def test_n_components_and_max_pca_components_none(): """Test n_components and max_pca_components=None.""" raw = read_raw_fif(raw_fname).crop(1.5, stop).load_data() events = read_events(event_name) picks = pick_types(raw.info, eeg=True, meg=False) epochs = Epochs(raw, events, event_id, tmin, tmax, picks=picks, baseline=(None, 0), preload=True) max_pca_components = None n_components = None random_state = 12345 tempdir = _TempDir() output_fname = op.join(tempdir, 'test_ica-ica.fif') ica = ICA(max_pca_components=max_pca_components, n_components=n_components, random_state=random_state) with warnings.catch_warnings(record=True): # convergence ica.fit(epochs) ica.save(output_fname) ica = read_ica(output_fname) # ICA.fit() replaced max_pca_components, which was previously None, # with the appropriate integer value. assert_equal(ica.max_pca_components, epochs.info['nchan']) assert_is_none(ica.n_components)
def clean_fif(fif_path, ica_sol_path, ica_bads_path, cleaned_fif_path): raw = read_raw_fif(fif_path, preload=True) ica = read_ica(ica_sol_path) ica.exclude = read_ica_bads(ica_bads_path, logger) logger.info(f"Excluding ICs {ica.exclude}") ica.apply(raw) raw.save(cleaned_fif_path, overwrite=True)
def apply_ICA(subject, runlist, badEEG, badICA): from mne.io.pick import _picks_by_type as picks_by_type from mne.preprocessing import read_ica from mne.io import Raw data_path = '/neurospin/meg/meg_tmp/MTT_MEG_Baptiste/MEG/' for run in runlist: raw_fname = (data_path + subject + '/' + run + '_trans_sss.fif') # read raw data raw = [] raw = Raw(raw_fname, preload=True) raw.info['bads'] = badEEG # Load ICA file for each data type (MEG and EEG) for ch_type, picks in picks_by_type(raw.info, meg_combined=True): # Read ICA file ica = [] ica = read_ica(data_path + subject + '/mne_python/ICA/ICA_' + ch_type + '_allRuns') # Apply ICA projection ica.exclude += badICA[ch_type] raw = ica.apply(raw, copy=True) # Interpolate bad EEG channels raw = raw.copy().interpolate_bads() # Save artifacts-corrected raw data raw.save((data_path + subject + '/' + run + 'ICAcorr_trans_sss.fif'), overwrite='True')
def test_ica_n_iter_(method): """Test that ICA.n_iter_ is set after fitting.""" _skip_check_picard(method) raw = read_raw_fif(raw_fname).crop(0.5, stop).load_data() n_components = 3 max_iter = 1 ica = ICA(n_components=n_components, max_iter=max_iter, method=method) if method == 'infomax': ica.fit(raw) else: with pytest.warns(UserWarning, match='did not converge'): ica.fit(raw) assert_equal(ica.n_iter_, max_iter) # Test I/O roundtrip. tempdir = _TempDir() output_fname = op.join(tempdir, 'test_ica-ica.fif') _assert_ica_attributes(ica) ica.save(output_fname) ica = read_ica(output_fname) _assert_ica_attributes(ica) assert_equal(ica.n_iter_, max_iter)
def test_n_components_none(): """Test n_components=None.""" raw = read_raw_fif(raw_fname).crop(1.5, stop).load_data() events = read_events(event_name) picks = pick_types(raw.info, eeg=True, meg=False) epochs = Epochs(raw, events, event_id, tmin, tmax, picks=picks, baseline=(None, 0), preload=True) max_pca_components = 10 n_components = None random_state = 12345 tempdir = _TempDir() output_fname = op.join(tempdir, 'test_ica-ica.fif') ica = ICA(max_pca_components=max_pca_components, n_components=n_components, random_state=random_state) with warnings.catch_warnings(record=True): # convergence ica.fit(epochs) ica.save(output_fname) ica = read_ica(output_fname) # ICA.fit() replaced max_pca_components, which was previously None, # with the appropriate integer value. assert_equal(ica.max_pca_components, 10) assert_is_none(ica.n_components)
def test_fit_params(method, tmpdir): """Test fit_params for ICA.""" _skip_check_picard(method) fit_params = {} ICA(fit_params=fit_params, method=method) # test no side effects assert fit_params == {} # Test I/O roundtrip. # Only picard and infomax support the "extended" keyword, so limit the # tests to those. if method in ['picard', 'infomax']: tmpdir = str(tmpdir) output_fname = op.join(tmpdir, 'test_ica-ica.fif') raw = read_raw_fif(raw_fname).crop(0.5, stop).load_data() n_components = 3 max_iter = 1 fit_params = dict(extended=True) ica = ICA(fit_params=fit_params, n_components=n_components, max_iter=max_iter, method=method) fit_params_after_instantiation = ica.fit_params if method == 'infomax': ica.fit(raw) else: with pytest.warns(UserWarning, match='did not converge'): ica.fit(raw) ica.save(output_fname) ica = read_ica(output_fname) assert ica.fit_params == fit_params_after_instantiation
def load_saved_icas(dir_icas): icas = [] for dir, _, file in os.walk(dir_icas): for fi in file: ica = read_ica(os.path.join(dir, fi)) icas.append(ica) return icas
def test_n_components_and_max_pca_components_none(method): """Test n_components and max_pca_components=None.""" _skip_check_picard(method) raw = read_raw_fif(raw_fname).crop(1.5, stop).load_data() events = read_events(event_name) picks = pick_types(raw.info, eeg=True, meg=False) epochs = Epochs(raw, events, event_id, tmin, tmax, picks=picks, baseline=(None, 0), preload=True) max_pca_components = None n_components = None random_state = 12345 tempdir = _TempDir() output_fname = op.join(tempdir, 'test_ica-ica.fif') ica = ICA(max_pca_components=max_pca_components, method=method, n_components=n_components, random_state=random_state) with pytest.warns(None): # convergence ica.fit(epochs) ica.save(output_fname) ica = read_ica(output_fname) # ICA.fit() replaced max_pca_components, which was previously None, # with the appropriate integer value. assert_equal(ica.max_pca_components, epochs.info['nchan']) assert ica.n_components is None
def test_max_pca_components_none(method): """Test max_pca_components=None.""" _skip_check_picard(method) raw = read_raw_fif(raw_fname).crop(1.5, stop).load_data() events = read_events(event_name) picks = pick_types(raw.info, eeg=True, meg=False) epochs = Epochs(raw, events, event_id, tmin, tmax, picks=picks, baseline=(None, 0), preload=True) max_pca_components = None n_components = 10 random_state = 12345 tempdir = _TempDir() output_fname = op.join(tempdir, 'test_ica-ica.fif') ica = ICA(max_pca_components=max_pca_components, method=method, n_components=n_components, random_state=random_state) with pytest.warns(None): ica.fit(epochs) ica.save(output_fname) ica = read_ica(output_fname) # ICA.fit() replaced max_pca_components, which was previously None, # with the appropriate integer value. assert_equal(ica.max_pca_components, epochs.info['nchan']) assert_equal(ica.n_components, 10)
def inspect_ica(filt_path, ica_sol_path, ica_bads_path): raw = read_raw_fif(filt_path, preload=True) ica = read_ica(ica_sol_path) if ica_bads_path.exists(): ica.exclude = read_ica_bads(ica_bads_path, logger) ica.plot_sources(raw, block=True) logger.info(f"Excluding ICs {ica.exclude}") write_ica_bads(ica_bads_path, ica, logger)
def browse_components(subject, runlist, badEEG): import numpy as np import mne import os.path as op import os from mne.report import Report from mne.io.pick import _picks_by_type as picks_by_type from mne.preprocessing import read_ica from mne.io import Raw data_path = '/neurospin/meg/meg_tmp/MTT_MEG_Baptiste/MEG/' report = Report(subject) raw_fnames = [] for run in runlist: raw_fnames.append(data_path + subject + '/' + run + '_trans_sss.fif') # read raw data raw = Raw(raw_fnames, preload=True) raw.info['bads'] = badEEG # Highpass filter 1Hz on EOG/ECG channels #picks = mne.pick_types(raw.info, meg=False,eeg=False, eog=True, ecg=True) #raw.filter(l_freq = 1, h_freq=30, picks = picks) #picks = mne.pick_types(raw.info, meg=True,eeg=True, eog=True, ecg=True) #raw.filter(l_freq = None, h_freq=30, picks = picks,n_jobs = 4) picks = mne.pick_types(raw.info, meg=False, eeg=False, eog=False, ecg=True) raw.filter(l_freq=1, h_freq=30, picks=picks) picks = mne.pick_types(raw.info, meg=False, eeg=False, eog=True, ecg=False) raw.filter(l_freq=1, h_freq=5, picks=picks) picks = mne.pick_types(raw.info, meg=True, eeg=True, eog=True, ecg=True) raw.filter(l_freq=None, h_freq=30, picks=picks, n_jobs=4) results_dir = op.join(data_path, subject, 'artefactICA') if not op.exists(results_dir): os.makedirs(results_dir) # Plot all ICA component for ch_type, picks in picks_by_type( raw.info, meg_combined=True): # bad EEG channels are excluded # Read ICA file for each data type (MEG and EEG) - created in preprocessing_ica ica = read_ica(data_path + subject + '/mne_python/ICA/ICA_' + ch_type + '_allRuns') print subject + ' ' + ch_type #fig = ica.plot_sources(raw, block = True) # the viewer will open and ICA component can be screened #report.add_figs_to_section(fig, 'All ICA sources (%s)' % ch_type,'ICA decomposition') fig = ica.plot_components(colorbar=True) for i in range(np.shape(fig)[0]): report.add_figs_to_section(fig[i], 'All ICA components (%s)' % ch_type, 'ICA decomposition') report.save((results_dir + '/AllRuns_checkcomponents.html'), open_browser=False, overwrite=True) del raw
def load_ica(subject, description, ica_data_root=None): if ica_data_root is None: # use default data root import deepthought data_root = os.path.join(deepthought.DATA_PATH, 'OpenMIIR') ica_data_root = os.path.join(data_root, 'eeg', 'preprocessing', 'ica') ica_filepath = os.path.join(ica_data_root, '{}-{}-ica.fif'.format(subject, description)) return read_ica(ica_filepath)
def loading_icas (): icas = [] for subj in range (len(subjects)): icas_names = os.path.join(dir_icas,'S'+ str(subjects[subj]) + '_ica.fif') loaded_ica = read_ica(icas_names[subj]) icas.append(loaded_ica) return icas
def get_ica(subject): """ a function to get the ica corresponding to a subject ID parameters: ----------- - subject : str correspond to the ID of the subject returns: mne ICA object ------- """ path_ica = os.path.join(ICA_DIR, f'P{subject}-100p_64c-ica.fif') return read_ica(path_ica)
def reconstructICA(subjectID): subject = 'dh{:#02d}a'.format(subjectID) logFile = open(outPath + subject + '/removedICAcomponents.log', 'w') for block in ['1','2']: logFile.write('Processing subject ' + subject + ', block ' + block + '\n') subjectStub = subject + '/block' + block raw_fname = rawPath + subjectStub + '.fif' icaFile = rawPath + subjectStub + '_ica.fif' outFile = outPath + subjectStub + '.fif' if not os.path.isdir(outPath + subject): os.makedirs(outPath + subject) if os.path.exists(raw_fname): raw = Raw(raw_fname, preload=True) raw.info['bads'] = badChanLibrary[subjectID][int(block)] ica = read_ica(icaFile) #raw.ch_names = ica.ch_names # Select and filter interesting channels picks_eog = mne.pick_types(raw.info, meg=False, eeg=False, stim=False, eog=True, ecg=False) picks_ecg = mne.pick_types(raw.info, meg=False, eeg=False, stim=False, eog=False, ecg=True) logFile.write('Rejecting components that correlate with EOG and ECG channels...\n') excluded_components = [] eogChannel = picks_eog[1] eogNames = raw.ch_names[eogChannel] eog_idx, eog_scores = ica.find_bads_eog(raw, eogNames) for i in eog_idx: if i not in excluded_components: excluded_components.append(i) logFile.write("Excluding component {}, Correlation with EOG: {} \n".format(i, eog_scores[i])) ecgChannel = picks_ecg ecgNames = raw.ch_names[ecgChannel] ecg_idx, ecg_scores = ica.find_bads_ecg(raw, ecgNames) for i in ecg_idx: if i not in excluded_components: excluded_components.append(i) logFile.write("Excluding component {}, Correlation with ECG: {} \n".format(i, ecg_scores[i])) # Save corrected fif file if len(excluded_components) > 0: logFile.write('Saving corrected fif file\n') ica.apply(raw, exclude=excluded_components) raw.save(outFile, overwrite=True) else: logFile.write('Nothing to do; creating symlink\n') force_symlink(raw_fname, outFile) logFile.close()
def cli(subjdirs): """ Show the variance explained for mne ica solution EXAMPLES: Show explained variances for ica solutions for each subject in FIF_DATASET and write them to file vars.txt: $ ica_var FIF_DATASET/*/*-ica.fif >> vars.txt """ for fname in subjdirs: with nostdout(): ica = read_ica(fname) n_comp = ica.n_components_ tot_var = ica.pca_explained_variance_.sum() n_comp_var = ica.pca_explained_variance_[:n_comp].sum() PVE = n_comp_var / tot_var click.echo(PVE)
def preprocess_set_ICA_comp_fif_to_ts(fif_file, subject_id, n_comp_exclude, is_sensor_space): import os import sys import mne from mne.preprocessing import read_ica from nipype.utils.filemanip import split_filename as split_f from ephypype.preproc import create_ts subj_path, basename, ext = split_f(fif_file) (data_path, sbj_name) = os.path.split(subj_path) print(('*** SBJ %s' % subject_id + '***')) # Read raw current_dir = os.getcwd() if os.path.exists(os.path.join(current_dir, '../ica', basename + '_ica' + ext)): raw_ica_file = os.path.join( current_dir, '../ica', basename + '_ica' + ext) elif os.path.exists(os.path.join(current_dir, '../ica', basename + '_filt_ica' + ext)): raw_ica_file = os.path.join( current_dir, '../ica', basename + '_filt_ica' + ext) elif os.path.exists(os.path.join(current_dir, '../ica', basename + '_filt_dsamp_ica' + ext)): raw_ica_file = os.path.join( current_dir, '../ica', basename + '_filt_dsamp_ica' + ext) print(('*** raw_ica_file %s' % raw_ica_file + '***')) raw = mne.io.read_raw_fif(raw_ica_file, preload=True) # load ICA if os.path.exists(os.path.join(current_dir, '../ica', basename + '_ica_solution.fif')): ica_sol_file = os.path.join( current_dir, '../ica', basename + '_ica_solution.fif') elif os.path.exists(os.path.join(current_dir, '../ica', basename + '_filt_ica_solution.fif')): ica_sol_file = os.path.join( current_dir, '../ica', basename + '_filt_ica_solution.fif') elif os.path.exists(os.path.join(current_dir, '../ica', basename + '_filt_dsamp_ica_solution.fif')): ica_sol_file = os.path.join( current_dir, '../ica', basename + '_filt_dsamp_ica_solution.fif') if os.path.exists(ica_sol_file) is False: print(('$$$ Warning, no %s found' % ica_sol_file)) sys.exit() else: ica = read_ica(ica_sol_file) print(('\n *** ica.exclude before set components= ', ica.exclude)) if subject_id in n_comp_exclude: print(('*** ICA to be excluded for sbj %s ' % subject_id)) print((' ' + str(n_comp_exclude[subject_id]) + '***')) session_dict = n_comp_exclude[subject_id] session_names = list(session_dict.keys()) componentes = [] for s in session_names: componentes = session_dict[s] if len(componentes) == 0: print('\n no ICA to be excluded \n') else: print(('\n *** ICA to be excluded for session %s ' % s + ' ' + str(componentes) + ' *** \n')) ica.exclude = componentes print(('\n *** ica.exclude after set components = ', ica.exclude)) # apply ICA to raw data new_raw_ica_file = os.path.join(subj_path, basename + '_ica-raw.fif') raw_ica = ica.apply(raw) raw_ica.save(new_raw_ica_file, overwrite=True) # save ICA solution print(ica_sol_file) ica.save(ica_sol_file) ts_file, channel_coords_file, channel_names_file, raw.info['sfreq'] = create_ts( new_raw_ica_file) if is_sensor_space: return ts_file, channel_coords_file, channel_names_file, raw.info['sfreq'] else: return raw_ica, channel_coords_file, channel_names_file, raw.info['sfreq']
