[ome-users] [Software Feedback] a question on Matlab code to read Bio-Format

[Melissa Linkert]

Hi Honglin,

> yes we are aware of this bug and it is currently being fixed.
> Briefly, bfGetReader is not automatically checking/adding loci_tools.jar to the Java class path right now. This explains your first error message.
> In the mean time, you can always add loci_tools.jar to your Java class path,
>  1) statically using >> edit classpath.txt (see header of bfopen)
>  2) dynamically using >> javaaddpath(path_to_loci_tools.jar);

Thanks to Sebastien, this problem should now be solved if you update to
the latest *.m files here:

http://loci.wisc.edu/bio-formats/matlab

If you continue to notice any problems, please let us know.

Regards,
-Melissa

On Thu, Apr 19, 2012 at 08:36:09AM +0000, Sebastien Besson wrote:
> Hi Honglin,
> 
> yes we are aware of this bug and it is currently being fixed.
> Briefly, bfGetReader is not automatically checking/adding loci_tools.jar to the Java class path right now. This explains your first error message.
> In the mean time, you can always add loci_tools.jar to your Java class path,
>  1) statically using >> edit classpath.txt (see header of bfopen)
>  2) dynamically using >> javaaddpath(path_to_loci_tools.jar);
> 
> Now the second error with bfopen is more suspicious. Do you always experience a Matlab crash when running bfopen. Or is it only once bfGetReder has failed?
> 
> Cheers,
> Sebastien
> 
> On 18 Apr 2012, at 20:18, Curtis Rueden wrote:
> 
> Hi Honglin,
> 
> I am forwarding your message to the OME-users mailing list.
> 
> -Curtis
> 
> 
> ---------- Forwarded message ----------
> From: <honglin.zhang at hiphealth.ca<mailto:honglin.zhang at hiphealth.ca>>
> Date: Wed, Apr 18, 2012 at 1:49 PM
> Subject: [Software Feedback] a question on Matlab code to read Bio-Format
> To: ctrueden at wisc.edu<mailto:ctrueden at wisc.edu>
> 
> 
> Honglin Zhang sent a message using the contact form at http://loci.wisc.edu/contact.
> 
> Hello,
> 
> I want to use your code for Matlab to read my data in Bio Format.  I downloaded bfopen, bfGetReader, bfGetPlane, and loci_tools.jar and saved them in the working directory according to the instructions.
> 
> If I run bfGetReader first, there will be an error message says:
> ??? Undefined variable "loci" or class "loci.common.DebugTools.enableLogging".
> 
> Error in ==> bfGetReader at 27
> loci.common.DebugTools.enableLogging('INFO');
> 
> If I run bfopen, a window will popped up and says "Matlab has encountered an internal problem and needs to close".  What do you think is the problem?
> 
> Thank you very much!
> 
> Cheers, Honglin
> 
> 
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