image-js 0.31.3 → 0.33.1

package/README.md

@@ -1,10 +1,5 @@
 # image-js
 
-[![NPM version][npm-image]][npm-url]
-[![build status][ci-image]][ci-url]
-[![Test coverage][codecov-image]][codecov-url]
-[![npm download][download-image]][download-url]
-
 Advanced image processing and manipulation in JavaScript.
 
 image-js is a full-featured library that can deal with simple image processing
@@ -12,6 +7,23 @@ image-js is a full-featured library that can deal with simple image processing
 processing on scientific images (Region of interest (ROI), Hull curve, minimal
 boundary rectangle (MBR), particle size and orientation, cell imaging, etc.).
 
+<h3 align="center">
+
+  <a href="https://www.zakodium.com">
+    <img src="https://www.zakodium.com/brand/zakodium-logo-white.svg" width="50" alt="Zakodium logo" />
+  </a>
+
+  <p>
+    Maintained by <a href="https://www.zakodium.com">Zakodium</a>
+  </p>
+
+[![NPM version][npm-image]][npm-url]
+[![build status][ci-image]][ci-url]
+[![Test coverage][codecov-image]][codecov-url]
+[![npm download][download-image]][download-url]
+
+</h3>
+
 ## [API Documentation](https://image-js.github.io/image-js/)
 
 ## Installation

package/index.d.ts

@@ -61,8 +61,9 @@ export declare class Image {
   // exportMethods
   save(path: string, options?: SaveOptions): Promise<void>;
   toDataURL(type?: string, options?: SaveOptions): string;
-  toBase64(type?: string, options?: SaveOptions): string;
-  toBlob(type?: string, quality?: number): Blob;
+  toBase64(type?: string, options?: SaveOptions): string | Promise<string>;
+  toBuffer(options?: SaveOptions): Uint8Array;
+  toBlob(type?: string, quality?: number): Promise<Blob>;
   getCanvas(): HTMLCanvasElement;
 
   checkProcessable(processName: string, options: object): void;
@@ -83,8 +84,8 @@ export declare class Image {
   // divide
   // hypotenuse
   // background
-  // flipX
-  // flipY
+  flipX(): this;
+  flipY(): this;
 
   blurFilter(options?: { radius?: number }): Image;
   medianFilter(options?: {
@@ -290,7 +291,7 @@ export interface ResizeOptions {
   width?: number;
   height?: number;
   factor?: number;
-  interpolation?: InterpolationAlgorithm;
+  interpolation?: 'nearestNeighbor';
   preserveAspectRatio?: boolean;
 }
 

package/lib/browser/environment.js

@@ -3,11 +3,12 @@
 Object.defineProperty(exports, "__esModule", {
   value: true
 });
+exports.ImageData = exports.DOMImage = void 0;
 exports.createCanvas = createCanvas;
-exports.fetchBinary = fetchBinary;
 exports.createWriteStream = createWriteStream;
+exports.env = void 0;
+exports.fetchBinary = fetchBinary;
 exports.writeFile = writeFile;
-exports.DOMImage = exports.ImageData = exports.env = void 0;
 const env = 'browser';
 exports.env = env;
 const ImageData = self.ImageData;

package/lib/image/Image.js

@@ -55,7 +55,7 @@ const objectToString = Object.prototype.toString;
  *      8 and 16 bit depth images.
  * * position : an array of 2 elements that allows to define a relative position
  *      to a parent image. This will be used in a crop or in the management
- *      of Region Of Interests (Roi) for exmaple
+ *      of Region Of Interests (Roi) for example
  * * data : an array that contains all the points of the image.
  *      Depending the bitDepth Uint8Array (1 bit), Uint8Array (8 bits),
  *      Uint16Array (16 bits), Float32Array (32 bits)
@@ -135,7 +135,7 @@ const objectToString = Object.prototype.toString;
  * // the RoiManager. A RoiManager will be applied on the original image
  * // in order to be able to extract from the original image the regions
  *
- * // the result of this console.log result can diretly be pasted
+ * // the result of this console.log result can directly be pasted
  * // in the browser
  * // console.log(mask.toDataURL());
  *
@@ -178,6 +178,24 @@ const objectToString = Object.prototype.toString;
  *  var canvas = document.getElementById('myCanvasID');
  *  var image = IJS.fromCanvas(canvas);
  * </script>
+ *
+ * @example
+ * // Image from matrix of values
+ * const [min, max] = d3.extent(temperatures)
+ * const colorScaler = d3.scaleSequential([min, max], d3.interpolateRdYlBu);
+ *
+ * // size = rows * columns * channels
+ * const data = new Uint8Array(2*3*3);
+ * for (let i = 0; i < temperatures.length; i++) {
+ *   const {r, g, b} = d3.rgb(colorScaler(temperatures[i]));
+ *   data[i*3] = r;
+ *   data[i*3 + 1] = g;
+ *   data[i*3 + 2] = b;
+ * }
+ *
+ * const image = new Image(2, 3, data, { kind: 'RGB' });
+ * // or
+ * const image = new Image({ width: 2, height: 3, data, kind: 'RGB'});
  */
 
