[ImageJ-devel] [fiji-devel] LOCI crashes with current Fiji build on runtime
Curtis Rueden
ctrueden at wisc.edu
Fri Dec 14 15:12:29 CST 2012
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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