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