 class Image {

package/lib/image/compute/extendedPoints.js

@@ -8,6 +8,7 @@ exports.default = extendedPoints;
 /**
  * Allows to generate an array of points for a binary image (bit depth = 1)
  * The points consider the beginning and the end of each pixel
+ * This method is only used to calculate minimalBoundRectangle
  * @memberof Image
  * @instance
  * @return {Array<Array<number>>} - an array of [x,y] corresponding to the set pixels in the binary image
@@ -35,6 +36,11 @@ function extendedPoints() {
             pixels.push([x, y + 1]);
             pixels.push([x + 1, y + 1]);
           }
+        } // this small optimization allows to reduce dramatically the number of points for MBR calculation
+
+
+        while (x < this.width - 2 && this.getBitXY(x + 1, y) === 1 && this.getBitXY(x + 2, y) === 1) {
+          x++;
         }
       }
     }

package/lib/image/core/environment.js

@@ -3,20 +3,21 @@
 Object.defineProperty(exports, "__esModule", {
   value: true
 });
-exports.fetchBinary = fetchBinary;
+exports.createCanvas = exports.ImageData = exports.DOMImage = void 0;
 Object.defineProperty(exports, "createWriteStream", {
   enumerable: true,
   get: function () {
     return _fs.createWriteStream;
   }
 });
+exports.env = void 0;
+exports.fetchBinary = fetchBinary;
 Object.defineProperty(exports, "writeFile", {
   enumerable: true,
   get: function () {
     return _fs.writeFile;
   }
 });
-exports.DOMImage = exports.ImageData = exports.createCanvas = exports.env = void 0;
 
 var _fs = require("fs");
 
@@ -27,6 +28,7 @@ exports.DOMImage = DOMImage;
 exports.createCanvas = createCanvas;
 
 try {
+  // eslint-disable-next-line import/no-unresolved
   const canvas = require('canvas');
 
   exports.createCanvas = createCanvas = canvas.createCanvas;

package/lib/image/core/kind.js

@@ -3,18 +3,18 @@
 Object.defineProperty(exports, "__esModule", {
   value: true
 });
+exports.createPixelArray = createPixelArray;
 exports.getKind = getKind;
-exports.verifyKindDefinition = verifyKindDefinition;
 exports.getTheoreticalPixelArraySize = getTheoreticalPixelArraySize;
-exports.createPixelArray = createPixelArray;
+exports.verifyKindDefinition = verifyKindDefinition;
 
 var ColorModel = _interopRequireWildcard(require("../model/model"));
 
 var Kind = _interopRequireWildcard(require("./kindNames"));
 
-function _getRequireWildcardCache() { if (typeof WeakMap !== "function") return null; var cache = new WeakMap(); _getRequireWildcardCache = function () { return cache; }; return cache; }
+function _getRequireWildcardCache(nodeInterop) { if (typeof WeakMap !== "function") return null; var cacheBabelInterop = new WeakMap(); var cacheNodeInterop = new WeakMap(); return (_getRequireWildcardCache = function (nodeInterop) { return nodeInterop ? cacheNodeInterop : cacheBabelInterop; })(nodeInterop); }
 
-function _interopRequireWildcard(obj) { if (obj && obj.__esModule) { return obj; } if (obj === null || typeof obj !== "object" && typeof obj !== "function") { return { default: obj }; } var cache = _getRequireWildcardCache(); if (cache && cache.has(obj)) { return cache.get(obj); } var newObj = {}; var hasPropertyDescriptor = Object.defineProperty && Object.getOwnPropertyDescriptor; for (var key in obj) { if (Object.prototype.hasOwnProperty.call(obj, key)) { var desc = hasPropertyDescriptor ? Object.getOwnPropertyDescriptor(obj, key) : null; if (desc && (desc.get || desc.set)) { Object.defineProperty(newObj, key, desc); } else { newObj[key] = obj[key]; } } } newObj.default = obj; if (cache) { cache.set(obj, newObj); } return newObj; }
+function _interopRequireWildcard(obj, nodeInterop) { if (!nodeInterop && obj && obj.__esModule) { return obj; } if (obj === null || typeof obj !== "object" && typeof obj !== "function") { return { default: obj }; } var cache = _getRequireWildcardCache(nodeInterop); if (cache && cache.has(obj)) { return cache.get(obj); } var newObj = {}; var hasPropertyDescriptor = Object.defineProperty && Object.getOwnPropertyDescriptor; for (var key in obj) { if (key !== "default" && Object.prototype.hasOwnProperty.call(obj, key)) { var desc = hasPropertyDescriptor ? Object.getOwnPropertyDescriptor(obj, key) : null; if (desc && (desc.get || desc.set)) { Object.defineProperty(newObj, key, desc); } else { newObj[key] = obj[key]; } } } newObj.default = obj; if (cache) { cache.set(obj, newObj); } return newObj; }
 
 const kinds = {};
 kinds[Kind.BINARY] = {

package/lib/image/core/kindNames.js

@@ -3,7 +3,7 @@
 Object.defineProperty(exports, "__esModule", {
   value: true
 });
-exports.CMYKA = exports.CMYK = exports.RGBA = exports.RGB = exports.GREYA = exports.GREY = exports.BINARY = void 0;
+exports.RGBA = exports.RGB = exports.GREYA = exports.GREY = exports.CMYKA = exports.CMYK = exports.BINARY = void 0;
 // Shortcuts for common image kinds
 const BINARY = 'BINARY';
 exports.BINARY = BINARY;

