Open Microscopy Environment

Hi,

I use the bioformats_package.jar in my java library, in order to read images.
But every time I read an image, I have a lot of information because the debug mode is on. See an example:

[main] DEBUG loci.common.IniParser - Line 1:
01:22:05.191 [main] DEBUG loci.common.IniParser - Line 2:
01:22:05.191 [main] DEBUG loci.common.IniParser - Line 3: [autoscale]
01:22:05.191 [main] DEBUG loci.common.IniParser - Line 4: type = boolean
01:22:05.191 [main] DEBUG loci.common.IniParser - Line 5: label = Autoscale
...

I have tens of those lines.

How can I stop the debug mode?
Thank you for your help!

Hi,

to tune the logging level, you should be able to use the DebugTools.enableLogging method.

As an example, this block shows how the command-line showinf tool sets the level to DEBUG when the -debug option is passed.

Sebastien

Thank you very much, that's exactly what I needed!!!

One last question (related).
Even when I set DebugTools.enableLogging ("OFF"), for one of my image, this information is display: Populating metadata
I tried to modify the ImporterOptions, but it didn't work.
Any idea?


[Edit] I tried to read a tif file containing a stack, and I got all these informations:

Reading header
Populating core metadata
Reading extended header
Populating original metadata
Populating OME metadata
Reading header
Populating original metadata
Populating OME metadata

I would really like shutdown all these informations.

Hi,

is the code you are using available publicly to help us debugging the issue here? Also can you give us more specifics about "one of my image": is this image from a different file format?

Sebastien

Hi,
the text I shared is the outputs displayed when I read the image, even when I set DebugTools.enableLogging ("OFF").
About the image, it is a TIFF file representing a stack with four channels.

So far the code I use is this simple line:

Code: Select all

ImagePlus[] images = BF.openImagePlus("...")  ;

Hi,

Would it be possible for you to upload this TIFF file to http://qa.openmicroscopy.org.uk/qa/upload?
On the code side, I understand you are using a custom Java code or a custom ImageJ/Fiji macro? Is the code on GitHub? Otherwise, could you upload it either as a Gist or as part of the TIFF upload (you should be able to zip files together and upload them as a zip)?

Best,
Sebastien

Hi,
thank you for your answer.
I don't use any custom java code, just the simple line I share in my previous post. I found the class BF to read images for ImageJ.
And my bad, the image is not a TIFF, but a DV. I only have this huge file to share right now, but it generates the text I was talking about: www.thibault.biz/Developpez/test.dv

Hi,

Thank you for submitting your file.
We were able to reproduce the issue locally and I have filed a ticket on this regard,
https://trac.openmicroscopy.org/ome/ticket/13151#ticket

This will get looked into at the earliest.

Best,
Balaji