@cornerstonejs/tools 0.34.2 → 0.35.1

package/dist/cjs/utilities/segmentation/rectangleROIThresholdVolumeByRange.d.ts

@@ -1,9 +1,13 @@
 import type { Types } from '@cornerstonejs/core';
-export declare type ThresholdRangeOptions = {
+export declare type ThresholdInformation = {
+    volume: Types.IImageVolume;
     lower: number;
     upper: number;
+};
+export declare type ThresholdOptions = {
     numSlicesToProject?: number;
     overwrite: boolean;
+    overlapType?: number;
 };
 export declare type AnnotationForThresholding = {
     data: {
@@ -15,5 +19,5 @@ export declare type AnnotationForThresholding = {
         };
     };
 };
-declare function rectangleROIThresholdVolumeByRange(annotationUIDs: string[], segmentationVolume: Types.IImageVolume, referenceVolumes: Types.IImageVolume[], options: ThresholdRangeOptions): Types.IImageVolume;
+declare function rectangleROIThresholdVolumeByRange(annotationUIDs: string[], segmentationVolume: Types.IImageVolume, thresholdVolumeInformation: ThresholdInformation[], options: ThresholdOptions): Types.IImageVolume;
 export default rectangleROIThresholdVolumeByRange;

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

@@ -7,23 +7,19 @@ const annotation_1 = require("../../stateManagement/annotation");
 const tools_1 = require("../../tools");
 const thresholdVolumeByRange_1 = __importDefault(require("./thresholdVolumeByRange"));
 const getBoundsIJKFromRectangleAnnotations_1 = __importDefault(require("../rectangleROITool/getBoundsIJKFromRectangleAnnotations"));
-function rectangleROIThresholdVolumeByRange(annotationUIDs, segmentationVolume, referenceVolumes, options) {
-    if (referenceVolumes.length > 1) {
-        throw new Error('thresholding based on more than one reference volumes data is not supported yet');
-    }
-    const referenceVolume = referenceVolumes[0];
+function rectangleROIThresholdVolumeByRange(annotationUIDs, segmentationVolume, thresholdVolumeInformation, options) {
     const annotations = annotationUIDs.map((annotationUID) => {
         return annotation_1.state.getAnnotation(annotationUID);
     });
     _validateAnnotations(annotations);
-    const boundsIJK = (0, getBoundsIJKFromRectangleAnnotations_1.default)(annotations, referenceVolume, options);
-    const optionsToUse = {
-        lower: options.lower,
-        upper: options.upper,
-        overwrite: options.overwrite,
-        boundsIJK,
-    };
-    const outputSegmentationVolume = (0, thresholdVolumeByRange_1.default)(segmentationVolume, referenceVolume, optionsToUse);
+    let boundsIJK;
+    for (let i = 0; i < thresholdVolumeInformation.length; i++) {
+        const volumeSize = thresholdVolumeInformation[i].volume.scalarData.length;
+        if (volumeSize === segmentationVolume.scalarData.length || i === 0) {
+            boundsIJK = (0, getBoundsIJKFromRectangleAnnotations_1.default)(annotations, thresholdVolumeInformation[i].volume, options);
+        }
+    }
+    const outputSegmentationVolume = (0, thresholdVolumeByRange_1.default)(segmentationVolume, thresholdVolumeInformation, Object.assign(Object.assign({}, options), { boundsIJK }));
     return outputSegmentationVolume;
 }
 function _validateAnnotations(annotations) {

