BlueBrain / morphoclass

Neuronal morphology preparation and classification using Machine Learning.
https://morphoclass.readthedocs.io
Apache License 2.0
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Morphometrics: feature extraction + classification model training #29

Closed FrancescoCasalegno closed 2 years ago

FrancescoCasalegno commented 2 years ago

Fixes #14.

Description

Introduce the two commands:

How to test?

All the following needs to be run from dvc/:

cd dvc/

Testing morphoclass morphometrics extract-features

Feature extraction can be tested with the following command.

dvc stage list --names-only | grep "morphometrics-feature-extraction" | xargs dvc repro -f -s

Notice that this command takes a few hour, so if you only need to fetch the results you can just do:

dvc stage list --names-only | grep "morphometrics-feature-extraction" | xargs dvc pull

Testing morphoclass morphometrics extract-features

Model training can be tested with the following command. You can safely run it on your laptop, it will only take a couple of minutes.

dvc stage list --names-only | grep "train-morphometrics" | xargs dvc repro -f -s

Checklist