image-js 1.0.0-alpha.3 → 1.1.0

package/lib/roi/RoiMapManager.js

@@ -0,0 +1,51 @@
+import { Matrix } from 'ml-matrix';
+import { fromMask } from './fromMask.js';
+import { getRois } from './getRois.js';
+export class RoiMapManager {
+    map;
+    whiteRois;
+    blackRois;
+    constructor(map) {
+        this.map = map;
+        this.whiteRois = [];
+        this.blackRois = [];
+    }
+    /**
+     * Return the ROI map of the RoiMapManager.
+     * @returns - The ROI map.
+     */
+    getMap() {
+        return this.map;
+    }
+    /**
+     * Return the value at the given coordinates in an ROI map.
+     * @param column - Column of the value.
+     * @param row - Row of the value.
+     * @returns The value at the given coordinates.
+     */
+    getMapValue(column, row) {
+        return this.map.data[this.map.width * row + column];
+    }
+    /**
+     * Returns the ROI map as a correct width and height matrix.
+     * @returns The ROI map matrix.
+     */
+    getMapMatrix() {
+        return Matrix.from1DArray(this.map.height, this.map.width, this.map.data).to2DArray();
+    }
+    getRois(options = {}) {
+        return getRois(this, options);
+    }
+    getRoiById(roiID) {
+        const rois = this.getRois({ kind: 'bw' });
+        const foundRoi = rois.find((roi) => roi.id === roiID);
+        if (!foundRoi) {
+            throw new Error(`invalid ID: ${roiID}`);
+        }
+        return foundRoi;
+    }
+    static fromMask(mask, options = {}) {
+        return fromMask(mask, options);
+    }
+}
+//# sourceMappingURL=RoiMapManager.js.map

package/lib/roi/RoiMapManager.js.map

@@ -0,0 +1 @@
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package/lib/roi/colorRois.d.ts

@@ -0,0 +1,38 @@
+import { Image } from '../Image.js';
+import type { RoiMapManager } from './RoiMapManager.js';
+import type { RoiKind } from './getRois.js';
+export declare const RoisColorMode: {
+    /**
+     * Only two acceptable values: red or green.
+     */
+    readonly BINARY: "binary";
+    /**
+     * Palette of reds and blues.
+     */
+    readonly SATURATION: "saturation";
+    /**
+     * All possible hues (gradient of colors).
+     */
+    readonly RAINBOW: "rainbow";
+};
+export type RoisColorMode = (typeof RoisColorMode)[keyof typeof RoisColorMode];
+export interface ColorRoisOptions {
+    /**
+     * Define the color mode to use to color the ROIs.
+     * @default `'binary'`
+     */
+    mode?: RoisColorMode;
+    /**
+     * Specify which ROIs to color.
+     * @default `'bw'`
+     */
+    roiKind?: RoiKind;
+}
+/**
+ * Generate an image with all the ROIs of various colors.
+ * @param roiMapManager - The ROI map manager.
+ * @param options - Color ROIs options.
+ * @returns The colored image.
+ */
+export declare function colorRois(roiMapManager: RoiMapManager, options?: ColorRoisOptions): Image;
+//# sourceMappingURL=colorRois.d.ts.map

package/lib/roi/colorRois.d.ts.map

@@ -0,0 +1 @@
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package/lib/roi/colorRois.js

@@ -0,0 +1,41 @@
+import { Image } from '../Image.js';
+import { getColorMap } from './utils/getColorMap.js';
+export const RoisColorMode = {
+    /**
+     * Only two acceptable values: red or green.
+     */
+    BINARY: 'binary',
+    /**
+     * Palette of reds and blues.
+     */
+    SATURATION: 'saturation',
+    /**
+     * All possible hues (gradient of colors).
+     */
+    RAINBOW: 'rainbow',
+};
+/**
+ * Generate an image with all the ROIs of various colors.
+ * @param roiMapManager - The ROI map manager.
+ * @param options - Color ROIs options.
+ * @returns The colored image.
+ */
+export function colorRois(roiMapManager, options = {}) {
+    const { roiKind = 'bw', mode = 'binary' } = options;
+    const map = roiMapManager.getMap();
+    const image = new Image(map.width, map.height, {
+        colorModel: 'RGBA',
+    });
+    const colorMap = getColorMap({
+        roiKind,
+        mode,
+        nbNegative: map.nbNegative,
+        nbPositive: map.nbPositive,
+    });
+    const data32 = new Uint32Array(image.getRawImage().data.buffer);
+    for (let index = 0; index < image.size; index++) {
+        data32[index] = colorMap[map.data[index] + map.nbNegative];
+    }
+    return image;
+}
+//# sourceMappingURL=colorRois.js.map