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

@@ -1 +1 @@
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+{"version":3,"file":"rectangleROIThresholdVolumeByRange.js","sourceRoot":"","sources":["../../../../src/utilities/segmentation/rectangleROIThresholdVolumeByRange.ts"],"names":[],"mappings":";;;;;AACA,iEAAyD;AACzD,uCAGqB;AAErB,sFAA8D;AAC9D,oIAA4G;AAoC5G,SAAS,kCAAkC,CACzC,cAAwB,EACxB,kBAAsC,EACtC,0BAAkD,EAClD,OAAyB;IAEzB,MAAM,WAAW,GAAG,cAAc,CAAC,GAAG,CAAC,CAAC,aAAa,EAAE,EAAE;QACvD,OAAO,kBAAK,CAAC,aAAa,CAAC,aAAa,CAAC,CAAC;IAC5C,CAAC,CAAC,CAAC;IAEH,oBAAoB,CAAC,WAAW,CAAC,CAAC;IAElC,IAAI,SAAS,CAAC;IACd,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,0BAA0B,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE;QAE1D,MAAM,UAAU,GAAG,0BAA0B,CAAC,CAAC,CAAC,CAAC,MAAM,CAAC,UAAU,CAAC,MAAM,CAAC;QAC1E,IAAI,UAAU,KAAK,kBAAkB,CAAC,UAAU,CAAC,MAAM,IAAI,CAAC,KAAK,CAAC,EAAE;YAClE,SAAS,GAAG,IAAA,8CAAoC,EAC9C,WAAW,EACX,0BAA0B,CAAC,CAAC,CAAC,CAAC,MAAM,EACpC,OAAO,CACR,CAAC;SACH;KACF;IAED,MAAM,wBAAwB,GAAG,IAAA,gCAAsB,EACrD,kBAAkB,EAClB,0BAA0B,kCACrB,OAAO,KAAE,SAAS,IACxB,CAAC;IAEF,OAAO,wBAAwB,CAAC;AAClC,CAAC;AAED,SAAS,oBAAoB,CAAC,WAAW;IACvC,MAAM,cAAc,GAAG;QACrB,iCAAyB,CAAC,QAAQ;QAClC,yCAAiC,CAAC,QAAQ;KAC3C,CAAC;IAEF,KAAK,MAAM,UAAU,IAAI,WAAW,EAAE;QACpC,MAAM,IAAI,GAAG,UAAU,CAAC,QAAQ,CAAC,QAAQ,CAAC;QAC1C,IAAI,CAAC,cAAc,CAAC,QAAQ,CAAC,IAAI,CAAC,EAAE;YAClC,MAAM,IAAI,KAAK,CACb,sHAAsH,CACvH,CAAC;SACH;KACF;AACH,CAAC;AAED,kBAAe,kCAAkC,CAAC"}

package/dist/cjs/utilities/segmentation/thresholdVolumeByRange.d.ts

@@ -1,10 +1,14 @@
-import type { Types } from '@cornerstonejs/core';
+import { Types } from '@cornerstonejs/core';
 import { BoundsIJK } from '../../types';
 export declare type ThresholdRangeOptions = {
-    upper: number;
-    lower: number;
-    boundsIJK: BoundsIJK;
     overwrite: boolean;
+    boundsIJK: BoundsIJK;
+    overlapType?: number;
+};
+export declare type ThresholdInformation = {
+    volume: Types.IImageVolume;
+    lower: number;
+    upper: number;
 };
-declare function thresholdVolumeByRange(segmentationVolume: Types.IImageVolume, referenceVolume: Types.IImageVolume, options: ThresholdRangeOptions): Types.IImageVolume;
+declare function thresholdVolumeByRange(segmentationVolume: Types.IImageVolume, thresholdVolumeInformation: ThresholdInformation[], options: ThresholdRangeOptions): Types.IImageVolume;
 export default thresholdVolumeByRange;

