:orphan: .. _api_reference: ==================== Python API Reference ==================== This is the reference for classes (``CamelCase`` names) and functions (``underscore_case`` names) of MNE-Python, grouped thematically by analysis stage. Functions and classes that are not below a module heading are found in the ``mne`` namespace. MNE-Python also provides multiple command-line scripts that can be called directly from a terminal, see :ref:`python_commands`. .. contents:: :local: :depth: 2 :py:mod:`mne`: .. automodule:: mne :no-members: :no-inherited-members: Most-used classes ================= .. currentmodule:: mne .. autosummary:: :toctree: generated/ :template: class.rst io.Raw Epochs Evoked Info Reading raw data ================ :py:mod:`mne.io`: .. currentmodule:: mne.io .. automodule:: mne.io :no-members: :no-inherited-members: .. autosummary:: :toctree: generated/ :template: function.rst anonymize_info get_edf_events read_events_eeglab read_raw_artemis123 read_raw_bti read_raw_cnt read_raw_ctf read_raw_edf read_raw_kit read_raw_nicolet read_raw_eeglab read_raw_brainvision read_raw_egi read_raw_fif Base class: .. autosummary:: :toctree: generated :template: class.rst BaseRaw :py:mod:`mne.io.kit`: .. currentmodule:: mne.io.kit .. automodule:: mne.io.kit :no-members: :no-inherited-members: .. autosummary:: :toctree: generated/ :template: function.rst read_mrk File I/O ======== .. currentmodule:: mne .. autosummary:: :toctree: generated :template: function.rst decimate_surface get_head_surf get_meg_helmet_surf get_volume_labels_from_aseg get_volume_labels_from_src parse_config read_labels_from_annot read_bem_solution read_bem_surfaces read_cov read_dipole read_epochs read_epochs_kit read_epochs_eeglab 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 read_tri 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 io.read_info io.show_fiff Base class: .. autosummary:: :toctree: generated :template: class.rst BaseEpochs Creating data objects from arrays ================================= .. currentmodule:: mne .. autosummary:: :toctree: generated/ :template: class.rst EvokedArray EpochsArray io.RawArray .. currentmodule:: mne .. autosummary:: :toctree: generated/ :template: function.rst create_info Datasets ======== .. currentmodule:: mne.datasets :py:mod:`mne.datasets`: .. automodule:: mne.datasets :no-members: :no-inherited-members: .. autosummary:: :toctree: generated/ :template: function.rst brainstorm.bst_auditory.data_path brainstorm.bst_resting.data_path brainstorm.bst_raw.data_path eegbci.load_data megsim.data_path megsim.load_data mtrf.data_path fetch_hcp_mmp_parcellation multimodal.data_path sample.data_path somato.data_path spm_face.data_path visual_92_categories.data_path Visualization ============= .. currentmodule:: mne.viz :py:mod:`mne.viz`: .. automodule:: mne.viz :no-members: :no-inherited-members: .. autosummary:: :toctree: generated/ :template: class.rst ClickableImage .. autosummary:: :toctree: generated/ :template: function.rst add_background_image compare_fiff circular_layout mne_analyze_colormap plot_bem 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_topo plot_evoked_topomap plot_evoked_joint plot_evoked_field plot_evoked_white plot_filter plot_head_positions plot_ideal_filter plot_compare_evokeds plot_ica_sources plot_ica_components plot_ica_properties plot_ica_scores plot_ica_overlay plot_epochs_image plot_layout plot_montage plot_projs_topomap plot_raw plot_raw_psd plot_sensors plot_snr_estimate plot_source_estimates plot_sparse_source_estimates plot_tfr_topomap plot_topo_image_epochs plot_topomap plot_alignment snapshot_brain_montage Preprocessing ============= Projections: .. currentmodule:: mne .. autosummary:: :toctree: generated/ :template: class.rst Projection .. autosummary:: :toctree: generated/ :template: function.rst