image-js 0.0.0-next-e30968a2d8

package/lib-esm/roi/RoiManager.d.ts

@@ -0,0 +1,32 @@
+export declare enum RoiKind {
+    BLACK = "BLACK",
+    WHITE = "WHITE",
+    BW = "BW"
+}
+export interface GetRoisOptions {
+    /**
+     * Minimal surface of the ROIs to keep
+     *
+     * @default 0
+     */
+    minSurface?: number;
+    /**
+     * Maximal surface of the ROIs to keep
+     *
+     * @default Number.POSITIVE_INFINITY
+     */
+    maxSurface?: number;
+    /**
+     * Kind of ROIs to keep
+     *
+     * @default 'BW'
+     */
+    kind?: RoiKind;
+}
+export interface Roi {
+    getSurface(): number;
+}
+export interface RoiManager {
+    getRois(options: GetRoisOptions): Roi[];
+}
+//# sourceMappingURL=RoiManager.d.ts.map

package/lib-esm/roi/RoiManager.d.ts.map

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package/lib-esm/roi/RoiManager.js

@@ -0,0 +1,7 @@
+export var RoiKind;
+(function (RoiKind) {
+    RoiKind["BLACK"] = "BLACK";
+    RoiKind["WHITE"] = "WHITE";
+    RoiKind["BW"] = "BW";
+})(RoiKind || (RoiKind = {}));
+//# sourceMappingURL=RoiManager.js.map

package/lib-esm/roi/RoiManager.js.map

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

@@ -0,0 +1,33 @@
+import { Roi, RoiManager } from './RoiManager';
+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: Int16Array;
+    /**
+     * 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 {
+    map: RoiMap;
+    constructor(map: RoiMap);
+    getRois(): Roi[];
+    getMapMatrix(): number[][];
+}
+//# sourceMappingURL=RoiMapManager.d.ts.map

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

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package/lib-esm/roi/RoiMapManager.js

@@ -0,0 +1,13 @@
+import { Matrix } from 'ml-matrix';
+export class RoiMapManager {
+    constructor(map) {
+        this.map = map;
+    }
+    getRois() {
+        return [];
+    }
+    getMapMatrix() {
+        return Matrix.from1DArray(this.map.height, this.map.width, this.map.data).to2DArray();
+    }
+}
+//# sourceMappingURL=RoiMapManager.js.map

package/lib-esm/roi/RoiMapManager.js.map

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

@@ -0,0 +1,39 @@
+import { IJS } from '..';
+import { RoiKind, RoiMapManager } from '.';
+export declare enum 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"
+}
+export interface ColorRoisOptions {
+    /**
+     * Define the color mode to use to color the ROIs.
+     *
+     * @default ColorMode.BINARY
+     */
+    mode?: RoisColorMode;
+    /**
+     * Specify which ROIs to colour.
+     *
+     * @default RoiKind.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): IJS;
+//# sourceMappingURL=colorRois.d.ts.map

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

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

@@ -0,0 +1,44 @@
+import { IJS, ImageColorModel } from '..';
+import { colorMapCenter } from './utils/constants';
+import { getColorMap } from './utils/getColorMap';
+import { RoiKind } from '.';
+export var RoisColorMode;
+(function (RoisColorMode) {
+    /**
+     * Only two acceptable values: red or green
+     */
+    RoisColorMode["BINARY"] = "BINARY";
+    /**
+     * Palette of reds and blues.
+     */
+    RoisColorMode["SATURATION"] = "SATURATION";
+    /**
+     * All possible hues (gradient of colors).
+     */
+    RoisColorMode["RAINBOW"] = "RAINBOW";
+})(RoisColorMode || (RoisColorMode = {}));
+/**
+ * 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 = RoiKind.BW, mode = RoisColorMode.BINARY } = options;
+    let image = new IJS(roiMapManager.map.width, roiMapManager.map.height, {
+        colorModel: ImageColorModel.RGBA,
+    });
+    const colorMap = getColorMap({
+        roiKind,
+        mode,
+        nbNegative: roiMapManager.map.nbNegative,
+        nbPositive: roiMapManager.map.nbPositive,
+    });
+    let data32 = new Uint32Array(image.getRawImage().data.buffer);
+    for (let index = 0; index < image.size; index++) {
+        data32[index] = colorMap[roiMapManager.map.data[index] + colorMapCenter];
+    }
+    return image;
+}
+//# sourceMappingURL=colorRois.js.map

package/lib-esm/roi/colorRois.js.map

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

@@ -0,0 +1,19 @@
+import { Mask } from '..';
+import { RoiMapManager } from './RoiMapManager';
+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 - fromMask options
+ * @returns The corresponding ROI manager.
+ */
+export declare function fromMask(mask: Mask, options?: FromMaskOptions): RoiMapManager;
+//# sourceMappingURL=fromMask.d.ts.map

