image-js 0.35.2 → 0.35.4

package/index.d.ts

@@ -2,6 +2,8 @@
 // Project: https://github.com/image-js/image-js
 // Definitions by: Michaël Zasso <https://github.com/targos>
 
+import Matrix from 'ml-matrix';
+
 // Global variable exposed by UMD bundle
 export as namespace IJS;
 
@@ -157,7 +159,7 @@ export declare class Image {
   getRow(row: number, channel?: number): Array<number>;
   getColumn(row: number, channel?: number): Array<number>;
   getMatrix(options?: { channel?: number }): Matrix;
-  setMatrix(matrix: Matrix, options?: { channel?: number });
+  setMatrix(matrix: Matrix, options?: { channel?: number }): this;
   getPixelsArray(): Array<Array<number>>;
   getIntersection(mask2: Image): object;
   getClosestCommonParent(mask: Image): Image;
@@ -328,15 +330,6 @@ export declare class Stack extends Array<Image> {
 
 export declare class RoiManager {}
 
-export declare class Matrix extends Array<Array<number>> {
-  constructor();
-  constructor(width: number, height: number, defaultValue?: number);
-
-  localMin(x: number, y: number): { position: Array<number>; value: number };
-  localMax(x: number, y: number): { position: Array<number>; value: number };
-  localSearch(x: number, y: number, value: number): Array<Array<number>>;
-}
-
 export interface ImageConstructorOptions {
   width?: number;
   height?: number;

package/lib/browser/environment.js

@@ -15,14 +15,12 @@ const ImageData = self.ImageData;
 exports.ImageData = ImageData;
 const DOMImage = self.Image;
 exports.DOMImage = DOMImage;
-
 function createCanvas(width, height) {
   let canvas = self.document.createElement('canvas');
   canvas.width = width;
   canvas.height = height;
   return canvas;
 }
-
 function fetchBinary(url, {
   withCredentials = false
 } = {}) {
@@ -31,20 +29,16 @@ function fetchBinary(url, {
     xhr.open('GET', url, true);
     xhr.responseType = 'arraybuffer';
     xhr.withCredentials = withCredentials;
-
     xhr.onload = function (e) {
       if (this.status !== 200) reject(e);else resolve(this.response);
     };
-
     xhr.onerror = reject;
     xhr.send();
   });
 }
-
 function createWriteStream() {
   throw new Error('createWriteStream does not exist in the browser');
 }
-
 function writeFile() {
   throw new Error('writeFile does not exist in the browser');
 }

package/lib/browser/worker/extend.js

@@ -4,11 +4,8 @@ Object.defineProperty(exports, "__esModule", {
   value: true
 });
 exports.default = extend;
-
 var _background = _interopRequireDefault(require("./process/background"));
-
 function _interopRequireDefault(obj) { return obj && obj.__esModule ? obj : { default: obj }; }
-
 function extend(Worker) {
   Worker.extendMethod('background', _background.default);
 }

package/lib/browser/worker/process/background.js

@@ -4,11 +4,8 @@ Object.defineProperty(exports, "__esModule", {
   value: true
 });
 exports.default = void 0;
-
 var _Image = _interopRequireDefault(require("../../../image/Image"));
-
 function _interopRequireDefault(obj) { return obj && obj.__esModule ? obj : { default: obj }; }
-
 const defaultOptions = {
   regression: {
     kernelType: 'polynomial',
@@ -25,36 +22,29 @@ const defaultOptions = {
   sampling: 20,
   include: []
 };
-
 function run(image, options, onStep) {
   options = Object.assign({}, defaultOptions, options);
   const manager = this.manager;
-
   if (Array.isArray(image)) {
     return Promise.all(image.map(function (img) {
       const run = runOnce(manager, img, options);
-
       if (typeof onStep === 'function') {
         run.then(onStep);
       }
-
       return run;
     }));
   } else {
     return runOnce(manager, image, options);
   }
 }
-
 function runOnce(manager, image, options) {
   return manager.post('data', [image, options]).then(function (response) {
     for (let i in response) {
       response[i] = new _Image.default(response[i]);
     }
-
     return response;
   });
 }
-
 function work() {
   worker.on('data', function (send, image, options) {
     image = new IJS(image);
@@ -81,7 +71,6 @@ function work() {
     result.result = corrected;
     toTransfer.push(corrected.data.buffer);
     send(result, toTransfer);
-
     function maybeInclude(name, image) {
       if (options.include.includes(name)) {
         result[name] = image;
@@ -90,7 +79,6 @@ function work() {
     }
   });
 }
-
 const background = {
   run,
   work