compute_proj_epochs compute_proj_evoked compute_proj_raw read_proj write_proj :py:mod:`mne.channels`: .. currentmodule:: mne.channels .. automodule:: mne.channels :no-members: :no-inherited-members: .. autosummary:: :toctree: generated/ :template: class.rst Layout Montage DigMontage .. autosummary:: :toctree: generated/ :template: function.rst fix_mag_coil_types read_montage get_builtin_montages read_dig_montage read_layout find_layout make_eeg_layout make_grid_layout find_ch_connectivity read_ch_connectivity equalize_channels rename_channels generate_2d_layout :py:mod:`mne.preprocessing`: .. currentmodule:: mne.preprocessing .. automodule:: mne.preprocessing :no-members: :no-inherited-members: .. autosummary:: :toctree: generated/ :template: class.rst ICA Xdawn .. autosummary:: :toctree: generated/ :template: function.rst compute_proj_ecg compute_proj_eog create_ecg_epochs create_eog_epochs find_ecg_events find_eog_events fix_stim_artifact ica_find_ecg_events ica_find_eog_events infomax maxwell_filter read_ica run_ica corrmap EEG referencing: .. currentmodule:: mne .. autosummary:: :toctree: generated/ :template: function.rst add_reference_channels set_bipolar_reference set_eeg_reference :py:mod:`mne.filter`: .. currentmodule:: mne.filter .. automodule:: mne.filter :no-members: :no-inherited-members: .. autosummary:: :toctree: generated/ :template: function.rst construct_iir_filter create_filter estimate_ringing_samples filter_data notch_filter resample :py:mod:`mne.chpi` .. currentmodule:: mne.chpi .. automodule:: mne.chpi :no-members: :no-inherited-members: .. autosummary:: :toctree: generated/ :template: function.rst filter_chpi head_pos_to_trans_rot_t read_head_pos write_head_pos :py:mod:`mne.transforms` .. currentmodule:: mne.transforms .. automodule:: mne.transforms :no-members: :no-inherited-members: .. autosummary:: :toctree: generated/ :template: class.rst Transform .. autosummary:: :toctree: generated/ :template: function.rst quat_to_rot rot_to_quat Events ====== .. currentmodule:: mne .. autosummary:: :toctree: generated/ :template: class.rst Annotations AcqParserFIF .. 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 concatenate_epochs :py:mod:`mne.event`: .. automodule:: mne.event :no-members: :no-inherited-members: .. currentmodule:: mne.event .. autosummary:: :toctree: generated/ :template: function.rst define_target_events :py:mod:`mne.epochs`: .. automodule:: mne.epochs :no-members: :no-inherited-members: .. currentmodule:: mne.epochs .. autosummary:: :toctree: generated/ :template: function.rst add_channels_epochs average_movements combine_event_ids equalize_epoch_counts Sensor Space Data ================= .. currentmodule:: mne .. autosummary:: :toctree: generated/ :template: function.rst combine_evoked concatenate_raws equalize_channels grand_average pick_channels pick_channels_cov pick_channels_forward pick_channels_regexp pick_types pick_types_forward pick_info read_epochs read_reject_parameters read_selection rename_channels Covariance computation ====================== .. currentmodule:: mne .. autosummary:: :toctree: generated/ :template: class.rst Covariance .. autosummary:: :toctree: generated/ :template: function.rst compute_covariance compute_raw_covariance cov.regularize make_ad_hoc_cov read_cov write_cov 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 ================ .. currentmodule:: mne .. autosummary:: :toctree: generated/ :template: class.rst Forward SourceSpaces .. autosummary:: :toctree: generated/ :template: function.rst add_source_space_distances apply_forward apply_forward_raw average_forward_solutions convert_forward_solution forward.restrict_forward_to_label forward.restrict_forward_to_stc make_bem_model make_bem_solution make_forward_dipole 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 surface.complete_surface_info