || annotation === void 0 ? void 0 : 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 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.TOOL_NAMES = {};
+AnnotationToPointData.register(RectangleROIStartEndThreshold_1.default);
+exports.default = AnnotationToPointData;
+//# sourceMappingURL=AnnotationToPointData.js.map

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

@@ -0,0 +1 @@
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package/dist/cjs/utilities/contours/RectangleROIStartEndThreshold.d.ts

@@ -0,0 +1,6 @@
+declare class RectangleROIStartEndThreshold {
+    static toolName: string;
+    constructor();
+    static getContourSequence(toolData: any, metadataProvider: any): any;
+}
+export default RectangleROIStartEndThreshold;

package/dist/cjs/utilities/contours/RectangleROIStartEndThreshold.js

@@ -0,0 +1,43 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+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,
+    };
+}
+exports.default = RectangleROIStartEndThreshold;
+//# sourceMappingURL=RectangleROIStartEndThreshold.js.map

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

@@ -0,0 +1 @@
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package/dist/cjs/utilities/contours/contourFinder.d.ts

@@ -0,0 +1,7 @@
+export declare function findContours(lines: any): any;
+export declare function findContoursFromReducedSet(lines: any): any;
+declare const _default: {
+    findContours: typeof findContours;
+    findContoursFromReducedSet: typeof findContoursFromReducedSet;
+};
+export default _default;

package/dist/cjs/utilities/contours/contourFinder.js

@@ -0,0 +1,68 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.findContoursFromReducedSet = exports.findContours = void 0;
+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',
+    };
+}
+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;
+    }
+}
+exports.findContours = findContours;
+function findContoursFromReducedSet(lines) {
+    return findContours(lines);
+}
+exports.findContoursFromReducedSet = findContoursFromReducedSet;
+exports.default = {
+    findContours,
+    findContoursFromReducedSet,
+};
+//# sourceMappingURL=contourFinder.js.map

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

@@ -0,0 +1 @@
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package/dist/cjs/utilities/contours/detectContourHoles.d.ts

@@ -0,0 +1,5 @@
+export declare function processContourHoles(contours: any, points: any, useXOR?: boolean): any;
+declare const _default: {
+    processContourHoles: typeof processContourHoles;
+};
+export default _default;

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

@@ -0,0 +1,78 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.processContourHoles = void 0;
+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;
+}
+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;
+}
+exports.processContourHoles = processContourHoles;
+exports.default = { processContourHoles };
+//# sourceMappingURL=detectContourHoles.js.map

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

@@ -0,0 +1 @@
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package/dist/cjs/utilities/contours/generateContourSetsFromLabelmap.d.ts

@@ -0,0 +1,4 @@
+declare function generateContourSetsFromLabelmap({ segmentations }: {
+    segmentations: any;
+}): any[];
+export { generateContourSetsFromLabelmap };

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

@@ -0,0 +1,124 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.generateContourSetsFromLabelmap = void 0;
+const core_1 = require("@cornerstonejs/core");
+const ImageMarchingSquares_1 = __importDefault(require("@kitware/vtk.js/Filters/General/ImageMarchingSquares"));
+const DataArray_1 = __importDefault(require("@kitware/vtk.js/Common/Core/DataArray"));
+const ImageData_1 = __importDefault(require("@kitware/vtk.js/Common/DataModel/ImageData"));
+const mergePoints_1 = require("./mergePoints");
+const contourFinder_1 = require("./contourFinder");
+const SegmentationRepresentations_1 = __importDefault(require("../../enums/SegmentationRepresentations"));
+const { Labelmap } = SegmentationRepresentations_1.default;
+function generateContourSetsFromLabelmap({ segmentations }) {
+    var _a;
+    const { representationData, segments = [0, 1] } = segmentations;
+    const { volumeId: segVolumeId } = representationData[Labelmap];
+    const vol = core_1.cache.getVolume(segVolumeId);
+    if (!vol) {
+        console.warn(`No volume found for ${segVolumeId}`);
+        return;
+    }
+    const numSlices = vol.dimensions[2];
+    const imageVol = core_1.cache.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 = DataArray_1.default.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 === null || containedSegmentIndices === void 0 ? void 0 : containedSegmentIndices.has(value))) {
+                        scalars.setValue(i + frameStart, 1);
+                    }
+                    else {
+                        scalars.setValue(i, 0);
+                    }
+                }
+                const mSquares = ImageMarchingSquares_1.default.newInstance({
+                    slice: sliceIndex,
+                });
+                const imageDataCopy = ImageData_1.default.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 = (0, mergePoints_1.removeDuplicatePoints)(msOutput);
+                if ((_a = reducedSet.points) === null || _a === void 0 ? void 0 : _a.length) {
+                    const contours = (0, contourFinder_1.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;
+}
+exports.generateContourSetsFromLabelmap = generateContourSetsFromLabelmap;
+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;
+}
+//# sourceMappingURL=generateContourSetsFromLabelmap.js.map

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

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package/dist/cjs/utilities/contours/index.d.ts

