Index

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) AnalysisLevelType (class in nipoppy.config.pipeline_step)

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 (class in nipoppy.tabular) (class in nipoppy.tabular.bagel) BagelModel (class in nipoppy.tabular.bagel) Base (class in nipoppy.base) BasePipelineConfig (class in nipoppy.config) (class in nipoppy.config.pipeline) BasePipelineStepConfig (class in nipoppy.config) (class in nipoppy.config.pipeline_step) BasePipelineWorkflow (class in nipoppy.workflows) (class in nipoppy.workflows.pipeline) BaseTabular (class in nipoppy.tabular.base) BaseTabularModel (class in nipoppy.tabular.base) BaseWorkflow (class in nipoppy.workflows) (class in nipoppy.workflows.base) 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_SUBJECT_PREFIX (in module nipoppy.env) BidsConversionRunner (class in nipoppy.workflows) (class in nipoppy.workflows.bids_conversion) BidsPipelineConfig (class in nipoppy.config) (class in nipoppy.config.pipeline) BidsPipelineStepConfig (class in nipoppy.config) (class in nipoppy.config.pipeline_step) Boutiques boutiques_config() (nipoppy.workflows.BasePipelineWorkflow method) (nipoppy.workflows.pipeline.BasePipelineWorkflow method) BOUTIQUES_CONFIG_KEY (in module nipoppy.config.boutiques) BOUTIQUES_CUSTOM_KEY (in module nipoppy.config.boutiques) BoutiquesConfig (class in nipoppy.config) (class in 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_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_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 (class in nipoppy.config) (class in nipoppy.config.main) config() (nipoppy.workflows.base.BaseWorkflow method) (nipoppy.workflows.BaseWorkflow method) CONTAINER_CONFIG (nipoppy.config.container.SchemaWithContainerConfig attribute) CONTAINER_INFO (nipoppy.config.BasePipelineConfig attribute) (nipoppy.config.pipeline.BasePipelineConfig attribute) CONTAINER_SUBCOMMAND (nipoppy.config.boutiques.BoutiquesConfig attribute) (nipoppy.config.BoutiquesConfig attribute) ContainerConfig (class in nipoppy.config) (class in nipoppy.config.container) ContainerInfo (class in nipoppy.config.container) copy() (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) DatasetLayout (class in nipoppy.layout) 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 method) (nipoppy.workflows.pipeline.BasePipelineWorkflow method) DESCRIPTOR_FILE (nipoppy.config.BasePipelineStepConfig attribute) (nipoppy.config.pipeline_step.BasePipelineStepConfig attribute) dicom_dir_map() (nipoppy.workflows.base.BaseWorkflow method) (nipoppy.workflows.BaseWorkflow method) 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) DicomDirMap (class in nipoppy.tabular.dicom_dir_map) DicomDirMapModel (class in nipoppy.tabular.dicom_dir_map) DicomReorgWorkflow (class in nipoppy.workflows) (class in nipoppy.workflows.dicom_reorg) Doughnut (class in nipoppy.tabular) (class in nipoppy.tabular.doughnut) Doughnut file doughnut() (nipoppy.workflows.base.BaseWorkflow method) (nipoppy.workflows.BaseWorkflow method) DoughnutModel (class in nipoppy.tabular.doughnut) DoughnutWorkflow (class in nipoppy.workflows) (class in nipoppy.workflows.doughnut) dpath_assessments (nipoppy.layout.LayoutConfig attribute) dpath_bids (nipoppy.layout.LayoutConfig attribute) dpath_bids_db (nipoppy.layout.LayoutConfig attribute) dpath_bids_ignore_patterns (nipoppy.layout.LayoutConfig attribute)

