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

Fri Dec 14 15:19:00 CST 2012

Hey again!

Sorry I wasn't clear in the previous message - all really is good.

After running last updates I can import all my images fine. I just uploaded
the sample image so you could reproduce if you wanted to look further into
what was causing it *before* I ran the update.

Sincerely,
JonasD

On Fri, Dec 14, 2012 at 10:12 PM, Curtis Rueden <ctrueden at wisc.edu> wrote:

> Hi Melissa, Jonas & everyone,
>
> > As long as Jonas is able to see the image in Fiji and there is truly
> > no physical pixel size, this is not a bug.
>
> I agree, but what I meant was that from his prior message, it sounded like
> he was getting an exception:
>
> > java.lang.IllegalArgumentException: 0 must not be null and positive.
>
> So by my vague question "can you reproduce?" I actually meant "can you
> reproduce the IllegalArgumentException". Apologies for being unclear.
>
> From your mail, it sounds like you see the same behavior as me: a
> relatively harmless warning, rather than exception that prevents the image
> window from appearing.
>
> Jonas: Did you double check that your Fiji is 100% up to date? Help >
> Update Fiji, no "locally modified" or "local-only" files at all? And if so,
> do you still receive an exception?
>
> Thanks,
> Curtis
>
>
> On Fri, Dec 14, 2012 at 3:04 PM, Melissa Linkert <
> melissa at glencoesoftware.com> wrote:
>
>> Hi,
>>
>> > > 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?
>>
>> Yes, and that is the correct behavior.  So far as I can see from opening
>> the file in Nikon's Elements software, this file contains no physical
>> size/calibration information.  Bio-Formats is simply warning that a
>> physical pixel size of 0 was found, which means that it will not be
>> preserved if you were to convert the file to some other format (only
>> values greater than 0 are preserved).
>>
>> As long as Jonas is able to see the image in Fiji and there is truly no
>> physical pixel size, this is not a bug.
>>
>> Regards,
>> -Melissa
>>
>> On Fri, Dec 14, 2012 at 02:06:41PM -0600, Curtis Rueden wrote:
>> > 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
>> > >
>> >
>> > --
>> > 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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