Index _ | A | B | C | D | E | F | G | H | I | L | M | N | O | P | R | S | T | U | V | W | Z _ __getattr__() (neurodent.results.ZeitgeberAnalysisResult method) __init__() (neurodent.analysis.LongRecordingAnalyzer method) (neurodent.loading.AnimalOrganizer method) (neurodent.loading.DDFBinaryMetadata method) (neurodent.loading.LongRecordingOrganizer method) (neurodent.loading.RecordingMetadata method) (neurodent.plotting.AnimalPlotter method) (neurodent.plotting.ExperimentPlotter method) (neurodent.plotting.ZeitgeberPlotter method) (neurodent.results.FrequencyDomainSpikeAnalysisResult method) (neurodent.results.WindowAnalysisResult method) (neurodent.results.ZeitgeberAnalysisResult method) __repr__() (neurodent.loading.LongRecordingOrganizer method) __str__() (neurodent.loading.LongRecordingOrganizer method) (neurodent.results.FrequencyDomainSpikeAnalysisResult method) A add_unique_hash() (neurodent.results.WindowAnalysisResult method) aggregate_time_windows() (neurodent.results.WindowAnalysisResult method) algorithm() (neurodent.core.utils.Natural_Neighbor method) AnimalOrganizer (class in neurodent.loading) AnimalPlotter (class in neurodent.plotting) apply_filters() (neurodent.results.WindowAnalysisResult method) apply_lof_threshold() (neurodent.loading.AnimalOrganizer method) (neurodent.loading.LongRecordingOrganizer method) asserts() (neurodent.core.utils.Natural_Neighbor method) atomic_output_path() (in module neurodent.core.utils) atomic_write_json() (in module neurodent.core.utils) B BAND (neurodent.constants.analysis.FeatureType attribute) BAND_FEATURES (in module neurodent.constants.analysis) BAND_NAMES (in module neurodent.constants.analysis) band_scale() (neurodent.plotting.ExperimentPlotter static method) BANDED_MATRIX (neurodent.constants.analysis.FeatureType attribute) BANDED_MATRIX_FEATURES (in module neurodent.constants.analysis) C cache_fragments_to_zarr() (in module neurodent.core.utils) CHANNEL_ABBREV_BY_RAW (in module neurodent.constants.mappings) CHANNEL_ABBREVS (in module neurodent.constants.mappings) channel_axes (neurodent.constants.analysis.FeatureType property) CHANNEL_MAP (in module neurodent.constants.mappings) chunked_channel_distance_matrix() (in module neurodent.core.utils) classify_feature() (in module neurodent.constants.analysis) cleanup_rec() (neurodent.loading.AnimalOrganizer method) (neurodent.loading.LongRecordingOrganizer method) COMPONENT_LABELS (in module neurodent.constants.analysis) compute_ampvar() (neurodent.analysis.FragmentAnalyzer static method) (neurodent.analysis.LongRecordingAnalyzer method) compute_bad_channels() (neurodent.loading.AnimalOrganizer method) (neurodent.loading.LongRecordingOrganizer method) compute_cohere() (neurodent.analysis.FragmentAnalyzer static method) (neurodent.analysis.LongRecordingAnalyzer method) compute_coherency() (neurodent.analysis.FragmentAnalyzer static method) compute_frequency_domain_spike_analysis() (neurodent.loading.AnimalOrganizer method) compute_imcoh() (neurodent.analysis.FragmentAnalyzer static method) (neurodent.analysis.LongRecordingAnalyzer method) compute_logampvar() (neurodent.analysis.FragmentAnalyzer static method) (neurodent.analysis.LongRecordingAnalyzer method) compute_lognspike() (neurodent.analysis.FragmentAnalyzer static method) (neurodent.analysis.LongRecordingAnalyzer method) compute_logpsdband() (neurodent.analysis.FragmentAnalyzer static method) (neurodent.analysis.LongRecordingAnalyzer method) compute_logpsdfrac() (neurodent.analysis.FragmentAnalyzer static method) (neurodent.analysis.LongRecordingAnalyzer