package/lib/image/core/load.js

@@ -169,9 +169,30 @@ function loadJPEG(data) {
     useTArray: true,
     maxMemoryUsageInMB: 1024
   });
-  return new _Image.default(jpeg.width, jpeg.height, jpeg.data, {
+  let image = new _Image.default(jpeg.width, jpeg.height, jpeg.data, {
     meta
   });
+
+  if (meta && meta.tiff.tags.Orientation) {
+    const orientation = meta.tiff.tags.Orientation;
+
+    if (orientation > 2) {
+      image = image.rotate({
+        3: 180,
+        4: 180,
+        5: 90,
+        6: 90,
+        7: 270,
+        8: 270
+      }[orientation]);
+    }
+
+    if ([2, 4, 5, 7].includes(orientation)) {
+      image = image.flipX();
+    }
+  }
+
+  return image;
 }
 
 function loadTIFF(data) {

package/lib/image/filter/subtractImage.js

@@ -7,24 +7,18 @@ exports.default = subtractImage;
 
 var _channel = require("../../util/channel");
 
-var _Image = _interopRequireDefault(require("../Image"));
-
-function _interopRequireDefault(obj) { return obj && obj.__esModule ? obj : { default: obj }; }
-
 /**
  * Calculate a new image that is the subtraction between the current image and the otherImage.
  * @memberof Image
  * @instance
  * @param {Image} otherImage
  * @param {object} [options={}]
- * @param {number} [options.bitDepth=this.bitDepth]
  * @param {number[]|string[]} [options.channels] : to which channel to apply the filter. By default all but alpha.
  * @param {number[]|string[]} [options.absolute=false] :.take the absolute value of the difference (default minimum=0)
  * @return {Image}
  */
 function subtractImage(otherImage, options = {}) {
   let {
-    bitDepth = this.bitDepth,
     channels,
     absolute = false
   } = options;
@@ -44,10 +38,7 @@ function subtractImage(otherImage, options = {}) {
     throw new Error('subtractImage: both images must have the same number of channels');
   }
 
-  let newImage = _Image.default.createFrom(this, {
-    bitDepth: bitDepth
-  });
-
+  let newImage = this.clone();
   channels = (0, _channel.validateArrayOfChannels)(this, {
     channels: channels
   });

package/lib/image/internal/checks.js

@@ -3,10 +3,10 @@
 Object.defineProperty(exports, "__esModule", {
   value: true
 });
-exports.checkRow = checkRow;
-exports.checkColumn = checkColumn;
 exports.checkChannel = checkChannel;
+exports.checkColumn = checkColumn;
 exports.checkInterpolation = checkInterpolation;
+exports.checkRow = checkRow;
 exports.validInterpolations = void 0;
 
 function checkRow(image, row) {

package/lib/image/model/model.js

@@ -3,7 +3,7 @@
 Object.defineProperty(exports, "__esModule", {
   value: true
 });
-exports.CMYK = exports.HSV = exports.HSL = exports.RGB = exports.GREY = void 0;
+exports.RGB = exports.HSV = exports.HSL = exports.GREY = exports.CMYK = void 0;
 
 /**
  * Color model of an image

package/lib/image/roi/Roi.js

@@ -21,9 +21,9 @@ var KindNames = _interopRequireWildcard(require("../core/kindNames"));
 
 var _feretDiameters = _interopRequireDefault(require("./feretDiameters"));
 
-function _getRequireWildcardCache() { if (typeof WeakMap !== "function") return null; var cache = new WeakMap(); _getRequireWildcardCache = function () { return cache; }; return cache; }
+function _getRequireWildcardCache(nodeInterop) { if (typeof WeakMap !== "function") return null; var cacheBabelInterop = new WeakMap(); var cacheNodeInterop = new WeakMap(); return (_getRequireWildcardCache = function (nodeInterop) { return nodeInterop ? cacheNodeInterop : cacheBabelInterop; })(nodeInterop); }
 
-function _interopRequireWildcard(obj) { if (obj && obj.__esModule) { return obj; } if (obj === null || typeof obj !== "object" && typeof obj !== "function") { return { default: obj }; } var cache = _getRequireWildcardCache(); if (cache && cache.has(obj)) { return cache.get(obj); } var newObj = {}; var hasPropertyDescriptor = Object.defineProperty && Object.getOwnPropertyDescriptor; for (var key in obj) { if (Object.prototype.hasOwnProperty.call(obj, key)) { var desc = hasPropertyDescriptor ? Object.getOwnPropertyDescriptor(obj, key) : null; if (desc && (desc.get || desc.set)) { Object.defineProperty(newObj, key, desc); } else { newObj[key] = obj[key]; } } } newObj.default = obj; if (cache) { cache.set(obj, newObj); } return newObj; }
+function _interopRequireWildcard(obj, nodeInterop) { if (!nodeInterop && obj && obj.__esModule) { return obj; } if (obj === null || typeof obj !== "object" && typeof obj !== "function") { return { default: obj }; } var cache = _getRequireWildcardCache(nodeInterop); if (cache && cache.has(obj)) { return cache.get(obj); } var newObj = {}; var hasPropertyDescriptor = Object.defineProperty && Object.getOwnPropertyDescriptor; for (var key in obj) { if (key !== "default" && Object.prototype.hasOwnProperty.call(obj, key)) { var desc = hasPropertyDescriptor ? Object.getOwnPropertyDescriptor(obj, key) : null; if (desc && (desc.get || desc.set)) { Object.defineProperty(newObj, key, desc); } else { newObj[key] = obj[key]; } } } newObj.default = obj; if (cache) { cache.set(obj, newObj); } return newObj; }
 
 function _interopRequireDefault(obj) { return obj && obj.__esModule ? obj : { default: obj }; }
 
