Update and fixes in dwiml_create_hdf5 and associated doc

scil-vital / dwi_ml

Code for people working on machine learning for diffusion MRI

MIT License

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Update and fixes in dwiml_create_hdf5 and associated doc #222

Closed EmmaRenauld closed 7 months ago

EmmaRenauld commented 9 months ago

Script dwiml_create_hdf5:

Removed option std_mask in the script. Is now an option of each volume group in the config file.
Fixed the spelling of "connectivty" in the code.
Small modif: use our io method add_logging_arg.

Script dwiml_compute_connectivity_from_labels:

Fixes.
Better figure.

Doc:

Add the std options explanation.
Add the connectivity options explanation.
Delete the preprocessing explanation. People know how to preprocess their data. (link to tractoflow is now deleted).

Sneeking in a .gitignore modification.

pep8speaks commented 9 months ago

Hello @EmmaRenauld, Thank you for updating !

In the file dwi_ml/data/hdf5/utils.py:

Line 62:80: E501 line too long (80 > 79 characters) Line 65:80: E501 line too long (80 > 79 characters) Line 79:80: E501 line too long (80 > 79 characters)

In the file dwi_ml/training/batch_samplers.py:

Line 279:80: E501 line too long (80 > 79 characters)

Comment last updated at 2024-03-01 14:32:06 UTC

EmmaRenauld commented 9 months ago

See associated issue #223

EmmaRenauld commented 7 months ago

Ran at least two epochs on beluga on > 1 subject. Merging current state of code.