`nipoppy.tabular.bagel`¶

Class for bagel tracker files.

Module Contents¶

class nipoppy.tabular.bagel.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.bagel.BagelModel(/, **data)¶

Bases: nipoppy.tabular.base.BaseTabularModel

A file generated by the trackers.

Contains process statuses for image processing pipelines.

Note: This class is called “model” to be consistent with Pydantic nomenclature, but it can be thought of as a schema for each row in the bagel file.

Parameters:: data (Any)

bids_participant: str | None¶

participant_id: str¶

pipeline_complete: str¶

pipeline_name: str¶

pipeline_starttime: str¶

pipeline_version: str¶

session: str | None¶

session_id: str¶

classmethod check_status(value)¶

Check that a status field has a valid value.

Parameters:: value (str)

validate_after()¶: Check fields.

nipoppy.tabular.bagel.STATUS_FAIL = 'FAIL'¶

nipoppy.tabular.bagel.STATUS_INCOMPLETE = 'INCOMPLETE'¶

nipoppy.tabular.bagel.STATUS_SUCCESS = 'SUCCESS'¶

nipoppy.tabular.bagel.STATUS_UNAVAILABLE = 'UNAVAILABLE'¶