@@ -728,7 +728,7 @@ class Roi {
 
   get roundness() {
     /*Slide 24 https://static.horiba.com/fileadmin/Horiba/Products/Scientific/Particle_Characterization/Webinars/Slides/TE011.pdf */
-    return 4 * this.surface / (Math.PI * this.feretDiameters.max) ** 2;
+    return 4 * this.surface / (Math.PI * this.feretDiameters.max ** 2);
   }
 
   get sphericity() {

package/lib/image/transform/mask/renyiEntropy.js

@@ -5,8 +5,6 @@ Object.defineProperty(exports, "__esModule", {
 });
 exports.default = renyiEntropy;
 
-var _numSort = require("num-sort");
-
 // 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"
@@ -136,7 +134,7 @@ function renyiEntropy(histogram, total) {
 
 
   let tStars = [threshold1, threshold2, threshold3];
-  tStars.sort(_numSort.ascending);
+  tStars.sort((a, b) => a - b);
   let betas;
   /* Adjust beta values */
 

package/lib/image/utility/getMatrix.js

@@ -5,9 +5,7 @@ Object.defineProperty(exports, "__esModule", {
 });
 exports.default = getMatrix;
 
-var _mlMatrix = _interopRequireDefault(require("ml-matrix"));
-
-function _interopRequireDefault(obj) { return obj && obj.__esModule ? obj : { default: obj }; }
+var _mlMatrix = require("ml-matrix");
 
 /**
  * @memberof Image
@@ -32,7 +30,7 @@ function getMatrix(options = {}) {
     channel = 0;
   }
 
-  let matrix = new _mlMatrix.default(this.height, this.width);
+  let matrix = new _mlMatrix.Matrix(this.height, this.width);
 
   for (let x = 0; x < this.height; x++) {
     for (let y = 0; y < this.width; y++) {

package/lib/index.js

@@ -3,16 +3,17 @@
 Object.defineProperty(exports, "__esModule", {
   value: true
 });
-Object.defineProperty(exports, "default", {
+Object.defineProperty(exports, "Image", {
   enumerable: true,
   get: function () {
     return _Image.default;
   }
 });
-Object.defineProperty(exports, "Image", {
+exports.Kernel = void 0;
+Object.defineProperty(exports, "Shape", {
   enumerable: true,
   get: function () {
-    return _Image.default;
+    return _Shape.default;
   }
 });
 Object.defineProperty(exports, "Stack", {
@@ -21,19 +22,19 @@ Object.defineProperty(exports, "Stack", {
     return _Stack.default;
   }
 });
-Object.defineProperty(exports, "Shape", {
+exports.Static = void 0;
+Object.defineProperty(exports, "Worker", {
   enumerable: true,
   get: function () {
-    return _Shape.default;
+    return _worker.default;
   }
 });
-Object.defineProperty(exports, "Worker", {
+Object.defineProperty(exports, "default", {
   enumerable: true,
   get: function () {
-    return _worker.default;
+    return _Image.default;
   }
 });
-exports.Kernel = exports.Static = void 0;
 
 var _Image = _interopRequireDefault(require("./image/Image"));
 
@@ -51,9 +52,9 @@ var _Shape = _interopRequireDefault(require("./util/Shape"));
 
 var _worker = _interopRequireDefault(require("./worker/worker"));
 
-function _getRequireWildcardCache() { if (typeof WeakMap !== "function") return null; var cache = new WeakMap(); _getRequireWildcardCache = function () { return cache; }; return cache; }
+function _getRequireWildcardCache(nodeInterop) { if (typeof WeakMap !== "function") return null; var cacheBabelInterop = new WeakMap(); var cacheNodeInterop = new WeakMap(); return (_getRequireWildcardCache = function (nodeInterop) { return nodeInterop ? cacheNodeInterop : cacheBabelInterop; })(nodeInterop); }
 
-function _interopRequireWildcard(obj) { if (obj && obj.__esModule) { return obj; } if (obj === null || typeof obj !== "object" && typeof obj !== "function") { return { default: obj }; } var cache = _getRequireWildcardCache(); if (cache && cache.has(obj)) { return cache.get(obj); } var newObj = {}; var hasPropertyDescriptor = Object.defineProperty && Object.getOwnPropertyDescriptor; for (var key in obj) { if (Object.prototype.hasOwnProperty.call(obj, key)) { var desc = hasPropertyDescriptor ? Object.getOwnPropertyDescriptor(obj, key) : null; if (desc && (desc.get || desc.set)) { Object.defineProperty(newObj, key, desc); } else { newObj[key] = obj[key]; } } } newObj.default = obj; if (cache) { cache.set(obj, newObj); } return newObj; }
+function _interopRequireWildcard(obj, nodeInterop) { if (!nodeInterop && obj && obj.__esModule) { return obj; } if (obj === null || typeof obj !== "object" && typeof obj !== "function") { return { default: obj }; } var cache = _getRequireWildcardCache(nodeInterop); if (cache && cache.has(obj)) { return cache.get(obj); } var newObj = {}; var hasPropertyDescriptor = Object.defineProperty && Object.getOwnPropertyDescriptor; for (var key in obj) { if (key !== "default" && Object.prototype.hasOwnProperty.call(obj, key)) { var desc = hasPropertyDescriptor ? Object.getOwnPropertyDescriptor(obj, key) : null; if (desc && (desc.get || desc.set)) { Object.defineProperty(newObj, key, desc); } else { newObj[key] = obj[key]; } } } newObj.default = obj; if (cache) { cache.set(obj, newObj); } return newObj; }
 
