[ome-users] Exception when loading vsi image

[Melissa Linkert]

Hi Robert,

> Just wondering if you had any idea whether this bug would get scheduled to be fixed? Or if there is any additional information or sample data we could provide in order to be of assistance?
>

No additional information is necessary; this will be fixed with next
week's 4.4.7 release of Bio-Formats.

Regards,
-Melissa

On Fri, Apr 12, 2013 at 03:53:13PM +0000, Robert Schuler wrote:
> Hi Melissa,
> 
> Just wondering if you had any idea whether this bug would get scheduled to be fixed? Or if there is any additional information or sample data we could provide in order to be of assistance?
> 
> Thank you,
> 
> RS
> 
> On Mar 26, 2013, at 4:59 PM, Melissa Linkert <melissa at glencoesoftware.com> wrote:
> 
> > 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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> >> ome-users at lists.openmicroscopy.org.uk
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> > 
> 
>