method) compute_logpsdtotal() (neurodent.analysis.FragmentAnalyzer static method) (neurodent.analysis.LongRecordingAnalyzer method) compute_logrms() (neurodent.analysis.FragmentAnalyzer static method) (neurodent.analysis.LongRecordingAnalyzer method) compute_nspike() (neurodent.analysis.FragmentAnalyzer static method) (neurodent.analysis.LongRecordingAnalyzer method) compute_pcorr() (neurodent.analysis.FragmentAnalyzer static method) (neurodent.analysis.LongRecordingAnalyzer method) compute_psd() (neurodent.analysis.FragmentAnalyzer static method) (neurodent.analysis.LongRecordingAnalyzer method) compute_psdband() (neurodent.analysis.FragmentAnalyzer static method) (neurodent.analysis.LongRecordingAnalyzer method) compute_psdfrac() (neurodent.analysis.FragmentAnalyzer static method) (neurodent.analysis.LongRecordingAnalyzer method) compute_psdslope() (neurodent.analysis.FragmentAnalyzer static method) (neurodent.analysis.LongRecordingAnalyzer method) compute_psdtotal() (neurodent.analysis.FragmentAnalyzer static method) (neurodent.analysis.LongRecordingAnalyzer method) compute_rms() (neurodent.analysis.FragmentAnalyzer static method) (neurodent.analysis.LongRecordingAnalyzer method) compute_windowed_analysis() (neurodent.loading.AnimalOrganizer method) compute_zcohere() (neurodent.analysis.FragmentAnalyzer static method) (neurodent.analysis.LongRecordingAnalyzer method) compute_zimcoh() (neurodent.analysis.FragmentAnalyzer static method) (neurodent.analysis.LongRecordingAnalyzer method) compute_zpcorr() (neurodent.analysis.FragmentAnalyzer static method) (neurodent.analysis.LongRecordingAnalyzer method) convert_colbins_to_rowbins() (neurodent.loading.AnimalOrganizer method) convert_colpath_to_rowpath() (in module neurodent.core.utils) convert_file_with_mne_to_recording() (neurodent.loading.LongRecordingOrganizer method) convert_file_with_si_to_recording() (neurodent.loading.LongRecordingOrganizer method) convert_idx_to_timebound() (neurodent.analysis.LongRecordingAnalyzer method) convert_rowbins_to_rec() (neurodent.loading.AnimalOrganizer method) convert_sa_to_np() (neurodent.results.FrequencyDomainSpikeAnalysisResult static method) convert_sas_to_mne() (neurodent.results.FrequencyDomainSpikeAnalysisResult static method) convert_to_mne() (neurodent.loading.LongRecordingOrganizer method) (neurodent.results.FrequencyDomainSpikeAnalysisResult method) convert_units_to_multiplier() (in module neurodent.core.utils) copy() (neurodent.results.WindowAnalysisResult method) count() (neurodent.core.utils.Natural_Neighbor method) D DATEPARSER_PATTERNS_TO_REMOVE (in module neurodent.constants.mappings) DDFBinaryMetadata (class in neurodent.loading) DEFAULT_DAY (in module neurodent.constants.mappings) DEFAULT_GENOTYPE_MAP (in module neurodent.constants.mappings) DEFAULT_PARAMS (neurodent.analysis.FrequencyDomainSpikeDetector attribute) DEFAULT_SEX_MAP (in module neurodent.constants.mappings) detect_and_load_data() (neurodent.loading.LongRecordingOrganizer method) detect_spikes_recording() (neurodent.analysis.FrequencyDomainSpikeDetector static method) DF_SORT_ORDER (in module neurodent.constants.mappings) display_name (neurodent.loading.LongRecordingOrganizer property) E evaluate_lof_threshold_binary() (neurodent.results.WindowAnalysisResult method) ExperimentPlotter (class in neurodent.plotting) extract_mne_unit_info() (in module neurodent.core.utils) extracted_shape (neurodent.constants.analysis.FeatureType property) F FEATURE_DEPENDENCIES (neurodent.analysis.FragmentAnalyzer attribute) FEATURE_LABELS (in module neurodent.constants.mappings) FEATURE_PLOT_HEIGHT_RATIOS (in