Index A | B | C | D | E | F | G | H | I | J | L | M | N | P | R | S | T | U | V A add_bind_path() (nipoppy.config.container.ContainerConfig method) (nipoppy.config.ContainerConfig method) add_bind_path_to_args() (in module nipoppy.config.container) add_logfile() (in module nipoppy.logger) add_or_update_records() (nipoppy.tabular.base.BaseTabular method) add_path_suffix() (in module nipoppy.utils) add_path_timestamp() (in module nipoppy.utils) add_pybids_ignore_patterns() (in module nipoppy.utils) ANALYSIS_LEVEL (nipoppy.config.BasePipelineStepConfig attribute) (nipoppy.config.pipeline_step.BasePipelineStepConfig attribute) API apply_analysis_level() (in module nipoppy.workflows.pipeline) apply_fname_mapping() (nipoppy.workflows.dicom_reorg.DicomReorgWorkflow method) (nipoppy.workflows.DicomReorgWorkflow method) apply_substitutions_to_json() (in module nipoppy.utils) (nipoppy.config.Config method) (nipoppy.config.main.Config method) APPTAINER_BIND_FLAG (in module nipoppy.config.container) APPTAINER_BIND_SEP (in module nipoppy.config.container) APPTAINER_ENVVAR_PREFIXES (in module nipoppy.config.container) ARGS (nipoppy.config.container.ContainerConfig attribute) (nipoppy.config.ContainerConfig attribute) B bagel (nipoppy.workflows.PipelineTracker attribute) (nipoppy.workflows.tracker.PipelineTracker attribute) BIDS bids_participant (nipoppy.tabular.bagel.BagelModel attribute) BIDS_PIPELINES (nipoppy.config.Config attribute) (nipoppy.config.main.Config attribute) BIDS_SESSION_PREFIX (in module nipoppy.env) bids_source (nipoppy.workflows.dataset_init.InitWorkflow attribute) (nipoppy.workflows.InitWorkflow attribute) BIDS_SUBJECT_PREFIX (in module nipoppy.env) Boutiques boutiques_config (nipoppy.workflows.BasePipelineWorkflow property) (nipoppy.workflows.pipeline.BasePipelineWorkflow property) BOUTIQUES_CONFIG_KEY (in module nipoppy.config.boutiques) BOUTIQUES_CUSTOM_KEY (in module nipoppy.config.boutiques) C capture_warnings() (in module nipoppy.logger) check_container_args() (in module nipoppy.config.container) check_container_command() (in module nipoppy.config.container) check_dicoms (nipoppy.workflows.dicom_reorg.DicomReorgWorkflow attribute) (nipoppy.workflows.DicomReorgWorkflow attribute) check_dir() (nipoppy.workflows.BasePipelineWorkflow method) (nipoppy.workflows.pipeline.BasePipelineWorkflow method) check_input() (nipoppy.config.Config class method) (nipoppy.config.main.Config class method) check_participant_id() (in module nipoppy.utils) check_pipeline_step() (nipoppy.workflows.BasePipelineWorkflow method) (nipoppy.workflows.pipeline.BasePipelineWorkflow method) check_pipeline_version() (nipoppy.workflows.BasePipelineWorkflow method) (nipoppy.workflows.pipeline.BasePipelineWorkflow method) check_session_id() (in module nipoppy.utils) check_status() (nipoppy.tabular.bagel.BagelModel class method) (nipoppy.workflows.PipelineTracker method) (nipoppy.workflows.tracker.PipelineTracker method) check_tracker_configs() (in module nipoppy.config.tracker) CLI col_bids_participant (nipoppy.tabular.Bagel attribute) (nipoppy.tabular.bagel.Bagel attribute) col_bids_session (nipoppy.tabular.Bagel attribute) (nipoppy.tabular.bagel.Bagel attribute) col_datatype (nipoppy.tabular.Manifest attribute) (nipoppy.tabular.manifest.Manifest attribute) col_in_bids (nipoppy.tabular.Doughnut attribute) (nipoppy.tabular.doughnut.Doughnut attribute) col_in_raw_imaging (nipoppy.tabular.Doughnut attribute) (nipoppy.tabular.doughnut.Doughnut attribute) col_in_sourcedata (nipoppy.tabular.Doughnut attribute) (nipoppy.tabular.doughnut.Doughnut attribute) col_participant_dicom_dir (nipoppy.tabular.dicom_dir_map.DicomDirMap attribute) (nipoppy.tabular.Doughnut attribute) (nipoppy.tabular.doughnut.Doughnut attribute) col_participant_id (nipoppy.tabular.Bagel attribute) (nipoppy.tabular.bagel.Bagel attribute) (nipoppy.tabular.dicom_dir_map.DicomDirMap attribute) (nipoppy.tabular.Manifest attribute) (nipoppy.tabular.manifest.Manifest attribute) col_pipeline_complete (nipoppy.tabular.Bagel attribute) (nipoppy.tabular.bagel.Bagel attribute) col_pipeline_name (nipoppy.tabular.Bagel attribute) (nipoppy.tabular.bagel.Bagel attribute) col_pipeline_version (nipoppy.tabular.Bagel attribute) (nipoppy.tabular.bagel.Bagel