package/lib/roi/colorRois.js.map

@@ -0,0 +1 @@
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package/lib/roi/computeRois.d.ts

@@ -0,0 +1,7 @@
+import type { RoiMapManager } from './RoiMapManager.js';
+/**
+ * Generate an array of ROIs based on an ROI map manager.
+ * @param roiMapManager - Roi map manager to use.
+ */
+export declare function computeRois(roiMapManager: RoiMapManager): void;
+//# sourceMappingURL=computeRois.d.ts.map

package/lib/roi/computeRois.d.ts.map

@@ -0,0 +1 @@
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package/lib/roi/computeRois.js

@@ -0,0 +1,81 @@
+import { Roi } from './Roi.js';
+/**
+ * Generate an array of ROIs based on an ROI map manager.
+ * @param roiMapManager - Roi map manager to use.
+ */
+export function computeRois(roiMapManager) {
+    const map = roiMapManager.getMap();
+    const whites = new Array(map.nbPositive);
+    const blacks = new Array(map.nbNegative);
+    for (let i = 0; i < map.nbPositive; i++) {
+        whites[i] = {
+            minRow: map.height,
+            minColumn: map.width,
+            maxRow: -1,
+            maxColumn: -1,
+            surface: 0,
+            id: i + 1,
+        };
+    }
+    for (let i = 0; i < map.nbNegative; i++) {
+        blacks[i] = {
+            borderLengths: [],
+            borderIDs: [],
+            minRow: map.height,
+            minColumn: map.width,
+            maxRow: -1,
+            maxColumn: -1,
+            surface: 0,
+            id: -i - 1,
+        };
+    }
+    for (let row = 0; row < map.height; row++) {
+        for (let column = 0; column < map.width; column++) {
+            const currentIndex = roiMapManager.getMapValue(column, row);
+            if (currentIndex === 0) {
+                continue;
+            }
+            let currentRoi;
+            if (currentIndex < 0) {
+                currentRoi = blacks[-currentIndex - 1];
+            }
+            else {
+                currentRoi = whites[currentIndex - 1];
+            }
+            currentRoi.surface++;
+            if (row < currentRoi.minRow) {
+                currentRoi.minRow = row;
+            }
+            if (row > currentRoi.maxRow) {
+                currentRoi.maxRow = row;
+            }
+            if (column < currentRoi.minColumn) {
+                currentRoi.minColumn = column;
+            }
+            if (column > currentRoi.maxColumn) {
+                currentRoi.maxColumn = column;
+            }
+        }
+    }
+    roiMapManager.whiteRois = new Array(map.nbPositive);
+    roiMapManager.blackRois = new Array(map.nbNegative);
+    for (let i = 0; i < map.nbNegative; i++) {
+        const width = blacks[i].maxColumn - blacks[i].minColumn + 1;
+        const height = blacks[i].maxRow - blacks[i].minRow + 1;
+        const origin = { row: blacks[i].minRow, column: blacks[i].minColumn };
+        const id = blacks[i].id;
+        const surface = blacks[i].surface;
+        const blackRoi = new Roi(map, id, width, height, origin, surface);
+        roiMapManager.blackRois[i] = blackRoi;
+    }
+    for (let i = 0; i < map.nbPositive; i++) {
+        const width = whites[i].maxColumn - whites[i].minColumn + 1;
+        const height = whites[i].maxRow - whites[i].minRow + 1;
+        const origin = { row: whites[i].minRow, column: whites[i].minColumn };
+        const id = whites[i].id;
+        const surface = whites[i].surface;
+        const whiteRoi = new Roi(map, id, width, height, origin, surface);
+        roiMapManager.whiteRois[i] = whiteRoi;
+    }
+}
+//# sourceMappingURL=computeRois.js.map

package/lib/roi/computeRois.js.map

@@ -0,0 +1 @@
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package/lib/roi/fromMask.d.ts

