image-js 1.0.0-alpha.3 → 1.0.0

package/lib/Stack.d.ts.map

@@ -0,0 +1 @@
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package/lib/Stack.js

@@ -0,0 +1,165 @@
+import { histogram, maxImage, meanImage, medianImage, minImage, sum, } from './stack/index.js';
+import { checkImagesValid, verifySameDimensions, } from './stack/utils/checkImagesValid.js';
+export class Stack {
+    /**
+     * The array of images.
+     */
+    images;
+    /**
+     * The stack size.
+     */
+    size;
+    /**
+     * Do the images have an alpha channel?
+     */
+    alpha;
+    /**
+     * The color model of the images.
+     */
+    colorModel;
+    /**
+     * The bit depth of the images.
+     */
+    bitDepth;
+    /**
+     * Whether all the images of the stack have the same dimensions.
+     */
+    sameDimensions;
+    /**
+     * The number of channels of the images.
+     */
+    channels;
+    /**
+     * Create a new stack from an array of images.
+     * The images must have the same bit depth and color model.
+     * @param images - Array of images from which to create the stack.
+     */
+    constructor(images) {
+        checkImagesValid(images);
+        this.images = images;
+        this.size = images.length;
+        this.alpha = images[0].alpha;
+        this.colorModel = images[0].colorModel;
+        this.channels = images[0].channels;
+        this.bitDepth = images[0].bitDepth;
+        this.sameDimensions = verifySameDimensions(images);
+    }
+    *[Symbol.iterator]() {
+        for (const image of this.images) {
+            yield image;
+        }
+    }
+    /**
+     * Clone a stack. The images are a copy of the original images.
+     * @returns A new stack with the same images.
+     */
+    clone() {
+        return new Stack(this.images.map((image) => image.clone()));
+    }
+    /**
+     * Get the images of the stack. Mainly for debugging purposes.
+     * @returns The images.
+     */
+    getImages() {
+        return this.images;
+    }
+    /**
+     * Get the image at the given index.
+     * @param index - The index of the image.
+     * @returns The image.
+     */
+    getImage(index) {
+        return this.images[index];
+    }
+    /**
+     * Get a value from an image of the stack.
+     * @param stackIndex - Index of the image in the stack.
+     * @param row - Row index of the pixel.
+     * @param column - Column index of the pixel.
+     * @param channel - The channel to retrieve.
+     * @returns The value at the given position.
+     */
+    getValue(stackIndex, row, column, channel) {
+        return this.images[stackIndex].getValue(row, column, channel);
+    }
+    /**
+     * Get a value from an image of the stack. Specify the pixel position using its index.
+     * @param stackIndex - Index of the image in the stack.
+     * @param index - The index of the pixel.
+     * @param channel - The channel to retrieve.
+     * @returns The value at the given position.
+     */
+    getValueByIndex(stackIndex, index, channel) {
+        return this.images[stackIndex].getValueByIndex(index, channel);
+    }
+    /**
+     * Return the image containing the minimum values of all the images in the stack for
+     * each pixel. All the images must have the same dimensions.
+     * @returns The minimum image.
+     */
+    minImage() {
+        return minImage(this);
+    }
+    /**
+     * Return the image containing the maximum values of all the images in the stack for
+     * each pixel. All the images must have the same dimensions.
+     * @returns The maximum image.
+     */
+    maxImage() {
+        return maxImage(this);
+    }
+    /**
+     * Return the image containing the median values of all the images in the stack for
+     * each pixel. All the images must have the same dimensions.
+     * @returns The median image.
+     */
+    medianImage() {
+        return medianImage(this);
+    }
+    /**
+     * Return the image containing the average values of all the images in the stack for
+     * each pixel. All the images must have the same dimensions.
+     * @returns The mean image.
+     */
+    meanImage() {
+        return meanImage(this);
+    }
+    /**
+     * Return a 16 bits depth image containing the sum values of all the images in the stack for
+     * each pixel.
+     * @returns The sum image.
+     */
+    sum() {
+        return sum(this);
+    }
+    /**
+     * Get the sum of all the histograms of the stack's images. If no channel is specified in the options, the images must be GREY.
+     * @param options - Histogram options.
+     * @returns The histogram of the stack.
+     */
+    histogram(options = {}) {
+        return histogram(this, options);
+    }
+    /**
+     * Align all the images of the stack on the image at the given index.
+     * @param refIndex - The index of the reference image.
+     */
+    // public alignImages(refIndex: number): Stack {}
+    /**
+     * Map a function on all the images of the stack.
+     * @param callback - Function to apply on each image.
+     * @returns New stack with the modified images.
+     */
+    map(callback) {
+        return new Stack(this.images.map(callback));
+    }
+    /**
+     * Filter the images in the stack.
+     * @param callback - Function to decide which images to keep.
+     * @returns New filtered stack.
+     */
+    filter(callback) {
+        return new Stack(this.images.filter(callback));
+    }
+}
+//# sourceMappingURL=Stack.js.map

