image-js 1.0.0-alpha.3 → 1.0.0

package/lib/geometry/transform.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"transform.d.ts","sourceRoot":"","sources":["../../src/geometry/transform.ts"],"names":[],"mappings":"AAEA,OAAO,EAAE,KAAK,EAAE,MAAM,aAAa,CAAC;AAEpC,OAAO,KAAK,EAAE,UAAU,EAAE,MAAM,+BAA+B,CAAC;AAEhE,OAAO,KAAK,EAAE,iBAAiB,EAAE,MAAM,8BAA8B,CAAC;AAGtE,MAAM,WAAW,gBAAgB;IAC/B;;OAEG;IACH,KAAK,CAAC,EAAE,MAAM,CAAC;IACf;;OAEG;IACH,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB;;;OAGG;IAEH,iBAAiB,CAAC,EAAE,iBAAiB,CAAC;IACtC;;;OAGG;IACH,UAAU,CAAC,EAAE,UAAU,CAAC;IACxB;;;OAGG;IACH,WAAW,CAAC,EAAE,MAAM,CAAC;IACrB;;OAEG;IACH,OAAO,CAAC,EAAE,OAAO,CAAC;IAClB;;;OAGG;IACH,SAAS,CAAC,EAAE,OAAO,CAAC;CACrB;AAED;;;;;;GAMG;AACH,wBAAgB,SAAS,CACvB,KAAK,EAAE,KAAK,EACZ,eAAe,EAAE,MAAM,EAAE,EAAE,EAC3B,OAAO,GAAE,gBAAqB,GAC7B,KAAK,CA2HP"}