attribute) col_session_id (nipoppy.tabular.Bagel attribute) (nipoppy.tabular.bagel.Bagel attribute) (nipoppy.tabular.dicom_dir_map.DicomDirMap attribute) (nipoppy.tabular.Manifest attribute) (nipoppy.tabular.manifest.Manifest attribute) col_visit_id (nipoppy.tabular.Manifest attribute) (nipoppy.tabular.manifest.Manifest attribute) COMMAND (nipoppy.config.container.ContainerConfig attribute) (nipoppy.config.ContainerConfig attribute) concatenate() (nipoppy.tabular.base.BaseTabular method) conda config (nipoppy.layout.DatasetLayout attribute) (nipoppy.workflows.base.BaseWorkflow property) (nipoppy.workflows.BaseWorkflow property) CONTAINER_CONFIG CONTAINER_INFO (nipoppy.config.BasePipelineConfig attribute) (nipoppy.config.pipeline.BasePipelineConfig attribute) CONTAINER_SUBCOMMAND (nipoppy.config.boutiques.BoutiquesConfig attribute) (nipoppy.config.BoutiquesConfig attribute) copy() (nipoppy.workflows.base.BaseWorkflow method) (nipoppy.workflows.BaseWorkflow method) copy_files (nipoppy.workflows.dicom_reorg.DicomReorgWorkflow attribute) (nipoppy.workflows.DicomReorgWorkflow attribute) copytree() (nipoppy.workflows.base.BaseWorkflow method) (nipoppy.workflows.BaseWorkflow method) create_bids_db() (in module nipoppy.utils) create_symlink() (nipoppy.workflows.base.BaseWorkflow method) (nipoppy.workflows.BaseWorkflow method) CUSTOM (nipoppy.config.Config attribute) (nipoppy.config.main.Config attribute) D DATASET_NAME (nipoppy.config.Config attribute) (nipoppy.config.main.Config attribute) datatype (nipoppy.tabular.manifest.ManifestModel attribute) DATE_FORMAT (in module nipoppy.logger) DEFAULT_LAYOUT_INFO (in module nipoppy.layout) DESCRIPTION (nipoppy.config.BasePipelineConfig attribute) (nipoppy.config.pipeline.BasePipelineConfig attribute) description (nipoppy.layout.PathInfo attribute) descriptor (nipoppy.workflows.BasePipelineWorkflow property) (nipoppy.workflows.pipeline.BasePipelineWorkflow property) DESCRIPTOR_FILE (nipoppy.config.BasePipelineStepConfig attribute) (nipoppy.config.pipeline_step.BasePipelineStepConfig attribute) dicom_dir_map (nipoppy.workflows.base.BaseWorkflow property) (nipoppy.workflows.BaseWorkflow property) DICOM_DIR_MAP_FILE (nipoppy.config.Config attribute) (nipoppy.config.main.Config attribute) DICOM_DIR_PARTICIPANT_FIRST (nipoppy.config.Config attribute) (nipoppy.config.main.Config attribute) dname_pipeline_output (nipoppy.layout.DatasetLayout attribute) dname_pipeline_work (nipoppy.layout.DatasetLayout attribute) doughnut (nipoppy.workflows.base.BaseWorkflow property) (nipoppy.workflows.BaseWorkflow property) Doughnut file dpath_assessments (nipoppy.layout.DatasetLayout attribute) (nipoppy.layout.LayoutConfig attribute) dpath_bids (nipoppy.layout.DatasetLayout attribute) (nipoppy.layout.LayoutConfig attribute) dpath_bids_db (nipoppy.layout.DatasetLayout attribute) (nipoppy.layout.LayoutConfig attribute) dpath_bids_ignore_patterns (nipoppy.layout.DatasetLayout attribute) (nipoppy.layout.LayoutConfig attribute) dpath_containers (nipoppy.layout.DatasetLayout attribute) (nipoppy.layout.LayoutConfig attribute) DPATH_DATA (in module nipoppy.utils) dpath_demographics (nipoppy.layout.DatasetLayout attribute) (nipoppy.layout.LayoutConfig attribute) dpath_derivatives (nipoppy.layout.DatasetLayout attribute) (nipoppy.layout.LayoutConfig attribute) dpath_descriptions (nipoppy.layout.DatasetLayout property) DPATH_DESCRIPTORS (in module nipoppy.utils) dpath_descriptors (nipoppy.layout.DatasetLayout attribute) (nipoppy.layout.LayoutConfig attribute) dpath_downloads (nipoppy.layout.DatasetLayout attribute) (nipoppy.layout.LayoutConfig attribute) DPATH_EXAMPLES (in module nipoppy.utils) DPATH_INVOCATIONS (in module nipoppy.utils) dpath_invocations (nipoppy.layout.DatasetLayout attribute) (nipoppy.layout.LayoutConfig attribute) DPATH_LAYOUTS (in module nipoppy.utils) dpath_logs (nipoppy.layout.DatasetLayout attribute) (nipoppy.layout.LayoutConfig attribute) dpath_pipeline (nipoppy.workflows.BasePipelineWorkflow property) (nipoppy.workflows.pipeline.BasePipelineWorkflow property) dpath_pipeline_bids_db (nipoppy.workflows.BasePipelineWorkflow property) (nipoppy.workflows.pipeline.BasePipelineWorkflow property) dpath_pipeline_output (nipoppy.workflows.BasePipelineWorkflow