image-js 1.0.0-alpha.3 → 1.0.0

package/lib/roi/Roi.js

@@ -0,0 +1,553 @@
+import { getConvexHull } from '../maskAnalysis/getConvexHull.js';
+import { getFeret } from '../maskAnalysis/getFeret.js';
+import { getMbr } from '../maskAnalysis/getMbr.js';
+import { getBorderPoints } from './getBorderPoints.js';
+import { getMask } from './getMask.js';
+import { getEllipse } from './properties/getEllipse.js';
+export class Roi {
+    /**
+     * Original map with all the ROI IDs.
+     */
+    map;
+    /**
+     * ID of the ROI. Positive for white ROIs and negative for black ones.
+     */
+    id;
+    /**
+     * Origin of the ROI. The top-left corner of the rectangle around
+     * the ROI relative to the original image.
+     */
+    origin;
+    /**
+     * Width of the ROI.
+     */
+    width;
+    /**
+     * Height of the ROI.
+     */
+    height;
+    /**
+     * Surface of the ROI.
+     */
+    surface;
+    /**
+     * Cached values of properties to improve performance.
+     */
+    #computed;
+    constructor(map, id, width, height, origin, surface) {
+        this.map = map;
+        this.id = id;
+        this.origin = origin;
+        this.width = width;
+        this.height = height;
+        this.surface = surface;
+        this.#computed = {};
+    }
+    /**
+     * 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 ratio between the width and the height of the bounding rectangle of the ROI.
+     * @returns The width by height ratio.
+     */
+    getRatio() {
+        return this.width / this.height;
+    }
+    /**
+     * Generates a mask of an ROI. You can specify the kind of mask you want using the `kind` option.
+     * @param options - Get Mask options.
+     * @returns The ROI mask.
+     */
+    getMask(options) {
+        return getMask(this, options);
+    }
+    /**
+     * Computes the diameter of a circle that has the same perimeter as the particle image.
+     * @returns Ped value in pixels.
+     */
+    get ped() {
+        return this.perimeter / Math.PI;
+    }
+    /**
+     * Return an array with the coordinates of the pixels that are on the border of the ROI.
+     * The points are defined as [column, row].
+     * @param options - Get border points options.
+     * @returns The array of border pixels.
+     */
+    getBorderPoints(options) {
+        return getBorderPoints(this, options);
+    }
+    /**
+     * Returns an array of ROIs IDs that are included in the current ROI.
+     * This will be useful to know if there are some holes in the ROI.
+     * @returns InternalIDs.
+     */
+    get internalIDs() {
+        return this.#getComputed('internalIDs', () => {
+            const internal = [this.id];
+            const roiMap = this.map;
+            const data = roiMap.data;
+            if (this.height > 2) {
+                for (let column = 0; column < this.width; column++) {
+                    const target = this.#computeIndex(0, column);
+                    if (internal.includes(data[target])) {
+                        const id = data[target + roiMap.width];
+                        if (!internal.includes(id) && !this.boxIDs.includes(id)) {
+                            internal.push(id);
+                        }
+                    }
+                }
+            }
+            const array = new Array(4);
+            for (let column = 1; column < this.width - 1; column++) {
+                for (let row = 1; row < this.height - 1; row++) {
+                    const target = this.#computeIndex(row, column);
+                    if (internal.includes(data[target])) {
+                        // We check if one of the neighbor is not yet in.
+                        array[0] = data[target - 1];
+                        array[1] = data[target + 1];
+                        array[2] = data[target - roiMap.width];
+                        array[3] = data[target + roiMap.width];
+                        for (let i = 0; i < 4; i++) {
+                            const id = array[i];
+                            if (!internal.includes(id) && !this.boxIDs.includes(id)) {
+                                internal.push(id);
+                            }
+                        }
+                    }
+                }
+            }
+            return internal;
+        });
+    }
+    /**
+     * Returns an array of ROIs IDs that touch the current ROI.
+     * @returns The array of Borders.
+     */
+    get externalBorders() {
+        return this.#getComputed('externalBorders', () => {
+            // Takes all the borders and removes the internal one ...