@@ -0,0 +1,17 @@
+import type { Mask } from '../Mask.js';
+import { RoiMapManager } from './RoiMapManager.js';
+export interface FromMaskOptions {
+    /**
+     * Consider pixels connected by corners as same ROI?
+     * @default `false`
+     */
+    allowCorners?: boolean;
+}
+/**
+ * Extract the ROIs of an image.
+ * @param mask - Mask to extract the ROIs from.
+ * @param options - From mask options.
+ * @returns The corresponding ROI manager.
+ */
+export declare function fromMask(mask: Mask, options?: FromMaskOptions): RoiMapManager;
+//# sourceMappingURL=fromMask.d.ts.map

package/lib/roi/fromMask.d.ts.map

@@ -0,0 +1 @@
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package/lib/roi/fromMask.js

@@ -0,0 +1,139 @@
+import { assert } from '../utils/validators/assert.js';
+import { RoiMapManager } from './RoiMapManager.js';
+/**
+ * Extract the ROIs of an image.
+ * @param mask - Mask to extract the ROIs from.
+ * @param options - From mask options.
+ * @returns The corresponding ROI manager.
+ */
+export function fromMask(mask, options = {}) {
+    const { allowCorners = false } = options;
+    const MAX_TODO_ARRAY_FILTER = 65535; // 65535 should be enough for most of the cases
+    const MAX_POSITIVE_ID = 2 ** 31 - 1;
+    const MAX_NEGATIVE_ID = -(2 ** 31 - 1);
+    // based on a binary image we will create plenty of small images
+    const data = new Int32Array(mask.size); // maxValue: maxPositiveId, minValue: maxNegativeId
+    // split will always return an array of images
+    let positiveId = 0;
+    let negativeId = 0;
+    const columnToProcess = new Uint16Array(MAX_TODO_ARRAY_FILTER + 1);
+    const rowToProcess = new Uint16Array(MAX_TODO_ARRAY_FILTER + 1);
+    for (let column = 0; column < mask.width; column++) {
+        for (let row = 0; row < mask.height; row++) {
+            if (data[row * mask.width + column] === 0) {
+                // need to process the whole surface
+                analyseSurface(column, row);
+            }
+        }
+    }
+    // x column
+    // y row
+    function analyseSurface(column, row) {
+        let from = 0;
+        let to = 0;
+        const targetState = mask.getBit(column, row);
+        const id = targetState ? ++positiveId : --negativeId;
+        assert(positiveId <= MAX_POSITIVE_ID && negativeId >= MAX_NEGATIVE_ID, 'too many regions of interest');
+        columnToProcess[0] = column;
+        rowToProcess[0] = row;
+        while (from <= to) {
+            const currentColumn = columnToProcess[from & MAX_TODO_ARRAY_FILTER];
+            const currentRow = rowToProcess[from & MAX_TODO_ARRAY_FILTER];
+            data[currentRow * mask.width + currentColumn] = id;
+            // need to check all around mask pixel
+            if (currentColumn > 0 &&
+                data[currentRow * mask.width + currentColumn - 1] === 0 &&
+                mask.getBit(currentColumn - 1, currentRow) === targetState) {
+                // LEFT
+                to++;
+                columnToProcess[to & MAX_TODO_ARRAY_FILTER] = currentColumn - 1;
+                rowToProcess[to & MAX_TODO_ARRAY_FILTER] = currentRow;
+                data[currentRow * mask.width + currentColumn - 1] = MAX_NEGATIVE_ID;
+            }
+            if (currentRow > 0 &&
+                data[(currentRow - 1) * mask.width + currentColumn] === 0 &&
+                mask.getBit(currentColumn, currentRow - 1) === targetState) {
+                // TOP
+                to++;
+                columnToProcess[to & MAX_TODO_ARRAY_FILTER] = currentColumn;
+                rowToProcess[to & MAX_TODO_ARRAY_FILTER] = currentRow - 1;
+                data[(currentRow - 1) * mask.width + currentColumn] = MAX_NEGATIVE_ID;
+            }
+            if (currentColumn < mask.width - 1 &&
+                data[currentRow * mask.width + currentColumn + 1] === 0 &&
+                mask.getBit(currentColumn + 1, currentRow) === targetState) {