property) (nipoppy.workflows.pipeline.BasePipelineWorkflow property) dpath_pipeline_work (nipoppy.workflows.BasePipelineWorkflow property) (nipoppy.workflows.pipeline.BasePipelineWorkflow property) dpath_proc (nipoppy.layout.DatasetLayout attribute) (nipoppy.layout.LayoutConfig attribute) dpath_pybids (nipoppy.layout.DatasetLayout attribute) (nipoppy.layout.LayoutConfig attribute) dpath_raw_imaging (nipoppy.layout.DatasetLayout attribute) (nipoppy.layout.LayoutConfig attribute) dpath_releases (nipoppy.layout.DatasetLayout attribute) (nipoppy.layout.LayoutConfig attribute) dpath_root (nipoppy.layout.DatasetLayout attribute) (nipoppy.workflows.base.BaseWorkflow attribute) (nipoppy.workflows.BaseWorkflow attribute) dpath_scratch (nipoppy.layout.DatasetLayout attribute) (nipoppy.layout.LayoutConfig attribute) dpath_sourcedata (nipoppy.layout.DatasetLayout attribute) (nipoppy.layout.LayoutConfig attribute) dpath_tabular (nipoppy.layout.DatasetLayout attribute) (nipoppy.layout.LayoutConfig attribute) DPATH_TRACKER_CONFIGS (in module nipoppy.utils) dpath_tracker_configs (nipoppy.layout.DatasetLayout attribute) (nipoppy.layout.LayoutConfig attribute) dpaths (nipoppy.layout.DatasetLayout property) dpaths_to_check (nipoppy.workflows.BasePipelineWorkflow property) (nipoppy.workflows.bids_conversion.BidsConversionRunner property) (nipoppy.workflows.BidsConversionRunner property) (nipoppy.workflows.pipeline.BasePipelineWorkflow property) (nipoppy.workflows.PipelineRunner property) (nipoppy.workflows.runner.PipelineRunner property) dry_run (nipoppy.workflows.base.BaseWorkflow attribute) (nipoppy.workflows.BaseWorkflow attribute) E empty (nipoppy.workflows.doughnut.DoughnutWorkflow attribute) (nipoppy.workflows.DoughnutWorkflow attribute) ENV_VARS (nipoppy.config.container.ContainerConfig attribute) (nipoppy.config.ContainerConfig attribute) equals() (nipoppy.tabular.base.BaseTabular method) F FAILURE (nipoppy.env.LogColor attribute) FIELD_DESCRIPTION_MAP (in module nipoppy.utils) FILE (nipoppy.config.container.ContainerInfo attribute) find_duplicates() (nipoppy.tabular.base.BaseTabular method) fname_readme (nipoppy.workflows.dataset_init.InitWorkflow attribute) (nipoppy.workflows.InitWorkflow attribute) FORMAT_FILE (in module nipoppy.logger) FORMAT_RICH (in module nipoppy.logger) fpath_config (nipoppy.layout.DatasetLayout attribute) (nipoppy.layout.LayoutConfig attribute) fpath_container (nipoppy.workflows.BasePipelineWorkflow property) (nipoppy.workflows.pipeline.BasePipelineWorkflow property) FPATH_DEFAULT_LAYOUT (in module nipoppy.utils) fpath_doughnut (nipoppy.layout.DatasetLayout attribute) (nipoppy.layout.LayoutConfig attribute) fpath_imaging_bagel (nipoppy.layout.DatasetLayout attribute) (nipoppy.layout.LayoutConfig attribute) fpath_layout (nipoppy.workflows.base.BaseWorkflow attribute) (nipoppy.workflows.BaseWorkflow attribute) fpath_manifest (nipoppy.layout.DatasetLayout attribute) (nipoppy.layout.LayoutConfig attribute) FPATH_SAMPLE_CONFIG (in module nipoppy.utils) FPATH_SAMPLE_CONFIG_FULL (in module nipoppy.utils) FPATH_SAMPLE_DICOM_DIR_MAP (in module nipoppy.utils) FPATH_SAMPLE_MANIFEST (in module nipoppy.utils) fpath_spec (nipoppy.layout.DatasetLayout attribute) fpaths (nipoppy.layout.DatasetLayout property) G generate_doughnut() (in module nipoppy.tabular) (in module nipoppy.tabular.doughnut) generate_fpath_log() (nipoppy.workflows.base.BaseWorkflow method) (nipoppy.workflows.BasePipelineWorkflow method) (nipoppy.workflows.BaseWorkflow method) (nipoppy.workflows.pipeline.BasePipelineWorkflow method) GENERATE_PYBIDS_DATABASE (nipoppy.config.pipeline_step.ProcPipelineStepConfig attribute) (nipoppy.config.ProcPipelineStepConfig attribute) get_bidsified_participants_sessions() (nipoppy.tabular.Doughnut method) (nipoppy.tabular.doughnut.Doughnut method) get_boutiques_config_from_descriptor() (in module nipoppy.config.boutiques) get_completed_participants_sessions() (nipoppy.tabular.Bagel method) (nipoppy.tabular.bagel.Bagel method) get_dicom_dir() (nipoppy.tabular.dicom_dir_map.DicomDirMap method) get_diff() (nipoppy.tabular.base.BaseTabular method) get_downloaded_participants_sessions() (nipoppy.tabular.Doughnut method) (nipoppy.tabular.doughnut.Doughnut method) get_dpath_bids_db() (nipoppy.layout.DatasetLayout