Register lamella image

[tieneupin]

This PR adds on the GridSquare creation and updating logic for the lamella image registration workflow. If an atlas image has already been registered (i.e., there is an ImagingSite database entry with data type "atlas") and a thumbnail exists for it (i.e. the thumbnail_pixels_... fields in the table have been populated), it will calculate the length, width, and position of the lamella image relative to the spatial region covered by the atlas image, and insert that into ISPyB.

This PR is a bit on the longer side, as a fair number of calculations need to be performed, and many attributes need to be updated.

Currently, we are still trying to establish a mathematical relationship between the values of y, z, and tilt_alpha and the part of the stage that's in focus. For now, if the z height between the atlas image and lamella images are similar (i.e. within 0.5 mm), the mapping will be fairly accurate.

[codecov]

Codecov Report

❌ Patch coverage is 79.31034% with 12 lines in your changes missing coverage. Please review.
✅ Project coverage is 55.42%. Comparing base (fc8355f) to head (fa81e28).

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #905      +/-   ##
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+ Coverage   55.29%   55.42%   +0.12%     
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  Files         103      103              
  Lines       11491    11546      +55     
  Branches     1534     1541       +7     
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+ Hits         6354     6399      +45     
- Misses       4793     4800       +7     
- Partials      344      347       +3     

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[stephen-riggs]

Looks fine from what I can see. One note is that for SPA/tomo we wrote in conditions to make murfey db registration work even if ispyb is not available (i.e. no _transport_object) which you haven't got here. Should be fine as this is only likely to be run with ispyb

[tieneupin]

Thanks for the review! I think I'll implement the transport object handling logic in a separate PR and merge this as-is for now.