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 _______________________________________________ ImageJ-devel mailing list [email protected] http://imagej.net/mailman/listinfo/imagej-devel
