[ome-devel] Cannot create loci.formats.in.FakeReader object in MATLAB bioformats

[Sebastien Besson (Staff)]

Hi,

Thanks for the additional information and notably including the MATLAB/Java version.

Bio-Formats 6.0.0 bumps the minimal supported Java version to 8 [1]. For MATLAB users, this means it is no longer possible to use old versions of MATLAB shipping JVM 7 natively with Bio-Formats 6. There are two possibilities:

- if possible, upgrading to MATLAB R2017b or later is recommended. R2017b is the first version which ships an embedded version of Java 8 [2]
- if upgrading is not a possibility, it should be possible to point MATLAB at a different JVM than the embedded  one [3].
I quickly tested the latter process on CentOS6/MATLAB R2013b to point at local JDK8 and was able to successfully load the Bio-Formats 6 toolbox.

Can you try one of these options and let us know if you encounter more issues?

From our side, we will clarify the impact of the Java bump for the MATLAB community in our technical documentation in an upcoming patch release. Thanks for bringing this problem to our attention.

Best,
Sebastien

[1] https://docs.openmicroscopy.org/bio-formats/6.0.0/about/whats-new.html
[2] https://mathworks.com/help/matlab/release-notes.html?rntext=Java&startrelease=R2017b&endrelease=R2017b&category=advanced-software-development&groupby=release&sortby=descending&searchHighlight=Java
[3] https://uk.mathworks.com/matlabcentral/answers/103056-how-do-i-change-the-java-virtual-machine-jvm-that-matlab-is-using-on-macos


On 21 Feb 2019, at 12:06, Biofysikos Biologos <biofysikos at gmail.com<mailto:biofysikos at gmail.com>> wrote:

Hi David,

Here are the results I get:
[status, version] = bfCheckJavaPath(true)

status =

 logical

  0


version =

 0×0 empty char array

and yes the .jar file is in the same folder as the rest of the MATLAB scripts.

Is it possible that my java version is not up to date? I am using R2017a.

version -java

ans =

   'Java 1.7.0_60-b19 with Oracle Corporation Java HotSpot(TM) 64-Bit
Server VM mixed mode'

Best,
Biofysikos

On Wed, Feb 20, 2019 at 3:04 PM David Gault (Staff)
<d.gault at dundee.ac.uk<mailto:d.gault at dundee.ac.uk>> wrote:

Hi Biofysikos,

It looks as though the bioformats_package jar is not part of the MATLAB path.
If you run the below it will quickly tell you if the jar can be found and if so which version.

[status, version] = bfCheckJavaPath(true)

Is the bioformats_package jar in the same folder as the rest of the MATLAB scripts?

With Thanks,
David Gault

On 19 Feb 2019, at 20:48, Biofysikos Biologos <biofysikos at gmail.com<mailto:biofysikos at gmail.com>> wrote:

Hello,

I have downloaded the latest Bioformats for MATLAB and it seems that
the .jar file is not loading.

The error I get is the following:

Error using bfopen (line 100)
Missing Bio-Formats library. Either add bioformats_package.jar to the
static Java path or add it to the Matlab path.

I have traced it to this line:

reader = javaObject('loci.formats.in.FakeReader');

Any help would be appreciated. Thanks.

Biofysikos
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