image-js 1.0.0-alpha.3 → 1.1.0

package/lib/roi/properties/getEllipse.js

@@ -0,0 +1,96 @@
+import { EigenvalueDecomposition } from 'ml-matrix';
+import { xVariance, xyCovariance } from 'ml-spectra-processing';
+import { getAngle } from '../../maskAnalysis/utils/getAngle.js';
+import { toDegrees } from '../../utils/geometry/angles.js';
+import { assert } from '../../utils/validators/assert.js';
+/**
+ * Calculates ellipse on around ROI.
+ * @param roi - Region of interest.
+ * @returns Ellipse.
+ */
+export function getEllipse(roi) {
+    const xCenter = roi.centroid.column;
+    const yCenter = roi.centroid.row;
+    const xCentered = roi.relativePoints.map((point) => point.column - xCenter);
+    const yCentered = roi.relativePoints.map((point) => point.row - yCenter);
+    const centeredXVariance = xVariance(xCentered, { unbiased: false });
+    const centeredYVariance = xVariance(yCentered, { unbiased: false });
+    const centeredCovariance = xyCovariance({
+        x: xCentered,
+        y: yCentered,
+    }, { unbiased: false });
+    //spectral decomposition of the sample covariance matrix
+    const sampleCovarianceMatrix = [
+        [centeredXVariance, centeredCovariance],
+        [centeredCovariance, centeredYVariance],
+    ];
+    const e = new EigenvalueDecomposition(sampleCovarianceMatrix);
+    const eigenvalues = e.realEigenvalues;
+    const vectors = e.eigenvectorMatrix;
+    assert(eigenvalues[0] <= eigenvalues[1]);
+    let radiusMajor = Math.sqrt(eigenvalues[1]);
+    let radiusMinor = Math.sqrt(eigenvalues[0]);
+    const vectorMajor = vectors.getColumn(1);
+    const vectorMinor = vectors.getColumn(0);
+    let majorAxisPoint1 = {
+        column: xCenter + radiusMajor * vectorMajor[0],
+        row: yCenter + radiusMajor * vectorMajor[1],
+    };
+    let majorAxisPoint2 = {
+        column: xCenter - radiusMajor * vectorMajor[0],
+        row: yCenter - radiusMajor * vectorMajor[1],
+    };
+    let minorAxisPoint1 = {
+        column: xCenter + radiusMinor * vectorMinor[0],
+        row: yCenter + radiusMinor * vectorMinor[1],
+    };
+    let minorAxisPoint2 = {
+        column: xCenter - radiusMinor * vectorMinor[0],
+        row: yCenter - radiusMinor * vectorMinor[1],
+    };
+    let majorLength = Math.hypot(majorAxisPoint1.column - majorAxisPoint2.column, majorAxisPoint1.row - majorAxisPoint2.row);
+    let minorLength = Math.hypot(minorAxisPoint1.column - majorAxisPoint2.column, minorAxisPoint1.row - minorAxisPoint2.row);
+    let ellipseSurface = (((minorLength / 2) * majorLength) / 2) * Math.PI;
+    if (ellipseSurface !== roi.surface) {
+        const scaleFactor = Math.sqrt(roi.surface / ellipseSurface);
+        radiusMajor *= scaleFactor;
+        radiusMinor *= scaleFactor;
+        majorAxisPoint1 = {
+            column: xCenter + radiusMajor * vectorMajor[0],
+            row: yCenter + radiusMajor * vectorMajor[1],
+        };
+        majorAxisPoint2 = {
+            column: xCenter - radiusMajor * vectorMajor[0],
+            row: yCenter - radiusMajor * vectorMajor[1],
+        };
+        minorAxisPoint1 = {
+            column: xCenter + radiusMinor * vectorMinor[0],
+            row: yCenter + radiusMinor * vectorMinor[1],
+        };
+        minorAxisPoint2 = {
+            column: xCenter - radiusMinor * vectorMinor[0],
+            row: yCenter - radiusMinor * vectorMinor[1],
+        };
+        majorLength *= scaleFactor;
+        minorLength *= scaleFactor;
+        ellipseSurface *= scaleFactor ** 2;
+    }
+    return {
+        center: {
+            column: xCenter,
+            row: yCenter,
+        },
+        majorAxis: {
+            points: [majorAxisPoint1, majorAxisPoint2],
+            length: majorLength,
+            angle: toDegrees(getAngle(majorAxisPoint1, majorAxisPoint2)),
+        },
+        minorAxis: {
+            points: [minorAxisPoint1, minorAxisPoint2],
+            length: minorLength,
+            angle: toDegrees(getAngle(minorAxisPoint1, minorAxisPoint2)),
+        },
+        surface: ellipseSurface,
+    };
+}
+//# sourceMappingURL=getEllipse.js.map

