Index

_

__init__() (AlignPeriodicBlockTriggers method) (ArtifactRemovalMWF method) (AttachSave method) (BasenameComparisonFn method) (BIDSPathGenerator method) (BIDSStimulusGrouper method) (BIDSStimulusInfoExtractor method) (CachingPreprocessingPipeline method) (CheckFunctor method) (CLI method) (ColorFormatter method) (CommonAverageRereference method) (DataLoader method) (DefaultCLI method) (DefaultFilenameFn method) (DefaultFormatter method) (DefaultPipeline method) (DefaultPipelineCache method) (DefaultRunner method) (DefaultSave method) (DefaultSaveMetadata method) (EnvelopeFromGammatone method) (FileLoadMixin method) (FileParser method) (Finder method) (GammatoneEnvelope method) (GlobLoader method) (InterpolateArtifacts method) (IsDoneCheck method) (IsReloadableCheck method) (LibrosaMelSpectrogram method) (LinkStimulusToBrainResponse method) (LoadEEGNumpy method) (LoadStimuli method) (MidSplit method) (MNELoader method) (MultiprocessingSingleton method) (ObjectsWithConfig method) (OldMetadataCompliant method) (Parser method) (Pipeline method) (PipelineCache method) (PipelineStep method) (ProgressCallbackFn method) (ResamplePoly method) (Runner method) (Save method) (SaveMetadata method) (SequentialSplit method) (SimpleCallbackFn method) (SimpleDictParser method) (SosFiltFilt method) (SplitEpochs method) (Splitter method) (SplitterOperation method) (Standardize method) (TemplateFileParser method) (TemplateTextParser method) (TextParser method) (Transpose method) (Wrapper method) (YAMLFileParser method) (YAMLMixin method) (YAMLTemplateFileParser method) (YAMLTextParser method)

A

add() (DefaultSaveMetadata method) (SaveMetadata method) add_arguments_to_argparser() (DefaultCLI method) AlignPeriodicBlockTriggers (class in brain_pipe.preprocessing.brain.trigger) apply_config() (FileParser method) (ObjectsWithConfig method) (SimpleDictParser method) (TemplateFileParser method) (TemplateTextParser method) (TextParser method) (YAMLFileParser method) (YAMLTemplateFileParser method) (YAMLTextParser method)

apply_mwf() (ArtifactRemovalMWF method) ArtifactRemovalMWF (class in brain_pipe.preprocessing.brain.artifact) attach_saver() (AttachSave method) (CheckFunctor method) (DefaultSaveMetadata method) (IsDoneCheck method) (IsReloadableCheck method) (SaveMetadata method) AttachSave (class in brain_pipe.save.default)

B

BasenameComparisonFn (class in brain_pipe.preprocessing.brain.link) BIDSPathGenerator (class in brain_pipe.utils.path) BIDSStimulusGrouper (class in brain_pipe.utils.path) BIDSStimulusInfoExtractor (class in brain_pipe.preprocessing.brain.link) biosemi_trigger_processing_fn() (in module brain_pipe.preprocessing.brain.eeg.biosemi) brain_pipe module brain_pipe.cli module brain_pipe.cli.base module brain_pipe.cli.default module brain_pipe.dataloaders module brain_pipe.dataloaders.base module brain_pipe.dataloaders.path module brain_pipe.parser module brain_pipe.parser.base module brain_pipe.parser.file module brain_pipe.parser.simple_dict module brain_pipe.parser.template_text module brain_pipe.parser.text module brain_pipe.parser.yaml module brain_pipe.pipeline module brain_pipe.pipeline.base module brain_pipe.pipeline.cache module brain_pipe.pipeline.cache.base module brain_pipe.pipeline.cache.default module brain_pipe.pipeline.cache.pipeline module brain_pipe.pipeline.default module brain_pipe.pipeline.wrapper module brain_pipe.preprocessing module brain_pipe.preprocessing.brain module brain_pipe.preprocessing.brain.artifact module brain_pipe.preprocessing.brain.eeg module brain_pipe.preprocessing.brain.eeg.biosemi module brain_pipe.preprocessing.brain.eeg.load module brain_pipe.preprocessing.brain.epochs module

brain_pipe.preprocessing.brain.link module brain_pipe.preprocessing.brain.load module brain_pipe.preprocessing.brain.rereference module brain_pipe.preprocessing.brain.trigger module brain_pipe.preprocessing.filter module brain_pipe.preprocessing.resample module brain_pipe.preprocessing.stimulus module brain_pipe.preprocessing.stimulus.audio module brain_pipe.preprocessing.stimulus.audio.envelope module brain_pipe.preprocessing.stimulus.audio.spectrogram module brain_pipe.preprocessing.stimulus.load module brain_pipe.preprocessing.transpose module brain_pipe.runner module brain_pipe.runner.base module brain_pipe.runner.default module brain_pipe.save module brain_pipe.save.base module brain_pipe.save.default module brain_pipe.split module brain_pipe.split.base module brain_pipe.split.mid module brain_pipe.split.operations module brain_pipe.split.operations.base module brain_pipe.split.operations.normalize module brain_pipe.split.sequential module brain_pipe.utils module brain_pipe.utils.find module brain_pipe.utils.list module brain_pipe.utils.log module brain_pipe.utils.parallellization module brain_pipe.utils.path module brain_pipe.utils.serialization module

