Update and fixes in dwiml_create_hdf5 and associated doc

[EmmaRenauld]

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]

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]

See associated issue #223

[EmmaRenauld]

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