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

[Curtis Rueden]

Hi Joe,

> 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.

Yes, that is correct.

So: in your C++ code, which JAR files are you putting on the classpath? You
must have lines of code somewhere that look like this:

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

Right?

Regards,
Curtis


On Mon, Aug 17, 2015 at 10:09 AM, Joe Ping-Lin Hsiao <phsiao at cs.unc.edu>
wrote:

> 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
>>>
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>>
>>
>
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