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

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package/lib-esm/roi/fromMask.js

@@ -0,0 +1,144 @@
+import { RoiMapManager } from './RoiMapManager';
+import { maxNumberRois, maxRoiId } from './utils/constants';
+/**
+ * Extract the ROIs of an image.
+ *
+ * @param mask - Mask to extract the ROIs from
+ * @param options - fromMask options
+ * @returns The corresponding ROI manager.
+ */
+export function fromMask(mask, options = {}) {
+    const { allowCorners = false } = options;
+    const MAX_ARRAY = maxNumberRois - 1; // 65535 should be enough for most of the cases
+    const maxPositiveId = maxRoiId - 1;
+    const maxNegativeId = -maxRoiId;
+    // based on a binary image we will create plenty of small images
+    let data = new Int16Array(mask.size); // maxValue: maxPositiveId, minValue: maxNegativeId
+    // split will always return an array of images
+    let positiveId = 0;
+    let negativeId = 0;
+    let columnToProcess = new Uint16Array(maxNumberRois);
+    let rowToProcess = new Uint16Array(maxNumberRois);
+    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;
+        let targetState = mask.getBit(row, column);
+        let id = targetState ? ++positiveId : --negativeId;
+        if (positiveId > maxPositiveId || negativeId < maxNegativeId) {
+            throw new Error('Too many regions of interest');
+        }
+        columnToProcess[0] = column;
+        rowToProcess[0] = row;
+        while (from <= to) {
+            let currentColumn = columnToProcess[from & MAX_ARRAY];
+            let currentRow = rowToProcess[from & MAX_ARRAY];
+            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(currentRow, currentColumn - 1) === targetState) {
+                // LEFT
+                to++;
+                columnToProcess[to & MAX_ARRAY] = currentColumn - 1;
+                rowToProcess[to & MAX_ARRAY] = currentRow;
+                data[currentRow * mask.width + currentColumn - 1] = maxNegativeId;
+            }
+            if (currentRow > 0 &&
+                data[(currentRow - 1) * mask.width + currentColumn] === 0 &&
+                mask.getBit(currentRow - 1, currentColumn) === targetState) {
+                // TOP
+                to++;
+                columnToProcess[to & MAX_ARRAY] = currentColumn;
+                rowToProcess[to & MAX_ARRAY] = currentRow - 1;
+                data[(currentRow - 1) * mask.width + currentColumn] = maxNegativeId;
+            }
+            if (currentColumn < mask.width - 1 &&
+                data[currentRow * mask.width + currentColumn + 1] === 0 &&
+                mask.getBit(currentRow, currentColumn + 1) === targetState) {
+                // RIGHT
+                to++;
+                columnToProcess[to & MAX_ARRAY] = currentColumn + 1;
+                rowToProcess[to & MAX_ARRAY] = currentRow;
+                data[currentRow * mask.width + currentColumn + 1] = maxNegativeId;
+            }
+            if (currentRow < mask.height - 1 &&
+                data[(currentRow + 1) * mask.width + currentColumn] === 0 &&
+                mask.getBit(currentRow + 1, currentColumn) === targetState) {
+                // BOTTOM
+                to++;
+                columnToProcess[to & MAX_ARRAY] = currentColumn;
+                rowToProcess[to & MAX_ARRAY] = currentRow + 1;
+                data[(currentRow + 1) * mask.width + currentColumn] = maxNegativeId;
+            }
+            if (allowCorners) {
+                if (currentColumn > 0 &&
+                    currentRow > 0 &&
+                    data[(currentRow - 1) * mask.width + currentColumn - 1] === 0 &&
+                    mask.getBit(currentRow - 1, currentColumn - 1) === targetState) {
+                    // TOP LEFT
+                    to++;
+                    columnToProcess[to & MAX_ARRAY] = currentColumn - 1;
+                    rowToProcess[to & MAX_ARRAY] = currentRow - 1;
+                    data[(currentRow - 1) * mask.width + currentColumn - 1] =
+                        maxNegativeId;
+                }
+                if (currentColumn < mask.width - 1 &&
+                    currentRow > 0 &&
+                    data[(currentRow - 1) * mask.width + currentColumn + 1] === 0 &&
+                    mask.getBit(currentRow - 1, currentColumn + 1) === targetState) {
+                    // TOP RIGHT
+                    to++;
+                    columnToProcess[to & MAX_ARRAY] = currentColumn + 1;
+                    rowToProcess[to & MAX_ARRAY] = currentRow - 1;
+                    data[(currentRow - 1) * mask.width + currentColumn + 1] =
+                        maxNegativeId;
+                }
+                if (currentColumn > 0 &&
+                    currentRow < mask.height - 1 &&
+                    data[(currentRow + 1) * mask.width + currentColumn - 1] === 0 &&
+                    mask.getBit(currentRow + 1, currentColumn - 1) === targetState) {
+                    // BOTTOM LEFT
+                    to++;
+                    columnToProcess[to & MAX_ARRAY] = currentColumn - 1;
+                    rowToProcess[to & MAX_ARRAY] = currentRow + 1;
+                    data[(currentRow + 1) * mask.width + currentColumn - 1] =
+                        maxNegativeId;
+                }
+                if (currentColumn < mask.width - 1 &&
+                    currentRow < mask.height - 1 &&
+                    data[(currentRow + 1) * mask.width + currentColumn + 1] === 0 &&
+                    mask.getBit(currentRow + 1, currentColumn + 1) === targetState) {
+                    // BOTTOM RIGHT
+                    to++;
+                    columnToProcess[to & MAX_ARRAY] = currentColumn + 1;
+                    rowToProcess[to & MAX_ARRAY] = currentRow + 1;
+                    data[(currentRow + 1) * mask.width + currentColumn + 1] =
+                        maxNegativeId;
+                }
+            }
+            from++;
+            if (to - from > MAX_ARRAY) {
+                throw new Error('analyseMask 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-esm/roi/fromMask.js.map

