image-js 0.33.0 → 0.34.0

package/index.d.ts

@@ -32,7 +32,7 @@ export declare class Image {
   static createFrom(other: Image, options: ImageConstructorOptions): Image;
   static load(
     image: string | ArrayBuffer | Uint8Array,
-    options?: RequestInit,
+    options?: RequestInit & { ignorePalette: boolean },
   ): Promise<Image>;
 
   getRoiManager(): RoiManager;
@@ -149,7 +149,14 @@ export declare class Image {
   // paintPoints
   // paintPolyline
   // paintPolylines
-  // paintPolygon
+  paintPolygon(
+    points: Array<Array<number>>,
+    options?: {
+      color?: Array<number>;
+      filled?: boolean;
+    },
+  ): Image;
+
   // paintPolygons
 
   // countAlphaPixels

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/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");
 

package/lib/image/core/kind.js

@@ -3,10 +3,10 @@
 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"));
 

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

@@ -34,7 +34,10 @@ const isDataURL = /^data:[a-z]+\/(?:[a-z]+);base64,/;
  * @static
  * @param {string|ArrayBuffer|Buffer|Uint8Array} image - URL of the image (browser, can be a dataURL) or path (Node.js)
  * or buffer containing the binary data
- * @param {object} [options] - In the browser, the options object is passed to the underlying `fetch` call.
+ * @param {object} [options] - In the browser, the options object is passed to the underlying `fetch` call, along with
+ * the data URL. For binary data, the option specify decoding options.
+ * @param {boolean} [options.ignorePalette] - When set to true and loading a tiff from binary data, if the tiff is of
+ * type 3 (palette), load as single channel greyscale rather than as a pseudo-colored RGB.
  * @return {Promise<Image>}
  * @example
  * const image = await Image.load('https://example.com/image.png');
@@ -44,15 +47,15 @@ function load(image, options) {
   if (typeof image === 'string') {
     return loadURL(image, options);
   } else if (image instanceof ArrayBuffer) {
-    return Promise.resolve(loadBinary(new Uint8Array(image)));
+    return Promise.resolve(loadBinary(new Uint8Array(image), undefined, options && options.ignorePalette));
   } else if (image.buffer) {
-    return Promise.resolve(loadBinary(image));
+    return Promise.resolve(loadBinary(image, undefined, options && options.ignorePalette));
   } else {
     throw new Error('argument to "load" must be a string or buffer.');
   }
 }
 
-function loadBinary(image, base64Url) {
+function loadBinary(image, base64Url, ignorePalette) {
   const type = (0, _imageType.default)(image);
 
   if (type) {
@@ -64,7 +67,7 @@ function loadBinary(image, base64Url) {
         return loadJPEG(image);
 
       case 'image/tiff':
-        return loadTIFF(image);
+        return loadTIFF(image, ignorePalette);
 
       default:
         return loadGeneric(getBase64(type.mime));
@@ -94,7 +97,7 @@ function loadURL(url, options) {
 
   return binaryDataP.then(binaryData => {
     const uint8 = new Uint8Array(binaryData);
-    return loadBinary(uint8, dataURL ? url : undefined);
+    return loadBinary(uint8, dataURL ? url : undefined, options && options.ignorePalette);
   });
 }
 
@@ -195,13 +198,15 @@ function loadJPEG(data) {
   return image;
 }
 
-function loadTIFF(data) {
+function loadTIFF(data, ignorePalette) {
   let result = (0, _tiff.decode)(data);
 
   if (result.length === 1) {
-    return getImageFromIFD(result[0]);
+    return getImageFromIFD(result[0], ignorePalette);
   } else {
-    return new _Stack.default(result.map(getImageFromIFD));
+    return new _Stack.default(result.map(function (image) {
+      return getImageFromIFD(image, ignorePalette);
+    }));
   }
 }
 