+            const borders = this.borders;
+            const externalBorders = [];
+            const externalIDs = [];
+            const internals = this.internalIDs;
+            for (const border of borders) {
+                if (!internals.includes(border.connectedID)) {
+                    const element = {
+                        connectedID: border.connectedID,
+                        length: border.length,
+                    };
+                    externalIDs.push(element.connectedID);
+                    externalBorders.push(element);
+                }
+            }
+            return externalBorders;
+        });
+    }
+    /**
+     * Calculates and caches the number of sides by which each pixel is touched externally.
+     * @returns An object which tells how many pixels are exposed externally to how many sides.
+     */
+    get perimeterInfo() {
+        return this.#getComputed('perimeterInfo', () => {
+            const roiMap = this.map;
+            const data = roiMap.data;
+            let one = 0;
+            let two = 0;
+            let three = 0;
+            let four = 0;
+            const externalIDs = new Set(this.externalBorders.map((element) => element.connectedID));
+            for (let column = 0; column < this.width; column++) {
+                for (let row = 0; row < this.height; row++) {
+                    const target = this.#computeIndex(row, column);
+                    if (data[target] === this.id) {
+                        let nbAround = 0;
+                        if (column === 0) {
+                            nbAround++;
+                        }
+                        else if (externalIDs.has(data[target - 1])) {
+                            nbAround++;
+                        }
+                        if (column === roiMap.width - 1) {
+                            nbAround++;
+                        }
+                        else if (externalIDs.has(data[target + 1])) {
+                            nbAround++;
+                        }
+                        if (row === 0) {
+                            nbAround++;
+                        }
+                        else if (externalIDs.has(data[target - roiMap.width])) {
+                            nbAround++;
+                        }
+                        if (row === roiMap.height - 1) {
+                            nbAround++;
+                        }
+                        else if (externalIDs.has(data[target + roiMap.width])) {
+                            nbAround++;
+                        }
+                        switch (nbAround) {
+                            case 1:
+                                one++;
+                                break;
+                            case 2:
+                                two++;
+                                break;
+                            case 3:
+                                three++;
+                                break;
+                            case 4:
+                                four++;
+                                break;
+                            default:
+                        }
+                    }
+                }
+            }
+            return { one, two, three, four };
+        });
+    }
+    /**
+     * Perimeter of the ROI.
+     * The perimeter is calculated using the sum of all the external borders of the ROI to which we subtract:
+     * (2 - √2) * the number of pixels that have 2 external borders
+     * 2 * (2 - √2) * the number of pixels that have 3 external borders
+     * @returns Perimeter value in pixels.
+     */
+    get perimeter() {
+        const info = this.perimeterInfo;
+        const delta = 2 - Math.sqrt(2);
+        return (info.one +
+            info.two * 2 +
+            info.three * 3 +
+            info.four * 4 -
+            delta * (info.two + info.three * 2 + info.four));
+    }
+    /**
+     * Computes ROI points relative to ROIs point of `origin`.
+     * @returns Array of points with relative ROI coordinates.
+     */
+    get relativePoints() {
+        return this.#getComputed(`relativePoints`, () => {
+            const points = Array.from(this.points(false));
+            return points;
+        });
+    }
+    /**
+     * Computes ROI points relative to Image's/Mask's point of `origin`.
+     * @returns Array of points with absolute ROI coordinates.
+     */
+    get absolutePoints() {
+        return this.#getComputed(`absolutePoints`, () => {
+            const points = Array.from(this.points(true));
+            return points;
+        });
+    }
+    get boxIDs() {
+        return this.#getComputed('boxIDs', () => {
+            const surroundingIDs = new Set(); // Allows to get a unique list without indexOf.
+            const roiMap = this.map;
+            const data = roiMap.data;
+            // We check the first line and the last line.