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

@@ -0,0 +1,5 @@
+export * from './fromMask';
+export * from './RoiManager';
+export * from './RoiMapManager';
+export * from './colorRois';
+//# sourceMappingURL=index.d.ts.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../src/roi/index.ts"],"names":[],"mappings":"AAAA,cAAc,YAAY,CAAC;AAC3B,cAAc,cAAc,CAAC;AAC7B,cAAc,iBAAiB,CAAC;AAChC,cAAc,aAAa,CAAC"}

package/lib-esm/roi/index.js

@@ -0,0 +1,5 @@
+export * from './fromMask';
+export * from './RoiManager';
+export * from './RoiMapManager';
+export * from './colorRois';
+//# sourceMappingURL=index.js.map

package/lib-esm/roi/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/roi/index.ts"],"names":[],"mappings":"AAAA,cAAc,YAAY,CAAC;AAC3B,cAAc,cAAc,CAAC;AAC7B,cAAc,iBAAiB,CAAC;AAChC,cAAc,aAAa,CAAC"}

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

@@ -0,0 +1,37 @@
+import { RoiKind } from '../../RoiManager';
+export interface GetBinaryMapOptions {
+    /**
+     * Number of black ROIs
+     */
+    nbNegative: number;
+    /**
+     * Number of white ID ROIs
+     */
+    nbPositive: number;
+    /**
+     * Specify which ROIs to colour.
+     *
+     * @default RoiKind.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-esm/roi/utils/colorMaps/getBinaryMap.d.ts.map

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

@@ -0,0 +1,30 @@
+import { RoiKind } from '../../RoiManager';
+import { maxNumberRois, colorMapCenter } from '../constants';
+import { hsvToRgb } from '../hsvToRgb';
+import { rgbToNumber } from '../rgbToNumber';
+/**
+ * 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 = RoiKind.BW, } = options;
+    let colorMap = new Uint32Array(maxNumberRois);
+    // negative values
+    if (roiKind === RoiKind.BW || roiKind === RoiKind.BLACK) {
+        for (let i = colorMapCenter - nbNegative; i < colorMapCenter; i++) {
+            const hsv = [blackHue, 255, 255];
+            colorMap[i] = rgbToNumber(hsvToRgb(hsv));
+        }
+    }
+    if (roiKind === RoiKind.BW || roiKind === RoiKind.WHITE) {
+        // positive values
+        for (let i = colorMapCenter + 1; i < colorMapCenter + 1 + nbPositive; i++) {
+            const hsv = [whiteHue, 255, 255];
+            colorMap[i] = rgbToNumber(hsvToRgb(hsv));
+        }
+    }
+    return colorMap;
+}
+//# sourceMappingURL=getBinaryMap.js.map

