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