Update shutter behavior and LF acquisition channel order

[ieivanov]

This PR fixes #111. It also starts to address #110 and #142

To fully fix #142 we also need to:

• ask the user to manually close and open the shutter if an auto shutter is not available
• provide the option to manually enter a black level - either in the GUI or the CLI
  @talonchandler could you please help me with those?

Towards addressing #110 I've added a check to ensure that all LF channel exposures are the same. If they are not, all exposures are set to the exposure for State0. That's not a complete solution, but will prevent acquiring corrupted data.

[codecov-commenter]

Codecov Report

Merging #160 (ef9de8f) into main (3c570ec) will increase coverage by 0.09%.
The diff coverage is 0.00%.

@@            Coverage Diff             @@
##             main     #160      +/-   ##
==========================================
+ Coverage   11.20%   11.30%   +0.09%     
==========================================
  Files          45       45              
  Lines        5990     5938      -52     
==========================================
  Hits          671      671              
+ Misses       5319     5267      -52     

Impacted Files	Coverage Δ
recOrder/acq/acq_functions.py	0.00% <0.00%> (ø)
recOrder/calib/Calibration.py	0.00% <0.00%> (ø)
recOrder/plugin/widget/main_widget.py	0.00% <0.00%> (ø)
recOrder/plugin/workers/acquisition_workers.py	0.00% <0.00%> (ø)
recOrder/plugin/workers/calibration_workers.py	0.00% <0.00%> (ø)
recOrder/io/utils.py	0.00% <0.00%> (ø)
recOrder/pipelines/qlipp_pipeline.py	0.00% <0.00%> (ø)

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[deprecated-napari-hub-preview-bot]

Preview page for your plugin is ready here:
https://preview.napari-hub.org/mehta-lab/recOrder/160
Updated: 2022-09-12T21:30:29.088358

[talonchandler]

This is excellent, Ivan, thanks so much. I'll definitely be able to take this over the finish line.

I really like your "warning + default to State0" solution for #110---good call. This fix moved to #162.

In the interests of onboarding Ziwen, I'm thinking of testing and completing the fixes for #110, #111, and #142 on three different branches. Thanks for giving us a major headstart!

[talonchandler]

I've moved the exposure check to a different PR #162 since the implementation needs work, and this PR will benefit from narrowed scope.

[talonchandler]

This PR is on the larger side. It includes:

Features

• keeping the shutter open during multi-channel and multi-slice acquisitions
• options for users to calibrate when a shutter isn't available
  • if a shutter isn't available, a warning appears prompting an input on the command line
  • the user can enter a number that will be used as a black level, or close the shutter manually and let recOrder estimate the black level
• slice-first acquisition instead of channel-first acquisition

Non-features

• To allow for testing of import statements, I have made napari[all] a requirement (and updated the docs accordingly).
• Dropped support for python 3.7 because napari has also dropped support.

@ziw-liu much of this depends on hardware, but I'd still appreciate a quick second set of eyes on the code before merging. Thanks!

[ieivanov]

Quick note: I see that you've removed run_calibration, run_5state_calibration, and run_4state_calibration from calib.Calibration. These function used to let users run LC calibration outside of the recOrder widget (e.g. in a script). I think that's OK, as this is not a commonly used mode of recOrder right now, and we don't test and debug it.

[talonchandler]

Thanks for the context @ieivanov.

I'm totally in favor of script-based calibration if it's useful. For the sake of maintenance/updates, it will be great to have a single function that the GUI/scripts/others can call. I think we can revisit these design choices when we address #120.