HeadlessQR for this page
ImageJ 1.x was never meant as anything else than a desktop application with one user in front of one screen attached to one computer.
Java does support a headless mode via the
java.awt.headless property; setting this property to
true enables it.
Unfortunately, with X11-based Java (such as on Linux, which is the most prevalent platform for running clusters), headless mode does not allow to instantiate any GUI components that would want to display text. The reason is that the font-metrics on X11 are provided by the X11 server (and are indeed different between servers) and therefore the dimensions of such elements simply cannot be calculated without a graphical desktop.
Since ImageJ 1.x was devised as a desktop application, everything -- including macros -- works through the GUI. For example, a simple
run("Open..."); will look for the action in the menu.
On MacOSX, there is no problem: Aqua provides GUI-independent text rendering (mapping to the actual display using anti-aliasing). There, running in headless mode allows instantiating GUI elements such as the menu bar.
Fiji provides the capability to execute ImageJ plugins, macros and scripts in headless mode. This feature uses bytecode manipulation to patch ImageJ 1.x's behavior at runtime, making it possible to start ImageJ in batch mode without instantiating GUI components.
Shortcoming: There are plugins which are even more bound to a GUI than ImageJ 1.x is. Naturally, these plugins will still try to instantiate GUI elements when being called in headless mode, failing.
Running macros in headless mode
To run a macro in headless mode, use the
-macro command line argument along with the
--headless option, as follows:
ImageJ --headless -macro path-to-Macro.ijm
If the macro resides in ImageJ's macro directory, it is possible to specify the macro name instead of the actual file path. The file extension is always very recommended but for backwards compatibility, it is not strictly required only when specifying the macro name instead of a path.
Running scripts in headless mode
To run a script (JRuby, Jython, etc.) simply skip the
-batch argument and pass the path to the script only.
ImageJ --headless path-to-script
Another method is to have a virtual desktop, e.g. Xvfb. This will allow Fiji to start with a virtualised graphical desktop.
Advantage: No run-time patching is required.
Shortcomings: It is slower than it needs to be because of the overhead of starting the GUI, it is harder to configure, and plugins might get stuck because they wait for user input which never comes.
Example: Here is an example shell script that wraps a macro for use with Xvfb (thanks to Nestor Milyaev!):
export DISPLAY=:1 Xvfb $DISPLAY -auth /dev/null & ( # the '(' starts a new sub shell. In this sub shell we start the worker processes: script=$scriptDir"lsmrotate2nrrd.ijm \"dir="$1"&angle-x=$2&angle-y= $3&angle-z=$4&reverse=$5\" -batch" $fijiBin -macro $script # running the actual ijm script wait # waits until all 'program' processes are finished # this wait sees only the 'program' processes, not the Xvfb process )
Rewriting as scripts or plugins
The most robust method is to rewrite macros as scripts that do not require interaction with the GUI to begin with. Unfortunately, this is the most involved solution, too, since it usually takes some time to convert macros.