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Remove background debugging print statement #261

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merged 2 commits into from
Nov 8, 2022

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talonchandler
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This PR removes a debugging print statement that was left behind, solving #258.

@mattersoflight brought up a potential concern that "local_fit" background corrections were being applied to phase reconstructions, but I have reread the code closely and found that this is not the case. Background corrections are only being applied to polarization acquisition.

@talonchandler talonchandler added this to the 0.3.0 milestone Nov 8, 2022
@talonchandler talonchandler self-assigned this Nov 8, 2022
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deprecated-napari-hub-preview-bot bot commented Nov 8, 2022

Preview page for your plugin is ready here:
https://preview.napari-hub.org/mehta-lab/recOrder/261
Updated: 2022-11-08T18:05:09.666405

@ziw-liu
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ziw-liu commented Nov 8, 2022

I found this behavior confusing too. Also when initializing the reconstructor for phase from BF, maybe we can explicitly pass in "None" for the bg_correction keyword argument (which defaults to "local_fit") here:

recon = initialize_reconstructor(
"PhaseFromBF",
image_dim=(stack.shape[-2], stack.shape[-1]),
wavelength_nm=int(
self.calib_window.ui.le_recon_wavelength.text()
),
NA_obj=self.calib_window.obj_na,
NA_illu=self.calib_window.cond_na,
mag=self.calib_window.mag,
n_slices=self.img_dim[-1],
z_step_um=self.calib_window.z_step,
pad_z=self.calib_window.pad_z,
pixel_size_um=self.calib_window.ps,
n_obj_media=self.calib_window.n_media,
mode=self.calib_window.acq_mode,
use_gpu=self.calib_window.use_gpu,
gpu_id=self.calib_window.gpu_id,
)

@talonchandler
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Agreed. Changing the keyword argument to "None" is much cleaner. Thanks!

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codecov-commenter commented Nov 8, 2022

Codecov Report

Merging #261 (c4b7ad5) into main (ecca6ff) will increase coverage by 0.01%.
The diff coverage is 0.00%.

@@           Coverage Diff            @@
##            main    #261      +/-   ##
========================================
+ Coverage   4.37%   4.38%   +0.01%     
========================================
  Files         22      22              
  Lines       4986    4971      -15     
========================================
  Hits         218     218              
+ Misses      4768    4753      -15     
Impacted Files Coverage Δ
recOrder/compute/qlipp_compute.py 0.00% <ø> (ø)
recOrder/plugin/main_widget.py 0.00% <0.00%> (ø)
recOrder/plugin/gui.py 0.00% <0.00%> (ø)

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@talonchandler talonchandler merged commit eff8b7d into main Nov 8, 2022
@talonchandler talonchandler deleted the suprress-bg-mode-print branch November 8, 2022 18:13
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recOrder prints local_fit terminal, even when "BG Correction Method" is set to None
3 participants