mehta-lab / recOrder

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

Collect and unify color overlays #473

Closed talonchandler closed 3 months ago

talonchandler commented 3 months ago

Paired with https://github.com/czbiohub-sf/shrimPy/pull/141, which will close without merging.

This PR merges @edyoshikun's color overlays from shrimpy into recOrder while making necessary changes to both sets of functions:

The new function signatures are: det ret_ori_overlay(czyx, ret_max: Union[float, Literal["auto"]] = 10, cmap: Literal["JCh", "HSV"] = "JCh"): def ret_ori_phase_overlay(czyx, max_val_V: float = 1.0, max_val_S: float = 1.0):

I have tested the new ret_ori_overlay on the example datasets (to check the lazy-computed dask arrays), and I've tested both new functions in CI.

Notes:

codecov[bot] commented 3 months ago

Codecov Report

Attention: Patch coverage is 8.51064% with 43 lines in your changes missing coverage. Please review.

Project coverage is 9.54%. Comparing base (57f611e) to head (26f8a79).

Files Patch % Lines
recOrder/io/visualization.py 0.00% 41 Missing :warning:
recOrder/plugin/main_widget.py 0.00% 2 Missing :warning:
Additional details and impacted files ```diff @@ Coverage Diff @@ ## main #473 +/- ## ======================================== + Coverage 9.49% 9.54% +0.04% ======================================== Files 29 30 +1 Lines 4594 4591 -3 ======================================== + Hits 436 438 +2 + Misses 4158 4153 -5 ```

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