package/lib/Stack.js.map

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package/lib/align/affineTransfrom/affineFitFunction.d.ts

@@ -0,0 +1,10 @@
+import type { Point } from '../../geometry/index.js';
+/**
+ * The fit function for an affine transformation.
+ * Get the best transformation parameters for the given source and destination.
+ * @param source - Source points.
+ * @param destination - Destination points.
+ * @returns The model parameters in the format [angle, xTranslation, yTranslation]
+ */
+export declare function affineFitFunction(source: Point[], destination: Point[]): number[];
+//# sourceMappingURL=affineFitFunction.d.ts.map

package/lib/align/affineTransfrom/affineFitFunction.d.ts.map

@@ -0,0 +1 @@
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package/lib/align/affineTransfrom/affineFitFunction.js

@@ -0,0 +1,21 @@
+import { getAffineTransform } from 'ml-affine-transform';
+import { getMatrixFromPoints } from './getMatrixFromPoints.js';
+/**
+ * The fit function for an affine transformation.
+ * Get the best transformation parameters for the given source and destination.
+ * @param source - Source points.
+ * @param destination - Destination points.
+ * @returns The model parameters in the format [angle, xTranslation, yTranslation]
+ */
+export function affineFitFunction(source, destination) {
+    const sourceMatrix = getMatrixFromPoints(source);
+    const destinationMatrix = getMatrixFromPoints(destination);
+    const result = getAffineTransform(sourceMatrix, destinationMatrix);
+    return [
+        result.rotation,
+        result.translation.x,
+        result.translation.y,
+        result.scale,
+    ];
+}
+//# sourceMappingURL=affineFitFunction.js.map

package/lib/align/affineTransfrom/affineFitFunction.js.map

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package/lib/align/affineTransfrom/applyAffineTransform.d.ts

@@ -0,0 +1,10 @@
+import type { ModelFunction } from 'ml-ransac';
+import type { Point } from '../../geometry/index.js';
+/**
+ * Apply a given transform to a set of points.
+ * @param points - Points to process.
+ * @param model - The transformation function.
+ * @returns The transformed points.
+ */
+export declare function applyAffineTransfom(points: Point[], model: ModelFunction<Point>): Point[];
+//# sourceMappingURL=applyAffineTransform.d.ts.map

package/lib/align/affineTransfrom/applyAffineTransform.d.ts.map

@@ -0,0 +1 @@
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package/lib/align/affineTransfrom/applyAffineTransform.js

@@ -0,0 +1,19 @@
+/**
+ * Apply a given transform to a set of points.
+ * @param points - Points to process.
+ * @param model - The transformation function.
+ * @returns The transformed points.
+ */
+export function applyAffineTransfom(points, model) {
+    const result = [];
+    for (const point of points) {
+        const transformed = model(point);
+        const roundedPoint = {
+            row: Math.round(transformed.row),
+            column: Math.round(transformed.column),
+        };
+        result.push(roundedPoint);
+    }
+    return result;
+}
+//# sourceMappingURL=applyAffineTransform.js.map

package/lib/align/affineTransfrom/applyAffineTransform.js.map

@@ -0,0 +1 @@
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package/lib/align/affineTransfrom/createAffineTransformModel.d.ts

