Examples with Size org.bytedeco.opencv.opencv_core.Size used on opensource projects

Example 11 with Size

use of org.bytedeco.opencv.opencv_core.Size in project qupath by qupath.

the class WandToolCV method createShape.

@Override
protected Geometry createShape(MouseEvent e, double x, double y, boolean useTiles, Geometry addToShape) {
    GeometryFactory factory = getGeometryFactory();
    if (addToShape != null && pLast != null && pLast.distanceSq(x, y) < 2)
        return null;
    long startTime = System.currentTimeMillis();
    QuPathViewer viewer = getViewer();
    if (viewer == null)
        return null;
    double downsample = Math.max(1, Math.round(viewer.getDownsampleFactor() * 4)) / 4.0;
    var regionStore = viewer.getImageRegionStore();
    // Paint the image as it is currently being viewed
    var type = wandType.get();
    boolean doGray = type == WandType.GRAY;
    BufferedImage imgTemp = doGray ? imgGray : imgBGR;
    int nChannels = doGray ? 1 : 3;
    Graphics2D g2d = imgTemp.createGraphics();
    g2d.setColor(Color.BLACK);
    g2d.setClip(0, 0, w, w);
    g2d.fillRect(0, 0, w, w);
    double xStart = Math.round(x - w * downsample * 0.5);
    double yStart = Math.round(y - w * downsample * 0.5);
    bounds.setFrame(xStart, yStart, w * downsample, w * downsample);
    g2d.scale(1.0 / downsample, 1.0 / downsample);
    g2d.translate(-xStart, -yStart);
    regionStore.paintRegion(viewer.getServer(), g2d, bounds, viewer.getZPosition(), viewer.getTPosition(), downsample, null, null, viewer.getImageDisplay());
    // regionStore.paintRegionCompletely(viewer.getServer(), g2d, bounds, viewer.getZPosition(), viewer.getTPosition(), viewer.getDownsampleFactor(), null, viewer.getImageDisplay(), 250);
    // Optionally include the overlay information when using the wand
    float opacity = viewer.getOverlayOptions().getOpacity();
    if (opacity > 0 && getWandUseOverlays()) {
        ImageRegion region = ImageRegion.createInstance((int) bounds.getX() - 1, (int) bounds.getY() - 1, (int) bounds.getWidth() + 2, (int) bounds.getHeight() + 2, viewer.getZPosition(), viewer.getTPosition());
        if (opacity < 1)
            g2d.setComposite(AlphaComposite.getInstance(AlphaComposite.SRC_OVER, opacity));
        for (PathOverlay overlay : viewer.getOverlayLayers().toArray(PathOverlay[]::new)) {
            if (!(overlay instanceof HierarchyOverlay))
                overlay.paintOverlay(g2d, region, downsample, viewer.getImageData(), true);
        }
    }
    // Ensure we have Mats & the correct channel number
    if (mat != null && (mat.channels() != nChannels || mat.depth() != opencv_core.CV_8U)) {
        mat.close();
        mat = null;
    }
    if (mat == null || mat.isNull() || mat.empty())
        mat = new Mat(w, w, CV_8UC(nChannels));
    // if (matMask == null)
    // matMask = new Mat(w+2, w+2, CV_8U);
    // if (matSelected == null)
    // matSelected = new Mat(w+2, w+2, CV_8U);
    // Put pixels into an OpenCV image
    byte[] buffer = ((DataBufferByte) imgTemp.getRaster().getDataBuffer()).getData();
    ByteBuffer matBuffer = mat.createBuffer();
    matBuffer.put(buffer);
    // mat.put(0, 0, buffer);
    // opencv_imgproc.cvtColor(mat, mat, opencv_imgproc.COLOR_BGR2Lab);
    // blurSigma = 4;
    boolean doSimpleSelection = e.isShortcutDown() && !e.isShiftDown();
    if (doSimpleSelection) {
        matMask.put(Scalar.ZERO);
        // opencv_imgproc.circle(matMask, seed, radius, Scalar.ONE);
        opencv_imgproc.floodFill(mat, matMask, seed, Scalar.ONE, null, Scalar.ZERO, Scalar.ZERO, 4 | (2 << 8) | opencv_imgproc.FLOODFILL_MASK_ONLY | opencv_imgproc.FLOODFILL_FIXED_RANGE);
        subtractPut(matMask, Scalar.ONE);
    } else {
        double blurSigma = Math.max(0.5, getWandSigmaPixels());
        int size = (int) Math.ceil(blurSigma * 2) * 2 + 1;
        blurSize.width(size);
        blurSize.height(size);
        // Smooth a little
        opencv_imgproc.GaussianBlur(mat, mat, blurSize, blurSigma);
        // Choose mat to threshold (may be adjusted)
        Mat matThreshold = mat;
        // Apply color transform if required
        if (type == WandType.LAB_DISTANCE) {
            mat.convertTo(matFloat, opencv_core.CV_32F, 1.0 / 255.0, 0.0);
            opencv_imgproc.cvtColor(matFloat, matFloat, opencv_imgproc.COLOR_BGR2Lab);
            double max = 0;
            double mean = 0;
            try (FloatIndexer idx = matFloat.createIndexer()) {
                int k = w / 2;
                double v1 = idx.get(k, k, 0);
                double v2 = idx.get(k, k, 1);
                double v3 = idx.get(k, k, 2);
                double meanScale = 1.0 / (w * w);
                for (int row = 0; row < w; row++) {
                    for (int col = 0; col < w; col++) {
                        double L = idx.get(row, col, 0) - v1;
                        double A = idx.get(row, col, 1) - v2;
                        double B = idx.get(row, col, 2) - v3;
