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mehta-lab / recOrder

3D quantitative label-free imaging with phase and polarization
BSD 3-Clause "New" or "Revised" License
11 stars 4 forks source link

Pass metadata #464

Closed talonchandler closed 6 months ago

talonchandler commented 6 months ago

Before: recorder reconstruct does not pass any plate-level metadata because it takes single position as input. This was very inconvenient for @dsundarraman's work, where we need to reconstruct each FOV then use the plate-level stage-position metatdata for a first pass at stitching the FOVs.

After: recorder reconstruct checks to see if the position is a part of a plate, and passes the plate-level metadata if is.

@dsundarraman, this PR will let you run reconstructions, then merge the reconstructions directly. Here's a snippet to get you started...I expect these to be some of the first lines in zebrapro stitch:

plate = open_ome_zarr("./reconstruction.zarr")
positions = plate.zattrs["Summary"]["StagePositions"]
zyx_stage_position_list = [[positions[k]["DevicePositions"][0]["Position_um"][0], positions[k]["DevicePositions"][1]["Position_um"][0], positions[k]["DevicePositions"][1]["Position_um"][1]] for k in range(len(positions))]
codecov[bot] commented 6 months ago

Codecov Report

All modified and coverable lines are covered by tests :white_check_mark:

Comparison is base (d31ad91) 9.45% compared to head (3b1f7fb) 9.49%. Report is 1 commits behind head on main.

Additional details and impacted files ```diff @@ Coverage Diff @@ ## main #464 +/- ## ======================================== + Coverage 9.45% 9.49% +0.03% ======================================== Files 29 29 Lines 4592 4594 +2 ======================================== + Hits 434 436 +2 Misses 4158 4158 ```

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talonchandler commented 6 months ago

@dsundarraman can you try this out before we merge? (for some reason I can't request your review)