module neurodent.constants.plotting) FEATURE_SHAPES (in module neurodent.constants.analysis) FEATURE_TYPES (in module neurodent.constants.analysis) FEATURES (in module neurodent.constants.analysis) FeatureType (class in neurodent.constants.analysis) filepath_to_index() (in module neurodent.core.utils) filter_all() (neurodent.results.WindowAnalysisResult method) filter_high_beta() (neurodent.results.WindowAnalysisResult method) filter_high_rms() (neurodent.results.WindowAnalysisResult method) filter_logrms_range() (neurodent.results.WindowAnalysisResult method) filter_low_rms() (neurodent.results.WindowAnalysisResult method) filter_reject_channels() (neurodent.results.WindowAnalysisResult method) filter_reject_channels_by_session() (neurodent.results.WindowAnalysisResult method) finalize_file_timestamps() (neurodent.loading.LongRecordingOrganizer method) findKNN() (neurodent.core.utils.Natural_Neighbor method) FragmentAnalyzer (class in neurodent.analysis) FREQ_BAND_TOTAL (in module neurodent.constants.analysis) FREQ_BANDS (in module neurodent.constants.analysis) FREQ_MAXS (in module neurodent.constants.analysis) FREQ_MINS (in module neurodent.constants.analysis) FrequencyDomainSpikeAnalysisResult (class in neurodent.results) FrequencyDomainSpikeDetector (class in neurodent.analysis) from_detection_results() (neurodent.results.FrequencyDomainSpikeAnalysisResult class method) from_dict() (neurodent.loading.DDFBinaryMetadata class method) (neurodent.loading.RecordingMetadata class method) from_json() (neurodent.loading.DDFBinaryMetadata class method) (neurodent.loading.RecordingMetadata class method) from_lros() (neurodent.loading.AnimalOrganizer class method) G GENOTYPE_MAP (in module neurodent.constants.mappings) get_all_lof_scores() (neurodent.loading.AnimalOrganizer method) get_bad_channels_by_lof_threshold() (neurodent.results.WindowAnalysisResult method) get_cache_status_message() (in module neurodent.core.utils) get_channel_averaged_result() (neurodent.results.WindowAnalysisResult method) (neurodent.results.ZeitgeberAnalysisResult method) get_date_string() (neurodent.loading.LongRecordingOrganizer method) get_datetime_fragment() (neurodent.loading.LongRecordingOrganizer method) get_dur_fragment() (neurodent.loading.LongRecordingOrganizer method) get_feature_label() (in module neurodent.core.utils) get_file_end() (neurodent.analysis.LongRecordingAnalyzer method) get_file_stem() (in module neurodent.core.utils) get_filter_high_beta() (neurodent.results.WindowAnalysisResult method) get_filter_high_rms() (neurodent.results.WindowAnalysisResult method) get_filter_logrms_range() (neurodent.results.WindowAnalysisResult method) get_filter_low_rms() (neurodent.results.WindowAnalysisResult method) get_filter_morphological_smoothing() (neurodent.results.WindowAnalysisResult method) get_filter_reject_channels() (neurodent.results.WindowAnalysisResult method) get_filter_reject_channels_by_recording_session() (neurodent.results.WindowAnalysisResult method) get_fragment() (neurodent.loading.LongRecordingOrganizer method) get_fragment_mne() (neurodent.analysis.LongRecordingAnalyzer method) get_fragment_np() (neurodent.analysis.LongRecordingAnalyzer method) get_fragment_rec() (neurodent.analysis.LongRecordingAnalyzer method) get_fragment_timestamp() (neurodent.core.utils.TimestampMapper method) get_groupavg_result() (neurodent.results.WindowAnalysisResult method) (neurodent.results.ZeitgeberAnalysisResult method) get_grouprows_result() (neurodent.results.WindowAnalysisResult method) (neurodent.results.ZeitgeberAnalysisResult