+            for (const row of [0, this.height - 1]) {
+                for (let column = 0; column < this.width; column++) {
+                    const target = this.#computeIndex(row, column);
+                    if (column - this.origin.column > 0 &&
+                        data[target] === this.id &&
+                        data[target - 1] !== this.id) {
+                        const value = data[target - 1];
+                        surroundingIDs.add(value);
+                    }
+                    if (roiMap.width - column - this.origin.column > 1 &&
+                        data[target] === this.id &&
+                        data[target + 1] !== this.id) {
+                        const value = data[target + 1];
+                        surroundingIDs.add(value);
+                    }
+                }
+            }
+            // We check the first column and the last column.
+            for (const column of [0, this.width - 1]) {
+                for (let row = 0; row < this.height; row++) {
+                    const target = this.#computeIndex(row, column);
+                    if (row - this.origin.row > 0 &&
+                        data[target] === this.id &&
+                        data[target - roiMap.width] !== this.id) {
+                        const value = data[target - roiMap.width];
+                        surroundingIDs.add(value);
+                    }
+                    if (roiMap.height - row - this.origin.row > 1 &&
+                        data[target] === this.id &&
+                        data[target + roiMap.width] !== this.id) {
+                        const value = data[target + roiMap.width];
+                        surroundingIDs.add(value);
+                    }
+                }
+            }
+            return Array.from(surroundingIDs); // The selection takes the whole rectangle.
+        });
+    }
+    /**
+     * Computes the diameter of a circle of equal projection area (EQPC).
+     * It is a diameter of a circle that has the same surface as the ROI.
+     * @returns `eqpc` value in pixels.
+     */
+    get eqpc() {
+        return 2 * Math.sqrt(this.surface / Math.PI);
+    }
+    /**
+     * Computes ellipse of ROI. It is the smallest ellipse that fits the ROI.
+     * @returns Ellipse
+     */
+    get ellipse() {
+        return this.#getComputed('ellipse', () => {
+            return getEllipse(this);
+        });
+    }
+    /**
+     * Number of holes in the ROI and their total surface.
+     * Used to calculate fillRatio.
+     * @returns The surface of holes in ROI in pixels.
+     */
+    get holesInfo() {
+        return this.#getComputed('holesInfo', () => {
+            let surface = 0;
+            const data = this.map.data;
+            for (let column = 1; column < this.width - 1; column++) {
+                for (let row = 1; row < this.height - 1; row++) {
+                    const target = this.#computeIndex(row, column);
+                    if (this.internalIDs.includes(data[target]) &&
+                        data[target] !== this.id) {
+                        surface++;
+                    }
+                }
+            }
+            return {
+                number: this.internalIDs.length - 1,
+                surface,
+            };
+        });
+    }
+    /**
+     * Calculates and caches border's length and their IDs.
+     * @returns Borders' length and their IDs.
+     */
+    get borders() {
+        return this.#getComputed('borders', () => {
+            const roiMap = this.map;
+            const data = roiMap.data;
+            const surroudingIDs = new Set();
+            const surroundingBorders = new Map();
+            const visitedData = new Set();
+            const dx = [1, 0, -1, 0];
+            const dy = [0, 1, 0, -1];
+            for (let column = this.origin.column; column <= this.origin.column + this.width; column++) {
+                for (let row = this.origin.row; row <= this.origin.row + this.height; row++) {
+                    const target = column + row * roiMap.width;
+                    if (data[target] === this.id) {
+                        for (let dir = 0; dir < 4; dir++) {
+                            const newX = column + dx[dir];
+                            const newY = row + dy[dir];
+                            if (newX >= 0 &&
+                                newY >= 0 &&
+                                newX < roiMap.width &&
+                                newY < roiMap.height) {
+                                const neighbour = newX + newY * roiMap.width;
+                                if (data[neighbour] !== this.id &&
+                                    !visitedData.has(neighbour)) {
+                                    visitedData.add(neighbour);
+                                    surroudingIDs.add(data[neighbour]);
+                                    let surroundingBorder = surroundingBorders.get(data[neighbour]);
+                                    if (!surroundingBorder) {
+                                        surroundingBorders.set(data[neighbour], 1);
+                                    }
+                                    else {
+                                        surroundingBorders.set(data[neighbour], ++surroundingBorder);
+                                    }
+                                }
+                            }
+                        }
+                    }
+                }
+            }
+            const id = Array.from(surroudingIDs);
+            return id.map((id) => {
+                return {
+                    connectedID: id,
+                    length: surroundingBorders.get(id),
+                };
+            });
+        });
+    }
+    /**
+     * Computes fill ratio of the ROI. It is calculated by dividing ROI's actual surface over the surface combined with holes, to see how holes affect its surface.
