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 <[email protected]> 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 < > [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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