ImageJ was never meant as anything else than a desktop application with one user in front of one screen attached to one computer.
To address all of these needs, ImageJ2 provides the capability to execute ImageJ plugins, macros and scripts in headless mode. This feature uses bytecode manipulation to patch ImageJ’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 is. Naturally, these plugins will still try to instantiate GUI elements when being called in headless mode, failing.
Running scripts in headless mode
Please see the headless scripting guide.
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.
You can even pass parameters to the macro; e.g.:
./ImageJ-win64.exe --headless --console -macro ./RunBatch.ijm 'folder=../folder1 parameters=a.properties output=../samples/Output'
In that case, the RunBatch.ijm file should be something like:
arg = getArgument() print("Running batch analysis with arguments:") print(arg) run("Batch process", arg ) print("Done.") eval("script", "System.exit(0);");
getArgument() is used to grab the parameter string itself, and it is then passed to an IJ command.
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 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 macOS, 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.
Xvfb virtual desktop
Another method is to have a virtual desktop, e.g. Xvfb. This will allow ImageJ 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.
Here are a couple of simple examples.
Passing direct arguments:
$ cat hello.js importClass(Packages.ij.IJ); IJ.log("hello " + arguments); $ xvfb-run -a $IMAGEJ_DIR/ImageJ-linux64 hello.js Emerson hello Emerson
$ cat hello-with-params.js // @String name importClass(Packages.ij.IJ); IJ.log("hello " + name); $ xvfb-run -a $IMAGEJ_DIR/ImageJ-linux64 --ij2 --headless --run hello-with-params.js 'name="Emerson"' hello Emerson
A more complex 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" $imagejBin -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 )
See also this post on the ImageJ mailing list.
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.