Refactoring

[thisFreya]

Refactored according to Nina's requests - reorganized file structure and renamed many functions accordingly.

[codecov[bot]]

Codecov Report

Merging #46 (ee100db) into master (1bc504f) will decrease coverage by 1.50%. The diff coverage is 97.15%.

@@            Coverage Diff             @@
##           master      #46      +/-   ##
==========================================
- Coverage   95.32%   93.83%   -1.49%     
==========================================
  Files           7        6       -1     
  Lines         363      259     -104     
==========================================
- Hits          346      243     -103     
+ Misses         17       16       -1     

Impacted Files	Coverage Δ
ioSPI/micrographs.py	96.43% <96.43%> (ø)
ioSPI/particle_metadata.py	97.23% <97.23%> (ø)
ioSPI/atomic_models.py	98.22% <100.00%> (ø)
ioSPI/fourier.py	98.51% <0.00%> (-1.49%)	:arrow_down:

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[ninamiolane]

And yes, please fix the linting error. It might be coming from an update in black, it has been popping up on other projects that I manage.

It could be fixed by running black . in the root of this repo.

[thisFreya]

@ninamiolane Changes implemented, please let me know if there's anything else that can be better represented!