Hi everyone,<div><br></div><div>> I somehow keep deleting loci_plugins.jar but it keeps coming back ... that caused the problem.</div><div><br></div><div>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.</div>
<div><br></div><div>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.</div><div><br></div>
<div>
Sorry,</div><div>Curtis</div><div><br><br><div class="gmail_quote">On Mon, Jul 23, 2012 at 6:44 PM, Stephan Preibisch <span dir="ltr"><<a href="mailto:preibisch@mpi-cbg.de" target="_blank">preibisch@mpi-cbg.de</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">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.<br>
<br>
Bye bye,<br>
Steffi<br>
<br>
<br>
Am Jul 23, 2012 um 19:30 schrieb Melissa Linkert <<a href="mailto:melissa@glencoesoftware.com" target="_blank">melissa@glencoesoftware.com</a>>:<br>
<div><div><br>
> Hi Steffi,<br>
><br>
>> 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<br>
>><br>
>> A similar error (setAcquiredDate instead of setDisplayName) can be reproduced using the Script editor with beanshell and the mitosis.tif (ImageJ example image):<br>
> *snip*<br>
>><br>
>> Does anyone know why this happens (was fine some days ago)...<br>
><br>
> As far as I can tell, this is because when you build Fiji you now get<br>
> two different versions of Bio-Formats in the 'jars' and 'plugins'<br>
> directories. plugins/loci_tools.jar is a specific version from April<br>
> 2012, where plugins/loci_plugins.jar and jars/bio-formats.jar (and<br>
> jars/loci-common.jar etc.) are the latest 4.4-SNAPSHOT version from<br>
> Maven. 4.4-SNAPSHOT had some subtle API changes a couple of weeks ago,<br>
> which would cause this error if older and newer JARs were mixed on the<br>
> CLASSPATH.<br>
><br>
> I would guess that this is somewhat related to this thread:<br>
><br>
> <a href="https://groups.google.com/forum/?fromgroups#!topic/fiji-devel/r1JOg4C8_68" target="_blank">https://groups.google.com/forum/?fromgroups#!topic/fiji-devel/r1JOg4C8_68</a><br>
><br>
> ...but I could easily be wrong.<br>
><br>
> Regards,<br>
> -Melissa<br>
><br>
> On Thu, Jul 19, 2012 at 12:02:36PM -0400, Stephan Preibisch wrote:<br>
>> Hi,<br>
>><br>
>> 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<br>
>><br>
>> A similar error (setAcquiredDate instead of setDisplayName) can be reproduced using the Script editor with beanshell and the mitosis.tif (ImageJ example image):<br>
>><br>
>> import loci.formats.ChannelSeparator;<br>
>> import loci.formats.MetadataTools;<br>
>> import loci.formats.meta.IMetadata;<br>
>> import loci.formats.IFormatReader;<br>
>><br>
>> final IFormatReader r = new ChannelSeparator();<br>
>><br>
>> final IMetadata omexmlMeta = MetadataTools.createOMEXMLMetadata();<br>
>> r.setMetadataStore( omexmlMeta );<br>
>> r.setId( "/Users/preibischs/Desktop/mitosis.tif" );<br>
>><br>
>> -> Target exception: java.lang.NoSuchMethodError: ome.xml.model.Image.setAcquiredDate(Ljava/lang/String;)V<br>
>><br>
>> Does anyone know why this happens (was fine some days ago)...<br>
>><br>
>> Thanks a lot,<br>
>> Steffi<br>
>><br>
>><br>
>> java.lang.reflect.InvocationTargetException<br>
>> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)<br>
>> at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)<br>
>> at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)<br>
>> at java.lang.reflect.Method.invoke(Method.java:597)<br>
>> at ij.Command.runPlugIn(Command.java:146)<br>
>> at ij.Command.runCommand(Command.java:95)<br>
>> at ij.Executer.run(Executer.java:64)<br>
>> at java.lang.Thread.run(Thread.java:680)<br>
>> Caused by: java.lang.NoSuchMethodError: ome.xml.model.Experimenter.setDisplayName(Ljava/lang/String;)V<br>
>> at loci.formats.ome.OMEXMLMetadataImpl.setExperimenterDisplayName(OMEXMLMetadataImpl.java:7386)<br>
>> at loci.formats.meta.FilterMetadata.setExperimenterDisplayName(FilterMetadata.java:889)<br>
>> at loci.formats.in.ZeissLSMReader.initMetadata(ZeissLSMReader.java:1192)<br>
>> at loci.formats.in.ZeissLSMReader.initFile(ZeissLSMReader.java:520)<br>
>> at loci.formats.FormatReader.setId(FormatReader.java:1091)<br>
>> at loci.formats.ImageReader.setId(ImageReader.java:682)<br>
>> at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:492)<br>
>> at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:261)<br>
>> at mpicbg.imglib.io.LOCI.openLOCIFloatType(LOCI.java:638)<br>
>> at mpicbg.imglib.io.LOCI.openLOCIFloatType(LOCI.java:583)<br>
>> at mpicbg.imglib.io.LOCI.openLOCIFloatType(LOCI.java:573)<br>
>> at mpicbg.imglib.io.LOCI.openLOCIFloatType(LOCI.java:568)<br>
>> at fiji.plugin.Bead_Registration.getInteractiveDoGParameters(Bead_Registration.java:673)<br>
>> at fiji.plugin.Bead_Registration.getConfiguration(Bead_Registration.java:320)<br>
>> at fiji.plugin.Bead_Registration.access$100(Bead_Registration.java:40)<br>
>> at fiji.plugin.Bead_Registration$1.dialogItemChanged(Bead_Registration.java:208)<br>
>> at ij.gui.GenericDialog.showDialog(GenericDialog.java:1052)<br>
>> at fiji.plugin.Bead_Registration.singleChannel(Bead_Registration.java:265)<br>
>> at fiji.plugin.Bead_Registration.run(Bead_Registration.java:75)<br>
>> at ij.IJ.runUserPlugIn(IJ.java:185)<br>
>> at ij.IJ.runPlugIn(IJ.java:152)<br>
>><br>
>> --<br>
>> Please avoid top-posting, and please make sure to reply-to-all!<br>
>><br>
>> Mailing list web interface: <a href="http://groups.google.com/group/fiji-devel" target="_blank">http://groups.google.com/group/fiji-devel</a><br>
<br>
--<br>
Please avoid top-posting, and please make sure to reply-to-all!<br>
<br>
Mailing list web interface: <a href="http://groups.google.com/group/fiji-devel" target="_blank">http://groups.google.com/group/fiji-devel</a><br>
</div></div></blockquote></div><br></div>