image-js 1.0.0-alpha.3 → 1.1.0

package/lib/operations/split.js

@@ -1,16 +1,20 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-const Image_1 = require("../Image");
-function split(image) {
-    const result = [];
-    for (let c = 0; c < image.channels; c++) {
-        const channel = Image_1.Image.createFrom(image, { kind: Image_1.ImageKind.GREY });
-        for (let i = 0; i < channel.data.length; i++) {
-            channel.data[i] = image.data[i * image.channels + c];
-        }
-        result.push(channel);
-    }
-    return result;
-}
-exports.split = split;
+import { Image } from '../Image.js';
+/**
+ * Create an array of single-channel images based on a multi-channel image.
+ * @param image - The image with many channels.
+ * @returns Array of single-channel images.
+ */
+export function split(image) {
+    const result = [];
+    for (let c = 0; c < image.channels; c++) {
+        const channel = Image.createFrom(image, {
+            colorModel: 'GREY',
+        });
+        for (let i = 0; i < channel.size; i++) {
+            channel.setValueByIndex(i, 0, image.getValueByIndex(i, c));
+        }
+        result.push(channel);
+    }
+    return result;
+}
 //# sourceMappingURL=split.js.map

package/lib/operations/split.js.map

@@ -1 +1 @@
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package/lib/operations/threshold.d.ts

@@ -1,19 +1,61 @@
-import { Image } from '../Image';
-export declare enum ThresholdAlgorithm {
-    OTSU = "OTSU",
-    TRIANGLE = "TRIANGLE"
-}
-interface IThresholdOptionsBase {
-    out?: Image;
-}
-export interface IThresholdOptionsThreshold extends IThresholdOptionsBase {
-    threshold: number;
-}
-export interface IThresholdOptionsAlgorithm extends IThresholdOptionsBase {
-    algorithm: ThresholdAlgorithm;
-}
-export declare type ThresholdOptions = IThresholdOptionsThreshold | IThresholdOptionsAlgorithm;
-export declare function computeThreshold(image: Image, algorithm: ThresholdAlgorithm): number;
-export declare function threshold(image: Image, options: ThresholdOptions): Image;
-export {};
+import type { Image } from '../Image.js';
+import type { Mask } from '../Mask.js';
+export declare const ThresholdAlgorithm: {
+    readonly HUANG: "huang";
+    readonly INTERMODES: "intermodes";
+    readonly ISODATA: "isodata";
+    readonly LI: "li";
+    readonly MAX_ENTROPY: "maxEntropy";
+    readonly MEAN: "mean";
+    readonly MIN_ERROR: "minError";
+    readonly MINIMUM: "minimum";
+    readonly MOMENTS: "moments";
+    readonly OTSU: "otsu";
+    readonly PERCENTILE: "percentile";
+    readonly RENYI_ENTROPY: "renyiEntropy";
+    readonly SHANBHAG: "shanbhag";
+    readonly TRIANGLE: "triangle";
+    readonly YEN: "yen";
+};
+export type ThresholdAlgorithm = (typeof ThresholdAlgorithm)[keyof typeof ThresholdAlgorithm];
+interface ThresholdOptionsBase {
+    /**
+     * Number of slots that histogram can have. Slots must be a power of 2.
+     */
+    slots?: number;
+    /**
+     * Image to use as the output.
+     */
+    out?: Mask;
+}
+export interface ThresholdOptionsThreshold extends ThresholdOptionsBase {
+    /**
+     * Threshold value that should be used. Threshold is a value in range [0,1],
+     * which will be interpreted as a percentage of image.maxValue.
+     */
+    threshold: number;
+}
+export interface ThresholdOptionsAlgorithm extends ThresholdOptionsBase {
+    /**
+     * Specify a function to computes the threshold value.
+     *   @default `'otsu'`
+     */
+    algorithm?: ThresholdAlgorithm;
+}
+export type ThresholdOptions = ThresholdOptionsThreshold | ThresholdOptionsAlgorithm;
+/**
+ * Compute threshold value for an image using the specified algorithm.
+ * @param image - The grey image.
+ * @param options - Threshold options.
+ * @returns The threshold value for the image.
+ */
+export declare function computeThreshold(image: Image, options?: ThresholdOptionsAlgorithm): number;
+/**
+ * Create a black and white image based on a threshold value.
+ * @param image - The grey image to convert.
+ * @param options - Threshold options.
+ * @returns The resulting mask.
+ */
+export declare function threshold(image: Image, options?: ThresholdOptions): Mask;
+export {};
 //# sourceMappingURL=threshold.d.ts.map