dpath_containers (nipoppy.layout.LayoutConfig attribute) DPATH_DATA (in module nipoppy.utils) dpath_demographics (nipoppy.layout.LayoutConfig attribute) dpath_derivatives (nipoppy.layout.LayoutConfig attribute) dpath_descriptions() (nipoppy.layout.DatasetLayout method) DPATH_DESCRIPTORS (in module nipoppy.utils) dpath_descriptors (nipoppy.layout.LayoutConfig attribute) dpath_downloads (nipoppy.layout.LayoutConfig attribute) DPATH_EXAMPLES (in module nipoppy.utils) DPATH_INVOCATIONS (in module nipoppy.utils) dpath_invocations (nipoppy.layout.LayoutConfig attribute) DPATH_LAYOUTS (in module nipoppy.utils) dpath_logs (nipoppy.layout.LayoutConfig attribute) dpath_pipeline() (nipoppy.workflows.BasePipelineWorkflow method) (nipoppy.workflows.pipeline.BasePipelineWorkflow method) dpath_pipeline_bids_db() (nipoppy.workflows.BasePipelineWorkflow method) (nipoppy.workflows.pipeline.BasePipelineWorkflow method) dpath_pipeline_output() (nipoppy.workflows.BasePipelineWorkflow method) (nipoppy.workflows.pipeline.BasePipelineWorkflow method) dpath_pipeline_work() (nipoppy.workflows.BasePipelineWorkflow method) (nipoppy.workflows.pipeline.BasePipelineWorkflow method) dpath_proc (nipoppy.layout.LayoutConfig attribute) dpath_pybids (nipoppy.layout.LayoutConfig attribute) dpath_raw_imaging (nipoppy.layout.LayoutConfig attribute) dpath_releases (nipoppy.layout.LayoutConfig attribute) dpath_scratch (nipoppy.layout.LayoutConfig attribute) dpath_sourcedata (nipoppy.layout.LayoutConfig attribute) dpath_tabular (nipoppy.layout.LayoutConfig attribute) DPATH_TRACKER_CONFIGS (in module nipoppy.utils) dpath_tracker_configs (nipoppy.layout.LayoutConfig attribute) DpathInfo (class in nipoppy.layout) dpaths() (nipoppy.layout.DatasetLayout method) dpaths_to_check() (nipoppy.workflows.BasePipelineWorkflow method) (nipoppy.workflows.bids_conversion.BidsConversionRunner method) (nipoppy.workflows.BidsConversionRunner method) (nipoppy.workflows.pipeline.BasePipelineWorkflow method) (nipoppy.workflows.PipelineRunner method) (nipoppy.workflows.runner.PipelineRunner method)

E

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) FORMAT_FILE (in module nipoppy.logger) FORMAT_RICH (in module nipoppy.logger) fpath_config (nipoppy.layout.LayoutConfig attribute) fpath_container() (nipoppy.workflows.BasePipelineWorkflow method) (nipoppy.workflows.pipeline.BasePipelineWorkflow method)

FPATH_DEFAULT_LAYOUT (in module nipoppy.utils) fpath_doughnut (nipoppy.layout.LayoutConfig attribute) fpath_imaging_bagel (nipoppy.layout.LayoutConfig attribute) fpath_manifest (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) FpathInfo (class in nipoppy.layout) fpaths() (nipoppy.layout.DatasetLayout method)

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) get_analysis_level() (nipoppy.config.BasePipelineConfig method) (nipoppy.config.pipeline.BasePipelineConfig method) 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_container_config() (nipoppy.config.container.SchemaWithContainerConfig method) get_descriptor_file() (nipoppy.config.BasePipelineConfig method) (nipoppy.config.pipeline.BasePipelineConfig 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_invocation_file() (nipoppy.config.BasePipelineConfig method) (nipoppy.config.pipeline.BasePipelineConfig 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_pybids_ignore_file() (nipoppy.config.pipeline.ProcPipelineConfig method) (nipoppy.config.ProcPipelineConfig 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) get_update_doughnut() (nipoppy.config.BidsPipelineConfig method) (nipoppy.config.pipeline.BidsPipelineConfig 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) InitWorkflow (class in nipoppy.workflows) (class in nipoppy.workflows.dataset_init) invocation() (nipoppy.workflows.BasePipelineWorkflow method) (nipoppy.workflows.pipeline.BasePipelineWorkflow method) INVOCATION_FILE (nipoppy.config.BasePipelineStepConfig attribute) (nipoppy.config.pipeline_step.BasePipelineStepConfig attribute) is_derived_dicom() (in module nipoppy.workflows.dicom_reorg)

