Live reconstruction compatibility features

[talonchandler]

This PR adds two features to make recOrder's CLI reconstruction workflow more compatible with live reconstructions:

1. a new time_indices option for reconstructing a subset of all time points. time_indices can be an integer, a list of integers, or all (default). This allows the user to reconstruct all time points (typical for offline), or individual time points (typical for faster online reconstructions).

2. support for passing ReconstructionSettings objects directly into apply_inverse_transfer_function_cli. This feature makes it more convenient for an online reconstruction routine to call the same reconstruction on different time points...instead of modifying and save a configuration yaml file for each time point, the user can modify the time_indices attribute of the ReconstructionSettings object directly.

@ziw-liu I'm not sure if I implemented (2) in the way that you had in mind...please suggest improvements.
@clinton-huynh please feel free to add or modify this branch.

[codecov]

Codecov Report

Merging #388 (3fe47ad) into main (96dca01) will increase coverage by 0.06%.
The diff coverage is 100.00%.

❗ Current head 3fe47ad differs from pull request most recent head d2331d9. Consider uploading reports for the commit d2331d9 to get more accurate results

@@           Coverage Diff            @@
##            main    #388      +/-   ##
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+ Coverage   7.23%   7.29%   +0.06%     
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  Files         25      25              
  Lines       4439    4442       +3     
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+ Hits         321     324       +3     
  Misses      4118    4118              

Files Changed	Coverage Δ
recOrder/tests/cli_tests/test_reconstruct.py	97.36% <100.00%> (+0.22%)	⬆️

[deprecated-napari-hub-preview-bot]

Preview page for your plugin is ready here:
https://preview.napari-hub.org/mehta-lab/recOrder/388
Updated: 2023-07-28T18:15:49.415886

[talonchandler]

I'm going to change this to draft because the tests aren't passing and we made some suboptimal choices here to enable a demo. The work in this branch is useful for demonstrating live reconstructions from micromanager, though, so this does not need to be closed until we've found a good solution for that.

@edyoshikun I am planning to move the time_indices option to it's own PR because that feature is useful for multiprocessing.

[talonchandler]

Replaced by #398. Closing.