nipoppy.workflows.PipelineTracker

class nipoppy.workflows.PipelineTracker(dpath_root, pipeline_name, pipeline_version=None, pipeline_step=None, participant_id=None, session_id=None, fpath_layout=None, logger=None, dry_run=False)

Pipeline tracker.

Parameters:

  • dpath_root (nipoppy.env.StrOrPathLike)

  • pipeline_name (str)

  • pipeline_version (Optional[str])

  • pipeline_step (Optional[str])

  • participant_id (str)

  • session_id (str)

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

  • logger (Optional[logging.Logger])

  • dry_run (bool)

check_status(relative_paths)

Check the processing status based on a list of expected paths.

Parameters:

relative_paths (nipoppy.env.StrOrPathLike)

get_participants_sessions_to_run(participant_id, session_id)

Get participant-session pairs with BIDS data to run the tracker on.

Parameters:

  • participant_id (Optional[str])

  • session_id (Optional[str])

run_cleanup()

Save the bagel file.

run_setup()

Load/initialize the bagel file.

run_single(participant_id, session_id)

Run tracker on a single participant/session.

Parameters:

  • participant_id (str)

  • session_id (str)

bagel: nipoppy.tabular.bagel.Bagel