 function _interopRequireDefault(obj) { return obj && obj.__esModule ? obj : { default: obj }; }
 

package/lib/util/base64.js

@@ -3,8 +3,8 @@
 Object.defineProperty(exports, "__esModule", {
   value: true
 });
-exports.encode = encode;
 exports.decode = decode;
+exports.encode = encode;
 exports.toBase64URL = toBase64URL;
 
 /*

package/lib/util/channel.js

@@ -8,9 +8,9 @@ exports.validateChannel = validateChannel;
 
 var Model = _interopRequireWildcard(require("../image/model/model"));
 
-function _getRequireWildcardCache() { if (typeof WeakMap !== "function") return null; var cache = new WeakMap(); _getRequireWildcardCache = function () { return cache; }; return cache; }
+function _getRequireWildcardCache(nodeInterop) { if (typeof WeakMap !== "function") return null; var cacheBabelInterop = new WeakMap(); var cacheNodeInterop = new WeakMap(); return (_getRequireWildcardCache = function (nodeInterop) { return nodeInterop ? cacheNodeInterop : cacheBabelInterop; })(nodeInterop); }
 
-function _interopRequireWildcard(obj) { if (obj && obj.__esModule) { return obj; } if (obj === null || typeof obj !== "object" && typeof obj !== "function") { return { default: obj }; } var cache = _getRequireWildcardCache(); if (cache && cache.has(obj)) { return cache.get(obj); } var newObj = {}; var hasPropertyDescriptor = Object.defineProperty && Object.getOwnPropertyDescriptor; for (var key in obj) { if (Object.prototype.hasOwnProperty.call(obj, key)) { var desc = hasPropertyDescriptor ? Object.getOwnPropertyDescriptor(obj, key) : null; if (desc && (desc.get || desc.set)) { Object.defineProperty(newObj, key, desc); } else { newObj[key] = obj[key]; } } } newObj.default = obj; if (cache) { cache.set(obj, newObj); } return newObj; }
+function _interopRequireWildcard(obj, nodeInterop) { if (!nodeInterop && obj && obj.__esModule) { return obj; } if (obj === null || typeof obj !== "object" && typeof obj !== "function") { return { default: obj }; } var cache = _getRequireWildcardCache(nodeInterop); if (cache && cache.has(obj)) { return cache.get(obj); } var newObj = {}; var hasPropertyDescriptor = Object.defineProperty && Object.getOwnPropertyDescriptor; for (var key in obj) { if (key !== "default" && Object.prototype.hasOwnProperty.call(obj, key)) { var desc = hasPropertyDescriptor ? Object.getOwnPropertyDescriptor(obj, key) : null; if (desc && (desc.get || desc.set)) { Object.defineProperty(newObj, key, desc); } else { newObj[key] = obj[key]; } } } newObj.default = obj; if (cache) { cache.set(obj, newObj); } return newObj; }
 
 /**
  * Specify which channels should be processed

package/lib/util/color.js

@@ -4,9 +4,9 @@ Object.defineProperty(exports, "__esModule", {
   value: true
 });
 exports.css2array = css2array;
+exports.getColors = getColors;
 exports.getDistinctColors = getDistinctColors;
 exports.getRandomColor = getRandomColor;
-exports.getColors = getColors;
 
 var _colorFns = require("@swiftcarrot/color-fns");
 

package/lib/util/converter.js

@@ -3,9 +3,9 @@
 Object.defineProperty(exports, "__esModule", {
   value: true
 });
+exports.factorDimensions = factorDimensions;
 exports.getFactor = getFactor;
 exports.getThreshold = getThreshold;
-exports.factorDimensions = factorDimensions;
 
 /**
  * Converts a factor value to a number between 0 and 1

package/lib/util/histogram.js

@@ -3,8 +3,8 @@
 Object.defineProperty(exports, "__esModule", {
   value: true
 });
-exports.median = median;
 exports.mean = mean;
+exports.median = median;
 
