[ImageJ-devel] [fiji-devel] LOCI crashes with current Fiji build on runtime

Fri Dec 14 04:49:39 CST 2012

Hi,

Now all is good!
Thanks a ton and more.

I uploaded a sample image (seq1615.jp2) anyway for testing (but where did
it go?)

Sincerely,
JonasD

On Thu, Dec 13, 2012 at 5:11 PM, Jonas D. S. Øgaard
<jonas.ogaard at gmail.com>wrote:

> Essentially any (Nikon NIS) JPEG2000 formatted images fails. Will sen one
> when home.
>
> //JonasD
>
> Den 13. des. 2012 kl. 17:08 skrev Curtis Rueden <ctrueden at wisc.edu>:
>
> Hi Jonas,
>
> > java.lang.IllegalArgumentException: 0 must not be null and positive.
>
> That is actually great news. It means we fixed the problem with the update
> site. Now there is most likely a bona fide bug in Bio-Formats.
>
> Would you be willing to send us a problematic dataset, so that we can
> address the issue? You can use Fiji's Help > Upload Sample Image feature to
> send it if is smaller than ~250MB.
>
> But first, just to be sure: please run Help > Update Fiji and make sure it
> says your Fiji is fully up to date, with no locally modified files.
>
> Thanks,
> Curtis
>
>
> On Thu, Dec 13, 2012 at 6:42 AM, Jonas Øgaard <jonas at ogaard.no> wrote:
>
>> OK, back at work today. Here is trace log after attempting to import
>> using LOCI:
>>
>> java.lang.reflect.InvocationTargetException
>> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
>>  at
>> sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
>> at
>> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
>>  at java.lang.reflect.Method.invoke(Method.java:601)
>> at ij.Command.runPlugIn(Command.java:146)
>>  at ij.Command.runCommand(Command.java:95)
>> at ij.Executer.run(Executer.java:64)
>>  at java.lang.Thread.run(Thread.java:722)
>> Caused by: java.lang.IllegalArgumentException: 0 must not be null and
>> positive.
>>  at
>> ome.xml.model.primitives.PositiveInteger.<init>(PositiveInteger.java:56)
>> at loci.formats.MetadataTools.populatePixelsOnly(MetadataTools.java:272)
>>  at loci.formats.MetadataTools.populatePixelsOnly(MetadataTools.java:246)
>> at loci.formats.ChannelFiller.setId(ChannelFiller.java:267)
>>  at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:552)
>> at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:274)
>>  at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:552)
>> at loci.formats.DimensionSwapper.setId(DimensionSwapper.java:285)
>>  at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:552)
>> at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:552)
>>  at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:552)
>> at loci.plugins.in.ImportProcess.setId(ImportProcess.java:682)
>>  at loci.plugins.in.ImportProcess.initializeStack(ImportProcess.java:519)
>> at loci.plugins.in.ImportProcess.execute(ImportProcess.java:150)
>>  at loci.plugins.in.Importer.showDialogs(Importer.java:141)
>> at loci.plugins.in.Importer.run(Importer.java:79)
>>  at loci.plugins.LociImporter.run(LociImporter.java:81)
>> at ij.IJ.runUserPlugIn(IJ.java:184)
>>  at ij.IJ.runPlugIn(IJ.java:151)
>> ... 8 more
>>
>> Sincerely,
>> Jonas Ogaard
>>
>>
>> On Tue, Dec 11, 2012 at 11:17 PM, Jonas Øgaard <jonas at ogaard.no> wrote:
>>
>>> Hi again, Curtis!
>>>
>>> > I sat at work all day today pulling my hair - I could not make it
>>>> > work.
>>>>
>>>> My sincerest apologies for the pain. It is almost certainly due to
>>>> problems on the update site, not your configuration.
>>>>
>>>
>>> Please don't apologize for providing me with tools for science (;
>>> I will try it out first thing tomorrow. Pretty much done with
>>> developing, now it's time for analysis (:
>>>
>>> Besides, I like a challenge - although I have to admit this time I was
>>> in over my head.
>>>
>>> Oh, by the way, I'm not sure if the Maven dependencies are all sorted
>>> with regards to a certain Jama package... It looks for version 1.0.2
>>> whereas the latest release is 1.0.3 so it cannot be found... I managed to
>>> get it working through manually installing 1.0.2. It also works by changing
>>> the pom files of VIB-lib, VIB_ and 3D_viewer making them up to date. Having
>>> said that I only have a faintest clue of the infrastructure of Maven
>>> repositories...
>>>
>>> Anyway, it didn't help me with my loci (;
>>>
>>> Sincerely,
>>> Jonas
>>>
>>>
>>>>
>>>> I have updated the Bio-Formats installation in Fiji to the absolute
>>>> latest available, and hopefully ironed out these problems. Can you please
>>>> run Help > Update Fiji to install all the updates, and let me know if