#!/usr/bin/env python3 # -*- coding: utf-8 -*- """ Created on Fri Apr 10 01:58:13 2020 @author: wexu """ import mne import numpy as np from config_SYN_Human import study_path, exp import os from mne.preprocessing import read_ica for ID in exp.index: fname = os.path.join(study_path, ID + '.edf') ica = read_ica(fname.replace(".edf", "-ica.fif")) epochs = mne.read_epochs(fname.replace(".edf", "_cleaned-epo.fif")) ica.plot_sources(epochs, block=True) print(ica.exclude) ica.plot_components(inst=epochs) print(ica.exclude) ica.plot_sources(epochs, block=True) np.save(fname.replace(".edf", 'ICA_excludes.npy'), ica.exclude)
def apply_ica(*, cfg, subject, session): bids_basename = BIDSPath(subject=subject, session=session, task=cfg.task, acquisition=cfg.acq, run=None, recording=cfg.rec, space=cfg.space, datatype=cfg.datatype, root=cfg.deriv_root, check=False) fname_epo_in = bids_basename.copy().update(suffix='epo', extension='.fif') fname_epo_out = bids_basename.copy().update(processing='ica', suffix='epo', extension='.fif') fname_ica = bids_basename.copy().update(suffix='ica', extension='.fif') fname_ica_components = bids_basename.copy().update(processing='ica', suffix='components', extension='.tsv') report_fname = (bids_basename.copy().update(processing='ica', suffix='report', extension='.html')) title = f'ICA artifact removal – sub-{subject}' if session is not None: title += f', ses-{session}' if cfg.task is not None: title += f', task-{cfg.task}' # Load ICA. msg = f'Reading ICA: {fname_ica}' logger.debug( **gen_log_kwargs(message=msg, subject=subject, session=session)) ica = read_ica(fname=fname_ica) # Select ICs to remove. tsv_data = pd.read_csv(fname_ica_components, sep='\t') ica.exclude = (tsv_data.loc[tsv_data['status'] == 'bad', 'component'].to_list()) # Load epochs to reject ICA components. msg = f'Input: {fname_epo_in}, Output: {fname_epo_out}' logger.info( **gen_log_kwargs(message=msg, subject=subject, session=session)) epochs = mne.read_epochs(fname_epo_in, preload=True) epochs.drop_bad(cfg.ica_reject) # Now actually reject the components. msg = f'Rejecting ICs: {", ".join([str(ic) for ic in ica.exclude])}' logger.info( **gen_log_kwargs(message=msg, subject=subject, session=session)) epochs_cleaned = ica.apply(epochs.copy()) # Copy b/c works in-place! msg = 'Saving reconstructed epochs after ICA.' logger.info( **gen_log_kwargs(message=msg, subject=subject, session=session)) epochs_cleaned.save(fname_epo_out, overwrite=True, split_naming='bids') # Compare ERP/ERF before and after ICA artifact rejection. The evoked # response is calculated across ALL epochs, just like ICA was run on # all epochs, regardless of their respective experimental condition. # # We apply baseline correction here to (hopefully!) make the effects of # ICA easier to see. Otherwise, individual channels might just have # arbitrary DC shifts, and we wouldn't be able to easily decipher what's # going on! report = Report(report_fname, title=title, verbose=False) picks = ica.exclude if ica.exclude else None report.add_ica(ica=ica, title='Effects of ICA cleaning', inst=epochs.copy().apply_baseline(cfg.baseline), picks=picks) report.save(report_fname, overwrite=True, open_browser=cfg.interactive)
raw = mne.io.read_raw_fif(run_fname, preload=True, add_eeg_ref=False) ############################################################################### # We change the channel type for ECG and EOG. raw.set_channel_types({'EEG061': 'eog', 'EEG062': 'eog', 'EEG063': 'ecg', 'EEG064': 'misc'}) # EEG064 free floating el. raw.rename_channels({'EEG061': 'EOG061', 'EEG062': 'EOG062', 'EEG063': 'ECG063'}) ############################################################################### # Bad sensors are repaired. raw.info['bads'] = bads raw.interpolate_bads() raw.set_eeg_reference() ############################################################################### # Now let's get to some serious ICA preprocessing ica_name = op.join(meg_dir, subject, 'run_%02d-ica.fif' % run) ica = read_ica(ica_name) n_max_ecg = 3 # use max 3 components ecg_epochs = create_ecg_epochs(raw, tmin=-.5, tmax=.5) ecg_inds, scores_ecg = ica.find_bads_ecg(ecg_epochs, method='ctps', threshold=0.8) ica.plot_sources(raw, exclude=ecg_inds) ica.plot_scores(scores_ecg, exclude=ecg_inds) ica.plot_properties(raw, ecg_inds) ica.exclude += ecg_inds[:n_max_ecg]
for sub_string in sub_list: # Define the Subject ID and paths deriv_path = deriv_dir / sub_string print(f'Preprocessing task-{task} data for {sub_string}') print(f' Derivatives Folder: {deriv_path}') # Load ICA Epochs epochs_fif_file = deriv_path / \ f'{sub_string}_task-{task}_ref-FCz_desc-ica_epo.fif.gz' epochs = read_epochs(epochs_fif_file) # Load ICA ica_file = deriv_path / \ f'{sub_string}_task-{task}_ref-FCz_desc-ica_ica.fif.gz' ica = read_ica(ica_file) # Plot ICA ica.plot_components(inst=epochs, reject=None, psd_args=dict(fmax=70)) ica.exclude.sort() ica.save(ica_file) print(f'ICs Flagged for Removal: {ica.exclude}') # Load json file for updating json_file = deriv_path / \ f'{sub_string}_task-{task}_ref-FCz_desc-ica_ica.json' with open(json_file, 'r') as f: json_info = json.load(f) # Only update description, proportion of flagged components, # and flagged components
cond_names = ad.analysis_dict[subj][input_files].keys() # sort names so that VS comes before FFA! cond_names.sort(reverse=True) for cond in cond_names: if 'empty' not in cond: raw_path = ad._scratch_folder + '/' + input_files + '/' + subj in_fnames = ad.analysis_dict[subj][input_files][cond]['files'] for fname in in_fnames: img_prefix = img_folder + '/' + cond print 'In: ', fname raw = Raw(fname, preload=True) # for finding events from raw, must be preloaded ica = read_ica(ica_folder + '/' + cond + '-ica.fif') # 2) identify bad components by analyzing latent sources. title = 'Sources related to %s artifacts (red)' # generate ECG epochs use detection via phase statistics picks = mne.pick_types(raw.info, meg=True, eeg=False, eog=True, ecg=True, stim=False, exclude='bads') # create_ecg_epochs is strange: it strips the channels of anything non M/EEG # UNLESS picks=None #picks=None # This will work with the above, but uses MASSIVE RAM # Not sure the ECG quality is good enough for the QRS-detector ecg_inds, scores = ica.find_bads_ecg(raw, method='ctps', ch_name='ECG002', threshold=0.25) if len(ecg_inds) < 1: # destroy the ECG channel by changing it to an EMG!
fname = op.join(MEG_data_path, subject, task + '_%d' % (day + subject_id) + '_tsss_mc.fif') raw_tsss_mc = mne.io.read_raw_fif(fname, preload=True) if op.isfile(fname.replace("tsss_mc", "annot")): raw_tsss_mc.set_annotations( mne.read_annotations(fname.replace("tsss_mc", "annot"))) print("Annotion loaded!") raw_tsss_mc.filter(l_freq=1, h_freq=40.0, fir_design='firwin', n_jobs=-1) # band-pass filter data ica = read_ica( op.join(MEG_data_path, subject, task + '_%d' % (day + subject_id) + '-ica.fif')) ICA_reject_threshold = np.load( fname.replace("tsss_mc.fif", 'ICA_reject_threshold.npy')) if op.isfile(fname.replace("tsss_mc.fif", 'ICA_excludes.npy')): ica.exclude.extend( np.load(fname.replace("tsss_mc.fif", 'ICA_excludes.npy')).tolist()) events = pd.read_csv(fname.replace('tsss_mc.fif', 'events.csv'))[[ "stim_onset", "button_press", "trigger_code" ]].astype(int).values epochs = mne.Epochs(raw_tsss_mc, events=events, tmin=-0.2, tmax=1,
def main(): ################################################# ## SETUP ## Get list of subject files subj_files = listdir(DAT_PATH) subj_files = [file for file in subj_files if EXT.lower() in file.lower()] ## Set up FOOOF Objects # Initialize FOOOF settings & objects objects fooof_settings = FOOOFSettings(peak_width_limits=PEAK_WIDTH_LIMITS, max_n_peaks=MAX_N_PEAKS, min_peak_amplitude=MIN_PEAK_AMP, peak_threshold=PEAK_THRESHOLD, aperiodic_mode=APERIODIC_MODE) fm = FOOOF(*fooof_settings, verbose=False) fg = FOOOFGroup(*fooof_settings, verbose=False) # Save out a settings file fg.save('0-FOOOF_Settings', pjoin(RES_PATH, 'FOOOF'), save_settings=True) # Set up the dictionary to store all the FOOOF results fg_dict = dict() for load_label in LOAD_LABELS: fg_dict[load_label] = dict() for side_label in SIDE_LABELS: fg_dict[load_label][side_label] = dict() for seg_label in SEG_LABELS: fg_dict[load_label][side_label][seg_label] = [] ## Initialize group level data stores n_subjs, n_conds, n_times = len(subj_files), 3, N_TIMES group_fooofed_alpha_freqs = np.zeros(shape=[n_subjs]) dropped_components = np.ones(shape=[n_subjs, 50]) * 999 dropped_trials = np.ones(shape=[n_subjs, 1500]) * 999 canonical_group_avg_dat = np.zeros(shape=[n_subjs, n_conds, n_times]) fooofed_group_avg_dat = np.zeros(shape=[n_subjs, n_conds, n_times]) # Set channel types ch_types = {'LHor' : 'eog', 'RHor' : 'eog', 'IVer' : 'eog', 'SVer' : 'eog', 'LMas' : 'misc', 'RMas' : 'misc', 'Nose' : 'misc', 'EXG8' : 'misc'} ################################################# ## RUN ACROSS ALL SUBJECTS # Run analysis across each subject for s_ind, subj_file in enumerate(subj_files): # Get subject label and print status subj_label = subj_file.split('.')[0] print('\nCURRENTLY RUNNING SUBJECT: ', subj_label, '\n') ################################################# ## LOAD / ORGANIZE / SET-UP DATA # Load subject of data, apply apply fixes for channels, etc eeg_dat = mne.io.read_raw_edf(pjoin(DAT_PATH, subj_file), preload=True, verbose=False) # Fix channel name labels eeg_dat.info['ch_names'] = [chl[2:] for chl in \ eeg_dat.ch_names[:-1]] + [eeg_dat.ch_names[-1]] for ind, chi in enumerate(eeg_dat.info['chs']): eeg_dat.info['chs'][ind]['ch_name'] = eeg_dat.info['ch_names'][ind] # Update channel types eeg_dat.set_channel_types(ch_types) # Set reference - average reference eeg_dat = eeg_dat.set_eeg_reference(ref_channels='average', projection=False, verbose=False) # Set channel montage chs = mne.channels.read_montage('standard_1020', eeg_dat.ch_names) eeg_dat.set_montage(chs) # Get event information & check all used event codes evs = mne.find_events(eeg_dat, shortest_event=1, verbose=False) # Pull out sampling rate srate = eeg_dat.info['sfreq'] ################################################# ## Pre-Processing: ICA # High-pass filter data for running ICA eeg_dat.filter(l_freq=1., h_freq=None, fir_design='firwin') if RUN_ICA: print("\nICA: CALCULATING SOLUTION\n") # ICA settings method = 'fastica' n_components = 0.99 random_state = 47 reject = {'eeg': 20e-4} # Initialize ICA object ica = ICA(n_components=n_components, method=method, random_state=random_state) # Fit ICA ica.fit(eeg_dat, reject=reject) # Save out ICA solution ica.save(pjoin(RES_PATH, 'ICA', subj_label + '-ica.fif')) # Otherwise: load previously saved ICA to apply else: print("\nICA: USING PRECOMPUTED\n") ica = read_ica(pjoin(RES_PATH, 'ICA', subj_label + '-ica.fif')) # Find components to drop, based on correlation with EOG channels drop_inds = [] for chi in EOG_CHS: inds, _ = ica.find_bads_eog(eeg_dat, ch_name=chi, threshold=2.5, l_freq=1, h_freq=10, verbose=False) drop_inds.extend(inds) drop_inds = list(set(drop_inds)) # Set which components to drop, and collect record of this ica.exclude = drop_inds dropped_components[s_ind, 0:len(drop_inds)] = drop_inds # Apply ICA to data eeg_dat = ica.apply(eeg_dat) ################################################# ## SORT OUT EVENT CODES # Extract a list of all the event labels all_trials = [it for it2 in EV_DICT.values() for it in it2] # Create list of new event codes to be used to label correct trials (300s) all_trials_new = [it + 100 for it in all_trials] # This is an annoying way to collapse across the doubled event markers from above all_trials_new = [it - 1 if not ind%2 == 0 else it for ind, it in enumerate(all_trials_new)] # Get labelled dictionary of new event names ev_dict2 = {k:v for k, v in zip(EV_DICT.keys(), set(all_trials_new))} # Initialize variables to store new event definitions evs2 = np.empty(shape=[0, 3], dtype='int64') lags = np.array([]) # Loop through, creating new events for all correct trials t_min, t_max = -0.4, 3.0 for ref_id, targ_id, new_id in zip(all_trials, CORR_CODES * 6, all_trials_new): t_evs, t_lags = mne.event.define_target_events(evs, ref_id, targ_id, srate, t_min, t_max, new_id) if len(t_evs) > 0: evs2 = np.vstack([evs2, t_evs]) lags = np.concatenate([lags, t_lags]) ################################################# ## FOOOF # Set channel of interest ch_ind = eeg_dat.ch_names.index(CHL) # Calculate PSDs over ~ first 2 minutes of data, for specified channel fmin, fmax = 1, 50 tmin, tmax = 5, 125 psds, freqs = mne.time_frequency.psd_welch(eeg_dat, fmin=fmin, fmax=fmax, tmin=tmin, tmax=tmax, n_fft=int(2*srate), n_overlap=int(srate), n_per_seg=int(2*srate), verbose=False) # Fit FOOOF across all channels fg.fit(freqs, psds, FREQ_RANGE, n_jobs=-1) # Save out FOOOF results fg.save(subj_label + '_fooof', pjoin(RES_PATH, 'FOOOF'), save_results=True) # Extract individualized CF from specified channel, add to group collection fm = fg.get_fooof(ch_ind, False) fooof_freq, _, _ = get_band_peak(fm.peak_params_, [7, 14]) group_fooofed_alpha_freqs[s_ind] = fooof_freq # If not FOOOF alpha extracted, reset to 10 if np.isnan(fooof_freq): fooof_freq = 10 ################################################# ## ALPHA FILTERING # CANONICAL: Filter data to canonical alpha band: 8-12 Hz alpha_dat = eeg_dat.copy() alpha_dat.filter(8, 12, fir_design='firwin', verbose=False) alpha_dat.apply_hilbert(envelope=True, verbose=False) # FOOOF: Filter data to FOOOF derived alpha band fooof_dat = eeg_dat.copy() fooof_dat.filter(fooof_freq-2, fooof_freq+2, fir_design='firwin') fooof_dat.apply_hilbert(envelope=True) ################################################# ## EPOCH