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Hi Kouichi,
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<div class="">thanks for the update and glad you found a workaround.</div>
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<div class="">I checked and the bfopen utility shipped with Bio-Formats 5.8.1 [1] is definitely</div>
<div class="">using the getSeriesMetadata() API as well.</div>
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<div class="">Reading the error and the problematic lines, I suspect your local copy of bfopen</div>
<div class="">is a modified version of the file shipped with the Bio-Formats MATLAB toolbox.</div>
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<div class="">For future issues, you might consider:</div>
<div class="">- either updating your code to consume the upstream bfopen function shipped with</div>
<div class=""> the toolbox and potentially wrap it with your custom functionality</div>
<div class="">- and/or share your version e.g. via GitHub to facilitate the troubleshooting.</div>
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<div class="">Best,</div>
<div class="">Sebastien</div>
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<div class="">[1] <a href="https://github.com/openmicroscopy/bioformats/blob/v5.8.1/components/formats-gpl/matlab/bfopen.m#L218" class="">
https://github.com/openmicroscopy/bioformats/blob/v5.8.1/components/formats-gpl/matlab/bfopen.m#L218</a></div>
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<blockquote type="cite" class="">
<div class="">On 27 Mar 2018, at 23:58, Kouichi C. Nakamura <<a href="mailto:kouichi.c.nakamura@gmail.com" class="">kouichi.c.nakamura@gmail.com</a>> wrote:</div>
<br class="Apple-interchange-newline">
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<div class="">Hi,</div>
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<div class="">Looking at <a href="https://github.com/ome/bio-formats-matlab/blob/51295373fc6a121c9ea94be686e86772cac4f23e/src/bfopen.m" class="">https://github.com/ome/bio-formats-matlab/blob/51295373fc6a121c9ea94be686e86772cac4f23e/src/bfopen.m</a>, the following
appears to fix the problem (bfopen worked with this change).</div>
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<div class=""> metadataList = r.getSeriesMetadata();</div>
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<div class="">Best,</div>
<div class="">Kouichi</div>
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<pre class="">To whom it may concern,
|<i class="">bfopen.m| does not work and issues an error as below:
</i>
|<i class=""> >> data = bfopen('Z:\xxxxx\xxxxx\Image000.png') Warning: Invalid file
</i>or directory 'D:\Fiji.app\scripts\..\plugins\loci_tools.jar'. > In
javaclasspath>local_validate_dynamic_path (line 271) In
javaclasspath>local_javapath (line 187) In javaclasspath (line 124) In
javaaddpath (line 71) In bfopen (line 103) APNGReader initializing
Z:\Analysis\Images from Otto\Image000.png Reading series #1 ...Undefined
function or variable 'getMetadata'. Error in bfopen (line 268)
metadataList = r.getMetadata(); 268 metadataList = r.getMetadata(); |
Output of |methods(loci.formats.ChannelSeparator)| or |methods(r)| does
not contain |getMetadata| method. I suspect that the method has been
recently renamed.
environments:
MATLAB Version: 9.4.0.813654 (R2018a)
Java 1.8.0_144-b01 with Oracle Corporation Java HotSpot(TM) 64-Bit
Server VM mixed mode
Bio-formats MATLAB toolbox 5.8.1 (2018 March 22)
Best regards,
Kouichi
--
Kouichi C. Nakamura, PhD
Senior Postdoctoral Neuroscientist
MRC Brain Network Dynamics Unit
University of Oxford
Mansfield Road, Oxford OX1 3TH, United Kingdom
+44-1865-271582 (office)
<a href="http://www.mrcbndu.ox.ac.uk/people/dr-kouichi-c-nakamura" class="">http://www.mrcbndu.ox.ac.uk/people/dr-kouichi-c-nakamura</a>
<a href="http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users" class="">kouichi.c.nakamura at gmail.com</a>
<a href="http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users" class="">kouichi.nakamura at pharm.ox.ac.uk</a></pre>
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