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

[Sebastien Besson]

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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