TRIALS # Set epoch timings tmin, tmax = -0.85, 1.1 # Epoch trials - raw data for trial rejection epochs = mne.Epochs(eeg_dat, evs2, ev_dict2, tmin=tmin, tmax=tmax, baseline=None, preload=True, verbose=False) # Epoch trials - filtered version epochs_alpha = mne.Epochs(alpha_dat, evs2, ev_dict2, tmin=tmin, tmax=tmax, baseline=(-0.5, -0.35), preload=True, verbose=False) epochs_fooof = mne.Epochs(fooof_dat, evs2, ev_dict2, tmin=tmin, tmax=tmax, baseline=(-0.5, -0.35), preload=True, verbose=False) ################################################# ## PRE-PROCESSING: AUTO-REJECT if RUN_AUTOREJECT: print('\nAUTOREJECT: CALCULATING SOLUTION\n') # Initialize and run autoreject across epochs ar = AutoReject(n_jobs=4, verbose=False) ar.fit(epochs) # Save out AR solution ar.save(pjoin(RES_PATH, 'AR', subj_label + '-ar.hdf5'), overwrite=True) # Otherwise: load & apply previously saved AR solution else: print('\nAUTOREJECT: USING PRECOMPUTED\n') ar = read_auto_reject(pjoin(RES_PATH, 'AR', subj_label + '-ar.hdf5')) ar.verbose = 'tqdm' # Apply autoreject to the original epochs object it was learnt on epochs, rej_log = ar.transform(epochs, return_log=True) # Apply autoreject to the copies of the data - apply interpolation, then drop same epochs _apply_interp(rej_log, epochs_alpha, ar.threshes_, ar.picks_, ar.verbose) epochs_alpha.drop(rej_log.bad_epochs) _apply_interp(rej_log, epochs_fooof, ar.threshes_, ar.picks_, ar.verbose) epochs_fooof.drop(rej_log.bad_epochs) # Collect which epochs were dropped dropped_trials[s_ind, 0:sum(rej_log.bad_epochs)] = np.where(rej_log.bad_epochs)[0] ################################################# ## SET UP CHANNEL CLUSTERS # Set channel clusters - take channels contralateral to stimulus presentation # Note: channels will be used to extract data contralateral to stimulus presentation le_chs = ['P3', 'P5', 'P7', 'P9', 'O1', 'PO3', 'PO7'] # Left Side Channels le_inds = [epochs.ch_names.index(chn) for chn in le_chs] ri_chs = ['P4', 'P6', 'P8', 'P10', 'O2', 'PO4', 'PO8'] # Right Side Channels ri_inds = [epochs.ch_names.index(chn) for chn in ri_chs] ################################################# ## TRIAL-RELATED ANALYSIS: CANONICAL vs. FOOOF ## Pull out channels of interest for each load level # Channels extracted are those contralateral to stimulus presentation # Canonical Data lo1_a = np.concatenate([epochs_alpha['LeLo1']._data[:, ri_inds, :], epochs_alpha['RiLo1']._data[:, le_inds, :]], 0) lo2_a = np.concatenate([epochs_alpha['LeLo2']._data[:, ri_inds, :], epochs_alpha['RiLo2']._data[:, le_inds, :]], 0) lo3_a = np.concatenate([epochs_alpha['LeLo3']._data[:, ri_inds, :], epochs_alpha['RiLo3']._data[:, le_inds, :]], 0) # FOOOFed data lo1_f = np.concatenate([epochs_fooof['LeLo1']._data[:, ri_inds, :], epochs_fooof['RiLo1']._data[:, le_inds, :]], 0) lo2_f = np.concatenate([epochs_fooof['LeLo2']._data[:, ri_inds, :], epochs_fooof['RiLo2']._data[:, le_inds, :]], 0) lo3_f = np.concatenate([epochs_fooof['LeLo3']._data[:, ri_inds, :], epochs_fooof['RiLo3']._data[:, le_inds, :]], 0) ## Calculate average across trials and channels - add to group data collection # Canonical data canonical_group_avg_dat[s_ind, 0, :] = np.mean(lo1_a, 1).mean(0) canonical_group_avg_dat[s_ind, 1, :] = np.mean(lo2_a, 1).mean(0) canonical_group_avg_dat[s_ind, 2, :] = np.mean(lo3_a, 1).mean(0) # FOOOFed data fooofed_group_avg_dat[s_ind, 0, :] = np.mean(lo1_f, 1).mean(0) fooofed_group_avg_dat[s_ind, 1, :] = np.mean(lo2_f, 1).mean(0) fooofed_group_avg_dat[s_ind, 2, :] = np.mean(lo3_f, 1).mean(0) ################################################# ## FOOOFING TRIAL AVERAGED DATA # Loop loop loads & trials segments for seg_label, seg_time in zip(SEG_LABELS, SEG_TIMES): tmin, tmax = seg_time[0], seg_time[1] # Calculate PSDs across trials, fit FOOOF models to averages for le_label, ri_label, load_label in zip(['LeLo1', 'LeLo2', 'LeLo3'], ['RiLo1', 'RiLo2', 'RiLo3'], LOAD_LABELS): ## Calculate trial wise PSDs for left & right side trials trial_freqs, le_trial_psds = periodogram( epochs[le_label]._data[:, :, _time_mask(epochs.times, tmin, tmax, srate)], srate, window='hann', nfft=4*srate) trial_freqs, ri_trial_psds = periodogram( epochs[ri_label]._data[:, :, _time_mask(epochs.times, tmin, tmax, srate)], srate, window='hann', nfft=4*srate) ## FIT ALL CHANNELS VERSION if FIT_ALL_CHANNELS: ## Average spectra across trials within a given load & side le_avg_psd_contra = avg_func(le_trial_psds[:, ri_inds, :], 0) le_avg_psd_ipsi = avg_func(le_trial_psds[:, le_inds, :], 0) ri_avg_psd_contra = avg_func(ri_trial_psds[:, le_inds, :], 0) ri_avg_psd_ipsi = avg_func(ri_trial_psds[:, ri_inds, :], 0) ## Combine spectra across left & right trials for given load ch_psd_contra = np.vstack([le_avg_psd_contra, ri_avg_psd_contra]) ch_psd_ipsi = np.vstack([le_avg_psd_ipsi, ri_avg_psd_ipsi]) ## Fit FOOOFGroup to all channels, average & and collect results fg.fit(trial_freqs, ch_psd_contra, FREQ_RANGE) fm = avg_fg(fg) fg_dict[load_label]['Contra'][seg_label].append(fm.copy()) fg.fit(trial_freqs, ch_psd_ipsi, FREQ_RANGE) fm = avg_fg(fg) fg_dict[load_label]['Ipsi'][seg_label].append(fm.copy()) ## COLLAPSE ACROSS CHANNELS VERSION else: ## Average spectra across trials and channels within a given load & side le_avg_psd_contra = avg_func(avg_func(le_trial_psds[:, ri_inds, :], 0), 0) le_avg_psd_ipsi = avg_func(avg_func(le_trial_psds[:, le_inds, :], 0), 0) ri_avg_psd_contra = avg_func(avg_func(ri_trial_psds[:, le_inds, :], 0), 0) ri_avg_psd_ipsi = avg_func(avg_func(ri_trial_psds[:, ri_inds, :], 0), 0) ## Collapse spectra across left & right trials for given load avg_psd_contra = avg_func(np.vstack([le_avg_psd_contra, ri_avg_psd_contra]), 0) avg_psd_ipsi = avg_func(np.vstack([le_avg_psd_ipsi, ri_avg_psd_ipsi]), 0) ## Fit FOOOF, and collect results fm.fit(trial_freqs, avg_psd_contra, FREQ_RANGE) fg_dict[load_label]['Contra'][seg_label].append(fm.copy()) fm.fit(trial_freqs, avg_psd_ipsi, FREQ_RANGE) fg_dict[load_label]['Ipsi'][seg_label].append(fm.copy()) ################################################# ## SAVE OUT RESULTS # Save out group data np.save(pjoin(RES_PATH, 'Group', 'alpha_freqs_group'), group_fooofed_alpha_freqs) np.save(pjoin(RES_PATH, 'Group', 'canonical_group'), canonical_group_avg_dat) np.save(pjoin(RES_PATH, 'Group', 'fooofed_group'), fooofed_group_avg_dat) np.save(pjoin(RES_PATH, 'Group', 'dropped_trials'), dropped_trials) np.save(pjoin(RES_PATH, 'Group', 'dropped_components'), dropped_components) # Save out second round of FOOOFing for load_label in LOAD_LABELS: for side_label in SIDE_LABELS: for seg_label in SEG_LABELS: fg = combine_fooofs(fg_dict[load_label][side_label][seg_label]) fg.save('Group_' + load_label + '_' + side_label + '_' + seg_label, pjoin(RES_PATH, 'FOOOF'), save_results=True)
def test_ica_additional(): """Test additional ICA functionality """ stop2 = 500 raw = io.Raw(raw_fname, preload=True).crop(0, stop, False).crop(1.5) picks = pick_types(raw.info, meg=True, stim=False, ecg=False, eog=False, exclude='bads') test_cov = read_cov(test_cov_name) events = read_events(event_name) picks = pick_types(raw.info, meg=True, stim=False, ecg=False, eog=False, exclude='bads') epochs = Epochs(raw, events[:4], event_id, tmin, tmax, picks=picks, baseline=(None, 0), preload=True) # for testing eog functionality picks2 = pick_types(raw.info, meg=True, stim=False, ecg=False, eog=True, exclude='bads') epochs_eog = Epochs(raw, events[:4], event_id, tmin, tmax, picks=picks2, baseline=(None, 0), preload=True) test_cov2 = deepcopy(test_cov) ica = ICA(noise_cov=test_cov2, n_components=3, max_pca_components=4, n_pca_components=4) assert_true(ica.info is None) ica.decompose_raw(raw, picks[:5]) assert_true(isinstance(ica.info, Info)) assert_true(ica.n_components_ < 5) ica = ICA(n_components=3, max_pca_components=4, n_pca_components=4) assert_raises(RuntimeError, ica.save, '') ica.decompose_raw(raw, picks=None, start=start, stop=stop2) # test warnings on bad filenames with warnings.catch_warnings(record=True) as w: warnings.simplefilter('always') ica_badname = op.join(op.dirname(tempdir), 'test-bad-name.fif.gz') ica.save(ica_badname) read_ica(ica_badname) assert_true(len(w) == 2) # test decim ica = ICA(n_components=3, max_pca_components=4, n_pca_components=4) raw_ = raw.copy() for _ in range(3): raw_.append(raw_) n_samples = raw_._data.shape[1] ica.decompose_raw(raw, picks=None, decim=3) assert_true(raw_._data.shape[1], n_samples) # test expl var ica = ICA(n_components=1.0, max_pca_components=4, n_pca_components=4) ica.decompose_raw(raw, picks=None, decim=3) assert_true(ica.n_components_ == 4) # epochs extraction from raw fit assert_raises(RuntimeError, ica.get_sources_epochs, epochs) # test reading and writing test_ica_fname = op.join(op.dirname(tempdir), 'test-ica.fif') for cov in (None, test_cov): ica = ICA(noise_cov=cov, n_components=2, max_pca_components=4, n_pca_components=4) with warnings.catch_warnings(record=True): # ICA does not converge ica.decompose_raw(raw, picks=picks, start=start, stop=stop2) sources = ica.get_sources_epochs(epochs) assert_true(ica.mixing_matrix_.shape == (2, 2)) assert_true(ica.unmixing_matrix_.shape == (2, 2)) assert_true(ica.pca_components_.shape == (4, len(picks))) assert_true(sources.shape[1] == ica.n_components_) for exclude in [[], [0]]: ica.exclude = [0] ica.save(test_ica_fname) ica_read = read_ica(test_ica_fname) assert_true(ica.exclude == ica_read.exclude) # test pick merge -- add components ica.pick_sources_raw(raw, exclude=[1]) assert_true(ica.exclude == [0, 1]) # -- only as arg ica.exclude = [] ica.pick_sources_raw(raw, exclude=[0, 1]) assert_true(ica.exclude == [0, 1]) # -- remove duplicates ica.exclude += [1] ica.pick_sources_raw(raw, exclude=[0, 1]) assert_true(ica.exclude == [0, 1]) # test basic include ica.exclude = [] ica.pick_sources_raw(raw, include=[1]) ica_raw = ica.sources_as_raw(raw) assert_true(ica.exclude == [ica_raw.ch_names.index(e) for e in ica_raw.info['bads']]) # test filtering d1 = ica_raw._data[0].copy() with warnings.catch_warnings(record=True): # dB warning ica_raw.filter(4, 20) assert_true((d1 != ica_raw._data[0]).any()) d1 = ica_raw._data[0].copy() with warnings.catch_warnings(record=True): # dB warning ica_raw.notch_filter([10]) assert_true((d1 != ica_raw._data[0]).any()) ica.n_pca_components = 2 ica.save(test_ica_fname) ica_read = read_ica(test_ica_fname) assert_true(ica.n_pca_components == ica_read.n_pca_components) # check type consistency attrs = ('mixing_matrix_ unmixing_matrix_ pca_components_ ' 'pca_explained_variance_ _pre_whitener') f = lambda x, y: getattr(x, y).dtype for attr in attrs.split(): assert_equal(f(ica_read, attr), f(ica, attr)) ica.n_pca_components = 4 ica_read.n_pca_components = 4 ica.exclude = [] ica.save(test_ica_fname) ica_read = read_ica(test_ica_fname) for attr in ['mixing_matrix_', 'unmixing_matrix_', 'pca_components_', 'pca_mean_', 'pca_explained_variance_', '_pre_whitener']: assert_array_almost_equal(getattr(ica, attr), getattr(ica_read, attr)) assert_true(ica.ch_names == ica_read.ch_names) assert_true(isinstance(ica_read.info, Info)) assert_raises(RuntimeError, ica_read.decompose_raw, raw) sources = ica.get_sources_raw(raw) sources2 = ica_read.get_sources_raw(raw) assert_array_almost_equal(sources, sources2) _raw1 = ica.pick_sources_raw(raw, exclude=[1]) _raw2 = ica_read.pick_sources_raw(raw, exclude=[1]) assert_array_almost_equal(_raw1[:, :][0], _raw2[:, :][0]) os.remove(test_ica_fname) # check scrore funcs for name, func in score_funcs.items(): if name in score_funcs_unsuited: continue scores = ica.find_sources_raw(raw, target='EOG 061', score_func=func, start=0, stop=10) assert_true(ica.n_components_ == len(scores)) # check univariate stats scores = ica.find_sources_raw(raw, score_func=stats.skew) # check exception handling assert_raises(ValueError, ica.find_sources_raw, raw, target=np.arange(1)) params = [] params += [(None, -1, slice(2), [0, 1])] # varicance, kurtosis idx params params += [(None, 'MEG 1531')] # ECG / EOG channel params for idx, ch_name in product(*params): ica.detect_artifacts(raw, start_find=0, stop_find=50, ecg_ch=ch_name, eog_ch=ch_name, skew_criterion=idx, var_criterion=idx, kurt_criterion=idx) ## score funcs epochs ## # check score funcs for name, func in score_funcs.items(): if name in score_funcs_unsuited: continue scores = ica.find_sources_epochs(epochs_eog, target='EOG 061', score_func=func) assert_true(ica.n_components_ == len(scores)) # check univariate stats scores = ica.find_sources_epochs(epochs, score_func=stats.skew) # check exception handling assert_raises(ValueError, ica.find_sources_epochs, epochs, target=np.arange(1)) # ecg functionality ecg_scores = ica.find_sources_raw(raw, target='MEG 1531', score_func='pearsonr') with warnings.catch_warnings(record=True): # filter attenuation warning ecg_events = ica_find_ecg_events(raw, sources[np.abs(ecg_scores).argmax()]) assert_true(ecg_events.ndim == 2) # eog functionality eog_scores = ica.find_sources_raw(raw, target='EOG 061', score_func='pearsonr') with warnings.catch_warnings(record=True): # filter attenuation warning eog_events = ica_find_eog_events(raw, sources[np.abs(eog_scores).argmax()]) assert_true(eog_events.ndim == 2) # Test ica fiff export ica_raw = ica.sources_as_raw(raw, start=0, stop=100) assert_true(ica_raw.last_samp - ica_raw.first_samp == 100) assert_true(len(ica_raw._filenames) == 0) # API consistency ica_chans = [ch for ch in ica_raw.ch_names if 'ICA' in ch] assert_true(ica.n_components_ == len(ica_chans)) test_ica_fname = op.join(op.abspath(op.curdir), 'test-ica_raw.fif') ica.n_components = np.int32(ica.n_components) ica_raw.save(test_ica_fname, overwrite=True) ica_raw2 = io.Raw(test_ica_fname, preload=True) assert_allclose(ica_raw._data, ica_raw2._data, rtol=1e-5, atol=1e-4) ica_raw2.close() os.remove(test_ica_fname) # Test ica epochs export ica_epochs = ica.sources_as_epochs(epochs) assert_true(ica_epochs.events.shape == epochs.events.shape) sources_epochs = ica.get_sources_epochs(epochs) assert_array_equal(ica_epochs.get_data(), sources_epochs) ica_chans = [ch for ch in ica_epochs.ch_names if 'ICA' in ch] assert_true(ica.n_components_ == len(ica_chans)) assert_true(ica.n_components_ == ica_epochs.get_data().shape[1]) assert_true(ica_epochs.raw is None) assert_true(ica_epochs.preload is True) # test float n pca components ica.pca_explained_variance_ = np.array([0.2] * 5) ica.n_components_ = 0 for ncomps, expected in [[0.3, 1], [0.9, 4], [1, 1]]: ncomps_ = _check_n_pca_components(ica, ncomps) assert_true(ncomps_ == expected)
