.. _api_reference: ============= API Reference ============= This is the classes and functions reference of mne-python. Functions are grouped thematically by analysis stage. Functions and classes that are not below a module heading are found in the :py:mod:`mne` namespace. .. contents:: :local: :depth: 2 Classes ======= .. currentmodule:: mne .. autosummary:: :toctree: generated/ :template: class.rst io.Raw io.RawFIF Epochs Evoked SourceSpaces SourceEstimate VolSourceEstimate MixedSourceEstimate Covariance Dipole Label BiHemiLabel Transform preprocessing.ICA decoding.CSP decoding.Scaler decoding.ConcatenateChannels decoding.FilterEstimator decoding.PSDEstimator decoding.GeneralizationAcrossTime decoding.TimeDecoding realtime.RtEpochs realtime.RtClient realtime.MockRtClient realtime.StimServer realtime.StimClient report.Report Logging and Configuration ========================= .. currentmodule:: mne .. autosummary:: :toctree: generated/ :template: function.rst get_config_path get_config set_log_level set_log_file set_config :py:mod:`mne.cuda`: .. automodule:: mne.cuda :no-members: :no-inherited-members: .. currentmodule:: mne.cuda .. autosummary:: :toctree: generated/ :template: function.rst init_cuda Reading raw data ================ :py:mod:`mne.io`: .. currentmodule:: mne.io Classes: .. autosummary:: :toctree: generated/ :template: class.rst Raw Functions: .. autosummary:: :toctree: generated/ :template: function.rst read_raw_bti read_raw_edf read_raw_kit read_raw_brainvision read_raw_egi read_raw_fif .. currentmodule:: mne.io.kit :py:mod:`mne.io.kit`: .. autosummary:: :toctree: generated/ :template: function.rst read_mrk File I/O ======== .. currentmodule:: mne Functions: .. autosummary:: :toctree: generated :template: function.rst decimate_surface get_head_surf get_meg_helmet_surf get_volume_labels_from_aseg parse_config read_labels_from_annot read_bem_solution read_bem_surfaces read_cov read_dipole read_epochs read_epochs_kit read_events read_evokeds read_forward_solution read_label read_morph_map read_proj read_reject_parameters read_selection read_source_estimate read_source_spaces read_surface read_trans save_stc_as_volume write_labels_to_annot write_bem_solution write_bem_surfaces write_cov write_events write_evokeds write_forward_solution write_label write_proj write_source_spaces write_surface write_trans Creating data objects from arrays ================================= Classes: .. currentmodule:: mne :py:mod:`mne`: .. autosummary:: :toctree: generated/ :template: class.rst EvokedArray EpochsArray .. currentmodule:: mne.io :py:mod:`mne.io`: .. autosummary:: :toctree: generated/ :template: class.rst RawArray Functions: .. currentmodule:: mne :py:mod:`mne`: .. autosummary:: :toctree: generated/ :template: function.rst create_info Sample datasets =============== :py:mod:`mne.datasets.sample`: .. automodule:: mne.datasets.sample :no-members: :no-inherited-members: .. currentmodule:: mne.datasets.sample .. autosummary:: :toctree: generated/ :template: function.rst data_path :py:mod:`mne.datasets.spm_face`: .. automodule:: mne.datasets.spm_face :no-members: :no-inherited-members: .. currentmodule:: mne.datasets.spm_face .. autosummary:: :toctree: generated/ :template: function.rst data_path :py:mod:`mne.datasets.brainstorm`: .. automodule:: mne.datasets.brainstorm :no-members: :no-inherited-members: .. currentmodule:: mne.datasets.brainstorm .. autosummary:: :toctree: generated/ :template: function.rst bst_auditory.data_path bst_resting.data_path bst_raw.data_path :py:mod:`mne.datasets.megsim`: .. automodule:: mne.datasets.megsim :no-members: :no-inherited-members: .. currentmodule:: mne.datasets.megsim .. autosummary:: :toctree: generated/ :template: function.rst data_path load_data Visualization ============= :py:mod:`mne.viz`: .. automodule:: mne.viz :no-members: :no-inherited-members: .. currentmodule:: mne.viz Classes: .. autosummary:: :toctree: generated/ :template: class.rst ClickableImage Functions: .. autosummary:: :toctree: generated/ :template: function.rst circular_layout mne_analyze_colormap plot_connectivity_circle plot_cov plot_dipole_amplitudes plot_dipole_locations plot_drop_log plot_epochs plot_events plot_evoked plot_evoked_image plot_evoked_topomap plot_evoked_field plot_evoked_white plot_ica_sources plot_ica_components plot_ica_scores plot_ica_overlay plot_epochs_image plot_montage plot_projs_topomap plot_raw plot_raw_psd plot_snr_estimate