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

[Stephan Preibisch]

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!
>> 
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