[ome-users] bfopen error

[Kouichi C. Nakamura]

Hi,

Looking at https://github.com/ome/bio-formats-matlab/blob/51295373fc6a121c9ea94be686e86772cac4f23e/src/bfopen.m <https://github.com/ome/bio-formats-matlab/blob/51295373fc6a121c9ea94be686e86772cac4f23e/src/bfopen.m>, the following appears to fix the problem (bfopen worked with this change).

  metadataList = r.getSeriesMetadata();

Best,
Kouichi


> To whom it may concern,
> 
> |bfopen.m| does not work and issues an error as below:
> 
> | >> data = bfopen('Z:\xxxxx\xxxxx\Image000.png') Warning: Invalid file 
> 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)
> http://www.mrcbndu.ox.ac.uk/people/dr-kouichi-c-nakamura <http://www.mrcbndu.ox.ac.uk/people/dr-kouichi-c-nakamura>
> kouichi.c.nakamura at gmail.com <http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users>
> kouichi.nakamura at pharm.ox.ac.uk <http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users>
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