J

JSON

L

launch_boutiques_run() (nipoppy.workflows.PipelineRunner method) (nipoppy.workflows.runner.PipelineRunner method) LayoutConfig (class in nipoppy.layout) 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) LogColor (class in nipoppy.env)

M

Manifest (class in nipoppy.tabular) (class in nipoppy.tabular.manifest) manifest() (nipoppy.workflows.base.BaseWorkflow method) (nipoppy.workflows.BaseWorkflow method) ManifestModel (class in nipoppy.tabular.manifest) 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

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) nipoppy module nipoppy.base module nipoppy.config module nipoppy.config.boutiques module nipoppy.config.container module nipoppy.config.main module nipoppy.config.pipeline module nipoppy.config.pipeline_step module nipoppy.config.tracker module nipoppy.env module nipoppy.layout module nipoppy.logger module nipoppy.tabular module

nipoppy.tabular.bagel module nipoppy.tabular.base module nipoppy.tabular.dicom_dir_map module nipoppy.tabular.doughnut module nipoppy.tabular.manifest module nipoppy.utils module nipoppy.workflows module nipoppy.workflows.base module nipoppy.workflows.bids_conversion module nipoppy.workflows.dataset_init module nipoppy.workflows.dicom_reorg module nipoppy.workflows.doughnut module nipoppy.workflows.pipeline module nipoppy.workflows.runner module nipoppy.workflows.tracker module

O

OptionalFpathInfo (class in nipoppy.layout)

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) 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 method) path_labels() (nipoppy.layout.LayoutConfig method) path_sep (nipoppy.workflows.base.BaseWorkflow attribute) (nipoppy.workflows.BaseWorkflow attribute) PathInfo (class in nipoppy.layout) PATHS (nipoppy.config.tracker.TrackerConfig attribute) (nipoppy.config.TrackerConfig attribute) pipeline_complete (nipoppy.tabular.bagel.BagelModel attribute) pipeline_config() (nipoppy.workflows.BasePipelineWorkflow method) (nipoppy.workflows.bids_conversion.BidsConversionRunner method) (nipoppy.workflows.BidsConversionRunner method) (nipoppy.workflows.pipeline.BasePipelineWorkflow method) pipeline_name (nipoppy.tabular.bagel.BagelModel attribute) (nipoppy.workflows.base.BaseWorkflow attribute) (nipoppy.workflows.BaseWorkflow attribute) pipeline_starttime (nipoppy.tabular.bagel.BagelModel attribute)

pipeline_version (nipoppy.tabular.bagel.BagelModel attribute) (nipoppy.workflows.base.BaseWorkflow attribute) (nipoppy.workflows.BaseWorkflow attribute) PipelineRunner (class in nipoppy.workflows) (class in nipoppy.workflows.runner) PipelineTracker (class in nipoppy.workflows) (class in nipoppy.workflows.tracker) 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) ProcPipelineConfig (class in nipoppy.config) (class in nipoppy.config.pipeline) ProcPipelineStepConfig (class in nipoppy.config) (class in nipoppy.config.pipeline_step) 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 method) (nipoppy.workflows.pipeline.BasePipelineWorkflow method) PyPI

R

ReturnCode (class in nipoppy.env) 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) SchemaWithContainerConfig (class in nipoppy.config.container) 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) session_id_to_bids_session() (in module nipoppy.utils) SESSION_IDS (nipoppy.config.Config attribute) (nipoppy.config.main.Config 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)

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)

TrackerConfig (class in nipoppy.config) (class in nipoppy.config.tracker)

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) VISITS