Index _ | A | B | C | D | E | F | G | H | I | K | L | M | N | P | R | S | T | U | V | W _ __init__() (neurodent.core.DDFBinaryMetadata method) (neurodent.core.LongRecordingAnalyzer method) (neurodent.core.LongRecordingOrganizer method) (neurodent.core.utils.Natural_Neighbor method) (neurodent.core.utils.TimestampMapper method) (neurodent.visualization.AnimalOrganizer method) (neurodent.visualization.AnimalPlotter method) (neurodent.visualization.ExperimentPlotter method) (neurodent.visualization.FrequencyDomainSpikeAnalysisResult method) (neurodent.visualization.SpikeAnalysisResult method) (neurodent.visualization.WindowAnalysisResult method) __repr__() (neurodent.core.LongRecordingOrganizer method) __str__() (neurodent.core.LongRecordingOrganizer method) (neurodent.visualization.FrequencyDomainSpikeAnalysisResult method) A add_unique_hash() (neurodent.visualization.WindowAnalysisResult method) aggregate_time_windows() (neurodent.visualization.WindowAnalysisResult method) algorithm() (neurodent.core.utils.Natural_Neighbor method) AnimalOrganizer (class in neurodent.visualization) AnimalPlotter (class in neurodent.visualization) apply_filters() (neurodent.visualization.WindowAnalysisResult method) apply_lof_threshold() (neurodent.core.LongRecordingOrganizer method) (neurodent.visualization.AnimalOrganizer method) asserts() (neurodent.core.utils.Natural_Neighbor method) B BAND_FEATURES (in module neurodent.constants) BAND_NAMES (in module neurodent.constants) C cache_fragments_to_zarr() (in module neurodent.core.utils) cleanup_rec() (neurodent.core.LongRecordingOrganizer method) (neurodent.visualization.AnimalOrganizer method) compute_ampvar() (neurodent.core.FragmentAnalyzer static method) (neurodent.core.LongRecordingAnalyzer method) compute_bad_channels() (neurodent.core.LongRecordingOrganizer method) (neurodent.visualization.AnimalOrganizer method) compute_cohere() (neurodent.core.FragmentAnalyzer static method) (neurodent.core.LongRecordingAnalyzer method) compute_coherency() (neurodent.core.FragmentAnalyzer static method) compute_frequency_domain_spike_analysis() (neurodent.visualization.AnimalOrganizer method) compute_imcoh() (neurodent.core.FragmentAnalyzer static method) (neurodent.core.LongRecordingAnalyzer method) compute_logampvar() (neurodent.core.FragmentAnalyzer static method) (neurodent.core.LongRecordingAnalyzer method) compute_lognspike() (neurodent.core.FragmentAnalyzer static method) (neurodent.core.LongRecordingAnalyzer method) compute_logpsdband() (neurodent.core.FragmentAnalyzer static method) (neurodent.core.LongRecordingAnalyzer method) compute_logpsdfrac() (neurodent.core.FragmentAnalyzer static method) (neurodent.core.LongRecordingAnalyzer method) compute_logpsdtotal() (neurodent.core.FragmentAnalyzer static method) (neurodent.core.LongRecordingAnalyzer method) compute_logrms() (neurodent.core.FragmentAnalyzer static method) (neurodent.core.LongRecordingAnalyzer method) compute_nspike() (neurodent.core.FragmentAnalyzer static method) (neurodent.core.LongRecordingAnalyzer method) compute_pcorr() (neurodent.core.FragmentAnalyzer static method) (neurodent.core.LongRecordingAnalyzer method) compute_psd() (neurodent.core.FragmentAnalyzer static method) (neurodent.core.LongRecordingAnalyzer method) compute_psdband() (neurodent.core.FragmentAnalyzer static method) (neurodent.core.LongRecordingAnalyzer method) compute_psdfrac() (neurodent.core.FragmentAnalyzer static method) (neurodent.core.LongRecordingAnalyzer method) compute_psdslope() (neurodent.core.FragmentAnalyzer static method) (neurodent.core.LongRecordingAnalyzer method) compute_psdtotal() (neurodent.core.FragmentAnalyzer static method) (neurodent.core.LongRecordingAnalyzer method) compute_rms() (neurodent.core.FragmentAnalyzer static method) (neurodent.core.LongRecordingAnalyzer method) compute_spike_analysis() (neurodent.visualization.AnimalOrganizer method) compute_windowed_analysis() (neurodent.visualization.AnimalOrganizer method) compute_zcohere() (neurodent.core.FragmentAnalyzer static method) (neurodent.core.LongRecordingAnalyzer method) compute_zimcoh() (neurodent.core.FragmentAnalyzer static method) (neurodent.core.LongRecordingAnalyzer method) compute_zpcorr() (neurodent.core.FragmentAnalyzer static method) (neurodent.core.LongRecordingAnalyzer method) convert_colbins_rowbins_to_rec() (neurodent.core.LongRecordingOrganizer method) convert_colbins_to_rowbins() (neurodent.core.LongRecordingOrganizer method) (neurodent.visualization.AnimalOrganizer method) convert_colpath_to_rowpath() (in module