package/lib/operations/threshold.d.ts.map

@@ -1 +1 @@
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package/lib/operations/threshold.js

@@ -1,59 +1,91 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-const validators_1 = require("../utils/validators");
-const getOutputImage_1 = require("../utils/getOutputImage");
-const otsu_1 = require("./thresholds/otsu");
-const triangle_1 = require("./thresholds/triangle");
-// TODO: convert more algorithms to TS.
-var ThresholdAlgorithm;
-(function (ThresholdAlgorithm) {
-    // HUANG,
-    // INTERMODES,
-    // ISODATA,
-    // LI,
-    // MAX_ENTROPY,
-    // MEAN,
-    // MIN_ERROR,
-    // MINIMUM,
-    // MOMENTS,
-    ThresholdAlgorithm["OTSU"] = "OTSU";
-    // PERCENTILE,
-    // RENYI_ENTROPY,
-    // SHANBHAG,
-    ThresholdAlgorithm["TRIANGLE"] = "TRIANGLE";
-    // YEN
-})(ThresholdAlgorithm = exports.ThresholdAlgorithm || (exports.ThresholdAlgorithm = {}));
-function computeThreshold(image, algorithm) {
-    if (image.channels !== 1) {
-        throw new Error('threshold can only be computed on images with one channel');
-    }
-    const histogram = image.histogram();
-    switch (algorithm) {
-        case ThresholdAlgorithm.OTSU:
-            return otsu_1.otsu(histogram, image.size);
-        case ThresholdAlgorithm.TRIANGLE:
-            return triangle_1.triangle(histogram);
-        default:
-            throw new RangeError(`unsupported threshold algorithm: ${algorithm}`);
-    }
-}
-exports.computeThreshold = computeThreshold;
-// TODO: add support for other threshold types.
-// See: https://docs.opencv.org/4.0.1/d7/d1b/group__imgproc__misc.html#gaa9e58d2860d4afa658ef70a9b1115576
-function threshold(image, options) {
-    let thresholdValue;
-    if ('threshold' in options) {
-        thresholdValue = options.threshold;
-    }
-    else {
-        thresholdValue = computeThreshold(image, options.algorithm);
-    }
-    validators_1.validateValue(thresholdValue, image);
-    const result = getOutputImage_1.getOutputImage(image, options);
-    for (let i = 0; i < image.data.length; i++) {
-        result.data[i] = image.data[i] > thresholdValue ? image.maxValue : 0;
-    }
-    return result;
-}
-exports.threshold = threshold;
+import { match } from 'ts-pattern';
+import { imageToOutputMask } from '../utils/getOutputImage.js';
+import huang from './thresholds/huang.js';
+import intermodes from './thresholds/intermodes.js';
+import isodata from './thresholds/isodata.js';
+import li from './thresholds/li.js';
+import maxEntropy from './thresholds/maxEntropy.js';
+import mean from './thresholds/mean.js';
+import minError from './thresholds/minError.js';
+import minimum from './thresholds/minimum.js';
+import moments from './thresholds/moments.js';
+import { otsu } from './thresholds/otsu.js';
+import percentile from './thresholds/percentile.js';
+import renyiEntropy from './thresholds/renyiEntropy.js';
+import shanbhag from './thresholds/shanbhag.js';
+import { triangle } from './thresholds/triangle.js';
