Non-integer focus support

[talonchandler]

Fixes #470.

Enables sub-pixel precision for focus detection and z_focus_offset values, improving 2D phase reconstructions for coarsely sampled data.

Changes:

• Settings: z_focus_offset now accepts float values (previously int only)
• Focus detection: Added optional sub-pixel precision to focus_from_transverse_band()
  • New parameter: enable_subpixel_precision: bool = False
  • Uses a polynomial fit to find a continuous maximum
  • Returns float indices when enabled, maintains integer behavior by default
• Backwards compatible. Default behavior return integers to continue to support mantis and other applications.

Old usage (unchanged):

focus_slice = focus_from_transverse_band(data, NA_det, lambda_ill, pixel_size)

New usage:

focus_slice = focus_from_transverse_band(
    data, NA_det, lambda_ill, pixel_size,
    polynomial_fit_order=2,
    enable_subpixel_precision=True
)  # Returns float like 5.3 instead of 5

Config files now support float offsets:

transfer_function:
  z_focus_offset: 0.5  # Previously only integers

[gav-sturm]

@talonchandler one thing that might help in the documentation is selecting a reasonable polynomial fit order if subpixel_precission is set to True. I saw in your tests that 4 is a good default?

[talonchandler]

@talonchandler one thing that might help in the documentation is selecting a reasonable polynomial fit order if subpixel_precission is set to True. I saw in your tests that 4 is a good default?

Good suggestion. @gav-sturm, for your use case I suggest starting with order=2, then increasing to 3 or 4 if you're unhappy with the fits you're seeing in the plots. If this suggestion works well, I'll add it to the docstring.

[codecov]

Codecov Report

❌ Patch coverage is 91.66667% with 2 lines in your changes missing coverage. Please review.
✅ Project coverage is 38.11%. Comparing base (bf46c27) to head (855a68b).
⚠️ Report is 10 commits behind head on main.

Files with missing lines	Patch %	Lines
waveorder/focus.py	91.30%	2 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #473      +/-   ##
==========================================
+ Coverage   36.55%   38.11%   +1.56%     
==========================================
  Files          49       49              
  Lines       10186     9791     -395     
==========================================
+ Hits         3723     3732       +9     
+ Misses       6463     6059     -404     

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