package/lib/geometry/transform.js

@@ -1,85 +1,103 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-const ml_matrix_1 = require("ml-matrix");
-const Image_1 = require("../Image");
-const interpolatePixel_1 = require("../utils/interpolatePixel");
-const types_1 = require("../types");
-const interpolateBorder_1 = require("../utils/interpolateBorder");
-const clamp_1 = require("../utils/clamp");
-function transform(image, transformMatrix, options = {}) {
-    const { borderType = types_1.BorderType.CONSTANT, borderValue = 0, interpolationType = types_1.InterpolationType.BILINEAR } = options;
-    let { width = image.width, height = image.height } = options;
-    if (options.fullImage) {
-        transformMatrix = transformMatrix.map((row) => row.slice());
-        transformMatrix[0][2] = 0;
-        transformMatrix[1][2] = 0;
-        const corners = [
-            image.getCoordinates(Image_1.ImageCoordinates.TOP_LEFT),
-            image.getCoordinates(Image_1.ImageCoordinates.TOP_RIGHT),
-            image.getCoordinates(Image_1.ImageCoordinates.BOTTOM_RIGHT),
-            image.getCoordinates(Image_1.ImageCoordinates.BOTTOM_LEFT)
-        ];
-        corners[1][0] += 1;
-        corners[2][0] += 1;
-        corners[2][1] += 1;
-        corners[3][1] += 1;
-        const transformedCorners = corners.map((corner) => {
-            return [
-                transformPoint(transformMatrix[0], corner[0], corner[1]),
-                transformPoint(transformMatrix[1], corner[0], corner[1])
-            ];
-        });
-        const xCoordinates = transformedCorners.map((c) => c[0]);
-        const yCoordinates = transformedCorners.map((c) => c[1]);
-        const maxX = Math.max(...xCoordinates);
-        const maxY = Math.max(...yCoordinates);
-        const minX = Math.min(...xCoordinates);
-        const minY = Math.min(...yCoordinates);
-        const center = [(image.width - 1) / 2, (image.height - 1) / 2];
-        width = maxX - minX;
-        height = maxY - minY;
-        const centerX = transformPoint(transformMatrix[0], center[0], center[1]);
-        const centerY = transformPoint(transformMatrix[1], center[0], center[1]);
-        const a = (width - 1) / 2 - centerX;
-        const b = (height - 1) / 2 - centerY;
-        transformMatrix[0][2] = a;
-        transformMatrix[1][2] = b;
-        width = Math.round(width);
-        height = Math.round(height);
-    }
-    if (transformMatrix.length !== 2 ||
-        transformMatrix[0].length !== 3 ||
-        transformMatrix[1].length !== 3) {
-        throw new Error(`transformation matrix must be 2x3, found ${transformMatrix.length}x${transformMatrix[1].length}`);
-    }
-    if (!options.inverse) {
-        transformMatrix = [transformMatrix[0], transformMatrix[1], [0, 0, 1]];
-        transformMatrix = ml_matrix_1.inverse(new ml_matrix_1.Matrix(transformMatrix)).to2DArray();
-    }
-    const newImage = Image_1.Image.createFrom(image, {
-        width,
-        height
-    });
-    const interpolateBorder = interpolateBorder_1.getBorderInterpolation(borderType, borderValue);
-    const clamp = clamp_1.getClamp(newImage);
-    const interpolate = interpolatePixel_1.getInterpolationFunction(interpolationType);
-    const hFactor = newImage.width * newImage.channels;
-    for (let y = 0; y < newImage.height; y++) {
-        const hOffset = hFactor * y;
-        for (let x = 0; x < newImage.width; x++) {
-            const wOffset = hOffset + x * image.channels;
-            const nx = transformPoint(transformMatrix[0], x, y);
-            const ny = transformPoint(transformMatrix[1], x, y);
-            for (let c = 0; c < newImage.channels; c++) {
-                const newValue = interpolate(image, nx, ny, c, interpolateBorder, clamp);
-                newImage.data[wOffset + c] = newValue;
-            }
-        }
-    }
-    return newImage;
-}
-exports.transform = transform;
-function transformPoint(transform, x, y) {
-    return transform[0] * x + transform[1] * y + transform[2];
-}
+import { Matrix, inverse } from 'ml-matrix';
+import { Image } from '../Image.js';
+import { getClamp } from '../utils/clamp.js';
+import { getBorderInterpolation } from '../utils/interpolateBorder.js';
+import { getInterpolationFunction } from '../utils/interpolatePixel.js';
+/**
+ * Transforms an image using a matrix.
+ * @param image - Original image.
+ * @param transformMatrix - 2×3 transform matrix.
+ * @param options - Transform options.
+ * @returns The new image.
+ */
+export function transform(image, transformMatrix, options = {}) {
+    const { borderType = 'constant', borderValue = 0, interpolationType = 'bilinear', fullImage, } = options;
+    let { width = image.width, height = image.height } = options;
+    if (!isValidMatrix(transformMatrix)) {
+        throw new TypeError(`transformation matrix must be 2x3 or 3x3. Received ${transformMatrix.length}x${transformMatrix[1].length}`);
+    }
+    if (transformMatrix.length === 2) {
+        transformMatrix.push([0, 0, 1]);
+    }
+    if (fullImage) {
+        transformMatrix = transformMatrix.map((row) => row.slice());
+        transformMatrix[0][2] = 0;
+        transformMatrix[1][2] = 0;
+        const corners = [
+            image.getCoordinates('top-left'),
+            image.getCoordinates('top-right'),
+            image.getCoordinates('bottom-right'),
+            image.getCoordinates('bottom-left'),
+        ];
+        corners[1].column += 1;
+        corners[2].column += 1;
+        corners[2].row += 1;
+        corners[3].row += 1;
+        const transformedCorners = corners.map((corner) => {
+            return [
+                transformPoint(transformMatrix[0], transformMatrix[2], corner.column, corner.row),
+                transformPoint(transformMatrix[1], transformMatrix[2], corner.column, corner.row),
+            ];
+        });
+        const xCoordinates = transformedCorners.map((c) => c[0]);
+        const yCoordinates = transformedCorners.map((c) => c[1]);
+        const maxX = Math.max(...xCoordinates);
+        const maxY = Math.max(...yCoordinates);
+        const minX = Math.min(...xCoordinates);
+        const minY = Math.min(...yCoordinates);
+        const center = [(image.width - 1) / 2, (image.height - 1) / 2];
+        width = maxX - minX;
+        height = maxY - minY;
+        const centerX = transformPoint(transformMatrix[0], transformMatrix[2], center[0], center[1]);
+        const centerY = transformPoint(transformMatrix[1], transformMatrix[2], center[0], center[1]);
+        const a = (width - 1) / 2 - centerX;
+        const b = (height - 1) / 2 - centerY;
+        transformMatrix[0][2] = a;
+        transformMatrix[1][2] = b;
+        width = Math.round(width);
+        height = Math.round(height);
+    }
+    if (!options.inverse) {
+        transformMatrix = inverse(new Matrix(transformMatrix)).to2DArray();
+    }
+    const newImage = Image.createFrom(image, {
+        width,
+        height,
+    });
+    const interpolateBorder = getBorderInterpolation(borderType, borderValue);
+    const clamp = getClamp(newImage);
+    const interpolate = getInterpolationFunction(interpolationType);
+    for (let row = 0; row < newImage.height; row++) {
+        for (let column = 0; column < newImage.width; column++) {
+            const nx = transformPoint(transformMatrix[0], transformMatrix[2], column, row);
+            const ny = transformPoint(transformMatrix[1], transformMatrix[2], column, row);
+            for (let channel = 0; channel < newImage.channels; channel++) {
+                const newValue = interpolate(image, nx, ny, channel, interpolateBorder, clamp);
+                newImage.setValue(column, row, channel, newValue);
+            }
+        }
+    }
+    return newImage;
+}
+/**
+ * Apply a transformation to a point.
+ * @param transform - Transformation matrix.
+ * @param perspective - Perspective matrix.
+ * @param column - Column of the point.
+ * @param row - Row of the point.
+ * @returns New value.
+ */
+function transformPoint(transform, perspective, column, row) {
+    return ((transform[0] * column + transform[1] * row + transform[2]) /
+        (perspective[0] * column + perspective[1] * row + perspective[2]));
+}
+function isValidMatrix(transformationMatrix) {
+    return ((transformationMatrix.length === 3 &&
+        transformationMatrix[0].length === 3 &&
+        transformationMatrix[1].length === 3 &&
+        transformationMatrix[2].length === 3) ||
+        (transformationMatrix.length === 2 &&
+            transformationMatrix[0].length === 3 &&
+            transformationMatrix[1].length === 3));
+}
 //# sourceMappingURL=transform.js.map