package/lib/browser/worker/worker.js

@@ -4,43 +4,33 @@ Object.defineProperty(exports, "__esModule", {
   value: true
 });
 exports.default = void 0;
-
 var _webWorkerManager = _interopRequireDefault(require("web-worker-manager"));
-
 var _extend = _interopRequireDefault(require("./extend"));
-
 function _interopRequireDefault(obj) { return obj && obj.__esModule ? obj : { default: obj }; }
-
 class Worker {
   constructor() {
     this._url = null;
     this._deps = [null];
   }
-
   checkUrl() {
     if (this._url === null) {
       throw new Error('image worker must be initialized with an URL');
     }
   }
-
   get url() {
     return this._url;
   }
-
   set url(value) {
     if (typeof value !== 'string') {
       throw new TypeError('worker URL must be a string');
     }
-
     this._url = value;
     this._deps[0] = value;
   }
-
   static extendMethod(name, method) {
     let manager;
     let url;
     let runner = {};
-
     function run(...args) {
       if (!manager) {
         this.checkUrl();
@@ -50,10 +40,8 @@ class Worker {
         });
         runner.manager = manager;
       }
-
       return method.run.call(runner, ...args);
     }
-
     run.reset = function () {
       if (manager) {
         manager.terminate();
@@ -63,14 +51,9 @@ class Worker {
         runner.manager = manager;
       }
     };
-
     Worker.prototype[name] = run;
   }
-
 }
-
 (0, _extend.default)(Worker);
-
 var _default = new Worker();
-
 exports.default = _default;

package/lib/image/Image.js

@@ -4,34 +4,21 @@ Object.defineProperty(exports, "__esModule", {
   value: true
 });
 exports.default = void 0;
-
 var _bitMethods = _interopRequireDefault(require("./core/bitMethods"));
-
 var _checkProcessable = _interopRequireDefault(require("./core/checkProcessable"));
-
 var _export = _interopRequireDefault(require("./core/export"));
-
 var _extend = require("./core/extend");
-
 var _getRGBAData = _interopRequireDefault(require("./core/getRGBAData"));
-
 var _kind = require("./core/kind");
-
 var _kindNames = require("./core/kindNames");
-
 var _load = _interopRequireDefault(require("./core/load"));
-
 var _valueMethods = _interopRequireDefault(require("./core/valueMethods"));
-
 var _extend2 = _interopRequireDefault(require("./extend"));
-
 var _getImageParameters = _interopRequireDefault(require("./internal/getImageParameters"));
-
 var _manager = _interopRequireDefault(require("./roi/manager"));
-
 function _interopRequireDefault(obj) { return obj && obj.__esModule ? obj : { default: obj }; }
-
 const objectToString = Object.prototype.toString;
+
 /**
  * Class representing an image.
  * This class allows to manipulate easily images directly in the browser or in node.
@@ -197,7 +184,6 @@ const objectToString = Object.prototype.toString;
  * // or
  * const image = new Image({ width: 2, height: 3, data, kind: 'RGB'});
  */
-
 class Image {
   constructor(width, height, data, options) {
     if (arguments.length === 1) {
@@ -213,40 +199,31 @@ class Image {
         data
       } = options);
     }
-
     if (width === undefined) width = 1;
     if (height === undefined) height = 1;
     if (options === undefined) options = {};
-
     if (typeof options !== 'object' || options === null) {
       throw new TypeError('options must be an object');
     }
-
     if (!Number.isInteger(width) || width <= 0) {
       throw new RangeError('width must be a positive integer');
     }
-
     if (!Number.isInteger(height) || height <= 0) {
       throw new RangeError('height must be a positive integer');
     }
-
     const {
       kind = _kindNames.RGBA
     } = options;
-
     if (typeof kind !== 'string') {
       throw new TypeError('kind must be a string');
     }
-
     const theKind = (0, _kind.getKind)(kind);
     const kindDefinition = Object.assign({}, options);
-
     for (const prop in theKind) {
       if (kindDefinition[prop] === undefined) {
         kindDefinition[prop] = theKind[prop];
       }
     }
-
     (0, _kind.verifyKindDefinition)(kindDefinition);
     const {
       components,
@@ -257,85 +234,83 @@ class Image {
     const size = width * height;
     const channels = components + alpha;
     const maxValue = bitDepth === 32 ? Number.MAX_VALUE : 2 ** bitDepth - 1;
-
     if (data === undefined) {
       data = (0, _kind.createPixelArray)(size, components, alpha, channels, bitDepth, maxValue);
     } else {
       const expectedLength = (0, _kind.getTheoreticalPixelArraySize)(size, channels, bitDepth);
-
       if (data.length !== expectedLength) {
         throw new RangeError(`incorrect data size: ${data.length}. Should be ${expectedLength}`);
       }
     }
+
     /**
      * Width of the image.
      * @member {number}
      */
-
-
     this.width = width;
+
     /**
      * Height of the image.
      * @member {number}
      */
-
     this.height = height;
+
     /**
      * Typed array holding the image data.
      * @member {TypedArray}
      */
-
     this.data = data;
+
     /**
      * Total number of pixels (width * height).
      * @member {number}
      */
-
     this.size = size;
+
     /**
      * Number of color channels in the image.
      * A grey image has 1 component. An RGB image has 3 components.
      * @member {number}
      */
-
     this.components = components;
+
     /**
      * Alpha is 1 if there is an alpha channel, 0 otherwise.
      * @member {number}
      */
-
     this.alpha = alpha;
+
     /**
      * Number of bits per value in each channel.
      * @member {number}
      */
-
     this.bitDepth = bitDepth;
+
     /**
      * Maximum value that a pixel can have.
      * @member {number}
      */
-
     this.maxValue = maxValue;
+
     /**
      * Color model of the image.
      * @member {ColorModel}
      */
-
     this.colorModel = colorModel;
+
     /**
      * Total number of channels. Is equal to `image.components + image.alpha`.
      * @member {number}
      */
-
     this.channels = channels;
+
     /**
      * Metadata associated with the image.
      * @member {object}
      */
+    this.meta = options.meta || {};
 
