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

Mon Aug 17 17:39:15 BST 2015

Hi Joe,

Right, so I see that the formats-gpl JAR is not on that list. But it needs
to be...

Regards,
Curtis

On Mon, Aug 17, 2015 at 11:28 AM, Joe Ping-Lin Hsiao <phsiao at cs.unc.edu>
wrote:

> Hi Curtis,
>
> Thanks for your reply.
> My code doesn't deal with any JAR file at all. The most likely place I
> found that collects all the JAR files is in JavaTools:createJVM(), and it
> is the first procedure that I called in my code. By default It puts all the
> following JAR files within a 'jar' folder into a 'classpath' string:
>
> bsh-2.0b4.jar
> formats-api-5.1.2.jar
> formats-bsd-5.1.2.jar
> formats-common-5.1.2.jar
> guava-17.0.jar
> hamcrest-core-1.1.jar
> jace-runtime.jar
> jai_imageio-5.1.2.jar
> jcommander-1.27.jar
> jgoodies-common-1.7.0.jar
> jgoodies-forms-1.7.2.jar
> joda-time-2.2.jar
> junit-4.10.jar
> kryo-2.24.0.jar
> logback-classic-1.1.1.jar
> logback-core-1.1.1.jar
> lwf-stubs-5.1.2.jar
> metadata-extractor-2.6.2.jar
> minlog-1.2.jar
> mipav-stubs-5.1.2.jar
> native-lib-loader-2.0.2.jar
> objenesis-2.1.jar
> ome-xml-5.1.2.jar
> perf4j-0.9.13.jar
> serializer-2.7.1.jar
> slf4j-api-1.7.6.jar
> snakeyaml-1.6.jar
> specification-5.1.2.jar
> testng-6.8.jar
> turbojpeg-5.1.2.jar
> xalan-2.7.1.jar
> xercesImpl-2.8.1.jar
> xml-apis-1.3.04.jar
> xmpcore-5.1.2.jar
>
>
> Joe
>
> On Mon, Aug 17, 2015 at 11:56 AM, Curtis Rueden <ctrueden at wisc.edu> wrote:
>
>> 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
>>>>>
>>>>> _______________________________________________
>>>>> ome-users mailing list
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>>>>>
>>>>
>>>>
>>>
>>
>
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