Public bug reported:

To reproduce, open a terminal window (not maximised) and run:

xdotool getactivewindow getwindowgeometry

The output of this includes the window's size.

Screen-grab the window and open in an editor such as Gimp.

Whilst the window is identical in size (when viewed at 1:1 zoom), the
dimensions of the grabbed version is actually larger by (as far as I can
tell) the window decoration such as the title bar, in my case 28px.

An alternative approach that doesn't require screen-grabbing is to drag
the terminal to the top of the screen and then manually extend it to the
full height of the screen.  My screen is 1920x1080 and the height of the
full-height window is reported by xdotool as 1052 which is exactly 1080
minus the height of the window's title bar.

I am using Linux Mint 18.1 Serena and the installed and candidate
versions of xdotool are both 1:3.20150503.1-2.

** Affects: xdotool (Ubuntu)
     Importance: Undecided
         Status: New

** Description changed:

  To reproduce, open a terminal window (not maximised) and run:
  
  xdotool getactivewindow getwindowgeometry
  
  The output of this includes the window's size.
  
  Screen-grab the window and open in an editor such as Gimp.
  
  Whilst the window is identical in size (when viewed at 1:1 zoom), the
  dimensions of the grabbed version is actually larger by (as far as I can
  tell) the window decoration such as the title bar, in my case 28px.
  
  An alternative approach that doesn't require screen-grabbing is to drag
  the terminal to the top of the screen and then manually extend it to the
  full height of the screen.  My screen is 1920x1080 and the height of the
- full-height window is reported by xdotool as 1052 which is exactly the
- height of the window's title bar.
+ full-height window is reported by xdotool as 1052 which is exactly 1080
+ minus the height of the window's title bar.
  
  I am using Linux Mint 18.1 Serena and the installed and candidate
  versions of xdotool are both 1:3.20150503.1-2.

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https://bugs.launchpad.net/bugs/1674373

Title:
  xdotool reports incorrect window dimensions

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