plot_source_estimates plot_sparse_source_estimates plot_tfr_topomap plot_topo plot_topo_image_epochs plot_topomap compare_fiff add_background_image .. currentmodule:: mne.io .. autosummary:: :toctree: generated/ :template: function.rst show_fiff Preprocessing ============= Projections: .. currentmodule:: mne .. autosummary:: :toctree: generated/ :template: function.rst compute_proj_epochs compute_proj_evoked compute_proj_raw read_proj write_proj Manipulate channels and set sensors locations for processing and plotting: .. currentmodule:: mne.channels Classes: .. autosummary:: :toctree: generated/ :template: class.rst Layout Montage DigMontage Functions: .. autosummary:: :toctree: generated/ :template: function.rst fix_mag_coil_types read_montage read_dig_montage read_layout find_layout make_eeg_layout make_grid_layout read_ch_connectivity equalize_channels rename_channels generate_2d_layout :py:mod:`mne.preprocessing`: .. automodule:: mne.preprocessing :no-members: :no-inherited-members: .. currentmodule:: mne.preprocessing .. autosummary:: :toctree: generated/ :template: function.rst compute_proj_ecg compute_proj_eog create_ecg_epochs create_eog_epochs find_ecg_events find_eog_events ica_find_ecg_events ica_find_eog_events read_ica run_ica EEG referencing: .. currentmodule:: mne.io .. autosummary:: :toctree: generated/ :template: function.rst add_reference_channels set_bipolar_reference set_eeg_reference :py:mod:`mne.filter`: .. automodule:: mne.filter :no-members: :no-inherited-members: .. currentmodule:: mne.filter .. autosummary:: :toctree: generated/ :template: function.rst band_pass_filter construct_iir_filter high_pass_filter low_pass_filter Events ====== .. currentmodule:: mne .. autosummary:: :toctree: generated/ :template: function.rst concatenate_events find_events find_stim_steps make_fixed_length_events merge_events parse_config pick_events read_events write_events .. currentmodule:: mne.event .. autosummary:: :toctree: generated/ :template: function.rst define_target_events .. currentmodule:: mne.epochs .. autosummary:: :toctree: generated/ :template: function.rst combine_event_ids equalize_epoch_counts add_channels_epochs concatenate_epochs Sensor Space Data ================= .. currentmodule:: mne .. autosummary:: :toctree: generated/ :template: function.rst combine_evoked concatenate_raws equalize_channels grand_average get_chpi_positions pick_channels pick_channels_cov pick_channels_forward pick_channels_regexp pick_types pick_types_forward read_epochs read_reject_parameters read_selection rename_channels Covariance ========== .. currentmodule:: mne .. autosummary:: :toctree: generated/ :template: function.rst compute_covariance compute_raw_covariance make_ad_hoc_cov read_cov write_cov .. currentmodule:: mne.cov .. autosummary:: :toctree: generated/ :template: function.rst regularize MRI Processing ============== .. currentmodule:: mne Step by step instructions for using :func:`gui.coregistration`: - `Coregistration for subjects with structural MRI `_ - `Scaling a template MRI for subjects for which no MRI is available `_ .. autosummary:: :toctree: generated/ :template: function.rst gui.coregistration gui.fiducials create_default_subject scale_mri scale_bem scale_labels scale_source_space Forward Modeling ================ :py:mod:`mne`: .. currentmodule:: mne Functions: .. autosummary:: :toctree: generated/ :template: function.rst add_source_space_distances apply_forward apply_forward_raw average_forward_solutions convert_forward_solution do_forward_solution make_bem_model make_bem_solution make_forward_solution make_field_map make_sphere_model morph_source_spaces read_bem_surfaces read_forward_solution read_trans read_source_spaces read_surface sensitivity_map setup_source_space setup_volume_source_space write_bem_surface write_trans .. currentmodule:: mne.bem .. autosummary:: :toctree: generated/ :template: function.rst make_watershed_bem make_flash_bem convert_flash_mris .. currentmodule:: mne.forward .. autosummary:: :toctree: generated/ :template: function.rst restrict_forward_to_label restrict_forward_to_stc :py:mod:`mne.source_space`: .. automodule:: mne.source_space :no-members: :no-inherited-members: Inverse Solutions ================= :py:mod:`mne.minimum_norm`: .. automodule:: mne.minimum_norm :no-members: :no-inherited-members: .. currentmodule:: mne.minimum_norm Classes: .. autosummary:: :toctree: generated/ :template: class.rst