Developer Guide - Anchor beans | Anchor Image Analysis

Edit me

What is an AnchorBean?

It is a JavaBean, subject to all the official conventions.
It inherits form the class AnchorBean
The fields which define bean properties are additionally annotated with @BeanField.
Serveral additional annotations are possible: @Optional @NonEmpty etc.

Why use AnchorBeans?

To separate the implementation of algorithms/components from their parameterization.
To allow for easy serialization of configuration back and forth to XML.
For a core-object model with certain repeated functionality (initialization, duplication).
To remember parameters and algorithms for scientific record-keeping.
To facilitate rapid ongoing development: low cost to add prototypes.

Tip: Application behavior can be changed via BeanXML without recompiling e.g. change configuration settings, define new experimental pipelines, modify existing pipelines, tweak parameters etc.

We implement principles of Dependency Injection and Inversion of Control (IoC) (similarly to the Spring Framework).

Anchor BeanXML

BeanXML is a basic XML standard for defining AnchorBeans, which just uses the Apache Commons Configuration framework for serializing JavaBeans to/from XML.

Important: Please read and understand the user-guide to BeanXML

Note: For technical Java coding on BeanXML please see Declaring and Creating Beans before proceeding.

Additional Anchor-specific aspects are added to standard BeanXML. e.g. duplication occurs not only on the bean itself, but recursively on all its child properties, thus giving a deep copy.

Important prior step before usage in code

Code must always first call RegisterBeanFactories.registerAllPackageBeanFactories() before loading any beans. This registers the additional-factories, and a replacement default factory (AnchorDefaultBeanFactory).

Initializable beans

Certain types of beans require initialization-parameters before they can be used. These beans should derive from InitializableBean, which provides helpful methods for recursively initializating a bean and all its nested children.

The type of parameter is application-dependent, and typically another abstract-base-class will subclass InitializableBean and specify both the parameter-type and some further interfaces.

Package namespaces in JARs

By convention, Anchor beans are always stored with bean in the root package namespace of the JAR e.g.

org.anchoranalysis.image.bean.threshold.ThresholderGlobal
org.anchoranalysis.bean.StringSet
org.anchoranalysis.image.bean.unitvalue.distance.UnitValueDistanceVoxels

The namespace to the left of bean is the root package namespace.

Note: Remember, a bean often inherits properties from parent-beans, so consider also all classes the bean inherits from.

Locating source-code for a particular bean

Read the bean-class from the config-class attribute
The relevant source-code repository can be inferred from the root package namespace (see Source Repositories).
Follow the maven structure of src/main/java/org/anchoranalysis/ etc. backwards along the package namespace to eventually locate the class.