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 < [email protected]> 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 <[email protected]> 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 < > > > [email protected]> 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 <[email protected]>: > > >> > > >> 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 <[email protected]> > 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 <[email protected]> > 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 <[email protected] > >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 <[email protected] > >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, <[email protected]> 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, [email protected] 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 > > >>>>>>>> [email protected] > > >>>>>>>> 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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