def apply_ica(subject, run, session): print("Processing subject: %s" % subject) # Construct the search path for the data file. `sub` is mandatory subject_path = op.join('sub-{}'.format(subject)) # `session` is optional if session is not None: subject_path = op.join(subject_path, 'ses-{}'.format(session)) subject_path = op.join(subject_path, config.kind) bids_basename = make_bids_basename(subject=subject, session=session, task=config.task, acquisition=config.acq, run=None, processing=config.proc, recording=config.rec, space=config.space ) fpath_deriv = op.join(config.bids_root, 'derivatives', config.PIPELINE_NAME, subject_path) fname_in = \ op.join(fpath_deriv, bids_basename + '-epo.fif') fname_out = \ op.join(fpath_deriv, bids_basename + '_cleaned-epo.fif') # load epochs to reject ICA components epochs = mne.read_epochs(fname_in, preload=True) print("Input: ", fname_in) print("Output: ", fname_out) # load first run of raw data for ecg /eog epochs print(" Loading one run from raw data") bids_basename = make_bids_basename(subject=subject, session=session, task=config.task, acquisition=config.acq, run=config.runs[0], processing=config.proc, recording=config.rec, space=config.space ) if config.use_maxwell_filter: raw_fname_in = \ op.join(fpath_deriv, bids_basename + '_sss_raw.fif') else: raw_fname_in = \ op.join(fpath_deriv, bids_basename + '_filt_raw.fif') raw = mne.io.read_raw_fif(raw_fname_in, preload=True) # run ICA on MEG and EEG picks_meg = mne.pick_types(raw.info, meg=True, eeg=False, eog=False, stim=False, exclude='bads') picks_eeg = mne.pick_types(raw.info, meg=False, eeg=True, eog=False, stim=False, exclude='bads') all_picks = {'meg': picks_meg, 'eeg': picks_eeg} for ch_type in config.ch_types: report = None print(ch_type) picks = all_picks[ch_type] # Load ICA fname_ica = \ op.join(fpath_deriv, bids_basename + '_%s-ica.fif' % ch_type) print('Reading ICA: ' + fname_ica) ica = read_ica(fname=fname_ica) pick_ecg = mne.pick_types(raw.info, meg=False, eeg=False, ecg=True, eog=False) # ECG # either needs an ecg channel, or avg of the mags (i.e. MEG data) ecg_inds = list() if pick_ecg or ch_type == 'meg': picks_ecg = np.concatenate([picks, pick_ecg]) # Create ecg epochs if ch_type == 'meg': reject = {'mag': config.reject['mag'], 'grad': config.reject['grad']} elif ch_type == 'eeg': reject = {'eeg': config.reject['eeg']} ecg_epochs = create_ecg_epochs(raw, picks=picks_ecg, reject=reject, baseline=(None, 0), tmin=-0.5, tmax=0.5) ecg_average = ecg_epochs.average() ecg_inds, scores = \ ica.find_bads_ecg(ecg_epochs, method='ctps', threshold=config.ica_ctps_ecg_threshold) del ecg_epochs report_fname = \ op.join(fpath_deriv, bids_basename + '_%s-reject_ica.html' % ch_type) report = Report(report_fname, verbose=False) # Plot r score report.add_figs_to_section(ica.plot_scores(scores, exclude=ecg_inds, show=config.plot), captions=ch_type.upper() + ' - ECG - ' + 'R scores') # Plot source time course report.add_figs_to_section(ica.plot_sources(ecg_average, exclude=ecg_inds, show=config.plot), captions=ch_type.upper() + ' - ECG - ' + 'Sources time course') # Plot source time course report.add_figs_to_section(ica.plot_overlay(ecg_average, exclude=ecg_inds, show=config.plot), captions=ch_type.upper() + ' - ECG - ' + 'Corrections') else: # XXX : to check when EEG only is processed print('no ECG channel is present. Cannot automate ICAs component ' 'detection for ECG!') # EOG pick_eog = mne.pick_types(raw.info, meg=False, eeg=False, ecg=False, eog=True) eog_inds = list() if pick_eog.any(): print('using EOG channel') picks_eog = np.concatenate([picks, pick_eog]) # Create eog epochs eog_epochs = create_eog_epochs(raw, picks=picks_eog, reject=None, baseline=(None, 0), tmin=-0.5, tmax=0.5) eog_average = eog_epochs.average() eog_inds, scores = ica.find_bads_eog(eog_epochs, threshold=3.0) del eog_epochs params = dict(exclude=eog_inds, show=config.plot) # Plot r score report.add_figs_to_section(ica.plot_scores(scores, **params), captions=ch_type.upper() + ' - EOG - ' + 'R scores') # Plot source time course report.add_figs_to_section(ica.plot_sources(eog_average, **params), captions=ch_type.upper() + ' - EOG - ' + 'Sources time course') # Plot source time course report.add_figs_to_section(ica.plot_overlay(eog_average, **params), captions=ch_type.upper() + ' - EOG - ' + 'Corrections') report.save(report_fname, overwrite=True, open_browser=False) else: print('no EOG channel is present. Cannot automate ICAs component ' 'detection for EOG!') ica_reject = (list(ecg_inds) + list(eog_inds) + list(config.rejcomps_man[subject][ch_type])) # now reject the components print('Rejecting from %s: %s' % (ch_type, ica_reject)) epochs = ica.apply(epochs, exclude=ica_reject) print('Saving cleaned epochs') epochs.save(fname_out) if report is not None: fig = ica.plot_overlay(raw, exclude=ica_reject, show=config.plot) report.add_figs_to_section(fig, captions=ch_type.upper() + ' - ALL(epochs) - Corrections') if config.plot: epochs.plot_image(combine='gfp', group_by='type', sigma=2., cmap="YlGnBu_r", show=config.plot)
# Read events from the stim channel mask = 4096 + 256 # mask for excluding high order bits events = mne.find_events(raw, stim_channel='STI101', consecutive='increasing', mask=mask, mask_type='not_and', min_duration=0.003) # Compensate for projector delay events[:, 0] += int(round(0.0345 * raw.info['sfreq'])) # Load the ICA object print(' Using ICA') ica = read_ica(fname.ica(subject=subject)) # Make epochs. Because the original 1000Hz sampling rate is a bit excessive # for what we're going for, we only read every 5th sample. This gives us a # sampling rate of ~200Hz. epochs = mne.Epochs(raw, events, events_id, epoch_tmin, epoch_tmax, baseline=baseline, decim=5, preload=True) # Save evoked plot to the report with mne.open_report(fname.report(subject=subject)) as report:
subject = group_name + "%d" % subject_id print("processing subject: %s" % subject) tasks = ['AVLearn', 'AVLearn'] days = [100, 200] for task, day in zip(tasks, days): fname = op.join(MEG_data_path, subject, task + '_%d' % (day + subject_id) + '_tsss_mc.fif') raw_tsss_mc = mne.io.read_raw_fif(fname, preload=True) raw_tsss_mc.filter(l_freq=None, h_freq=40.0, fir_design='firwin') # low-pass filter data ica = read_ica(fname.replace("_tsss_mc", "-ica")) ica.exclude = np.load(fname.replace("tsss_mc.fif", 'ICA_excludes.npy')).tolist() raw_tsss_mc = ica.apply(raw_tsss_mc, exclude=ica.exclude) events = pd.read_csv(fname.replace('tsss_mc.fif', 'events.csv')) artifacts = pd.read_csv(fname.replace('tsss_mc.fif', 'artifacts.csv')) df = pd.merge(events, artifacts, on='stim_onset') df['trigger_code2'] = df['trigger_code'] + df['block'] * 1000 df = df[df['artifacts'] == False] events = df[["stim_onset", "button_press", "trigger_code2"]].astype(int).values picks = mne.pick_types(raw_tsss_mc.info, meg=True,
def run_epochs(subject_id, tsss=False): subject = "sub%03d" % subject_id print("Processing subject: %s%s" % (subject, (' (tSSS=%d)' % tsss) if tsss else '')) data_path = op.join(meg_dir, subject) # map to correct subject for bad channels mapping = map_subjects[subject_id] raw_list = list() events_list = list() print(" Loading raw data") for run in range(1, 7): bads = list() bad_name = op.join('bads', mapping, 'run_%02d_raw_tr.fif_bad' % run) if os.path.exists(bad_name): with open(bad_name) as f: for line in f: bads.append(line.strip()) if tsss: run_fname = op.join(data_path, 'run_%02d_filt_tsss_%d_raw.fif' % (run, tsss)) else: run_fname = op.join( data_path, 'run_%02d_filt_sss_' 'highpass-%sHz_raw.fif' % (run, l_freq)) raw = mne.io.read_raw_fif(run_fname, preload=True) delay = int(round(0.0345 * raw.info['sfreq'])) events = mne.read_events(op.join(data_path, 'run_%02d-eve.fif' % run)) events[:, 0] = events[:, 0] + delay events_list.append(events) raw.info['bads'] = bads raw.interpolate_bads() raw_list.append(raw) raw, events = mne.concatenate_raws(raw_list, events_list=events_list) raw.set_eeg_reference(projection=True) del raw_list picks = mne.pick_types(raw.info, meg=True, eeg=True, stim=True, eog=True, exclude=()) # Epoch the data print(' Epoching') epochs = mne.Epochs(raw, events, events_id, tmin, tmax, proj=True, picks=picks, baseline=baseline, preload=False, decim=5, reject=None, reject_tmax=reject_tmax) print(' Interpolating bad channels') # ICA if tsss: ica_name = op.join(meg_dir, subject, 'run_concat-tsss_%d-ica.fif' % (tsss, )) ica_out_name = ica_name else: ica_name = op.join(meg_dir, subject, 'run_concat-ica.fif') ica_out_name = op.join(meg_dir, subject, 'run_concat_highpass-%sHz-ica.fif' % (l_freq, )) print(' Using ICA') ica = read_ica(ica_name) ica.exclude = [] filter_label = '-tsss_%d' % tsss if tsss else '_highpass-%sHz' % l_freq ecg_epochs = create_ecg_epochs(raw, tmin=-.3, tmax=.3, preload=False) eog_epochs = create_eog_epochs(raw, tmin=-.5, tmax=.5, preload=False) del raw n_max_ecg = 3 # use max 3 components ecg_epochs.decimate(5) ecg_epochs.load_data() ecg_epochs.apply_baseline((None, None)) ecg_inds, scores_ecg = ica.find_bads_ecg(ecg_epochs, method='ctps', threshold=0.8) print(' Found %d ECG indices' % (len(ecg_inds), )) ica.exclude.extend(ecg_inds[:n_max_ecg]) ecg_epochs.average().save( op.join(data_path, '%s%s-ecg-ave.fif' % (subject, filter_label))) np.save( op.join(data_path, '%s%s-ecg-scores.npy' % (subject, filter_label)), scores_ecg) del ecg_epochs n_max_eog = 3 # use max 2 components eog_epochs.decimate(5) eog_epochs.load_data() eog_epochs.apply_baseline((None, None)) eog_inds, scores_eog = ica.find_bads_eog(eog_epochs) print(' Found %d EOG indices' % (len(eog_inds), )) ica.exclude.extend(eog_inds[:n_max_eog]) eog_epochs.average().save( op.join(data_path, '%s%s-eog-ave.fif' % (subject, filter_label))) np.save( op.join(data_path, '%s%s-eog-scores.npy' % (subject, filter_label)), scores_eog) del eog_epochs ica.save(ica_out_name) epochs.load_data() ica.apply(epochs) print(' Getting rejection thresholds') reject = get_rejection_threshold(epochs.copy().crop(None, reject_tmax)) epochs.drop_bad(reject=reject) print(' Dropped %0.1f%% of epochs' % (epochs.drop_log_stats(), )) print(' Writing to disk') if tsss: epochs.save(op.join(data_path, '%s-tsss_%d-epo.fif' % (subject, tsss))) else: epochs.save( op.join(data_path, '%s_highpass-%sHz-epo.fif' % (subject, l_freq)))
def test_ica_additional(): """Test additional functionality """ stop2 = 500 test_cov2 = deepcopy(test_cov) ica = ICA(noise_cov=test_cov2, n_components=3, max_pca_components=4, n_pca_components=4) assert_true(ica.info is None) ica.decompose_raw(raw, picks[:5]) assert_true(isinstance(ica.info, Info)) assert_true(ica.n_components_ < 5) ica = ICA(n_components=3, max_pca_components=4, n_pca_components=4) assert_raises(RuntimeError, ica.save, '') ica.decompose_raw(raw, picks=None, start=start, stop=stop2) # epochs extraction from raw fit assert_raises(RuntimeError, ica.get_sources_epochs, epochs) # test reading and writing test_ica_fname = op.join(op.dirname(tempdir), 'ica_test.fif') for cov in (None, test_cov): ica = ICA(noise_cov=cov, n_components=3, max_pca_components=4, n_pca_components=4) ica.decompose_raw(raw, picks=picks, start=start, stop=stop2) sources = ica.get_sources_epochs(epochs) assert_true(sources.shape[1] == ica.n_components_) for exclude in [[], [0]]: ica.exclude = [0] ica.save(test_ica_fname) ica_read = read_ica(test_ica_fname) assert_true(ica.exclude == ica_read.exclude) # test pick merge -- add components ica.pick_sources_raw(raw, exclude=[1]) assert_true(ica.exclude == [0, 1]) # -- only as arg ica.exclude = [] ica.pick_sources_raw(raw, exclude=[0, 1]) assert_true(ica.exclude == [0, 1]) # -- remove duplicates ica.exclude += [1] ica.pick_sources_raw(raw, exclude=[0, 1]) assert_true(ica.exclude == [0, 1]) ica_raw = ica.sources_as_raw(raw) assert_true(ica.exclude == [ica_raw.ch_names.index(e) for e in ica_raw.info['bads']]) ica.n_pca_components = 2 ica.save(test_ica_fname) ica_read = read_ica(test_ica_fname) assert_true(ica.n_pca_components == ica_read.n_pca_components) ica.n_pca_components = 4 ica_read.n_pca_components = 4 ica.exclude = [] ica.save(test_ica_fname) ica_read = read_ica(test_ica_fname) assert_true(ica.ch_names == ica_read.ch_names) assert_true(isinstance(ica_read.info, Info)) # XXX improve later assert_true(np.allclose(ica.mixing_matrix_, ica_read.mixing_matrix_, rtol=1e-16, atol=1e-32)) assert_array_equal(ica.pca_components_, ica_read.pca_components_) assert_array_equal(ica.pca_mean_, ica_read.pca_mean_) assert_array_equal(ica.pca_explained_variance_, ica_read.pca_explained_variance_) assert_array_equal(ica._pre_whitener, ica_read._pre_whitener) # assert_raises(RuntimeError, ica_read.decompose_raw, raw) sources = ica.get_sources_raw(raw) sources2 = ica_read.get_sources_raw(raw) assert_array_almost_equal(sources, sources2) _raw1 = ica.pick_sources_raw(raw, exclude=[1]) _raw2 = ica_read.pick_sources_raw(raw, exclude=[1]) assert_array_almost_equal(_raw1[:, :][0], _raw2[:, :][0]) os.remove(test_ica_fname) # check scrore funcs for name, func in score_funcs.items(): if name in score_funcs_unsuited: continue scores = ica.find_sources_raw(raw, target='EOG 061', score_func=func, start=0, stop=10) assert_true(ica.n_components_ == len(scores)) # check univariate stats scores = ica.find_sources_raw(raw, score_func=stats.skew) # check exception handling assert_raises(ValueError, ica.find_sources_raw, raw, target=np.arange(1)) params = [] params += [(None, -1, slice(2), [0, 1])] # varicance, kurtosis idx params params += [(None, 'MEG 1531')] # ECG / EOG channel params for idx, ch_name in product(*params): ica.detect_artifacts(raw, start_find=0, stop_find=50, ecg_ch=ch_name, eog_ch=ch_name, skew_criterion=idx, var_criterion=idx, kurt_criterion=idx) ## score funcs epochs ## # check score funcs for name, func in score_funcs.items(): if name in score_funcs_unsuited: continue scores = ica.find_sources_epochs(epochs_eog, target='EOG 061', score_func=func) assert_true(ica.n_components_ == len(scores)) # check univariate stats scores = ica.find_sources_epochs(epochs, score_func=stats.skew) # check exception handling assert_raises(ValueError, ica.find_sources_epochs, epochs, target=np.arange(1)) # ecg functionality ecg_scores = ica.find_sources_raw(raw, target='MEG 1531', score_func='pearsonr') ecg_events = ica_find_ecg_events(raw, sources[np.abs(ecg_scores).argmax()]) assert_true(ecg_events.ndim == 2) # eog functionality eog_scores = ica.find_sources_raw(raw, target='EOG 061', score_func='pearsonr') eog_events = ica_find_eog_events(raw, sources[np.abs(eog_scores).argmax()]) assert_true(eog_events.ndim == 2) # Test ica fiff export ica_raw = ica.sources_as_raw(raw, start=0, stop=100) assert_true(ica_raw.last_samp - ica_raw.first_samp == 100) ica_chans = [ch for ch in ica_raw.ch_names if 'ICA' in ch] assert_true(ica.n_components_ == len(ica_chans)) test_ica_fname = op.join(op.abspath(op.curdir), 'test_ica.fif') ica_raw.save(test_ica_fname) ica_raw2 = fiff.Raw(test_ica_fname, preload=True) assert_array_almost_equal(ica_raw._data, ica_raw2._data) ica_raw2.close() os.remove(test_ica_fname) # Test ica epochs export ica_epochs = ica.sources_as_epochs(epochs) assert_true(ica_epochs.events.shape == epochs.events.shape) sources_epochs = ica.get_sources_epochs(epochs) assert_array_equal(ica_epochs.get_data(), sources_epochs) ica_chans = [ch for ch in ica_epochs.ch_names if 'ICA' in ch] assert_true(ica.n_components_ == len(ica_chans)) assert_true(ica.n_components_ == ica_epochs.get_data().shape[1]) assert_true(ica_epochs.raw is None) assert_true(ica_epochs.preload == True) # regression test for plot method assert_raises(ValueError, ica.plot_sources_raw, raw, order=np.arange(50)) assert_raises(ValueError, ica.plot_sources_epochs, epochs, order=np.arange(50))
