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Very recent problem opening OIB files

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Very recent problem opening OIB files

Vera, Pedro L.
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
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Re: Very recent problem opening OIB files

Vera, Pedro L.
I found a workaround, which is to save the files as .oif rather than .oib and ImageJ can open those. I still would like to find out what happened though.

Thanks.

Pedro
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Re: Very recent problem opening OIB files

Melissa Linkert-2
In reply to this post by Vera, Pedro L.
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
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Re: Very recent problem opening OIB files

Vera, Pedro L.
Hi Melissa:
Thanks for your suggestion. I tried both the daily build and the stable one and neither one worked. I would be happy to send you one of the files in question, if you provide me with the ftp server. I won't probably load it until tonight though.

Thanks.

Pedro
________________________________________
From: ImageJ Interest Group [[hidden email]] On Behalf Of Melissa Linkert [[hidden email]]
Sent: Wednesday, April 21, 2010 12:01 PM
To: [hidden email]
Subject: Re: Very recent problem opening OIB files

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
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Re: Very recent problem opening OIB files

Glen MacDonald-2
Pedro,
What version of Fluoview is running your confocal?  Versions prior to 2.0 would occasionally throw an OIB that no other software can open.  They could be opened only by Fluoview.  Because of this, I stick with the OIF format.  But, if the current build of the LOCI plugin has fixed the recent problems then I will test them with OIB files from newer FV versions.

Regards,
Glen

Glen MacDonald
Core for Communication Research
Virginia Merrill Bloedel Hearing Research Center
Box 357923
University of Washington
Seattle, WA 98195-7923  USA
(206) 616-4156
[hidden email]








On Apr 21, 2010, at 10:08 AM, Vera, Pedro L. wrote:

> Hi Melissa:
> Thanks for your suggestion. I tried both the daily build and the stable one and neither one worked. I would be happy to send you one of the files in question, if you provide me with the ftp server. I won't probably load it until tonight though.
>
> Thanks.
>
> Pedro
> ________________________________________
> From: ImageJ Interest Group [[hidden email]] On Behalf Of Melissa Linkert [[hidden email]]
> Sent: Wednesday, April 21, 2010 12:01 PM
> To: [hidden email]
> Subject: Re: Very recent problem opening OIB files
>
> 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
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