nipoppy.workflows.tracker.PipelineTracker¶

class nipoppy.workflows.tracker.PipelineTracker(dpath_root, pipeline_name, pipeline_version=None, pipeline_step=None, participant_id=None, session_id=None, n_jobs=1, fpath_layout=None, verbose=False, dry_run=False)¶

Pipeline tracker.

Parameters:

dpath_root (nipoppy.env.StrOrPathLike)
pipeline_name (str)
pipeline_version (str | None)
pipeline_step (str | None)
participant_id (str)
session_id (str)
n_jobs (int)
fpath_layout (nipoppy.env.StrOrPathLike | None)
verbose (bool)
dry_run (bool)

static apply_analysis_level(participants_sessions, analysis_level)¶

Tracker: level is always participant-session.

Parameters:

participants_sessions (collections.abc.Iterable[str])
analysis_level (nipoppy.config.pipeline_step.AnalysisLevelType)

Return type:

list[tuple[str]]

check_status(relative_paths, relative_dpath_tarred=None)¶

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

Parameters:

relative_paths (nipoppy.env.StrOrPathLike)
relative_dpath_tarred (nipoppy.env.StrOrPathLike | None)

get_participants_sessions_to_run(participant_id, session_id)¶

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

Parameters:

participant_id (str | None)
session_id (str | None)

run_main()¶: Run the tracker workflow.

run_setup()¶: Load/initialize the processing status file.

run_single(participant_id, session_id)¶

Run tracker on a single participant/session.

Parameters:

participant_id (str)
session_id (str)

progress_bar_description = 'Tracking...'¶