@@ -224,8 +229,8 @@ function getMetadata(image) {
   return metadata;
 }
 
-function getImageFromIFD(image) {
-  if (image.type === 3) {
+function getImageFromIFD(image, ignorePalette) {
+  if (!ignorePalette && image.type === 3) {
     // Palette
     const data = new Uint16Array(3 * image.width * image.height);
     const palette = image.palette;

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/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"));
 

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/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": "0.33.0",
+  "version": "0.34.0",
   "description": "Image processing and manipulation in JavaScript",
   "keywords": [
     "image",
@@ -59,21 +59,21 @@
     ]
   },
   "devDependencies": {
-    "@babel/cli": "^7.14.5",
-    "@babel/core": "^7.14.6",
-    "@babel/plugin-transform-block-scoping": "^7.14.5",
-    "@babel/plugin-transform-modules-commonjs": "^7.14.5",
-    "@babel/preset-env": "^7.14.7",
-    "@types/jest": "^26.0.23",
+    "@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",
     "cheminfo-build": "^1.1.11",
     "cross-env": "^7.0.3",
-    "eslint": "^7.30.0",
-    "eslint-config-cheminfo": "^5.2.4",
+    "eslint": "^8.1.0",
+    "eslint-config-cheminfo": "^7.1.2",
     "esm": "^3.2.25",
-    "jest": "^27.0.6",
-    "jest-matcher-deep-close-to": "^2.0.1",
-    "prettier": "^2.3.2",
+    "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"
   },
@@ -84,7 +84,7 @@
     "fast-bmp": "^1.0.0",
     "fast-jpeg": "^1.0.1",
     "fast-list": "^1.0.3",
-    "fast-png": "^5.0.4",
+    "fast-png": "^6.1.0",
     "has-own": "^1.0.1",
     "image-type": "^4.1.0",
     "is-array-type": "^1.0.0",
@@ -101,7 +101,7 @@
     "monotone-chain-convex-hull": "^1.0.0",
     "new-array": "^1.0.0",
     "robust-point-in-polygon": "^1.0.3",
-    "tiff": "^5.0.0",
+    "tiff": "^5.0.2",
     "web-worker-manager": "^0.2.0"
   },
   "engines": {

package/src/browser/worker/worker.js

@@ -26,6 +26,7 @@ class Worker {
     let manager;
     let url;
     let runner = {};
+
     function run(...args) {
       if (!manager) {
         this.checkUrl();
@@ -35,6 +36,7 @@ class Worker {
       }
       return method.run.call(runner, ...args);
     }
+
     run.reset = function () {
       if (manager) {
         manager.terminate();

package/src/image/core/export.js

@@ -125,10 +125,12 @@ const exportMethods = {
     }
     const { useCanvas = false, encoder: encoderOptions = undefined } = options;
     type = getType(type);
+
     function dataUrl(encoder, ctx) {
       const u8 = encoder(ctx, encoderOptions);
       return toBase64URL(u8, type);
     }
+
     if (type === 'image/bmp') {
       return dataUrl(encodeBmp, this);
     } else if (type === 'image/png' && !useCanvas) {

package/src/image/core/load.js

@@ -19,7 +19,10 @@ const isDataURL = /^data:[a-z]+\/(?:[a-z]+);base64,/;
  * @static
  * @param {string|ArrayBuffer|Buffer|Uint8Array} image - URL of the image (browser, can be a dataURL) or path (Node.js)
  * or buffer containing the binary data
- * @param {object} [options] - In the browser, the options object is passed to the underlying `fetch` call.
+ * @param {object} [options] - In the browser, the options object is passed to the underlying `fetch` call, along with
+ * the data URL. For binary data, the option specify decoding options.
+ * @param {boolean} [options.ignorePalette] - When set to true and loading a tiff from binary data, if the tiff is of
+ * type 3 (palette), load as single channel greyscale rather than as a pseudo-colored RGB.
  * @return {Promise<Image>}
  * @example
  * const image = await Image.load('https://example.com/image.png');
@@ -28,15 +31,23 @@ export default function load(image, options) {
   if (typeof image === 'string') {
     return loadURL(image, options);
   } else if (image instanceof ArrayBuffer) {
-    return Promise.resolve(loadBinary(new Uint8Array(image)));
+    return Promise.resolve(
+      loadBinary(
+        new Uint8Array(image),
+        undefined,
+        options && options.ignorePalette,
+      ),
+    );
   } else if (image.buffer) {
-    return Promise.resolve(loadBinary(image));
+    return Promise.resolve(
+      loadBinary(image, undefined, options && options.ignorePalette),
+    );
   } else {
     throw new Error('argument to "load" must be a string or buffer.');
   }
 }
 