@@ -0,0 +1,6 @@
+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, };

package/dist/cjs/utilities/contours/index.js

@@ -0,0 +1,17 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.AnnotationToPointData = exports.generateContourSetsFromLabelmap = exports.detectContourHoles = exports.mergePoints = exports.contourFinder = void 0;
+const contourFinder_1 = __importDefault(require("./contourFinder"));
+exports.contourFinder = contourFinder_1.default;
+const mergePoints_1 = __importDefault(require("./mergePoints"));
+exports.mergePoints = mergePoints_1.default;
+const detectContourHoles_1 = __importDefault(require("./detectContourHoles"));
+exports.detectContourHoles = detectContourHoles_1.default;
+const generateContourSetsFromLabelmap_1 = require("./generateContourSetsFromLabelmap");
+Object.defineProperty(exports, "generateContourSetsFromLabelmap", { enumerable: true, get: function () { return generateContourSetsFromLabelmap_1.generateContourSetsFromLabelmap; } });
+const AnnotationToPointData_1 = __importDefault(require("./AnnotationToPointData"));
+exports.AnnotationToPointData = AnnotationToPointData_1.default;
+//# sourceMappingURL=index.js.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../../../src/utilities/contours/index.ts"],"names":[],"mappings":";;;;;;AAAA,oEAA4C;AAQ1C,wBARK,uBAAa,CAQL;AAPf,gEAAwC;AAQtC,sBARK,qBAAW,CAQL;AAPb,8EAAsD;AAQpD,6BARK,4BAAkB,CAQL;AAPpB,uFAAoF;AAQlF,gHARO,iEAA+B,OAQP;AANjC,oFAA4D;AAO1D,gCAPK,+BAAqB,CAOL"}

package/dist/cjs/utilities/contours/mergePoints.d.ts

@@ -0,0 +1,8 @@
+export declare function removeDuplicatePoints(polyData: any, bypass?: boolean): {
+    points: any[];
+    lines: any[];
+};
+declare const _default: {
+    removeDuplicatePoints: typeof removeDuplicatePoints;
+};
+export default _default;

package/dist/cjs/utilities/contours/mergePoints.js

@@ -0,0 +1,77 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.removeDuplicatePoints = void 0;
+function ptInArray(array, pt) {
+    let index = -1;
+    for (let i = 0; i < array.length; i++) {
+        if (isSamePoint(pt, array[i])) {
+            index = i;
+        }
+    }
+    return index;
+}
+function isSamePoint(ptA, ptB) {
+    if (ptA[0] == ptB[0] && ptA[1] == ptB[1] && ptA[2] == ptB[2]) {
+        return true;
+    }
+    else {
+        return false;
+    }
+}
+function replacePointIndexReferences(linesArray, oldIndex, newIndex) {
+    for (let i = 0; i < linesArray.length; i++) {
+        const line = linesArray[i];
+        if (line.a == oldIndex) {
+            line.a = newIndex;
+        }
+        else if (line.b == oldIndex) {
+            line.b = newIndex;
+        }
+    }
+}
+function removeDuplicatePoints(polyData, bypass = false) {
+    const points = polyData.getPoints();
+    const lines = polyData.getLines();
+    const pointsArray = [];
+    for (let i = 0; i < points.getNumberOfPoints(); i++) {
+        const pt = points.getPoint(i).slice();
+        pointsArray.push(pt);
+    }
+    const linesArray = [];
+    for (let i = 0; i < lines.getNumberOfCells(); i++) {
+        const cell = lines.getCell(i * 3).slice();
+        const a = cell[0];
+        const b = cell[1];
+        const line = {
+            a,
+            b,
+        };
+        linesArray.push(line);
+    }
+    if (bypass) {
+        return { points: pointsArray, lines: linesArray };
+    }
+    const newPoints = [];
+    for (let i = 0; i < pointsArray.length; i++) {
+        const pt = pointsArray[i];
+        let index = ptInArray(newPoints, pt);
+        if (index >= 0) {
+            replacePointIndexReferences(linesArray, i, index);
+        }
+        else {
+            index = newPoints.length;
+            newPoints.push(pt);
+            replacePointIndexReferences(linesArray, i, index);
+        }
+    }
+    const newLines = [];
+    linesArray.forEach((line) => {
+        if (line.a != line.b) {
+            newLines.push(line);
+        }
+    });
+    return { points: newPoints, lines: newLines };
+}
+exports.removeDuplicatePoints = removeDuplicatePoints;
+exports.default = { removeDuplicatePoints };
+//# sourceMappingURL=mergePoints.js.map

package/dist/cjs/utilities/contours/mergePoints.js.map

@@ -0,0 +1 @@
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package/dist/cjs/utilities/getCalibratedUnits.d.ts

@@ -1,6 +1,20 @@
 declare const getCalibratedLengthUnits: (handles: any, image: any) => string;
 declare const getCalibratedAreaUnits: (handles: any, image: any) => string;
-declare const getCalibratedScale: (image: any) => any;
+declare const getCalibratedScale: (image: any, handles?: any[]) => any;
+declare const getCalibratedLengthUnitsAndScale: (image: any, handles: any) => {
+    units: string;
+    areaUnits: string;
+    scale: number;
+};
+declare const getCalibratedProbeUnitsAndValue: (image: any, handles: any) => {
+    units: string[];
+    values: any[];
+    calibrationType?: undefined;
+} | {
+    units: string[];
+    values: any[];
+    calibrationType: string;
+};
 declare const getCalibratedAspect: (image: any) => any;
 export default getCalibratedLengthUnits;
-export { getCalibratedAreaUnits, getCalibratedLengthUnits, getCalibratedScale, getCalibratedAspect, };
+export { getCalibratedAreaUnits, getCalibratedLengthUnits, getCalibratedLengthUnitsAndScale, getCalibratedScale, getCalibratedAspect, getCalibratedProbeUnitsAndValue, };