session_no = '' ica_check_eves = dict(FFA=['A','B']) ica_cond = 'FFA' ica_excludes = load_excludes(ica_excludes_path, subj, ica_cond) print 30*'*' print 'ICA excludes:', ica_excludes print 30*'*' raw_path = opj(ad._scratch_folder, input_files, subj) in_fnames = ad.analysis_dict[subj][input_files][cond]['files'] events = mne.read_events(opj(eve_folder, cond + '-eve.fif')) eve_dict, id_dict = \ split_events_by_trialtype(events, condition=cond) for fname in in_fnames: ica = read_ica(opj(ica_folder, cond + '-ica.fif')) print 'In: ', fname raw = Raw(fname, preload=performBandpassFilter) rep_section_name = '' if performBandpassFilter: raw.filter(filter_params['highpass'], filter_params['lowpass'], method='iir', n_jobs=1 ) picks = mne.pick_types(raw.info, meg=True, eog=True) for trial_type in trial_types: epochs = mne.Epochs(raw, eve_dict[trial_type], id_dict[trial_type],
def run_epochs(subject_id): subject = "sub%03d" % subject_id print("processing subject: %s" % subject) data_path = op.join(meg_dir, subject) all_epochs = list() # Get all bad channels mapping = map_subjects[subject_id] # map to correct subject all_bads = list() for run in range(1, 7): bads = list() bad_name = op.join('bads', mapping, 'run_%02d_raw_tr.fif_bad' % run) if os.path.exists(bad_name): with open(bad_name) as f: for line in f: bads.append(line.strip()) all_bads += [bad for bad in bads if bad not in all_bads] for run in range(1, 7): print " - Run %s" % run run_fname = op.join(data_path, 'run_%02d_filt_sss_raw.fif' % run) if not os.path.exists(run_fname): continue raw = mne.io.Raw(run_fname, preload=True, add_eeg_ref=False) raw.set_channel_types({'EEG061': 'eog', 'EEG062': 'eog', 'EEG063': 'ecg', 'EEG064': 'misc'}) # EEG064 free floating el. raw.rename_channels({'EEG061': 'EOG061', 'EEG062': 'EOG062', 'EEG063': 'ECG063'}) eog_events = mne.preprocessing.find_eog_events(raw) eog_events[:, 0] -= int(0.25 * raw.info['sfreq']) annotations = mne.Annotations(eog_events[:, 0] / raw.info['sfreq'], np.repeat(0.5, len(eog_events)), 'BAD_blink', raw.info['meas_date']) raw.annotations = annotations # Remove epochs with blinks delay = int(0.0345 * raw.info['sfreq']) events = mne.read_events(op.join(data_path, 'run_%02d_filt_sss-eve.fif' % run)) events[:, 0] = events[:, 0] + delay raw.info['bads'] = all_bads raw.interpolate_bads() raw.set_eeg_reference() picks = mne.pick_types(raw.info, meg=True, eeg=True, stim=True, eog=True) # Read epochs epochs = mne.Epochs(raw, events, events_id, tmin, tmax, proj=True, picks=picks, baseline=baseline, preload=True, decim=2, reject=reject, add_eeg_ref=False) # ICA ica_name = op.join(meg_dir, subject, 'run_%02d-ica.fif' % run) ica = read_ica(ica_name) n_max_ecg = 3 # use max 3 components ecg_epochs = create_ecg_epochs(raw, tmin=-.5, tmax=.5) ecg_inds, scores_ecg = ica.find_bads_ecg(ecg_epochs, method='ctps', threshold=0.8) ica.exclude += ecg_inds[:n_max_ecg] ica.apply(epochs) all_epochs.append(epochs) epochs = mne.epochs.concatenate_epochs(all_epochs) epochs.save(op.join(data_path, '%s-epo.fif' % subject))
return eve_dict, id_dict # Set epoch parameters tmin, tmax = -0.4, 0.6 # no need to take more than this, wide enough to see eyemov though rej_tmin, rej_tmax = -0.2, 0.2 # reject trial only if blinks in the 400 ms middle portion! baseline = (-0.2, 0.) reject = dict(eog=150e-6, mag=4e-12, grad=4000e-13) # compare to standard rejection raw_path = ad._scratch_folder + '/tsss_initial/007_SGF' eve_path = ad._scratch_folder + '/events.fif/007_SGF/raw' fname = raw_path + '/VS_1a_1_tsss_mc.fif' raw = Raw(fname, preload=True) ica = read_ica(raw_path + '/ica_pre.fif') print 'Excluding', ica.exclude raw_ica = ica.apply(raw, copy=True) events = mne.read_events(eve_path + '/VS_1a_1-eve.fif') picks = pick_types(raw.info, meg=True, eeg=False, stim=True, eog=True, misc=True) eve_dict, id_dict = split_events_by_trialtype(events) for trial_type in ['VS']: epochs = mne.Epochs(raw, eve_dict[trial_type], id_dict, tmin, tmax, picks=picks, verbose=False, baseline=baseline, reject=reject, preload=True, reject_tmin=rej_tmin, reject_tmax=rej_tmax) # Check rejection settings epochs_ica = mne.Epochs(raw_ica, eve_dict[trial_type], id_dict, tmin, tmax, picks=picks, verbose=False, baseline=baseline, reject=None, preload=True)
def preprocess_set_ICA_comp_fif_to_ts(fif_file, n_comp_exclude, l_freq, h_freq, down_sfreq, is_sensor_space): import os import numpy as np import sys import mne from mne.io import Raw from mne.preprocessing import read_ica from mne.report import Report from nipype.utils.filemanip import split_filename as split_f report = Report() subj_path, basename, ext = split_f(fif_file) (data_path, sbj_name) = os.path.split(subj_path) print '*** SBJ %s' % sbj_name + '***' # n_session = int(filter(str.isdigit, basename)) # print '*** n session = %d' % n_session + '***' # Read raw raw = Raw(fif_file, preload=True) # select sensors select_sensors = mne.pick_types(raw.info, meg=True, ref_meg=False, exclude='bads') picks_meeg = mne.pick_types(raw.info, meg=True, eeg=True, exclude='bads') # save electrode locations sens_loc = [raw.info['chs'][i]['loc'][:3] for i in select_sensors] sens_loc = np.array(sens_loc) channel_coords_file = os.path.abspath("correct_channel_coords.txt") np.savetxt(channel_coords_file, sens_loc, fmt='%s') # save electrode names sens_names = np.array([raw.ch_names[pos] for pos in select_sensors], dtype="str") channel_names_file = os.path.abspath("correct_channel_names.txt") np.savetxt(channel_names_file, sens_names, fmt='%s') # filtering + downsampling # TODO n_jobs=8 raw.filter(l_freq=l_freq, h_freq=h_freq, picks=picks_meeg, method='iir',n_jobs=8) # raw.resample(sfreq=down_sfreq, npad=0) # load ICA is_show = False # visualization ica_filename = os.path.join(subj_path, basename + '-ica.fif') if os.path.exists(ica_filename) is False: print "$$$ Warning, no %s found" % ica_filename sys.exit() else: ica = read_ica(ica_filename) # AP 210316 ''' print '*** ica.exclude before set components= ', ica.exclude if n_comp_exclude.has_key(sbj_name): print '*** ICA to be excluded for sbj %s ' % sbj_name + ' ' + str(n_comp_exclude[sbj_name]) + '***' matrix_c_ICA = n_comp_exclude[sbj_name] if not matrix_c_ICA[n_session-1]: print 'no ICA' else: print '*** ICA to be excluded for session %d ' %n_session + ' ' + str(matrix_c_ICA[n_session-1]) + '***' ica.exclude = matrix_c_ICA[n_session-1] ''' # AP new dict print '*** ica.exclude before set components= ', ica.exclude if n_comp_exclude.has_key(sbj_name): print '*** ICA to be excluded for sbj %s ' % sbj_name + ' ' + str(n_comp_exclude[sbj_name]) + '***' session_dict = n_comp_exclude[sbj_name] session_names = session_dict.keys() componentes = [] for s in session_names: if basename.find(s) > -1: componentes = session_dict[s] break if len(componentes) == 0: print '\n no ICA to be excluded \n' else: print '\n *** ICA to be excluded for session %s ' % s + \ ' ' + str(componentes) + ' *** \n' ica.exclude = componentes print '\n *** ica.exclude after set components = ', ica.exclude fig1 = ica.plot_overlay(raw, show=is_show) report.add_figs_to_section(fig1, captions=['Signal'], section='Signal quality') report_filename = os.path.join(subj_path, basename + "-report_NEW.html") print report_filename report.save(report_filename, open_browser=False, overwrite=True) # 3) apply ICA to raw data and save solution and report # check the amplitudes do not change # raw_ica_file = os.path.abspath(basename[:i_raw] + 'ica-raw.fif') raw_ica_file = os.path.join(subj_path, basename + '-preproc-raw.fif') raw_ica = ica.apply(raw) raw_ica.resample(sfreq=down_sfreq, npad=0) raw_ica.save(raw_ica_file, overwrite=True) # save ICA solution print ica_filename ica.save(ica_filename) # 4) save data data_noIca, times = raw[select_sensors, :] data, times = raw_ica[select_sensors, :] print data.shape print raw.info['sfreq'] ts_file = os.path.abspath(basename + '_ica.npy') np.save(ts_file, data) print '*** TS FILE ' + ts_file + '***' print '*** raw.info[sfreq] = ' + str(raw.info['sfreq']) if is_sensor_space: return ts_file, channel_coords_file, channel_names_file, raw.info['sfreq'] else: return raw_ica_file, channel_coords_file, channel_names_file, raw.info['sfreq']
def test_ica_additional(method): """Test additional ICA functionality.""" _skip_check_picard(method) tempdir = _TempDir() stop2 = 500 raw = read_raw_fif(raw_fname).crop(1.5, stop).load_data() raw.del_proj() # avoid warnings raw.set_annotations(Annotations([0.5], [0.5], ['BAD'])) # XXX This breaks the tests :( # raw.info['bads'] = [raw.ch_names[1]] test_cov = read_cov(test_cov_name) events = read_events(event_name) picks = pick_types(raw.info, meg=True, stim=False, ecg=False, eog=False, exclude='bads')[1::2] epochs = Epochs(raw, events, None, tmin, tmax, picks=picks, baseline=(None, 0), preload=True, proj=False) epochs.decimate(3, verbose='error') assert len(epochs) == 4 # test if n_components=None works ica = ICA(n_components=None, max_pca_components=None, n_pca_components=None, random_state=0, method=method, max_iter=1) with pytest.warns(UserWarning, match='did not converge'): ica.fit(epochs) # for testing eog functionality picks2 = np.concatenate([picks, pick_types(raw.info, False, eog=True)]) epochs_eog = Epochs(raw, events[:4], event_id, tmin, tmax, picks=picks2, baseline=(None, 0), preload=True) del picks2 test_cov2 = test_cov.copy() ica = ICA(noise_cov=test_cov2, n_components=3, max_pca_components=4, n_pca_components=4, method=method) assert (ica.info is None) with pytest.warns(RuntimeWarning, match='normalize_proj'): ica.fit(raw, picks[:5]) assert (isinstance(ica.info, Info)) assert (ica.n_components_ < 5) ica = ICA(n_components=3, max_pca_components=4, method=method, n_pca_components=4, random_state=0) pytest.raises(RuntimeError, ica.save, '') ica.fit(raw, picks=[1, 2, 3, 4, 5], start=start, stop=stop2) # check passing a ch_name to find_bads_ecg with pytest.warns(RuntimeWarning, match='longer'): _, scores_1 = ica.find_bads_ecg(raw) _, scores_2 = ica.find_bads_ecg(raw, raw.ch_names[1]) assert scores_1[0] != scores_2[0] # test corrmap ica2 = ica.copy() ica3 = ica.copy() corrmap([ica, ica2], (0, 0), threshold='auto', label='blinks', plot=True, ch_type="mag") corrmap([ica, ica2], (0, 0), threshold=2, plot=False, show=False) assert (ica.labels_["blinks"] == ica2.labels_["blinks"]) assert (0 in ica.labels_["blinks"]) # test retrieval of component maps as arrays components = ica.get_components() template = components[:, 0] EvokedArray(components, ica.info, tmin=0.).plot_topomap([0], time_unit='s') corrmap([ica, ica3], template, threshold='auto', label='blinks', plot=True, ch_type="mag") assert (ica2.labels_["blinks"] == ica3.labels_["blinks"]) plt.close('all') ica_different_channels = ICA(n_components=2, random_state=0).fit( raw, picks=[2, 3, 4, 5]) pytest.raises(ValueError, corrmap, [ica_different_channels, ica], (0, 0)) # test warnings on bad filenames ica_badname = op.join(op.dirname(tempdir), 'test-bad-name.fif.gz') with pytest.warns(RuntimeWarning, match='-ica.fif'): ica.save(ica_badname) with pytest.warns(RuntimeWarning, match='-ica.fif'): read_ica(ica_badname) # test decim ica = ICA(n_components=3, max_pca_components=4, n_pca_components=4, method=method, max_iter=1) raw_ = raw.copy() for _ in range(3): raw_.append(raw_) n_samples = raw_._data.shape[1] with pytest.warns(UserWarning, match='did not converge'): ica.fit(raw, picks=picks[:5], decim=3) assert raw_._data.shape[1] == n_samples # test expl var ica = ICA(n_components=1.0, max_pca_components=4, n_pca_components=4, method=method, max_iter=1) with pytest.warns(UserWarning, match='did not converge'): ica.fit(raw, picks=None, decim=3) assert (ica.n_components_ == 4) ica_var = _ica_explained_variance(ica, raw, normalize=True) assert (np.all(ica_var[:-1] >= ica_var[1:])) # test ica sorting ica.exclude = [0] ica.labels_ = dict(blink=[0], think=[1]) ica_sorted = _sort_components(ica, [3, 2, 1, 0], copy=True) assert_equal(ica_sorted.exclude, [3]) assert_equal(ica_sorted.labels_, dict(blink=[3], think=[2])) # epochs extraction from raw fit pytest.raises(RuntimeError, ica.get_sources, epochs) # test reading and writing test_ica_fname = op.join(op.dirname(tempdir), 'test-ica.fif') for cov in (None, test_cov): ica = ICA(noise_cov=cov, n_components=2, max_pca_components=4, n_pca_components=4, method=method, max_iter=1) with pytest.warns(None): # ICA does not converge ica.fit(raw, picks=picks[:10], start=start, stop=stop2) sources = ica.get_sources(epochs).get_data() assert (ica.mixing_matrix_.shape == (2, 2)) assert (ica.unmixing_matrix_.shape == (2, 2)) assert (ica.pca_components_.shape == (4, 10)) assert (sources.shape[1] == ica.n_components_) for