-    this.meta = options.meta || {}; // TODO review those props
-
+    // TODO review those props
     Object.defineProperty(this, 'parent', {
       enumerable: false,
       writable: true,
@@ -354,22 +329,21 @@ class Image {
   get [Symbol.toStringTag]() {
     return 'IJSImage';
   }
-
   static isImage(object) {
     return objectToString.call(object) === '[object IJSImage]';
   }
+
   /**
    * Creates an image from an HTML Canvas object
    * @param {Canvas} canvas
    * @return {Image}
    */
-
-
   static fromCanvas(canvas) {
     const ctx = canvas.getContext('2d');
     const imageData = ctx.getImageData(0, 0, canvas.width, canvas.height);
     return new Image(imageData.width, imageData.height, imageData.data);
   }
+
   /**
    * Create a new Image based on the characteristics of another one.
    * @param {Image} other
@@ -378,8 +352,6 @@ class Image {
    * @example
    * const newImage = Image.createFrom(image, { width: 100 });
    */
-
-
   static createFrom(other, options) {
     const newOptions = (0, _getImageParameters.default)(other);
     Object.assign(newOptions, {
@@ -388,28 +360,25 @@ class Image {
     }, options);
     return new Image(newOptions);
   }
+
   /**
    * Create a new manager for regions of interest based on the current image.
    * @param {object} [options]
    * @return {RoiManager}
    */
-
-
   getRoiManager(options) {
     return new _manager.default(this, options);
   }
+
   /**
    * Create a copy a the current image, including its data.
    * @instance
    * @return {Image}
    */
-
-
   clone() {
     const newData = this.data.slice();
     return new Image(this.width, this.height, newData, this);
   }
-
   apply(filter) {
     for (let y = 0; y < this.height; y++) {
       for (let x = 0; x < this.width; x++) {
@@ -418,9 +387,7 @@ class Image {
       }
     }
   }
-
 }
-
 exports.default = Image;
 (0, _valueMethods.default)(Image);
 (0, _bitMethods.default)(Image);

package/lib/image/compute/colorHistogram.js

@@ -4,11 +4,8 @@ Object.defineProperty(exports, "__esModule", {
   value: true
 });
 exports.default = getColorHistogram;
-
 var _newArray = _interopRequireDefault(require("new-array"));
-
 function _interopRequireDefault(obj) { return obj && obj.__esModule ? obj : { default: obj }; }
-
 /**
  * @memberof Image
  * @instance
@@ -27,26 +24,21 @@ function getColorHistogram(options = {}) {
     components: [3]
   });
   let nbSlotsCheck = Math.log(nbSlots) / Math.log(8);
-
   if (nbSlotsCheck !== Math.floor(nbSlotsCheck)) {
     throw new RangeError('nbSlots must be a power of 8. Usually 8, 64, 512 or 4096');
   }
-
   let bitShift = this.bitDepth - nbSlotsCheck;
   let data = this.data;
   let result = (0, _newArray.default)(Math.pow(8, nbSlotsCheck), 0);
   let factor2 = Math.pow(2, nbSlotsCheck * 2);
   let factor1 = Math.pow(2, nbSlotsCheck);
-
   for (let i = 0; i < data.length; i += this.channels) {
     let slot = (data[i] >> bitShift) * factor2 + (data[i + 1] >> bitShift) * factor1 + (data[i + 2] >> bitShift);
-
     if (useAlpha && this.alpha) {
       result[slot] += data[i + this.channels - 1] / this.maxValue;
     } else {
       result[slot]++;
     }
   }
-
   return result;
 }

