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This is probably a little late, but may be others can benefit from this answer:

Ok, in the line

//im = new BufferedImage(im.getWidth(), im.getHeight(),BufferedImage.TYPE_3BYTE_BGR);

just an empty instance of BufferedImage is created, resulting output of a black image.

The cause of the problems is that depending on the case either a DataBufferedByte or DataBufferInt is created. A look in class Robot's method createScreenCapture() reveals the encoding. A case distinction is needed here, converting a DataBufferInt if necessary. I have added a (very crude) conversion routine to your method above:

public Mat matify(BufferedImage sourceImg) {

    long millis = System.currentTimeMillis();

    DataBuffer dataBuffer = sourceImg.getRaster().getDataBuffer();
    byte[] imgPixels = null;
    Mat imgMat = null;

    int width = sourceImg.getWidth();
    int height = sourceImg.getHeight();

    if(dataBuffer instanceof DataBufferByte) {      
            imgPixels = ((DataBufferByte)dataBuffer).getData();
    }

    if(dataBuffer instanceof DataBufferInt) {

        int byteSize = width * height;      
        imgPixels = new byte[byteSize*3];

        int[] imgIntegerPixels = ((DataBufferInt)dataBuffer).getData();

        for(int p = 0; p < byteSize; p++) {         
            imgPixels[p*3 + 0] = (byte) ((imgIntegerPixels[p] & 0x00FF0000) >> 16);
            imgPixels[p*3 + 1] = (byte) ((imgIntegerPixels[p] & 0x0000FF00) >> 8);
            imgPixels[p*3 + 2] = (byte) (imgIntegerPixels[p] & 0x000000FF);
        }
    }

    if(imgPixels != null) {
        imgMat = new Mat(height, width, CvType.CV_8UC3);
        imgMat.put(0, 0, imgPixels);
    }

    System.out.println("matify exec millis: " + (System.currentTimeMillis() - millis));

    return imgMat;
}

The runtime measurement can be omitted obviously.

Greetings