Pixel Size/Scaling Cleanup

[garrettwrong]

Cleans up multiple issues with pixel size across the image/xform/filter/source components.

Resolves #1318 and fixes the introduced bugs, closing #1395 .

Adds unit tests covering the triggering situations of the bugs.

This should probably be rebased after the larger PR 1388.

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Ironically, it was the single # Assign correct pixel_size line in Simulation that caused all the original problems, because it was assigning the wrong pixel_size under downsampling.

This caused some bugs (the math error in 1395) to be cancelled out, and workarounds to be added in other components... most of which I think only worked for Simulations, not real data.... Hopefully that's better now.

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 90.66%. Comparing base (5836ad2) to head (822bc17).

Additional details and impacted files

@@             Coverage Diff             @@
##           develop    #1396      +/-   ##
===========================================
+ Coverage    90.65%   90.66%   +0.01%     
===========================================
  Files          135      135              
  Lines        14926    14921       -5     
===========================================
- Hits         13531    13528       -3     
+ Misses        1395     1393       -2     

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