Add option to specify a mask during embedding

[thorstenwagner]

As requested by @cmccaffe

Its currently building, but should then be available as v0.4.4b0 at https://pypi.org/project/tomotwin-cryoet/#history

Once installed, you will find a --mask option in the embed command.

Inspired by isonet, I'm also playing with a method to generate meaningful masks quickly. But thats not yet included in this PR

[codecov]

Codecov Report

Patch coverage: 52.72% and project coverage change: -0.15 ⚠️

Comparison is base (3834518) 66.75% compared to head (31b1a0f) 66.61%.

❗ Current head 31b1a0f differs from pull request most recent head a9bdfc7. Consider uploading reports for the commit a9bdfc7 to get more accurate results

Additional details and impacted files

@@            Coverage Diff             @@
##             main      #27      +/-   ##
==========================================
- Coverage   66.75%   66.61%   -0.15%     
==========================================
  Files          60       60              
  Lines        2975     3028      +53     
==========================================
+ Hits         1986     2017      +31     
- Misses        989     1011      +22     

Impacted Files	Coverage Δ
tomotwin/modules/tools/embedding_mask.py	0.00% <0.00%> (ø)
tomotwin/modules/tools/umap.py	0.00% <0.00%> (ø)
tomotwin/embed_main.py	80.67% <66.66%> (-0.91%)	⬇️
tomotwin/modules/inference/volumedata.py	97.43% <93.75%> (+1.98%)	⬆️
tomotwin/modules/inference/boxer.py	91.37% <97.22%> (+4.28%)	⬆️
tomotwin/modules/inference/argparse_embed_ui.py	98.18% <100.00%> (+0.10%)	⬆️
tomotwin/modules/inference/embed_ui.py	100.00% <100.00%> (ø)

... and 1 file with indirect coverage changes

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[thorstenwagner]

Alright @cmccaffe, I also added now a tool to calculate a mask. Two important changes:

1. The tomotwin_tools.py umap command now calculates the embedding label mask internally and save it into the output directory of the umap commmand

2. The tomotwin_tools.py emedding_mask now calculate a embedding mask that defines a ROI and can be used during embedding.

There should be soon a version 0.4.4b1 available:
https://pypi.org/project/tomotwin-cryoet/#history