Open Microscopy Environment

Hi Jonathan,

jwarren wrote:OK - so there are at least two things going on here 1) thumbnails not showing if not accessed the render_image url before (occurs with any sized image) and 2) pyramids not created for some of the larger images.

What URL are you using for the thumbnails in 1)?

re: 2) I assume pyramids aren't generated _until_ render_image is called (plus some extra time).

To get over these I've written a python crawler to request the render_image urls so the thumbnails and if necessary pyramids are created and stored. This appears to be having the desired effect so I'm not going to spend time right now tracing any bug.

Fair enough.

So the waiting for pyramid to load is the standard behaviour for the larger images? So my crawler will be useful in future?

For the immediate future, yes. Pyramids are generated inherently asynchronously, so you could also trigger their creation immediately. There's not a background service for the thumbnails at the moment.

Cheers,
~Josh.

Hi,

Just an update: The thumbnail refreshing in web during pyramid generation should be fixed in 5.1.1 (out soon) with https://github.com/openmicroscopy/openm ... /pull/3750 and https://github.com/openmicroscopy/openm ... /pull/3713.

The strategy is for the thumbnail version to be set to -1 during pyramid generation.
During this time, web displays thumbnails with a random number as version:

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src=" <render_thumbnail_url>?version=<random>


so each time you refresh the dataset, the browser will request a new thumbnail for any unfinished images.
Once the pyramid is complete for a given image, requesting a thumbnail for it will generate a new thumbnail with version=0. The browser will then cache this until the version changes for some other reason.

Hope that helps.

Will.

Hi

I was just after an update of the current status of pyramid generation? We have version omero 5.1.3 at the moment and after weeks of uploading the images in the "normal" fashion -not in place import we have some images that don't have thumbnails. Can I check there is a background process creating pyramids or should I run my image crawler that requests urls like these to force pyramids to be created for each image we have uploaded?

/omero/webgateway/render_image/19052/

Any tips or pointers to relevant documentation welcome!

Cheers

Jonathan.

You can see if any Pyramids are being generated on the server by watching the PixelData log:

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$ tail -f var/log/PixelData-0.log


You might have missing thumbnails for images that imported successfully, in which case your crawler should work as before for kicking off pyramid / thumbnail generation.
If any of your images are quite large then the render_image/ url will ask the server to do a lot of work and this will probably fail over approx 12 k * 12 k.
A better solution seems to be using the /render_thumbnail/<iid>/ url, which seems to work for starting Pyramid generation (just tried this on latest development OMERO, but I don't think this has changed recently).
This will also be far less intensive for images that have already created thumbnails.

It's also possible that some imports have failed for some reason, in which case thumbnails won't be created, but hopefully this won't be the case.

I don't know of a docs page specifically about pyramids, but a search of the OME site for "pyramids" returns a bunch of results that you might find useful:
https://www.openmicroscopy.org/site/gsearch/?q=pyramid

Hope that helps,

Will.