Apply clipping to user initial model if not a cube

[stephen-riggs]

Uses imod clip to resize the image into a cube.
Won't resolve the issue we saw with the particle being cropped.

[codecov]

Codecov Report

❌ Patch coverage is 0% with 10 lines in your changes missing coverage. Please review.
✅ Project coverage is 34.29%. Comparing base (24d6628) to head (bdb954f).
⚠️ Report is 3 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #677      +/-   ##
==========================================
- Coverage   34.32%   34.29%   -0.04%     
==========================================
  Files          92       92              
  Lines       11157    11167      +10     
  Branches     1474     1476       +2     
==========================================
  Hits         3830     3830              
- Misses       7202     7212      +10     
  Partials      125      125              

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