image-js 0.0.0-next-e30968a2d8

package/lib-esm/operations/thresholds/moments.js

@@ -0,0 +1,59 @@
+// see https://github.com/fiji/Auto_Threshold/blob/master/src/main/java/fiji/threshold/Auto_Threshold.java
+// W. Tsai, "Moment-preserving thresholding: a new approach," Computer Vision,
+// Graphics, and Image Processing, vol. 29, pp. 377-393, 1985.
+// Ported to ImageJ plugin by G.Landini from the the open source project FOURIER 0.8
+// by M. Emre Celebi , Department of Computer Science, Louisiana State University in Shreveport
+// Shreveport, LA 71115, USA
+// http://sourceforge.net/projects/fourier-ipal
+// http://www.lsus.edu/faculty/~ecelebi/fourier.htm
+/**
+ * Return a threshold for a histogram.
+ *
+ * @param histogram - Image histogram.
+ * @param total - Number of pixels in the image.
+ * @returns The threshold.
+ */
+export default function moments(histogram, total) {
+    // moments
+    const m0 = 1.0;
+    let m1 = 0.0;
+    let m2 = 0.0;
+    let m3 = 0.0;
+    let sum = 0.0;
+    let threshold = -1;
+    const histogramLength = histogram.length;
+    const normalizedHistogram = new Array(histogramLength);
+    for (let i = 0; i < histogramLength; i++) {
+        normalizedHistogram[i] = histogram[i] / total;
+    }
+    /* Calculate the first, second, and third order moments */
+    for (let i = 0; i < histogramLength; i++) {
+        m1 += i * normalizedHistogram[i];
+        m2 += i * i * normalizedHistogram[i];
+        m3 += i * i * i * normalizedHistogram[i];
+    }
+    /*
+       First 4 moments of the gray-level image should match the first 4 moments
+       of the target binary image. This leads to 4 equalities whose solutions
+       are given in the Appendix of Ref. 1
+       */
+    const cd = m0 * m2 - m1 * m1; // determinant of the matriz of hankel for moments 2x2
+    const c0 = (-m2 * m2 + m1 * m3) / cd;
+    const c1 = (m0 * -m3 + m2 * m1) / cd;
+    // new two gray values where z0<z1
+    const z0 = 0.5 * (-c1 - Math.sqrt(c1 * c1 - 4.0 * c0));
+    const z1 = 0.5 * (-c1 + Math.sqrt(c1 * c1 - 4.0 * c0));
+    const p0 = (z1 - m1) /
+        (z1 -
+            z0); /* Fraction of the object pixels in the target binary image (p0z0+p1z1=m1) */
+    // The threshold is the gray-level closest to the p0-tile of the normalized histogram
+    for (let i = 0; i < histogramLength; i++) {
+        sum += normalizedHistogram[i];
+        if (sum > p0) {
+            threshold = i;
+            break;
+        }
+    }
+    return threshold;
+}
+//# sourceMappingURL=moments.js.map

package/lib-esm/operations/thresholds/moments.js.map

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package/lib-esm/operations/thresholds/otsu.d.ts

@@ -0,0 +1,9 @@
+/**
+ * Return a threshold for a histogram using Otsu algorithm.
+ *
+ * @param histogramCounts - The image histogram.
+ * @param total - Total number of pixels of the image.
+ * @returns The threshold.
+ */
+export declare function otsu(histogramCounts: Uint32Array, total: number): number;
+//# sourceMappingURL=otsu.d.ts.map

package/lib-esm/operations/thresholds/otsu.d.ts.map

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package/lib-esm/operations/thresholds/otsu.js

