How to load and invoke ImageJ2 plugins

KnipImageJ.java

//
// KnipImageJ.java
//

/*
ImageJ software for multidimensional image processing and analysis.

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      names of its contributors may be used to endorse or promote products
      derived from this software without specific prior written permission.

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AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
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*/

package imagej;

import imagej.data.Dataset;
import imagej.data.display.DatasetView;
import imagej.data.display.ImageDisplay;
import imagej.data.display.OverlayView;
import imagej.data.overlay.Overlay;
import imagej.event.EventHandler;
import imagej.event.EventService;
import imagej.event.StatusEvent;
import imagej.ext.module.Module;
import imagej.ext.module.ModuleException;
import imagej.ext.module.ModuleInfo;
import imagej.ext.module.ModuleItem;
import imagej.ext.module.ModuleRunner;
import imagej.ext.module.ModuleService;
import imagej.ext.module.process.ModulePostprocessor;
import imagej.ext.module.process.ModulePreprocessor;
import imagej.ext.plugin.DynamicPlugin;
import imagej.ext.plugin.InitPreprocessor;
import imagej.ext.plugin.PluginService;
import imagej.ext.plugin.ServicePreprocessor;
import imagej.util.ClassUtils;

import java.util.ArrayList;
import java.util.List;

/**
 * Exploration of ImageJ plugin integration from other tools
 * (e.g., KNIP, OMERO, ICY).
 * 
 * @author Curtis Rueden
 */
public final class KnipImageJ {

	private KnipImageJ() {
		// prevent instantiation of utility class
	}

	private static Object subscribers;

	public static void main(final String[] args) {
//		final ImageJ context = ImageJ.createContext();
//		context.getService(UIService.class).processArgs(args);
		@SuppressWarnings("unchecked")
		final ImageJ context =
			ImageJ.createContext(EventService.class, ModuleService.class,
				PluginService.class);

		// Note: the above context will contain only the minimal services needed
		// to discover plugins. But the plugins themselves may depend on
		// additional services. So it may be a good idea to instead use
		// ImageJ.createContext() which will load all available services, rather
		// than only the minimal ones.

		// listen to status events
		// need to keep a reference, so the subscribers aren't GCed
		final EventService eventService = context.getService(EventService.class);
		subscribers = eventService.subscribe(new KnipImageJ());

		// get list of modules, and filter them to those acceptable to KNIME/KNIP
		final ModuleService moduleService =
			context.getService(ModuleService.class);
		final List<ModuleInfo> modules = moduleService.getModules();
		final List<ModuleInfo> legalModules = findLegalModules(modules);

		final SettingsModel settingsModel = null;

		final ModuleInfo sampleInfo = legalModules.get(0);
		final Module module;
		try {
			module = sampleInfo.createModule();
		}
		catch (final ModuleException e) {
			return;
		}
		final List<ModulePreprocessor> pre = new ArrayList<ModulePreprocessor>();
		pre.add(new InitPreprocessor());
		pre.add(new ServicePreprocessor(context));
		pre.add(new KnipPreprocessor(settingsModel));
		final List<ModulePostprocessor> post =
			new ArrayList<ModulePostprocessor>();
		final Object something = new Object();
		post.add(new KnipPostprocessor(something));
		final ModuleRunner runner = new ModuleRunner(module, pre, post);
		runner.run();
	}

	public static class SettingsModel {

		public Object getValue() {
			return null;
		}
	}

	public static class KnipPreprocessor implements ModulePreprocessor {

		private final SettingsModel settingsModel;

		public KnipPreprocessor(final SettingsModel settingsModel) {
			this.settingsModel = settingsModel;
		}

		@Override
		public boolean canceled() {
			return false;
		}

		@Override
		public String getMessage() {
			// TODO Auto-generated method stub
			return null;
		}

		@Override
		public void process(final Module module) {
			// TODO Auto-generated method stub
			for (final ModuleItem<?> item : module.getInfo().inputs()) {
				processItem(item, module);
			}
		}

		public <T> void processItem(final ModuleItem<T> item, final Module module)
		{
			if (module.isResolved(item.getName())) return;
			module.setInput(item.getName(), settingsModel.getValue());
		}

	}

	public static class KnipPostprocessor implements ModulePostprocessor {

		public KnipPostprocessor(final Object something) {}

		@Override
		public void process(final Module module) {
			// TODO Auto-generated method stub
			for (final ModuleItem<?> item : module.getInfo().outputs()) {
				processItem(item, module);
			}

		}

		private <T> void
			processItem(final ModuleItem<T> item, final Module module)
		{
			// TODO: do something with this output
		}
	}

	@EventHandler
	protected void onEvent(final StatusEvent event) {
		// do something
	}

	private static List<ModuleInfo> findLegalModules(
		final List<ModuleInfo> modules)
	{
		final ArrayList<ModuleInfo> legal = new ArrayList<ModuleInfo>();
		for (final ModuleInfo info : modules) {
			if (isEvilPlugin(info)) continue;
			for (final ModuleItem<?> item : info.inputs()) {
				final Class<?> type = item.getType();
				if (!isLegalType(type)) continue;
				legal.add(info);
			}
		}
		return legal;
	}

	private static boolean isEvilPlugin(final ModuleInfo info) {
		// SO UGLY! TODO: add API to ModuleInfo to query whether the module has
		// dynamically generated inputs and outputs (isStatic? isDynamic?)
		final String className = info.getDelegateClassName();
		final Class<?> c = ClassUtils.loadClass(className);
		return !DynamicPlugin.class.isAssignableFrom(c);
	}

	private static final Class<?>[] LEGAL_TYPES = { String.class, Number.class,
		Dataset.class, Overlay.class, DatasetView.class, OverlayView.class,
		ImageDisplay.class,
	// TODO: primitive types?
		};

	private static boolean isLegalType(final Class<?> type) {
		for (final Class<?> candidate : LEGAL_TYPES) {
			if (candidate.isAssignableFrom(type)) return true;
		}
		return false;
	}

}