API

cubids.cubids: Main Module

cubids.cubids.CuBIDS(data_root[, ...])

The main CuBIDS class.

cubids.workflows: Workflow Functions

cubids.workflows.validate(bids_dir, ...)	Run the bids validator.
cubids.workflows.bids_sidecar_merge(...)	Merge critical keys from one sidecar to another.
cubids.workflows.group(bids_dir, container, ...)	Find key and param groups.
cubids.workflows.apply(bids_dir, ...)	Apply the tsv changes.
cubids.workflows.datalad_save(bids_dir, ...)	Perform datalad save.
cubids.workflows.undo(bids_dir, container)	Revert the most recent commit.
cubids.workflows.copy_exemplars(bids_dir, ...)	Create and save a directory with one subject from each acquisition group.
cubids.workflows.add_nifti_info(bids_dir, ...)	Add information from nifti files to the dataset's sidecars.
cubids.workflows.purge(bids_dir, container, ...)	Purge scan associations.
cubids.workflows.remove_metadata_fields(...)	Delete fields from metadata.
cubids.workflows.print_metadata_fields(...)	Print unique metadata fields.

cubids.metadata_merge: Merging Metadata

cubids.metadata_merge.check_merging_operations(...)	Check that the merges in an action tsv are possible.
cubids.metadata_merge.merge_without_overwrite(...)	Perform a safe metadata copy.
cubids.metadata_merge.merge_json_into_json(...)	Merge imaging metadata into JSON.
cubids.metadata_merge.get_acq_dictionary()	Create a BIDS data dictionary from dataframe columns.
cubids.metadata_merge.group_by_acquisition_sets(...)	Find unique sets of Key/Param groups across subjects.

cubids.validator: Validation

cubids.validator.build_validator_call(path)	Build a subprocess command to the bids validator.
cubids.validator.build_subject_paths(bids_dir)	Build a list of BIDS dirs with 1 subject each.
cubids.validator.run_validator(call)	Run the validator with subprocess.
cubids.validator.parse_validator_output(output)	Parse the JSON output of the BIDS validator into a pandas dataframe.
cubids.validator.get_val_dictionary()	Get value dictionary.