axondeepseg / axondeepseg / 16234456046

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Add nerve section morphometrics + axon density (#869)

* Add option for nerve section morphometrics

* Refactor: new state var morphometrics_mode + closure check_mask_exists

* Add a row for total nerve area in morphometrics file

* Only write index img (numbers only) for myelinated mode

* Add TODOs

* Fix clash with merged PR #867 causing tests to fail

* Add density computation for the nerve morphometrics file

* Add prints in remove_outside_nerve fn

* Comment axon density part

* Remove try execpt block

* Change nerve morphometrics xlsx to json format

* Change nerve morphometrics file format to json

* Update -n help str

* Minor cleanup

* Add axon density for each fascicle feat

* Move functions to compute_morphometrics.py

* Code cleanup, hints for next steps

* Add axon density calculation for each fascicle

* chore: removed clean mask fn

* Add print for num regions identified

* Add documentation for feat

* Add details on the feature and reformat subsections

* Remove subsections and improve readability

* Add integrity test

* Update pipy release alpha version

* Use ads.imread instead of image.imread

* Improve readability and remove unused dependency

* Add unit test for save_nerve_morpho_to_json function

* Fix current tests and typo

* Remove missing key from save_nerve_morphometrics_to_json check

* Add unit test for remove_outside_nerve function

* Add integration test for nerve mode without axon mask present

* Add unit tests for compute_axon_density fn

* Add unit test for compute_fascicle_axon_density fn

* Compute total axons after fascicle assignment

* Add simple 1D test case for remove outside nerve

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Co-authored-by: Edgar Kappauf <edgar.kappauf@polymtl.ca>
Co-authored-by: Mathieu Boudreau, PhD <emb6150@gmail.com>

120 of 120 new or added lines in 4 files covered. (100.0%)

1759 of 1964 relevant lines covered (89.56%)

2.5 hits per line