image-js 1.0.0-alpha.3 → 1.1.0

package/lib/operations/thresholds/renyiEntropy.js

@@ -0,0 +1,127 @@
+// 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;
+    let maxEnt2 = 0;
+    let maxEnt3 = 0;
+    const alpha2 = 0.5;
+    const term2 = 1 / (1 - alpha2);
+    const alpha3 = 2;
+    const term3 = 1 / (1 - alpha3);
+    for (let ih = 0; ih < histogram.length; ih++) {
+        normHisto[ih] = histogram[ih] / total;
+    }
+    P1[0] = normHisto[0];
+    P2[0] = 1 - P1[0];
+    for (let ih = 1; ih < histogram.length; ih++) {
+        P1[ih] = P1[ih - 1] + normHisto[ih];
+        P2[ih] = 1 - 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;
+        let entBack2 = 0;
+        let entBack3 = 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;
+        let entObj2 = 0;
+        let entObj3 = 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 ? Math.log(entBack2 * entObj2) : 0);
+        const totEnt3 = term3 * (entBack3 * entObj3 > 0 ? Math.log(entBack3 * entObj3) : 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/operations/thresholds/renyiEntropy.js.map

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

@@ -0,0 +1,8 @@
+/**
+ * Return a threshold for a histogram using Shanbhag algorithm.
+ * @param histogram - The image histogram.
+ * @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/operations/thresholds/shanbhag.d.ts.map

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

@@ -0,0 +1,72 @@
+// 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 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 - P1[0];
+    for (let ih = 1; ih < histogram.length; ih++) {
+        P1[ih] = P1[ih - 1] + normHisto[ih];
+        P2[ih] = 1 - 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;
+        term = 0.5 / P1[it];
+        for (let ih = 1; ih <= it; ih++) {
+            entBack -= normHisto[ih] * Math.log(1 - term * P1[ih - 1]);
+        }
+        entBack *= term;
+        /* Entropy of the object pixels */
+        entObj = 0;
+        term = 0.5 / P2[it];
+        for (let ih = it + 1; ih < histogram.length; ih++) {
+            entObj -= normHisto[ih] * Math.log(1 - 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/operations/thresholds/shanbhag.js.map

@@ -0,0 +1 @@
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package/lib/operations/thresholds/triangle.d.ts

@@ -1,2 +1,7 @@
-export declare function triangle(histogram: number[]): number;
+/**
+ * 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/operations/thresholds/triangle.d.ts.map

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package/lib/operations/thresholds/triangle.js

@@ -1,106 +1,108 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-// 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
-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;
-    }
-}
-exports.triangle = triangle;
+// 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.hypot(nx, 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

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

@@ -0,0 +1,8 @@
+/**
+ * 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/operations/thresholds/yen.d.ts.map

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

package/lib/operations/thresholds/yen.js

@@ -0,0 +1,55 @@
+// 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;
+    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 * (P1Sq[it] * P2Sq[it] > 0 ? Math.log(P1Sq[it] * P2Sq[it]) : 0) +
+                2 * (P1[it] * (1 - P1[it]) > 0 ? Math.log(P1[it] * (1 - P1[it])) : 0);
+        if (crit > maxCrit) {
+            maxCrit = crit;
+            threshold = it;
+        }
+    }
+    return threshold;
+}
+//# sourceMappingURL=yen.js.map

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

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package/lib/point/operations.d.ts

@@ -0,0 +1,10 @@
+import type { Point } from '../utils/geometry/points.js';
+/**
+ * Rotate a point around a center by a given angle.
+ * @param point - The point to rotate
+ * @param rotationCenter - The center of rotation
+ * @param angle - The angle of rotation in radians
+ * @returns The rotated point
+ */
+export declare function rotatePoint(point: Point, rotationCenter: Point, angle: number): Point;
+//# sourceMappingURL=operations.d.ts.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"operations.d.ts","sourceRoot":"","sources":["../../src/point/operations.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,KAAK,EAAE,MAAM,6BAA6B,CAAC;AAEzD;;;;;;GAMG;AACH,wBAAgB,WAAW,CACzB,KAAK,EAAE,KAAK,EACZ,cAAc,EAAE,KAAK,EACrB,KAAK,EAAE,MAAM,GACZ,KAAK,CAeP"}

package/lib/point/operations.js

@@ -0,0 +1,21 @@
+/**
+ * Rotate a point around a center by a given angle.
+ * @param point - The point to rotate
+ * @param rotationCenter - The center of rotation
+ * @param angle - The angle of rotation in radians
+ * @returns The rotated point
+ */
+export function rotatePoint(point, rotationCenter, angle) {
+    const angleCos = Math.cos(angle);
+    const angleSin = Math.sin(angle);
+    const column = point.column * angleCos -
+        point.row * angleSin +
+        (1 - angleCos) * rotationCenter.column +
+        rotationCenter.row * angleSin;
+    const row = point.column * angleSin +
+        point.row * angleCos +
+        (1 - angleCos) * rotationCenter.row -
+        rotationCenter.column * angleSin;
+    return { column, row };
+}
+//# sourceMappingURL=operations.js.map

package/lib/point/operations.js.map

@@ -0,0 +1 @@
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