package/lib/image/compute/countAlphaPixels.js

@@ -4,7 +4,6 @@ Object.defineProperty(exports, "__esModule", {
   value: true
 });
 exports.default = countAlphaPixels;
-
 /**
  * Returns the number of transparent pixels
  * @memberof Image
@@ -22,14 +21,12 @@ function countAlphaPixels(options = {}) {
     alpha: 1
   });
   let count = 0;
-
   if (alpha !== undefined) {
     for (let i = this.components; i < this.data.length; i += this.channels) {
       if (this.data[i] === alpha) {
         count++;
       }
     }
-
     return count;
   } else {
     // because there is an alpha channel all the pixels have an alpha

package/lib/image/compute/extendedPoints.js

@@ -4,7 +4,6 @@ Object.defineProperty(exports, "__esModule", {
   value: true
 });
 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
@@ -18,16 +17,13 @@ function extendedPoints() {
     bitDepth: [1]
   });
   const pixels = [];
-
   for (let y = 0; y < this.height; y++) {
     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]);
-
           if (this.getBitXY(x, y + 1) !== 1) {
             pixels.push([x, y + 1]);
           }
@@ -36,15 +32,14 @@ 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
-
+        }
 
+        // 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++;
         }
       }
     }
   }
-
   return pixels;
 }

package/lib/image/compute/histogram.js

@@ -5,13 +5,9 @@ Object.defineProperty(exports, "__esModule", {
 });
 exports.getHistogram = getHistogram;
 exports.getHistograms = getHistograms;
-
 var _isInteger = _interopRequireDefault(require("is-integer"));
-
 var _newArray = _interopRequireDefault(require("new-array"));
-
 function _interopRequireDefault(obj) { return obj && obj.__esModule ? obj : { default: obj }; }
-
 /**
  * Returns a histogram for the specified channel
  * @memberof Image
@@ -31,20 +27,18 @@ function getHistogram(options = {}) {
   this.checkProcessable('getHistogram', {
     bitDepth: [1, 8, 16]
   });
-
   if (channel === undefined) {
     if (this.components > 1) {
       throw new RangeError('You need to define the channel for an image that contains more than one channel');
     }
-
     channel = 0;
   }
-
   return getChannelHistogram.call(this, channel, {
     useAlpha,
     maxSlots
   });
 }
+
 /**
  * Returns an array (number of channels) of array (number of slots) containing
  * the number of data of a specific intensity.
@@ -64,8 +58,6 @@ function getHistogram(options = {}) {
  *          useAlpha: false
  *      });
  */
-
-
 function getHistograms(options = {}) {
   const {
     maxSlots = 256,
@@ -75,30 +67,27 @@ function getHistograms(options = {}) {
     bitDepth: [8, 16]
   });
   let results = new Array(useAlpha ? this.components : this.channels);
-
   for (let i = 0; i < results.length; i++) {
     results[i] = getChannelHistogram.call(this, i, {
       useAlpha,
       maxSlots
     });
   }
-
   return results;
 }
-
 function getChannelHistogram(channel, options) {
   let {
     useAlpha,
     maxSlots
-  } = options; // for a mask, return a number array containing count of black and white points (black = array[0], white = array[1])
+  } = options;
+
+  // for a mask, return a number array containing count of black and white points (black = array[0], white = array[1])
 
   if (this.bitDepth === 1) {
     let blackWhiteCount = [0, 0];
-
     for (let i = 0; i < this.height; i++) {
       for (let j = 0; j < this.width; j++) {
         let value = this.getBitXY(i, j);
-
         if (value === 0) {
           blackWhiteCount[0] += 1;
         } else if (value === 1) {
@@ -106,31 +95,24 @@ function getChannelHistogram(channel, options) {
         }
       }
     }
-
     return blackWhiteCount;
   }
-
   let bitSlots = Math.log2(maxSlots);
-
   if (!(0, _isInteger.default)(bitSlots)) {
     throw new RangeError('maxSlots must be a power of 2, for example: 64, 256, 1024');
-  } // we will compare the bitSlots to the bitDepth of the image
+  }
+  // we will compare the bitSlots to the bitDepth of the image
   // based on this we will shift the values. This allows to generate a histogram
   // of 16 grey even if the images has 256 shade of grey
 
-
   let bitShift = 0;
-
   if (this.bitDepth > bitSlots) {
     bitShift = this.bitDepth - bitSlots;
   }
-
   let data = this.data;
   let result = (0, _newArray.default)(Math.pow(2, Math.min(this.bitDepth, bitSlots)), 0);
-
   if (useAlpha && this.alpha) {
     let alphaChannelDiff = this.channels - channel - 1;
-
     for (let i = channel; i < data.length; i += this.channels) {
       result[data[i] >> bitShift] += data[i + alphaChannelDiff] / this.maxValue;
     }
@@ -139,6 +121,5 @@ function getChannelHistogram(channel, options) {
       result[data[i] >> bitShift]++;
     }
   }
-
   return result;
 }