@@ -0,0 +1,10 @@
+import type { ModelFunction } from 'ml-ransac';
+import type { Point } from '../../geometry/index.js';
+/**
+ * Generate a function that applies the given transformation parameters to a point.
+ * The transform is an array of number in the format: [angle, x, y, scale].
+ * @param transform - Transformation to apply.
+ * @returns Function to transform a point.
+ */
+export declare function createAffineTransformModel(transform: number[]): ModelFunction<Point>;
+//# sourceMappingURL=createAffineTransformModel.d.ts.map

package/lib/align/affineTransfrom/createAffineTransformModel.d.ts.map

@@ -0,0 +1 @@
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package/lib/align/affineTransfrom/createAffineTransformModel.js

@@ -0,0 +1,23 @@
+/**
+ * Generate a function that applies the given transformation parameters to a point.
+ * The transform is an array of number in the format: [angle, x, y, scale].
+ * @param transform - Transformation to apply.
+ * @returns Function to transform a point.
+ */
+export function createAffineTransformModel(transform) {
+    if (transform.length !== 4) {
+        throw new Error('Transform had wrong number of parameters');
+    }
+    return (point) => {
+        const angle = (transform[0] * Math.PI) / 180;
+        const xTranslation = transform[1];
+        const yTranslation = transform[2];
+        const scale = transform[3];
+        const column = scale * (Math.cos(angle) * point.column - Math.sin(angle) * point.row) +
+            xTranslation;
+        const row = scale * (Math.sin(angle) * point.column + Math.cos(angle) * point.row) +
+            yTranslation;
+        return { column, row };
+    };
+}
+//# sourceMappingURL=createAffineTransformModel.js.map

package/lib/align/affineTransfrom/createAffineTransformModel.js.map

@@ -0,0 +1 @@
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package/lib/align/affineTransfrom/drawResult.d.ts

@@ -0,0 +1,12 @@
+import { Image } from '../../Image.js';
+import type { Point } from '../../geometry/index.js';
+/**
+ * Draw source, destination and transformed points on an image.
+ * @param source - Source points.
+ * @param destination - Destination points.
+ * @param result - Transformed points.
+ * @param imageSide - Dimension of the image. Should be odd integer.
+ * @returns The image with the points.
+ */
+export declare function drawResult(source: Point[], destination: Point[], result: Point[], imageSide?: number): Image;
+//# sourceMappingURL=drawResult.d.ts.map

package/lib/align/affineTransfrom/drawResult.d.ts.map

@@ -0,0 +1 @@
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package/lib/align/affineTransfrom/drawResult.js

@@ -0,0 +1,38 @@
+import { Image } from '../../Image.js';
+import { Mask } from '../../Mask.js';
+import { ImageColorModel } from '../../utils/constants/colorModels.js';
+/**
+ * Draw source, destination and transformed points on an image.
+ * @param source - Source points.
+ * @param destination - Destination points.
+ * @param result - Transformed points.
+ * @param imageSide - Dimension of the image. Should be odd integer.
+ * @returns The image with the points.
+ */
+export function drawResult(source, destination, result, imageSide = 21) {
+    const center = (imageSide - 1) / 2;
+    const image = new Image(imageSide, imageSide, {
+        colorModel: ImageColorModel.RGB,
+    });
+    // draw coordinates axes
+    image.drawLine({ row: center, column: 0 }, { row: center, column: imageSide }, { out: image, strokeColor: [255, 255, 255] });
+    image.drawLine({ row: 0, column: center }, { row: imageSide, column: center }, { out: image, strokeColor: [255, 255, 255] });
+    // draw points: source (green), destination (blue), result (red)
+    drawBlendedPoints(source, [null, 255, null]);
+    drawBlendedPoints(destination, [null, null, 255]);
+    drawBlendedPoints(result, [255, null, null]);
+    return image;
+    function drawBlendedPoints(points, color) {
+        const mask = new Mask(imageSide, imageSide);
+        const withPoints = mask.drawPoints(points, {
+            color: [1],
+            origin: { row: center, column: center },
+        });
+        image.paintMask(withPoints, {
+            out: image,
+            color,
+            blend: false,
+        });
+    }
+}
+//# sourceMappingURL=drawResult.js.map