+import yen from './thresholds/yen.js';
+export const ThresholdAlgorithm = {
+    HUANG: 'huang',
+    INTERMODES: 'intermodes',
+    ISODATA: 'isodata',
+    LI: 'li',
+    MAX_ENTROPY: 'maxEntropy',
+    MEAN: 'mean',
+    MIN_ERROR: 'minError',
+    MINIMUM: 'minimum',
+    MOMENTS: 'moments',
+    OTSU: 'otsu',
+    PERCENTILE: 'percentile',
+    RENYI_ENTROPY: 'renyiEntropy',
+    SHANBHAG: 'shanbhag',
+    TRIANGLE: 'triangle',
+    YEN: 'yen',
+};
+/**
+ * Compute threshold value for an image using the specified algorithm.
+ * @param image - The grey image.
+ * @param options - Threshold options.
+ * @returns The threshold value for the image.
+ */
+export function computeThreshold(image, options = {}) {
+    const { algorithm = 'otsu', slots } = options;
+    if (image.channels !== 1) {
+        throw new TypeError('threshold can only be computed on images with one channel');
+    }
+    const histogram = image.histogram({ slots });
+    const scale = slots ? 2 ** image.bitDepth / slots : 1;
+    return match(algorithm)
+        .with('huang', () => huang(histogram) * scale)
+        .with('intermodes', () => intermodes(histogram) * scale)
+        .with('isodata', () => isodata(histogram) * scale)
+        .with('li', () => li(histogram, image.size) * scale)
+        .with('maxEntropy', () => maxEntropy(histogram, image.size) * scale)
+        .with('mean', () => mean(histogram, image.size) * scale)
+        .with('minimum', () => minimum(histogram) * scale)
+        .with('minError', () => minError(histogram, image.size) * scale)
+        .with('moments', () => moments(histogram, image.size) * scale)
+        .with('otsu', () => otsu(histogram, image.size) * scale)
+        .with('percentile', () => percentile(histogram) * scale)
+        .with('renyiEntropy', () => renyiEntropy(histogram, image.size) * scale)
+        .with('shanbhag', () => shanbhag(histogram, image.size) * scale)
+        .with('triangle', () => triangle(histogram) * scale)
+        .with('yen', () => yen(histogram, image.size) * scale)
+        .exhaustive();
+}
+// See: https://docs.opencv.org/4.0.1/d7/d1b/group__imgproc__misc.html#gaa9e58d2860d4afa658ef70a9b1115576
+/**
+ * Create a black and white image based on a threshold value.
+ * @param image - The grey image to convert.
+ * @param options - Threshold options.
+ * @returns The resulting mask.
+ */
+export function threshold(image, options = {}) {
+    let thresholdValue;
+    if ('threshold' in options) {
+        const threshold = options.threshold;
+        if (threshold < 0 || threshold > 1) {
+            throw new RangeError('threshold must be a value between 0 and 1');
+        }
+        thresholdValue = threshold * image.maxValue;
+    }
+    else {
+        thresholdValue = computeThreshold(image, options);
+    }
+    const result = imageToOutputMask(image, options);
+    for (let i = 0; i < image.size; i++) {
+        result.setBitByIndex(i, image.getValueByIndex(i, 0) > thresholdValue ? 1 : 0);
+    }
+    return result;
+}
 //# sourceMappingURL=threshold.js.map