                        double dist = Math.sqrt(L * L + A * A + B * B);
                        if (dist > max)
                            max = dist;
                        mean += dist * meanScale;
                        idx.put(row, col, 0, (float) dist);
                    }
                }
            }
            if (matThreshold == null)
                matThreshold = new Mat();
            opencv_core.extractChannel(matFloat, matThreshold, 0);
            // There are various ways we might choose a threshold now...
            // Here, we use a multiple of the mean. Since values are 'distances'
            // they are all >= 0
            matThreshold.convertTo(matThreshold, opencv_core.CV_8U, 255.0 / max, 0);
            threshold.put(mean * getWandSensitivity());
            // //			OpenCVTools.matToImagePlus(matThreshold, "Before").show();
            // // Apply local Otsu threshold
            // opencv_imgproc.threshold(matThreshold, matThreshold,
            // 0,
            // 255, opencv_imgproc.THRESH_BINARY + opencv_imgproc.THRESH_OTSU);
            // threshold.put(Scalar.ZERO);
            nChannels = 1;
        } else {
            // Base threshold on local standard deviation
            meanStdDev(matThreshold, mean, stddev);
            DoubleBuffer stddevBuffer = stddev.createBuffer();
            double[] stddev2 = new double[nChannels];
            stddevBuffer.get(stddev2);
            double scale = 1.0 / getWandSensitivity();
            if (scale < 0)
                scale = 0.01;
            for (int i = 0; i < stddev2.length; i++) stddev2[i] = stddev2[i] * scale;
            threshold.put(stddev2);
        }
        // Limit maximum radius by pen
        int radius = (int) Math.round(w / 2 * QuPathPenManager.getPenManager().getPressure());
        if (radius == 0)
            return null;
        matMask.put(Scalar.ZERO);
        opencv_imgproc.circle(matMask, seed, radius, Scalar.ONE);
        opencv_imgproc.floodFill(matThreshold, matMask, seed, Scalar.ONE, null, threshold, threshold, 4 | (2 << 8) | opencv_imgproc.FLOODFILL_MASK_ONLY | opencv_imgproc.FLOODFILL_FIXED_RANGE);
        subtractPut(matMask, Scalar.ONE);
        if (strel == null)
            strel = opencv_imgproc.getStructuringElement(opencv_imgproc.MORPH_ELLIPSE, new Size(5, 5));
        opencv_imgproc.morphologyEx(matMask, matMask, opencv_imgproc.MORPH_CLOSE, strel);
    }
    MatVector contours = new MatVector();
    if (contourHierarchy == null)
        contourHierarchy = new Mat();
    opencv_imgproc.findContours(matMask, contours, contourHierarchy, opencv_imgproc.RETR_EXTERNAL, opencv_imgproc.CHAIN_APPROX_SIMPLE);
    // logger.trace("Contours: " + contours.size());
    List<Coordinate> coords = new ArrayList<>();
    List<Geometry> geometries = new ArrayList<>();
    for (Mat contour : contours.get()) {
        // Discard single pixels / lines
        if (contour.size().height() <= 2)
            continue;
        // Create a polygon geometry
        try (IntIndexer idxrContours = contour.createIndexer()) {
            for (long r = 0; r < idxrContours.size(0); r++) {
                int px = idxrContours.get(r, 0L, 0L);
                int py = idxrContours.get(r, 0L, 1L);
                // * downsample + x;
                double xx = (px - w / 2 - 1);
                // * downsample + y;
                double yy = (py - w / 2 - 1);
                coords.add(new Coordinate(xx, yy));
            }
        }
        if (coords.size() > 1) {
            // Ensure closed
            if (!coords.get(coords.size() - 1).equals(coords.get(0)))
                coords.add(coords.get(0));
            // Exclude single pixels
            var polygon = factory.createPolygon(coords.toArray(Coordinate[]::new));
            if (coords.size() > 5 || polygon.getArea() > 1)
                geometries.add(polygon);
        }
    }
    contours.close();
    if (geometries.isEmpty())
        return null;
    // Handle the fact that OpenCV contours are defined using the 'pixel center' by dilating the boundary
    var geometry = geometries.size() == 1 ? geometries.get(0) : GeometryCombiner.combine(geometries);
    geometry = geometry.buffer(0.5);
    // Transform to map to integer pixel locations in the full-resolution image
    var transform = new AffineTransformation().scale(downsample, downsample).translate(x, y);
    geometry = transform.transform(geometry);
    geometry = GeometryTools.roundCoordinates(geometry);
    geometry = GeometryTools.constrainToBounds(geometry, 0, 0, viewer.getServerWidth(), viewer.getServerHeight());
    if (geometry.getArea() <= 1)
        return null;
    long endTime = System.currentTimeMillis();
    logger.trace(getClass().getSimpleName() + " time: " + (endTime - startTime));
    if (pLast == null)
        pLast = new Point2D.Double(x, y);
    else
        pLast.setLocation(x, y);
    return geometry;
}

