ignore irrelevant modalities when initializing layout

[jdkent]

In theory, BIDS datasets should be completely valid, in practice, sometimes not all files are valid in a dataset yet.
If a lab is working on converting their project to a BIDS valid dataset that contains many modalities, they may focus on getting anat, func, and fmap to get things right, but may not have finished:

• dwi
• perf
• meg
• eeg
• ieeg
• beh

Currently, one can skip validation (even if you do not, a multitude of irrelevant errors are ignored)

fmriprep/fmriprep/utils/bids.py

Lines 77 to 124 in a42d929

	validator_config_dict = {
	"ignore": [
	"EVENTS_COLUMN_ONSET",
	"EVENTS_COLUMN_DURATION",
	"TSV_EQUAL_ROWS",
	"TSV_EMPTY_CELL",
	"TSV_IMPROPER_NA",
	"VOLUME_COUNT_MISMATCH",
	"BVAL_MULTIPLE_ROWS",
	"BVEC_NUMBER_ROWS",
	"DWI_MISSING_BVAL",
	"INCONSISTENT_SUBJECTS",
	"INCONSISTENT_PARAMETERS",
	"BVEC_ROW_LENGTH",
	"B_FILE",
	"PARTICIPANT_ID_COLUMN",
	"PARTICIPANT_ID_MISMATCH",
	"TASK_NAME_MUST_DEFINE",
	"PHENOTYPE_SUBJECTS_MISSING",
	"STIMULUS_FILE_MISSING",
	"DWI_MISSING_BVEC",
	"EVENTS_TSV_MISSING",
	"TSV_IMPROPER_NA",
	"ACQTIME_FMT",
	"Participants age 89 or higher",
	"DATASET_DESCRIPTION_JSON_MISSING",
	"FILENAME_COLUMN",
	"WRONG_NEW_LINE",
	"MISSING_TSV_COLUMN_CHANNELS",
	"MISSING_TSV_COLUMN_IEEG_CHANNELS",
	"MISSING_TSV_COLUMN_IEEG_ELECTRODES",
	"UNUSED_STIMULUS",
	"CHANNELS_COLUMN_SFREQ",
	"CHANNELS_COLUMN_LOWCUT",
	"CHANNELS_COLUMN_HIGHCUT",
	"CHANNELS_COLUMN_NOTCH",
	"CUSTOM_COLUMN_WITHOUT_DESCRIPTION",
	"ACQTIME_FMT",
	"SUSPICIOUSLY_LONG_EVENT_DESIGN",
	"SUSPICIOUSLY_SHORT_EVENT_DESIGN",
	"MALFORMED_BVEC",
	"MALFORMED_BVAL",
	"MISSING_TSV_COLUMN_EEG_ELECTRODES",
	"MISSING_SESSION"
	],
	"error": ["NO_T1W"],
	"ignoredFiles": ['/dataset_description.json', '/participants.tsv']
	}

but if one has malformed json files, the pybids indexer will still fail on potentially irrelevant (to fmriprep) files.

So my proposed solution is to ignore all the directories above when creating the bids layout so they will not be indexed (e.g., re.compile("sub-.*/beh")):

fmriprep/fmriprep/config.py

Lines 448 to 455 in 4bb8a61

	ignore=(
	"code",
	"stimuli",
	"sourcedata",
	"models",
	re.compile(r"^\."),
	),
	)

This may also have the added benefit of making indexing faster on larger datasets with many modalities.

[oesteban]

I think this is a pretty low-hanging fruit - don't you all agree?

[oesteban]

We can address this at the same time we remove the following warning:

/home/oesteban/.miniconda/lib/python3.8/site-packages/bids/layout/validation.py:46: UserWarning: The ability to pass arguments to BIDSLayout that control indexing is likely to be removed in future; possibly as e
arly as PyBIDS 0.14. This includes the `config_filename`, `ignore`, `force_index`, and `index_metadata` arguments. The recommended usage pattern is to initialize a new BIDSLayoutIndexer with these arguments, and
 pass it to the BIDSLayout via the `indexer` argument.
  warnings.warn("The ability to pass arguments to BIDSLayout that control "