VTK/Java Wrapping
Configuration
Bartlomiej Wilkowski has created a nice tutorial of configuring Java wrapping with VTK.
Java Wrapper Refactoring (Oct 8, 2007)
There were a few problems with the old Java wrappers. One was that, as you said, objects were being deleted before they were supposed to. We hacked in a fix at one point about a year ago which basically made all VTK objects accessed from Java stay around forever, but this was not acceptable either.
Ref:
The other major concern was that the map from Java objects to VTK objects was in the C++ JNI layer, and while we tried to keep this map synchronized with a mutex, race conditions could still occur because other Java threads could advance while the JNI layer was being called (a thread could access a C++ object just as it is being garbage-collected and deleted). There does not seem to be a way to atomically call a JNI method, or ensure the collector doesn't run while a method is called. This second issue forced us to rethink how the map is done, and the solution was to keep the map in Java instead of C++. But we didn't want this Java map to prohibit objects from being garbage collected. Fortunately, Java has a WeakReference class for just this type of purpose. When accessed, the reference will either be valid or null depending on whether it has been garbage-collected.
http://java.sun.com/j2se/1.4.2/docs/api/java/lang/ref/WeakReference.html
Thus, the wrapper code can lookup objects in this map when returning objects from methods, and if it is not there, or null, it creates a new Java object representing that C++ object.
A final issue was that we wanted a way to guarantee all C++ destructors are called before the program exits. The natural place to decrement the reference count of the C++ object is in finalize(), which works when things are garbage-collected, but Java does not guarantee that finalize will ever be called. So the method vtkGlobalJavaHash.DeleteAll() will plow through the remaining VTK objects and call Delete on them.
