[ome-users] bfopen error

[Sebastien Besson (Staff)]

Hi Kouichi,

thanks for the update and glad you found a workaround.

I checked and the bfopen utility shipped with Bio-Formats 5.8.1 [1] is definitely
using the getSeriesMetadata() API as well.

Reading the error and the problematic lines, I suspect your local copy of bfopen
is a modified version of the file shipped with the Bio-Formats MATLAB toolbox.

For future issues, you might consider:
- either updating your code to consume the upstream bfopen function shipped with
  the toolbox and potentially wrap it with your custom functionality
- and/or share your version e.g. via GitHub to facilitate the troubleshooting.

Best,
Sebastien

[1] https://github.com/openmicroscopy/bioformats/blob/v5.8.1/components/formats-gpl/matlab/bfopen.m#L218


On 27 Mar 2018, at 23:58, Kouichi C. Nakamura <kouichi.c.nakamura at gmail.com<mailto:kouichi.c.nakamura at gmail.com>> wrote:

Hi,

Looking at 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
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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