package/dist/cjs/utilities/segmentation/thresholdVolumeByRange.js

@@ -1,24 +1,112 @@
 "use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
 Object.defineProperty(exports, "__esModule", { value: true });
+const core_1 = require("@cornerstonejs/core");
 const utilities_1 = require("../../utilities");
 const triggerSegmentationEvents_1 = require("../../stateManagement/segmentation/triggerSegmentationEvents");
-function thresholdVolumeByRange(segmentationVolume, referenceVolume, options) {
-    const { scalarData, imageData: segmentationImageData } = segmentationVolume;
-    const { overwrite, boundsIJK, upper, lower } = options;
-    const { imageData } = referenceVolume;
-    const referenceValues = imageData.getPointData().getScalars().getData();
+const getBoundingBoxAroundShape_1 = __importDefault(require("../boundingBox/getBoundingBoxAroundShape"));
+const equalsCheck = (a, b) => {
+    return JSON.stringify(a) === JSON.stringify(b);
+};
+function thresholdVolumeByRange(segmentationVolume, thresholdVolumeInformation, options) {
+    const { scalarData, spacing: segmentationSpacing, imageData: segmentationImageData, } = segmentationVolume;
+    const { overwrite, boundsIJK } = options;
+    const overlapType = (options === null || options === void 0 ? void 0 : options.overlapType) || 0;
     if (overwrite) {
         for (let i = 0; i < scalarData.length; i++) {
             scalarData[i] = 0;
         }
     }
-    const callback = ({ index, pointIJK }) => {
+    const volumeInfoList = [];
+    let baseVolumeIdx = 0;
+    for (let i = 0; i < thresholdVolumeInformation.length; i++) {
+        const { imageData, spacing, dimensions } = thresholdVolumeInformation[i].volume;
+        const volumeSize = thresholdVolumeInformation[i].volume.scalarData.length;
+        if (volumeSize === scalarData.length &&
+            equalsCheck(spacing, segmentationSpacing)) {
+            baseVolumeIdx = i;
+        }
+        const referenceValues = imageData.getPointData().getScalars().getData();
+        const lower = thresholdVolumeInformation[i].lower;
+        const upper = thresholdVolumeInformation[i].upper;
+        volumeInfoList.push({
+            imageData,
+            referenceValues,
+            lower,
+            upper,
+            spacing,
+            dimensions,
+            volumeSize,
+        });
+    }
+    let overlaps, total, range;
+    const testOverlapRange = (volumeInfo, voxelSpacing, voxelCenter) => {
+        const callbackOverlap = ({ value }) => {
+            total = total + 1;
+            if (value >= range.lower && value <= range.upper) {
+                overlaps = overlaps + 1;
+            }
+        };
+        const { imageData, dimensions, lower, upper } = volumeInfo;
+        const overlapBounds = getVoxelOverlap(imageData, dimensions, voxelSpacing, voxelCenter);
+        total = 0;
+        overlaps = 0;
+        range = { lower, upper };
+        let overlapTest = false;
+        (0, utilities_1.pointInShapeCallback)(imageData, () => true, callbackOverlap, overlapBounds);
+        if (overlapType === 0) {
+            overlapTest = overlaps > 0;
+        }
+        else if (overlapType == 1) {
+            overlapTest = overlaps === total;
+        }
+        return overlapTest;
+    };
+    const testRange = (volumeInfo, pointIJK) => {
+        const { imageData, referenceValues, lower, upper } = volumeInfo;
         const offset = imageData.computeOffsetIndex(pointIJK);
         const value = referenceValues[offset];
         if (value <= lower || value >= upper) {
-            return;
+            return false;
+        }
+        else {
+            return true;
+        }
+    };
+    const getVoxelOverlap = (imageData, dimensions, voxelSpacing, voxelCenter) => {
+        const voxelCornersWorld = [];
+        for (let i = 0; i < 2; i++) {
+            for (let j = 0; j < 2; j++) {
+                for (let k = 0; k < 2; k++) {
+                    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;
+                    voxelCornersWorld.push(point);
+                }
+            }
+        }
+        const voxelCornersIJK = voxelCornersWorld.map((world) => core_1.utilities.transformWorldToIndex(imageData, world));
+        const overlapBounds = (0, getBoundingBoxAroundShape_1.default)(voxelCornersIJK, dimensions);
+        return overlapBounds;
+    };
+    const callback = ({ index, pointIJK, pointLPS }) => {
+        let insert = volumeInfoList.length > 0;
+        for (let i = 0; i < volumeInfoList.length; i++) {
+            if (volumeInfoList[i].volumeSize === scalarData.length) {
+                insert = testRange(volumeInfoList[i], pointIJK);
+            }
+            else {
+                insert = testOverlapRange(volumeInfoList[i], volumeInfoList[baseVolumeIdx].spacing, pointLPS);
+            }
+            if (!insert) {
+                break;
+            }
         }
-        scalarData[index] = 1;
+        if (insert)
+            scalarData[index] = 1;
     };
     (0, utilities_1.pointInShapeCallback)(segmentationImageData, () => true, callback, boundsIJK);
     (0, triggerSegmentationEvents_1.triggerSegmentationDataModified)(segmentationVolume.volumeId);

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

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package/dist/esm/utilities/segmentation/rectangleROIThresholdVolumeByRange.d.ts

