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

Melissa Linkert melissa at glencoesoftware.com
Fri Dec 14 15:04:06 CST 2012 

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

More information about the ImageJ-devel mailing list