neurodent.core.utils) convert_file_with_mne_to_recording() (neurodent.core.LongRecordingOrganizer method) convert_file_with_si_to_recording() (neurodent.core.LongRecordingOrganizer method) convert_idx_to_timebound() (neurodent.core.LongRecordingAnalyzer method) convert_rowbins_to_rec() (neurodent.core.LongRecordingOrganizer method) (neurodent.visualization.AnimalOrganizer method) convert_sa_to_np() (neurodent.visualization.SpikeAnalysisResult static method) convert_sas_to_mne() (neurodent.visualization.SpikeAnalysisResult static method) convert_to_mne() (neurodent.core.LongRecordingOrganizer method) (neurodent.visualization.FrequencyDomainSpikeAnalysisResult method) (neurodent.visualization.SpikeAnalysisResult method) convert_units_to_multiplier() (in module neurodent.core.utils) copy() (neurodent.visualization.WindowAnalysisResult method) count() (neurodent.core.utils.Natural_Neighbor method) cumulative_durations (neurodent.core.utils.TimestampMapper attribute) D data (neurodent.core.utils.Natural_Neighbor attribute) DDFBinaryMetadata (class in neurodent.core) DEFAULT_PARAMS (neurodent.core.FrequencyDomainSpikeDetector attribute) detect_and_load_data() (neurodent.core.LongRecordingOrganizer method) detect_spikes_recording() (neurodent.core.FrequencyDomainSpikeDetector static method) E evaluate_lof_threshold_binary() (neurodent.visualization.WindowAnalysisResult method) ExperimentPlotter (class in neurodent.visualization) extract_mne_unit_info() (in module neurodent.core.utils) F FEATURE_DEPENDENCIES (neurodent.core.FragmentAnalyzer attribute) file_durations (neurodent.core.utils.TimestampMapper attribute) file_end_datetimes (neurodent.core.utils.TimestampMapper attribute) file_start_datetimes (neurodent.core.utils.TimestampMapper attribute) filepath_to_index() (in module neurodent.core.utils) filter_all() (neurodent.visualization.WindowAnalysisResult method) filter_high_beta() (neurodent.visualization.WindowAnalysisResult method) filter_high_rms() (neurodent.visualization.WindowAnalysisResult method) filter_logrms_range() (neurodent.visualization.WindowAnalysisResult method) filter_low_rms() (neurodent.visualization.WindowAnalysisResult method) filter_morphological_smoothing() (neurodent.visualization.WindowAnalysisResult method) filter_reject_channels() (neurodent.visualization.WindowAnalysisResult method) filter_reject_channels_by_session() (neurodent.visualization.WindowAnalysisResult method) finalize_file_timestamps() (neurodent.core.LongRecordingOrganizer method) findKNN() (neurodent.core.utils.Natural_Neighbor method) FragmentAnalyzer (class in neurodent.core) FREQ_BANDS (in module neurodent.constants), [1] FrequencyDomainSpikeAnalysisResult (class in neurodent.visualization) FrequencyDomainSpikeDetector (class in neurodent.core) from_detection_results() (neurodent.visualization.FrequencyDomainSpikeAnalysisResult class method) from_dict() (neurodent.core.DDFBinaryMetadata class method) from_json() (neurodent.core.DDFBinaryMetadata class method) G get_all_lof_scores() (neurodent.visualization.AnimalOrganizer method) get_bad_channels_by_lof_threshold() (neurodent.visualization.WindowAnalysisResult method) get_cache_status_message() (in module neurodent.core.utils) get_datetime_fragment() (neurodent.core.LongRecordingOrganizer method) get_dur_fragment() (neurodent.core.LongRecordingOrganizer method) get_file_end() (neurodent.core.LongRecordingAnalyzer method) get_file_stem() (in module neurodent.core.utils) get_filter_high_beta() (neurodent.visualization.WindowAnalysisResult method) get_filter_high_rms() (neurodent.visualization.WindowAnalysisResult method) get_filter_logrms_range() (neurodent.visualization.WindowAnalysisResult method) get_filter_low_rms() (neurodent.visualization.WindowAnalysisResult method) get_filter_morphological_smoothing() (neurodent.visualization.WindowAnalysisResult method) get_filter_reject_channels() (neurodent.visualization.WindowAnalysisResult method) get_filter_reject_channels_by_recording_session() (neurodent.visualization.WindowAnalysisResult method) get_fragment() (neurodent.core.LongRecordingOrganizer method) get_fragment_mne() (neurodent.core.LongRecordingAnalyzer method) get_fragment_np() (neurodent.core.LongRecordingAnalyzer method) get_fragment_rec() (neurodent.core.LongRecordingAnalyzer method) get_fragment_timestamp() (neurodent.core.utils.TimestampMapper method) get_groupavg_result() (neurodent.visualization.WindowAnalysisResult method) get_grouprows_result() (neurodent.visualization.WindowAnalysisResult method) get_info() (neurodent.visualization.WindowAnalysisResult method) get_lof_scores() (neurodent.core.LongRecordingOrganizer