package/lib/align/affineTransfrom/drawResult.js.map

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package/lib/align/affineTransfrom/getAffineTransform.d.ts

@@ -0,0 +1,97 @@
+import type { Image } from '../../Image.js';
+import type { Point } from '../../geometry/index.js';
+export interface GetAffineTransformOptions {
+    /**
+     * @default `31`
+     */
+    centroidPatchDiameter?: number;
+    /**
+     * @default `10`
+     */
+    bestKeypointRadius?: number;
+    /**
+     * Should only the crossckeck matches be considered.
+     * @default `true`
+     */
+    crosscheck?: boolean;
+    /**
+     * Should the contrast of the images be enhanced before feature matching.
+     * @default `true`
+     */
+    enhanceContrast?: boolean;
+    /**
+     * Origin of the destination image relative to the top-left corner of the source image.
+     * Roughly indicates the position of the destination image in the source image. Is used
+     * to filter matches by distance as well as to define a subarea of the source image to
+     * use for contrast enhancement.
+     * @default `{ column: 0, row: 0 }`
+     */
+    destinationOrigin?: Point;
+    /**
+     * Max number of iterations of the ransac algorithm.
+     */
+    maxRansacNbIterations?: number;
+    /**
+     * Save images with matches for debugging.
+     * @default `false`
+     */
+    debug?: boolean;
+    /**
+     * Path of the debug image.
+     * @default `${import.meta.dirname}/montage.png`
+     */
+    debugImagePath?: string;
+}
+export interface AffineTransform {
+    /**
+     * Translation of source points along x and y axes.
+     */
+    translation: Point;
+    /**
+     * Clockwise angle in degrees.
+     */
+    rotation: number;
+    /**
+     * Scaling factor from source to destination.
+     */
+    scale: number;
+}
+export interface GetAffineTransformResult {
+    /**
+     * Affine transformation from source to destination.
+     */
+    transform: AffineTransform;
+    stats: {
+        /**
+         * Number of matches of feature matching between source and destination.
+         * The bigger this number is, the better.
+         */
+        nbMatches: number;
+        /**
+         * Number of inliers resulting from the ransac algorithm.
+         */
+        nbInliers: number;
+        /**
+         * Number of iterations of the RANSAC algorithm.
+         */
+        nbRansacIterations: number;
+        /**
+         * Number of source keypoints used for matching.
+         */
+        nbSourceKeypoints: number;
+        /**
+         * Number of destination keypoints used for matching.
+         */
+        nbDestinationKeypoints: number;
+    };
+}
+/**
+ * Get the affine transformation from the source to the destination image.
+ * @param source - Source image. Should be the image to align on the reference image.
+ * It can have an additional margin, specified in the options.
+ * @param destination - Destination image. Should be the reference image.
+ * @param options - Get destination translation options.
+ * @returns The affine transformation from source to destination image.
+ */
+export declare function getAffineTransform(source: Image, destination: Image, options?: GetAffineTransformOptions): GetAffineTransformResult;
+//# sourceMappingURL=getAffineTransform.d.ts.map

package/lib/align/affineTransfrom/getAffineTransform.d.ts.map

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package/lib/align/affineTransfrom/getAffineTransform.js

