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

Example 66 with Mat

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

the class OpenCVTools method mergeChannels.

/**
 * Merge channels from a multichannel {@link Mat}.
 * May be more convenient than OpenCV's built-in approach.
 *
 * @param channels separate channels
 * @param dest optional destination (may be null)
 * @return merged {@link Mat}, which will be the same as dest if provided
 * @throws IllegalArgumentException if the number of channels in the output would be greater than {@link opencv_core#CV_CN_MAX}
 */
@SuppressWarnings("unchecked")
public static Mat mergeChannels(Collection<? extends Mat> channels, Mat dest) throws IllegalArgumentException {
    if (dest == null)
        dest = new Mat();
    boolean firstMat = true;
    boolean allSingleChannel = true;
    int rows = -1;
    int cols = -1;
    int depth = 0;
    int nChannels = 0;
    for (var m : channels) {
        if (firstMat) {
            rows = m.rows();
            cols = m.cols();
            depth = m.depth();
            if (rows < 0 || cols < 0)
                throw new IllegalArgumentException("Rows and columns must be >= 0");
            firstMat = false;
        }
        int nc = m.channels();
        allSingleChannel = allSingleChannel && nc == 1;
        nChannels += nc;
        if (depth != m.depth() || rows != m.rows() || cols != m.cols())
            throw new IllegalArgumentException("mergeChannels() requires all Mats to have the same dimensions and depth!");
    }
    // We can only use OpenCV's merge if all Mats are single-channel
    boolean mixChannels = !allSingleChannel;
    if (nChannels > opencv_core.CV_CN_MAX)
        throw new IllegalArgumentException("Can't merge more than " + opencv_core.CV_CN_MAX + " channels (you requested " + nChannels + ")");
    try (var scope = new PointerScope()) {
        if (mixChannels) {
            dest.create(rows, cols, opencv_core.CV_MAKETYPE(depth, nChannels));
            var vecSource = new MatVector(channels.toArray(Mat[]::new));
            var vecDest = new MatVector(dest);
            int[] inds = new int[nChannels * 2];
            for (int i = 0; i < nChannels; i++) {
                inds[i * 2] = i;
                inds[i * 2 + 1] = i;
            }
            opencv_core.mixChannels(vecSource, vecDest, new IntPointer(inds));
        } else {
            opencv_core.merge(new MatVector(channels.toArray(Mat[]::new)), dest);
        }
    // scope.deallocate();
    }
    return dest;
}

Example 67 with Mat

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

the class OpenCVTools method extractPixels.

/**
 * Extract pixels as a float[] array.
 * <p>
 * <p>
 * In QuPath v0.2 this would return only the pixels in the first channel.
 * In v0.3+ it should return all pixels.
 *
 * @param mat
 * @param pixels
 * @return
 * @implNote in its current form, this is not very efficient.
 */
public static float[] extractPixels(Mat mat, float[] pixels) {
    if (pixels == null)
        pixels = new float[(int) totalPixels(mat)];
    Mat mat2 = null;
    if (mat.depth() != opencv_core.CV_32F) {
        mat2 = new Mat();
        mat.convertTo(mat2, opencv_core.CV_32F);
        ensureContinuous(mat2, true);
    } else
        mat2 = ensureContinuous(mat, false);
    FloatIndexer idx = mat2.createIndexer();
    idx.get(0L, pixels);
    idx.release();
    // buffer.get(pixels);
    if (mat2 != mat)
        mat2.close();
    return pixels;
}

Example 68 with Mat

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

the class OpenCVTools method fillSmallHoles.

/**
 * Fill holes in a binary image (1-channel, 8-bit unsigned) with an area <= maxArea.
 *
 * @param matBinary
 * @param maxArea
 */
public static void fillSmallHoles(Mat matBinary, double maxArea) {
    Mat matHoles = new Mat();
    invertBinary(matBinary, matHoles);
    MatVector contours = new MatVector();
    Mat hierarchy = new Mat();
    opencv_imgproc.findContours(matHoles, contours, hierarchy, opencv_imgproc.RETR_CCOMP, opencv_imgproc.CHAIN_APPROX_SIMPLE);
    Scalar color = Scalar.WHITE;
    int ind = 0;
    Point offset = new Point(0, 0);
    Indexer indexerHierarchy = hierarchy.createIndexer();
    for (int c = 0; c < contours.size(); c++) {
        Mat contour = contours.get(c);
        // TODO: Check hierarchy indexing after switch to JavaCPP!!
        if (indexerHierarchy.getDouble(0, ind, 3) >= 0 || opencv_imgproc.contourArea(contour) > maxArea) {
            ind++;
            continue;
        }
        opencv_imgproc.drawContours(matBinary, contours, c, color, -1, opencv_imgproc.LINE_8, null, Integer.MAX_VALUE, offset);
        ind++;
    }
}

Example 69 with Mat

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

the class OpenCVTools method extractZStack.

/**
 * Extract a list of Mats, where each Mat corresponds to a z-slice.
 *
 * @param server
 * @param request
 * @param zMin first z slice, inclusive
 * @param zMax last z slice, exclusive
 * @return
 * @throws IOException
 */
public static List<Mat> extractZStack(ImageServer<BufferedImage> server, RegionRequest request, int zMin, int zMax) throws IOException {
    List<Mat> list = new ArrayList<>();
    for (int z = zMin; z < zMax; z++) {
        RegionRequest request2 = RegionRequest.createInstance(server.getPath(), request.getDownsample(), request.getX(), request.getY(), request.getWidth(), request.getHeight(), z, request.getT());
        BufferedImage img = server.readBufferedImage(request2);
        list.add(imageToMat(img));
    }
    return list;
}

Example 70 with Mat

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

the class OpenCVTools method stdDev.

/**
 * Get the standard deviation of an image, across all pixels (regardless of channels), ignoring NaNs.
 * @param mat
 * @return the standard deviation of all pixels in the image
 */
public static double stdDev(Mat mat) {
    Mat temp;
    if (mat.channels() == 1)
        temp = mat;
    else
        temp = mat.reshape(1, mat.rows() * mat.cols());
    var output = channelStdDev(temp);
    assert output.length == 1;
    return output[0];
}