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

Tutorial:

https://ancplaboldenburg.github.io/docker_workshop_template/

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]
  • [PSD]
• QC_derivative, MEG_channel classes
  • MEG_channel
    • MEG_channel.add_ecg_info()
    • MEG_channel.add_eog_info()
    • MEG_channel.to_df()
  • 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()
• Calculation pipeline
  • add_raw_to_config_json()
  • ask_user_rerun_subs()
  • check_config_saved_ask_user()
  • check_ds_paths()
  • check_sub_list()
  • create_config_artifact()
  • get_files_list()
  • get_list_of_raws_for_config()
  • make_derivative_meg_qc()
• Initial processing
  • Epoch_meg()
  • add_3d_ch_locations()
  • assign_channels_properties()
  • change_ch_type_CTF()
  • check_chosen_ch_types()
  • choose_channels()
  • chs_dict_to_csv()
  • get_all_config_params()
  • get_internal_config_params()
  • initial_processing()
  • load_data()
  • sort_channels_by_lobe()
  • stim_data_to_df()
• Standard deviation
  • STD_meg_qc()
  • get_big_small_std_ptp_all_data()
  • 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()
  • 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_bands_amplitude_per_ch()
  • 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.amplitude_ratio
    • Avg_artif.similarity_score
    • 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.smooth_artif()
  • ECG_meg_qc()
  • EOG_meg_qc()
  • align_artif_data()
  • 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_amplitude_ratio()
  • find_affected_by_correlation()
  • find_affected_by_similarity_score()
  • 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()
  • minmax_amplitude()
  • reconstruct_ecg_and_check()
  • rms_amplitude()
  • shift_mean_wave()
  • split_correlated_artifacts_into_3_groups()
• High frequency (muscle) disturbancies
  • MUSCLE_meg_qc()
  • attach_dummy_data()
  • calculate_muscle_NO_threshold()
  • filter_noise_before_muscle_detection()
  • find_powerline_noise_short()
  • make_simple_metric_muscle()
  • save_muscle_to_csv()
• Head movement artifacts
  • HEAD_movement_meg_qc()
  • compute_head_pos_std_and_max_rotation_movement()
  • get_head_positions()
  • head_pos_to_csv()
  • make_simple_metric_head()
• Plots and reports pipeline
  • Deriv_to_plot
    • Deriv_to_plot.path
    • Deriv_to_plot.metric
    • Deriv_to_plot.deriv_entity_obj
    • Deriv_to_plot.raw_entity_name
    • Deriv_to_plot.subject
    • Deriv_to_plot.__repr__()
    • Deriv_to_plot.print_detailed_entities()
    • Deriv_to_plot.find_raw_entity_name()
    • Deriv_to_plot.find_raw_entity_name()
    • Deriv_to_plot.print_detailed_entities()
  • create_categories_for_selector()
  • csv_to_html_report()
  • extract_raw_entities_from_obj()
  • get_ds_entities()
  • make_plots_meg_qc()
  • select_subcategory()
  • selector()
  • sort_tsvs_by_raw()
• Plotting functions
  • Plot_psd_csv()
  • add_log_buttons()
  • assign_epoched_std_ptp_to_channels()
  • boxplot_all_time_csv()
  • boxplot_epoched_xaxis_channels_csv()
  • boxplot_epoched_xaxis_epochs_csv()
  • boxplot_epochs()
  • edit_legend_pie_SNR()
  • figure_x_axis()
  • get_meg_system()
  • get_tit_and_unit()
  • keep_unique_locs()
  • make_3d_sensors_trace()
  • make_head_annots_plot()
  • make_head_pos_plot_mne()
  • plot_3d_topomap_std_ptp_csv()
  • plot_ECG_EOG_channel_csv()
  • plot_affected_channels_csv()
  • plot_artif_per_ch_3_groups()
  • plot_ch_df_as_lines_by_lobe_csv()
  • plot_correlation_csv()
  • plot_ecg_eog_mne()
  • plot_head_pos_csv()
  • plot_mean_rwave_csv()
  • plot_mean_rwave_shifted()
  • plot_muscle_annotations_mne()
  • plot_muscle_csv()
  • plot_pie_chart_freq_csv()
  • plot_sensors_3d_csv()
  • plot_stim_csv()
  • plot_stim_csv_colored_leveled()
  • plot_stim_csv_simple()
  • plot_topomap_std_ptp_csv()
  • split_affected_into_3_groups_csv()
  • switch_names_on_off()
• Report functions
  • combine_howto_sensors_and_metric()
  • keep_fig_derivs()
  • make_howto_use_plots_section()
  • make_joined_report()
  • make_joined_report_mne()
  • make_metric_section()
  • make_sensor_figs_section()
  • simple_metric_basic()