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

[Joe Ping-Lin Hsiao]

Curtis,

My code is all written in C++, and I am using the JACE C++ binding method.
The reader is an ImageReader object. Just like the 'showinf' program
provide from the source, I believe when given a file input, it goes through
a .txt file and tries all the file formats listed there.

Thanks,
Joe

On Thu, Aug 13, 2015 at 10:20 PM, Curtis Rueden <ctrueden at wisc.edu> wrote:

> 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)
>>
>> > _______________________________________________
>> > ome-users mailing list
>> > ome-users at lists.openmicroscopy.org.uk
>> > http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>>
>> _______________________________________________
>> ome-users mailing list
>> ome-users at lists.openmicroscopy.org.uk
>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>>
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.openmicroscopy.org.uk/pipermail/ome-users/attachments/20150817/2d22c01e/attachment.html>