package/lib/roi/properties/getEllipse.js.map

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

@@ -0,0 +1,29 @@
+import type { Point } from '../utils/geometry/points.js';
+export interface Ellipse {
+    center: {
+        column: number;
+        row: number;
+    };
+    majorAxis: {
+        points: [Point, Point];
+        length: number;
+        angle: number;
+    };
+    minorAxis: {
+        points: [Point, Point];
+        length: number;
+        angle: number;
+    };
+    surface: number;
+}
+export interface Border {
+    /**
+     * Refers  to the roiID of the contiguous ROI.
+     */
+    connectedID: number;
+    /**
+     * Length of the border with connectedID.
+     */
+    length: number;
+}
+//# sourceMappingURL=roi.types.d.ts.map

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

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

@@ -0,0 +1,2 @@
+export {};
+//# sourceMappingURL=roi.types.js.map

package/lib/roi/roi.types.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"roi.types.js","sourceRoot":"","sources":["../../src/roi/roi.types.ts"],"names":[],"mappings":""}

package/lib/roi/utils/colorMaps/getBinaryMap.d.ts

@@ -0,0 +1,33 @@
+import type { RoiKind } from '../../getRois.js';
+export interface GetBinaryMapOptions {
+    /**
+     * Number of black ROIs.
+     */
+    nbNegative: number;
+    /**
+     * Number of white ID ROIs.
+     */
+    nbPositive: number;
+    /**
+     * Specify which ROIs to color.
+     * @default `'bw'`
+     */
+    roiKind?: RoiKind;
+    /**
+     * Hue of white ROIs.
+     * @default `120`
+     */
+    whiteHue?: number;
+    /**
+     * Hue of black ROIs.
+     * @default `0`
+     */
+    blackHue?: number;
+}
+/**
+ * Return a map where ROIs are red (negative) or green (positive) depending on the ROI index.
+ * @param options - Color maps options.
+ * @returns The colored map.
+ */
+export declare function getBinaryMap(options: GetBinaryMapOptions): Uint32Array;
+//# sourceMappingURL=getBinaryMap.d.ts.map

package/lib/roi/utils/colorMaps/getBinaryMap.d.ts.map

@@ -0,0 +1 @@
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package/lib/roi/utils/colorMaps/getBinaryMap.js

@@ -0,0 +1,27 @@
+import { hsvToRgb } from '../hsvToRgb.js';
+import { rgbToNumber } from '../rgbToNumber.js';
+/**
+ * Return a map where ROIs are red (negative) or green (positive) depending on the ROI index.
+ * @param options - Color maps options.
+ * @returns The colored map.
+ */
+export function getBinaryMap(options) {
+    const { nbNegative, nbPositive, whiteHue = 120, blackHue = 0, roiKind = 'bw', } = options;
+    const colorMap = new Uint32Array(nbNegative + nbPositive + 1);
+    // negative values
+    if (roiKind === 'bw' || roiKind === 'black') {
+        for (let i = -nbNegative; i < 0; i++) {
+            const hsv = [blackHue, 255, 255];
+            colorMap[i + nbNegative] = rgbToNumber(hsvToRgb(hsv));
+        }
+    }
+    if (roiKind === 'bw' || roiKind === 'white') {
+        // positive values
+        for (let i = 1; i <= nbPositive; i++) {
+            const hsv = [whiteHue, 255, 255];
+            colorMap[i + nbNegative] = rgbToNumber(hsvToRgb(hsv));
+        }
+    }
+    return colorMap;
+}
+//# sourceMappingURL=getBinaryMap.js.map

package/lib/roi/utils/colorMaps/getBinaryMap.js.map

@@ -0,0 +1 @@
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package/lib/roi/utils/colorMaps/getRainbowMap.d.ts

