Re: netcdf accepted / resume work on bioformats

[Josh Moore <josh@glencoesoftware.com>]

All,

Sorry for the long pause. Finally got around to discussing with the team today[1].

On May 4, 2012, at 2:41 PM, Mathieu Malaterre wrote:

> Ok, netcdf has been -painfully- accepted in debian main I can resume
> work on bioformats.
> 
> On Wed, Apr 11, 2012 at 11:31 AM, Josh Moore <josh@glencoesoftware.com> wrote:
>> What are the issues you've run into for the other targets? Specific jars missing from Debian?
> 
> 
> Ok here is another -nasty- one. How badly is JAI Image I/O Tools
> required in bioformats ?

JAI Image I/O Tools is required for all JPEG2000 support.


> As you know JAI Image I/O does not have a free license (you do not
> even have access to the source code), therefore I have two options:
> 
> - if JAI Image I/O is required to build bioformats, then bioformats
> will go into non-free (better than nothing)

Another also better-than-nothing alternative would be to build Bio-Formats such that there's a free and a non-free package, but if we don't have to, that'd be optimal.


> - if JAI Image I/O is not really required, then I can just simply
> repack the orig-upstream source and push a reduced bioformats to
> debian main

There's quite a bit that's then lost.


> Thanks again for your comment,
> -M


On May 4, 2012, at 3:30 PM, Andreas Tille wrote:

> On Fri, May 04, 2012 at 02:41:31PM +0200, Mathieu Malaterre wrote:
>> Ok, netcdf has been -painfully- accepted in debian main I can resume
>> work on bioformats.
> 
> Thanks!
> 
>> required in bioformats ?
>> As you know JAI Image I/O does not have a free license (you do not
>> even have access to the source code), therefore I have two options:
> 
> BTW, JAI Image I/O is also needed for dcm4che which would be really
> nice to have.  If anybody knows whom to bother for a free license for
> Image I/O this would be *really* cool ...


The fork that we maintain [2] is derived from the java.net project [3] which lists itself as BSD. Roger has pointed out that the major issue may be that the headers of the files were not updated to reflect BSD. If so, that may be something we contact upstream about.

Let us know how we can help.
Cheers,
~Josh.


[1] https://www.openmicroscopy.org/site/community/minutes/conference-calls/2012/2012-05-15-tuesday-meeting
[2] https://github.com/openmicroscopy/bioformats/tree/develop/components/forks/jai
[3] http://java.net/projects/jai-imageio-core