exclude in [[], [0], np.array([1, 2, 3])]: ica.exclude = exclude ica.labels_ = {'foo': [0]} ica.save(test_ica_fname) ica_read = read_ica(test_ica_fname) assert (list(ica.exclude) == ica_read.exclude) assert_equal(ica.labels_, ica_read.labels_) ica.apply(raw) ica.exclude = [] ica.apply(raw, exclude=[1]) assert (ica.exclude == []) ica.exclude = [0, 1] ica.apply(raw, exclude=[1]) assert (ica.exclude == [0, 1]) ica_raw = ica.get_sources(raw) assert (ica.exclude == [ica_raw.ch_names.index(e) for e in ica_raw.info['bads']]) # test filtering d1 = ica_raw._data[0].copy() ica_raw.filter(4, 20, fir_design='firwin2') assert_equal(ica_raw.info['lowpass'], 20.) assert_equal(ica_raw.info['highpass'], 4.) assert ((d1 != ica_raw._data[0]).any()) d1 = ica_raw._data[0].copy() ica_raw.notch_filter([10], trans_bandwidth=10, fir_design='firwin') assert ((d1 != ica_raw._data[0]).any()) ica.n_pca_components = 2 ica.method = 'fake' ica.save(test_ica_fname) ica_read = read_ica(test_ica_fname) assert (ica.n_pca_components == ica_read.n_pca_components) assert_equal(ica.method, ica_read.method) assert_equal(ica.labels_, ica_read.labels_) # check type consistency attrs = ('mixing_matrix_ unmixing_matrix_ pca_components_ ' 'pca_explained_variance_ pre_whitener_') def f(x, y): return getattr(x, y).dtype for attr in attrs.split(): assert_equal(f(ica_read, attr), f(ica, attr)) ica.n_pca_components = 4 ica_read.n_pca_components = 4 ica.exclude = [] ica.save(test_ica_fname) ica_read = read_ica(test_ica_fname) for attr in ['mixing_matrix_', 'unmixing_matrix_', 'pca_components_', 'pca_mean_', 'pca_explained_variance_', 'pre_whitener_']: assert_array_almost_equal(getattr(ica, attr), getattr(ica_read, attr)) assert (ica.ch_names == ica_read.ch_names) assert (isinstance(ica_read.info, Info)) sources = ica.get_sources(raw)[:, :][0] sources2 = ica_read.get_sources(raw)[:, :][0] assert_array_almost_equal(sources, sources2) _raw1 = ica.apply(raw, exclude=[1]) _raw2 = ica_read.apply(raw, exclude=[1]) assert_array_almost_equal(_raw1[:, :][0], _raw2[:, :][0]) os.remove(test_ica_fname) # check score funcs for name, func in get_score_funcs().items(): if name in score_funcs_unsuited: continue scores = ica.score_sources(raw, target='EOG 061', score_func=func, start=0, stop=10) assert (ica.n_components_ == len(scores)) # check univariate stats scores = ica.score_sources(raw, start=0, stop=50, score_func=stats.skew) # check exception handling pytest.raises(ValueError, ica.score_sources, raw, target=np.arange(1)) params = [] params += [(None, -1, slice(2), [0, 1])] # variance, kurtosis params params += [(None, 'MEG 1531')] # ECG / EOG channel params for idx, ch_name in product(*params): ica.detect_artifacts(raw, start_find=0, stop_find=50, ecg_ch=ch_name, eog_ch=ch_name, skew_criterion=idx, var_criterion=idx, kurt_criterion=idx) # Make sure detect_artifacts marks the right components. # For int criterion, the doc says "E.g. range(2) would return the two # sources with the highest score". Assert that's what it does. # Only test for skew, since it's always the same code. ica.exclude = [] ica.detect_artifacts(raw, start_find=0, stop_find=50, ecg_ch=None, eog_ch=None, skew_criterion=0, var_criterion=None, kurt_criterion=None) assert np.abs(scores[ica.exclude]) == np.max(np.abs(scores)) evoked = epochs.average() evoked_data = evoked.data.copy() raw_data = raw[:][0].copy() epochs_data = epochs.get_data().copy() with pytest.warns(RuntimeWarning, match='longer'): idx, scores = ica.find_bads_ecg(raw, method='ctps') assert_equal(len(scores), ica.n_components_) with pytest.warns(RuntimeWarning, match='longer'): idx, scores = ica.find_bads_ecg(raw, method='correlation') assert_equal(len(scores), ica.n_components_) with pytest.warns(RuntimeWarning, match='longer'): idx, scores = ica.find_bads_eog(raw) assert_equal(len(scores), ica.n_components_) idx, scores = ica.find_bads_ecg(epochs, method='ctps') assert_equal(len(scores), ica.n_components_) pytest.raises(ValueError, ica.find_bads_ecg, epochs.average(), method='ctps') pytest.raises(ValueError, ica.find_bads_ecg, raw, method='crazy-coupling') with pytest.warns(RuntimeWarning, match='longer'): idx, scores = ica.find_bads_eog(raw) assert_equal(len(scores), ica.n_components_) raw.info['chs'][raw.ch_names.index('EOG 061') - 1]['kind'] = 202 with pytest.warns(RuntimeWarning, match='longer'): idx, scores = ica.find_bads_eog(raw) assert (isinstance(scores, list)) assert_equal(len(scores[0]), ica.n_components_) idx, scores = ica.find_bads_eog(evoked, ch_name='MEG 1441') assert_equal(len(scores), ica.n_components_) idx, scores = ica.find_bads_ecg(evoked, method='correlation') assert_equal(len(scores), ica.n_components_) assert_array_equal(raw_data, raw[:][0]) assert_array_equal(epochs_data, epochs.get_data()) assert_array_equal(evoked_data, evoked.data) # check score funcs for name, func in get_score_funcs().items(): if name in score_funcs_unsuited: continue scores = ica.score_sources(epochs_eog, target='EOG 061', score_func=func) assert (ica.n_components_ == len(scores)) # check univariate stats scores = ica.score_sources(epochs, score_func=stats.skew) # check exception handling pytest.raises(ValueError, ica.score_sources, epochs, target=np.arange(1)) # ecg functionality ecg_scores = ica.score_sources(raw, target='MEG 1531', score_func='pearsonr') with pytest.warns(RuntimeWarning, match='longer'): ecg_events = ica_find_ecg_events( raw, sources[np.abs(ecg_scores).argmax()]) assert (ecg_events.ndim == 2) # eog functionality eog_scores = ica.score_sources(raw, target='EOG 061', score_func='pearsonr') with pytest.warns(RuntimeWarning, match='longer'): eog_events = ica_find_eog_events( raw, sources[np.abs(eog_scores).argmax()]) assert (eog_events.ndim == 2) # Test ica fiff export ica_raw = ica.get_sources(raw, start=0, stop=100) assert (ica_raw.last_samp - ica_raw.first_samp == 100) assert_equal(len(ica_raw._filenames), 1) # API consistency ica_chans = [ch for ch in ica_raw.ch_names if 'ICA' in ch] assert (ica.n_components_ == len(ica_chans)) test_ica_fname = op.join(op.abspath(op.curdir), 'test-ica_raw.fif') ica.n_components = np.int32(ica.n_components) ica_raw.save(test_ica_fname, overwrite=True) ica_raw2 = read_raw_fif(test_ica_fname, preload=True) assert_allclose(ica_raw._data, ica_raw2._data, rtol=1e-5, atol=1e-4) ica_raw2.close() os.remove(test_ica_fname) # Test ica epochs export ica_epochs = ica.get_sources(epochs) assert (ica_epochs.events.shape == epochs.events.shape) ica_chans = [ch for ch in ica_epochs.ch_names if 'ICA' in ch] assert (ica.n_components_ == len(ica_chans)) assert (ica.n_components_ == ica_epochs.get_data().shape[1]) assert (ica_epochs._raw is None) assert (ica_epochs.preload is True) # test float n pca components ica.pca_explained_variance_ = np.array([0.2] * 5) ica.n_components_ = 0 for ncomps, expected in [[0.3, 1], [0.9, 4], [1, 1]]: ncomps_ = ica._check_n_pca_components(ncomps) assert (ncomps_ == expected) ica = ICA(method=method) with pytest.warns(None): # sometimes does not converge ica.fit(raw, picks=picks[:5]) with pytest.warns(RuntimeWarning, match='longer'): ica.find_bads_ecg(raw) ica.find_bads_eog(epochs, ch_name='MEG 0121') assert_array_equal(raw_data, raw[:][0]) raw.drop_channels(['MEG 0122']) pytest.raises(RuntimeError, ica.find_bads_eog, raw) with pytest.warns(RuntimeWarning, match='longer'): pytest.raises(RuntimeError, ica.find_bads_ecg, raw)
def preprocess_ICA_fif_to_ts(fif_file, ECG_ch_name, EoG_ch_name, l_freq, h_freq, down_sfreq, variance, is_sensor_space, data_type): import os import numpy as np import mne from mne.io import Raw from mne.preprocessing import ICA, read_ica from mne.preprocessing import create_ecg_epochs, create_eog_epochs from mne.report import Report from nipype.utils.filemanip import split_filename as split_f report = Report() subj_path, basename, ext = split_f(fif_file) (data_path, sbj_name) = os.path.split(subj_path) print data_path # Read raw # If None the compensation in the data is not modified. # If set to n, e.g. 3, apply gradient compensation of grade n as for # CTF systems (compensation=3) raw = Raw(fif_file, preload=True) # select sensors select_sensors = mne.pick_types(raw.info, meg=True, ref_meg=False, exclude='bads') picks_meeg = mne.pick_types(raw.info, meg=True, eeg=True, exclude='bads') # save electrode locations sens_loc = [raw.info['chs'][i]['loc'][:3] for i in select_sensors] sens_loc = np.array(sens_loc) channel_coords_file = os.path.abspath("correct_channel_coords.txt") print '*** ' + channel_coords_file + '***' np.savetxt(channel_coords_file, sens_loc, fmt='%s') # save electrode names sens_names = np.array([raw.ch_names[pos] for pos in select_sensors],dtype = "str") # AP 21032016 # channel_names_file = os.path.join(data_path, "correct_channel_names.txt") channel_names_file = os.path.abspath("correct_channel_names.txt") np.savetxt(channel_names_file,sens_names , fmt = '%s') ### filtering + downsampling raw.filter(l_freq=l_freq, h_freq=h_freq, picks=picks_meeg, method='iir', n_jobs=8) # raw.filter(l_freq = l_freq, h_freq = h_freq, picks = picks_meeg, # method='iir') # raw.resample(sfreq=down_sfreq, npad=0) ### 1) Fit ICA model using the FastICA algorithm # Other available choices are `infomax` or `extended-infomax` # We pass a float value between 0 and 1 to select n_components based on the # percentage of variance explained by the PCA components. ICA_title = 'Sources related to %s artifacts (red)' is_show = False # visualization reject = dict(mag=4e-12, grad=4000e-13) # check if we have an ICA, if yes, we load it ica_filename = os.path.join(subj_path,basename + "-ica.fif") if os.path.exists(ica_filename) is False: ica = ICA(n_components=variance, method='fastica', max_iter=500) # , max_iter=500 ica.fit(raw, picks=select_sensors, reject=reject) # decim = 3, has_ICA = False else: has_ICA = True print ica_filename + ' exists!!!' ica = read_ica(ica_filename) ica.exclude = [] # 2) identify bad components by analyzing latent sources. # generate ECG epochs use detection via phase statistics # if we just have exclude channels we jump these steps # if len(ica.exclude)==0: n_max_ecg = 3 n_max_eog = 2 # check if ECG_ch_name is in the raw channels if ECG_ch_name in raw.info['ch_names']: ecg_epochs = create_ecg_epochs(raw, tmin=-.5, tmax=.5, picks=select_sensors, ch_name=ECG_ch_name) # if not a synthetic ECG channel is created from cross channel average else: ecg_epochs = create_ecg_epochs(raw, tmin=-.5, tmax=.5, picks=select_sensors) # ICA for ECG artifact # threshold=0.25 come default ecg_inds, scores = ica.find_bads_ecg(ecg_epochs, method='ctps') print scores print '\n len ecg_inds *** ' + str(len(ecg_inds)) + '***\n' if len(ecg_inds) > 0: ecg_evoked = ecg_epochs.average() fig1 = ica.plot_scores(scores, exclude=ecg_inds, title=ICA_title % 'ecg', show=is_show) show_picks = np.abs(scores).argsort()[::-1][:5] # Pick the five largest scores and plot them # Plot estimated latent sources given the unmixing matrix. #ica.plot_sources(raw, show_picks, exclude=ecg_inds, title=ICA_title % 'ecg', show=is_show) t_start = 0 t_stop = 30 # take the fist 30s fig2 = ica.plot_sources(raw, show_picks, exclude=ecg_inds, title=ICA_title % 'ecg' + ' in 30s' ,start = t_start, stop = t_stop, show=is_show) # topoplot of unmixing matrix columns fig3 = ica.plot_components(show_picks, title=ICA_title % 'ecg', colorbar=True, show=is_show) ecg_inds = ecg_inds[:n_max_ecg] ica.exclude += ecg_inds fig4 = ica.plot_sources(ecg_evoked, exclude=ecg_inds, show=is_show) # plot ECG sources + selection fig5 = ica.plot_overlay(ecg_evoked, exclude=ecg_inds, show=is_show) # plot ECG cleaning fig = [fig1, fig2, fig3, fig4, fig5] report.add_figs_to_section(fig, captions=['Scores of ICs related to ECG', 'Time Series plots of ICs (ECG)', 'TopoMap of ICs (ECG)', 'Time-locked ECG sources', 'ECG overlay'], section = 'ICA - ECG') # check if EoG_ch_name is in the raw channels # if EoG_ch_name is empty if data_type is fif, ICA routine automatically looks for EEG61, EEG62 # otherwise if data_type is ds we jump this step if not EoG_ch_name and data_type=='ds': eog_inds = [] else: if EoG_ch_name in raw.info['ch_names']: ### ICA for eye blink artifact - detect EOG by correlation eog_inds, scores = ica.find_bads_eog(raw, ch_name = EoG_ch_name) else: eog_inds, scores = ica.find_bads_eog(raw) if len(eog_inds) > 0: fig6 = ica.plot_scores(scores, exclude=eog_inds, title=ICA_title % 'eog', show=is_show) report.add_figs_to_section(fig6, captions=['Scores of ICs related to EOG'], section = 'ICA - EOG') # check how many EoG ch we have rs = np.shape(scores) if len(rs)>1: rr = rs[0] show_picks = [np.abs(scores[i][:]).argsort()[::-1][:5] for i in range(rr)] for i in range(rr): fig7 = ica.plot_sources(raw, show_picks[i][:], exclude=eog_inds, start = raw.times[0], stop = raw.times[-1], title=ICA_title % 'eog',show=is_show) fig8 = ica.plot_components(show_picks[i][:], title=ICA_title % 'eog', colorbar=True, show=is_show) # ICA nel tempo fig = [fig7, fig8] report.add_figs_to_section(fig, captions=['Scores of ICs related to EOG', 'Time Series plots of ICs (EOG)'], section = 'ICA - EOG') else: show_picks = np.abs(scores).argsort()[::-1][:5] fig7 = ica.plot_sources(raw, show_picks, exclude=eog_inds, title=ICA_title % 'eog', show=is_show) fig8 = ica.plot_components(show_picks, title=ICA_title % 'eog', colorbar=True, show=is_show) fig = [fig7, fig8] report.add_figs_to_section(fig, captions=['Time Series plots of ICs (EOG)', 'TopoMap of ICs (EOG)',], section = 'ICA - EOG') eog_inds = eog_inds[:n_max_eog] ica.exclude += eog_inds if EoG_ch_name in raw.info['ch_names']: eog_evoked = create_eog_epochs(raw, tmin=-.5, tmax=.5, picks=select_sensors, ch_name=EoG_ch_name).average() else: eog_evoked = create_eog_epochs(raw, tmin=-.5, tmax=.5, picks=select_sensors).average() fig9 = ica.plot_sources(eog_evoked, exclude=eog_inds, show=is_show) # plot EOG sources + selection fig10 = ica.plot_overlay(eog_evoked, exclude=eog_inds, show=is_show) # plot EOG cleaning fig = [fig9, fig10] report.add_figs_to_section(fig, captions=['Time-locked EOG sources', 'EOG overlay'], section = 'ICA - EOG') fig11 = ica.plot_overlay(raw, show=is_show) report.add_figs_to_section(fig11, captions=['Signal'], section = 'Signal quality') ### plot all topographies and time seris of the ICA components n_ica_components = ica.mixing_matrix_.shape[1] n_topo = 10; n_fig = n_ica_components/n_topo; n_plot = n_ica_components%n_topo; print '*************** n_fig = ' + str(n_fig) + ' n_plot = ' + str(n_plot) + '********************' fig = [] t_start = 0 t_stop = None # 60 if we want to take the fist 60s for n in range(0,n_fig): fig_tmp = ica.plot_components(range(n_topo*n,n_topo*(n+1)),title='ICA components', show=is_show) fig.append(fig_tmp) fig_tmp = ica.plot_sources(raw, range(n_topo*n,n_topo*(n+1)), start = t_start, stop = t_stop, title='ICA components') fig.append(fig_tmp) # if n_plot > 0: # fig_tmp = ica.plot_components(range(n_fig*n_topo,n_ica_components), title='ICA components', show=is_show) # fig.append(fig_tmp) # fig_tmp = ica.plot_sources(raw, range(n_fig*n_topo,n_ica_components), # start = t_start, stop = t_stop, # title='ICA components') # fig.append(fig_tmp) # # for n in range(0, len(fig)): # report.add_figs_to_section(fig[n], captions=['TOPO'], section = 'ICA Topo Maps') if n_plot > 5: n_fig_l = n_plot//5 print '*************************** ' + str(n_fig_l) + ' *********************************' for n in range(0,n_fig_l): print range(n_fig*n_topo+5*n, n_fig*n_topo+5*(n+1)) fig_tmp = ica.plot_components(range(n_fig*n_topo+5*n, n_fig*n_topo+5*(n+1)),title='ICA components') fig.append(fig_tmp) fig_tmp = ica.plot_sources(raw, range(n_fig*n_topo+5*n, n_fig*n_topo+5*(n+1)), start = t_start, stop = t_stop, title='ICA components') fig.append(fig_tmp) print range(n_fig*n_topo+5*(n+1),n_ica_components) fig_tmp = ica.plot_components(range(n_fig*n_topo+5*(n+1),n_ica_components), title='ICA components') fig.append(fig_tmp) fig_tmp = ica.plot_sources(raw, range(n_fig*n_topo+5*(n+1),n_ica_components), start = t_start, stop = t_stop, title='ICA components') fig.append(fig_tmp) for n in range(0, len(fig)): report.add_figs_to_section(fig[n], captions=['TOPO'], section = 'ICA Topo Maps') report_filename = os.path.join(subj_path,basename + "-report.html") print '******* ' + report_filename report.save(report_filename, open_browser=False, overwrite=True) # 3) apply ICA to raw data and save solution and report # check the amplitudes do not change # raw_ica_file = os.path.abspath(basename[:i_raw] + 'ica-raw.fif') raw_ica_file = os.path.join(subj_path, basename + '-preproc-raw.fif') raw_ica = ica.apply(raw) raw_ica.resample(sfreq=down_sfreq, npad=0) raw_ica.save(raw_ica_file, overwrite=True) # save ICA solution print ica_filename if has_ICA is False: ica.save(ica_filename) # 4) save data data_noIca, times = raw[select_sensors, :] data, times = raw_ica[select_sensors, :] print data.shape print raw.info['sfreq'] ts_file = os.path.abspath(basename + "_ica.npy") np.save(ts_file, data) print '***** TS FILE ' + ts_file + '*****' if is_sensor_space: return ts_file, channel_coords_file, channel_names_file, raw.info['sfreq'] else: # return raw_ica, channel_coords_file, channel_names_file, raw.info['sfreq'] return raw_ica_file, channel_coords_file, channel_names_file, raw.info['sfreq']
def test_ica_additional(method): """Test additional ICA functionality.""" _skip_check_picard(method) tempdir = _TempDir() stop2 = 500 raw = read_raw_fif(raw_fname).crop(1.5, stop).load_data() raw.del_proj() # avoid warnings raw.set_annotations(Annotations([0.5], [0.5], ['BAD'])) # XXX This breaks the tests :( # raw.info['bads'] = [raw.ch_names[1]] test_cov = read_cov(test_cov_name) events = read_events(event_name) picks = pick_types(raw.info, meg=True, stim=False, ecg=False, eog=False, exclude='bads')[1::2] epochs = Epochs(raw, events, None, tmin, tmax, picks=picks, baseline=(None, 0), preload=True, proj=False) epochs.decimate(3, verbose='error') assert len(epochs) == 4 # test if n_components=None works ica = ICA(n_components=None, max_pca_components=None, n_pca_components=None, random_state=0, method=method, max_iter=1) with pytest.warns(UserWarning, match='did not converge'): ica.fit(epochs) # for testing eog functionality picks2 = np.concatenate([picks, pick_types(raw.info, False, eog=True)]) epochs_eog = Epochs(raw, events[:4], event_id, tmin, tmax, picks=picks2, baseline=(None, 0), preload=True) del picks2 test_cov2 = test_cov.copy() ica = ICA(noise_cov=test_cov2, n_components=3, max_pca_components=4, n_pca_components=4, method=method) assert (ica.info is None) with pytest.warns(RuntimeWarning, match='normalize_proj'): ica.fit(raw, picks[:5]) assert (isinstance(ica.info, Info)) assert (ica.n_components_ < 5) ica = ICA(n_components=3, max_pca_components=4, method=method, n_pca_components=4, random_state=0) pytest.raises(RuntimeError, ica.save, '') ica.fit(raw, picks=[1, 2, 3, 4, 5], start=start, stop=stop2) # check passing a ch_name to find_bads_ecg with pytest.warns(RuntimeWarning, match='longer'): _, scores_1 = ica.find_bads_ecg(raw) _, scores_2 = ica.find_bads_ecg(raw, raw.ch_names[1]) assert scores_1[0] != scores_2[0] # test corrmap ica2 = ica.copy() ica3 = ica.copy() corrmap([ica, ica2], (0, 0), threshold='auto', label='blinks', plot=True, ch_type="mag") corrmap([ica, ica2], (0, 0), threshold=2, plot=False, show=False) assert (ica.labels_["blinks"] == ica2.labels_["blinks"]) assert (0 in ica.labels_["blinks"]) # test retrieval of component maps as arrays components = ica.get_components() template = components[:, 0] EvokedArray(components, ica.info, tmin=0.).plot_topomap([0], time_unit='s') corrmap([ica, ica3], template, threshold='auto', label='blinks', plot=True, ch_type="mag") assert (ica2.labels_["blinks"] == ica3.labels_["blinks"]) plt.close('all') # make sure a single threshold in a list works corrmap([ica, ica3], template, threshold=[0.5], label='blinks', plot=True, ch_type="mag") ica_different_channels = ICA(n_components=2, random_state=0).fit(raw, picks=[2, 3, 4, 5]) pytest.raises(ValueError, corrmap, [ica_different_channels, ica], (0, 0)) # test warnings on bad filenames ica_badname = op.join(op.dirname(tempdir), 'test-bad-name.fif.gz') with pytest.warns(RuntimeWarning, match='-ica.fif'): ica.save(ica_badname) with pytest.warns(RuntimeWarning, match='-ica.fif'): read_ica(ica_badname) # test decim ica = ICA(n_components=3, max_pca_components=4, n_pca_components=4, method=method, max_iter=1) raw_ = raw.copy() for _ in range(3): raw_.append(raw_) n_samples = raw_._data.shape[1] with pytest.warns(UserWarning, match='did not converge'): ica.fit(raw, picks=picks[:5], decim=3) assert raw_._data.shape[1] == n_samples # test expl var ica = ICA(n_components=1.0, max_pca_components=4, n_pca_components=4, method=method, max_iter=1) with pytest.warns(UserWarning, match='did not converge'): ica.fit(raw, picks=None, decim=3) assert (ica.n_components_ == 4) ica_var = _ica_explained_variance(ica, raw, normalize=True) assert (np.all(ica_var[:-1] >= ica_var[1:])) # test ica sorting ica.exclude = [0] ica.labels_ = dict(blink=[0], think=[1]) ica_sorted = _sort_components(ica, [3, 2, 1, 0], copy=True) assert_equal(ica_sorted.exclude, [3]) assert_equal(ica_sorted.labels_, dict(blink=[3], think=[2])) # epochs extraction from raw fit pytest.raises(RuntimeError, ica.get_sources, epochs) # test reading and writing test_ica_fname = op.join(op.dirname(tempdir), 'test-ica.fif') for cov in (None, test_cov): ica = ICA(noise_cov=cov, n_components=2, max_pca_components=4, n_pca_components=4, method=method, max_iter=1) with pytest.warns(None): # ICA does not converge ica.fit(raw, picks=picks[:10], start=start, stop=stop2) sources = ica.get_sources(epochs).get_data() assert (ica.mixing_matrix_.shape == (2, 2)) assert (ica.unmixing_matrix_.shape == (2, 2)) assert (ica.pca_components_.shape == (4, 10)) assert (sources.shape[1] == ica.n_components_) for exclude in [[], [0], np.array([1, 2, 3])]: ica.exclude = exclude ica.labels_ = {'foo': [0]} ica.save(test_ica_fname) ica_read = read_ica(test_ica_fname) assert (list(ica.exclude) == ica_read.exclude) assert_equal(ica.labels_, ica_read.labels_) ica.apply(raw) ica.exclude = [] ica.apply(raw, exclude=[1]) assert (ica.exclude == []) ica.exclude = [0, 1] ica.apply(raw, exclude=[1]) assert (ica.exclude == [0, 1]) ica_raw = ica.get_sources(raw) assert (ica.exclude == [ ica_raw.ch_names.index(e) for e in ica_raw.info['bads'] ]) # test filtering d1 = ica_raw._data[0].copy() ica_raw.filter(4, 20, fir_design='firwin2') assert_equal(ica_raw.info['lowpass'], 20.) assert_equal(ica_raw.info['highpass'], 4.) assert ((d1 != ica_raw._data[0]).any()) d1 = ica_raw._data[0].copy() ica_raw.notch_filter([10], trans_bandwidth=10, fir_design='firwin') assert ((d1 != ica_raw._data[0]).any()) ica.n_pca_components = 2 ica.method = 'fake' ica.save(test_ica_fname) ica_read = read_ica(test_ica_fname) assert (ica.n_pca_components == ica_read.n_pca_components) assert_equal(ica.method, ica_read.method) assert_equal(ica.labels_, ica_read.labels_) # check type consistency attrs = ('mixing_matrix_ unmixing_matrix_ pca_components_ ' 'pca_explained_variance_ pre_whitener_') def f(x, y): return getattr(x, y).dtype for attr in attrs.split(): assert_equal(f(ica_read, attr), f(ica, attr)) ica.n_pca_components = 4 ica_read.n_pca_components = 4 ica.exclude = [] ica.save(test_ica_fname) ica_read = read_ica(test_ica_fname) for attr in [ 'mixing_matrix_', 'unmixing_matrix_', 'pca_components_', 'pca_mean_', 'pca_explained_variance_', 'pre_whitener_' ]: assert_array_almost_equal(getattr(ica, attr), getattr(ica_read, attr)) assert (ica.ch_names == ica_read.ch_names) assert (isinstance(ica_read.info, Info)) sources = ica.get_sources(raw)[:, :][0] sources2 = ica_read.get_sources(raw)[:, :][0] assert_array_almost_equal(sources, sources2) _raw1 = ica.apply(raw, exclude=[1]) _raw2 = ica_read.apply(raw, exclude=[1]) assert_array_almost_equal(_raw1[:, :][0], _raw2[:, :][0]) os.remove(test_ica_fname) # check score funcs for name, func in get_score_funcs().items(): if name in score_funcs_unsuited: continue scores = ica.score_sources(raw, target='EOG 061', score_func=func, start=0, stop=10) assert (ica.n_components_ == len(scores)) # check univariate stats scores = ica.score_sources(raw, start=0, stop=50, score_func=stats.skew) # check exception handling pytest.raises(ValueError, ica.score_sources, raw, target=np.arange(1)) params = [] params += [(None, -1, slice(2), [0, 1])] # variance, kurtosis params params += [(None, 'MEG 1531')] # ECG / EOG channel params for idx, ch_name in product(*params): ica.detect_artifacts(raw, start_find=0, stop_find=50, ecg_ch=ch_name, eog_ch=ch_name, skew_criterion=idx, var_criterion=idx, kurt_criterion=idx) # Make sure detect_artifacts marks the right components. # For int criterion, the doc says "E.g. range(2) would return the two # sources with the highest score". Assert that's what it does. # Only test for skew, since it's always the same code. ica.exclude = [] ica.detect_artifacts(raw, start_find=0, stop_find=50, ecg_ch=None, eog_ch=None, skew_criterion=0, var_criterion=None, kurt_criterion=None) assert np.abs(scores[ica.exclude]) == np.max(np.abs(scores)) evoked = epochs.average() evoked_data = evoked.data.copy() raw_data = raw[:][0].copy() epochs_data = epochs.get_data().copy() with pytest.warns(RuntimeWarning, match='longer'): idx, scores = ica.find_bads_ecg(raw, method='ctps') assert_equal(len(scores), ica.n_components_) with pytest.warns(RuntimeWarning, match='longer'): idx, scores = ica.find_bads_ecg(raw, method='correlation') assert_equal(len(scores), ica.n_components_) with pytest.warns(RuntimeWarning, match='longer'): idx, scores = ica.find_bads_eog(raw) assert_equal(len(scores), ica.n_components_) idx, scores = ica.find_bads_ecg(epochs, method='ctps') assert_equal(len(scores), ica.n_components_) pytest.raises(ValueError, ica.find_bads_ecg, epochs.average(), method='ctps') pytest.raises(ValueError, ica.find_bads_ecg, raw, method='crazy-coupling') with pytest.warns(RuntimeWarning, match='longer'): idx, scores = ica.find_bads_eog(raw) assert_equal(len(scores), ica.n_components_) raw.info['chs'][raw.ch_names.index('EOG 061') - 1]['kind'] = 202 with pytest.warns(RuntimeWarning, match='longer'): idx, scores = ica.find_bads_eog(raw) assert (isinstance(scores, list)) assert_equal(len(scores[0]), ica.n_components_) idx, scores = ica.find_bads_eog(evoked, ch_name='MEG 1441') assert_equal(len(scores), ica.n_components_) idx, scores = ica.find_bads_ecg(evoked, method='correlation') assert_equal(len(scores), ica.n_components_) assert_array_equal(raw_data, raw[:][0]) assert_array_equal(epochs_data, epochs.get_data()) assert_array_equal(evoked_data, evoked.data) # check score funcs for name, func in get_score_funcs().items(): if name in score_funcs_unsuited: continue scores = ica.score_sources(epochs_eog, target='EOG 061', score_func=func) assert (ica.n_components_ == len(scores)) # check univariate stats scores = ica.score_sources(epochs, score_func=stats.skew) # check exception handling pytest.raises(ValueError, ica.score_sources, epochs, target=np.arange(1)) # ecg functionality ecg_scores = ica.score_sources(raw, target='MEG 1531', score_func='pearsonr') with pytest.warns(RuntimeWarning, match='longer'): ecg_events = ica_find_ecg_events(raw, sources[np.abs(ecg_scores).argmax()]) assert (ecg_events.ndim == 2) # eog functionality eog_scores = ica.score_sources(raw, target='EOG 061', score_func='pearsonr') with pytest.warns(RuntimeWarning, match='longer'): eog_events = ica_find_eog_events(raw, sources[np.abs(eog_scores).argmax()]) assert (eog_events.ndim == 2) # Test ica fiff export ica_raw = ica.get_sources(raw, start=0, stop=100) assert (ica_raw.last_samp - ica_raw.first_samp == 100) assert_equal(len(ica_raw._filenames), 1) # API consistency ica_chans = [ch for ch in ica_raw.ch_names if 'ICA' in ch] assert (ica.n_components_ == len(ica_chans)) test_ica_fname = op.join(op.abspath(op.curdir), 'test-ica_raw.fif') ica.n_components = np.int32(ica.n_components) ica_raw.save(test_ica_fname, overwrite=True) ica_raw2 = read_raw_fif(test_ica_fname, preload=True) assert_allclose(ica_raw._data, ica_raw2._data, rtol=1e-5, atol=1e-4) ica_raw2.close() os.remove(test_ica_fname) # Test ica epochs export ica_epochs = ica.get_sources(epochs) assert (ica_epochs.events.shape == epochs.events.shape) ica_chans = [ch for ch in ica_epochs.ch_names if 'ICA' in ch] assert (ica.n_components_ == len(ica_chans)) assert (ica.n_components_ == ica_epochs.get_data().shape[1]) assert (ica_epochs._raw is None) assert (ica_epochs.preload is True) # test float n pca components ica.pca_explained_variance_ = np.array([0.2] * 5) ica.n_components_ = 0 for ncomps, expected in [[0.3, 1], [0.9, 4], [1, 1]]: ncomps_ = ica._check_n_pca_components(ncomps) assert (ncomps_ == expected) ica = ICA(method=method) with pytest.warns(None): # sometimes does not converge ica.fit(raw, picks=picks[:5]) with pytest.warns(RuntimeWarning, match='longer'): ica.find_bads_ecg(raw) ica.find_bads_eog(epochs, ch_name='MEG 0121') assert_array_equal(raw_data, raw[:][0]) raw.drop_channels(['MEG 0122']) pytest.raises(RuntimeError, ica.find_bads_eog, raw) with pytest.warns(RuntimeWarning, match='longer'): pytest.raises(RuntimeError, ica.find_bads_ecg, raw)