@@ -0,0 +1,39 @@
+/*
+ * The method is present in: Otsu, N (1979), "A threshold selection method from gray-level histograms", IEEE Trans. Sys., Man., Cyber. 9: 62-66
+ * The Otsu implementation is based on: https://en.wikipedia.org/wiki/Otsu's_method
+ * @param histogram - the histogram of the image
+ * @returns {number} - the threshold
+ */
+/**
+ * Return a threshold for a histogram using Otsu algorithm.
+ *
+ * @param histogramCounts - The image histogram.
+ * @param total - Total number of pixels of the image.
+ * @returns The threshold.
+ */
+export function otsu(histogramCounts, total) {
+    let sumB = 0;
+    let wB = 0;
+    let maximum = 0;
+    let level = 0;
+    let sum1 = 0;
+    for (let i = 0; i < histogramCounts.length; i++) {
+        sum1 += i * histogramCounts[i];
+    }
+    for (let ii = 0; ii < histogramCounts.length; ii++) {
+        wB = wB + histogramCounts[ii];
+        const wF = total - wB;
+        if (wB === 0 || wF === 0) {
+            continue;
+        }
+        sumB = sumB + ii * histogramCounts[ii];
+        const mF = (sum1 - sumB) / wF;
+        const between = wB * wF * (sumB / wB - mF) * (sumB / wB - mF);
+        if (between >= maximum) {
+            level = ii;
+            maximum = between;
+        }
+    }
+    return level;
+}
+//# sourceMappingURL=otsu.js.map

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package/lib-esm/operations/thresholds/percentile.d.ts

@@ -0,0 +1,8 @@
+/**
+ * Return a threshold for a histogram using percentiles.
+ *
+ * @param histogram - Image histogram.
+ * @returns The threshold.
+ */
+export default function percentile(histogram: Uint32Array): number;
+//# sourceMappingURL=percentile.d.ts.map

package/lib-esm/operations/thresholds/percentile.d.ts.map

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

@@ -0,0 +1,36 @@
+// See http://imagej.nih.gov/ij/download/tools/source/ij/process/AutoThresholder.java
+// W. Doyle, "Operation useful for similarity-invariant pattern recognition,"
+// Journal of the Association for Computing Machinery, vol. 9,pp. 259-267, 1962.
+// ported to ImageJ plugin by G.Landini from Antti Niemisto's Matlab code (GPL)
+// Original Matlab code Copyright (C) 2004 Antti Niemisto
+// See http://www.cs.tut.fi/~ant/histthresh/ for an excellent slide presentation
+// and the original Matlab code.
+/**
+ * Return a threshold for a histogram using percentiles.
+ *
+ * @param histogram - Image histogram.
+ * @returns The threshold.
+ */
+export default function percentile(histogram) {
+    let threshold = -1;
+    const percentile = 0.5; // default fraction of foreground pixels
+    const avec = new Array(histogram.length);
+    const total = partialSum(histogram, histogram.length - 1);
+    let temp = 1.0;
+    for (let i = 0; i < histogram.length; i++) {
+        avec[i] = Math.abs(partialSum(histogram, i) / total - percentile);
+        if (avec[i] < temp) {
+            temp = avec[i];
+            threshold = i;
+        }
+    }
+    return threshold;
+}
+function partialSum(histogram, endIndex) {
+    let x = 0;
+    for (let i = 0; i <= endIndex; i++) {
+        x += histogram[i];
+    }
+    return x;
+}
+//# sourceMappingURL=percentile.js.map

package/lib-esm/operations/thresholds/percentile.js.map

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package/lib-esm/operations/thresholds/renyiEntropy.d.ts

@@ -0,0 +1,9 @@
+/**
+ * Return a threshold for a histogram using its entropy.
+ *
+ * @param histogram - The image histogram.
+ * @param total - Total number of pixels of the image.
+ * @returns The threshold.
+ */
+export default function renyiEntropy(histogram: Uint32Array, total: number): number;
+//# sourceMappingURL=renyiEntropy.d.ts.map