 /**
  * Returns the median of an histogram

package/lib/util/kernels.js

@@ -3,7 +3,7 @@
 Object.defineProperty(exports, "__esModule", {
   value: true
 });
-exports.SECOND_DERIVATIVE_INV = exports.SECOND_DERIVATIVE = exports.SCHARR_Y = exports.SCHARR_X = exports.SOBEL_Y = exports.SOBEL_X = exports.DISCRETE_LAPLACE_8 = exports.DISCRETE_LAPLACE_4 = void 0;
+exports.SOBEL_Y = exports.SOBEL_X = exports.SECOND_DERIVATIVE_INV = exports.SECOND_DERIVATIVE = exports.SCHARR_Y = exports.SCHARR_X = exports.DISCRETE_LAPLACE_8 = exports.DISCRETE_LAPLACE_4 = void 0;
 const DISCRETE_LAPLACE_4 = [[0, 1, 0], [1, -4, 1], [0, 1, 0]];
 exports.DISCRETE_LAPLACE_4 = DISCRETE_LAPLACE_4;
 const DISCRETE_LAPLACE_8 = [[1, 1, 1], [1, -8, 1], [1, 1, 1]];

package/lib/util/points.js

@@ -3,17 +3,17 @@
 Object.defineProperty(exports, "__esModule", {
   value: true
 });
-exports.round = round;
-exports.difference = difference;
-exports.normalize = normalize;
-exports.rotate = rotate;
-exports.dot = dot;
 exports.angle = angle;
 exports.boundary = boundary;
-exports.perimeter = perimeter;
-exports.surface = surface;
+exports.difference = difference;
+exports.dot = dot;
 exports.minMax = minMax;
 exports.moveToZeroZero = moveToZeroZero;
+exports.normalize = normalize;
+exports.perimeter = perimeter;
+exports.rotate = rotate;
+exports.round = round;
+exports.surface = surface;
 
 /**
  * Rounds all the x and y values of an array of points

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "image-js",
-  "version": "0.31.3",
+  "version": "0.33.1",
   "description": "Image processing and manipulation in JavaScript",
   "keywords": [
     "image",
@@ -44,8 +44,10 @@
     "compile": "npm run clean-lib && cross-env NODE_ENV=npm babel src --out-dir lib --ignore \"**/__tests__\" --quiet",
     "eslint": "eslint src test/common.js test/nodeScripts --cache",
     "eslint-fix": "npm run eslint -- --fix",
-    "prepublishOnly": "npm run compile",
-    "test": "npm run test-only && npm run eslint",
+    "prepack": "npm run compile",
+    "prettier": "prettier --check .",
+    "prettier-write": "prettier --write .",
+    "test": "npm run test-only && npm run eslint && npm run prettier",
     "test-coverage": "jest --coverage --runInBand",
     "test-only": "jest"
   },
@@ -56,33 +58,22 @@
       "<rootDir>/node_modules/"
     ]
   },
-  "prettier": {
-    "arrowParens": "always",
-    "semi": true,
-    "singleQuote": true,
-    "tabWidth": 2,
-    "trailingComma": "all"
-  },
   "devDependencies": {
-    "@babel/cli": "^7.12.10",
-    "@babel/core": "^7.12.10",
-    "@babel/plugin-transform-block-scoping": "^7.12.1",
-    "@babel/plugin-transform-modules-commonjs": "^7.12.1",
-    "@babel/preset-env": "^7.12.10",
-    "@babel/register": "^7.12.10",
-    "@types/jest": "^26.0.19",
-    "babel-core": "^7.0.0-bridge.0",
-    "babel-jest": "^26.6.3",
+    "@babel/cli": "^7.16.0",
+    "@babel/core": "^7.16.0",
+    "@babel/plugin-transform-block-scoping": "^7.16.0",
+    "@babel/plugin-transform-modules-commonjs": "^7.16.0",
+    "@babel/preset-env": "^7.16.0",
+    "@types/jest": "^27.0.2",
     "benchmark": "^2.1.4",
-    "canvas": "^2.6.1",
-    "cheminfo-build": "^1.1.8",
+    "cheminfo-build": "^1.1.11",
     "cross-env": "^7.0.3",
-    "eslint": "^7.15.0",
-    "eslint-config-cheminfo": "^5.2.2",
+    "eslint": "^8.1.0",
+    "eslint-config-cheminfo": "^7.1.2",
     "esm": "^3.2.25",
-    "jest": "^26.6.3",
-    "jest-matcher-deep-close-to": "^2.0.1",
-    "prettier": "^2.2.1",
+    "jest": "^27.3.1",
+    "jest-matcher-deep-close-to": "^3.0.2",
+    "prettier": "^2.4.1",
     "rimraf": "^3.0.2",
     "sha.js": "^2.4.11"
   },
@@ -93,28 +84,27 @@
     "fast-bmp": "^1.0.0",
     "fast-jpeg": "^1.0.1",
     "fast-list": "^1.0.3",
-    "fast-png": "^5.0.3",
+    "fast-png": "^6.1.0",
     "has-own": "^1.0.1",
     "image-type": "^4.1.0",
     "is-array-type": "^1.0.0",
     "is-integer": "^1.0.7",
-    "jpeg-js": "^0.4.2",
+    "jpeg-js": "^0.4.3",
     "js-priority-queue": "^0.1.5",
     "js-quantities": "^1.7.6",
     "median-quickselect": "^1.0.1",
     "ml-convolution": "0.2.0",
     "ml-disjoint-set": "^1.0.0",
-    "ml-matrix": "^6.5.3",
+    "ml-matrix": "^6.8.0",
     "ml-matrix-convolution": "0.4.3",
     "ml-regression": "^5.0.0",
     "monotone-chain-convex-hull": "^1.0.0",
     "new-array": "^1.0.0",
-    "num-sort": "^2.1.0",
     "robust-point-in-polygon": "^1.0.3",
-    "tiff": "^4.3.0",
+    "tiff": "^5.0.2",
     "web-worker-manager": "^0.2.0"
   },
   "engines": {
-    "node": ">= 10.0.0"
+    "node": ">= 12.0.0"
   }
 }