method) (neurodent.visualization.WindowAnalysisResult method) get_num_fragments() (neurodent.core.LongRecordingOrganizer method) get_result() (neurodent.visualization.WindowAnalysisResult method) get_spike_counts_per_channel() (neurodent.visualization.FrequencyDomainSpikeAnalysisResult method) get_temp_directory() (in module neurodent.core.utils) get_timeline_summary() (neurodent.visualization.AnimalOrganizer method) get_total_spike_count() (neurodent.visualization.FrequencyDomainSpikeAnalysisResult method) H HIST_FEATURES (in module neurodent.constants) I is_day() (in module neurodent.core.utils) K knn (neurodent.core.utils.Natural_Neighbor attribute) L LINEAR_FEATURES (in module neurodent.constants) load() (neurodent.core.utils.Natural_Neighbor method) load_fif_and_json() (neurodent.visualization.FrequencyDomainSpikeAnalysisResult class method) (neurodent.visualization.SpikeAnalysisResult class method) load_pickle_and_json() (neurodent.visualization.WindowAnalysisResult class method) log_transform() (in module neurodent.core.utils) LongRecordingAnalyzer (class in neurodent.core) LongRecordingOrganizer (class in neurodent.core) M MATRIX_FEATURES (in module neurodent.constants) merge() (neurodent.core.LongRecordingOrganizer method) module neurodent.constants neurodent.core neurodent.core.utils neurodent.visualization MountainSortAnalyzer (class in neurodent.core) N nan_edges (neurodent.core.utils.Natural_Neighbor attribute) nan_num (neurodent.core.utils.Natural_Neighbor attribute) 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.core module neurodent.core.utils module neurodent.visualization module P parse_chname_to_abbrev() (in module neurodent.core.utils) parse_path_to_animalday() (in module neurodent.core.utils) parse_str_to_animal() (in module neurodent.core.utils) parse_str_to_day() (in module neurodent.core.utils) parse_str_to_genotype() (in module neurodent.core.utils) parse_truncate() (in module neurodent.core.utils) plot_catplot() (neurodent.visualization.ExperimentPlotter method) plot_coherecorr_diff() (neurodent.visualization.AnimalPlotter method) plot_coherecorr_matrix() (neurodent.visualization.AnimalPlotter method) plot_coherecorr_spectral() (neurodent.visualization.AnimalPlotter method) plot_diffheatmap() (neurodent.visualization.ExperimentPlotter method) plot_diffheatmap_faceted() (neurodent.visualization.ExperimentPlotter method) plot_heatmap() (neurodent.visualization.ExperimentPlotter method) plot_heatmap_faceted() (neurodent.visualization.ExperimentPlotter method) plot_linear_temporal() (neurodent.visualization.AnimalPlotter method) plot_psd_histogram() (neurodent.visualization.AnimalPlotter method) plot_psd_spectrogram() (neurodent.visualization.AnimalPlotter method) plot_qqplot() (neurodent.visualization.ExperimentPlotter method) plot_spike_averaged_traces() (neurodent.visualization.FrequencyDomainSpikeAnalysisResult method) plot_temporal_heatmap() (neurodent.visualization.AnimalPlotter method) prepare_colbins_rowbins_metas() (neurodent.core.LongRecordingOrganizer method) process_fragment_with_dependencies() (neurodent.core.FragmentAnalyzer static method) pull_timeseries_dataframe() (neurodent.visualization.ExperimentPlotter method) R read() (neurodent.core.utils.Natural_Neighbor method) read_mnes_spikes() (neurodent.visualization.WindowAnalysisResult method) read_sars_spikes() (neurodent.visualization.WindowAnalysisResult method) reorder_and_pad_channels() (neurodent.visualization.WindowAnalysisResult method) repeat (neurodent.core.utils.Natural_Neighbor attribute) S save_fif_and_json() (neurodent.visualization.FrequencyDomainSpikeAnalysisResult method) (neurodent.visualization.SpikeAnalysisResult method) save_pickle_and_json() (neurodent.visualization.WindowAnalysisResult method) set_temp_directory() (in module neurodent.core.utils) should_use_cache_unified() (in module neurodent.core.utils) should_use_cached_file() (in module neurodent.core.utils) sort_dataframe_by_plot_order() (in module neurodent.core.utils) sort_recording() (neurodent.core.MountainSortAnalyzer static method) SpikeAnalysisResult (class in neurodent.visualization) T target (neurodent.core.utils.Natural_Neighbor attribute) TimestampMapper (class in neurodent.core.utils) to_dict() (neurodent.core.DDFBinaryMetadata method) to_json() (neurodent.core.DDFBinaryMetadata method) U update_sampling_rate() (neurodent.core.DDFBinaryMetadata method) V validate_plot_order() (neurodent.visualization.ExperimentPlotter method) validate_timestamps() (in module neurodent.core.utils) W WindowAnalysisResult (class in neurodent.visualization)