C

CachingPreprocessingPipeline (class in brain_pipe.pipeline.cache.pipeline) check_reload() (CachingPreprocessingPipeline method) (DefaultPipeline method) check_symmetric() (ArtifactRemovalMWF method) CheckFunctor (class in brain_pipe.save.default) clean() (MultiprocessingSingleton class method) clear() (DefaultSaveMetadata method) (SaveMetadata method) CLI (class in brain_pipe.cli.base) cli_entrypoint() (in module brain_pipe.cli)

cli_factory() (in module brain_pipe.cli) ColorFormatter (class in brain_pipe.utils.log) CommonAverageRereference (class in brain_pipe.preprocessing.brain.rereference) compute_length() (DataLoader method) (GlobLoader method) compute_mwf() (ArtifactRemovalMWF method) convert_old_format() (DefaultSaveMetadata method) (OldMetadataCompliant method) converter() (ColorFormatter method) (DefaultFormatter method)

D

data_dict_copy() (SplitEpochs method) DataLoader (class in brain_pipe.dataloaders.base) default_drift_correction() (in module brain_pipe.preprocessing.brain.trigger) default_error_handler_fn() (in module brain_pipe.pipeline.default) default_logging() (in module brain_pipe.utils.log) default_metadata_key_fn() (in module brain_pipe.save.default) default_multiprocessing_key_fn() (in module brain_pipe.preprocessing.brain.link) DefaultCLI (class in brain_pipe.cli.default)

DefaultFilenameFn (class in brain_pipe.save.default) DefaultFormatter (class in brain_pipe.utils.log) DefaultPipeline (class in brain_pipe.pipeline.default) DefaultPipelineCache (class in brain_pipe.pipeline.cache.default) DefaultRunner (class in brain_pipe.runner.default) DefaultSave (class in brain_pipe.save.default) DefaultSaveMetadata (class in brain_pipe.save.default) duration (EnvelopeFromGammatone property)

E

EnvelopeFromGammatone (class in brain_pipe.preprocessing.stimulus.audio.envelope)

F

FileLoadMixin (class in brain_pipe.parser.file) FileParser (class in brain_pipe.parser.file) filter() (Finder method) filter_fn() (Finder method) find_existing_cache_from_data_dict() (DefaultPipelineCache method) (PipelineCache method) find_existing_cache_from_previous_filename() (DefaultPipelineCache method) (PipelineCache method) Finder (class in brain_pipe.utils.find)

fix_symmetric() (ArtifactRemovalMWF method) flatten() (in module brain_pipe.utils.list) format() (ColorFormatter method) (DefaultFormatter method) formatException() (ColorFormatter method) (DefaultFormatter method) formatStack() (ColorFormatter method) (DefaultFormatter method) formatTime() (ColorFormatter method) (DefaultFormatter method)

G

GammatoneEnvelope (class in brain_pipe.preprocessing.stimulus.audio.envelope) get() (DefaultSaveMetadata method) get_additional_kwargs() (FileLoadMixin method) (FileParser method) (Parser method) (SimpleDictParser method) (TemplateFileParser method) (TemplateTextParser method) (TextParser method) (YAMLFileParser method) (YAMLTemplateFileParser method) (YAMLTextParser method) get_argparser() (DefaultCLI method) get_artifact_segments() (ArtifactRemovalMWF method) get_cache_dict() (DefaultPipelineCache method) (PipelineCache method) get_channels() (LoadEEGNumpy method) get_existing_cache_paths() (DefaultPipelineCache method) (PipelineCache method) get_filename() (DefaultPipelineCache method) (PipelineCache method) get_foldername() (DefaultPipelineCache method) (PipelineCache method)

get_lock() (MultiprocessingSingleton class method) get_map_fn() (MultiprocessingSingleton class method) get_matlab_arguments() (SosFiltFilt method) get_metadata_for_savepath() (DefaultSaveMetadata method) get_parser() (CLI method) (DefaultCLI method) get_path() (DefaultPipelineCache method) (DefaultSaveMetadata method) (PipelineCache method) get_relpath() (DefaultSaveMetadata method) get_run_options() (CLI method) (DefaultCLI method) get_runner_from_parsed_config() (FileParser method) (SimpleDictParser method) (TemplateFileParser method) (TemplateTextParser method) (TextParser method) (YAMLFileParser method) (YAMLTemplateFileParser method) (YAMLTextParser method) get_trigger_indices() (AlignPeriodicBlockTriggers method) GlobLoader (class in brain_pipe.dataloaders.path)

