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ome / omero-iviewer

An OMERO.web app allowing to view images
https://www.openmicroscopy.org/omero/iviewer/
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Tiling threshold max projection bytes #349

Closed will-moore closed 3 years ago

will-moore commented 4 years ago

Fixes #341.

This boosts the "Big Image" (use tiles) threshold in iviewer from 2k 2k to `2048 2048. Also, it makes iviewer respect the value of the server config:omero config set omero.pixeldata.max_projection_bytes. So, if you boost this value on the server, iviewer will use that value, instead of needing to also update the corresponding config ofomero.web.iviewer.max_projection_bytes` in iviewer.

To test, an image should be enabled for projection in iviewer IF...

With default settings:

If omero.web.iviewer.max_projection_bytes setting is set to LESS than omero.pixeldata.max_projection_bytes then this lower threshold will be used:

jburel commented 4 years ago

https://merge-ci.openmicroscopy.org/web/webclient/img_detail/138051/?dataset=24051 (user3) has a dimension of 2048 x 2044 and 31 z-sections. The projection is not enabled

will-moore commented 4 years ago

The default max_projection_bytes on the server and iviewer is 1024 * 1024 * 256. So if you have a 2048 x 2048 x 31 image then you are only allowed 2 bytes per pixel. e.g. a 2-channel 8-bit image. That image above has 4 channels of uint16 so it is quite a bit over that threshold.

We need to test setting of a higher values for omero.pixeldata.max_projection_bytes on the merge-ci server.

jburel commented 4 years ago

That does not match an image of 2048 x 2048 should be enabled for Max-intensity projection

will-moore commented 4 years ago

OK, sorry - I forgot to say that it still has to be below the max_projection_bytes threshold, which is quite a low cut-off for images that are 2048 x 2048, as discussed at https://github.com/ome/omero-iviewer/issues/341#issuecomment-677465843

So, if we leave the omero.pixeldata.max_projection_bytes at the default setting then we need an image of just the right size to test that smaller 2048 x 2048 images can be projected. But we also need to test that different settings are respected by iviewer (and the server) to allow bigger images to be projected.

imagesc-bot commented 3 years ago

This pull request has been mentioned on Image.sc Forum. There might be relevant details there:

https://forum.image.sc/t/z-projection-disabled-big-images/26125/7

jburel commented 3 years ago

retested, it works as expected Thanks

sbesson commented 3 years ago

See https://github.com/IDR/deployment/pull/322#issuecomment-808046899 for a compatibility issue with OMERO.server 5.6.0

imagesc-bot commented 3 years ago

This pull request has been mentioned on Image.sc Forum. There might be relevant details there:

https://forum.image.sc/t/z-projection-disabled-in-viewers-for-big-images/54181/2

imagesc-bot commented 3 years ago

This pull request has been mentioned on Image.sc Forum. There might be relevant details there:

https://forum.image.sc/t/maximum-intensity-projection-feature-in-omero-web/54392/2