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…nto a computed field in the CLEM model instead
…set of a pre-existing one, and to overwrite existing ImagingSite database entry if it is
…dantic model when registering things in the databases
…re that the ISPyB entries all register the denoised datasets in their final state
This reverts commit 1f224ab.
tieneupin
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enhancement
Codecov Report❌ Patch coverage is Additional details and impacted files@@ Coverage Diff @@
## main #776 +/- ##
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+ Coverage 48.89% 48.99% +0.10%
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Files 94 94
Lines 10008 10026 +18
Branches 1326 1328 +2
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+ Hits 4893 4912 +19
Misses 4860 4860
+ Partials 255 254 -1 🚀 New features to boost your workflow:
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stephen-riggs
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Apr 7, 2026
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This all looks fine to me.
You make an assumption that the thumbnail and image sizes will be the same for the raw and denoised data, but that seems reasonable.
…fields when a denoised dataset is received in case denoised dataset is different in size from original one
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That's a good point, and worth taking on board now. I have updated the workflow logic so that it overwrites all the column values barring session ID and site name when a denoised dataset comes in. Let me know what you think! |
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The CLEM can be configured to acquire a second, denoised image set of a position, which is saved in its own folder with
_Lng_LVCC(and other suffixes, as we discover them) appended to the position name (e.g.,Position 12_Lng_LVCC--...).Previously, these datasets were registered as separate entries in Murfey and ISPyB, but we have received feedback that where denoised datasets are acquired, the originals no longer need to be displayed.
This PR addresses this request by adjusting the grid square registration logic for the CLEM workflow. If the image set to be registered has
_Lng_LVCCin its name and the original, un-denoised image set has already been registered, it will overwrite the existing entry in both Murfey and ISPyB. If the denoised one was registered first and the un-denoised one comes along, the original won't overwrite the current entry in Murfey and ISPyB.Similar logic will eventually have to be implemented for the atlas registration, but that can be done in a separate PR to prevent this one from becoming too massive.