write_bem_surfaces write_trans :py:mod:`mne.bem`: .. automodule:: mne.bem :no-members: :no-inherited-members: .. currentmodule:: mne.bem .. autosummary:: :toctree: generated/ :template: class.rst ConductorModel .. autosummary:: :toctree: generated/ :template: function.rst fit_sphere_to_headshape get_fitting_dig make_watershed_bem make_flash_bem convert_flash_mris Inverse Solutions ================= :py:mod:`mne.minimum_norm`: .. automodule:: mne.minimum_norm :no-members: :no-inherited-members: .. currentmodule:: mne.minimum_norm .. autosummary:: :toctree: generated/ :template: class.rst InverseOperator .. 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 make_stc_from_dipoles :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 make_lcmv apply_lcmv apply_lcmv_epochs apply_lcmv_raw dics dics_epochs dics_source_power rap_music tf_dics tf_lcmv .. currentmodule:: mne .. autosummary:: :toctree: generated/ :template: class.rst Dipole DipoleFixed .. autosummary:: :toctree: generated/ :template: function.rst fit_dipole :py:mod:`mne.dipole`: .. automodule:: mne.dipole :no-members: :no-inherited-members: .. currentmodule:: mne.dipole .. autosummary:: :toctree: generated/ :template: function.rst get_phantom_dipoles Source Space Data ================= .. currentmodule:: mne .. autosummary:: :toctree: generated/ :template: class.rst BiHemiLabel Label MixedSourceEstimate SourceEstimate VolSourceEstimate .. 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 .. autosummary:: :toctree: generated/ :template: class.rst AverageTFR EpochsTFR Functions that operate on mne-python objects: .. autosummary:: :toctree: generated/ :template: function.rst csd_epochs psd_welch psd_multitaper fit_iir_model_raw tfr_morlet tfr_multitaper tfr_stockwell tfr_array_morlet tfr_array_multitaper tfr_array_stockwell read_tfrs write_tfrs Functions that operate on ``np.ndarray`` objects: .. autosummary:: :toctree: generated/ :template: function.rst csd_array dpss_windows morlet stft istft stftfreq psd_array_multitaper psd_array_welch :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_oneway f_mway_rm f_threshold_mway_rm summarize_clusters_stc Functions to compute neighbor/adjacency matrices for cluster-level statistics: .. currentmodule:: mne .. autosummary:: :toctree: generated/ :template: function.rst spatial_dist_connectivity spatial_src_connectivity spatial_tris_connectivity spatial_inter_hemi_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 .. _api_decoding: Decoding ======== :py:mod:`mne.decoding`: .. automodule:: mne.decoding :no-members: :no-inherited-members: .. autosummary:: :toctree: generated/ :template: class.rst CSP EMS FilterEstimator LinearModel PSDEstimator Scaler TemporalFilter TimeFrequency UnsupervisedSpatialFilter Vectorizer ReceptiveField TimeDelayingRidge SlidingEstimator GeneralizingEstimator SPoC Functions that assist with decoding and model fitting: .. autosummary:: :toctree: generated/ :template: function.rst compute_ems cross_val_multiscore get_coef Realtime ======== :py:mod:`mne.realtime`: .. automodule:: mne.realtime :no-members: :no-inherited-members: .. autosummary:: :toctree: generated/ :template: class.rst RtEpochs RtClient MockRtClient FieldTripClient StimServer StimClient MNE-Report ========== :py:mod:`mne.report`: .. currentmodule:: mne.report .. automodule:: mne.report :no-members: :no-inherited-members: .. autosummary:: :toctree: generated/ :template: class.rst Report Logging and Configuration ========================= .. currentmodule:: mne .. autosummary:: :toctree: generated/ :template: function.rst get_config_path get_config open_docs set_log_level set_log_file set_config sys_info verbose :py:mod:`mne.cuda`: .. currentmodule:: mne.cuda .. automodule:: mne.cuda :no-members: :no-inherited-members: .. autosummary:: :toctree: generated/ :template: function.rst init_cuda