package/lib-esm/operations/thresholds/renyiEntropy.d.ts.map

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

@@ -0,0 +1,130 @@
+// see https://github.com/fiji/Auto_Threshold/blob/master/src/main/java/fiji/threshold/Auto_Threshold.java
+// Kapur J.N., Sahoo P.K., and Wong A.K.C. (1985) "A New Method for
+// Gray-Level Picture Thresholding Using the Entropy of the Histogram"
+// Graphical Models and Image Processing, 29(3): 273-285
+// M. Emre Celebi
+// 06.15.2007
+// Ported to ImageJ plugin by G.Landini from E Celebi's fourier_0.8 routines
+/**
+ * Return a threshold for a histogram using its entropy.
+ *
+ * @param histogram - The image histogram.
+ * @param total - Total number of pixels of the image.
+ * @returns The threshold.
+ */
+export default function renyiEntropy(histogram, total) {
+    let firstBin; // First non-zero bin
+    let lastBin; // last non-zero bin
+    const normHisto = new Array(histogram.length); // normalized histogram
+    const P1 = new Array(histogram.length); // accumulative normalized histogram
+    const P2 = new Array(histogram.length); // accumulative normalized histogram
+    // Entropy Variables
+    let threshold1 = 0;
+    let threshold2 = 0;
+    let threshold3 = 0;
+    let maxEnt1 = 0.0;
+    let maxEnt2 = 0.0;
+    let maxEnt3 = 0.0;
+    const alpha2 = 0.5;
+    const term2 = 1.0 / (1.0 - alpha2);
+    const alpha3 = 2.0;
+    const term3 = 1.0 / (1.0 - alpha3);
+    for (let ih = 0; ih < histogram.length; ih++) {
+        normHisto[ih] = histogram[ih] / total;
+    }
+    P1[0] = normHisto[0];
+    P2[0] = 1.0 - P1[0];
+    for (let ih = 1; ih < histogram.length; ih++) {
+        P1[ih] = P1[ih - 1] + normHisto[ih];
+        P2[ih] = 1.0 - P1[ih];
+    }
+    /* Determine the first non-zero bin */
+    firstBin = 0;
+    for (let ih = 0; ih < histogram.length; ih++) {
+        if (Math.abs(P1[ih]) >= Number.EPSILON) {
+            firstBin = ih;
+            break;
+        }
+    }
+    /* Determine the last non-zero bin */
+    lastBin = histogram.length - 1;
+    for (let ih = histogram.length - 1; ih >= firstBin; ih--) {
+        if (Math.abs(P2[ih]) >= Number.EPSILON) {
+            lastBin = ih;
+            break;
+        }
+    }
+    /* Maximum Entropy Thresholding - BEGIN */
+    /* ALPHA = 1.0 */
+    /* Calculate the total entropy each gray-level
+       and find the threshold that maximizes it
+       */
+    for (let it = firstBin; it <= lastBin; it++) {
+        /* Entropy of the background pixels */
+        let entBack1 = 0.0;
+        let entBack2 = 0.0;
+        let entBack3 = 0.0;
+        for (let ih = 0; ih <= it; ih++) {
+            if (histogram[ih] !== 0) {
+                entBack1 -= (normHisto[ih] / P1[it]) * Math.log(normHisto[ih] / P1[it]);
+            }
+            entBack2 += Math.sqrt(normHisto[ih] / P1[it]);
+            entBack3 += (normHisto[ih] * normHisto[ih]) / (P1[it] * P1[it]);
+        }
+        /* Entropy of the object pixels */
+        let entObj1 = 0.0;
+        let entObj2 = 0.0;
+        let entObj3 = 0.0;
+        for (let ih = it + 1; ih < histogram.length; ih++) {
+            if (histogram[ih] !== 0) {
+                entObj1 -= (normHisto[ih] / P2[it]) * Math.log(normHisto[ih] / P2[it]);
+            }
+            entObj2 += Math.sqrt(normHisto[ih] / P2[it]);
+            entObj3 += (normHisto[ih] * normHisto[ih]) / (P2[it] * P2[it]);
+        }
+        /* Total entropy */
+        const totEnt1 = entBack1 + entObj1;
+        const totEnt2 = term2 * (entBack2 * entObj2 > 0.0 ? Math.log(entBack2 * entObj2) : 0.0);
+        const totEnt3 = term3 * (entBack3 * entObj3 > 0.0 ? Math.log(entBack3 * entObj3) : 0.0);
+        if (totEnt1 > maxEnt1) {
+            maxEnt1 = totEnt1;
+            threshold1 = it;
+        }
+        if (totEnt2 > maxEnt2) {
+            maxEnt2 = totEnt2;
+            threshold2 = it;
+        }
+        if (totEnt3 > maxEnt3) {
+            maxEnt3 = totEnt3;
+            threshold3 = it;
+        }
+    }
+    /* End Maximum Entropy Thresholding */
+    const tStars = new Uint32Array([threshold1, threshold2, threshold3]);
+    tStars.sort();
+    let betas;
+    /* Adjust beta values */
+    if (Math.abs(tStars[0] - tStars[1]) <= 5) {
+        if (Math.abs(tStars[1] - tStars[2]) <= 5) {
+            betas = [1, 2, 1];
+        }
+        else {
+            betas = [0, 1, 3];
+        }
+    }
+    else {
+        if (Math.abs(tStars[1] - tStars[2]) <= 5) {
+            betas = [3, 1, 0];
+        }
+        else {
+            betas = [1, 2, 1];
+        }
+    }
+    /* Determine the optimal threshold value */
+    const omega = P1[tStars[2]] - P1[tStars[0]];
+    const optThreshold = Math.round(tStars[0] * (P1[tStars[0]] + 0.25 * omega * betas[0]) +
+        0.25 * tStars[1] * omega * betas[1] +
+        tStars[2] * (P2[tStars[2]] + 0.25 * omega * betas[2]));
+    return optThreshold;
+}
+//# sourceMappingURL=renyiEntropy.js.map