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package/lib/operations/thresholds/huang.d.ts

@@ -0,0 +1,7 @@
+/**
+ * Return a threshold for a histogram using Huang algorithm.
+ * @param histogram - Image histogram.
+ * @returns The threshold.
+ */
+export default function huang(histogram: Uint32Array): number;
+//# sourceMappingURL=huang.d.ts.map

package/lib/operations/thresholds/huang.d.ts.map

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package/lib/operations/thresholds/huang.js

@@ -0,0 +1,78 @@
+/*
+ * * see http://rsb.info.nih.gov/ij/developer/source/ij/process/AutoThresholder.java.html.
+ * Huang: Implements Huang's fuzzy thresholding method: Huang, L-K & Wang, M-J J (1995),
+ * "Image thresholding by minimizing the measure of fuzziness", Pattern Recognition 28(1): 41-51
+ */
+/**
+ * Return a threshold for a histogram using Huang algorithm.
+ * @param histogram - Image histogram.
+ * @returns The threshold.
+ */
+export default function huang(histogram) {
+    /* Determine the first non-zero bin */
+    let firstBin = 0;
+    for (let ih = 0; ih < histogram.length; ih++) {
+        if (histogram[ih] !== 0) {
+            firstBin = ih;
+            break;
+        }
+    }
+    /* Determine the last non-zero bin */
+    let lastBin = histogram.length - 1;
+    for (let ih = histogram.length - 1; ih >= firstBin; ih--) {
+        if (histogram[ih] !== 0) {
+            lastBin = ih;
+            break;
+        }
+    }
+    const term = 1 / (lastBin - firstBin);
+    const mu0 = new Array(histogram.length);
+    let sumPix = 0;
+    let numPix = 0;
+    for (let ih = firstBin; ih < histogram.length; ih++) {
+        sumPix += ih * histogram[ih];
+        numPix += histogram[ih];
+        mu0[ih] = sumPix / numPix;
+    }
+    const mu1 = new Array(histogram.length);
+    sumPix = 0;
+    numPix = 0;
+    for (let ih = lastBin; ih > 0; ih--) {
+        sumPix += ih * histogram[ih];
+        numPix += histogram[ih];
+        mu1[ih - 1] = sumPix / numPix;
+    }
+    /* Determine the threshold that minimizes the fuzzy entropy*/
+    let threshold = -1;
+    let minEnt = Number.MAX_VALUE;
+    for (let it = 0; it < histogram.length; it++) {
+        let ent = 0;
+        let muX;
+        for (let ih = 0; ih <= it; ih++) {
+            /* Equation (4) in Ref. 1 */
+            muX = 1 / (1 + term * Math.abs(ih - mu0[it]));
+            if (!(muX < 1e-6 || muX > 0.999999)) {
+                /* Equation (6) & (8) in Ref. 1 */
+                ent +=
+                    histogram[ih] *
+                        (-muX * Math.log(muX) - (1 - muX) * Math.log(1 - muX));
+            }
+        }
+        for (let ih = it + 1; ih < histogram.length; ih++) {
+            /* Equation (4) in Ref. 1 */
+            muX = 1 / (1 + term * Math.abs(ih - mu1[it]));
+            if (!(muX < 1e-6 || muX > 0.999999)) {
+                /* Equation (6) & (8) in Ref. 1 */
+                ent +=
+                    histogram[ih] *
+                        (-muX * Math.log(muX) - (1 - muX) * Math.log(1 - muX));
+            }
+        }
+        if (ent < minEnt) {
+            minEnt = ent;
+            threshold = it;
+        }
+    }
+    return threshold;
+}
+//# sourceMappingURL=huang.js.map

package/lib/operations/thresholds/huang.js.map

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package/lib/operations/thresholds/intermodes.d.ts

@@ -0,0 +1,7 @@
+/**
+ * Return a threshold for a histogram using Intermodes algorithm.
+ * @param histogram - Image histogram.
+ * @returns The threshold.
+ */
+export default function intermodes(histogram: Uint32Array): number;
+//# sourceMappingURL=intermodes.d.ts.map

package/lib/operations/thresholds/intermodes.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"intermodes.d.ts","sourceRoot":"","sources":["../../../src/operations/thresholds/intermodes.ts"],"names":[],"mappings":"AAUA;;;;GAIG;AACH,MAAM,CAAC,OAAO,UAAU,UAAU,CAAC,SAAS,EAAE,WAAW,GAAG,MAAM,CA2BjE"}