package/lib/geometry/transform.js.map

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package/lib/geometry/transformRotate.d.ts

@@ -0,0 +1,24 @@
+import type { Image, ImageCoordinates } from '../Image.js';
+import type { Point } from '../utils/geometry/points.js';
+import type { TransformOptions } from './transform.js';
+export interface TransformRotateOptions extends TransformOptions {
+    /**
+     * Specify the rotation center point as a predefined string or a Point.
+     * @default `'center'`.
+     */
+    center?: ImageCoordinates | Point;
+    /**
+     * Scaling factor for the rotated image.
+     *  @default `1`
+     */
+    scale?: number;
+}
+/**
+ * Rotate an image anti-clockwise of a given angle.
+ * @param image - Original image.
+ * @param angle - Angle in degrees.
+ * @param options - Rotate options.
+ * @returns A new rotated image.
+ */
+export declare function transformRotate(image: Image, angle: number, options?: TransformRotateOptions): Image;
+//# sourceMappingURL=transformRotate.d.ts.map

package/lib/geometry/transformRotate.d.ts.map

@@ -0,0 +1 @@
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package/lib/geometry/transformRotate.js

@@ -0,0 +1,38 @@
+import { transform } from './transform.js';
+/**
+ * Rotate an image anti-clockwise of a given angle.
+ * @param image - Original image.
+ * @param angle - Angle in degrees.
+ * @param options - Rotate options.
+ * @returns A new rotated image.
+ */
+export function transformRotate(image, angle, options = {}) {
+    const { center = 'center', scale = 1, ...otherOptions } = options;
+    let centerCoordinates;
+    if (typeof center === 'string') {
+        centerCoordinates = image.getCoordinates(center);
+    }
+    else {
+        centerCoordinates = center;
+    }
+    const transformMatrix = getRotationMatrix(angle, centerCoordinates, scale);
+    return transform(image, transformMatrix, otherOptions);
+}
+/**
+ * Generates a rotation matrix for the given angle.
+ * @param angle - Angle in degrees.
+ * @param center - Center point of the image.
+ * @param scale - Scaling factor.
+ * @returns 3 x 3 rotation matrix.
+ */
+function getRotationMatrix(angle, center, scale) {
+    const angleRadians = (angle * Math.PI) / 180;
+    const cos = scale * Math.cos(angleRadians);
+    const sin = scale * Math.sin(angleRadians);
+    return [
+        [cos, sin, (1 - cos) * center.column - sin * center.row],
+        [-sin, cos, sin * center.column + (1 - cos) * center.row],
+        [0, 0, 1],
+    ];
+}
+//# sourceMappingURL=transformRotate.js.map

package/lib/geometry/transformRotate.js.map

@@ -0,0 +1 @@
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package/lib/index.d.ts

