Reformat coordinate transforms

[MaxHellstrom]

Reformat coordinate transforms and orientation to make the calculation model consistent.

This includes phantom rotation and directions, rotational matrices, patient positioning, etc.

[codecov-io]

Codecov Report

Merging #17 (2e0c900) into master (9c1d97e) will increase coverage by 5.02%. The diff coverage is 29.67%.

:exclamation: Current head 2e0c900 differs from pull request most recent head be73834. Consider uploading reports for the commit be73834 to get more accurate results

@@            Coverage Diff             @@
##           master      #17      +/-   ##
==========================================
+ Coverage   52.01%   57.03%   +5.02%     
==========================================
  Files          28       30       +2     
  Lines        1094     1173      +79     
==========================================
+ Hits          569      669     +100     
+ Misses        525      504      -21     

Impacted Files	Coverage Δ
src/pyskindose/beam_class.py	15.90% <0.00%> (-0.76%)	:arrow_down:
src/pyskindose/constants.py	100.00% <ø> (ø)
src/pyskindose/plotting/create_wireframes.py	19.23% <0.00%> (-2.51%)	:arrow_down:
src/pyskindose/rdsr_normalizer.py	19.56% <ø> (ø)
src/pyskindose/settings_pyskindose.py	97.01% <ø> (ø)
...rc/pyskindose/plotting/create_ploty_ijk_indices.py	2.43% <2.43%> (ø)
src/pyskindose/geom_calc.py	37.50% <12.50%> (+1.50%)	:arrow_up:
src/pyskindose/phantom_class.py	62.87% <40.74%> (+50.57%)	:arrow_up:
src/pyskindose/__init__.py	100.00% <100.00%> (ø)
tests/unittests/test_positioning.py	100.00% <100.00%> (ø)
... and 3 more

---

Continue to review full report at Codecov.

Legend - Click here to learn more Δ = absolute <relative> (impact), ø = not affected, ? = missing data Powered by Codecov. Last update 9c1d97e...be73834. Read the comment docs.

[codecov-commenter]

Codecov Report

Merging #17 (358e297) into master (57eea3a) will increase coverage by 5.02%. The diff coverage is 28.57%.

@@            Coverage Diff             @@
##           master      #17      +/-   ##
==========================================
+ Coverage   52.01%   57.03%   +5.02%     
==========================================
  Files          28       30       +2     
  Lines        1094     1173      +79     
==========================================
+ Hits          569      669     +100     
+ Misses        525      504      -21     

Impacted Files	Coverage Δ
src/pyskindose/beam_class.py	15.90% <0.00%> (-0.76%)	:arrow_down:
src/pyskindose/constants.py	100.00% <ø> (ø)
src/pyskindose/plotting/create_wireframes.py	19.23% <0.00%> (-2.51%)	:arrow_down:
src/pyskindose/rdsr_normalizer.py	19.56% <ø> (ø)
src/pyskindose/settings_pyskindose.py	97.01% <ø> (ø)
...rc/pyskindose/plotting/create_ploty_ijk_indices.py	2.43% <2.43%> (ø)
src/pyskindose/geom_calc.py	37.50% <7.14%> (+1.50%)	:arrow_up:
src/pyskindose/phantom_class.py	62.87% <40.74%> (+50.57%)	:arrow_up:
src/pyskindose/__init__.py	100.00% <100.00%> (ø)
tests/unittests/test_positioning.py	100.00% <100.00%> (ø)
... and 3 more

---

Continue to review full report at Codecov.

Legend - Click here to learn more Δ = absolute <relative> (impact), ø = not affected, ? = missing data Powered by Codecov. Last update 57eea3a...358e297. Read the comment docs.