image-js 0.0.0-next-e30968a2d8

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

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

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package/lib/operations/thresholds/triangle.js

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+"use strict";
+// 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
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.triangle = void 0;
+/**
+ * Return a threshold for a histogram using Triangle algorithm.
+ *
+ * @param histogram - The image histogram.
+ * @returns The threshold.
+ */
+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;
+//# sourceMappingURL=triangle.js.map

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

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

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

@@ -0,0 +1,62 @@
+"use strict";
+// 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
+Object.defineProperty(exports, "__esModule", { value: true });
+/**
+ * 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.
+ */
+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;
+}
+exports.default = yen;
+//# sourceMappingURL=yen.js.map

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

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

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package/lib/roi/RoiManager.js

@@ -0,0 +1,10 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.RoiKind = void 0;
+var RoiKind;
+(function (RoiKind) {
+    RoiKind["BLACK"] = "BLACK";
+    RoiKind["WHITE"] = "WHITE";
+    RoiKind["BW"] = "BW";
+})(RoiKind = exports.RoiKind || (exports.RoiKind = {}));
+//# sourceMappingURL=RoiManager.js.map

package/lib/roi/RoiManager.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"RoiManager.js","sourceRoot":"","sources":["../../src/roi/RoiManager.ts"],"names":[],"mappings":";;;AAAA,IAAY,OAIX;AAJD,WAAY,OAAO;IACjB,0BAAe,CAAA;IACf,0BAAe,CAAA;IACf,oBAAS,CAAA;AACX,CAAC,EAJW,OAAO,GAAP,eAAO,KAAP,eAAO,QAIlB"}

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

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

@@ -0,0 +1,17 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.RoiMapManager = void 0;
+const ml_matrix_1 = require("ml-matrix");
+class RoiMapManager {
+    constructor(map) {
+        this.map = map;
+    }
+    getRois() {
+        return [];
+    }
+    getMapMatrix() {
+        return ml_matrix_1.Matrix.from1DArray(this.map.height, this.map.width, this.map.data).to2DArray();
+    }
+}
+exports.RoiMapManager = RoiMapManager;
+//# sourceMappingURL=RoiMapManager.js.map

package/lib/roi/RoiMapManager.js.map

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

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

@@ -0,0 +1,48 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.colorRois = exports.RoisColorMode = void 0;
+const __1 = require("..");
+const constants_1 = require("./utils/constants");
+const getColorMap_1 = require("./utils/getColorMap");
+const _1 = require(".");
+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 = exports.RoisColorMode || (exports.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.
+ */
+function colorRois(roiMapManager, options = {}) {
+    const { roiKind = _1.RoiKind.BW, mode = RoisColorMode.BINARY } = options;
+    let image = new __1.IJS(roiMapManager.map.width, roiMapManager.map.height, {
+        colorModel: __1.ImageColorModel.RGBA,
+    });
+    const colorMap = (0, getColorMap_1.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] + constants_1.colorMapCenter];
+    }
+    return image;
+}
+exports.colorRois = colorRois;
+//# sourceMappingURL=colorRois.js.map

package/lib/roi/colorRois.js.map

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

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

@@ -0,0 +1,148 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.fromMask = void 0;
+const RoiMapManager_1 = require("./RoiMapManager");
+const constants_1 = require("./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.
+ */
+function fromMask(mask, options = {}) {
+    const { allowCorners = false } = options;
+    const MAX_ARRAY = constants_1.maxNumberRois - 1; // 65535 should be enough for most of the cases
+    const maxPositiveId = constants_1.maxRoiId - 1;
+    const maxNegativeId = -constants_1.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(constants_1.maxNumberRois);
+    let rowToProcess = new Uint16Array(constants_1.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_1.RoiMapManager({
+        width: mask.width,
+        height: mask.height,
+        data,
+        nbNegative: Math.abs(negativeId),
+        nbPositive: positiveId,
+    });
+}
+exports.fromMask = fromMask;
+//# sourceMappingURL=fromMask.js.map

package/lib/roi/fromMask.js.map

@@ -0,0 +1 @@
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package/lib/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/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"}