@@ -1,9 +1,25 @@
-export * from './Image';
-export * from './compute';
-export * from './filters';
-export * from './load';
-export * from './operations';
-export * from './geometry';
-export * from './save';
-export * from './types';
+export * from './align/index.js';
+export * from './compare/index.js';
+export * from './compute/index.js';
+export * from './correctColor/index.js';
+export * from './draw/index.js';
+export * from './featureMatching/index.js';
+export * from './filters/index.js';
+export * from './geometry/index.js';
+export * from './utils/geometry/index.js';
+export * from './Image.js';
+export * from './load/index.js';
+export * from './Mask.js';
+export * from './maskAnalysis/index.js';
+export * from './morphology/index.js';
+export * from './operations/index.js';
+export * from './roi/index.js';
+export * from './save/index.js';
+export * from './Stack.js';
+export { decodeStack } from './stack/load/decodeStack.js';
+export * from './utils/utils.types.js';
+export * from './utils/constants/channelLabels.js';
+export * from './utils/constants/colorModels.js';
+export { BorderType } from './utils/interpolateBorder.js';
+export { InterpolationType } from './utils/interpolatePixel.js';
 //# sourceMappingURL=index.d.ts.map

package/lib/index.d.ts.map

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package/lib/index.js

@@ -1,14 +1,25 @@
-"use strict";
-function __export(m) {
-    for (var p in m) if (!exports.hasOwnProperty(p)) exports[p] = m[p];
-}
-Object.defineProperty(exports, "__esModule", { value: true });
-__export(require("./Image"));
-__export(require("./compute"));
-__export(require("./filters"));
-__export(require("./load"));
-__export(require("./operations"));
-__export(require("./geometry"));
-__export(require("./save"));
-__export(require("./types"));
+export * from './align/index.js';
+export * from './compare/index.js';
+export * from './compute/index.js';
+export * from './correctColor/index.js';
+export * from './draw/index.js';
+export * from './featureMatching/index.js';
+export * from './filters/index.js';
+export * from './geometry/index.js';
+export * from './utils/geometry/index.js';
+export * from './Image.js';
+export * from './load/index.js';
+export * from './Mask.js';
+export * from './maskAnalysis/index.js';
+export * from './morphology/index.js';
+export * from './operations/index.js';
+export * from './roi/index.js';
+export * from './save/index.js';
+export * from './Stack.js';
+export { decodeStack } from './stack/load/decodeStack.js';
+export * from './utils/utils.types.js';
+export * from './utils/constants/channelLabels.js';
+export * from './utils/constants/colorModels.js';
+export { BorderType } from './utils/interpolateBorder.js';
+export { InterpolationType } from './utils/interpolatePixel.js';
 //# sourceMappingURL=index.js.map

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package/lib/load/decode.d.ts

@@ -1,8 +1,9 @@
-import { Image } from '../Image';
-/**
- * Decode input data. Data format is automatically detected.
- * Possible formats: png and jpeg.
- * @param data - data to decode
- */
-export declare function decode(data: ArrayBufferView): Image;
+import type { Image } from '../Image.js';
+/**
+ * Decode input data. Data format is automatically detected.
+ * Possible formats: png, jpeg and tiff.
+ * @param data - Data to decode.
+ * @returns The decoded image.
+ */
+export declare function decode(data: ArrayBufferView): Image;
 //# sourceMappingURL=decode.d.ts.map

package/lib/load/decode.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"decode.d.ts","sourceRoot":"","sources":["../../src/load/decode.ts"],"names":[],"mappings":"AAGA,OAAO,KAAK,EAAE,KAAK,EAAE,MAAM,aAAa,CAAC;AAMzC;;;;;GAKG;AACH,wBAAgB,MAAM,CAAC,IAAI,EAAE,eAAe,GAAG,KAAK,CAcnD"}

package/lib/load/decode.js

@@ -1,29 +1,23 @@
-"use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-const checkHeader_1 = __importDefault(require("./checkHeader"));
-const decodePng_1 = require("./decodePng");
-const decodeJpeg_1 = require("./decodeJpeg");
-const pngHeader = [0x89, 0x50, 0x4e, 0x47, 0x0d, 0x0a, 0x1a, 0x0a];
-const jpegHeader = [0xff, 0xd8, 0xff];
-/**
- * Decode input data. Data format is automatically detected.
- * Possible formats: png and jpeg.
- * @param data - data to decode
- */
-function decode(data) {
-    const typedArray = new Uint8Array(data.buffer, data.byteOffset, data.byteLength);
-    if (checkHeader_1.default(typedArray, pngHeader)) {
-        return decodePng_1.decodePng(typedArray);
-    }
-    else if (checkHeader_1.default(typedArray, jpegHeader)) {
-        return decodeJpeg_1.decodeJpeg(typedArray);
-    }
-    else {
-        throw new Error('unrecognized data format');
-    }
-}
-exports.decode = decode;
+import imageType from 'image-type';
+import { match } from 'ts-pattern';
+import { decodeJpeg } from './decodeJpeg.js';
+import { decodePng } from './decodePng.js';
+import { decodeTiff } from './decodeTiff.js';
+/**
+ * Decode input data. Data format is automatically detected.
+ * Possible formats: png, jpeg and tiff.
+ * @param data - Data to decode.
+ * @returns The decoded image.
+ */
+export function decode(data) {
+    const typedArray = new Uint8Array(data.buffer, data.byteOffset, data.byteLength);
+    const type = imageType(typedArray);
+    return match(type)
+        .with({ mime: 'image/png' }, () => decodePng(typedArray))
+        .with({ mime: 'image/jpeg' }, () => decodeJpeg(typedArray))
+        .with({ mime: 'image/tiff' }, () => decodeTiff(typedArray))
+        .otherwise(() => {
+        throw new RangeError(`invalid data format: ${type?.mime}`);
+    });
+}
 //# sourceMappingURL=decode.js.map

