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

Thu Dec 13 06:42:46 CST 2012

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
>>>>>
>>>>>
>>>>
>>>
>>
>
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