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Bug 458 - LOCI Import Problem
LOCI Import Problem
Status: RESOLVED FIXED
Product: Fiji
Classification: Unclassified
Component: Plugins
unspecified
PC Windows
: P2 major
Assigned To: ImageJ Bugs Mailing List
Depends on:
Blocks:
 
Reported: 2012-07-31 15:46 CDT by Sebastian Rhode
Modified: 2012-08-02 22:14 CDT
2 users (show)

See Also:
Description Sebastian Rhode 2012-07-31 15:46:18 CDT 
Hi,

I tried to open a tiff image file using the LOCI Import. and got the following error message:

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 ij.IJ.run(IJ.java:251)
	at ij.IJ.run(IJ.java:229)
	at ij.macro.Functions.doRun(Functions.java:581)
	at ij.macro.Functions.doFunction(Functions.java:82)
	at ij.macro.Interpreter.doStatement(Interpreter.java:216)
	at ij.macro.Interpreter.doStatements(Interpreter.java:204)
	at ij.macro.Interpreter.run(Interpreter.java:103)
	at ij.macro.Interpreter.run(Interpreter.java:73)
	at ij.macro.MacroRunner.run(MacroRunner.java:130)
	at java.lang.Thread.run(Thread.java:662)
Caused by: java.lang.NoSuchMethodError: ome.xml.model.Image.getAcquiredDate()Ljava/lang/String;
	at loci.formats.ome.OMEXMLMetadataImpl.getImageAcquiredDate(OMEXMLMetadataImpl.java:2068)
	at loci.formats.in.OMETiffReader.initFile(OMETiffReader.java:345)
	at loci.formats.FormatReader.setId(FormatReader.java:1091)
	at loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:480)
	at loci.plugins.in.ImportProcess.execute(ImportProcess.java:144)
	at loci.plugins.in.Importer.showDialogs(Importer.java:139)
	at loci.plugins.in.Importer.run(Importer.java:77)
	at loci.plugins.LociImporter.run(LociImporter.java:79)
	at ij.IJ.runUserPlugIn(IJ.java:185)
	at ij.IJ.runPlugIn(IJ.java:152)
	... 17 more

It should be the latest version of the LOCI.

Sebi
Comment 1 Melissa Linkert 2012-07-31 15:53:26 CDT 
This is the same as what was reported here:

https://groups.google.com/forum/?fromgroups#!topic/fiji-devel/frm00CCOe_g

Which is to say, the issue is that there are two mismatched versions of Bio-Formats present.
Comment 2 Sebastian Rhode 2012-07-31 16:37:02 CDT 
Hi melissa,

I also ried to update Loci to the daily build and got during the update process:

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:662)
Caused by: java.lang.NegativeArraySizeException
	at loci.formats.UpgradeChecker.install(UpgradeChecker.java:274)
	at loci.plugins.Updater.install(Updater.java:96)
	at loci.plugins.Updater.run(Updater.java:85)
	at ij.IJ.runUserPlugIn(IJ.java:185)
	at ij.IJ.runPlugIn(IJ.java:152)
	... 8 more

And you are right, I have loci_tools.jar (in plugins) and loci-common-4.4-SNAPSHOT.jar (in jars).

But if I remove the one from the jars folder, the update process still does not work and neither does the import an image works. And if I remove the loci_tools.jar, I can not use the loci import any more ...

Cheers,

Sebi
Comment 3 Curtis Rueden 2012-07-31 16:44:23 CDT 
My understanding is that this is a bug in the current plugin dependency structure. There are some plugins that depend one flavor of Bio-Formats (loci_tools.jar), and others that depend on another flavor (individual JARs including loci_plugins.jar, bio-formats.jar, scifio.jar, etc.).

So I think the fix will be for the Bio-Formats & Fiji maintainers (i.e., Dscho & me) to update the Fiji build system to only build the individual Bio-Formats JARs instead of loci_tools.jar, and then update the plugin dependency tree to use only those.

The weird thing is that I cannot duplicate this problem on my Mac OS X system: after fully updating Fiji, I have only loci_tools.jar and not any of the individual JARs present.

Sebastian, what is your operating system?
Comment 4 Curtis Rueden 2012-07-31 16:47:25 CDT 
Also, are you having this problem with a developer install (i.e., built from source) or a user install (i.e., downloaded bundle from fiji.sc)?
Comment 5 Sebastian Rhode 2012-07-31 16:51:05 CDT 
Hi,

I just downloaded fiji today from the website:

http://jenkins.imagej.net/job/Stable-Fiji/lastSuccessfulBuild/artifact/fiji-nojre.zip

to have the latest versuion due some other issues I was trying to sort out. and then I addes the java folder from my old fiji to have the jre´s.

I use Windows7, 64bit.

Sebi
Comment 6 Sebastian Rhode 2012-08-01 09:41:40 CDT 
Hi guys,

when I use the latest download from

http://jenkins.imagej.net/job/Stable-Fiji/lastSuccessfulBuild/artifact/fiji-nojre.zip

it contains the loci_tools.jar as well as the individual jars. So whar should I do?

Sebi
Comment 7 Johannes Schindelin 2012-08-01 19:05:06 CDT 
Sorry, that is my mistake. I actually fixed it yesterday but was short on time to actually upload the fixed updater. The problem is that the updater would keep the locally-cached database of available files and not update files as being obsolete now.

To work around this, you can safely delete loci_tools.jar from your fiji-nojre for now, while I am busy trying to get a procedure in place that makes uploading a new updater easier than it is right now.
Comment 8 Johannes Schindelin 2012-08-02 22:14:41 CDT 
This is now fixed.