method) get_dpath_pipeline() (nipoppy.layout.DatasetLayout method) get_dpath_pipeline_output() (nipoppy.layout.DatasetLayout method) get_dpath_pipeline_work() (nipoppy.layout.DatasetLayout method) get_fpath_container() (nipoppy.config.BasePipelineConfig method) (nipoppy.config.pipeline.BasePipelineConfig method) get_fpaths_to_reorg() (nipoppy.workflows.dicom_reorg.DicomReorgWorkflow method) (nipoppy.workflows.DicomReorgWorkflow method) get_full_path() (nipoppy.layout.DatasetLayout method) get_imaging_subset() (nipoppy.tabular.Manifest method) (nipoppy.tabular.manifest.Manifest method) get_logger() (in module nipoppy.logger) get_organized_participants_sessions() (nipoppy.tabular.Doughnut method) (nipoppy.tabular.doughnut.Doughnut method) get_participants_sessions() (nipoppy.tabular.Manifest method) (nipoppy.tabular.manifest.Manifest method) get_participants_sessions_to_run() (nipoppy.workflows.BasePipelineWorkflow method) (nipoppy.workflows.bids_conversion.BidsConversionRunner method) (nipoppy.workflows.BidsConversionRunner method) (nipoppy.workflows.dicom_reorg.DicomReorgWorkflow method) (nipoppy.workflows.DicomReorgWorkflow method) (nipoppy.workflows.pipeline.BasePipelineWorkflow method) (nipoppy.workflows.PipelineRunner method) (nipoppy.workflows.PipelineTracker method) (nipoppy.workflows.runner.PipelineRunner method) (nipoppy.workflows.tracker.PipelineTracker method) get_path_info() (nipoppy.layout.LayoutConfig method) get_paths() (nipoppy.layout.DatasetLayout method) get_pipeline_config() (nipoppy.config.Config method) (nipoppy.config.main.Config method) get_pipeline_tag() (in module nipoppy.utils) get_pipeline_version() (nipoppy.config.Config method) (nipoppy.config.main.Config method) get_series_class() (nipoppy.tabular.base.BaseTabular method) get_status() (nipoppy.tabular.Doughnut method) (nipoppy.tabular.doughnut.Doughnut method) get_step_config() (nipoppy.config.BasePipelineConfig method) (nipoppy.config.pipeline.BasePipelineConfig method) group (nipoppy.config.pipeline_step.AnalysisLevelType attribute) H HPC I in_bids (nipoppy.tabular.doughnut.DoughnutModel attribute) in_raw_imaging (nipoppy.tabular.doughnut.DoughnutModel attribute) in_sourcedata (nipoppy.tabular.doughnut.DoughnutModel attribute) index_cols (nipoppy.tabular.Bagel attribute) (nipoppy.tabular.bagel.Bagel attribute) (nipoppy.tabular.base.BaseTabular attribute) (nipoppy.tabular.dicom_dir_map.DicomDirMap attribute) (nipoppy.tabular.Doughnut attribute) (nipoppy.tabular.doughnut.Doughnut attribute) (nipoppy.tabular.Manifest attribute) (nipoppy.tabular.manifest.Manifest attribute) INHERIT (nipoppy.config.container.ContainerConfig attribute) (nipoppy.config.ContainerConfig attribute) invocation (nipoppy.workflows.BasePipelineWorkflow property) (nipoppy.workflows.pipeline.BasePipelineWorkflow property) INVOCATION_FILE (nipoppy.config.BasePipelineStepConfig attribute) (nipoppy.config.pipeline_step.BasePipelineStepConfig attribute) is_derived_dicom() (in module nipoppy.workflows.dicom_reorg) IS_TESTING (in module nipoppy.env) J JSON L launch_boutiques_run() (nipoppy.workflows.PipelineRunner method) (nipoppy.workflows.runner.PipelineRunner method) layout (nipoppy.workflows.base.BaseWorkflow attribute) (nipoppy.workflows.BaseWorkflow attribute) load() (nipoppy.config.Config class method) (nipoppy.config.main.Config class method) (nipoppy.tabular.base.BaseTabular class method) (nipoppy.tabular.Manifest class method) (nipoppy.tabular.manifest.Manifest class method) load_json() (in module nipoppy.utils) load_or_generate() (nipoppy.tabular.dicom_dir_map.DicomDirMap class method) log_command() (nipoppy.workflows.base.BaseWorkflow method) (nipoppy.workflows.BaseWorkflow method) log_prefix_run (nipoppy.workflows.base.BaseWorkflow attribute) (nipoppy.workflows.BaseWorkflow attribute) log_prefix_run_stderr (nipoppy.workflows.base.BaseWorkflow attribute) (nipoppy.workflows.BaseWorkflow attribute) log_prefix_run_stdout (nipoppy.workflows.base.BaseWorkflow attribute) (nipoppy.workflows.BaseWorkflow attribute) LOG_SUFFIX (in module nipoppy.workflows.base) logger (nipoppy.workflows.base.BaseWorkflow attribute) (nipoppy.workflows.BaseWorkflow attribute) M manifest (nipoppy.workflows.base.BaseWorkflow