IMOD processing bypass and file copying

[stephen-riggs]

Updates imod dockerfile to include some missing libraries, then runs using -bypass to avoid the java dependency.

Also sets up a mechanism to copy the output files to a higher level. This was requested by b24 as the output folders can be messy and they want an easy way to access the tomograms.

[codecov]

Codecov Report

❌ Patch coverage is 95.45455% with 1 line in your changes missing coverage. Please review.
✅ Project coverage is 83.39%. Comparing base (b0b700d) to head (bd3375c).
⚠️ Report is 4 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #279      +/-   ##
==========================================
+ Coverage   83.13%   83.39%   +0.25%     
==========================================
  Files          75       75              
  Lines        9291     9580     +289     
  Branches     1264     1352      +88     
==========================================
+ Hits         7724     7989     +265     
- Misses       1075     1093      +18     
- Partials      492      498       +6     

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[tieneupin]

Looks good to me! I don't think running re.match(...) on the path parts in a NumPy array is needed, but the code should work nonetheless.