API

cubids.cubids: Main Module

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

The main CuBIDS class.

cubids.workflows: Workflow Functions

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

cubids.metadata_merge: Merging Metadata

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

cubids.validator: Validation

validator.build_validator_call(path[, ...])	Build a subprocess command to the bids validator.
validator.build_subject_paths(bids_dir)	Build a dictionary of BIDS directories with one subject each.
validator.run_validator(call)	Run the validator with subprocess.
validator.parse_validator_output(output)	Parse the JSON output of the BIDS validator into a pandas dataframe.
validator.get_val_dictionary()	Get value dictionary.