property) (nipoppy.workflows.BaseWorkflow property) merge() (nipoppy.config.container.ContainerConfig method) (nipoppy.config.ContainerConfig method) mkdir() (nipoppy.workflows.base.BaseWorkflow method) (nipoppy.workflows.BaseWorkflow method) model (nipoppy.tabular.Bagel attribute) (nipoppy.tabular.bagel.Bagel attribute) (nipoppy.tabular.base.BaseTabular property) (nipoppy.tabular.dicom_dir_map.DicomDirMap attribute) (nipoppy.tabular.Doughnut attribute) (nipoppy.tabular.doughnut.Doughnut attribute) (nipoppy.tabular.Manifest attribute) (nipoppy.tabular.manifest.Manifest attribute) model_config (nipoppy.config.BidsPipelineConfig attribute) (nipoppy.config.BidsPipelineStepConfig attribute) (nipoppy.config.boutiques.BoutiquesConfig attribute) (nipoppy.config.BoutiquesConfig attribute) (nipoppy.config.Config attribute) (nipoppy.config.container.ContainerConfig attribute) (nipoppy.config.container.ContainerInfo attribute) (nipoppy.config.ContainerConfig attribute) (nipoppy.config.main.Config attribute) (nipoppy.config.pipeline.BidsPipelineConfig attribute) (nipoppy.config.pipeline.ProcPipelineConfig attribute) (nipoppy.config.pipeline_step.BidsPipelineStepConfig attribute) (nipoppy.config.pipeline_step.ProcPipelineStepConfig attribute) (nipoppy.config.ProcPipelineConfig attribute) (nipoppy.config.ProcPipelineStepConfig attribute) (nipoppy.config.tracker.TrackerConfig attribute) (nipoppy.config.TrackerConfig attribute) (nipoppy.layout.LayoutConfig attribute) (nipoppy.tabular.manifest.ManifestModel attribute) module nipoppy nipoppy.base nipoppy.config nipoppy.config.boutiques nipoppy.config.container nipoppy.config.main nipoppy.config.pipeline nipoppy.config.pipeline_step nipoppy.config.tracker nipoppy.env nipoppy.layout nipoppy.logger nipoppy.tabular nipoppy.tabular.bagel nipoppy.tabular.base nipoppy.tabular.dicom_dir_map nipoppy.tabular.doughnut nipoppy.tabular.manifest nipoppy.utils nipoppy.workflows nipoppy.workflows.base nipoppy.workflows.bids_conversion nipoppy.workflows.dataset_init nipoppy.workflows.dicom_reorg nipoppy.workflows.doughnut nipoppy.workflows.pipeline nipoppy.workflows.runner nipoppy.workflows.tracker MRI N n_success (nipoppy.workflows.BasePipelineWorkflow attribute) (nipoppy.workflows.dicom_reorg.DicomReorgWorkflow attribute) (nipoppy.workflows.DicomReorgWorkflow attribute) (nipoppy.workflows.pipeline.BasePipelineWorkflow attribute) n_total (nipoppy.workflows.BasePipelineWorkflow attribute) (nipoppy.workflows.dicom_reorg.DicomReorgWorkflow attribute) (nipoppy.workflows.DicomReorgWorkflow attribute) (nipoppy.workflows.pipeline.BasePipelineWorkflow attribute) NAME (nipoppy.config.BasePipelineConfig attribute) (nipoppy.config.BasePipelineStepConfig attribute) (nipoppy.config.pipeline.BasePipelineConfig attribute) (nipoppy.config.pipeline_step.BasePipelineStepConfig attribute) (nipoppy.config.tracker.TrackerConfig attribute) (nipoppy.config.TrackerConfig attribute) name (nipoppy.workflows.base.BaseWorkflow attribute) (nipoppy.workflows.BaseWorkflow attribute) (nipoppy.workflows.bids_conversion.BidsConversionRunner attribute) (nipoppy.workflows.BidsConversionRunner attribute) nipoppy module nipoppy.base module nipoppy.base.Base (built-in class) nipoppy.config module nipoppy.config.BasePipelineConfig (built-in class) nipoppy.config.BasePipelineStepConfig (built-in class) nipoppy.config.BidsPipelineConfig (built-in class) nipoppy.config.BidsPipelineStepConfig (built-in class) nipoppy.config.boutiques module nipoppy.config.boutiques.BoutiquesConfig (built-in class) nipoppy.config.BoutiquesConfig (built-in class) nipoppy.config.Config (built-in class) nipoppy.config.container module nipoppy.config.container.ContainerConfig (built-in class) nipoppy.config.container.ContainerInfo (built-in class) nipoppy.config.ContainerConfig (built-in class) nipoppy.config.main module nipoppy.config.main.Config (built-in class) nipoppy.config.pipeline module nipoppy.config.pipeline.BasePipelineConfig (built-in class) nipoppy.config.pipeline.BidsPipelineConfig (built-in class) nipoppy.config.pipeline.ProcPipelineConfig (built-in class) nipoppy.config.pipeline_step module nipoppy.config.pipeline_step.AnalysisLevelType (built-in class) nipoppy.config.pipeline_step.BasePipelineStepConfig (built-in