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GReD-Clermont / omero_batch-plugin

GNU General Public License v2.0
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Error: "INFORMATION: Warning: there is no new image." No saving of the new images #11

Closed JensWendt closed 2 years ago

JensWendt commented 2 years ago

Hello,

I was made aware of this script by Pierre Pouchin in the recent OMERO admin meeting. I love the functionality and the GUI. But unfortunately I am getting an error while trying to process a small dataset and saving it both to local or OMERO.

Mär 28, 2022 12:40:59 PM fr.igred.ij.macro.OMEROBatchRunner save
INFORMATION: Warning: there is no new image.

The log does not display any more information. Do you have any ideas on what might be the cause? Additional info: I downloaded the latest OMERO plugin for Fiji (5.7.0) and our server runs on 5.6.3. I do not think that the version discrepancy between plugin and server plays a role, as the exact same error occurs while trying to save the images locally.

Best regards

Jens

ppouchin commented 2 years ago

Hello,

Sorry to come back to you this late: I did not receive any notification from Github, and so your issue went unnoticed.

This message normally indicates that the macro does not produce a new image, but only works on the original one. To clarify, the batch plugin only saves images that remain open in ImageJ at the end of the macro.

To prevent re-importing the original image each time, we skip the image that was opened from OMERO in the first place, otherwise users could quickly fill the server with duplicates. (Maybe I should look if ImageJ provides a way to check whether the image has been modified or not, but I doubt it is possible.)

One way to circumvent this is to duplicate the original image in the macro, if it is possible: run("Duplicate...", "title=result duplicate");

However, I might misinterpret the cause of the problem. How does your macro work? Are the new images left open, or are they saved on disk?

JensWendt commented 2 years ago

Hello Pierre,

You were spot on. I just had a small test macro running two filters over the image, basically just modifiying the original image. I did not read the line "Only new images will be saved..." from the readme.md with the meaning you explained. Thank you.