package/lib/operations/thresholds/intermodes.js

@@ -0,0 +1,57 @@
+/*
+ *
+ * see https://github.com/fiji/Auto_Threshold/blob/master/src/main/java/fiji/threshold/Auto_Threshold.java
+ * Intermodes: This assumes a bimodal histogram. Implements the thresholding Prewitt, JMS & Mendelsohn, ML (1966),
+ * "The analysis of cell images", Annals of the NewYork Academy of Sciences 128: 1035-1053
+ *
+ */
+import { assert } from '../../utils/validators/assert.js';
+/**
+ * Return a threshold for a histogram using Intermodes algorithm.
+ * @param histogram - Image histogram.
+ * @returns The threshold.
+ */
+export default function intermodes(histogram) {
+    const iHisto = histogram.slice();
+    let iter = 0;
+    while (!bimodalTest(iHisto)) {
+        // smooth with a 3 point running mean filter
+        let previous = 0;
+        let current = 0;
+        let next = iHisto[0];
+        for (let i = 0; i < histogram.length - 1; i++) {
+            previous = current;
+            current = next;
+            next = iHisto[i + 1];
+            iHisto[i] = (previous + current + next) / 3;
+        }
+        iHisto[histogram.length - 1] = (current + next) / 3;
+        iter++;
+        assert(iter < 1000, 'Intermodes threshold not found after 1000 iterations');
+    }
+    // The threshold is the mean between the two peaks.
+    let tt = 0;
+    for (let i = 1; i < histogram.length - 1; i++) {
+        if (iHisto[i - 1] < iHisto[i] && iHisto[i + 1] < iHisto[i]) {
+            tt += i;
+        }
+    }
+    return Math.floor(tt / 2);
+}
+function bimodalTest(iHisto) {
+    let b = false;
+    let modes = 0;
+    for (let k = 1; k < iHisto.length - 1; k++) {
+        if (iHisto[k - 1] < iHisto[k] && iHisto[k + 1] < iHisto[k]) {
+            modes++;
+            if (modes > 2) {
+                return false;
+            }
+        }
+    }
+    if (modes === 2) {
+        b = true;
+    }
+    return b;
+}
+//# sourceMappingURL=intermodes.js.map

package/lib/operations/thresholds/intermodes.js.map

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package/lib/operations/thresholds/isodata.d.ts

@@ -0,0 +1,7 @@
+/**
+ * Return a threshold for a histogram using Isodata algorithm.
+ * @param histogram - Image histogram.
+ * @returns The threshold.
+ */
+export default function isodata(histogram: Uint32Array): number;
+//# sourceMappingURL=isodata.d.ts.map

package/lib/operations/thresholds/isodata.d.ts.map

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package/lib/operations/thresholds/isodata.js

@@ -0,0 +1,50 @@
+/*
+ * see https://github.com/fiji/Auto_Threshold/blob/master/src/main/java/fiji/threshold/Auto_Threshold.java
+ * Isodata: Ridler, TW & Calvard, S (1978), "Picture thresholding using an iterative selection method"
+ * IEEE Transactions on Systems, Man and Cybernetics 8: 630-632.
+ *
+ */
+import { assert } from '../../utils/validators/assert.js';
+/**
+ * Return a threshold for a histogram using Isodata algorithm.
+ * @param histogram - Image histogram.
+ * @returns The threshold.
+ */
+export default function isodata(histogram) {
+    let l; // the average grey value of pixels with intensities < g
+    let toth; // the the average grey value of pixels with intensities > g
+    let totl; // the total the average grey value of pixels with intensities < g
+    let h; // the average grey value of pixels with intensities > g
+    let g = 0; // threshold value
+    for (let i = 1; i < histogram.length; i++) {
+        if (histogram[i] > 0) {
+            g = i + 1;
+            break;
+        }
+    }
+    while (true) {
+        l = 0;
+        totl = 0;
+        for (let i = 0; i < g; i++) {
+            totl = totl + histogram[i];
+            l = l + histogram[i] * i;
+        }
+        h = 0;
+        toth = 0;
+        for (let i = g + 1; i < histogram.length; i++) {
+            toth += histogram[i];
+            h += histogram[i] * i;
+        }
+        if (totl > 0 && toth > 0) {
+            l /= totl;
+            h /= toth;
+            if (g === Math.round((l + h) / 2)) {
+                break;
+            }
+        }
+        g++;
+        assert(g <= histogram.length - 2, 'Threshold not found');
+    }
+    return g;
+}
+//# sourceMappingURL=isodata.js.map

package/lib/operations/thresholds/isodata.js.map

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package/lib/operations/thresholds/li.d.ts

