axondeepseg / axondeepseg / 23230110555

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Diameter approximation overlay (#961)

* Add logic to generate and save diameter overlays

* Add morphometric -d option

* Also allow axonshape=ellipse

* Overlay ellipses for ellipse axon shape

* Draw outer ellipse according to the actual approximation we use

* Clarify ellipse overlay model and myelin_thickness definition

* refactor params: rename side_effect_suffixes and fix missing entries, including one introduced in this PR

* correct stale help text and comment for -d flag: missing new ellipse feature

* add ellipse morphometric columns to column_names_ordered

* add diameter overlay layer for ellipse axon shape

* Add tests for diameter overlay feature and circle/ellipse mode equivalence

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Co-authored-by: Mathieu Boudreau <emb6150@gmail.com>

85 of 97 new or added lines in 6 files covered. (87.63%)

1864 of 2325 relevant lines covered (80.17%)

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