-function loadBinary(image, base64Url) {
+function loadBinary(image, base64Url, ignorePalette) {
   const type = imageType(image);
   if (type) {
     switch (type.mime) {
@@ -45,12 +56,13 @@ function loadBinary(image, base64Url) {
       case 'image/jpeg':
         return loadJPEG(image);
       case 'image/tiff':
-        return loadTIFF(image);
+        return loadTIFF(image, ignorePalette);
       default:
         return loadGeneric(getBase64(type.mime));
     }
   }
   return loadGeneric(getBase64('application/octet-stream'));
+
   function getBase64(type) {
     if (base64Url) {
       return base64Url;
@@ -70,7 +82,11 @@ function loadURL(url, options) {
   }
   return binaryDataP.then((binaryData) => {
     const uint8 = new Uint8Array(binaryData);
-    return loadBinary(uint8, dataURL ? url : undefined);
+    return loadBinary(
+      uint8,
+      dataURL ? url : undefined,
+      options && options.ignorePalette,
+    );
   });
 }
 
@@ -159,12 +175,16 @@ function loadJPEG(data) {
   return image;
 }
 
-function loadTIFF(data) {
+function loadTIFF(data, ignorePalette) {
   let result = decodeTiff(data);
   if (result.length === 1) {
-    return getImageFromIFD(result[0]);
+    return getImageFromIFD(result[0], ignorePalette);
   } else {
-    return new Stack(result.map(getImageFromIFD));
+    return new Stack(
+      result.map(function (image) {
+        return getImageFromIFD(image, ignorePalette);
+      }),
+    );
   }
 }
 
@@ -184,8 +204,8 @@ function getMetadata(image) {
   return metadata;
 }
 
-function getImageFromIFD(image) {
-  if (image.type === 3) {
+function getImageFromIFD(image, ignorePalette) {
+  if (!ignorePalette && image.type === 3) {
     // Palette
     const data = new Uint16Array(3 * image.width * image.height);
     const palette = image.palette;

package/src/image/roi/creator/fromMask.js

@@ -151,5 +151,6 @@ export default function fromMask(mask, options = {}) {
       }
     }
   }
+
   return new RoiMap(mask, data);
 }

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

@@ -31,6 +31,7 @@ export default function minimum(histogram) {
   threshold = minimumBetweenPeeks(histogramCopy, max);
   return threshold;
 }
+
 function smoothed(histogram) {
   // Smooth with a 3 point running mean filter
   let auHistogram = new Array(histogram.length); // a copy of the histograma for the smoothing process
@@ -42,6 +43,7 @@ function smoothed(histogram) {
     (histogram[histogram.length - 2] + histogram[histogram.length - 1]) / 3;
   return auHistogram;
 }
+
 function minimumBetweenPeeks(histogramBimodal, max) {
   let threshold;
   for (let i = 1; i < max; i++) {
@@ -55,6 +57,7 @@ function minimumBetweenPeeks(histogramBimodal, max) {
   }
   return threshold;
 }
+
 function bimodalTest(histogram) {
   // It is responsible for determining if a histogram is bimodal
   let len = histogram.length;