I

InterpolateArtifacts (class in brain_pipe.preprocessing.brain.artifact) is_already_done() (DefaultSave method) (Save method) is_old_format() (DefaultSaveMetadata class method) (SaveMetadata class method)

is_reloadable() (DefaultSave method) (Save method) IsDoneCheck (class in brain_pipe.save.default) IsReloadableCheck (class in brain_pipe.save.default) iterate_over_steps() (CachingPreprocessingPipeline method) (DefaultPipeline method)

L

LibrosaMelSpectrogram (class in brain_pipe.preprocessing.stimulus.audio.spectrogram) link_loader_to_pipeline() (FileParser method) (Parser method) (SimpleDictParser method) (TemplateFileParser method) (TemplateTextParser method) (TextParser method) (YAMLFileParser method) (YAMLTemplateFileParser method) (YAMLTextParser method) LinkStimulusToBrainResponse (class in brain_pipe.preprocessing.brain.link) load() (DefaultPipelineCache method) (PipelineCache method)

load_file() (FileLoadMixin method) (FileParser method) (TemplateFileParser method) (YAMLFileParser method) (YAMLTemplateFileParser method) load_from_data_dict() (DefaultPipelineCache method) (PipelineCache method) load_from_path() (Finder method) LoadEEGNumpy (class in brain_pipe.preprocessing.brain.eeg.load) LoadStimuli (class in brain_pipe.preprocessing.stimulus.load) lock (DefaultSaveMetadata property)

M

MidSplit (class in brain_pipe.split.mid) MNELoader (class in brain_pipe.preprocessing.brain.load) module brain_pipe brain_pipe.cli brain_pipe.cli.base brain_pipe.cli.default brain_pipe.dataloaders brain_pipe.dataloaders.base brain_pipe.dataloaders.path brain_pipe.parser brain_pipe.parser.base brain_pipe.parser.file brain_pipe.parser.simple_dict brain_pipe.parser.template_text brain_pipe.parser.text brain_pipe.parser.yaml brain_pipe.pipeline brain_pipe.pipeline.base brain_pipe.pipeline.cache brain_pipe.pipeline.cache.base brain_pipe.pipeline.cache.default brain_pipe.pipeline.cache.pipeline brain_pipe.pipeline.default brain_pipe.pipeline.wrapper brain_pipe.preprocessing brain_pipe.preprocessing.brain brain_pipe.preprocessing.brain.artifact brain_pipe.preprocessing.brain.eeg brain_pipe.preprocessing.brain.eeg.biosemi brain_pipe.preprocessing.brain.eeg.load brain_pipe.preprocessing.brain.epochs brain_pipe.preprocessing.brain.link brain_pipe.preprocessing.brain.load brain_pipe.preprocessing.brain.rereference brain_pipe.preprocessing.brain.trigger brain_pipe.preprocessing.filter brain_pipe.preprocessing.resample brain_pipe.preprocessing.stimulus brain_pipe.preprocessing.stimulus.audio brain_pipe.preprocessing.stimulus.audio.envelope brain_pipe.preprocessing.stimulus.audio.spectrogram brain_pipe.preprocessing.stimulus.load brain_pipe.preprocessing.transpose brain_pipe.runner brain_pipe.runner.base brain_pipe.runner.default brain_pipe.save brain_pipe.save.base brain_pipe.save.default brain_pipe.split brain_pipe.split.base brain_pipe.split.mid brain_pipe.split.operations brain_pipe.split.operations.base brain_pipe.split.operations.normalize brain_pipe.split.sequential brain_pipe.utils brain_pipe.utils.find brain_pipe.utils.list brain_pipe.utils.log brain_pipe.utils.parallellization brain_pipe.utils.path brain_pipe.utils.serialization

MultiprocessingSingleton (class in brain_pipe.utils.parallellization)

O

ObjectsWithConfig (class in brain_pipe.utils) OldMetadataCompliant (class in brain_pipe.save.default)

on_error (CachingPreprocessingPipeline property) (DefaultPipeline property) overwrite (DefaultSave property)