class) nipoppy.config.pipeline_step.BidsPipelineStepConfig (built-in class) nipoppy.config.pipeline_step.ProcPipelineStepConfig (built-in class) nipoppy.config.ProcPipelineConfig (built-in class) nipoppy.config.ProcPipelineStepConfig (built-in class) nipoppy.config.tracker module nipoppy.config.tracker.TrackerConfig (built-in class) nipoppy.config.TrackerConfig (built-in class) nipoppy.env module nipoppy.env.LogColor (built-in class) nipoppy.env.ReturnCode (built-in class) nipoppy.layout module nipoppy.layout.DatasetLayout (built-in class) nipoppy.layout.DpathInfo (built-in class) nipoppy.layout.FpathInfo (built-in class) nipoppy.layout.LayoutConfig (built-in class) nipoppy.layout.OptionalFpathInfo (built-in class) nipoppy.layout.PathInfo (built-in class) nipoppy.logger module nipoppy.tabular module nipoppy.tabular.bagel module nipoppy.tabular.Bagel (built-in class) nipoppy.tabular.bagel.Bagel (built-in class) nipoppy.tabular.bagel.BagelModel (built-in class) nipoppy.tabular.base module nipoppy.tabular.base.BaseTabular (built-in class) nipoppy.tabular.base.BaseTabularModel (built-in class) nipoppy.tabular.dicom_dir_map module nipoppy.tabular.dicom_dir_map.DicomDirMap (built-in class) nipoppy.tabular.dicom_dir_map.DicomDirMapModel (built-in class) nipoppy.tabular.doughnut module nipoppy.tabular.Doughnut (built-in class) nipoppy.tabular.doughnut.Doughnut (built-in class) nipoppy.tabular.doughnut.DoughnutModel (built-in class) nipoppy.tabular.manifest module nipoppy.tabular.Manifest (built-in class) nipoppy.tabular.manifest.Manifest (built-in class) nipoppy.tabular.manifest.ManifestModel (built-in class) nipoppy.utils module nipoppy.workflows module nipoppy.workflows.base module nipoppy.workflows.base.BaseWorkflow (built-in class) nipoppy.workflows.BasePipelineWorkflow (built-in class) nipoppy.workflows.BaseWorkflow (built-in class) nipoppy.workflows.bids_conversion module nipoppy.workflows.bids_conversion.BidsConversionRunner (built-in class) nipoppy.workflows.BidsConversionRunner (built-in class) nipoppy.workflows.dataset_init module nipoppy.workflows.dataset_init.InitWorkflow (built-in class) nipoppy.workflows.dicom_reorg module nipoppy.workflows.dicom_reorg.DicomReorgWorkflow (built-in class) nipoppy.workflows.DicomReorgWorkflow (built-in class) nipoppy.workflows.doughnut module nipoppy.workflows.doughnut.DoughnutWorkflow (built-in class) nipoppy.workflows.DoughnutWorkflow (built-in class) nipoppy.workflows.InitWorkflow (built-in class) nipoppy.workflows.pipeline module nipoppy.workflows.pipeline.BasePipelineWorkflow (built-in class) nipoppy.workflows.PipelineRunner (built-in class) nipoppy.workflows.PipelineTracker (built-in class) nipoppy.workflows.runner module nipoppy.workflows.runner.PipelineRunner (built-in class) nipoppy.workflows.tracker module nipoppy.workflows.tracker.PipelineTracker (built-in class) P PARTIAL_SUCCESS (nipoppy.env.LogColor attribute) (nipoppy.env.ReturnCode attribute) participant (nipoppy.config.pipeline_step.AnalysisLevelType attribute) participant_dicom_dir (nipoppy.tabular.dicom_dir_map.DicomDirMapModel attribute) (nipoppy.tabular.doughnut.DoughnutModel attribute) participant_id (nipoppy.tabular.bagel.BagelModel attribute) (nipoppy.tabular.dicom_dir_map.DicomDirMapModel attribute) (nipoppy.tabular.manifest.ManifestModel attribute) (nipoppy.workflows.BasePipelineWorkflow attribute) (nipoppy.workflows.pipeline.BasePipelineWorkflow attribute) participant_id_to_bids_participant() (in module nipoppy.utils) participant_session (nipoppy.config.pipeline_step.AnalysisLevelType attribute) path (nipoppy.layout.PathInfo attribute) path_infos (nipoppy.layout.LayoutConfig property) path_labels (nipoppy.layout.LayoutConfig property) path_sep (nipoppy.workflows.base.BaseWorkflow attribute) (nipoppy.workflows.BaseWorkflow attribute) PATHS (nipoppy.config.tracker.TrackerConfig attribute) (nipoppy.config.TrackerConfig attribute) pipeline_complete (nipoppy.tabular.bagel.BagelModel attribute) pipeline_config (nipoppy.workflows.BasePipelineWorkflow property) (nipoppy.workflows.bids_conversion.BidsConversionRunner property) (nipoppy.workflows.BidsConversionRunner property) (nipoppy.workflows.pipeline.BasePipelineWorkflow property) pipeline_name (nipoppy.tabular.bagel.BagelModel