Re: Very recent problem opening OIB files

Posted by Melissa Linkert-2 on Apr 21, 2010; 4:01pm
URL: http://imagej.273.s1.nabble.com/Very-recent-problem-opening-OIB-files-tp3688529p3688530.html

Hi Pedro,

The error message that you reported was a known problem in several
recent trunk builds of Bio-Formats.  The problem was recently fixed,
so if you update to the very latest trunk build your files should open
correctly.

If upgrading does not solve the problem, then we would be happy to
investigate further, provided that you can send one of the problematic
files.  I can provide you with the LOCI FTP server information
off-list if you need a place to put the file.

Regards,
-Melissa

On Wed, Apr 21, 2010 at 9:50 AM, Vera, Pedro L. <[hidden email]> wrote:

> Hello:
>
> I'm using ImageJ 1.43t (java 1.6.0_20) with the Bio-Formats plugin to import different file formats. It has been working great for Olympus confocal microscope files with oib extensions.
>
> Today I noticed a problem. I had saved some files today and could not open them, but previous files (2 days ago) open fine. I can't find a difference in the files using the Nikon fluoview software, which works fine for today's and earlier files.
>
> When I try to open today's oib files, the Bioformats import window comes up and after clicking on my choices it disappears and I get the following errors:
>
> java.lang.NullPointerException
>  at java.util.Hashtable.get(Unknown Source)
>  at loci.formats.POITools.getFileSize(POITools.java:109)
>  at loci.formats.POITools.getDocumentStream(POITools.java:82)
>  at loci.formats.in.FV1000Reader.getFile(FV1000Reader.java:1306)
>  at loci.formats.in.FV1000Reader.initFile(FV1000Reader.java:750)
>  at loci.formats.FormatReader.setId(FormatReader.java:330)
>  at loci.plugins.importer.Importer.run(Importer.java:266)
>  at loci.plugins.LociImporter.run(LociImporter.java:77)
>  at ij.IJ.runUserPlugIn(IJ.java:184)
>  at ij.IJ.runPlugIn(IJ.java:151)
>  at ij.IJ.runPlugIn(IJ.java:140)
>  at HandleExtraFileTypes.openImage(HandleExtraFileTypes.java:241)
>  at HandleExtraFileTypes.run(HandleExtraFileTypes.java:37)
>  at ij.IJ.runUserPlugIn(IJ.java:184)
>  at ij.IJ.runPlugIn(IJ.java:151)
>  at ij.IJ.runPlugIn(IJ.java:140)
>  at ij.io.Opener.openWithHandleExtraFileTypes(Opener.java:405)
>  at ij.io.Opener.openImage(Opener.java:282)
>  at ij.io.Opener.openImage(Opener.java:301)
>  at ij.io.Opener.open(Opener.java:137)
>  at ij.io.Opener.open(Opener.java:65)
>  at ij.plugin.Commands.run(Commands.java:23)
>  at ij.IJ.runPlugIn(IJ.java:157)
>  at ij.Executer.runCommand(Executer.java:124)
>  at ij.Executer.run(Executer.java:61)
>  at java.lang.Thread.run(Unknown Source)
>
>
> Again, the key point is that this does not occur with oib files saved 2 days ago which points away from an ImageJ problem. I should also mention that this problem occurs either under Windows or Linux.
>
> Any suggestion would be appreciated.
>
> Regards,
>
> Pedro