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Correct 'global' and 'local_fit' background corrections #139

Merged
merged 7 commits into from
Aug 10, 2022

Commits on Aug 5, 2022

  1. Cast ROI from config file to tuple

    JSON convert python tuples to lists. This caused a bug where a tuple was compared to a list which resulted in "False" when the result should have been "True".
    
    Specifically, this bug caused the `utils.bg_read` function to average over an ROI area when it shouldn't, which in turn made recOrder's BG correction incorrect (or at least different from expected).
    talonchandler committed Aug 5, 2022
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  2. Accomodate waveorder's Polscope_bg_correction requirements

    `waveorder`'s `Polscope_bg_correction` function requires a background to be supplied, and this background will be subtracted for all `bg_option` choices ('global', 'local_fit', and 'none').
    
    Before this commit, `local_fit` background correction was applying a background correction from file (which might be empty if the GUI wasn't present, or it might be a real file if read from a config file) before proceeding to the local_fit correction.
    
    After this commit, the 'local_fit' option is applying an "identity correction" (i.e. no correction) then proceeding to apply the local_fit correction.
    talonchandler committed Aug 5, 2022
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  3. Supply n_slices to the QLIPP pipeline so that 3D background correct…

    …ion works
    
    Applying a 2D background correction to 3D data in `waveorder` depends on `self.N_decocus` being set correctly. `recOrder`'s branching logic did not set these parameters correctly, and this commit fixes the issue.
    talonchandler committed Aug 5, 2022
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Commits on Aug 6, 2022

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Commits on Aug 8, 2022

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Commits on Aug 9, 2022

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