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If you now eye rectangle you can take submat of original image and save it to file. Your code will be something like this:

Rect[] facesArray = faces.toArray();
for (int i = 0; i < facesArray.length; i++) {
    Highgui.imwrite("/sdcard/image_" + Integer.toString(i) + ".jpg", mRgba.submat(facesArray[i]));
}