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

[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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