@@ -1,9 +1,13 @@
 import type { Types } from '@cornerstonejs/core';
-export declare type ThresholdRangeOptions = {
+export declare type ThresholdInformation = {
+    volume: Types.IImageVolume;
     lower: number;
     upper: number;
+};
+export declare type ThresholdOptions = {
     numSlicesToProject?: number;
     overwrite: boolean;
+    overlapType?: number;
 };
 export declare type AnnotationForThresholding = {
     data: {
@@ -15,5 +19,5 @@ export declare type AnnotationForThresholding = {
         };
     };
 };
-declare function rectangleROIThresholdVolumeByRange(annotationUIDs: string[], segmentationVolume: Types.IImageVolume, referenceVolumes: Types.IImageVolume[], options: ThresholdRangeOptions): Types.IImageVolume;
+declare function rectangleROIThresholdVolumeByRange(annotationUIDs: string[], segmentationVolume: Types.IImageVolume, thresholdVolumeInformation: ThresholdInformation[], options: ThresholdOptions): Types.IImageVolume;
 export default rectangleROIThresholdVolumeByRange;

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

@@ -2,23 +2,19 @@ import { state } from '../../stateManagement/annotation';
 import { RectangleROIStartEndThresholdTool, RectangleROIThresholdTool, } from '../../tools';
 import thresholdVolumeByRange from './thresholdVolumeByRange';
 import getBoundsIJKFromRectangleAnnotations from '../rectangleROITool/getBoundsIJKFromRectangleAnnotations';
-function rectangleROIThresholdVolumeByRange(annotationUIDs, segmentationVolume, referenceVolumes, options) {
-    if (referenceVolumes.length > 1) {
-        throw new Error('thresholding based on more than one reference volumes data is not supported yet');
-    }
-    const referenceVolume = referenceVolumes[0];
+function rectangleROIThresholdVolumeByRange(annotationUIDs, segmentationVolume, thresholdVolumeInformation, options) {
     const annotations = annotationUIDs.map((annotationUID) => {
         return state.getAnnotation(annotationUID);
     });
     _validateAnnotations(annotations);
-    const boundsIJK = getBoundsIJKFromRectangleAnnotations(annotations, referenceVolume, options);
-    const optionsToUse = {
-        lower: options.lower,
-        upper: options.upper,
-        overwrite: options.overwrite,
-        boundsIJK,
-    };
-    const outputSegmentationVolume = thresholdVolumeByRange(segmentationVolume, referenceVolume, optionsToUse);
+    let boundsIJK;
+    for (let i = 0; i < thresholdVolumeInformation.length; i++) {
+        const volumeSize = thresholdVolumeInformation[i].volume.scalarData.length;
+        if (volumeSize === segmentationVolume.scalarData.length || i === 0) {
+            boundsIJK = getBoundsIJKFromRectangleAnnotations(annotations, thresholdVolumeInformation[i].volume, options);
+        }
+    }
+    const outputSegmentationVolume = thresholdVolumeByRange(segmentationVolume, thresholdVolumeInformation, { ...options, boundsIJK });
     return outputSegmentationVolume;
 }
 function _validateAnnotations(annotations) {

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

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

@@ -1,10 +1,14 @@
-import type { Types } from '@cornerstonejs/core';
+import { Types } from '@cornerstonejs/core';
 import { BoundsIJK } from '../../types';
 export declare type ThresholdRangeOptions = {
-    upper: number;
-    lower: number;
-    boundsIJK: BoundsIJK;
     overwrite: boolean;
+    boundsIJK: BoundsIJK;
+    overlapType?: number;
+};
+export declare type ThresholdInformation = {
+    volume: Types.IImageVolume;
+    lower: number;
+    upper: number;
 };
-declare function thresholdVolumeByRange(segmentationVolume: Types.IImageVolume, referenceVolume: Types.IImageVolume, options: ThresholdRangeOptions): Types.IImageVolume;
+declare function thresholdVolumeByRange(segmentationVolume: Types.IImageVolume, thresholdVolumeInformation: ThresholdInformation[], options: ThresholdRangeOptions): Types.IImageVolume;
 export default thresholdVolumeByRange;

