axondeepseg / axondeepseg / 15408690993
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Morphometric aggregation + visualization (#898)

* Add entry point for morph aggregation

* Skeleton for load_morphometrics()

* added base file for aggregation from notebook

* added a plotting function for histogram of axon counts and table of statistics

* filters list added, aggregate method changed for directory structure

* visual of histogram fixed

* restructuring of the folders where excel and figures are saved, correction of logic for excel generation

* prints removed

* Fix syntax error

* added constants to separate file

* structure of output files remade, separation of output file creation to new method and running script from root directory fixed

* added description to methods

* removed automatic double quote transformation

* Add back logging and make input_dir arg required

* Close figures after saving

* fixed output files (combined all sub-subjects into one) and removed unused methods

* save_subject_statistics name change

* fixed output files (combined all sub-subjects into one) and removed unused methods

* header changed for structure of output file

* Cleaner console output and don't aggregate in agg_dir

* Fix indent error from previous commit

* Code cleanup and removal of useless function

* Also save raw subject-aggregated morphometrics

* Add documentation draft

* Updated documentation

* Add error handling when files are missing

* Add test

* Remove logging

* Update testing data version

* handled empty excel file

* Handle empty axons image files, add aggregate test, bug fixes

* Add missing character break

---------

Co-authored-by: Muriellehxh <90001299+Muriellehxh@users.noreply.github.com>
Co-authored-by: Mathieu Boudreau, PhD <emb6150@gmail.com>
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1 macos-latest - 15408690993.1 21
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2 ubuntu-latest - 15408690993.2 21
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3 windows-latest - 15408690993.3 21
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