@@ -0,0 +1,145 @@
+import { getAffineTransform as matrixGetAffineTransform } from 'ml-affine-transform';
+import { ransac } from 'ml-ransac';
+import { getBrief } from '../../featureMatching/descriptors/getBrief.js';
+import { Montage, MontageDisposition, bruteForceOneMatch, getCrosscheckMatches, } from '../../featureMatching/index.js';
+import { filterEuclideanDistance } from '../../featureMatching/matching/filterEuclideanDistance.js';
+import { writeSync } from '../../save/index.js';
+import { ImageColorModel } from '../../utils/constants/colorModels.js';
+import { getMinMax } from '../../utils/getMinMax.js';
+import { affineFitFunction } from './affineFitFunction.js';
+import { createAffineTransformModel } from './createAffineTransformModel.js';
+import { getEuclideanDistance } from './getEuclideanDistance.js';
+import { getMatrixFromPoints } from './getMatrixFromPoints.js';
+import { getSourceWithoutMargins } from './utils/getSourceWithoutMargins.js';
+/**
+ * Get the affine transformation from the source to the destination image.
+ * @param source - Source image. Should be the image to align on the reference image.
+ * It can have an additional margin, specified in the options.
+ * @param destination - Destination image. Should be the reference image.
+ * @param options - Get destination translation options.
+ * @returns The affine transformation from source to destination image.
+ */
+export function getAffineTransform(source, destination, options = {}) {
+    const { centroidPatchDiameter = 31, bestKeypointRadius = 5, enhanceContrast = true, crosscheck = true, destinationOrigin = { column: 0, row: 0 }, maxRansacNbIterations, debug = false, debugImagePath = `${import.meta.dirname}/montage.png`, } = options;
+    if (source.colorModel !== ImageColorModel.GREY) {
+        source = source.grey();
+    }
+    if (destination.colorModel !== ImageColorModel.GREY) {
+        destination = destination.grey();
+    }
+    // enhance images contrast
+    if (enhanceContrast) {
+        const sourceWithoutMargin = getSourceWithoutMargins(source, destination, destinationOrigin);
+        const sourceExtremums = getMinMax(sourceWithoutMargin);
+        source.level({
+            inputMin: sourceExtremums.min[0],
+            inputMax: sourceExtremums.max[0],
+            out: source,
+        });
+        const destinationExtremums = getMinMax(destination);
+        destination.level({
+            inputMin: destinationExtremums.min[0],
+            inputMax: destinationExtremums.max[0],
+            out: destination,
+        });
+    }
+    // compute briefs
+    const sourceBrief = getBrief(source, {
+        centroidPatchDiameter,
+        bestKptRadius: bestKeypointRadius,
+    });
+    const destinationBrief = getBrief(destination, {
+        centroidPatchDiameter,
+        bestKptRadius: bestKeypointRadius,
+    });
+    const nbSourceKeypoints = sourceBrief.keypoints.length;
+    const nbDestinationKeypoints = destinationBrief.keypoints.length;
+    // match reference and destination keypoints
+    let matches = [];
+    if (crosscheck) {
+        matches = getCrosscheckMatches(sourceBrief.descriptors, destinationBrief.descriptors);
+    }
+    else {
+        matches = bruteForceOneMatch(sourceBrief.descriptors, destinationBrief.descriptors);
+        matches = filterEuclideanDistance(matches, sourceBrief.keypoints, destinationBrief.keypoints, { origin: destinationOrigin });
+    }
+    if (matches.length < 2) {
+        throw new Error('Insufficient number of matches found to compute affine transform (less than 2).');
+    }
+    // extract source and destination points
+    let sourcePoints = [];
+    let destinationPoints = [];
+    for (const match of matches) {
+        sourcePoints.push(sourceBrief.keypoints[match.sourceIndex].origin);
+        destinationPoints.push(destinationBrief.keypoints[match.destinationIndex].origin);
+    }
+    // find inliers with ransac
+    let nbInliers = sourcePoints.length;
+    let nbRansacIterations = 0;
+    let inliers = [0, 1];
+    if (sourcePoints.length > 2) {
+        const ransacResult = ransac(sourcePoints, destinationPoints, {
+            distanceFunction: getEuclideanDistance,
+            modelFunction: createAffineTransformModel,
+            fitFunction: affineFitFunction,
+            maxNbIterations: maxRansacNbIterations,
+        });
+        nbRansacIterations = ransacResult.nbIterations;
+        inliers = ransacResult.inliers;
+        nbInliers = inliers.length;
+        const newSrcPoints = [];
+        const newDstPoints = [];
+        for (const inlier of inliers) {
+            newSrcPoints.push(sourcePoints[inlier]);
+            newDstPoints.push(destinationPoints[inlier]);
+        }
+        sourcePoints = newSrcPoints;
+        destinationPoints = newDstPoints;
+    }
+    // create debug image
+    if (debug) {
+        const montage = new Montage(source, destination, {
+            disposition: MontageDisposition.VERTICAL,
+        });
+        montage.drawMatches(matches, sourceBrief.keypoints, destinationBrief.keypoints, { showDistance: true });
+        const inlierMatches = [];
+        for (const inlier of inliers) {
+            inlierMatches.push(matches[inlier]);
+        }
+        montage.drawMatches(inlierMatches, sourceBrief.keypoints, destinationBrief.keypoints, { strokeColor: [0, 0, 255] });
+        const drawKeypointsBaseOptions = {
+            fill: true,
+            color: [0, 255, 0],
+            showScore: true,
+            markerSize: 3,
+        };
+        montage.drawKeypoints(sourceBrief.keypoints, drawKeypointsBaseOptions);
+        montage.drawKeypoints(destinationBrief.keypoints, {
+            origin: montage.destinationOrigin,
+            ...drawKeypointsBaseOptions,
+        });
+        writeSync(debugImagePath, montage.image);
+    }
+    // compute affine transform from destination to reference
+    const sourceMatrix = getMatrixFromPoints(sourcePoints);
+    const destinationMatrix = getMatrixFromPoints(destinationPoints);
+    const affineTransform = matrixGetAffineTransform(sourceMatrix, destinationMatrix);
+    return {
+        transform: {
+            rotation: affineTransform.rotation,
+            scale: affineTransform.scale,
+            translation: {
+                column: Math.round(affineTransform.translation.x),
+                row: Math.round(affineTransform.translation.y),
+            },
+        },
+        stats: {
+            nbMatches: matches.length,
+            nbInliers,
+            nbRansacIterations,
+            nbSourceKeypoints,
+            nbDestinationKeypoints,
+        },
+    };
+}
+//# sourceMappingURL=getAffineTransform.js.map

