nipoppy.workflows.ExtractionRunner¶
- class nipoppy.workflows.ExtractionRunner(dpath_root, pipeline_name, pipeline_version=None, pipeline_step=None, participant_id=None, session_id=None, simulate=False, write_list=None, fpath_layout=None, verbose=False, dry_run=False)¶
Extract imaging-derived phenotypes (IDPs) from processed data.
- Parameters:
dpath_root (nipoppy.env.StrOrPathLike)
pipeline_name (str)
pipeline_version (Optional[str])
pipeline_step (Optional[str])
participant_id (str)
session_id (str)
simulate (bool)
write_list (Optional[nipoppy.env.StrOrPathLike])
fpath_layout (Optional[nipoppy.env.StrOrPathLike])
verbose (bool)
dry_run (bool)
- get_participants_sessions_to_run(participant_id, session_id)¶
Return participant-session pairs to run the pipeline on.
- run_single(participant_id, session_id)¶
Run extractor on a single participant/session.
- property dpath_pipeline: pathlib.Path¶
Get the path to the derivatives directory associated with the extractor.
- Return type:
- property dpath_pipeline_idp: pathlib.Path¶
Return the path to the pipeline’s IDP directory.
- Return type:
- property dpath_pipeline_output: pathlib.Path¶
Return the path to the pipeline’s output directory.
- Return type:
- property dpaths_to_check: list[pathlib.Path]¶
Directory paths to create if needed during the setup phase.
- Return type:
- property pipeline_config: nipoppy.config.pipeline.ExtractionPipelineConfig¶
Get the user config for the extraction pipeline.
- Return type:
- property pipeline_step_config: nipoppy.config.pipeline_step.ExtractionPipelineStepConfig¶
Get the config for the relevant step of the extraction pipeline.
- property proc_pipeline_info: nipoppy.config.pipeline.PipelineInfo¶
Get info about the first processing pipeline associated with extractor.
Also make sure the it is in the config as a processing pipeline.
- Return type: