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Add ispyb inserts for SXT atlases and ROIs#840

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stephen-riggs wants to merge 25 commits into
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sxt-atlas
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Add ispyb inserts for SXT atlases and ROIs#840
stephen-riggs wants to merge 25 commits into
mainfrom
sxt-atlas

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@stephen-riggs

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Adds the functionality to insert SXT atlas and ROI images into both the murfey and ispyb databases. For ispyb the positions are adjusted to match the thumbnail images so that they display correctly on pato.

Requires atlas locations which weren't previously needed, so makes use of the ImagingSite table in addition to DataCollectionGroup. ROIs are inserted into the SearchMap table (matching GridSquare in ispyb).

Relatively low test coverage as I haven't written tests for the ispyb inserts.

Comment thread src/murfey/server/api/workflow_sxt.py Fixed
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codecov Bot commented Jul 9, 2026

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Codecov Report

❌ Patch coverage is 58.55856% with 46 lines in your changes missing coverage. Please review.
✅ Project coverage is 53.32%. Comparing base (975c2f3) to head (c9fc226).

Additional details and impacted files
@@           Coverage Diff           @@
##             main     #840   +/-   ##
=======================================
  Coverage   53.31%   53.32%           
=======================================
  Files         101      102    +1     
  Lines       10933    11029   +96     
  Branches     1452     1470   +18     
=======================================
+ Hits         5829     5881   +52     
- Misses       4788     4828   +40     
- Partials      316      320    +4     
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