P

parse_all() (FileParser method) (SimpleDictParser method) (TemplateFileParser method) (TemplateTextParser method) (TextParser method) (YAMLFileParser method) (YAMLTemplateFileParser method) (YAMLTextParser method) parse_cli_arguments() (CLI method) (DefaultCLI method) parse_cli_arguments_for_parser() (CLI method) (DefaultCLI method) parse_dict_keys() (AlignPeriodicBlockTriggers method) (ArtifactRemovalMWF method) (CachingPreprocessingPipeline method) (CommonAverageRereference method) (DefaultPipeline method) (DefaultSave method) (GammatoneEnvelope method) (InterpolateArtifacts method) (LibrosaMelSpectrogram method) (LinkStimulusToBrainResponse method) (LoadEEGNumpy method) (LoadStimuli method) (MidSplit method) (MNELoader method) (Pipeline method) (PipelineStep method) (ResamplePoly method) (Save method) (SequentialSplit method) (SosFiltFilt method) (SplitEpochs method) (Splitter method) (Transpose method) (Wrapper method)

parse_librosa_kwargs() (LibrosaMelSpectrogram method) parse_text_to_dict() (FileParser method) (TemplateFileParser method) (TemplateTextParser method) (TextParser method) (YAMLFileParser method) (YAMLMixin method) (YAMLTemplateFileParser method) (YAMLTextParser method) Parser (class in brain_pipe.parser.base) path_to_data_dict() (GlobLoader method) pickle_dump_wrapper() (in module brain_pipe.utils.serialization) pickle_load_wrapper() (in module brain_pipe.utils.serialization) Pipeline (class in brain_pipe.pipeline.base) PipelineCache (class in brain_pipe.pipeline.cache.base) PipelineStep (class in brain_pipe.pipeline.base) predicate_fn() (Finder method) predict_filenames_from_data_dict() (DefaultPipelineCache method) (PipelineCache method) predict_filenames_from_previous_filename() (DefaultPipelineCache method) (PipelineCache method) predict_paths_from_data_dict() (DefaultPipelineCache method) (PipelineCache method) predict_paths_from_previous_filename() (DefaultPipelineCache method) (PipelineCache method) process() (EnvelopeFromGammatone method) process_path() (BasenameComparisonFn method) ProgressCallbackFn (class in brain_pipe.utils.parallellization)

R

read_events() (BIDSStimulusInfoExtractor method) recursive_parse() (FileParser method) (SimpleDictParser method) (TemplateFileParser method) (TemplateTextParser method) (TextParser method) (YAMLFileParser method) (YAMLTemplateFileParser method) (YAMLTextParser method) reload() (DefaultSave method) (Save method)

ResamplePoly (class in brain_pipe.preprocessing.resample) reset() (SplitterOperation method) (Standardize method) run() (CLI method) (DefaultCLI method) (DefaultRunner method) (Runner method) run_step() (CachingPreprocessingPipeline method) (DefaultPipeline method) Runner (class in brain_pipe.runner.base)

S

Save (class in brain_pipe.save.base) save() (DefaultPipelineCache method) (PipelineCache method) SaveMetadata (class in brain_pipe.save.default) select_paths() (BIDSPathGenerator method) SequentialSplit (class in brain_pipe.split.sequential) set_additional_kwargs() (FileParser method) (Parser method) (SimpleDictParser method) (TemplateFileParser method) (TemplateTextParser method) (TextParser method) (YAMLFileParser method) (YAMLTemplateFileParser method) (YAMLTextParser method)

SimpleCallbackFn (class in brain_pipe.utils.parallellization) SimpleDictParser (class in brain_pipe.parser.simple_dict) sort_evd() (ArtifactRemovalMWF method) SosFiltFilt (class in brain_pipe.preprocessing.filter) source (EnvelopeFromGammatone property) split() (MidSplit method) (SequentialSplit method) (Splitter method) split_epochs() (AlignPeriodicBlockTriggers method) SplitEpochs (class in brain_pipe.preprocessing.brain.epochs) Splitter (class in brain_pipe.split.base) SplitterOperation (class in brain_pipe.split.operations.base) stack_delayed() (ArtifactRemovalMWF method) Standardize (class in brain_pipe.split.operations.normalize)

T

TemplateFileParser (class in brain_pipe.parser.file) TemplateTextParser (class in brain_pipe.parser.template_text)

TextParser (class in brain_pipe.parser.text) Transpose (class in brain_pipe.preprocessing.transpose)

U

usesTime() (ColorFormatter method) (DefaultFormatter method)

W

wrap_in_list() (in module brain_pipe.utils.list)

Wrapper (class in brain_pipe.pipeline.wrapper) write() (DefaultSaveMetadata method)

Y

YAMLFileParser (class in brain_pipe.parser.yaml) YAMLMixin (class in brain_pipe.parser.yaml)

YAMLTemplateFileParser (class in brain_pipe.parser.yaml) YAMLTextParser (class in brain_pipe.parser.yaml)