API documentation

As the result of analysis will be produced (for each data file (.fif)):

• html report for all metrics

• csv file with the results of the analysis for some of metrics

• machine readable json file with the results of the analysis for all metrics

In the html report:

• all the plots produced by MEQ-QC are interactive, they can be scrolled through and enlarged.

• a few plots from MNE (in ECG and EOG sections) are not interactive.

UML diagrams presenting the flow of the analysis for each module are available here: https://github.com/ANCPLabOldenburg/MEG-QC-code/tree/main/diagrams

Modules:

• Pipeline Settings
  • Default settings [DEFAULT]
  • Filtering [Filtering]
  • Epoching [Epoching]
  • Standard deviation [STD]
  • Power spectral density [PSD]
  • Peak-to-peak amplitude manual [PTP_manual]
  • Peak-to-peak amplitude auto (based on MNE annotatons) [PTP_auto]
  • Heart beat artifacts [ECG]
  • Eye movement artifacts [EOG]
  • Head_movement artifacts [Head_movement]
  • Muscle artifacts [Muscle]
• Internal Pipeline Settings
  • [ECG]
  • [EOG]
• Main
  • make_derivative_meg_qc()
• Initial processing
  • Epoch_meg()
  • get_all_config_params()
  • get_internal_config_params()
  • initial_processing()
  • sanity_check()
• Standard deviation
  • RMSE()
  • STD_meg_qc()
  • get_big_small_std_ptp_all_data()
  • get_big_small_std_ptp_epochs()
  • get_noisy_flat_std_ptp_epochs()
  • get_std_all_data()
  • get_std_epochs()
  • make_dict_global_std_ptp()
  • make_dict_local_std_ptp()
  • make_simple_metric_std()
• Frequency spectrum
  • PSD_meg_qc()
  • Plot_psd_old()
  • add_log_buttons()
  • assign_psds_to_channels()
  • cut_the_noise_from_psd()
  • find_noisy_freq_bands_complex()
  • find_noisy_freq_bands_simple()
  • find_number_and_ampl_of_noise_freqs()
  • get_ampl_of_brain_waves()
  • get_ampl_of_noisy_freqs()
  • get_mean_bands_amplitude()
  • get_nfft_nperseg()
  • make_dict_global_psd()
  • make_dict_local_psd()
  • make_simple_metric_psd()
  • plot_one_psd()
  • split_blended_freqs_at_the_lowest_point()
• Peak to peak amplitude manual
  • PP_manual_meg_qc()
  • get_ptp_all_data()
  • get_ptp_epochs()
  • make_simple_metric_ptp_manual()
  • neighbour_peak_amplitude()
• Peak to peak amplitude auto: based on MNE annotations
  • PP_auto_meg_qc()
  • get_amplitude_annots_per_channel()
• ECG and EOG
  • Avg_artif
    • Avg_artif.name
    • Avg_artif.artif_data
    • Avg_artif.peak_loc
    • Avg_artif.peak_magnitude
    • Avg_artif.wave_shape
    • Avg_artif.artif_over_threshold
    • Avg_artif.main_peak_loc
    • Avg_artif.main_peak_magnitude
    • Avg_artif.artif_data_smoothed
    • Avg_artif.peak_loc_smoothed
    • Avg_artif.peak_magnitude_smoothed
    • Avg_artif.wave_shape_smoothed
    • Avg_artif.artif_over_threshold_smoothed
    • Avg_artif.main_peak_loc_smoothed
    • Avg_artif.main_peak_magnitude_smoothed
    • Avg_artif.corr_coef
    • Avg_artif.p_value
    • Avg_artif.lobe
    • Avg_artif.color
    • Avg_artif.__init__()
    • Avg_artif.__repr__()
    • Avg_artif.detect_artif_above_threshold()
    • Avg_artif.detect_artif_above_threshold_smoothed()
    • Avg_artif.flip_artif()
    • Avg_artif.flip_artif_smoothed()
