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

Example 71 with Mat

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

the class OpenCVTools method watershedIntensitySplit.

/**
 * Apply a watershed transform to refine a binary image, guided either by a distance transform or a supplied intensity image.
 *
 * @param matBinary thresholded, 8-bit unsigned integer binary image
 * @param matWatershedIntensities optional intensity image for applying watershed transform; if not set, distance transform of binary will be used
 * @param threshold
 * @param maximaRadius
 */
public static void watershedIntensitySplit(Mat matBinary, Mat matWatershedIntensities, double threshold, int maximaRadius) {
    // Separate by intensity using the watershed transform
    // Find local maxima
    Mat matTemp = new Mat();
    Mat strel = getCircularStructuringElement(maximaRadius);
    opencv_imgproc.dilate(matWatershedIntensities, matTemp, strel);
    opencv_core.compare(matWatershedIntensities, matTemp, matTemp, opencv_core.CMP_EQ);
    opencv_imgproc.dilate(matTemp, matTemp, getCircularStructuringElement(2));
    Mat matWatershedSeedsBinary = matTemp;
    // Remove everything outside the thresholded region
    opencv_core.min(matWatershedSeedsBinary, matBinary, matWatershedSeedsBinary);
    // Create labels for watershed
    Mat matLabels = new Mat(matWatershedIntensities.size(), opencv_core.CV_32F, Scalar.ZERO);
    labelImage(matWatershedSeedsBinary, matLabels, opencv_imgproc.RETR_CCOMP);
    // Do watershed
    // 8-connectivity is essential for the watershed lines to be preserved - otherwise OpenCV's findContours could not be used
    ProcessingCV.doWatershed(matWatershedIntensities, matLabels, threshold, true);
    // Update the binary image to remove the watershed lines
    opencv_core.multiply(matBinary, matLabels, matBinary, 1, matBinary.type());
}

Example 72 with Mat

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

the class OpenCVTools method findRegionalMaxima.

/**
 * Get the regional maxima within a Mat, providing the output as a labeled image.
 * @param mat image containing maxima; must be 2D and single-channel
 * @return
 * @implNote the labels are not guaranteed to be consecutive; the behavior of this function may change in a future release.
 */
public static Mat findRegionalMaxima(Mat mat) {
    checkSingleChannel(mat);
    int connectivity = 8;
    // Apply 3x3 maximum filter & check equality
    var matMax = new Mat();
    var kernel = Mat.ones(3, 3, opencv_core.CV_32FC1).asMat();
    opencv_imgproc.dilate(mat, matMax, kernel);
    kernel.close();
    matMax.put(opencv_core.equals(mat, matMax));
    // Find connected components
    var matLabels = label(matMax, connectivity);
    // Calculate stats for labels
    int nLabels = (int) Math.ceil(maximum(matLabels));
    MaxLabelStat[] stats = updateMaxLabelStats(mat, matLabels, nLabels, connectivity);
    // If boundaries labels are >= inner labels, they can't correspond to regional max - so remove them
    var nonMaxima = Arrays.stream(stats).filter(s -> s.maxBoundary >= s.maxInside).map(s -> s.label).collect(Collectors.toSet());
    if (!nonMaxima.isEmpty()) {
        // TODO: Make this more efficient...
        for (var nonMax : nonMaxima) replaceValues(matLabels, nonMax, 0);
    }
    return matLabels;
}

Example 73 with Mat

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

the class OpenCVTools method addNoise.

/**
 * Add Gaussian noise with specified mean and standard deviation to all channels of a Mat.
 * This is similar to {@link opencv_core#randn(Mat, Mat, Mat)}, but supports any number of channels.
 * @param mat image to which noise should be added
 * @param mean noise mean
 * @param stdDev noise standard deviation
 */
public static void addNoise(Mat mat, double mean, double stdDev) {
    if (!Double.isFinite(mean) || !Double.isFinite(stdDev)) {
        throw new IllegalArgumentException("Noise mean and standard deviation must be finite (specified " + mean + " and " + stdDev + ")");
    }
    if (stdDev < 0) {
        throw new IllegalArgumentException("Noise standard deviation must be >= 0, but specified value is " + stdDev);
    }
    var matMean = new Mat(1, 1, opencv_core.CV_32FC1, Scalar.all(mean));
    var matStdDev = new Mat(1, 1, opencv_core.CV_32FC1, Scalar.all(stdDev));
    int nChannels = mat.channels();
    if (nChannels == 1)
        opencv_core.randn(mat, matMean, matStdDev);
    else
        OpenCVTools.applyToChannels(mat, m -> opencv_core.randn(m, matMean, matStdDev));
    matMean.close();
    matStdDev.close();
}

Example 74 with Mat

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

the class OpenCVTools method scalarMatWithType.

/**
 * Create a 1x1 Mat with a specific value, with 1 or more channels.
 * If necessary, clipping or rounding is applied.
 *
 * @param value the value to include in the Mat
 * @param type type of the image; this may contain additional channels if required.
 * @return a Mat with one pixel containing the closest value supported by the type
 */
public static Mat scalarMatWithType(double value, int type) {
    if (opencv_core.CV_MAT_CN(type) <= 4)
        return new Mat(1, 1, type, Scalar.all(value));
    var mat = new Mat(1, 1, type);
    fill(mat, value);
    return mat;
}

Example 75 with Mat

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

the class OpenCVTools method extractPixels.

/**
 * Extract pixels as a double array.
 * @param mat
 * @param pixels
 * @return
 */
public static double[] extractPixels(Mat mat, double[] pixels) {
    if (pixels == null)
        pixels = new double[(int) totalPixels(mat)];
    Mat mat2 = null;
    if (mat.depth() != opencv_core.CV_64F) {
        mat2 = new Mat();
        mat.convertTo(mat2, opencv_core.CV_64F);
        ensureContinuous(mat2, true);
    } else
        mat2 = ensureContinuous(mat, false);
    DoubleIndexer idx = mat2.createIndexer();
    idx.get(0L, pixels);
    idx.release();
    if (mat2 != mat)
        mat2.close();
    // assert mat.total() == pixels.length;
    return pixels;
}