[easy] Remove physical_coordinate_calculator.py

[ttung]

Most of the functions are now only used by test code. Move _get_physical_coordinates_of_z_plane, the remaining "mainline" code into physical_coordinates.py

Test plan: pytest -v -n4 starfish/core/imagestack/test/

Depends on #1351

[codecov-io]

Codecov Report

Merging #1352 into master will decrease coverage by 1.27%.
The diff coverage is 100%.

@@            Coverage Diff             @@
##           master    #1352      +/-   ##
==========================================
- Coverage    90.4%   89.13%   -1.28%     
==========================================
  Files         216      147      -69     
  Lines        8223     5337    -2886     
==========================================
- Hits         7434     4757    -2677     
+ Misses        789      580     -209

Impacted Files	Coverage Δ
starfish/core/imagestack/parser/tileset/_parser.py	83.54% <100%> (ø)	⬆️
...fish/core/imagestack/test/factories/with_coords.py	100% <100%> (ø)	⬆️
starfish/core/imagestack/physical_coordinates.py	100% <100%> (ø)
starfish/core/experiment/test/test_experiment.py
starfish/core/recipe/test/test_runnable.py
starfish/core/spacetx_format/test/test_validate.py
...table/test/test_stack_intensity_table_reshaping.py
...rfish/core/intensity_table/test/test_to_mermaid.py
starfish/core/test/factories.py
...tarfish/core/image/_filter/test/test_call_bases.py
... and 57 more

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