    • Avg_artif.get_highest_peak()
    • Avg_artif.get_highest_peak_smoothed()
    • Avg_artif.get_peaks_wave()
    • Avg_artif.get_peaks_wave_smoothed()
    • Avg_artif.plot_epoch_and_peak()
    • Avg_artif.smooth_artif()
  • ECG_meg_qc()
  • EOG_meg_qc()
  • align_mean_rwave()
  • assign_lobe_to_artifacts()
  • calculate_artifacts_on_channels()
  • check_3_conditions()
  • check_mean_wave()
  • detect_channels_above_norm()
  • detect_noisy_ecg()
  • estimate_t0()
  • find_affected_by_correlation()
  • find_affected_over_mean()
  • find_epoch_peaks()
  • find_mean_rwave_blink()
  • find_t0_channels()
  • find_t0_highest()
  • find_t0_mean()
  • flip_channels()
  • get_ECG_data_choose_method()
  • get_EOG_data()
  • make_dict_global_ECG_EOG()
  • make_simple_metric_ECG_EOG()
  • plot_affected_channels()
  • plot_artif_per_ch_correlated_lobes()
  • plot_correlation()
  • plot_ecg_eog_mne()
  • plot_mean_rwave_shifted()
  • shift_mean_wave()
  • split_correlated_artifacts_into_3_groups()
• Muscle artifacts
  • MUSCLE_meg_qc()
  • attach_dummy_data()
  • calculate_muscle_NO_threshold()
  • filter_noise_before_muscle_detection()
  • make_simple_metric_muscle()
  • plot_muscle()
• Head movement artifacts
  • HEAD_movement_meg_qc()
  • compute_head_pos_std_and_max_rotation_movement()
  • get_head_positions()
  • make_head_annots_plot()
  • make_head_pos_plot()
  • make_simple_metric_head()
• Universal plotting functions
  • MEG_channels
    • MEG_channels.add_ecg_info()
    • MEG_channels.add_eog_info()
    • MEG_channels.to_df()
  • Plot_psd_csv()
  • QC_derivative
    • QC_derivative.content
    • QC_derivative.name
    • QC_derivative.content_type
    • QC_derivative.description_for_user
    • QC_derivative.convert_fig_to_html()
    • QC_derivative.convert_fig_to_html_add_description()
    • QC_derivative.get_section()
  • add_log_buttons()
  • assign_channels_properties()
  • assign_epoched_std_ptp_to_channels()
  • boxplot_all_time()
  • boxplot_all_time_OLD()
  • boxplot_all_time_csv()
  • boxplot_epoched_xaxis_channels()
  • boxplot_epoched_xaxis_channels_csv()
  • boxplot_epoched_xaxis_epochs()
  • boxplot_epoched_xaxis_epochs_csv()
  • boxplot_epochs()
  • boxplot_epochs_old()
  • check_num_channels_correct()
  • figure_x_axis()
  • get_ch_color_knowing_name()
  • get_tit_and_unit()
  • make_3d_sensors_trace()
  • make_head_pos_plot_csv()
  • make_head_pos_plot_mne()
  • plot_ECG_EOG_channel()
  • plot_ECG_EOG_channel_csv()
  • plot_affected_channels_csv()
  • plot_artif_per_ch_correlated_lobes_csv()
  • plot_correlation_csv()
  • plot_df_of_channels_data_as_lines_by_lobe()
  • plot_df_of_channels_data_as_lines_by_lobe_OLD()
  • plot_df_of_channels_data_as_lines_by_lobe_csv()
  • plot_muscle_annotations_mne()
  • plot_muscle_csv()
  • plot_pie_chart_freq()
  • plot_pie_chart_freq_csv()
  • plot_sensors_3d()
  • plot_sensors_3d_csv()
  • plot_sensors_3d_separated()
  • plot_time_series()
  • plot_time_series_avg()
  • sort_channel_by_lobe()
  • split_correlated_artifacts_into_3_groups_csv()
  • switch_names_on_off()
• HTML report
  • get_tit_and_unit()
  • keep_fig_derivs()
  • make_html_section()
  • make_joined_report()
  • make_joined_report_mne()
  • simple_metric_basic()