nipoppy.tabular

Classes for tabular data representation/manipulation.

Submodules

Package Contents

class nipoppy.tabular.Bagel(*args, **kwargs)

Bases: nipoppy.tabular.base.BaseTabular

A file to track data availability/processing status.

col_bids_participant = 'bids_participant'
col_bids_session = 'session'
col_participant_id = 'participant_id'
col_pipeline_complete = 'pipeline_complete'
col_pipeline_name = 'pipeline_name'
col_pipeline_version = 'pipeline_version'
col_session_id = 'session_id'
index_cols
model
status_fail
status_incomplete
status_success
status_unavailable
get_completed_participants_sessions(pipeline_name, pipeline_version, participant_id=None, session_id=None)

Get participant-session pairs that have successfully completed a pipeline run.

Can optionally filter within a specific participant and/or session.

Parameters:

  • pipeline_name (str)

  • pipeline_version (str)

  • participant_id (Optional[str])

  • session_id (Optional[str])

class nipoppy.tabular.Doughnut(*args, session_ids=None, visit_ids=None, **kwargs)

Bases: nipoppy.tabular.manifest.Manifest

A dataset’s doughnut, for tracking DICOM-to-BIDS conversion status.

col_in_bids = 'in_bids'
col_in_raw_imaging = 'in_raw_imaging'
col_in_sourcedata = 'in_sourcedata'
col_participant_dicom_dir = 'participant_dicom_dir'
index_cols
model
status_cols
get_bidsified_participants_sessions(participant_id=None, session_id=None)

Get participants and sessions with BIDS data.

Parameters:

  • participant_id (Optional[str])

  • session_id (Optional[str])

get_downloaded_participants_sessions(participant_id=None, session_id=None)

Get participants and sessions with downloaded data.

Parameters:

  • participant_id (Optional[str])

  • session_id (Optional[str])

get_organized_participants_sessions(participant_id=None, session_id=None)

Get participants and sessions with organized data.

Parameters:

  • participant_id (Optional[str])

  • session_id (Optional[str])

get_status(participant_id, session_id, col)

Get one of the statuses for an existing record.

Parameters:

  • participant_id (str)

  • session_id (str)

  • col (str)

Return type:

bool

set_status(participant_id, session_id, col, status)

Set one of the statuses for an existing record.

Parameters:
Return type:

typing_extensions.Self

class nipoppy.tabular.Manifest(*args, session_ids=None, visit_ids=None, **kwargs)

Bases: nipoppy.tabular.base.BaseTabular

A dataset’s manifest.

col_datatype = 'datatype'
col_participant_id = 'participant_id'
col_session_id = 'session_id'
col_visit_id = 'visit_id'
index_cols
model
get_imaging_subset(session_id=None)

Get records with imaging data.

Parameters:

session_id (Optional[str])

get_participants_sessions(participant_id=None, session_id=None)

Get participant IDs and session IDs.

Parameters:

  • participant_id (Optional[str])

  • session_id (Optional[str])

classmethod load(*args, session_ids=None, visit_ids=None, validate=True, **kwargs)

Load the manifest.

Return type:

typing_extensions.Self

validate(*args, **kwargs)

Validate the manifest.

Return type:

typing_extensions.Self

nipoppy.tabular.generate_doughnut(manifest, dicom_dir_map, dpath_downloaded=None, dpath_organized=None, dpath_bidsified=None, empty=False, logger=None)

Generate a doughnut object.

Parameters:
Return type:

Doughnut

nipoppy.tabular.update_doughnut(doughnut, manifest, dicom_dir_map, dpath_downloaded=None, dpath_organized=None, dpath_bidsified=None, empty=False, logger=None)

Update an existing doughnut file.

Parameters:
Return type:

Doughnut