+     * @returns Fill ratio value.
+     */
+    get fillRatio() {
+        return this.surface / (this.surface + this.holesInfo.surface);
+    }
+    /**
+     * Computes sphericity of the ROI.
+     * Sphericity is a measure of the degree to which a particle approximates the shape of a sphere, and is independent of its size. The value is always between 0 and 1. The less spheric the ROI is the smaller is the number.
+     * @returns Sphericity value.
+     */
+    get sphericity() {
+        return (2 * Math.sqrt(this.surface * Math.PI)) / this.perimeter;
+    }
+    /**
+     * Computes the surface of the ROI, including the surface of the holes.
+     * @returns Surface including holes measured in pixels.
+     */
+    get filledSurface() {
+        return this.surface + this.holesInfo.surface;
+    }
+    /**
+     * The solidity describes the extent to which a shape is convex or concave.
+     * The solidity of a completely convex shape is 1, the farther the it deviates from 1, the greater the extent of concavity in the shape of the ROI.
+     * @returns Solidity value.
+     */
+    get solidity() {
+        return this.surface / this.convexHull.surface;
+    }
+    //TODO Should be refactored to not need creating a new Mask.
+    /**
+     *Computes convex hull. It is the smallest convex set that contains it.
+     * @see https://en.wikipedia.org/wiki/Convex_hull
+     * @returns Convex hull.
+     */
+    get convexHull() {
+        return this.#getComputed('convexHull', () => {
+            return getConvexHull(this.getMask());
+        });
+    }
+    /**
+     * Computes the minimum bounding rectangle.
+     * In digital image processing, the bounding box is merely the coordinates of the rectangular border that fully encloses a digital image when it is placed over a page, a canvas, a screen or other similar bidimensional background.
+     * @returns The minimum bounding rectangle.
+     */
+    get mbr() {
+        return this.#getComputed('mbr', () => {
+            return getMbr(this.getMask());
+        });
+    }
+    /*
+    * Computes roundness of ROI.
+    * Roundness is the measure of how closely the shape of an object approaches that of a mathematically perfect circle.
+   (See slide 24 https://static.horiba.com/fileadmin/Horiba/Products/Scientific/Particle_Characterization/Webinars/Slides/TE011.pdf) */
+    get roundness() {
+        return (4 * this.surface) / (Math.PI * this.feret.maxDiameter.length ** 2);
+    }
+    /**
+     * This is not a diameter in its actual sense but the common basis of a group of diameters derived from the distance of two tangents to the contour of the particle in a well-defined orientation.
+     * In simpler words, the method corresponds to the measurement by a slide gauge (slide gauge principle).
+     * In general it is defined as the distance between two parallel tangents of the particle at an arbitrary angle. The minimum Feret diameter is often used as the diameter equivalent to a sieve analysis.
+     * @returns The maximum and minimum Feret Diameters.
+     */
+    get feret() {
+        return this.#getComputed('feret', () => {
+            return getFeret(this.getMask());
+        });
+    }
+    /**
+     * A JSON object with all the data about ROI.
+     * @returns All current ROI properties as one object.
+     */
+    toJSON() {
+        return {
+            id: this.id,
+            origin: this.origin,
+            height: this.height,
+            width: this.width,
+            surface: this.surface,
+            eqpc: this.eqpc,
+            ped: this.ped,
+            feret: this.feret,
+            fillRatio: this.fillRatio,
+            sphericity: this.sphericity,
+            roundness: this.roundness,
+            solidity: this.solidity,
+            perimeter: this.perimeter,
+            convexHull: this.convexHull,
+            mbr: this.mbr,
+            filledSurface: this.filledSurface,
+            centroid: this.centroid,
+        };
+    }
+    /**
+     * Computes a center of mass of the current ROI.