package/lib/load/decode.js.map

@@ -1 +1 @@
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package/lib/load/decodeJpeg.d.ts

@@ -1,7 +1,8 @@
-import { Image } from '../Image';
-/**
- * Decode a jpeg. See the jpeg-js npm module.
- * @param buffer The data to decode
- */
-export declare function decodeJpeg(buffer: Uint8Array): Image;
+import { Image } from '../Image.js';
+/**
+ * Decode a jpeg. See the jpeg-js npm module.
+ * @param buffer - The data to decode.
+ * @returns The decoded image.
+ */
+export declare function decodeJpeg(buffer: Uint8Array): Image;
 //# sourceMappingURL=decodeJpeg.d.ts.map

package/lib/load/decodeJpeg.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"decodeJpeg.d.ts","sourceRoot":"","sources":["../../src/load/decodeJpeg.ts"],"names":[],"mappings":"AAGA,OAAO,EAAE,KAAK,EAAE,MAAM,aAAa,CAAC;AAIpC;;;;GAIG;AACH,wBAAgB,UAAU,CAAC,MAAM,EAAE,UAAU,GAAG,KAAK,CAkBpD"}

package/lib/load/decodeJpeg.js

@@ -1,17 +1,27 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-const jpeg_js_1 = require("jpeg-js");
-const Image_1 = require("../Image");
-/**
- * Decode a jpeg. See the jpeg-js npm module.
- * @param buffer The data to decode
- */
-function decodeJpeg(buffer) {
-    const jpeg = jpeg_js_1.decode(buffer, true);
-    return new Image_1.Image(jpeg.width, jpeg.height, {
-        data: jpeg.data,
-        kind: Image_1.ImageKind.RGBA
-    });
-}
-exports.decodeJpeg = decodeJpeg;
+import { decode as decodeExif } from 'fast-jpeg';
+import { decode } from 'jpeg-js';
+import { Image } from '../Image.js';
+import { getMetadata } from './getMetadata.js';
+/**
+ * Decode a jpeg. See the jpeg-js npm module.
+ * @param buffer - The data to decode.
+ * @returns The decoded image.
+ */
+export function decodeJpeg(buffer) {
+    const jpeg = decode(buffer, {
+        useTArray: true,
+        maxMemoryUsageInMB: Number.POSITIVE_INFINITY,
+        maxResolutionInMP: Number.POSITIVE_INFINITY,
+    });
+    const decodedExif = decodeExif(buffer);
+    // TODO : handle stacks (many IFDs?)
+    const meta = decodedExif.exif?.[0]
+        ? getMetadata(decodedExif.exif[0])
+        : undefined;
+    return new Image(jpeg.width, jpeg.height, {
+        data: jpeg.data,
+        colorModel: 'RGBA',
+        meta,
+    });
+}
 //# sourceMappingURL=decodeJpeg.js.map

package/lib/load/decodeJpeg.js.map

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package/lib/load/decodePng.d.ts

@@ -1,7 +1,8 @@
-import { Image } from '../Image';
-/**
- * Decode a png. See the fast-png npm module.
- * @param buffer The data to decode
- */
-export declare function decodePng(buffer: Uint8Array): Image;
+import { Image } from '../Image.js';
+/**
+ * Decode a PNG. See the fast-png npm module.
+ * @param buffer - The data to decode.
+ * @returns The decoded image.
+ */
+export declare function decodePng(buffer: Uint8Array): Image;
 //# sourceMappingURL=decodePng.d.ts.map

package/lib/load/decodePng.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"decodePng.d.ts","sourceRoot":"","sources":["../../src/load/decodePng.ts"],"names":[],"mappings":"AAIA,OAAO,EAAE,KAAK,EAAE,MAAM,aAAa,CAAC;AAIpC;;;;GAIG;AACH,wBAAgB,SAAS,CAAC,MAAM,EAAE,UAAU,GAAG,KAAK,CA+BnD"}