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The fastest way to iterate over all pixels should be reading directly from the data-member of cv::Mat. There is a nice tutorial about scanning an image here: http://docs.opencv.org/doc/tutorials/core/how_to_scan_images/how_to_scan_images.html (In java it looks a bit different, bit it should work similar: http://stackoverflow.com/questions/9920449/converting-opencv-matrix-looping-to-javacv )