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

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

@@ -0,0 +1,25 @@
+import { RoiKind } from '../../RoiManager';
+export interface GetRainbowMapOptions {
+    /**
+     * Number of black ROIs
+     */
+    nbNegative: number;
+    /**
+     * Number of white ID ROIs
+     */
+    nbPositive: number;
+    /**
+     * Specify which ROIs to colour.
+     *
+     * @default RoiKind.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-esm/roi/utils/colorMaps/getRainbowMap.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"getRainbowMap.d.ts","sourceRoot":"","sources":["../../../../src/roi/utils/colorMaps/getRainbowMap.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,OAAO,EAAE,MAAM,kBAAkB,CAAC;AAK3C,MAAM,WAAW,oBAAoB;IACnC;;OAEG;IACH,UAAU,EAAE,MAAM,CAAC;IACnB;;OAEG;IACH,UAAU,EAAE,MAAM,CAAC;IACnB;;;;OAIG;IACH,OAAO,CAAC,EAAE,OAAO,CAAC;CACnB;AAED;;;;;GAKG;AACH,wBAAgB,aAAa,CAAC,OAAO,EAAE,oBAAoB,GAAG,WAAW,CAoCxE"}

package/lib-esm/roi/utils/colorMaps/getRainbowMap.js

@@ -0,0 +1,47 @@
+import { RoiKind } from '../../RoiManager';
+import { maxNumberRois, colorMapCenter } from '../constants';
+import { hsvToRgb } from '../hsvToRgb';
+import { rgbToNumber } from '../rgbToNumber';
+/**
+ * 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 = RoiKind.BW } = options;
+    let colorMap = new Uint32Array(maxNumberRois);
+    const hueRange = 360;
+    let step;
+    if (roiKind === RoiKind.BW) {
+        step = hueRange / (nbNegative + nbPositive);
+    }
+    else if (roiKind === RoiKind.BLACK) {
+        step = hueRange / nbNegative;
+    }
+    else if (roiKind === RoiKind.WHITE) {
+        step = hueRange / nbPositive;
+    }
+    else {
+        throw new Error('getRainbowMap: unrecognised ROI kind');
+    }
+    // negative values
+    let hue = 0;
+    if (roiKind === RoiKind.BW || roiKind === RoiKind.BLACK) {
+        for (let i = colorMapCenter - nbNegative; i < colorMapCenter; i++) {
+            const hsv = [hue, 255, 255];
+            colorMap[i] = rgbToNumber(hsvToRgb(hsv));
+            hue += step;
+        }
+    }
+    // positive values
+    if (roiKind === RoiKind.BW || roiKind === RoiKind.WHITE) {
+        for (let i = colorMapCenter + 1; i < colorMapCenter + 1 + nbPositive; i++) {
+            const hsv = [hue, 255, 255];
+            colorMap[i] = rgbToNumber(hsvToRgb(hsv));
+            hue += step;
+        }
+    }
+    return colorMap;
+}
+//# sourceMappingURL=getRainbowMap.js.map

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

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

@@ -0,0 +1,42 @@
+import { RoiKind } from '../../RoiManager';
+export interface GetSaturationMapOptions {
+    /**
+     * Number of black ROIs
+     */
+    nbNegative: number;
+    /**
+     * Number of white ID ROIs
+     */
+    nbPositive: number;
+    /**
+     * Specify which ROIs to colour.
+     *
+     * @default RoiKind.BW
+     */
+    /**
+     * Specify which ROIs to colour.
+     *
+     * @default RoiKind.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-esm/roi/utils/colorMaps/getSaturationMap.d.ts.map

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package/lib-esm/roi/utils/colorMaps/getSaturationMap.js

@@ -0,0 +1,35 @@
+import { RoiKind } from '../../RoiManager';
+import { maxNumberRois, colorMapCenter } from '../constants';
+import { hsvToRgb } from '../hsvToRgb';
+import { rgbToNumber } from '../rgbToNumber';
+/**
+ * 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 = RoiKind.BW, whiteHue = 0, blackHue = 240, } = options;
+    let colorMap = new Uint32Array(maxNumberRois);
+    const range = 255 - 63;
+    const negativeStep = range / nbNegative;
+    const positiveStep = range / nbPositive;
+    // negative values
+    let counter = 0;
+    if (roiKind === RoiKind.BW || roiKind === RoiKind.BLACK) {
+        for (let i = colorMapCenter - nbNegative; i < colorMapCenter; i++) {
+            const hsv = [blackHue, 255 - counter++ * negativeStep, 255];
+            colorMap[i] = rgbToNumber(hsvToRgb(hsv));
+        }
+    }
+    // positive values
+    counter = 0;
+    if (roiKind === RoiKind.BW || roiKind === RoiKind.WHITE) {
+        for (let i = colorMapCenter + 1; i < colorMapCenter + 1 + nbPositive; i++) {
+            const hsv = [whiteHue, 255 - counter++ * positiveStep, 255];
+            colorMap[i] = rgbToNumber(hsvToRgb(hsv));
+        }
+    }
+    return colorMap;
+}
+//# sourceMappingURL=getSaturationMap.js.map

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

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