attribute) (nipoppy.workflows.BasePipelineWorkflow attribute) (nipoppy.workflows.pipeline.BasePipelineWorkflow attribute) pipeline_starttime (nipoppy.tabular.bagel.BagelModel attribute) pipeline_step (nipoppy.workflows.BasePipelineWorkflow attribute) (nipoppy.workflows.pipeline.BasePipelineWorkflow attribute) pipeline_step_config (nipoppy.workflows.BasePipelineWorkflow property) (nipoppy.workflows.bids_conversion.BidsConversionRunner property) (nipoppy.workflows.BidsConversionRunner property) (nipoppy.workflows.pipeline.BasePipelineWorkflow property) pipeline_version (nipoppy.tabular.bagel.BagelModel attribute) (nipoppy.workflows.BasePipelineWorkflow attribute) (nipoppy.workflows.pipeline.BasePipelineWorkflow attribute) prepare_container() (in module nipoppy.config.container) PROC_PIPELINES (nipoppy.config.Config attribute) (nipoppy.config.main.Config attribute) process_container_config() (nipoppy.workflows.PipelineRunner method) (nipoppy.workflows.runner.PipelineRunner method) process_template_json() (nipoppy.workflows.BasePipelineWorkflow method) (nipoppy.workflows.pipeline.BasePipelineWorkflow method) process_template_str() (in module nipoppy.utils) propagate_container_config() (nipoppy.config.Config method) (nipoppy.config.main.Config method) PYBIDS_IGNORE_FILE (nipoppy.config.pipeline_step.ProcPipelineStepConfig attribute) (nipoppy.config.ProcPipelineStepConfig attribute) pybids_ignore_patterns (nipoppy.workflows.BasePipelineWorkflow property) (nipoppy.workflows.pipeline.BasePipelineWorkflow property) PyPI R regenerate (nipoppy.workflows.doughnut.DoughnutWorkflow attribute) (nipoppy.workflows.DoughnutWorkflow attribute) return_code (nipoppy.workflows.base.BaseWorkflow attribute) (nipoppy.workflows.BaseWorkflow attribute) rm() (nipoppy.workflows.base.BaseWorkflow method) (nipoppy.workflows.BaseWorkflow method) run() (nipoppy.workflows.base.BaseWorkflow method) (nipoppy.workflows.BaseWorkflow method) run_cleanup() (nipoppy.workflows.base.BaseWorkflow method) (nipoppy.workflows.BasePipelineWorkflow method) (nipoppy.workflows.BaseWorkflow method) (nipoppy.workflows.bids_conversion.BidsConversionRunner method) (nipoppy.workflows.BidsConversionRunner method) (nipoppy.workflows.dataset_init.InitWorkflow method) (nipoppy.workflows.dicom_reorg.DicomReorgWorkflow method) (nipoppy.workflows.DicomReorgWorkflow method) (nipoppy.workflows.doughnut.DoughnutWorkflow method) (nipoppy.workflows.DoughnutWorkflow method) (nipoppy.workflows.InitWorkflow method) (nipoppy.workflows.pipeline.BasePipelineWorkflow method) (nipoppy.workflows.PipelineRunner method) (nipoppy.workflows.PipelineTracker method) (nipoppy.workflows.runner.PipelineRunner method) (nipoppy.workflows.tracker.PipelineTracker method) run_command() (nipoppy.workflows.base.BaseWorkflow method) (nipoppy.workflows.BaseWorkflow method) run_main() (nipoppy.workflows.base.BaseWorkflow method) (nipoppy.workflows.BasePipelineWorkflow method) (nipoppy.workflows.BaseWorkflow method) (nipoppy.workflows.dataset_init.InitWorkflow method) (nipoppy.workflows.dicom_reorg.DicomReorgWorkflow method) (nipoppy.workflows.DicomReorgWorkflow method) (nipoppy.workflows.doughnut.DoughnutWorkflow method) (nipoppy.workflows.DoughnutWorkflow method) (nipoppy.workflows.InitWorkflow method) (nipoppy.workflows.pipeline.BasePipelineWorkflow method) run_setup() (nipoppy.workflows.base.BaseWorkflow method) (nipoppy.workflows.BasePipelineWorkflow method) (nipoppy.workflows.BaseWorkflow method) (nipoppy.workflows.dicom_reorg.DicomReorgWorkflow method) (nipoppy.workflows.DicomReorgWorkflow method) (nipoppy.workflows.pipeline.BasePipelineWorkflow method) (nipoppy.workflows.PipelineTracker method) (nipoppy.workflows.tracker.PipelineTracker method) run_single() (nipoppy.workflows.BasePipelineWorkflow method) (nipoppy.workflows.bids_conversion.BidsConversionRunner method) (nipoppy.workflows.BidsConversionRunner method) (nipoppy.workflows.dicom_reorg.DicomReorgWorkflow method) (nipoppy.workflows.DicomReorgWorkflow method) (nipoppy.workflows.pipeline.BasePipelineWorkflow method) (nipoppy.workflows.PipelineRunner method) (nipoppy.workflows.PipelineTracker method) (nipoppy.workflows.runner.PipelineRunner method) (nipoppy.workflows.tracker.PipelineTracker method) S save() (nipoppy.config.Config