[ImageJ-devel] [fiji-devel] LOCI crashes with current Fiji build on runtime
sebrhode at gmail.com
sebrhode at gmail.com
Wed Aug 1 02:33:31 CDT 2012
Hi Guys,
I tried to download the most up-to-date version (
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.
Do you still have an idea when this problem might get solved?
Cheers,
Sebi
Am Dienstag, 31. Juli 2012 20:32:09 UTC+2 schrieb Curtis Rueden:
>
> Hi everyone,
>
> > I somehow keep deleting loci_plugins.jar but it keeps coming back ...
> that caused the problem.
>
> I believe this problem is sorted out for user installations; that is,
> running "Update Fiji" should get the proper Bio-Formats JARs. We are no
> longer using loci_tools.jar, but rather the individual JARs.
>
> However, there is still work to be done with the Fiji build system, so for
> those using Fiji from source, there may continue to be these sorts of
> annoyances for a little while yet.
>
> Sorry,
> Curtis
>
>
> On Mon, Jul 23, 2012 at 6:44 PM, Stephan Preibisch <preibisch at mpi-cbg.de>wrote:
>
>> Thanks Melissa, that worked!! I somehow keep deleting loci_plugins.jar
>> but it keeps coming back ... that caused the problem. I will figure out
>> what always recreates it.
>>
>> Bye bye,
>> Steffi
>>
>>
>> Am Jul 23, 2012 um 19:30 schrieb Melissa Linkert <
>> melissa at glencoesoftware.com>:
>>
>> > Hi Steffi,
>> >
>> >> running the SPIM registration I run into the problem that it is not
>> possible to open images anymore because of a java.lang.NoSuchMethodError
>> (see full exception below):
>> ome.xml.model.Experimenter.setDisplayName(Ljava/lang/String;)V
>> >>
>> >> A similar error (setAcquiredDate instead of setDisplayName) can be
>> reproduced using the Script editor with beanshell and the mitosis.tif
>> (ImageJ example image):
>> > *snip*
>> >>
>> >> Does anyone know why this happens (was fine some days ago)...
>> >
>> > As far as I can tell, this is because when you build Fiji you now get
>> > two different versions of Bio-Formats in the 'jars' and 'plugins'
>> > directories. plugins/loci_tools.jar is a specific version from April
>> > 2012, where plugins/loci_plugins.jar and jars/bio-formats.jar (and
>> > jars/loci-common.jar etc.) are the latest 4.4-SNAPSHOT version from
>> > Maven. 4.4-SNAPSHOT had some subtle API changes a couple of weeks ago,
>> > which would cause this error if older and newer JARs were mixed on the
>> > CLASSPATH.
>> >
>> > I would guess that this is somewhat related to this thread:
>> >
>> >
>> https://groups.google.com/forum/?fromgroups#!topic/fiji-devel/r1JOg4C8_68
>> >
>> > ...but I could easily be wrong.
>> >
>> > Regards,
>> > -Melissa
>> >
>> > On Thu, Jul 19, 2012 at 12:02:36PM -0400, Stephan Preibisch wrote:
>> >> Hi,
>> >>
>> >> running the SPIM registration I run into the problem that it is not
>> possible to open images anymore because of a java.lang.NoSuchMethodError
>> (see full exception below):
>> ome.xml.model.Experimenter.setDisplayName(Ljava/lang/String;)V
>> >>
>> >> A similar error (setAcquiredDate instead of setDisplayName) can be
>> reproduced using the Script editor with beanshell and the mitosis.tif
>> (ImageJ example image):
>> >>
>> >> import loci.formats.ChannelSeparator;
>> >> import loci.formats.MetadataTools;
>> >> import loci.formats.meta.IMetadata;
>> >> import loci.formats.IFormatReader;
>> >>
>> >> final IFormatReader r = new ChannelSeparator();
>> >>
>> >> final IMetadata omexmlMeta = MetadataTools.createOMEXMLMetadata();
>> >> r.setMetadataStore( omexmlMeta );
>> >> r.setId( "/Users/preibischs/Desktop/mitosis.tif" );
>> >>
>> >> -> Target exception: java.lang.NoSuchMethodError:
>> ome.xml.model.Image.setAcquiredDate(Ljava/lang/String;)V
>> >>
>> >> Does anyone know why this happens (was fine some days ago)...
>> >>
>> >> Thanks a lot,
>> >> Steffi
>> >>
>> >>
>> >> java.lang.reflect.InvocationTargetException
>> >> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
>> >> at
>> sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
>> >> at
>> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
>> >> at java.lang.reflect.Method.invoke(Method.java:597)
>> >> 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:680)
>> >> Caused by: java.lang.NoSuchMethodError:
>> ome.xml.model.Experimenter.setDisplayName(Ljava/lang/String;)V
>> >> at
>> loci.formats.ome.OMEXMLMetadataImpl.setExperimenterDisplayName(OMEXMLMetadataImpl.java:7386)
>> >> at
>> loci.formats.meta.FilterMetadata.setExperimenterDisplayName(FilterMetadata.java:889)
>> >> at
>> loci.formats.in.ZeissLSMReader.initMetadata(ZeissLSMReader.java:1192)
>> >> at loci.formats.in.ZeissLSMReader.initFile(ZeissLSMReader.java:520)
>> >> at loci.formats.FormatReader.setId(FormatReader.java:1091)
>> >> at loci.formats.ImageReader.setId(ImageReader.java:682)
>> >> at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:492)
>> >> at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:261)
>> >> at mpicbg.imglib.io.LOCI.openLOCIFloatType(LOCI.java:638)
>> >> at mpicbg.imglib.io.LOCI.openLOCIFloatType(LOCI.java:583)
>> >> at mpicbg.imglib.io.LOCI.openLOCIFloatType(LOCI.java:573)
>> >> at mpicbg.imglib.io.LOCI.openLOCIFloatType(LOCI.java:568)
>> >> at
>> fiji.plugin.Bead_Registration.getInteractiveDoGParameters(Bead_Registration.java:673)
>> >> at
>> fiji.plugin.Bead_Registration.getConfiguration(Bead_Registration.java:320)
>> >> at
>> fiji.plugin.Bead_Registration.access$100(Bead_Registration.java:40)
>> >> at
>> fiji.plugin.Bead_Registration$1.dialogItemChanged(Bead_Registration.java:208)
>> >> at ij.gui.GenericDialog.showDialog(GenericDialog.java:1052)
>> >> at
>> fiji.plugin.Bead_Registration.singleChannel(Bead_Registration.java:265)
>> >> at fiji.plugin.Bead_Registration.run(Bead_Registration.java:75)
>> >> at ij.IJ.runUserPlugIn(IJ.java:185)
>> >> at ij.IJ.runPlugIn(IJ.java:152)
>> >>
>> >> --
>> >> 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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