Save GUI state with snapped images

[ziw-liu]

Resolves #262.

[deprecated-napari-hub-preview-bot]

Preview page for your plugin is ready here:
https://preview.napari-hub.org/mehta-lab/recOrder/279
Updated: 2022-11-18T18:00:31.822881

[codecov-commenter]

Codecov Report

Merging #279 (86f9a37) into main (d91889a) will decrease coverage by 0.01%.
The diff coverage is 0.00%.

❗ Current head 86f9a37 differs from pull request most recent head 4d4857f. Consider uploading reports for the commit 4d4857f to get more accurate results

@@           Coverage Diff            @@
##            main    #279      +/-   ##
========================================
- Coverage   4.37%   4.36%   -0.02%     
========================================
  Files         22      22              
  Lines       4979    4992      +13     
========================================
  Hits         218     218              
- Misses      4761    4774      +13     

Impacted Files	Coverage Δ
recOrder/acq/acquisition_workers.py	0.00% <0.00%> (ø)
recOrder/calib/calibration_workers.py	0.00% <0.00%> (ø)
recOrder/plugin/main_widget.py	0.00% <0.00%> (ø)

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[talonchandler]

When I acquired a background I received:
AttributeError: 'MainWidget' object has no attribute 'phase_regularizer'
because phase_regularizer hadn't been created yet.

I added a one-line fix calling enter_phase_denoiser in the main_widget constructor.

[talonchandler]

@Soorya19Pradeep @edyoshikun this PR addresses one of the issues we've run into recently: what parameters did you choose in recOrder when you acquired and reconstructed an image?

Our solution for 0.3.0 is to save a gui_state.yml file with each acquisition. Here's an example of one of these files:

Run Calibration:
  Swing: 0.1
  Wavelength: 532
  Illumination Scheme: 4-State
  Calibration Mode: MM-Voltage
  Config Group: Channel
Capture Background:
  Background Folder Name: BG
  Number of Images to Average: 5
Acquisition Settings:
  Z Start: -10.0
  Z End: 10.0
  Z Step: 1.0
  Acquisition Mode: 2D
  BF Channel: BF
General Reconstruction Settings:
  Background Correction: None
  Background Path: C:\Users\LabelFree
  Wavelength: 532
  Objective NA: 1.3
  Condenser NA: 0.5
  Camera Pixel Size: 6.9
  RI of Objective Media: 1.3
  Magnification: 60.0
  Orientation Offset: false
Phase Reconstruction Settings:
  Z Padding: 0
  Regularizer: Tikhonov
  Strength: 0.0001

Any comments @edyoshikun @Soorya19Pradeep? Does this solve most of the issues we've encountered?

This solution is a stop-gap on the way to 1.0.0 where we are aiming for the complete reconstruction to be exactly reproducible very quickly. For now, we think it's important to save the GUI state so that you can modify recOrder scripts.

[talonchandler]

Works really well...and I've received positive feedback from in-person conversations. Merging now...