[ome-users] Exception when loading vsi image

[Melissa Linkert]

Hi Robert,

> I am using loci_tools.jar to read vsi (and other image format) images. I recently ran into an exception when loading a vsi image, and it is now a recurring problem with some of our vsi images. To cancel out my own custom code, I have recreated the bug reported here by using loci_tools.jar as a plug-in via ImageJ. I get the same exception when using loci_tools.jar in ImageJ as with my custom code that calls the library directly.

Thank you for the detailed bug report.  I can reproduce the problem, and
have filed a ticket on our issue tracking system to fix it:

http://trac.openmicroscopy.org.uk/ome/ticket/10611

You have been CC'd on the ticket, and so will be automatically notified
when we update it.  If you prefer not to be notified, please let me
know.

Regards,
-Melissa

On Mon, Mar 25, 2013 at 06:15:32PM +0000, Robert Schuler wrote:
> Hello,
> 
> I am using loci_tools.jar to read vsi (and other image format) images. I recently ran into an exception when loading a vsi image, and it is now a recurring problem with some of our vsi images. To cancel out my own custom code, I have recreated the bug reported here by using loci_tools.jar as a plug-in via ImageJ. I get the same exception when using loci_tools.jar in ImageJ as with my custom code that calls the library directly.
> 
> Sample Image:
> 
> http://www.isi.edu/~schuler/vsi/bad.tar.gz
> 
> Versions:
> 
> ImageJ: 1.46r
> loci_tools.jar: 4.4.6 and Trunk
> Mac: OS X 10.7.5
> Linux: CentOS 5.5
> 
> Steps to recreate, from the ImageJ menu:
> 
> -> Plugins
> -> LOCI
> -> Bio-Formats Importer
> -> File dialog
>   -> select Lung_Mite.vsi
>   -> Open
> -> Bio-Formats Import Options Dialog
>   -> no changes to default settings
>   -> OK
> 
> Stack trace from the Exception window, using version 4.4.6:
> 
> java.lang.IllegalArgumentException
> 	at java.nio.Buffer.position(Buffer.java:216)
> 	at loci.common.NIOFileHandle.buffer(NIOFileHandle.java:535)
> 	at loci.common.NIOFileHandle.seek(NIOFileHandle.java:254)
> 	at loci.common.RandomAccessInputStream.seek(RandomAccessInputStream.java:140)
> 	at loci.formats.in.CellSensReader.readTags(CellSensReader.java:785)
> 	at loci.formats.in.CellSensReader.readTags(CellSensReader.java:826)
> 	at loci.formats.in.CellSensReader.readTags(CellSensReader.java:826)
> 	at loci.formats.in.CellSensReader.readTags(CellSensReader.java:826)
> 	at loci.formats.in.CellSensReader.readTags(CellSensReader.java:826)
> 	at loci.formats.in.CellSensReader.readTags(CellSensReader.java:826)
> 	at loci.formats.in.CellSensReader.readTags(CellSensReader.java:826)
> 	at loci.formats.in.CellSensReader.initFile(CellSensReader.java:355)
> 	at loci.formats.FormatReader.setId(FormatReader.java:1182)
> 	at loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:482)
> 	at loci.plugins.in.ImportProcess.execute(ImportProcess.java:146)
> 	at loci.plugins.in.Importer.showDialogs(Importer.java:141)
> 	at loci.plugins.in.Importer.run(Importer.java:79)
> 	at loci.plugins.LociImporter.run(LociImporter.java:81)
> 	at ij.IJ.runUserPlugIn(IJ.java:185)
> 	at ij.IJ.runPlugIn(IJ.java:152)
> 	at ij.Executer.runCommand(Executer.java:127)
> 	at ij.Executer.run(Executer.java:64)
> 	at java.lang.Thread.run(Thread.java:680)
> 
> After upgrading the plug-in to the Trunk build (on Mar 25 2013):
> 
> java.lang.IllegalArgumentException
> 	at java.nio.Buffer.position(Buffer.java:216)
> 	at ome.scifio.io.NIOFileHandle.buffer(NIOFileHandle.java:538)
> 	at ome.scifio.io.NIOFileHandle.seek(NIOFileHandle.java:257)
> 	at ome.scifio.io.RandomAccessInputStream.seek(RandomAccessInputStream.java:143)
> 	at loci.common.RandomAccessInputStream.seek(RandomAccessInputStream.java:108)
> 	at loci.formats.in.CellSensReader.readTags(CellSensReader.java:786)
> 	at loci.formats.in.CellSensReader.readTags(CellSensReader.java:827)
> 	at loci.formats.in.CellSensReader.readTags(CellSensReader.java:827)
> 	at loci.formats.in.CellSensReader.readTags(CellSensReader.java:827)
> 	at loci.formats.in.CellSensReader.readTags(CellSensReader.java:827)
> 	at loci.formats.in.CellSensReader.readTags(CellSensReader.java:827)
> 	at loci.formats.in.CellSensReader.readTags(CellSensReader.java:827)
> 	at loci.formats.in.CellSensReader.initFile(CellSensReader.java:355)
> 	at loci.formats.FormatReader.setId(FormatReader.java:1333)
> 	at loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:482)
> 	at loci.plugins.in.ImportProcess.execute(ImportProcess.java:146)
> 	at loci.plugins.in.Importer.showDialogs(Importer.java:141)
> 	at loci.plugins.in.Importer.run(Importer.java:79)
> 	at loci.plugins.LociImporter.run(LociImporter.java:81)
> 	at ij.IJ.runUserPlugIn(IJ.java:185)
> 	at ij.IJ.runPlugIn(IJ.java:152)
> 	at ij.Executer.runCommand(Executer.java:127)
> 	at ij.Executer.run(Executer.java:64)
> 	at java.lang.Thread.run(Thread.java:680)
> 
> Your help would be greatly appreciated.
> 
> Thanks,
> 
> RS
> 
> 
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