package/lib-esm/operations/thresholds/renyiEntropy.js.map

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package/lib-esm/operations/thresholds/shanbhag.d.ts

@@ -0,0 +1,10 @@
+/**
+ * Return a threshold for a histogram using Shanbhag algorithm.
+ *
+ * @param histogram - The image histogram.
+ * @param histogrami
+ * @param total - Total number of pixels of the image.
+ * @returns The threshold.
+ */
+export default function shanbhag(histogram: Uint32Array, total: number): number;
+//# sourceMappingURL=shanbhag.d.ts.map

package/lib-esm/operations/thresholds/shanbhag.d.ts.map

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package/lib-esm/operations/thresholds/shanbhag.js

@@ -0,0 +1,74 @@
+// see https://github.com/fiji/Auto_Threshold/blob/master/src/main/java/fiji/threshold/Auto_Threshold.java
+// Shanhbag A.G. (1994) "Utilization of Information Measure as a Means of
+// Image Thresholding" Graphical Models and Image Processing, 56(5): 414-419
+// Ported to ImageJ plugin by G.Landini from E Celebi's fourier_0.8 routines
+/**
+ * Return a threshold for a histogram using Shanbhag algorithm.
+ *
+ * @param histogram - The image histogram.
+ * @param histogrami
+ * @param total - Total number of pixels of the image.
+ * @returns The threshold.
+ */
+export default function shanbhag(histogram, total) {
+    const normHisto = new Array(histogram.length); // normalized histogram
+    for (let ih = 0; ih < histogram.length; ih++) {
+        normHisto[ih] = histogram[ih] / total;
+    }
+    const P1 = new Array(histogram.length); // cumulative normalized histogram
+    const P2 = new Array(histogram.length);
+    P1[0] = normHisto[0];
+    P2[0] = 1.0 - P1[0];
+    for (let ih = 1; ih < histogram.length; ih++) {
+        P1[ih] = P1[ih - 1] + normHisto[ih];
+        P2[ih] = 1.0 - P1[ih];
+    }
+    /* Determine the first non-zero bin */
+    let firstBin = 0;
+    for (let ih = 0; ih < histogram.length; ih++) {
+        if (Math.abs(P1[ih]) >= Number.EPSILON) {
+            firstBin = ih;
+            break;
+        }
+    }
+    /* Determine the last non-zero bin */
+    let lastBin = histogram.length - 1;
+    for (let ih = histogram.length - 1; ih >= firstBin; ih--) {
+        if (Math.abs(P2[ih]) >= Number.EPSILON) {
+            lastBin = ih;
+            break;
+        }
+    }
+    // Calculate the total entropy each gray-level
+    // and find the threshold that maximizes it
+    let threshold = -1;
+    let minEnt = Number.MAX_VALUE; // min entropy
+    let term;
+    let totEnt; // total entropy
+    let entBack; // entropy of the background pixels at a given threshold
+    let entObj; // entropy of the object pixels at a given threshold
+    for (let it = firstBin; it <= lastBin; it++) {
+        /* Entropy of the background pixels */
+        entBack = 0.0;
+        term = 0.5 / P1[it];
+        for (let ih = 1; ih <= it; ih++) {
+            entBack -= normHisto[ih] * Math.log(1.0 - term * P1[ih - 1]);
+        }
+        entBack *= term;
+        /* Entropy of the object pixels */
+        entObj = 0.0;
+        term = 0.5 / P2[it];
+        for (let ih = it + 1; ih < histogram.length; ih++) {
+            entObj -= normHisto[ih] * Math.log(1.0 - term * P2[ih]);
+        }
+        entObj *= term;
+        /* Total entropy */
+        totEnt = Math.abs(entBack - entObj);
+        if (totEnt < minEnt) {
+            minEnt = totEnt;
+            threshold = it;
+        }
+    }
+    return threshold;
+}
+//# sourceMappingURL=shanbhag.js.map

