This question is similar to this one
Fastest method of screen capturing
but for linux/X11.
To be more specific, i need a method to capture the pixel
This is just a wild guess, but I presume you could use x11vnc with the -id [windowid] (http://www.karlrunge.com/x11vnc/x11vnc_opts.html#opt-id) option to stream that single window over VNC. This will show you the whole window, with the exact same positioning as in the main screen (you might lose some popup menus), even when it is covered. You can fetch the window coordinates from the true X11 screen.