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Hi Honglin,
<div><br>
</div>
<div>yes we are aware of this bug and it is currently being fixed. </div>
<div>Briefly, bfGetReader is not automatically checking/adding loci_tools.jar to the Java class path right now. This explains your first error message. </div>
<div>In the mean time, you can always add loci_tools.jar to your Java class path,</div>
<div> 1) statically using >> edit classpath.txt (see header of bfopen)</div>
<div> 2) dynamically using >> javaaddpath(path_to_loci_tools.jar); </div>
<div><br>
</div>
<div>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?</div>
<div><br>
</div>
<div>Cheers,</div>
<div>Sebastien</div>
<div><br>
</div>
<div>
<div>On 18 Apr 2012, at 20:18, Curtis Rueden wrote:</div>
<br class="Apple-interchange-newline">
<blockquote type="cite">Hi Honglin,<br>
<br>
I am forwarding your message to the OME-users mailing list.<br>
<br>
-Curtis<br>
<br>
<br>
<div class="gmail_quote">---------- Forwarded message ----------<br>
From: <b class="gmail_sendername"></b><span dir="ltr"><<a href="mailto:honglin.zhang@hiphealth.ca">honglin.zhang@hiphealth.ca</a>></span><br>
Date: Wed, Apr 18, 2012 at 1:49 PM<br>
Subject: [Software Feedback] a question on Matlab code to read Bio-Format<br>
To: <a href="mailto:ctrueden@wisc.edu">ctrueden@wisc.edu</a><br>
<br>
<br>
Honglin Zhang sent a message using the contact form at <a href="http://loci.wisc.edu/contact" target="_blank">
http://loci.wisc.edu/contact</a>.<br>
<br>
Hello,<br>
<br>
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.<br>
<br>
If I run bfGetReader first, there will be an error message says:<br>
??? Undefined variable "loci" or class "loci.common.DebugTools.<u></u>enableLogging".<br>
<br>
Error in ==> bfGetReader at 27<br>
loci.common.DebugTools.<u></u>enableLogging('INFO');<br>
<br>
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?<br>
<br>
Thank you very much!<br>
<br>
Cheers, Honglin<br>
<br>
</div>
<br>
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</blockquote>
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