Posted by
Fong Koh on
Jun 04, 2008; 8:08am
URL: http://imagej.273.s1.nabble.com/oib-reader-tp3696051p3696054.html
Hi Melissa and Aparna,
I face a similar error as Aparna, so here goes:
1. OS: Windows XP Pro SP2
2. Java: Sun Java 6 Update 6 (Java SE Development Kit 6u6)
3. ImageJ: 1.40g
Not sure if you want an oib image file from me too. Email me anytime for it.
I can open Zeiss LSM 510 .lsm files with no errors. Thanks for your help!
Error when I use File->Open->myfile.oib:
java.util.NoSuchElementException
at java.util.StringTokenizer.nextToken(Unknown Source)
at loci.formats.POITools.setupFile(POITools.java:197)
at loci.formats.POITools.getFileSize(POITools.java:114)
at loci.formats.POITools.getDocumentStream(POITools.java:89)
at loci.formats.in.FV1000Reader.initFile(FV1000Reader.java:230)
at loci.formats.FormatReader.setId(FormatReader.java:633)
at loci.formats.FormatHandler.setId(FormatHandler.java:134)
at loci.plugins.Importer.run(Importer.java:145)
at loci.plugins.LociImporter.run(LociImporter.java:74)
at ij.IJ.runUserPlugIn(IJ.java:158)
at ij.IJ.runPlugIn(IJ.java:124)
at ij.IJ.runPlugIn(IJ.java:113)
at HandleExtraFileTypes.openImage(HandleExtraFileTypes.java:253)
at HandleExtraFileTypes.run(HandleExtraFileTypes.java:37)
at ij.IJ.runUserPlugIn(IJ.java:158)
at ij.IJ.runPlugIn(IJ.java:124)
at ij.IJ.runPlugIn(IJ.java:113)
at ij.io.Opener.openWithHandleExtraFileTypes(Opener.java:304)
at ij.io.Opener.openImage(Opener.java:233)
at ij.io.Opener.openImage(Opener.java:249)
at ij.io.Opener.open(Opener.java:116)
at ij.io.Opener.open(Opener.java:55)
at ij.plugin.Commands.run(Commands.java:23)
at ij.IJ.runPlugIn(IJ.java:131)
at ij.Executer.runCommand(Executer.java:104)
at ij.Executer.run(Executer.java:58)
at java.lang.Thread.run(Unknown Source)
A slightly different error when I use Plugins->LOCI->Bioformats Importer->myfile.oib
java.util.NoSuchElementException
at java.util.StringTokenizer.nextToken(StringTokenizer.java:332)
at loci.formats.POITools.setupFile(POITools.java:197)
at loci.formats.POITools.getFileSize(POITools.java:114)
at loci.formats.POITools.getDocumentStream(POITools.java:89)
at loci.formats.in.FV1000Reader.initFile(FV1000Reader.java:230)
at loci.formats.FormatReader.setId(FormatReader.java:633)
at loci.formats.FormatHandler.setId(FormatHandler.java:134)
at loci.plugins.Importer.run(Importer.java:145)
at loci.plugins.LociImporter.run(LociImporter.java:74)
at ij.IJ.runUserPlugIn(IJ.java:158)
at ij.IJ.runPlugIn(IJ.java:124)
at ij.Executer.runCommand(Executer.java:104)
at ij.Executer.run(Executer.java:58)
at java.lang.Thread.run(Thread.java:619)
aparna sadananda wrote
Hi Melissa!
I am furnishing the details you had asked for:
1) OS- Windows Vista Home Basic
2) Java Plugin 1.1
3) Image J version- 1.37v.
The contents of the exception window that I get while opening an oib file
are:
java.util.NoSuchElementException
at java.util.StringTokenizer.nextToken(Unknown Source)
at loci.formats.POITools.setupFile(POITools.java:197)
at loci.formats.POITools.getFileSize(POITools.java:114)
at loci.formats.POITools.getDocumentStream(POITools.java:89)
at loci.formats.in.FV1000Reader.initFile(FV1000Reader.java:230)
at loci.formats.FormatReader.setId(FormatReader.java:633)
at loci.formats.FormatHandler.setId(FormatHandler.java:134)
at loci.plugins.Importer.run(Importer.java:145)
at loci.plugins.LociImporter.run(LociImporter.java:74)
at ij.IJ.runUserPlugIn(IJ.java:266)
at ij.IJ.runPlugIn(IJ.java:120)
at ij.Executer.runCommand(Executer.java:95)
at ij.Executer.run(Executer.java:49)
at java.lang.Thread.run(Unknown Source)
I will send the 13.2 mb oib file in a separate mail.
Regards,
Aparna
On Sat, May 24, 2008 at 6:40 PM, Melissa Linkert <linkert@wisc.edu> wrote:
> Hi Aparna,
> I'm sorry to hear that Bio-Formats is not working correctly for you. We
> (the Bio-Formats developers) would be happy to fix this, but we need a
> little more information first.
>
> First of all, are you using the latest release of Bio-Formats (dated 17
> April, 2008)? If not, please upgrade to the latest version and see if the
> problem is fixed. To check the version, select "About>Plugins>LOCI
> Plugins"
> in ImageJ.
>
> If you are using the latest version of Bio-Formats, please supply the
> following information:
>
> 1) the operating system that you are using
> 2) the version of Java that you are using
> 3) the version of ImageJ that you are using
> 4) the exact contents of the "Exception" window - either a screenshot, or
> copy-and-pasted text
> 5) if possible, an OIB file that produces this problem (I will send details
> in a private email)
>
> Regards,
> -Melissa
>
> On Fri, May 23, 2008 at 12:08 PM, aparna sadananda <
> aparnasadananda@gmail.com> wrote:
>
> > Hi all,
> > I wish to open files of the oib format using Image J. For this, I
> > downloaded
> > the Bioformats reader and installed the zipped file in the Plugins folder
> > of
> > Image J files. To open the oib format file, I click on the plugins menu,
> > then the Loci tab followed by Bioformats importer. Then I browse for the
> > oib
> > file and click open. On doing this, I get a window titled "Exception".
> > Can anyone tell me, where I am wrong and how I can get Bioformats reader
> to
> > read my oib files?
> >
> > Thanks in Advance,
> > Aparna.
> >
>