+                // RIGHT
+                to++;
+                columnToProcess[to & MAX_TODO_ARRAY_FILTER] = currentColumn + 1;
+                rowToProcess[to & MAX_TODO_ARRAY_FILTER] = currentRow;
+                data[currentRow * mask.width + currentColumn + 1] = MAX_NEGATIVE_ID;
+            }
+            if (currentRow < mask.height - 1 &&
+                data[(currentRow + 1) * mask.width + currentColumn] === 0 &&
+                mask.getBit(currentColumn, currentRow + 1) === targetState) {
+                // BOTTOM
+                to++;
+                columnToProcess[to & MAX_TODO_ARRAY_FILTER] = currentColumn;
+                rowToProcess[to & MAX_TODO_ARRAY_FILTER] = currentRow + 1;
+                data[(currentRow + 1) * mask.width + currentColumn] = MAX_NEGATIVE_ID;
+            }
+            if (allowCorners) {
+                if (currentColumn > 0 &&
+                    currentRow > 0 &&
+                    data[(currentRow - 1) * mask.width + currentColumn - 1] === 0 &&
+                    mask.getBit(currentColumn - 1, currentRow - 1) === targetState) {
+                    // TOP LEFT
+                    to++;
+                    columnToProcess[to & MAX_TODO_ARRAY_FILTER] = currentColumn - 1;
+                    rowToProcess[to & MAX_TODO_ARRAY_FILTER] = currentRow - 1;
+                    data[(currentRow - 1) * mask.width + currentColumn - 1] =
+                        MAX_NEGATIVE_ID;
+                }
+                if (currentColumn < mask.width - 1 &&
+                    currentRow > 0 &&
+                    data[(currentRow - 1) * mask.width + currentColumn + 1] === 0 &&
+                    mask.getBit(currentColumn + 1, currentRow - 1) === targetState) {
+                    // TOP RIGHT
+                    to++;
+                    columnToProcess[to & MAX_TODO_ARRAY_FILTER] = currentColumn + 1;
+                    rowToProcess[to & MAX_TODO_ARRAY_FILTER] = currentRow - 1;
+                    data[(currentRow - 1) * mask.width + currentColumn + 1] =
+                        MAX_NEGATIVE_ID;
+                }
+                if (currentColumn > 0 &&
+                    currentRow < mask.height - 1 &&
+                    data[(currentRow + 1) * mask.width + currentColumn - 1] === 0 &&
+                    mask.getBit(currentColumn - 1, currentRow + 1) === targetState) {
+                    // BOTTOM LEFT
+                    to++;
+                    columnToProcess[to & MAX_TODO_ARRAY_FILTER] = currentColumn - 1;
+                    rowToProcess[to & MAX_TODO_ARRAY_FILTER] = currentRow + 1;
+                    data[(currentRow + 1) * mask.width + currentColumn - 1] =
+                        MAX_NEGATIVE_ID;
+                }
+                if (currentColumn < mask.width - 1 &&
+                    currentRow < mask.height - 1 &&
+                    data[(currentRow + 1) * mask.width + currentColumn + 1] === 0 &&
+                    mask.getBit(currentColumn + 1, currentRow + 1) === targetState) {
+                    // BOTTOM RIGHT
+                    to++;
+                    columnToProcess[to & MAX_TODO_ARRAY_FILTER] = currentColumn + 1;
+                    rowToProcess[to & MAX_TODO_ARRAY_FILTER] = currentRow + 1;
+                    data[(currentRow + 1) * mask.width + currentColumn + 1] =
+                        MAX_NEGATIVE_ID;
+                }
+            }
+            from++;
+            assert(to - from <= MAX_TODO_ARRAY_FILTER, 'fromMask can not finish, the array to manage internal data is not big enough.' +
+                'You could improve mask by changing MAX_ARRAY');
+        }
+    }
+    return new RoiMapManager({
+        width: mask.width,
+        height: mask.height,
+        data,
+        nbNegative: Math.abs(negativeId),
+        nbPositive: positiveId,
+    });
+}
+//# sourceMappingURL=fromMask.js.map