Example 12 with Size

use of org.bytedeco.opencv.opencv_core.Size in project qupath by qupath.

the class DefaultBlobFunction method toBlob.

@Override
public Mat toBlob(Mat... mats) {
    // Preprocess the images
    var preprocessed = new Mat[mats.length];
    int ind = 0;
    for (var mat : mats) {
        var temp = mat.clone();
        if (preprocessing != null) {
            temp = preprocessing.apply(temp);
        }
        if (inputSize != null) {
            if (crop) {
                int w = inputSize.width();
                int h = inputSize.height();
                double factor = Math.max(w / (double) temp.cols(), h / (double) temp.rows());
                opencv_imgproc.resize(temp, temp, new Size(), factor, factor, opencv_imgproc.INTER_LINEAR);
                int x = (temp.cols() - w) / 2;
                int y = (temp.rows() - h) / 2;
                temp.put(OpenCVTools.crop(temp, x, y, w, h));
            } else {
                opencv_imgproc.resize(temp, temp, inputSize, 0, 0, opencv_imgproc.INTER_LINEAR);
            }
        }
        preprocessed[ind] = temp;
        ind++;
    }
    // Convert images to blob
    return DnnTools.blobFromImages(preprocessed);
}

Example 13 with Size

use of org.bytedeco.opencv.opencv_core.Size in project javacv by bytedeco.