+     * @returns point
+     */
+    get centroid() {
+        return this.#getComputed('centroid', () => {
+            const roiMap = this.map;
+            const data = roiMap.data;
+            let sumColumn = 0;
+            let sumRow = 0;
+            for (let column = 0; column < this.width; column++) {
+                for (let row = 0; row < this.height; row++) {
+                    const target = this.#computeIndex(row, column);
+                    if (data[target] === this.id) {
+                        sumColumn += column;
+                        sumRow += row;
+                    }
+                }
+            }
+            return {
+                column: sumColumn / this.surface + this.origin.column,
+                row: sumRow / this.surface + this.origin.row,
+            };
+        });
+    }
+    //  A helper function to cache already calculated properties.
+    #getComputed(property, callback) {
+        if (this.#computed[property] === undefined) {
+            const result = callback();
+            this.#computed[property] = result;
+            return result;
+        }
+        return this.#computed[property];
+    }
+    //TODO Make this private.
+    /**
+     * Calculates the correct index on the map of ROI.
+     * @param y - Map row
+     * @param x - Map column
+     * @returns Index within the ROI map.
+     */
+    #computeIndex(y, x) {
+        const roiMap = this.map;
+        return (y + this.origin.row) * roiMap.width + x + this.origin.column;
+    }
+    /**
+     * Generator function to calculate point's coordinates.
+     * @param absolute - controls whether coordinates should be relative to ROI's point of `origin` (relative), or relative to ROI's position on the Image/Mask (absolute).
+     * @yields Coordinates of each point of ROI.
+     */
+    *points(absolute) {
+        for (let row = 0; row < this.height; row++) {
+            for (let column = 0; column < this.width; column++) {
+                const target = (row + this.origin.row) * this.map.width +
+                    column +
+                    this.origin.column;
+                if (this.map.data[target] === this.id) {
+                    if (absolute) {
+                        yield {
+                            column: this.origin.column + column,
+                            row: this.origin.row + row,
+                        };
+                    }
+                    else {
+                        yield { column, row };
+                    }
+                }
+            }
+        }
+    }
+}
+//# sourceMappingURL=Roi.js.map

package/lib/roi/Roi.js.map

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

@@ -0,0 +1,59 @@
+import type { Mask } from '../Mask.js';
+import type { Roi } from './Roi.js';
+import type { FromMaskOptions } from './fromMask.js';
+import type { GetRoisOptions } from './getRois.js';
+export interface RoiManager {
+    getRois(options: GetRoisOptions): Roi[];
+}
+export interface RoiMap {
+    /**
+     * Width of the map.
+     */
+    width: number;
+    /**
+     * Height of the map.
+     */
+    height: number;
+    /**
+     * Data of the ROIs. Each ROI is associated with a negative or a positive value,
+     * depending if it derives from a zone made of zeros or ones in the original mask.
+     */
+    data: Int32Array;
+    /**
+     * Number of distinct positive values in the ROI map.
+     *
+     */
+    nbPositive: number;
+    /**
+     * Number of distinct negative values in the ROI map.
+     *
+     */
+    nbNegative: number;
+}
+export declare class RoiMapManager implements RoiManager {
+    private map;
+    whiteRois: Roi[];
+    blackRois: Roi[];
+    constructor(map: RoiMap);
+    /**
+     * Return the ROI map of the RoiMapManager.
+     * @returns - The ROI map.
+     */
+    getMap(): RoiMap;
+    /**
+     * 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: number, row: number): number;
+    /**
+     * Returns the ROI map as a correct width and height matrix.
+     * @returns The ROI map matrix.
+     */
+    getMapMatrix(): number[][];
+    getRois(options?: GetRoisOptions): Roi[];
+    getRoiById(roiID: number): Roi;
+    static fromMask(mask: Mask, options?: FromMaskOptions): RoiMapManager;
+}
+//# sourceMappingURL=RoiMapManager.d.ts.map

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

@@ -0,0 +1 @@
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