package/lib/roi/fromMask.js.map

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package/lib/roi/getBorderPoints.d.ts

@@ -0,0 +1,12 @@
+import type { GetBorderPointsOptions } from '../maskAnalysis/index.js';
+import type { Point } from '../utils/geometry/points.js';
+import type { Roi } from './Roi.js';
+/**
+ * Return an array with the coordinates of the pixels that are on the border of the ROI.
+ * The reference is the top-left corner of the ROI.
+ * @param roi - ROI to process.
+ * @param options - Get border points options.
+ * @returns The array of border pixels.
+ */
+export declare function getBorderPoints(roi: Roi, options?: GetBorderPointsOptions): Point[];
+//# sourceMappingURL=getBorderPoints.d.ts.map

package/lib/roi/getBorderPoints.d.ts.map

@@ -0,0 +1 @@
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package/lib/roi/getBorderPoints.js

@@ -0,0 +1,12 @@
+/**
+ * Return an array with the coordinates of the pixels that are on the border of the ROI.
+ * The reference is the top-left corner of the ROI.
+ * @param roi - ROI to process.
+ * @param options - Get border points options.
+ * @returns The array of border pixels.
+ */
+export function getBorderPoints(roi, options = {}) {
+    const mask = roi.getMask();
+    return mask.getBorderPoints(options);
+}
+//# sourceMappingURL=getBorderPoints.js.map

package/lib/roi/getBorderPoints.js.map

@@ -0,0 +1 @@
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package/lib/roi/getMask.d.ts

@@ -0,0 +1,17 @@
+import { Mask } from '../Mask.js';
+import type { Roi } from './Roi.js';
+export interface GetMaskOptions {
+    /**
+     * Should the ROI holes be filled in the resulting mask?
+     * @default `false`
+     */
+    solidFill?: boolean;
+}
+/**
+ * Generate a mask of an ROI.
+ * @param roi - The ROI to generate a mask for.
+ * @param options - Get mask options.
+ * @returns The ROI mask.
+ */
+export declare function getMask(roi: Roi, options?: GetMaskOptions): Mask;
+//# sourceMappingURL=getMask.d.ts.map

package/lib/roi/getMask.d.ts.map

@@ -0,0 +1 @@
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package/lib/roi/getMask.js

@@ -0,0 +1,27 @@
+import { Mask } from '../Mask.js';
+/**
+ * Generate a mask of an ROI.
+ * @param roi - The ROI to generate a mask for.
+ * @param options - Get mask options.
+ * @returns The ROI mask.
+ */
+export function getMask(roi, options = {}) {
+    const { solidFill = false } = options;
+    const mask = new Mask(roi.width, roi.height, { origin: roi.origin });
+    for (let row = 0; row < roi.height; row++) {
+        for (let column = 0; column < roi.width; column++) {
+            if (roi.getMapValue(roi.origin.column + column, roi.origin.row + row) ===
+                roi.id) {
+                mask.setBit(column, row, 1);
+            }
+            else {
+                mask.setBit(column, row, 0);
+            }
+        }
+    }
+    if (solidFill) {
+        mask.solidFill({ out: mask });
+    }
+    return mask;
+}
+//# sourceMappingURL=getMask.js.map

package/lib/roi/getMask.js.map

@@ -0,0 +1 @@
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package/lib/roi/getRois.d.ts

