[ImageJ-devel] [VIGRA] Avian VM and Bio-Formats

[Johannes Schindelin]

Hi Ulli,

On Thu, 17 Oct 2013, Ullrich Koethe wrote:

> thank you for this very encouraging effort! Do I understand correctly
> that you achieved the following:
> 
> * embed Avian in a C++ program
> * call BioFormats via the embedded Avian to convert a file into another
> format

Yes, that is essentially what I did. Except that the C++ program was
Avian's default one.

> but you didn't yet try to use Avian/BioFormats to read the data directly
> into a C++ data structure (such as vigra::MultiArray)? Is this latter
> step easy to achieve using standard JNI tools once the embedding/running
> of BioFormats works?

That would be the next step after cleaning up my Avian patches and trying
to read files via SCIFIO.

Once I can call a Java class that uses SCIFIO to read a file, it should be
very, very easy to access the read data via C++. Of course, the ultimate
goal would be to let SCIFIO read the data *directly* into VIGRA's data
structures, something I hope ImgLib2 makes easy: I would simply wrap the
C++ arrays in an ImgLib2-compatible container and ask SCIFIO to use that
as the destination.

Step by step ;-)
Johannes