package/src/image/Image.js

@@ -41,7 +41,7 @@ const objectToString = Object.prototype.toString;
  *      8 and 16 bit depth images.
  * * position : an array of 2 elements that allows to define a relative position
  *      to a parent image. This will be used in a crop or in the management
- *      of Region Of Interests (Roi) for exmaple
+ *      of Region Of Interests (Roi) for example
  * * data : an array that contains all the points of the image.
  *      Depending the bitDepth Uint8Array (1 bit), Uint8Array (8 bits),
  *      Uint16Array (16 bits), Float32Array (32 bits)
@@ -121,7 +121,7 @@ const objectToString = Object.prototype.toString;
  * // the RoiManager. A RoiManager will be applied on the original image
  * // in order to be able to extract from the original image the regions
  *
- * // the result of this console.log result can diretly be pasted
+ * // the result of this console.log result can directly be pasted
  * // in the browser
  * // console.log(mask.toDataURL());
  *
@@ -164,6 +164,24 @@ const objectToString = Object.prototype.toString;
  *  var canvas = document.getElementById('myCanvasID');
  *  var image = IJS.fromCanvas(canvas);
  * </script>
+ *
+ * @example
+ * // Image from matrix of values
+ * const [min, max] = d3.extent(temperatures)
+ * const colorScaler = d3.scaleSequential([min, max], d3.interpolateRdYlBu);
+ *
+ * // size = rows * columns * channels
+ * const data = new Uint8Array(2*3*3);
+ * for (let i = 0; i < temperatures.length; i++) {
+ *   const {r, g, b} = d3.rgb(colorScaler(temperatures[i]));
+ *   data[i*3] = r;
+ *   data[i*3 + 1] = g;
+ *   data[i*3 + 2] = b;
+ * }
+ *
+ * const image = new Image(2, 3, data, { kind: 'RGB' });
+ * // or
+ * const image = new Image({ width: 2, height: 3, data, kind: 'RGB'});
  */
 export default class Image {
   constructor(width, height, data, options) {

package/src/image/compute/extendedPoints.js

@@ -1,6 +1,7 @@
 /**
  * Allows to generate an array of points for a binary image (bit depth = 1)
  * The points consider the beginning and the end of each pixel
+ * This method is only used to calculate minimalBoundRectangle
  * @memberof Image
  * @instance
  * @return {Array<Array<number>>} - an array of [x,y] corresponding to the set pixels in the binary image
@@ -15,6 +16,7 @@ export default function extendedPoints() {
     for (let x = 0; x < this.width; x++) {
       if (this.getBitXY(x, y) === 1) {
         pixels.push([x, y]);
+
         if (this.getBitXY(x + 1, y) !== 1) {
           pixels.push([x + 1, y]);
           pixels.push([x + 1, y + 1]);
@@ -27,6 +29,15 @@ export default function extendedPoints() {
             pixels.push([x + 1, y + 1]);
           }
         }
+
+        // this small optimization allows to reduce dramatically the number of points for MBR calculation
+        while (
+          x < this.width - 2 &&
+          this.getBitXY(x + 1, y) === 1 &&
+          this.getBitXY(x + 2, y) === 1
+        ) {
+          x++;
+        }
       }
     }
   }

package/src/image/core/environment.js

@@ -5,6 +5,7 @@ const message =
 
 let createCanvas, DOMImage, ImageData;
 try {
+  // eslint-disable-next-line import/no-unresolved
   const canvas = require('canvas');
   createCanvas = canvas.createCanvas;
   DOMImage = canvas.Image;

package/src/image/core/load.js

@@ -137,7 +137,26 @@ function loadJPEG(data) {
     meta = getMetadata(decodedExif.exif);
   }
   const jpeg = decodeJpeg(data, { useTArray: true, maxMemoryUsageInMB: 1024 });
-  return new Image(jpeg.width, jpeg.height, jpeg.data, { meta });
+  let image = new Image(jpeg.width, jpeg.height, jpeg.data, { meta });
+  if (meta && meta.tiff.tags.Orientation) {
+    const orientation = meta.tiff.tags.Orientation;
+    if (orientation > 2) {
+      image = image.rotate(
+        {
+          3: 180,
+          4: 180,
+          5: 90,
+          6: 90,
+          7: 270,
+          8: 270,
+        }[orientation],
+      );
+    }
+    if ([2, 4, 5, 7].includes(orientation)) {
+      image = image.flipX();
+    }
+  }
+  return image;
 }
 
 function loadTIFF(data) {

package/src/image/filter/subtractImage.js

@@ -1,5 +1,4 @@
 import { validateArrayOfChannels } from '../../util/channel';
-import Image from '../Image';
 
