API

`cubids.cubids`: Main Module

The main CuBIDS class.

`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[, n_cpus])	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, ...[, n_cpus])	Add information from nifti files to the dataset's sidecars.
`workflows.add_file_collections`(bids_dir, ...)	Add file collection metadata to the sidecars of each NIfTI file in the BIDS dataset.
`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.

`entity_sets.parse_entity_set`(value)	Validate an entity set copied from the summary and return it.
`entity_sets.load_entity_set_changes`(...)	Load exact entity set substitutions from CLI strings or mapping tables.
`entity_sets.load_entity_set_removals`(...)	Load exact entity sets to delete from CLI strings or table files.
`entity_sets.apply_entity_set_changes`(...)	Apply exact entity set substitutions to a summary dataframe in memory.
`entity_sets.apply_entity_set_removals`(...)	Mark parameter groups with exact planned entity sets for deletion.

`file_collections.get_collection_rules`(schema)	Build the file collection rules that apply to a dataset from the BIDS schema.
`file_collections.get_collection_rule`(rules, ...)	Return the rule for the collection a file can belong to.
`file_collections.collection_context`(...)	Build a key shared by exactly the files in one collection.
`file_collections.collect_file_collections`(...)	Build a list of files in a file collection for a given base file.
`file_collections.analyze_collection_variant_consistency`(...)	Inspect file collections and propose aligned variants.
`file_collections.apply_collection_variant_proposals`(...)	Write globally unambiguous file-collection rename suggestions into a summary.
`file_collections.validate_collection_deletions`(...)	Fail before mutation when deletions would split a file collection.
`file_collections.validate_collection_renames`(...)	Ensure every file collection being renamed has compatible planned entities.

`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.

`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.