@@ -0,0 +1,23 @@
+import type { RoiKind } from '../../getRois.js';
+export interface GetRainbowMapOptions {
+    /**
+     * Number of black ROIs.
+     */
+    nbNegative: number;
+    /**
+     * Number of white ID ROIs.
+     */
+    nbPositive: number;
+    /**
+     * Specify which ROIs to color.
+     * @default `'bw'`
+     */
+    roiKind?: RoiKind;
+}
+/**
+ * Return a map where ROIs are all different hues.
+ * @param options - Get temperature map options.
+ * @returns The colored map.
+ */
+export declare function getRainbowMap(options: GetRainbowMapOptions): Uint32Array;
+//# sourceMappingURL=getRainbowMap.d.ts.map

package/lib/roi/utils/colorMaps/getRainbowMap.d.ts.map

@@ -0,0 +1 @@
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package/lib/roi/utils/colorMaps/getRainbowMap.js

@@ -0,0 +1,37 @@
+import { match } from 'ts-pattern';
+import { hsvToRgb } from '../hsvToRgb.js';
+import { rgbToNumber } from '../rgbToNumber.js';
+/**
+ * Return a map where ROIs are all different hues.
+ * @param options - Get temperature map options.
+ * @returns The colored map.
+ */
+export function getRainbowMap(options) {
+    const { nbNegative, nbPositive, roiKind = 'bw' } = options;
+    const colorMap = new Uint32Array(nbNegative + nbPositive + 1);
+    const hueRange = 360;
+    const step = match(roiKind)
+        .with('bw', () => hueRange / (nbNegative + nbPositive))
+        .with('black', () => hueRange / nbNegative)
+        .with('white', () => hueRange / nbPositive)
+        .exhaustive();
+    // negative values
+    let hue = 0;
+    if (roiKind === 'bw' || roiKind === 'black') {
+        for (let i = -nbNegative; i < 0; i++) {
+            const hsv = [hue, 255, 255];
+            colorMap[i + nbNegative] = rgbToNumber(hsvToRgb(hsv));
+            hue += step;
+        }
+    }
+    // positive values
+    if (roiKind === 'bw' || roiKind === 'white') {
+        for (let i = 1; i <= nbPositive; i++) {
+            const hsv = [hue, 255, 255];
+            colorMap[i + nbNegative] = rgbToNumber(hsvToRgb(hsv));
+            hue += step;
+        }
+    }
+    return colorMap;
+}
+//# sourceMappingURL=getRainbowMap.js.map

package/lib/roi/utils/colorMaps/getRainbowMap.js.map

@@ -0,0 +1 @@
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package/lib/roi/utils/colorMaps/getSaturationMap.d.ts

@@ -0,0 +1,33 @@
+import type { RoiKind } from '../../getRois.js';
+export interface GetSaturationMapOptions {
+    /**
+     * Number of black ROIs.
+     */
+    nbNegative: number;
+    /**
+     * Number of white ID ROIs.
+     */
+    nbPositive: number;
+    /**
+     * Specify which ROIs to color.
+     * @default `'bw'`
+     */
+    roiKind?: RoiKind;
+    /**
+     * Hue of white ROIs.
+     *  @default `0`
+     */
+    whiteHue?: number;
+    /**
+     * Hue of black ROIs.
+     * @default `240`
+     */
+    blackHue?: number;
+}
+/**
+ * Return a map where ROIs are different shades of red (positive) or blue (negative) depending on the ROI index. It it the saturation of the HSV color model that is varied.
+ * @param options - Get temperature map options.
+ * @returns The colored map.
+ */
+export declare function getSaturationMap(options: GetSaturationMapOptions): Uint32Array;
+//# sourceMappingURL=getSaturationMap.d.ts.map

package/lib/roi/utils/colorMaps/getSaturationMap.d.ts.map

@@ -0,0 +1 @@
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package/lib/roi/utils/colorMaps/getSaturationMap.js

