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Allow user to set input and output domains#27

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PinkShnack wants to merge 12 commits into
RI-imaging:masterfrom
PinkShnack:26_input_output_domains
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Allow user to set input and output domains#27
PinkShnack wants to merge 12 commits into
RI-imaging:masterfrom
PinkShnack:26_input_output_domains

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@PinkShnack

@PinkShnack PinkShnack commented Jun 8, 2026

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Similar to RI-imaging/qpretrieve#28 and mentioned in issue #26, I want to have nrefocus part-take in a faster qpi analysis pipeline by allowing the user to specofy the input and output domain.

Todo

  • Merge 3d array compatibility #25, as this PR is built on that.
  • update changelog
  • keep default and new pipeline with fourier domains consistent
  • test above
  • add docs section
  • add added version 0.7.2 everywhere necessary

@PinkShnack

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The fourier-only pipeline is quite a bit faster which is great. Rough twice as fast as the default spatial when running only refocus, which is expected as we've removed two Fourier transforms.

tests\test_bm\test_bm_refocus_domains.py ....                                                                                                                                                                           [100%]


--------------------------------------------------------------------------------------------- benchmark: 4 tests --------------------------------------------------------------------------------------------
Name (time in ms)                                   Min               Max              Mean            StdDev            Median               IQR            Outliers       OPS            Rounds  Iterations
-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
test_bm_refocus_fourier_input_fourier_output     1.6907 (1.0)      3.7432 (1.0)      1.8912 (1.0)      0.2204 (1.0)      1.8113 (1.0)      0.1618 (1.0)         60;43  528.7702 (1.0)         532           1
test_bm_refocus_fourier_input_spatial_output     2.8073 (1.66)     6.9890 (1.87)     3.0909 (1.63)     0.3744 (1.70)     2.9543 (1.63)     0.2673 (1.65)        22;15  323.5258 (0.61)        248           1
test_bm_refocus_spatial_input_fourier_output     2.8315 (1.67)     6.1681 (1.65)     3.0503 (1.61)     0.2648 (1.20)     2.9686 (1.64)     0.2028 (1.25)        24;15  327.8386 (0.62)        268           1
test_bm_refocus_spatial_default                  4.0662 (2.41)     8.5916 (2.30)     4.8868 (2.58)     0.5602 (2.54)     4.8201 (2.66)     0.5841 (3.61)         23;4  204.6346 (0.39)        139           1
-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

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