Imaging refactor part 2 - Atoms: add_atoms(), refine_atoms(), plot(kind='atoms') and tests - #236

Imaging refactor part 2 - Atoms: add_atoms(), refine_atoms(), plot(kind='atoms') and tests#236

darshan-mali wants to merge 11 commits into

electronmicroscopy:develectronmicroscopy/quantem:devfrom

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