InverseOperator Functions: .. autosummary:: :toctree: generated/ :template: function.rst apply_inverse apply_inverse_epochs apply_inverse_raw compute_source_psd compute_source_psd_epochs compute_rank_inverse estimate_snr make_inverse_operator read_inverse_operator source_band_induced_power source_induced_power write_inverse_operator point_spread_function cross_talk_function :py:mod:`mne.inverse_sparse`: .. automodule:: mne.inverse_sparse :no-members: :no-inherited-members: .. currentmodule:: mne.inverse_sparse .. autosummary:: :toctree: generated/ :template: function.rst mixed_norm tf_mixed_norm gamma_map :py:mod:`mne.beamformer`: .. automodule:: mne.beamformer :no-members: :no-inherited-members: .. currentmodule:: mne.beamformer .. autosummary:: :toctree: generated/ :template: function.rst lcmv lcmv_epochs lcmv_raw dics dics_epochs dics_source_power rap_music :py:mod:`mne`: .. currentmodule:: mne Functions: .. autosummary:: :toctree: generated/ :template: function.rst fit_dipole Source Space Data ================= .. currentmodule:: mne .. autosummary:: :toctree: generated/ :template: function.rst compute_morph_matrix extract_label_time_course grade_to_tris grade_to_vertices grow_labels label_sign_flip morph_data morph_data_precomputed read_labels_from_annot read_dipole read_label read_source_estimate save_stc_as_volume split_label stc_to_label transform_surface_to vertex_to_mni write_labels_to_annot write_label Time-Frequency ============== :py:mod:`mne.time_frequency`: .. automodule:: mne.time_frequency :no-members: :no-inherited-members: .. currentmodule:: mne.time_frequency Classes: .. autosummary:: :toctree: generated/ :template: class.rst AverageTFR Functions that operate on mne-python objects: .. autosummary:: :toctree: generated/ :template: function.rst compute_epochs_csd compute_epochs_psd compute_raw_psd fit_iir_model_raw tfr_morlet tfr_multitaper tfr_stockwell read_tfrs write_tfrs Functions that operate on ``np.ndarray`` objects: .. autosummary:: :toctree: generated/ :template: function.rst cwt_morlet dpss_windows morlet multitaper_psd single_trial_power stft istft stftfreq :py:mod:`mne.time_frequency.tfr`: .. automodule:: mne.time_frequency.tfr :no-members: :no-inherited-members: .. currentmodule:: mne.time_frequency.tfr .. autosummary:: :toctree: generated/ :template: function.rst cwt morlet Connectivity Estimation ======================= :py:mod:`mne.connectivity`: .. automodule:: mne.connectivity :no-members: :no-inherited-members: .. currentmodule:: mne.connectivity .. autosummary:: :toctree: generated/ :template: function.rst seed_target_indices spectral_connectivity phase_slope_index Statistics ========== :py:mod:`mne.stats`: .. automodule:: mne.stats :no-members: :no-inherited-members: .. currentmodule:: mne.stats .. autosummary:: :toctree: generated/ :template: function.rst bonferroni_correction fdr_correction permutation_cluster_test permutation_cluster_1samp_test permutation_t_test spatio_temporal_cluster_test spatio_temporal_cluster_1samp_test ttest_1samp_no_p linear_regression linear_regression_raw f_mway_rm Functions to compute connectivity (adjacency) matrices for cluster-level statistics .. currentmodule:: mne .. autosummary:: :toctree: generated/ :template: function.rst spatial_dist_connectivity spatial_src_connectivity spatial_tris_connectivity spatio_temporal_src_connectivity spatio_temporal_tris_connectivity spatio_temporal_dist_connectivity Simulation ========== :py:mod:`mne.simulation`: .. automodule:: mne.simulation :no-members: :no-inherited-members: .. currentmodule:: mne.simulation .. autosummary:: :toctree: generated/ :template: function.rst simulate_evoked simulate_raw simulate_stc simulate_sparse_stc select_source_in_label Decoding ======== :py:mod:`mne.decoding`: .. automodule:: mne.decoding :no-members: :no-inherited-members: Classes: .. autosummary:: :toctree: generated/ :template: class.rst Scaler ConcatenateChannels PSDEstimator FilterEstimator CSP GeneralizationAcrossTime Realtime ======== :py:mod:`mne.realtime`: .. automodule:: mne.realtime :no-members: :no-inherited-members: Classes: .. autosummary:: :toctree: generated/ :template: class.rst RtEpochs RtClient MockRtClient FieldTripClient StimServer StimClient MNE-Report ========== :py:mod:`mne.report`: .. automodule:: mne.report :no-members: :no-inherited-members: .. currentmodule:: mne.report Classes: .. autosummary:: :toctree: generated/ :template: class.rst Report