currentShotArray = new ByteArrayOutputStream();
ImageIO.write(currentShot, "bmp", currentShotArray);

public class ScreenAnalyzer implements Runnable{

NativeCls compare = new NativeCls();
BufferedImage currentShot = null;//Текушее изображения региона
ByteArrayOutputStream currentShotArray=null;
BufferedImage previousShot = null;//Предыдущее изображение региона
ByteArrayOutputStream previousShotArray=null;
Thread checkTh=null;
Rectangle screen =new Rectangle(Toolkit.getDefaultToolkit().getScreenSize());
Robot robot=null;
boolean start = false;

public ScreenAnalyzer() {
	try {
	robot= new Robot();
	previousShot=robot.createScreenCapture(screen);
	previousShotArray= new ByteArrayOutputStream();
	ImageIO.write(previousShot, "bmp", previousShotArray);
	} catch (Exception e) {
	e.printStackTrace();
	}		
}

public void start()
{
	checkTh= new Thread(this);
	checkTh.setPriority(Thread.MAX_PRIORITY);
	start=true;
	checkTh.start();
}

public void run() {
	while(start)
	{
		try
		{
			long start = System.currentTimeMillis();

			currentShot =robot.createScreenCapture(screen);
            
			//Медленно(~500мс)
			currentShotArray = new ByteArrayOutputStream();
			ImageIO.write(currentShot, "bmp", currentShotArray);
                       //Медленно(~500мс)
			
			//Вызов native функции(~30мс)
			List<Rect> rects =compare.sendArray(currentShotArray.toByteArray(), previousShotArray.toByteArray(), (int)screen.getWidth(), (int)screen.getHeight());

			for (Rect rect : rects) {
				Rect rrr= rect;
			}

			if (rects.size() > 0)
			{
				previousShot = currentShot;
				previousShotArray.close();
				
				//Медленно(~500мс)
				previousShotArray= new ByteArrayOutputStream();
				ImageIO.write(previousShot, "bmp", previousShotArray);
				//Медленно(~500мс)
			}

			currentShotArray.close();

			long end = System.currentTimeMillis();

			System.out.print(end-start+"\r\n");
		}
		catch (Exception e) {
		
		}
	}
}

}

currentShotArray = ((DataBufferInt) currentShot.getRaster().getDataBuffer()).getData();