nipoppy.utils.bids

Utility functions for BIDS dataset manipulation.

Module Contents

nipoppy.utils.bids.add_pybids_ignore_patterns(current, new)

Add pattern(s) to ignore for PyBIDS.

Parameters:
nipoppy.utils.bids.check_participant_id(participant_id, raise_error=False)

Make sure a participant ID is valid.

Specifically: - Check that it does not have the sub- prefix, stripping it if it does - Check that it only has alphanumeric characters

Parameters:

  • participant_id (Optional[str]) – The participant ID to check. If None, returns None.

  • raise_error (bool, optional) – Whether to raise an error if the participant ID has the sub- prefix, by default False. Note: an error is always raised if the participant ID contains non-alphanumeric characters after being stripped of the sub- prefix.

Returns:

The participant ID without the BIDS prefix

Return type:

str

Raises:

ValueError –

nipoppy.utils.bids.check_session_id(session_id, raise_error=False)

Make sure a session ID is valid.

Specifically: - Check that it does not have the ses- prefix, stripping it if it does - Check that it only has alphanumeric characters

Parameters:

  • participant_id (Optional[str]) – The participant ID to check. If None, returns None.

  • raise_error (bool, optional) – Whether to raise an error if the session ID has the ses- prefix, by default False. Note: an error is always raised if the session ID contains non-alphanumeric characters even being stripped of the ses- prefix.

  • session_id (Optional[str])

Returns:

The session ID without the BIDS prefix

Return type:

str

Raises:

ValueError –

nipoppy.utils.bids.create_bids_db(dpath_bids, dpath_pybids_db=None, validate=False, reset_database=True, ignore_patterns=None, resolve_paths=True)

Create a BIDSLayout using an indexer.

Parameters:

  • dpath_bids (nipoppy.env.StrOrPathLike)

  • dpath_pybids_db (Optional[nipoppy.env.StrOrPathLike])

  • ignore_patterns (Optional[list[str | re.Pattern] | str | re.Pattern])

Return type:

bids.BIDSLayout

nipoppy.utils.bids.participant_id_to_bids_participant_id(participant_id)

Add the BIDS prefix to a participant ID.

Parameters:

participant_id (str)

Return type:

str

nipoppy.utils.bids.session_id_to_bids_session_id(session_id)

Add the BIDS prefix to a session ID.

If session_id is None, returns None.

Parameters:

session_id (Optional[str])

Return type:

str