package/lib/align/affineTransfrom/getAffineTransform.js.map

@@ -0,0 +1 @@
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package/lib/align/affineTransfrom/getEuclideanDistance.d.ts

@@ -0,0 +1,9 @@
+import type { Point } from '../../geometry/index.js';
+/**
+ * Compute the distance between point 1 and point 2.
+ * @param point1 - First point.
+ * @param point2 - Second  point.
+ * @returns Euclidean distance.
+ */
+export declare function getEuclideanDistance(point1: Point, point2: Point): number;
+//# sourceMappingURL=getEuclideanDistance.d.ts.map

package/lib/align/affineTransfrom/getEuclideanDistance.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"getEuclideanDistance.d.ts","sourceRoot":"","sources":["../../../src/align/affineTransfrom/getEuclideanDistance.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,KAAK,EAAE,MAAM,yBAAyB,CAAC;AAErD;;;;;GAKG;AACH,wBAAgB,oBAAoB,CAAC,MAAM,EAAE,KAAK,EAAE,MAAM,EAAE,KAAK,GAAG,MAAM,CAEzE"}

package/lib/align/affineTransfrom/getEuclideanDistance.js

@@ -0,0 +1,10 @@
+/**
+ * Compute the distance between point 1 and point 2.
+ * @param point1 - First point.
+ * @param point2 - Second  point.
+ * @returns Euclidean distance.
+ */
+export function getEuclideanDistance(point1, point2) {
+    return Math.hypot(point1.row - point2.row, point1.column - point2.column);
+}
+//# sourceMappingURL=getEuclideanDistance.js.map