BlueBrain / morphoclass

Neuronal morphology preparation and classification using Machine Learning.
https://morphoclass.readthedocs.io
Apache License 2.0
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Refactor `morphoclass morphometrics` CLI + Fix SSH #61

Closed FrancescoCasalegno closed 2 years ago

FrancescoCasalegno commented 2 years ago

Fixes #60

Description

  1. morphoclass morphometrics extract-features now takes in input the dataset-csv (i.e. only one CSV file) instead of organised-dataset-directory (i.e. a whole directory that is then explored to read CSV files for each layer). This makes the command more similar to morphoclass extract-features.
  2. The output filesystem structure produced of feature extraction and model training is now the same for morphoclass and other features. I.e. the naming convention follows the structure <dataset>-<layer>:
    extract-features-morphometrics/
    ├── in-L1
    ├── in-L23
    ├── in-L4
    ├── in-L5
    ├── in-L6
    ├── in-merged
    ├── in-merged-bc-merged
    ├── janelia-L5
    ├── pc-L2
    ├── pc-L3
    ├── pc-L4
    ├── pc-L5
    └── pc-L6
  3. Enable SSH: replace dvc by dvc[ssh] in requirements-extras.txt + add apt-get install ssh in the Dockerfile.

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