Creating an extension project

Prerequisities

• Java 8 (Java 9+ are not working)
  • If you are using Windows or a Linux distribution without Java 8, we recommend AdoptOpenJDK (Please choose OpenJDK 8)
• Maven

Creating the project

The project should have following structure:

Project root
└── pom.xml
└── src
    └── main
        ├── java
        └── resources

Both the java and resources folder should contain a folder structure that is equivalent the groupId and artifactId of the project. This is done to prevent conflicts with other plugins.

JIPipe is based on SciJava and requires libraries provided by the SciJava Maven repository.

Here is an example *.pom file that you can adapt for your project: https://github.com/applied-systems-biology/jipipe/blob/master/jipipe-strings/pom.xml

Creating an extension service

JIPipe uses the SciJava plugin API to register Java extensions. In your project, you can create as many extensions as you want.

Java extension inherit from JIPipeJavaExtension and require a @Plugin annotation.

We recommend to inherit from JIPipeDefaultJavaExtension that comes with some convenience-functions.

A minimal extension can be found here:

@Plugin(type = JIPipeJavaExtension.class)
public class MyExtension extends JIPipeDefaultJavaExtension {

    // We recommend to create a static AS_DEPENDENCY variable that contains the dependency ID, name, and version of the extension
    // This simplifies the usage in getDependencies() for extensions that are based on your library
    public static final JIPipeDependency AS_DEPENDENCY = new JIPipeMutableDependency("CHANGEME", "1.0.0", "My extension");

    // If you have custom icons, thumbnails etc., create a JIPipeResourceManager instance that points towards the root directory of your resources
    // Please read the documentation of JIPipeResourceManager for more information on how to structure the resources directory 
    public static final JIPipeResourceManager RESOURCES = new JIPipeResourceManager(MyExtension.class, "resource/directory/of/my/extension");

    public MyExtension() {
        getMetadata().addCategories(PluginCategoriesEnumParameter.CATEGORY_SCRIPTING); // You can annotate your extension with ImageJ Wiki categories (Optional)
        
    }

    @Override
    public String getName() {
        return "My extension";
    }

    @Override
    public HTMLText getDescription() {
        return new HTMLText("A Java extension");
    }

    @Override
    public String getDependencyId() {
        // We recommend the following structure: <groupId>.<artifactId>:<dependencyId>
        // (!) The dependency Id should be unique for each extension @Plugin (!)
        return "CHANGEME";
    }

    // You can optionally override the version.
    // @Override
    // public String getDependencyVersion() {
    //    return "1.0.0";
    // }

    @Override
    public String getAuthors() {
        return "Ruman Gerst";
    }

    @Override
    public String getWebsite() {
        return "https://jipipe.org/";
    }

    @Override
    public String getLicense() {
        return "BSD-2";
    }
    
        @Override
    public ImageParameter getThumbnail() {
        // An optional thumbnail. Here it is loaded from the extension's resource package
        // Remove the override if you do not want a thumbnail
        return new ImageParameter(RESOURCES.getResourceURL("thumbnail.png"));
    }

    // You can add one more multiple logos on the JIPipe splash screen
    // They must be 32x32 in size
    // Please do not add too many of them to not fill up all the space
    // @Override
    // public List<ImageIcon> getSplashIcons() {
    //     return Collections.singletonList(new ImageIcon(getClass().getResource("org/hkijena/jipipe/extensions/myextension/icon-32.png")));
    // }

    @Override
    public String getCitation() {
        // Here you can enter a citation for your publication
        // It will be displayed in the plugin manager
        return "";
    }

    @Override
    public void register(JIPipe jiPipe, Context context, JIPipeProgressInfo progressInfo) {
        // Content is registered here
        // You can have multiple registerNodeType, registerDataType etc. in this place
    }

    // Optional: run code after this and other extensions are registered (for example to create notifications; see https://github.com/applied-systems-biology/jipipe/blob/master/jipipe-python/src/main/java/org/hkijena/jipipe/extensions/python/PythonExtension.java)
    // @Override
    // public void postprocess() {
    // }
}

Testing your extension

You have two options that allow to test your extension:

1. Using a main() function
2. Using a dedicated launcher library

The main() function is faster to implement, but has the disadvantage of that you need to include JIPipe extensions that you require for testing your nodes into the list of dependencies. For certain extensions (e.g., OMERO) there might also be some additional issues.

Just insert the following code into your project:

public static void main(final String... args) {
    final ImageJ ij = new ImageJ();
    ij.ui().showUI(); // If your ImageJ freezes, you can leave this out. JIPipe will show anyways.
    ij.command().run(JIPipeGUICommand.class, true);
}

A dedicated launcher plugin allows to utilize all available JIPipe extensions without directly referencing in your plugin’s dependency list. Please take a look at jipipe-launcher if you want to include a similar library into your project.