 /**
  * Calculate a new image that is the subtraction between the current image and the otherImage.
@@ -7,13 +6,12 @@ import Image from '../Image';
  * @instance
  * @param {Image} otherImage
  * @param {object} [options={}]
- * @param {number} [options.bitDepth=this.bitDepth]
  * @param {number[]|string[]} [options.channels] : to which channel to apply the filter. By default all but alpha.
  * @param {number[]|string[]} [options.absolute=false] :.take the absolute value of the difference (default minimum=0)
  * @return {Image}
  */
 export default function subtractImage(otherImage, options = {}) {
-  let { bitDepth = this.bitDepth, channels, absolute = false } = options;
+  let { channels, absolute = false } = options;
   this.checkProcessable('subtractImage', {
     bitDepth: [8, 16],
   });
@@ -34,7 +32,7 @@ export default function subtractImage(otherImage, options = {}) {
     );
   }
 
-  let newImage = Image.createFrom(this, { bitDepth: bitDepth });
+  let newImage = this.clone();
 
   channels = validateArrayOfChannels(this, { channels: channels });
 

package/src/image/roi/Roi.js

@@ -705,7 +705,7 @@ export default class Roi {
 
   get roundness() {
     /*Slide 24 https://static.horiba.com/fileadmin/Horiba/Products/Scientific/Particle_Characterization/Webinars/Slides/TE011.pdf */
-    return (4 * this.surface) / (Math.PI * this.feretDiameters.max) ** 2;
+    return (4 * this.surface) / (Math.PI * this.feretDiameters.max ** 2);
   }
 
   get sphericity() {

package/src/image/transform/mask/renyiEntropy.js

@@ -5,8 +5,6 @@
 // M. Emre Celebi
 // 06.15.2007
 // Ported to ImageJ plugin by G.Landini from E Celebi's fourier_0.8 routines
-import { ascending as sortAsc } from 'num-sort';
-
 export default function renyiEntropy(histogram, total) {
   let optThreshold; // Optimal threshold
   let firstBin; // First non-zero bin
@@ -112,7 +110,7 @@ export default function renyiEntropy(histogram, total) {
   /* End Maximum Entropy Thresholding */
 
   let tStars = [threshold1, threshold2, threshold3];
-  tStars.sort(sortAsc);
+  tStars.sort((a, b) => a - b);
 
   let betas;
 

package/src/image/utility/getMatrix.js

@@ -1,4 +1,4 @@
-import Matrix from 'ml-matrix';
+import { Matrix } from 'ml-matrix';
 
 /**
  * @memberof Image

package/CHANGELOG.md

@@ -1,57 +0,0 @@
-# Changelog
-
-### [0.31.3](https://www.github.com/image-js/image-js/compare/v0.31.2...v0.31.3) (2020-12-14)
-
-
-### Bug Fixes
-
-* update dependencies ([#539](https://www.github.com/image-js/image-js/issues/539)) ([c972f63](https://www.github.com/image-js/image-js/commit/c972f63a181706c65ea144ec1e6a6edf92deba5a))
-
-### [0.31.2](https://www.github.com/image-js/image-js/compare/v0.31.1...v0.31.2) (2020-12-10)
-
-
-### Performance Improvements
-
-* improve medianFilter ([#537](https://www.github.com/image-js/image-js/issues/537)) ([c341fac](https://www.github.com/image-js/image-js/commit/c341facf65745641510b5c53d1c00e6b3c69697e))
-
-### [0.31.1](https://www.github.com/image-js/image-js/compare/v0.31.0...v0.31.1) (2020-11-17)
-
-
-### Bug Fixes
-
-* correct hull filled mask ([81a8cd7](https://www.github.com/image-js/image-js/commit/81a8cd713add86fdb46f78024dacc343880d71cd))
-
-## [0.31.0](https://www.github.com/image-js/image-js/compare/v0.30.3...v0.31.0) (2020-11-12)
-
-
-### Features
-
-* restore old implementations of getMask with hull or mbr ([#532](https://www.github.com/image-js/image-js/issues/532)) ([4d51dbd](https://www.github.com/image-js/image-js/commit/4d51dbd7baffc4cc32d625b2912e4fbdabdf13a0))
-
-### [0.30.3](https://www.github.com/image-js/image-js/compare/v0.30.2...v0.30.3) (2020-10-20)
-
-
-### Bug Fixes
-
-* **types:** correct return type of Stack.getAverageImage to Image ([#529](https://www.github.com/image-js/image-js/issues/529)) ([ec6588c](https://www.github.com/image-js/image-js/commit/ec6588c2b0152bd865013ffe6fb3e5668c83cae3))
-
-### [0.30.2](https://www.github.com/image-js/image-js/compare/v0.30.1...v0.30.2) (2020-10-18)
-
-
-### Bug Fixes
-
-* add basic Stack type definition ([#525](https://www.github.com/image-js/image-js/issues/525)) ([d5f1972](https://www.github.com/image-js/image-js/commit/d5f1972fc1f39b506882f46b7c6c7722157bfd4c))
-
-### [0.30.1](https://www.github.com/image-js/image-js/compare/v0.30.0...v0.30.1) (2020-10-13)
-
-
-### Bug Fixes
-
-* include less files in npm package ([03903a6](https://www.github.com/image-js/image-js/commit/03903a692a3f4801d44d8d017fced52f218d0369))
-
-## [0.30.0](https://www.github.com/image-js/image-js/compare/v0.29.0...v0.30.0) (2020-10-13)
-
-
-### Bug Fixes
-
-* correct TIFF support in documentation ([7f3993f](https://www.github.com/image-js/image-js/commit/7f3993f189fe8adb32467b9c8522273778392871))