What does this mean?

[Bas Jansen]

Hi:

When opening a .oib file in ImageJ, I get the following exception:

java.lang.NullPointerException
        at loci.plugins.Importer.displayStack(Importer.java:727)
        at loci.plugins.Importer.showStack(Importer.java:631)
        at loci.plugins.Importer.run(Importer.java:519)
        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(Thread.java:613)

I'm on a PowerBook G4, Mac OS X 10.4.11, and use ImageJ 1.40g and Java 1.5.0_13

Kind regards,
Bas

[Joachim Wesner]

Hi,

as nobody of the BIO-FORMATS people that AFAIK have written the oib reader
has answered yet, maybe the reader requires Java 6 (1.6)?

I could not find out on their website....

Just my 2 cents...

Joachim

ImageJ Interest Group <[hidden email]> schrieb am 06.06.2008 13:55:14:

> Hi:
>
> When opening a .oib file in ImageJ, I get the following exception:
>
> java.lang.NullPointerException
>    at loci.plugins.Importer.displayStack(Importer.java:727)
>    at loci.plugins.Importer.showStack(Importer.java:631)
>    at loci.plugins.Importer.run(Importer.java:519)
>    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(Thread.java:613)
>
> I'm on a PowerBook G4, Mac OS X 10.4.11, and use ImageJ 1.40g and Java
> 1.5.0_13
>
> Kind regards,
> Bas
> --
> View this message in context: http://www.nabble.com/What-does-this-
> mean--tp17688331p17688331.html
> Sent from the ImageJ mailing list archive at Nabble.com.

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[dscho]

Hi,

On Fri, 6 Jun 2008, Joachim Wesner wrote:

> as nobody of the BIO-FORMATS people that AFAIK have written the oib
> reader has answered yet, maybe the reader requires Java 6 (1.6)?

Typically, such an issue would be indicated by a class version mismatch,
not by a null pointer.  My guesss is that nobody can fix that without an
example image.  It's probably some expected field in the metadata that is
missing.

Ciao,
Dscho

[Melissa Linkert]

Hi,
This issue was fixed in the June 7 daily build of Bio-Formats.  I apologize
for not CC'ing the ImageJ list on that announcement - we received two copies
of this bug report, and while Bas received an email indicating that this was
fixed, I simply forgot to respond to the mailing list as well.

For those who are interested, the issue was that the Bio-Formats importer
was trying to retrieve the title of a non-existent image window.

Regards,
-Melissa

On Sat, Jun 7, 2008 at 9:45 AM, Johannes Schindelin <
[hidden email]> wrote:

> Hi,
>
> On Fri, 6 Jun 2008, Joachim Wesner wrote:
>
> > as nobody of the BIO-FORMATS people that AFAIK have written the oib
> > reader has answered yet, maybe the reader requires Java 6 (1.6)?
>
> Typically, such an issue would be indicated by a class version mismatch,
> not by a null pointer.  My guesss is that nobody can fix that without an
> example image.  It's probably some expected field in the metadata that is
> missing.
>
> Ciao,
> Dscho
>