[ome-users] Newbee question bio-formats in Matlab

[Melissa Linkert]

Hi Claudia,

(I'm moving this thread back to the ome-users list, in case anyone
else is interested)

> But when I run
> Matlab with the bfopen-command I get the following error:
>
> This feature requires Java 1.2 or greater
> ??? Attempt to reference field of non-structure array.
>
> Error in ==> javaclasspath>local_javapath at 134
>     jArray = jloader.getClassPath;

This is certainly a confusing error message!  After a little bit of
searching, it looks like this error message occurs in certain Matlab
versions with Java 1.6 - see this post on Mathworks' Matlab forum:

http://www.mathworks.com/matlabcentral/newsreader/view_thread/160076

If upgrading to a more recent version of Matlab is not an option, then
downgrading to Java 1.5 (using the same installation procedure as
before) should solve the problem.

Regards,
-Melissa

On Thu, Jan 14, 2010 at 3:47 AM, Claudia Dach <cdach at gmx.de> wrote:
> Hi Melissa,
>
> thanks for your response. I did install the new Java-Version. And running
> the java -version command gives me a positive response. But when I run
> Matlab with the bfopen-command I get the following error:
>
> This feature requires Java 1.2 or greater
> ??? Attempt to reference field of non-structure array.
>
> Error in ==> javaclasspath>local_javapath at 134
>     jArray = jloader.getClassPath;
>
> Error in ==> javaclasspath at 60
>       p = local_javapath('-dynamic');
>
> Error in ==> javaaddpath at 51
>   javaclasspath( p, javaclasspath );
>
> Error in ==> bfopen at 30
> javaaddpath(fullfile(fileparts(mfilename('fullpath')),'loci_tools.jar'));
>
> So, Matlab still tells me that I work with an older Java version. Did I miss
> some steps I had to do in Matlab for running Matlab with a new Java version?
>
> Thanks a lot for your help!
> claudia
>
>
>
> -------- Original-Nachricht --------
> Datum: Wed, 13 Jan 2010 14:10:20 -0600
> Von: Melissa Linkert <melissa at glencoesoftware.com>
> An: Claudia Dach <cdach at gmx.de>
> CC: ome-users at lists.openmicroscopy.org.uk
> Betreff: Re: [ome-users] Newbee question bio-formats in Matlab
>
> Hi Claudia,
>
> The installation steps that you describe are correct - just to be
> sure, I tried them on a fresh install of Matlab 7.0.4, and was able
> to run the bfopen command without any problems.
>
> There are a few possible reasons for seeing this error message:
>
> - Matlab was not restarted after 'classpath.txt' was edited
> - changes 'classpath.txt' somehow did not get saved
> - the JVM being used by Matlab is version 1.4 or earlier
>
> To check the last possibility, run the "version -java" command;
> Bio-Formats requires Java 1.5 or later, so you will need to upgrade if
> the reported version number is 1.4 or lower. Instructions for
> upgrading Matlab's JVM are available here:
>
> http://www.mathworks.com/access/helpdesk/help/techdoc/matlab_external/f98533.html#f122001
>
> Please let us know if none of these suggestions solve the problem.
>
> Regards,
> -Melissa
>
> On Tue, Jan 12, 2010 at 8:48 AM, Claudia Dach <cdach at gmx.de> wrote:
>> Hi,
>>
>> there was already a topic of importing zvi-files to Matlab. I tried to do
>> it, but it didn't work. I saved the "loci_tools.jar" to
>> "C:\Programme\MATLAB_SV7\java\jar".
>>
>> In the "classpath.txt" which I found under the path
>> "C:\Programme\MATLAB_SV7\toolbox\local", I just added the line
>> "$matlabroot/java/jar/loci_tools.jar" (is this it what you meant with
>> updating?).
>>
>> The "bfopen.m"-file I saved under "C:\Programme\MATLAB_SV7\work".
>>
>> When I then type in the command "data=bfopen('C:\Hela.zvi')", I always get
>> back this error:
>>
>> ??? Undefined variable "loci" or class "loci.formats.ChannelFiller".
>>
>> Error in ==> bfopen at 43
>> r = loci.formats.ChannelFiller();
>>
>> Could you tell me which step I'm doing wrong?
>>
>> Thanks a lot!
>> claudia
>>
>>
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>
>
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