method) (nipoppy.config.main.Config method) save_df_with_backup() (in module nipoppy.utils) save_json() (in module nipoppy.utils) save_tabular_file() (nipoppy.workflows.base.BaseWorkflow method) (nipoppy.workflows.BaseWorkflow method) save_with_backup() (nipoppy.tabular.base.BaseTabular method) session (nipoppy.config.pipeline_step.AnalysisLevelType attribute) (nipoppy.tabular.bagel.BagelModel attribute) Session ID session_id (nipoppy.tabular.bagel.BagelModel attribute) (nipoppy.tabular.dicom_dir_map.DicomDirMapModel attribute) (nipoppy.tabular.manifest.ManifestModel attribute) (nipoppy.workflows.BasePipelineWorkflow attribute) (nipoppy.workflows.pipeline.BasePipelineWorkflow attribute) session_id_to_bids_session() (in module nipoppy.utils) SESSION_IDS (nipoppy.config.Config attribute) (nipoppy.config.main.Config attribute) session_ids (nipoppy.tabular.Manifest attribute) (nipoppy.tabular.manifest.Manifest attribute) SESSIONS set_container_env_vars() (in module nipoppy.config.container) set_status() (nipoppy.tabular.Doughnut method) (nipoppy.tabular.doughnut.Doughnut method) set_up_bids_db() (nipoppy.workflows.BasePipelineWorkflow method) (nipoppy.workflows.pipeline.BasePipelineWorkflow method) simulate (nipoppy.workflows.PipelineRunner attribute) (nipoppy.workflows.runner.PipelineRunner attribute) sort_values() (nipoppy.tabular.base.BaseTabular method) status_cols (nipoppy.tabular.Doughnut attribute) (nipoppy.tabular.doughnut.Doughnut attribute) STATUS_FAIL (in module nipoppy.tabular.bagel) status_fail (nipoppy.tabular.Bagel attribute) (nipoppy.tabular.bagel.Bagel attribute) STATUS_INCOMPLETE (in module nipoppy.tabular.bagel) status_incomplete (nipoppy.tabular.Bagel attribute) (nipoppy.tabular.bagel.Bagel attribute) STATUS_SUCCESS (in module nipoppy.tabular.bagel) status_success (nipoppy.tabular.Bagel attribute) (nipoppy.tabular.bagel.Bagel attribute) STATUS_UNAVAILABLE (in module nipoppy.tabular.bagel) status_unavailable (nipoppy.tabular.Bagel attribute) (nipoppy.tabular.bagel.Bagel attribute) STEPS (nipoppy.config.BasePipelineConfig attribute) (nipoppy.config.pipeline.BasePipelineConfig attribute) StrOrPathLike (in module nipoppy.env) SUBSTITUTIONS (nipoppy.config.Config attribute) (nipoppy.config.main.Config attribute) SUCCESS (nipoppy.env.LogColor attribute) (nipoppy.env.ReturnCode attribute) T TEMPLATE_REPLACE_PATTERN (in module nipoppy.utils) TRACKER_CONFIG_FILE (nipoppy.config.pipeline.ProcPipelineConfig attribute) (nipoppy.config.ProcPipelineConfig attribute) U UPDATE_DOUGHNUT (nipoppy.config.BidsPipelineStepConfig attribute) (nipoppy.config.pipeline_step.BidsPipelineStepConfig attribute) update_doughnut() (in module nipoppy.tabular) (in module nipoppy.tabular.doughnut) URI (nipoppy.config.container.ContainerInfo attribute) V validate() (nipoppy.layout.DatasetLayout method) (nipoppy.tabular.base.BaseTabular method) (nipoppy.tabular.Manifest method) (nipoppy.tabular.manifest.Manifest method) validate_after() (nipoppy.config.BasePipelineConfig method) (nipoppy.config.pipeline.BasePipelineConfig method) (nipoppy.config.tracker.TrackerConfig method) (nipoppy.config.TrackerConfig method) (nipoppy.tabular.bagel.BagelModel method) (nipoppy.tabular.dicom_dir_map.DicomDirMapModel method) (nipoppy.tabular.manifest.ManifestModel method) validate_and_process() (nipoppy.config.Config method) (nipoppy.config.main.Config method) validate_before() (nipoppy.config.BasePipelineConfig class method) (nipoppy.config.BasePipelineStepConfig class method) (nipoppy.config.pipeline.BasePipelineConfig class method) (nipoppy.config.pipeline_step.BasePipelineStepConfig class method) (nipoppy.tabular.base.BaseTabularModel class method) validate_layout (nipoppy.workflows.base.BaseWorkflow attribute) (nipoppy.workflows.BaseWorkflow attribute) (nipoppy.workflows.dataset_init.InitWorkflow attribute) (nipoppy.workflows.InitWorkflow attribute) venv VERSION (nipoppy.config.BasePipelineConfig attribute) (nipoppy.config.pipeline.BasePipelineConfig attribute) Visit ID visit_id (nipoppy.tabular.manifest.ManifestModel attribute) VISIT_IDS (nipoppy.config.Config attribute) (nipoppy.config.main.Config attribute) visit_ids (nipoppy.tabular.Manifest attribute) (nipoppy.tabular.manifest.Manifest attribute) VISITS