@@ -0,0 +1,32 @@
+import { hsvToRgb } from '../hsvToRgb.js';
+import { rgbToNumber } from '../rgbToNumber.js';
+/**
+ * Return a map where ROIs are different shades of red (positive) or blue (negative) depending on the ROI index. It it the saturation of the HSV color model that is varied.
+ * @param options - Get temperature map options.
+ * @returns The colored map.
+ */
+export function getSaturationMap(options) {
+    const { nbNegative, nbPositive, roiKind = 'bw', whiteHue = 0, blackHue = 240, } = options;
+    const colorMap = new Uint32Array(nbNegative + nbPositive + 1);
+    const range = 255 - 63; // saturation range for good contrast
+    const negativeStep = range / nbNegative;
+    const positiveStep = range / nbPositive;
+    // negative values
+    let counter = 0;
+    if (roiKind === 'bw' || roiKind === 'black') {
+        for (let i = -nbNegative; i < 0; i++) {
+            const hsv = [blackHue, 255 - counter++ * negativeStep, 255];
+            colorMap[i + nbNegative] = rgbToNumber(hsvToRgb(hsv));
+        }
+    }
+    // positive values
+    counter = 0;
+    if (roiKind === 'bw' || roiKind === 'white') {
+        for (let i = 1; i <= nbPositive; i++) {
+            const hsv = [whiteHue, 255 - counter++ * positiveStep, 255];
+            colorMap[i + nbNegative] = rgbToNumber(hsvToRgb(hsv));
+        }
+    }
+    return colorMap;
+}
+//# sourceMappingURL=getSaturationMap.js.map

package/lib/roi/utils/colorMaps/getSaturationMap.js.map

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

@@ -0,0 +1,29 @@
+import type { RoisColorMode } from '../colorRois.js';
+import type { RoiKind } from '../getRois.js';
+export interface GetColorMapOptions {
+    /**
+     * Number of black ROIs.
+     */
+    nbNegative: number;
+    /**
+     * Number of white ID ROIs.
+     */
+    nbPositive: number;
+    /**
+     * Specify the mode: what colors to use in the color map.
+     * @default `'binary'`
+     */
+    mode?: RoisColorMode;
+    /**
+     * Specify which ROIs to color.
+     * @default `'bw'`
+     */
+    roiKind?: RoiKind;
+}
+/**
+ * Return a map of 32 bits integers corresponding to the colors of each ROI.
+ * @param options - Get color map options.
+ * @returns The color map.
+ */
+export declare function getColorMap(options: GetColorMapOptions): Uint32Array;
+//# sourceMappingURL=getColorMap.d.ts.map

package/lib/roi/utils/getColorMap.d.ts.map

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

@@ -0,0 +1,19 @@
+import { match } from 'ts-pattern';
+import { getBinaryMap } from './colorMaps/getBinaryMap.js';
+import { getRainbowMap } from './colorMaps/getRainbowMap.js';
+import { getSaturationMap } from './colorMaps/getSaturationMap.js';
+/**
+ * Return a map of 32 bits integers corresponding to the colors of each ROI.
+ * @param options - Get color map options.
+ * @returns The color map.
+ */
+export function getColorMap(options) {
+    const { mode = 'binary' } = options;
+    options = { roiKind: 'bw', ...options };
+    return match(mode)
+        .with('binary', () => getBinaryMap(options))
+        .with('saturation', () => getSaturationMap(options))
+        .with('rainbow', () => getRainbowMap(options))
+        .exhaustive();
+}
+//# sourceMappingURL=getColorMap.js.map

package/lib/roi/utils/getColorMap.js.map

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

@@ -0,0 +1,20 @@
+export interface HsvColor {
+    h: number;
+    s: number;
+    v: number;
+}
+export interface RgbColor {
+    r: number;
+    g: number;
+    b: number;
+}
+/**
+ * Convert HSV (hue, saturation, value) color code to RGB.
+ * - Hue: angle in the color wheel (from red to purple), in range 0-359.
+ * - Saturation: how strong the color is (from white to bright color), in range 0-255.
+ * - Value: basically the brightness (from black to intense color), in range 0-255.
+ * @param hsv - The HSV color.
+ * @returns The RGB color.
+ */
+export declare function hsvToRgb(hsv: number[]): Uint8Array;
+//# sourceMappingURL=hsvToRgb.d.ts.map

package/lib/roi/utils/hsvToRgb.d.ts.map

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

@@ -0,0 +1,53 @@
+/**
+ * Convert HSV (hue, saturation, value) color code to RGB.
+ * - Hue: angle in the color wheel (from red to purple), in range 0-359.
+ * - Saturation: how strong the color is (from white to bright color), in range 0-255.
+ * - Value: basically the brightness (from black to intense color), in range 0-255.
+ * @param hsv - The HSV color.
+ * @returns The RGB color.
+ */
+export function hsvToRgb(hsv) {
+    const h = hsv[0];
+    const s = hsv[1] / 255;
+    const v = hsv[2] / 255;
+    const C = s * v;
+    const X = C * (1 - Math.abs(((h / 60) % 2) - 1));
+    const m = v - C;
+    let r, g, b;
+    if (h >= 0 && h < 60) {
+        r = C;
+        g = X;
+        b = 0;
+    }
+    else if (h >= 60 && h < 120) {
+        r = X;
+        g = C;
+        b = 0;
+    }
+    else if (h >= 120 && h < 180) {
+        r = 0;
+        g = C;
+        b = X;
+    }
+    else if (h >= 180 && h < 240) {
+        r = 0;
+        g = X;
+        b = C;
+    }
+    else if (h >= 240 && h < 300) {
+        r = X;
+        g = 0;
+        b = C;
+    }
+    else {
+        r = C;
+        g = 0;
+        b = X;
+    }
+    const rgb = new Uint8Array(3);
+    rgb[0] = (r + m) * 255;
+    rgb[1] = (g + m) * 255;
+    rgb[2] = (b + m) * 255;
+    return rgb;
+}
+//# sourceMappingURL=hsvToRgb.js.map

package/lib/roi/utils/hsvToRgb.js.map

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

@@ -0,0 +1,7 @@
+/**
+ * Convert RGB array to 32 bits number where alpha is set to 255.
+ * @param rgb - The RGB color array.
+ * @returns 32 bits number encoding RGBA color.
+ */
+export declare function rgbToNumber(rgb: Uint8Array): number;
+//# sourceMappingURL=rgbToNumber.d.ts.map

package/lib/roi/utils/rgbToNumber.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"rgbToNumber.d.ts","sourceRoot":"","sources":["../../../src/roi/utils/rgbToNumber.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AACH,wBAAgB,WAAW,CAAC,GAAG,EAAE,UAAU,GAAG,MAAM,CAEnD"}

package/lib/roi/utils/rgbToNumber.js

@@ -0,0 +1,9 @@
+/**
+ * Convert RGB array to 32 bits number where alpha is set to 255.
+ * @param rgb - The RGB color array.
+ * @returns 32 bits number encoding RGBA color.
+ */
+export function rgbToNumber(rgb) {
+    return 0xff000000 + (rgb[2] << 16) + (rgb[1] << 8) + rgb[0];
+}
+//# sourceMappingURL=rgbToNumber.js.map

package/lib/roi/utils/rgbToNumber.js.map

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

@@ -0,0 +1,36 @@
+import type { Image } from '../Image.js';
+import type { Mask } from '../Mask.js';
+import type { Point } from '../geometry/index.js';
+import { RoiMapManager } from './RoiMapManager.js';
+export interface WaterShedOptions {
+    /**
+     * @param points - Points which should be filled by watershed filter.
+     * @default - minimum points from getExtrema() function.
+     */
+    points?: Point[];
+    /**
+     * @param mask - A binary image, the same size as the image. The algorithm will fill only if the current pixel in the binary mask is not null.
+     * @default undefined
+     */
+    mask?: Mask;
+    /**
+     * @param threshold - Limit of filling. Maximum value that pixel can have.
+     * @default 1
+     */
+    threshold?: number;
+}
+/**
+ * This method allows to create a ROIMap using the water shed algorithm. By default this algorithm
+ * will fill the holes and therefore the lowest value of the image (black zones).
+ * If no points are given, the function will look for all the minimal points.
+ * If no mask is given the algorithm will completely fill the image.
+ * Please take care about the value that has be in the mask ! In order to be coherent with the expected mask,
+ * meaning that if it is a dark zone, the mask will be dark the normal behavior to fill a zone
+ * is that the mask pixel is clear (value of 0) !
+ * If you are looking for 'maxima' the image must be inverted before applying the algorithm
+ * @param image - Image that the filter will be applied to.
+ * @param options - WaterShedOptions
+ * @returns RoiMapManager
+ */
+export declare function waterShed(image: Image, options: WaterShedOptions): RoiMapManager;
+//# sourceMappingURL=waterShed.d.ts.map

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

@@ -0,0 +1 @@
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