cubids.cubids.CuBIDS

class CuBIDS(data_root, use_datalad=False, acq_group_level='subject', grouping_config=None, force_unlock=False, schema_json=None, ignore_entities=None)[source]

The main CuBIDS class.

Parameters:

  • data_root (str) – Path to the root of the BIDS dataset.

  • use_datalad (bool, optional) – If True, use datalad to track changes to the BIDS dataset. Default is False.

  • acq_group_level (str, optional) – The level at which to group scans. Default is “subject”.

  • grouping_config (str, optional) – Path to the grouping config file. Default is None, in which case the default config in CuBIDS is used.

  • force_unlock (bool, optional) – If True, force unlock all files in the BIDS dataset. Default is False.

  • schema_json (str, optional) – Path to a BIDS schema JSON file. Default is None, in which case the default schema in CuBIDS is used.

  • ignore_entities (list[str] or None, optional) – BIDS entities to ignore when creating entity sets. Default is None.

Variables:

  • path (str) – Path to the root of the BIDS dataset.

  • _layout (bids.layout.BIDSLayout) – The BIDSLayout object.

  • keys_files (dict) – A dictionary of entity sets and the files that belong to them.

  • fieldmaps_cached (bool) – If True, the fieldmaps have been cached.

  • datalad_ready (bool) – If True, the datalad dataset has been initialized.

  • datalad_handle (datalad.api.Dataset) – The datalad dataset handle.

  • old_filenames (list) – A list of old filenames.

  • new_filenames (list) – A list of new filenames.

  • IF_rename_paths (list) – A list of IntendedFor paths that have been renamed.

  • grouping_config (dict) – The grouping config dictionary.

  • acq_group_level (str) – The level at which to group scans.

  • scans_txt (str) – Path to the .txt file that lists the scans you want to be deleted from the dataset, along with their associations.

  • force_unlock (bool) – If True, force unlock all files in the BIDS dataset.

  • cubids_code_dir (bool) – If True, the CuBIDS code directory exists.

  • data_dict (dict) – A data dictionary for TSV outputs.

  • use_datalad (bool) – If True, use datalad to track changes to the BIDS dataset.

  • schema (dict) – The BIDS schema dictionary.

  • is_longitudinal (bool) – If True, adds “ses” in filepath.