🚚 Replace integers suffixes with descriptive strings for regressor forks

[shnizzedy]

Fixes

Related to #1808 by @shnizzedy
Includes #1823, #1825 & #1830 by @shnizzedy

Description

• 🎨 Standardize naming for atlases used in RBC #1823
• 🎨 Change -s in BIDS values to camelCase #1825
• Replaces integer suffixes from forking at regressors with camelCased desc- value additions (e.g., desc-preproc-1, desc-preproc-2 becomes reg-36Parameter_desc-preproc, reg-aCompCor_desc-preproc)

I interpreted

All non-standard file entities SHOULD conform to BIDS-style naming conventions, including alphabetic entities and suffixes and alphanumeric labels/indices.

― Brain Imaging Data Structure v1.8.0: Common principles § Unspecified data

as allowing us to create a non-standard reg- entity here. If we decide to keep this info mashed into desc- we can just roll back to 02f93df.

Technical details

The main change here is

C-PAC/CPAC/pipeline/engine.py

Lines 938 to 962 in 2d354fd

	if num_variant:
	if (
	'regressors' in json_info.get('CpacVariant', {}) and
	json_info['CpacVariant']['regressors']
	):
	reg_value = json_info['CpacVariant'][
	'regressors'
	][0].replace('nuisance_regressors_generation_', '')
	out_dct['filename'] = insert_reg_entity(
	out_dct['filename'], reg_value)
	resource_idx = insert_reg_entity(resource, reg_value)
	else:
	for key in out_dct['filename'].split('_')[::-1]:
	if key.startswith('desc-'): # final `desc` entity
	out_dct['filename'] = out_dct[
	'filename'].replace(key,
	f'{key}-{num_variant}')
	resource_idx = resource.replace(
	key, f'{key}-{num_variant}')
	break
	suff = resource.split('_')[-1]
	newdesc_suff = f'desc-{num_variant}_{suff}'
	resource_idx = resource.replace(suff, newdesc_suff)
	else:
	resource_idx = resource

to get names like sub-NDARYX806FL1_ses-HBNsiteRU_task-rest_run-1_atlas-HOCPA_reg-aCompCor_desc-th25Mean_timeseries instead of sub-NDARYX806FL1_ses-HBNsiteRU_task-rest_run-1_atlas-HOCPA_desc-th25Mean1_timeseries

Since the atlas names and hyphen-to-camelCase changes are integral to this PR, I merged #1823 and #1825 into this branch and tested them together. We can just merge this one into develop and get all 3 unless we want to keep them separate.

Screenshots

Checklist

• My pull request has a descriptive title (not a vague title like Update index.md).
• My pull request targets the develop branch of the repository.
• My commit messages follow best practices.
• My code follows the established code style of the repository.
• I added tests for the changes I made (if applicable).
• I updated the changelog.
• I added or updated documentation (if applicable).
• I tried running the project locally and verified that there are no visible errors.

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[shnizzedy]

Question about this one: in #1808, I gave the examples

(e.g., desc-preproc-1, desc-preproc-2 becomes desc-preprocReg36Parameter, desc-preprocRegACompCor)

but here

(e.g., desc-preproc-1, desc-preproc-2 becomes desc-preproc36Parameter, desc-preprocACompCor)

I didn't add Reg.

How to we want these differentiations to be?

• Just mashed on the end of desc like desc-preproc36Parameter?
• Mashed on the end with a prefix (e.g., Reg) like desc-preprocReg36Parameter?
• Add a nonstandard entity like reg-36Parameter_desc-preproc?
• Something else?

[shnizzedy]

Seems like we could add a reg- (or regr- or someothersuch) key

All non-standard file entities SHOULD conform to BIDS-style naming conventions, including alphabetic entities and suffixes and alphanumeric labels/indices.

― Brain Imaging Data Structure v1.8.0: Common principles § Unspecified data