[ome-users] NumberFormatException import .zvi file

[Jason Swedlow]

Hi Susan-

On 24 Sep 2008, at 21:54, Curtis Rueden wrote:

> Hi Susan,
>
> I downloaded the latest trunk build of the loci_tools.jar and  
> placed it in the plugins folder and re-ran ImageJ.  The LOCI  
> Bioformats Importer gives the same error on that zvi file that  
> OMERO.insight does.
>
> Strange; I checked the source code and it should not be generating  
> this error. Would you be willing to send us the problematic file  
> for us to use for debugging? Once we have the problem solved in Bio- 
> Formats, the next version of OMERO.importer will also incorporate  
> the fix -- or I can provide you with instructions on how to update  
> your existing version of OMERO.importer if you like.
>

Can you let us know which version of Zeiss software produced the  
file.  We test .zvi files before every release, but our testing is  
only as good and as up-to-date as our test files, so knowing which  
versions are giving us problems is very helpful.

Thanks!

Cheers,

Jason


> -Curtis
>
> On Wed, Sep 24, 2008 at 3:48 PM, Susan Wilson  
> <smwilson at hpc.unm.edu> wrote:
> Hi again,
>
> I downloaded the latest trunk build of the loci_tools.jar and  
> placed it in the plugins folder and re-ran ImageJ.  The LOCI  
> Bioformats Importer gives the same error on that zvi file that  
> OMERO.insight does.
>
> Susan
>
> On Sep 24, 2008, at 2:20 PM, Curtis Rueden wrote:
>
>> Hi Susan,
>>
>> That exception looks like a bug in Bio-Formats to me. Are you able  
>> to import the ZVI file into ImageJ using the Bio-Formats Importer  
>> plugin (http://www.loci.wisc.edu/ome/formats-imagej.html) with the  
>> latest trunk build (http://www.loci.wisc.edu/ome/formats- 
>> download.html)?
>>
>> -Curtis
>>
>> On Wed, Sep 24, 2008 at 3:09 PM, Susan Wilson  
>> <smwilson at hpc.unm.edu> wrote:
>> Hi,
>>
>> Runniing Beta3.0.1 all around.  This is the error I get when I  
>> attempt
>> to import a .zvi file:
>>
>> java.lang.NumberFormatException: For input string: "9/17/2008 7:05:39
>> PM"
>>        at
>> java
>> .lang.NumberFormatException.forInputString 
>> (NumberFormatException.java:
>> 48)
>>        at java.lang.Long.parseLong(Long.java:412)
>>        at java.lang.Long.parseLong(Long.java:461)
>>        at loci.formats.in.ZeissZVIReader.initMetadata 
>> (ZeissZVIReader.java:623)
>>        at loci.formats.in.ZeissZVIReader.initFile 
>> (ZeissZVIReader.java:513)
>>        at loci.formats.FormatReader.setId(FormatReader.java:216)
>>        at loci.formats.ImageReader.setId(ImageReader.java:565)
>>        at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:71)
>>        at loci.formats.ChannelFiller.setId(ChannelFiller.java:186)
>>        at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:71)
>>        at loci.formats.ChannelSeparator.setId 
>> (ChannelSeparator.java:61)
>>        at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:71)
>>        at ome.formats.importer.ImportLibrary.open 
>> (ImportLibrary.java:181)
>>        at ome.formats.importer.ImportLibrary.importImage 
>> (ImportLibrary.java:
>> 355)
>>        at ome.formats.importer.ImportHandler.importImages 
>> (ImportHandler.java:
>> 172)
>>        at ome.formats.importer.ImportHandler.access$0 
>> (ImportHandler.java:106)
>>        at ome.formats.importer.ImportHandler$1.run 
>> (ImportHandler.java:87)
>>
>> Also, I may be crazy, but the documentation for OMERO.insight does  
>> not
>> match what I am seeing.  This error is on my MAC to OMERO.server on
>> debian.  I downloaded and ran both (linux) importer and insight on  
>> the
>> localhost debian host and got the same importer error and the same
>> insight application.  Help/About shows Beta3.0.1, which is the server
>> I am running, but insight has no categories, no "Browse Button"...
>> And importer won't import the zvi on either platform.
>>
>> Thanks.
>> Susan
>> _______________________________________________
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>> ome-users at lists.openmicroscopy.org.uk
>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>>
>
>
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