The designs of the C++ library VIGRA and of the Java library ImgLib2 resemble each other. This is not a coincidence: VIGRA (among other C++ libraries) was the inspiration for ImgLib2.
However, C++ and Java are different enough to make it relatively difficult to reconcile both. This lil' project is an attempt to bridge these projects: it demonstrates how to provide a VIGRA-backed ImgLib2 ImgFactory.
The major challenge is to access C++ data efficiently from Java. You see, Java does not like the way C++ manages memory (it wants to be able to release it when appropriate, or to shift things around, which C++ does not allow because it does not keep track of memory references explicitly).
So the first stab at solving this problem is to access the C++-allocated data
structure only via explicit JNI functions. Should that turn out to be too slow,
we will have to look at using the JNI function
NewDirectByteBuffer
in a new family of Img implementations that are still backed by
VIGRA-allocated data structures.
First make sure that you have built and installed VIGRA.
Then clone the example: git clone https://github.com/dscho/vigra-imglib2.
Then build it: mvn (if you do not have Maven yet, you might want to
download and install it.
After building it, you can run it with mvn exec:java.
Eclipse makes everything slightly more challenging, especially when you step outside Eclipse's box even for an iota.
Therefore, you need to do everything as described above but instead of running it from the command-line, you can now import the example as a Maven project via '''File>Import>Import Existing Maven Project...'''.
Whenever you change the native code in src/main/cxx/, you will have to
build from the command-line via mvn before you can try it in Eclipse.
First, copy all dependencies with mvn dependency:copy-dependencies. Then
call Avian VM's drop-in avian command:
-Dpath.separator=: -Dfile.separator=/ -classpath \
$(ls target/dependency/*.jar | tr '\n' :)target/vigra-imglib2-1.0.0-SNAPSHOT.jar \
Example```