Open Microscopy Environment

Hi

I am using the bioformats macro extension 'openImagePlus' in a macro that I am running from the command line using headless Fiji, and I am seeing different behaviour between a mac and linux os. When running on mac I see

[INFO ] OMETiffReader initializing

On linux I see a much more verbose output, and eventually get messages like this

[Run$_main] DEBUG loci.formats.FormatHandler - Plane[1]

for every plane. This seems to make the macro run much slower under linux (where I eventually want to work).

Any thoughts about why this happens and how I can stop it?

Cheers,

Dan.

P.S. Bioformats is up to date (5.0.4) and I tried a daily build version as well.

Hi,

Looks like something on your Linux machine is setting the log level to DEBUG (instead of the default INFO).

Two suggestions,
1) Can you check your Fiji updater and see if there are any differences between the two cases?
2) Please check if you have one of the following files (within your FIJI directory),
log4j.properties, log4j.xml, or logback.xml and check for the following lines

</appender>
<logger name="ome.formats" level="INFO"/>
<logger name="ome.client" level="WARN"/>
<logger name="org.apache" level="WARN"/>
<logger name="org.springframework" level="WARN"/>
<logger name="net.sf.ehcache" level="ERROR"/>
<logger name="loci" level="INFO"/>
<logger name="ome.system" level="WARN"/>
<root level="debug">

Changing the log levels (from DEBUG to INFO, in these files) might solve your problem.

Please let us know if you the problem persists (Despite making these changes).

Best,
Balaji

Hi Balaji

Thanks for the response. Sorted now but maybe I don't quite understand how the Fiji/Bioformats updaters work. The Bioformats plugin was telling me I had the same version installed (on Mac compared to Linux) but the thing that was different in my Fiji updaters were that I was using the "Bioformats 5" update site in the Mac version of Fiji but not the Linux version.

Cheers,

Dan.

Hi Dan,

Glad that the suggestion worked.

reg : The Bio-formats version,
The plugin details should also mention the revision number of Bioformats :
If the configuration of FIJI updater was different between the two cases, then you should have seen a different revision number of Bioformats (between Linux and Mac).

ex : Bio-Formats Plugins for ImageJ, revision 193047d, built 6 November 2014
Release : 5.0.5-DEV

Please check this part "revision 193047d, built 6 November 2014 " (this should have been different between the two cases)

Best,
Balaji