[ome-users] Exception when loading vsi image

[Robert Schuler]

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