method) get_info() (neurodent.results.WindowAnalysisResult method) get_lof_scores() (neurodent.loading.LongRecordingOrganizer method) (neurodent.results.WindowAnalysisResult method) get_num_fragments() (neurodent.loading.LongRecordingOrganizer method) get_result() (neurodent.results.WindowAnalysisResult method) (neurodent.results.ZeitgeberAnalysisResult method) get_spike_counts_per_channel() (neurodent.results.FrequencyDomainSpikeAnalysisResult method) get_temp_directory() (in module neurodent.core.utils) get_timeline_summary() (neurodent.loading.AnimalOrganizer method) get_total_spike_count() (neurodent.results.FrequencyDomainSpikeAnalysisResult method) GLOBAL_DTYPE (in module neurodent.constants.config) GLOBAL_SAMPLING_RATE (in module neurodent.constants.config) H HIST (neurodent.constants.analysis.FeatureType attribute) HIST_FEATURES (in module neurodent.constants.analysis) I is_day() (in module neurodent.core.utils) is_dict_stored (neurodent.constants.analysis.FeatureType property) is_linear (neurodent.constants.analysis.FeatureType property) is_matrix (neurodent.constants.analysis.FeatureType property) is_si_recording_folder() (in module neurodent.core.utils) L LINE_FREQ (in module neurodent.constants.config) LINEAR (neurodent.constants.analysis.FeatureType attribute) LINEAR_2D (neurodent.constants.analysis.FeatureType attribute) LINEAR_2D_FEATURES (in module neurodent.constants.analysis) LINEAR_FEATURES (in module neurodent.constants.analysis) load() (neurodent.core.utils.Natural_Neighbor method) load_fif_and_json() (neurodent.results.FrequencyDomainSpikeAnalysisResult class method) load_parquet_and_json() (neurodent.results.WindowAnalysisResult class method) load_pickle_and_json() (neurodent.results.WindowAnalysisResult class method) load_recording() (neurodent.loading.LongRecordingOrganizer class method) log_transform() (in module neurodent.core.utils) LongRecordingAnalyzer (class in neurodent.analysis) LongRecordingOrganizer (class in neurodent.loading) M MATRIX_FEATURES (in module neurodent.constants.analysis) merge() (neurodent.loading.LongRecordingOrganizer method) module neurodent.constants neurodent.constants.analysis neurodent.constants.config neurodent.constants.mappings neurodent.constants.plotting neurodent.core neurodent.core.utils neurodent.plotting N nanaverage() (in module neurodent.core.utils) nanmean_series_of_np() (in module neurodent.core.utils) Natural_Neighbor (class in neurodent.core.utils) neurodent.constants module neurodent.constants.analysis module neurodent.constants.config module neurodent.constants.mappings module neurodent.constants.plotting module neurodent.core module neurodent.core.utils module neurodent.plotting module NEURODENT_SIDECAR_NAME (in module neurodent.constants.config) normalize_value_from_aliases() (in module neurodent.core.utils) O OKABE_ITO_COLORS (in module neurodent.constants.plotting) P parse_str_to_animal() (in module neurodent.core.utils) parse_str_to_day() (in module neurodent.core.utils) parse_truncate() (in module neurodent.core.utils) path_safe_animal_day (neurodent.results.FrequencyDomainSpikeAnalysisResult property) path_safe_animal_id (neurodent.results.FrequencyDomainSpikeAnalysisResult property) (neurodent.results.WindowAnalysisResult property) path_safe_animaldays (neurodent.results.WindowAnalysisResult property) path_safe_save_stem (neurodent.results.FrequencyDomainSpikeAnalysisResult property) persist() (neurodent.loading.LongRecordingOrganizer method) plot_catplot() (neurodent.plotting.ExperimentPlotter method) plot_coherecorr_diff() (neurodent.plotting.AnimalPlotter