@@ -0,0 +1,33 @@
+import type { Roi } from './Roi.js';
+import type { RoiMapManager } from './RoiMapManager.js';
+export declare const RoiKind: {
+    readonly BLACK: "black";
+    readonly WHITE: "white";
+    readonly BW: "bw";
+};
+export type RoiKind = (typeof RoiKind)[keyof typeof RoiKind];
+export interface GetRoisOptions {
+    /**
+     * Minimal surface of the ROIs to keep.
+     * @default `0`
+     */
+    minSurface?: number;
+    /**
+     * Maximal surface of the ROIs to keep.
+     * @default `Number.MAX_SAFE_INTEGER`
+     */
+    maxSurface?: number;
+    /**
+     * Kind of ROIs to keep.
+     * @default `'white'`
+     */
+    kind?: RoiKind;
+}
+/**
+ * Return an array of ROIs matching the options.
+ * @param roiMapManager - The ROI map manager containing the ROIs.
+ * @param options - Get ROIs options.
+ * @returns The array of ROIs.
+ */
+export declare function getRois(roiMapManager: RoiMapManager, options?: GetRoisOptions): Roi[];
+//# sourceMappingURL=getRois.d.ts.map

package/lib/roi/getRois.d.ts.map

@@ -0,0 +1 @@
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package/lib/roi/getRois.js

@@ -0,0 +1,27 @@
+import { match } from 'ts-pattern';
+import { computeRois } from './computeRois.js';
+export const RoiKind = {
+    BLACK: 'black',
+    WHITE: 'white',
+    BW: 'bw',
+};
+/**
+ * Return an array of ROIs matching the options.
+ * @param roiMapManager - The ROI map manager containing the ROIs.
+ * @param options - Get ROIs options.
+ * @returns The array of ROIs.
+ */
+export function getRois(roiMapManager, options = {}) {
+    const { minSurface = 0, maxSurface = Number.MAX_SAFE_INTEGER, kind = 'white', } = options;
+    if (roiMapManager.blackRois.length === 0 &&
+        roiMapManager.whiteRois.length === 0) {
+        computeRois(roiMapManager);
+    }
+    const rois = match(kind)
+        .with('black', () => roiMapManager.blackRois)
+        .with('white', () => roiMapManager.whiteRois)
+        .with('bw', () => [...roiMapManager.whiteRois, ...roiMapManager.blackRois])
+        .exhaustive();
+    return rois.filter((roi) => roi.surface >= minSurface && roi.surface <= maxSurface);
+}
+//# sourceMappingURL=getRois.js.map

package/lib/roi/getRois.js.map

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package/lib/roi/index.d.ts

@@ -0,0 +1,11 @@
+export * from './colorRois.js';
+export * from './computeRois.js';
+export * from './fromMask.js';
+export * from './getBorderPoints.js';
+export * from './getMask.js';
+export * from './getRois.js';
+export * from './Roi.js';
+export * from './RoiMapManager.js';
+export * from './waterShed.js';
+export * from './roi.types.js';
+//# sourceMappingURL=index.d.ts.map

package/lib/roi/index.d.ts.map

@@ -0,0 +1 @@
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package/lib/roi/index.js

@@ -0,0 +1,11 @@
+export * from './colorRois.js';
+export * from './computeRois.js';
+export * from './fromMask.js';
+export * from './getBorderPoints.js';
+export * from './getMask.js';
+export * from './getRois.js';
+export * from './Roi.js';
+export * from './RoiMapManager.js';
+export * from './waterShed.js';
+export * from './roi.types.js';
+//# sourceMappingURL=index.js.map

package/lib/roi/index.js.map

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package/lib/roi/properties/getEllipse.d.ts

@@ -0,0 +1,9 @@
+import type { Roi } from '../Roi.js';
+import type { Ellipse } from '../roi.types.js';
+/**
+ * Calculates ellipse on around ROI.
+ * @param roi - Region of interest.
+ * @returns Ellipse.
+ */
+export declare function getEllipse(roi: Roi): Ellipse;
+//# sourceMappingURL=getEllipse.d.ts.map

package/lib/roi/properties/getEllipse.d.ts.map

@@ -0,0 +1 @@
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