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

[Joe Ping-Lin Hsiao]

Hi Curtis,

It works after I download formats-gpl.jar into the jar folder. Thanks!

Joe

On Mon, Aug 17, 2015 at 12:39 PM, Curtis Rueden <ctrueden at wisc.edu> wrote:

> 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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