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

Fri Dec 14 14:06:41 CST 2012

Hi Jonas,

> I uploaded a sample image (seq1615.jp2) anyway for testing

Thanks, I tested on my system. It prints a warning "Expected positive value
for PhysicalSizeZ; got 0.0" but the image window opens.

Other Bio-Formats devs: can you reproduce?

> (but where did it go?)

Files uploaded using that mechanism are placed on the Fiji web server (
fiji.sc) in a private folder; we assume you do not want your data shared
publicly unless you say otherwise.

Regards,
Curtis

On Fri, Dec 14, 2012 at 4:49 AM, Jonas Øgaard <jonas at ogaard.no> wrote:

> 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
>>>
>>
>>
>  --
> 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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