[ome-users] Having trouble opening .nd2 file in Bio-formats cppwrap

[Curtis Rueden]

Hi Melissa and Joe,

> > loci.formats.UnknownFormatException: Unknown file format:
> > /common1/phsiao/build/vst/sample_vid/samplet01xy1.nd2 at
> > loci.formats.ImageReader.getReader(ImageReader.java:190) at
> > loci.formats.ImageReader.setId(ImageReader.java:832)
>
> This is currently expected; at the moment, the cppwrap builds only
> contain BSD-licensed readers.

IIRC, it is not necessary to produce C++ proxies for every single
Bio-Formats class, because typical API usage on the C++ side does not
involve directly accessing those individual reader classes. All that is
necessary is that in the C++ client code, the classpath of the created JVM
includes formats-gpl.jar.

E.g. on Windows, something like:

list.push_back(jace::ClassPath("jace-runtime.jar;bioformats_package.jar"));

Or the individual list of JARs, if you are using those rather than the
uber-jar.

Joe: Are you in fact using Bio-Formats from C++ via the C++ bindings? Or
does this problem happen to you in pure Java?

Regards,
Curtis

On Thu, Aug 13, 2015 at 3:21 PM, Melissa Linkert <
melissa at glencoesoftware.com> wrote:

> Hi Joe,
>
> > I am using Bio-formats 5.1.2, and I have trouble opening a .nd2 file from
> > my program and from "showinf". The .nd2 file has been uploaded. The weird
> > thing is Fiji can open the file fine. The error message I got was:
> >
> > 11:35:54.179 [main] DEBUG loci.common.NIOByteBufferProvider - Using
> mapped
> > byte buffer? false
> > loci.formats.UnknownFormatException: Unknown file format:
> > /common1/phsiao/build/vst/sample_vid/samplet01xy1.nd2
> >     at loci.formats.ImageReader.getReader(ImageReader.java:190)
> >     at loci.formats.ImageReader.setId(ImageReader.java:832)
>
> This is currently expected; at the moment, the cppwrap builds only contain
> BSD-licensed readers.  The final column in the list of supported
> formats indicates which formats this includes:
>
>
> http://www.openmicroscopy.org/site/support/bio-formats5.1/supported-formats.html
>
> There is a ticket on our issue tracking system to add all remaining
> readers:
>
> https://trac.openmicroscopy.org/ome/ticket/11896
>
> If you would like to be CC'd on the ticket, please let us know.
>
> Regards,
> -Melissa
>
> On Thu, Aug 13, 2015 at 03:21:24PM -0400, Joe Ping-Lin Hsiao wrote:
> > Hi,
> >
> > I am using Bio-formats 5.1.2, and I have trouble opening a .nd2 file from
> > my program and from "showinf". The .nd2 file has been uploaded. The weird
> > thing is Fiji can open the file fine. The error message I got was:
> >
> > 11:35:54.179 [main] DEBUG loci.common.NIOByteBufferProvider - Using
> mapped
> > byte buffer? false
> > loci.formats.UnknownFormatException: Unknown file format:
> > /common1/phsiao/build/vst/sample_vid/samplet01xy1.nd2
> >     at loci.formats.ImageReader.getReader(ImageReader.java:190)
> >     at loci.formats.ImageReader.setId(ImageReader.java:832)
>
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> > ome-users at lists.openmicroscopy.org.uk
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>
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