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

Thu Dec 13 10:08:07 CST 2012

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!
>
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