package/lib-esm/operations/thresholds/shanbhag.js.map

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package/lib-esm/operations/thresholds/triangle.d.ts

@@ -0,0 +1,8 @@
+/**
+ * Return a threshold for a histogram using Triangle algorithm.
+ *
+ * @param histogram - The image histogram.
+ * @returns The threshold.
+ */
+export declare function triangle(histogram: Uint32Array): number;
+//# sourceMappingURL=triangle.d.ts.map

package/lib-esm/operations/thresholds/triangle.d.ts.map

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

@@ -0,0 +1,109 @@
+// see https://github.com/fiji/Auto_Threshold/blob/master/src/main/java/fiji/threshold/Auto_Threshold.java
+// Zack, G. W., Rogers, W. E. and Latt, S. A., 1977,
+// Automatic Measurement of Sister Chromatid Exchange Frequency,
+// Journal of Histochemistry and Cytochemistry 25 (7), pp. 741-753
+//
+//  modified from Johannes Schindelin plugin
+/**
+ * Return a threshold for a histogram using Triangle algorithm.
+ *
+ * @param histogram - The image histogram.
+ * @returns The threshold.
+ */
+export function triangle(histogram) {
+    // find min and max
+    let min = 0;
+    let dmax = 0;
+    let max = 0;
+    let min2 = 0;
+    for (let i = 0; i < histogram.length; i++) {
+        if (histogram[i] > 0) {
+            min = i;
+            break;
+        }
+    }
+    if (min > 0) {
+        // line to the (p==0) point, not to histogram[min]
+        min--;
+    }
+    // The Triangle algorithm cannot tell whether the data is skewed to one side or another.
+    // This causes a problem as there are 2 possible thresholds between the max and the 2 extremes
+    // of the histogram.
+    // Here I propose to find out to which side of the max point the data is furthest, and use that as
+    //  the other extreme.
+    for (let i = histogram.length - 1; i > 0; i--) {
+        if (histogram[i] > 0) {
+            min2 = i;
+            break;
+        }
+    }
+    if (min2 < histogram.length - 1) {
+        // line to the (p==0) point, not to data[min]
+        min2++;
+    }
+    for (let i = 0; i < histogram.length; i++) {
+        if (histogram[i] > dmax) {
+            max = i;
+            dmax = histogram[i];
+        }
+    }
+    // find which is the furthest side
+    let inverted = false;
+    if (max - min < min2 - max) {
+        // reverse the histogram
+        inverted = true;
+        let left = 0; // index of leftmost element
+        let right = histogram.length - 1; // index of rightmost element
+        while (left < right) {
+            // exchange the left and right elements
+            const temp = histogram[left];
+            histogram[left] = histogram[right];
+            histogram[right] = temp;
+            // move the bounds toward the center
+            left++;
+            right--;
+        }
+        min = histogram.length - 1 - min2;
+        max = histogram.length - 1 - max;
+    }
+    if (min === max) {
+        return min;
+    }
+    // describe line by nx * x + ny * y - d = 0
+    let nx, ny, d;
+    // nx is just the max frequency as the other point has freq=0
+    nx = histogram[max]; // -min; // data[min]; //  lowest value bmin = (p=0)% in the image
+    ny = min - max;
+    d = Math.sqrt(nx * nx + ny * ny);
+    nx /= d;
+    ny /= d;
+    d = nx * min + ny * histogram[min];
+    // find split point
+    let split = min;
+    let splitDistance = 0;
+    for (let i = min + 1; i <= max; i++) {
+        const newDistance = nx * i + ny * histogram[i] - d;
+        if (newDistance > splitDistance) {
+            split = i;
+            splitDistance = newDistance;
+        }
+    }
+    split--;
+    if (inverted) {
+        // The histogram might be used for something else, so let's reverse it back
+        let left = 0;
+        let right = histogram.length - 1;
+        while (left < right) {
+            const temp = histogram[left];
+            histogram[left] = histogram[right];
+            histogram[right] = temp;
+            left++;
+            right--;
+        }
+        return histogram.length - 1 - split;
+    }
+    else {
+        return split;
+    }
+}
+//# sourceMappingURL=triangle.js.map

