README.md

Welcome to the ImageJ patcher

What is it?

The ij1-patcher injects extension points into ImageJ -- i.e., code that allows code outside of ImageJ to override some functions in ways that ImageJ's design does not normally support. For example, it becomes possible to open a sophisticated, syntax-highlighting editor instead of ImageJ's default text editor.

The patches optionally include (limited) support for so-called "headless" mode: running ImageJ without a graphical user environment. See below for details.

It also offers a convenient way to encapsulate multiple ImageJ "instances" from each other (ImageJ relies heavily on static settings; IJ.getInstance() is supposed to return the only ImageJ instance): a LegacyEnvironment contains a completely insulated class loader that does not interfere with ImageJ instances living in other class loaders. Example:

	// The first parameter is a class loader, asking for a new,
	// special-purpose class loader to be created; the second parameter
	// asks for headless mode.
	LegacyEnvironment ij1 = new LegacyEnvironment(null, true);
	ij1.runMacro("print('Hello, world!');");

How can I use it?

Add the following section to your pom.xml file (if you do not use Maven yet, you should):

	<dependencies>
		...
		<dependency>
			<groupId>net.imagej</groupId>
			<artifactId>ij1-patcher</artifactId>
			<version>0.1.0</version>
		</dependency>
	</dependencies>

Then, create a LegacyEnvironment:

	// The first parameter is a class loader, asking for a new,
	// special-purpose class loader to be created; the second parameter
	// asks for headless mode.
	LegacyEnvironment ij1 = new LegacyEnvironment(null, true);
	ij1.runMacro("open('" + path + "');");
	[... process the image ...]
	ij1.runMacro("saveAs('jpeg', '" + outputPath + "');");

Note: it is not currently possible to inject an ImagePlus instance into the legacy environment directly: There will be two different definitions of the ImagePlus class involved -- the one from the calling class loader and the one in the encapsulated class loader. It is impossible to assign an instance of one to a variable of the other.

How does it work?

The runtime patches are applied through Javassist, a library offering tools to manipulate Java bytecode. This is needed to get the changes into ImageJ code. The runtime patches live in LegacyInjector, LegacyExtensions and LegacyHeadless (the latter being applied only when the headless hacks are asked for).

To offer an encapsulated ImageJ instance, a new special-purpose class loader (to be precise, a LegacyClassLoader) is created that contains only the patched ImageJ classes, plus a select few classes required for callbacks. In addition, it will share the very special LegacyHooks class with the calling class loader (i.e. this class will not be defined in the legacy class loader, but its class definition as per the calling class loader will be reused).

The patched ImageJ classes interact with the "outside" world via the LegacyHooks class, an abstract base class which gets called by the patched ImageJ classes at appropriate times, e.g. when an exception needs to be displayed.

By default, the patched ImageJ will instantiate the EssentialLegacyHooks specialization of the LegacyHooks and install these hooks into the _hooks field that gets patched into the ij.IJ class. That way, there is always an instance, and the patched code does not check for null first. The EssentialLegacyHooks will also look for an initializer class -- to be loaded in ImageJ PluginClassLoader -- and if one is found, instantiate and run it as a Runnable. By default, the initializer class is net.imagej.legacy.plugin.LegacyInitializer -- to support ImageJ2 -- but it can be overridden by setting the system property ij1.patcher.initializer to the class name to use instead.

To add new extensions, the LegacyExtensions class should be extended by

• adding the necessary extension points at the end of the LegacyHooks class (with default implementations, for forward compatibility, so that users of ij1-patcher are able to use subclasses of LegacyHooks without requiring changes after upgrading to a new ij1-patcher version),
• adding a new method to the end that applies the necessary runtime patches,
• and calling that method in LegacyExtensions' injectHooks method.

As the LegacyHooks class definition needs to be shared with the calling class loader, it must not use any ImageJ classes!

When configuring the LegacyEnvironment -- e.g. disabling handling for the ij1.plugin.dirs system property -- what really happens is that a Callback is added to the LegacyInjector instance of the environment. This callback will patch the constructor of the EssentialLegacyHooks accordingly. As that EssentialLegacyHooks class definition will be written out when using the writeJar method, the configuration will be hard-coded into the written-out .jar file, too.

For details about the headless mode, see the section below.

Where does it come from?

ImageJ is a very successful project that -- as any major project -- benefits from some refactoring from time to time:

• A first attempt at improving ImageJ was made in the ImageJA project, which started as a lightweight fork of ImageJ, then became a Mavenized version of ImageJ, automatically tracking ImageJ's releases, and finally was retired in 2022 once ImageJ itself started publishing its own releases to Maven Central.

• Fiji, a related project aiming to provide a distribution of ImageJ, tapped into the ImageJA project to provide extension points not offered by ImageJ, and later also to provide the headless mode (see below). Over time, maintaining the ImageJA fork became very burdensome.

• With ImageJ2, a major effort was started to provide a new software architecture. The benefits to the Fiji project were immediately obvious and over the course of time, Fiji first imitated ImageJ2's approach by replacing the ImageJA-specific ImageJ patches with runtime patches (see above). Later, the Fiji-specific patches moved from Fiji's fiji-compat component into ImageJ's ij-legacy component.

• In the last step, the runtime patching code in ImageJ was separated out from the legacy service code, giving rise to this here ij1-patcher project.

What is this "headless" mode about?

Traditionally, ImageJ was only ever intended to be a single application for a single user on one single machine with one single task at each given moment. That implementation detail shows through the way macros are recorded: in order to make a plugin recordable, one has to instantiate a GenericDialog and show it to the user. When the same plugin is played back from a macro, the dialog's values are populated from the macro options and the dialog is not displayed.

The problem is when the dialog cannot be instantiated because Java is running without a user interface. Which is quite common in today's clouds.

Originally devised in ImageJA (see above), ij1-patcher's headless mode provides limited support to run in a headless environment. It does so by replacing GenericDialog's superclass with a fake dialog class that does not require a graphical user environment. This works with well-behaved plugins that use the GenericDialog class in the intended way, but it breaks down when the plugin tries to display GUI elements or assumes that the dialog itself is a subclass of java.awt.Dialog.

Summary: the headless mode works for most plugins but fails for plugins assuming that a graphical user environment is readily available.

Please see the ImageJ wiki's Running Headless page for further details.