@@ -0,0 +1,8 @@
+/**
+ * Return a threshold for a histogram using Li algorithm.
+ * @param histogram - Image histogram.
+ * @param total - Number of pixels in the image.
+ * @returns The threshold.
+ */
+export default function li(histogram: Uint32Array, total: number): number;
+//# sourceMappingURL=li.d.ts.map

package/lib/operations/thresholds/li.d.ts.map

@@ -0,0 +1 @@
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package/lib/operations/thresholds/li.js

@@ -0,0 +1,73 @@
+/*
+ * see http://rsb.info.nih.gov/ij/developer/source/ij/process/AutoThresholder.java.html
+ * The method is present in: Implements Li's Minimum Cross Entropy thresholding method
+ * This implementation is based on the iterative version (Ref. 2nd reference below) of the algorithm.
+ *  1) Li, CH & Lee, CK (1993), "Minimum Cross Entropy Thresholding", Pattern Recognition 26(4): 61 625
+ *  2) Li, CH & Tam, PKS (1998), "An Iterative Algorithm for Minimum Cross Entropy Thresholding",
+ *     Pattern Recognition Letters 18(8): 771-776
+ *  3) Sezgin, M & Sankur, B (2004), "Survey over Image Thresholding Techniques and Quantitative Performance
+ *     Evaluation",Journal of Electronic Imaging 13(1): 146-165
+ * @param histogram - the histogram of the image
+ * @param total - the number of pixels in the image
+ * @returns {number} - the threshold
+ */
+/**
+ * Return a threshold for a histogram using Li algorithm.
+ * @param histogram - Image histogram.
+ * @param total - Number of pixels in the image.
+ * @returns The threshold.
+ */
+export default function li(histogram, total) {
+    let threshold;
+    let sumBack; /* sum of the background pixels at a given threshold */
+    let sumObj; /* sum of the object pixels at a given threshold */
+    let numBack; /* number of background pixels at a given threshold */
+    let numObj; /* number of object pixels at a given threshold */
+    let oldThresh;
+    let newThresh;
+    let meanBack; /* mean of the background pixels at a given threshold */
+    let meanObj; /* mean of the object pixels at a given threshold */
+    let mean; /* mean gray-level in the image */
+    const tolerance = 0.5; /* threshold tolerance */
+    let temp;
+    /* Calculate the mean gray-level */
+    mean = 0;
+    for (let ih = 0; ih < histogram.length; ih++) {
+        mean += ih * histogram[ih];
+    }
+    mean /= total;
+    /* Initial estimate */
+    newThresh = mean;
+    do {
+        oldThresh = newThresh;
+        threshold = (oldThresh + 0.5) | 0; /* range */
+        /* Calculate the means of background and object pixels */
+        /* Background */
+        sumBack = 0;
+        numBack = 0;
+        for (let ih = 0; ih <= threshold; ih++) {
+            sumBack += ih * histogram[ih];
+            numBack += histogram[ih];
+        }
+        meanBack = numBack === 0 ? 0 : sumBack / numBack;
+        /* Object */
+        sumObj = 0;
+        numObj = 0;
+        for (let ih = threshold + 1; ih < histogram.length; ih++) {
+            sumObj += ih * histogram[ih];
+            numObj += histogram[ih];
+        }
+        meanObj = numObj === 0 ? 0 : sumObj / numObj;
+        temp = (meanBack - meanObj) / (Math.log(meanBack) - Math.log(meanObj));
+        if (temp < -Number.EPSILON) {
+            newThresh = (temp - 0.5) | 0;
+        }
+        else {
+            newThresh = (temp + 0.5) | 0;
+        }
+        /*  Stop the iterations when the difference between the
+             new and old threshold values is less than the tolerance */
+    } while (Math.abs(newThresh - oldThresh) > tolerance);
+    return threshold;
+}
+//# sourceMappingURL=li.js.map