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

@@ -1,22 +1,107 @@
+import { utilities as csUtils } from '@cornerstonejs/core';
 import { pointInShapeCallback } from '../../utilities';
 import { triggerSegmentationDataModified } from '../../stateManagement/segmentation/triggerSegmentationEvents';
-function thresholdVolumeByRange(segmentationVolume, referenceVolume, options) {
-    const { scalarData, imageData: segmentationImageData } = segmentationVolume;
-    const { overwrite, boundsIJK, upper, lower } = options;
-    const { imageData } = referenceVolume;
-    const referenceValues = imageData.getPointData().getScalars().getData();
+import getBoundingBoxAroundShape from '../boundingBox/getBoundingBoxAroundShape';
+const equalsCheck = (a, b) => {
+    return JSON.stringify(a) === JSON.stringify(b);
+};
+function thresholdVolumeByRange(segmentationVolume, thresholdVolumeInformation, options) {
+    const { scalarData, spacing: segmentationSpacing, imageData: segmentationImageData, } = segmentationVolume;
+    const { overwrite, boundsIJK } = options;
+    const overlapType = options?.overlapType || 0;
     if (overwrite) {
         for (let i = 0; i < scalarData.length; i++) {
             scalarData[i] = 0;
         }
     }
-    const callback = ({ index, pointIJK }) => {
+    const volumeInfoList = [];
+    let baseVolumeIdx = 0;
+    for (let i = 0; i < thresholdVolumeInformation.length; i++) {
+        const { imageData, spacing, dimensions } = thresholdVolumeInformation[i].volume;
+        const volumeSize = thresholdVolumeInformation[i].volume.scalarData.length;
+        if (volumeSize === scalarData.length &&
+            equalsCheck(spacing, segmentationSpacing)) {
+            baseVolumeIdx = i;
+        }
+        const referenceValues = imageData.getPointData().getScalars().getData();
+        const lower = thresholdVolumeInformation[i].lower;
+        const upper = thresholdVolumeInformation[i].upper;
+        volumeInfoList.push({
+            imageData,
+            referenceValues,
+            lower,
+            upper,
+            spacing,
+            dimensions,
+            volumeSize,
+        });
+    }
+    let overlaps, total, range;
+    const testOverlapRange = (volumeInfo, voxelSpacing, voxelCenter) => {
+        const callbackOverlap = ({ value }) => {
+            total = total + 1;
+            if (value >= range.lower && value <= range.upper) {
+                overlaps = overlaps + 1;
+            }
+        };
+        const { imageData, dimensions, lower, upper } = volumeInfo;
+        const overlapBounds = getVoxelOverlap(imageData, dimensions, voxelSpacing, voxelCenter);
+        total = 0;
+        overlaps = 0;
+        range = { lower, upper };
+        let overlapTest = false;
+        pointInShapeCallback(imageData, () => true, callbackOverlap, overlapBounds);
+        if (overlapType === 0) {
+            overlapTest = overlaps > 0;
+        }
+        else if (overlapType == 1) {
+            overlapTest = overlaps === total;
+        }
+        return overlapTest;
+    };
+    const testRange = (volumeInfo, pointIJK) => {
+        const { imageData, referenceValues, lower, upper } = volumeInfo;
         const offset = imageData.computeOffsetIndex(pointIJK);
         const value = referenceValues[offset];
         if (value <= lower || value >= upper) {
-            return;
+            return false;
+        }
+        else {
+            return true;
+        }
+    };
+    const getVoxelOverlap = (imageData, dimensions, voxelSpacing, voxelCenter) => {
+        const voxelCornersWorld = [];
+        for (let i = 0; i < 2; i++) {
+            for (let j = 0; j < 2; j++) {
+                for (let k = 0; k < 2; k++) {
+                    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;
+                    voxelCornersWorld.push(point);
+                }
+            }
+        }
+        const voxelCornersIJK = voxelCornersWorld.map((world) => csUtils.transformWorldToIndex(imageData, world));
+        const overlapBounds = getBoundingBoxAroundShape(voxelCornersIJK, dimensions);
+        return overlapBounds;
+    };
+    const callback = ({ index, pointIJK, pointLPS }) => {
+        let insert = volumeInfoList.length > 0;
+        for (let i = 0; i < volumeInfoList.length; i++) {
+            if (volumeInfoList[i].volumeSize === scalarData.length) {
+                insert = testRange(volumeInfoList[i], pointIJK);
+            }
+            else {
+                insert = testOverlapRange(volumeInfoList[i], volumeInfoList[baseVolumeIdx].spacing, pointLPS);
+            }
+            if (!insert) {
+                break;
+            }
         }
-        scalarData[index] = 1;
+        if (insert)
+            scalarData[index] = 1;
     };
     pointInShapeCallback(segmentationImageData, () => true, callback, boundsIJK);
     triggerSegmentationDataModified(segmentationVolume.volumeId);

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

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