the class Similarity method getMSSIM.

private static Scalar getMSSIM(Mat i1, Mat i2) {
    double C1 = 6.5025, C2 = 58.5225;
    /**
     *************************** INITS *********************************
     */
    int d = opencv_core.CV_32F;
    Mat I1 = new Mat();
    Mat I2 = new Mat();
    // cannot calculate on one byte large values
    i1.convertTo(I1, d);
    i2.convertTo(I2, d);
    // I2^2
    Mat I2_2 = I2.mul(I2).asMat();
    // I1^2
    Mat I1_2 = I1.mul(I1).asMat();
    // I1 * I2
    Mat I1_I2 = I1.mul(I2).asMat();
    /**
     ************************* END INITS *********************************
     */
    // PRELIMINARY COMPUTING
    Mat mu1 = new Mat();
    Mat mu2 = new Mat();
    opencv_imgproc.GaussianBlur(I1, mu1, new Size(11, 11), 1.5);
    opencv_imgproc.GaussianBlur(I2, mu2, new Size(11, 11), 1.5);
    Mat mu1_2 = mu1.mul(mu1).asMat();
    Mat mu2_2 = mu2.mul(mu2).asMat();
    Mat mu1_mu2 = mu1.mul(mu2).asMat();
    Mat sigma1_2 = new Mat();
    Mat sigma2_2 = new Mat();
    Mat sigma12 = new Mat();
    opencv_imgproc.GaussianBlur(I1_2, sigma1_2, new Size(11, 11), 1.5);
    sigma1_2 = opencv_core.subtract(sigma1_2, mu1_2).asMat();
    opencv_imgproc.GaussianBlur(I2_2, sigma2_2, new Size(11, 11), 1.5);
    sigma2_2 = opencv_core.subtract(sigma2_2, mu2_2).asMat();
    opencv_imgproc.GaussianBlur(I1_I2, sigma12, new Size(11, 11), 1.5);
    sigma12 = opencv_core.subtract(sigma12, mu1_mu2).asMat();
    Mat t1, t2, t3;
    t1 = opencv_core.add(opencv_core.multiply(2, mu1_mu2), Scalar.all(C1)).asMat();
    t2 = opencv_core.add(opencv_core.multiply(2, sigma12), Scalar.all(C2)).asMat();
    // t3 = ((2*mu1_mu2 + C1).*(2*sigma12 + C2))
    t3 = t1.mul(t2).asMat();
    t1 = opencv_core.add(opencv_core.add(mu1_2, mu2_2), Scalar.all(C1)).asMat();
    t2 = opencv_core.add(opencv_core.add(sigma1_2, sigma2_2), Scalar.all(C2)).asMat();
    // t1 =((mu1_2 + mu2_2 + C1).*(sigma1_2 + sigma2_2 + C2))
    t1 = t1.mul(t2).asMat();
    Mat ssim_map = new Mat();
    // ssim_map =  t3./t1;
    opencv_core.divide(t3, t1, ssim_map);
    // mssim = average of ssim map
    Scalar mssim = opencv_core.mean(ssim_map);
    return mssim;
}

Example 14 with Size

use of org.bytedeco.opencv.opencv_core.Size in project karate by karatelabs.

the class OpenCvUtils method rescale.

public static Mat rescale(Mat mat, double scale) {
    Mat resized = new Mat();
    resize(mat, resized, new Size(), scale, scale, CV_INTER_AREA);
    return resized;
}

Example 15 with Size

use of org.bytedeco.opencv.opencv_core.Size in project blog_demos by zq2599.

the class TrainFromDirectory method read.

/**
 * 读取指定图片的灰度图，调整为指定大小
 * @param path
 * @return
 */
private static Mat read(String path) {
    Mat faceMat = opencv_imgcodecs.imread(path, IMREAD_GRAYSCALE);
    resize(faceMat, faceMat, new Size(Constants.RESIZE_WIDTH, Constants.RESIZE_HEIGHT));
    return faceMat;
}