method) plot_coherecorr_matrix() (neurodent.plotting.AnimalPlotter method) plot_coherecorr_spectral() (neurodent.plotting.AnimalPlotter method) plot_diffheatmap() (neurodent.plotting.ExperimentPlotter method) plot_diffheatmap_faceted() (neurodent.plotting.ExperimentPlotter method) plot_feature() (neurodent.plotting.ZeitgeberPlotter method) plot_heatmap() (neurodent.plotting.ExperimentPlotter method) plot_heatmap_faceted() (neurodent.plotting.ExperimentPlotter method) plot_linear_temporal() (neurodent.plotting.AnimalPlotter method) plot_psd_histogram() (neurodent.plotting.AnimalPlotter method) plot_psd_spectrogram() (neurodent.plotting.AnimalPlotter method) plot_qqplot() (neurodent.plotting.ExperimentPlotter method) plot_spike_averaged_traces() (neurodent.results.FrequencyDomainSpikeAnalysisResult method) plot_temporal_heatmap() (neurodent.plotting.AnimalPlotter method) process_fragment_with_dependencies() (neurodent.analysis.FragmentAnalyzer static method) pull_timeseries_dataframe() (neurodent.plotting.ExperimentPlotter method) R read() (neurodent.core.utils.Natural_Neighbor method) read_distance_matrix() (neurodent.core.utils.Natural_Neighbor method) read_mnes_spikes() (neurodent.results.WindowAnalysisResult method) read_sars_spikes() (neurodent.results.WindowAnalysisResult method) RecordingMetadata (class in neurodent.loading) rename_mne_channels() (in module neurodent.core.utils) reorder_and_pad_channels() (neurodent.results.WindowAnalysisResult method) resolve_channel() (in module neurodent.core.utils) resolve_channels() (in module neurodent.core.utils) S safe_rmtree() (in module neurodent.core.utils) safe_unlink() (in module neurodent.core.utils) save_fif_and_json() (neurodent.results.FrequencyDomainSpikeAnalysisResult method) save_parquet_and_json() (neurodent.results.WindowAnalysisResult method) save_pickle_and_json() (neurodent.results.WindowAnalysisResult method) save_recording() (neurodent.loading.LongRecordingOrganizer method) save_to_edf() (neurodent.loading.LongRecordingOrganizer method) scan_parquet_and_json() (neurodent.results.WindowAnalysisResult class method) select_channels() (neurodent.results.WindowAnalysisResult method) semantic_axes (neurodent.constants.analysis.FeatureType property) set_temp_directory() (in module neurodent.core.utils) SEX_MAP (in module neurodent.constants.mappings) should_use_cache_unified() (in module neurodent.core.utils) should_use_cached_file() (in module neurodent.core.utils) SIMPLE_MATRIX (neurodent.constants.analysis.FeatureType attribute) SIMPLE_MATRIX_FEATURES (in module neurodent.constants.analysis) slugify() (in module neurodent.core.utils) sort_dataframe_by_plot_order() (in module neurodent.core.utils) split() (neurodent.loading.AnimalOrganizer method) (neurodent.loading.LongRecordingOrganizer method) stream_fragments_to_zarr() (in module neurodent.core.utils) stream_recording_to_zarr() (in module neurodent.core.utils) T TimestampMapper (class in neurodent.core.utils) to_dict() (neurodent.loading.DDFBinaryMetadata method) (neurodent.loading.RecordingMetadata method) to_json() (neurodent.loading.DDFBinaryMetadata method) (neurodent.loading.RecordingMetadata method) U update_sampling_rate() (neurodent.loading.DDFBinaryMetadata method) (neurodent.loading.RecordingMetadata method) V validate_plot_order() (neurodent.plotting.ExperimentPlotter method) validate_timestamps() (in module neurodent.core.utils) W WAR_FEATURES (in module neurodent.constants.analysis) WindowAnalysisResult (class in neurodent.results) Z ZeitgeberAnalysisResult (class in neurodent.results) ZeitgeberPlotter (class in neurodent.plotting)