>>>> Bio-Formats becomes functional for you?
>>>>
>>>> Thanks,
>>>> Curtis
>>>>
>>>>
>>>> On Tue, Dec 11, 2012 at 10:55 AM, Jonas Øgaard <jonas at ogaard.no> wrote:
>>>>
>>>>> Hi there,
>>>>>
>>>>> I have a working version of Fiji running at home (where I'm at now)
>>>>> and don't dare to break it, but I sat at work all day today pulling my hair
>>>>> - I could not make it work.
>>>>>
>>>>> I tried fresh downloads (fiji with and without jre), I tried removing
>>>>> one LOCI-jar, then the other, then both. I tried updating both fiji and
>>>>> imagej in two seperate clean setups, and also tried repeating updates to
>>>>> make sure no more components where awaiting updates.
>>>>>
>>>>> It could be that the java-install is not entirely stable/up-to-date -
>>>>> it's running JRE6. Haven't tried 7.
>>>>>
>>>>> I have no clue. Working from home tomorrow where it's safe & stable!
>>>>>
>>>>> Sincerely,
>>>>> Jonas
>>>>>
>>>>>
>>>>> On Tue, Dec 11, 2012 at 5:47 PM, Curtis Rueden <ctrueden at wisc.edu>wrote:
>>>>>
>>>>>> Hi Jonas,
>>>>>>
>>>>>> > I am unable to import files with LOCI, no matter which loci-jar is
>>>>>> > deleted or not...
>>>>>>
>>>>>> I updated Fiji with the 4.4.5 release of Bio-Formats last night, so
>>>>>> these errors are almost certainly my fault.
>>>>>>
>>>>>> Unfortunately, I am unable to replicate the problem. I tried updating
>>>>>> an existing Fiji on another workstation, and all worked fine (though I did
>>>>>> have to click "break the dependency" in response to one prompt). I also
>>>>>> tried with a fresh continuous release downloaded from fiji.sc just
>>>>>> now, and it also worked.
>>>>>>
>>>>>> If you run Help > Update Fiji, click on Advanced mode, what do you
>>>>>> see for "Locally modified files" and "Uninstalled files only"? A fully
>>>>>> up-to-date Fiji should not have any entries.
>>>>>>
>>>>>> -Curtis
>>>>>>
>>>>>>
>>>>>> On Tue, Dec 11, 2012 at 6:31 AM, <jonas.ogaard at gmail.com> wrote:
>>>>>>
>>>>>>> Hi!
>>>>>>>
>>>>>>> I am still having difficulties with the latest Fiji (both w/w/out
>>>>>>> jre) and LOCI. Receiving same errors as described above.
>>>>>>>
>>>>>>> As of now I am unable to import files with LOCI, no matter which
>>>>>>> loci-jar is deleted or not...
>>>>>>>
>>>>>>> Have I magically jinxed my Fiji folder (again) or is this a problem
>>>>>>> shared by others?
>>>>>>>
>>>>>>> Awesome work btw, Johannes (:
>>>>>>>
>>>>>>> //Jonas
>>>>>>>
>>>>>>> On Wednesday, August 1, 2012 7:37:26 PM UTC+2, Johannes Schindelin
>>>>>>> wrote:
>>>>>>>
>>>>>>>> Hi Sebi,
>>>>>>>>
>>>>>>>> On Wed, 1 Aug 2012, sebr... at gmail.com wrote:
>>>>>>>>
>>>>>>>> > I tried to download the most up-to-date version (
>>>>>>>> > http://jenkins.imagej.net/job/**Stable-Fiji/**
>>>>>>>> lastSuccessfulBuild/artifact/**fiji-nojre.zip<http://jenkins.imagej.net/job/Stable-Fiji/lastSuccessfulBuild/artifact/fiji-nojre.zip>)
>>>>>>>>
>>>>>>>> >
>>>>>>>> >
>>>>>>>> > This contains the loci_tools.jar as well as the the individual
>>>>>>>> jars. So
>>>>>>>> > should i just delete which files? This issues is quite critical
>>>>>>>> for us,
>>>>>>>> > since the Loci Bio-Format import is cruicial for us (and
>>>>>>>> customer) to
>>>>>>>> > import the OME-TIFF data produced by our imaging software.
>>>>>>>>
>>>>>>>> Yes, it is safe to delete loci_tools.jar. My work last year on
>>>>>>>> enabling
>>>>>>>> multiple update sites introduced the bug that removing files from
>>>>>>>> update
>>>>>>>> sites does not mark them as obsolete if you updated the files
>>>>>>>> successfully
>>>>>>>> before. We just did not hit that bug because we did not remove
>>>>>>>> files in a
>>>>>>>> long time ;-)
>>>>>>>>
>>>>>>>> > Do you still have an idea when this problem might get solved?
>>>>>>>>
>>>>>>>> It is fixed in the source code, I just have to upload a new version
>>>>>>>> (for
>>>>>>>> which I need to be comfortable with the current state first, though
>>>>>>>> ;-).
>>>>>>>> Should be happening within the hour.
>>>>>>>>
>>>>>>>> Ciao,
>>>>>>>> Dscho
>>>>>>>>
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> ImageJ-devel mailing list
>>>>>>> ImageJ-devel at imagej.net
>>>>>>> http://imagej.net/mailman/listinfo/imagej-devel
>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>  --
>> Please avoid top-posting, and please make sure to reply-to-all!
>>
>> Mailing list web interface: http://groups.google.com/group/fiji-devel
>>
>
>
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