package/lib-esm/operations/thresholds/triangle.js.map

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package/lib-esm/operations/thresholds/yen.d.ts

@@ -0,0 +1,9 @@
+/**
+ * Return a threshold for a histogram using Yen algorithm.
+ *
+ * @param histogram - The image histogram.
+ * @param total - Total number of pixels of the image.
+ * @returns The threshold.
+ */
+export default function yen(histogram: Uint32Array, total: number): number;
+//# sourceMappingURL=yen.d.ts.map

package/lib-esm/operations/thresholds/yen.d.ts.map

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

@@ -0,0 +1,59 @@
+// see https://github.com/fiji/Auto_Threshold/blob/master/src/main/java/fiji/threshold/Auto_Threshold.java
+// Implements Yen  thresholding method
+// 1) Yen J.C., Chang F.J., and Chang S. (1995) "A New Criterion
+//    for Automatic Multilevel Thresholding" IEEE Trans. on Image
+//    Processing, 4(3): 370-378
+// 2) Sezgin M. and Sankur B. (2004) "Survey over Image Thresholding
+//    Techniques and Quantitative Performance Evaluation" Journal of
+//    Electronic Imaging, 13(1): 146-165
+//    http://citeseer.ist.psu.edu/sezgin04survey.html
+//
+// M. Emre Celebi
+// 06.15.2007
+// Ported to ImageJ plugin by G.Landini from E Celebi's fourier_0.8 routines
+/**
+ * Return a threshold for a histogram using Yen algorithm.
+ *
+ * @param histogram - The image histogram.
+ * @param total - Total number of pixels of the image.
+ * @returns The threshold.
+ */
+export default function yen(histogram, total) {
+    const normHisto = new Array(histogram.length); // normalized histogram
+    for (let ih = 0; ih < histogram.length; ih++) {
+        normHisto[ih] = histogram[ih] / total;
+    }
+    const P1 = new Array(histogram.length); // cumulative normalized histogram
+    P1[0] = normHisto[0];
+    for (let ih = 1; ih < histogram.length; ih++) {
+        P1[ih] = P1[ih - 1] + normHisto[ih];
+    }
+    const P1Sq = new Array(histogram.length);
+    P1Sq[0] = normHisto[0] * normHisto[0];
+    for (let ih = 1; ih < histogram.length; ih++) {
+        P1Sq[ih] = P1Sq[ih - 1] + normHisto[ih] * normHisto[ih];
+    }
+    const P2Sq = new Array(histogram.length);
+    P2Sq[histogram.length - 1] = 0.0;
+    for (let ih = histogram.length - 2; ih >= 0; ih--) {
+        P2Sq[ih] = P2Sq[ih + 1] + normHisto[ih + 1] * normHisto[ih + 1];
+    }
+    /* Find the threshold that maximizes the criterion */
+    let threshold = -1;
+    let maxCrit = Number.MIN_VALUE;
+    let crit;
+    for (let it = 0; it < histogram.length; it++) {
+        crit =
+            -1.0 * (P1Sq[it] * P2Sq[it] > 0.0 ? Math.log(P1Sq[it] * P2Sq[it]) : 0.0) +
+                2 *
+                    (P1[it] * (1.0 - P1[it]) > 0.0
+                        ? Math.log(P1[it] * (1.0 - P1[it]))
+                        : 0.0);
+        if (crit > maxCrit) {
+            maxCrit = crit;
+            threshold = it;
+        }
+    }
+    return threshold;
+}
+//# sourceMappingURL=yen.js.map

package/lib-esm/operations/thresholds/yen.js.map

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