def apply_ica(subject): print("Processing subject: %s" % subject) meg_subject_dir = op.join(config.meg_dir, subject) # load epochs to reject ICA components extension = '-epo' fname_in = op.join(meg_subject_dir, config.base_fname.format(**locals())) epochs = mne.read_epochs(fname_in, preload=True) extension = '_cleaned-epo' fname_out = op.join(meg_subject_dir, config.base_fname.format(**locals())) print("Input: ", fname_in) print("Output: ", fname_out) # load first run of raw data for ecg /eog epochs raw_list = list() print(" Loading one run from raw data") extension = config.runs[0] + '_sss_raw' raw_fname_in = op.join(meg_subject_dir, config.base_fname.format(**locals())) raw = mne.io.read_raw_fif(raw_fname_in, preload=True) # run ICA on MEG and EEG picks_meg = mne.pick_types(raw.info, meg=True, eeg=False, eog=False, stim=False, exclude='bads') picks_eeg = mne.pick_types(raw.info, meg=False, eeg=True, eog=False, stim=False, exclude='bads') all_picks = {'meg': picks_meg, 'eeg': picks_eeg} ch_types = [] if 'eeg' in config.ch_types: ch_types.append('eeg') if set(config.ch_types).intersection(('meg', 'grad', 'mag')): ch_types.append('meg') for ch_type in ch_types: print(ch_type) picks = all_picks[ch_type] # Load ICA fname_ica = op.join( meg_subject_dir, '{0}_{1}_{2}-ica.fif'.format(subject, config.study_name, ch_type)) print('Reading ICA: ' + fname_ica) ica = read_ica(fname=fname_ica) pick_ecg = mne.pick_types(raw.info, meg=False, eeg=False, ecg=True, eog=False) # ECG # either needs an ecg channel, or avg of the mags (i.e. MEG data) if pick_ecg or ch_type == 'meg': picks_ecg = np.concatenate([picks, pick_ecg]) # Create ecg epochs if ch_type == 'meg': reject = { 'mag': config.reject['mag'], 'grad': config.reject['grad'] } elif ch_type == 'eeg': reject = {'eeg': config.reject['eeg']} ecg_epochs = create_ecg_epochs(raw, picks=picks_ecg, reject=reject, baseline=(None, 0), tmin=-0.5, tmax=0.5) ecg_average = ecg_epochs.average() ecg_inds, scores = \ ica.find_bads_ecg(ecg_epochs, method='ctps', threshold=config.ica_ctps_ecg_threshold) del ecg_epochs report_fname = \ '{0}_{1}_{2}-reject_ica.html'.format(subject, config.study_name, ch_type) report_fname = op.join(meg_subject_dir, report_fname) report = Report(report_fname, verbose=False) # Plot r score report.add_figs_to_section(ica.plot_scores(scores, exclude=ecg_inds, show=config.plot), captions=ch_type.upper() + ' - ECG - ' + 'R scores') # Plot source time course report.add_figs_to_section(ica.plot_sources(ecg_average, exclude=ecg_inds, show=config.plot), captions=ch_type.upper() + ' - ECG - ' + 'Sources time course') # Plot source time course report.add_figs_to_section(ica.plot_overlay(ecg_average, exclude=ecg_inds, show=config.plot), captions=ch_type.upper() + ' - ECG - ' + 'Corrections') else: # XXX : to check when EEG only is processed print('no ECG channel is present. Cannot automate ICAs component ' 'detection for EOG!') # EOG pick_eog = mne.pick_types(raw.info, meg=False, eeg=False, ecg=False, eog=True) if pick_eog.any(): print('using EOG channel') picks_eog = np.concatenate([picks, pick_eog]) # Create eog epochs eog_epochs = create_eog_epochs(raw, picks=picks_eog, reject=None, baseline=(None, 0), tmin=-0.5, tmax=0.5) eog_average = eog_epochs.average() eog_inds, scores = ica.find_bads_eog(eog_epochs, threshold=3.0) del eog_epochs params = dict(exclude=eog_inds, show=config.plot) # Plot r score report.add_figs_to_section(ica.plot_scores(scores, **params), captions=ch_type.upper() + ' - EOG - ' + 'R scores') # Plot source time course report.add_figs_to_section(ica.plot_sources(eog_average, **params), captions=ch_type.upper() + ' - EOG - ' + 'Sources time course') # Plot source time course report.add_figs_to_section(ica.plot_overlay(eog_average, **params), captions=ch_type.upper() + ' - EOG - ' + 'Corrections') report.save(report_fname, overwrite=True, open_browser=False) else: print('no EOG channel is present. Cannot automate ICAs component ' 'detection for EOG!') ica_reject = (list(ecg_inds) + list(eog_inds) + list(config.rejcomps_man[subject][ch_type])) # now reject the components print('Rejecting from %s: %s' % (ch_type, ica_reject)) epochs = ica.apply(epochs, exclude=ica_reject) print('Saving cleaned epochs') epochs.save(fname_out) fig = ica.plot_overlay(raw, exclude=ica_reject, show=config.plot) report.add_figs_to_section(fig, captions=ch_type.upper() + ' - ALL(epochs) - Corrections') if config.plot: epochs.plot_image(combine='gfp', group_by='type', sigma=2., cmap="YlGnBu_r", show=config.plot)
#noise_cov_er.save(empty_room_fname[:-4]+'-cov.fif') ############################################################################### # 1) Fit ICA model using the FastICA algorithm # Other available choices are `infomax` or `extended-infomax` # We pass a float value between 0 and 1 to select n_components based on the # percentage of variance explained by the PCA components. raw = Raw(raw_fname, preload=True) picks = mne.pick_types(raw.info, meg=True, eeg=False, eog=False, ecg=False, stim=False, exclude='bads') # maximum number of components to reject n_max_ecg, n_max_eog = 2, 3 # here we expect horizontal EOG components try: ica = read_ica(raw_data_folder + '/ica_pre.fif') except: ica = ICA(n_components=0.95, max_pca_components = 64, method='fastica') #noise_cov = noise_cov_er) #ica.fit(raw, picks=picks, decim=3, reject=dict(mag=4e-12, grad=4000e-13)) ica.fit(raw, picks=picks, decim = 5, reject=dict(mag=4e-11, grad=4000e-12)) # To save an ICA solution you can say: ############################################################################### # 2) identify bad components by analyzing latent sources. title = 'Sources related to %s artifacts (red)' # generate ECG epochs use detection via phase statistics
def apply_ica(subject, run, session): deriv_path = config.get_subject_deriv_path(subject=subject, session=session, kind=config.get_kind()) bids_basename = make_bids_basename(subject=subject, session=session, task=config.get_task(), acquisition=config.acq, run=None, processing=config.proc, recording=config.rec, space=config.space) fname_in = op.join(deriv_path, bids_basename + '-epo.fif') fname_out = op.join(deriv_path, bids_basename + '_cleaned-epo.fif') # load epochs to reject ICA components epochs = mne.read_epochs(fname_in, preload=True) msg = f'Input: {fname_in}, Output: {fname_out}' logger.info( gen_log_message(message=msg, step=5, subject=subject, session=session)) # load first run of raw data for ecg / eog epochs msg = 'Loading first run from raw data' logger.debug( gen_log_message(message=msg, step=5, subject=subject, session=session)) bids_basename = make_bids_basename(subject=subject, session=session, task=config.get_task(), acquisition=config.acq, run=config.get_runs()[0], processing=config.proc, recording=config.rec, space=config.space) if config.use_maxwell_filter: raw_fname_in = op.join(deriv_path, bids_basename + '_sss_raw.fif') else: raw_fname_in = \ op.join(deriv_path, bids_basename + '_filt_raw.fif') raw = mne.io.read_raw_fif(raw_fname_in, preload=True) # run ICA on MEG and EEG picks_meg = mne.pick_types(raw.info, meg=True, eeg=False, eog=False, stim=False, exclude='bads') picks_eeg = mne.pick_types(raw.info, meg=False, eeg=True, eog=False, stim=False, exclude='bads') all_picks = {'meg': picks_meg, 'eeg': picks_eeg} for ch_type in config.ch_types: report = None picks = all_picks[ch_type] # Load ICA fname_ica = op.join(deriv_path, f'bids_basename_{ch_type}-ica.fif') msg = f'Reading ICA: {fname_ica}' logger.debug( gen_log_message(message=msg, step=5, subject=subject, session=session)) ica = read_ica(fname=fname_ica) pick_ecg = mne.pick_types(raw.info, meg=False, eeg=False, ecg=True, eog=False) # ECG # either needs an ecg channel, or avg of the mags (i.e. MEG data) ecg_inds = list() if pick_ecg or ch_type == 'meg': picks_ecg = np.concatenate([picks, pick_ecg]) # Create ecg epochs if ch_type == 'meg': reject = { 'mag': config.reject['mag'], 'grad': config.reject['grad'] } elif ch_type == 'eeg': reject = {'eeg': config.reject['eeg']} ecg_epochs = create_ecg_epochs(raw, picks=picks_ecg, reject=reject, baseline=(None, 0), tmin=-0.5, tmax=0.5) ecg_average = ecg_epochs.average() ecg_inds, scores = \ ica.find_bads_ecg(ecg_epochs, method='ctps', threshold=config.ica_ctps_ecg_threshold) del ecg_epochs report_fname = \ op.join(deriv_path, bids_basename + f'_{ch_type}-reject_ica.html') report = Report(report_fname, verbose=False) # Plot r score report.add_figs_to_section( ica.plot_scores(scores, exclude=ecg_inds, show=config.interactive), captions=ch_type.upper() + ' - ECG - R scores') # Plot source time course report.add_figs_to_section( ica.plot_sources(ecg_average, exclude=ecg_inds, show=config.interactive), captions=ch_type.upper() + ' - ECG - Sources time course') # Plot source time course report.add_figs_to_section( ica.plot_overlay(ecg_average, exclude=ecg_inds, show=config.interactive), captions=ch_type.upper() + ' - ECG - Corrections') else: # XXX : to check when EEG only is processed msg = ('No ECG channel is present. Cannot automate IC detection ' 'for ECG') logger.info( gen_log_message(message=msg, step=5, subject=subject, session=session)) # EOG pick_eog = mne.pick_types(raw.info, meg=False, eeg=False, ecg=False, eog=True) eog_inds = list() if pick_eog.any(): msg = 'Using EOG channel' logger.debug( gen_log_message(message=msg, step=5, subject=subject, session=session)) picks_eog = np.concatenate([picks, pick_eog]) # Create eog epochs eog_epochs = create_eog_epochs(raw, picks=picks_eog, reject=None, baseline=(None, 0), tmin=-0.5, tmax=0.5) eog_average = eog_epochs.average() eog_inds, scores = ica.find_bads_eog(eog_epochs, threshold=3.0) del eog_epochs params = dict(exclude=eog_inds, show=config.interactive) # Plot r score report.add_figs_to_section(ica.plot_scores(scores, **params), captions=ch_type.upper() + ' - EOG - ' + 'R scores') # Plot source time course report.add_figs_to_section(ica.plot_sources(eog_average, **params), captions=ch_type.upper() + ' - EOG - ' + 'Sources time course') # Plot source time course report.add_figs_to_section(ica.plot_overlay(eog_average, **params), captions=ch_type.upper() + ' - EOG - ' + 'Corrections') report.save(report_fname, overwrite=True, open_browser=False) else: msg = ('No EOG channel is present. Cannot automate IC detection ' 'for EOG') logger.info( gen_log_message(message=msg, step=5, subject=subject, session=session)) ica_reject = (list(ecg_inds) + list(eog_inds) + list(config.rejcomps_man[subject][ch_type])) # now reject the components msg = f'Rejecting from {ch_type}: {ica_reject}' logger.info( gen_log_message(message=msg, step=5, subject=subject, session=session)) epochs = ica.apply(epochs, exclude=ica_reject) msg = 'Saving cleaned epochs' logger.info( gen_log_message(message=msg, step=5, subject=subject, session=session)) epochs.save(fname_out) if report is not None: fig = ica.plot_overlay(raw, exclude=ica_reject, show=config.interactive) report.add_figs_to_section(fig, captions=ch_type.upper() + ' - ALL(epochs) - Corrections') if config.interactive: epochs.plot_image(combine='gfp', group_by='type', sigma=2., cmap="YlGnBu_r", show=config.interactive)
parser = ArgumentParser(description=__doc__) parser.add_argument("subject", help="subject id") subj = parser.parse_args().subject json_path = bp.root_json.fpath(subject=subj, task="rest", run=None) with open(json_path, "r") as f: er_relpath = json.load(f)["AssociatedEmptyRoom"] er_path = dirs.bids_root / er_relpath er_raw = read_raw_fif(er_path, preload=True) # remove ICA components marked for 'quesitions' data from ER data ica_sol_path = bp.ica_sol.fpath(subject=subj, task="questions") ica_bads_path = bp.ica_bads.fpath(subject=subj, task="questions") ica = read_ica(ica_sol_path) ica.exclude = read_ica_bads(ica_bads_path, logger) logger.info(f"Excluding ICs {ica.exclude} from ER data") ica.apply(er_raw) noise_cov = compute_raw_covariance(er_raw, method="auto") del er_raw info = read_info(bp.epochs.fpath(subject=subj)) fwd = read_forward_solution(bp.fwd.fpath(subject=subj)) inv_path = bp.inv.fpath(subject=subj) inverse_operator = make_inverse_operator(info, fwd, noise_cov, rank="info") write_inverse_operator(inv_path, inverse_operator)
def test_ica_additional(): """Test additional functionality """ stop2 = 500 test_cov2 = deepcopy(test_cov) ica = ICA(noise_cov=test_cov2, n_components=3, max_pca_components=4, n_pca_components=4) ica.decompose_raw(raw, picks[:5]) assert_true(ica.n_components_ < 5) ica = ICA(n_components=3, max_pca_components=4, n_pca_components=4) assert_raises(RuntimeError, ica.save, '') ica.decompose_raw(raw, picks=None, start=start, stop=stop2) # epochs extraction from raw fit assert_raises(RuntimeError, ica.get_sources_epochs, epochs) # test reading and writing test_ica_fname = op.join(op.dirname(tempdir), 'ica_test.fif') for cov in (None, test_cov): ica = ICA(noise_cov=cov, n_components=3, max_pca_components=4, n_pca_components=4) ica.decompose_raw(raw, picks=picks, start=start, stop=stop2) sources = ica.get_sources_epochs(epochs) assert_true(sources.shape[1] == ica.n_components_) for exclude in [[], [0]]: ica.exclude = [0] ica.save(test_ica_fname) ica_read = read_ica(test_ica_fname) assert_true(ica.exclude == ica_read.exclude) # test pick merge -- add components ica.pick_sources_raw(raw, exclude=[1]) assert_true(ica.exclude == [0, 1]) # -- only as arg ica.exclude = [] ica.pick_sources_raw(raw, exclude=[0, 1]) assert_true(ica.exclude == [0, 1]) # -- remove duplicates ica.exclude += [1] ica.pick_sources_raw(raw, exclude=[0, 1]) assert_true(ica.exclude == [0, 1]) ica_raw = ica.sources_as_raw(raw) assert_true(ica.exclude == [ica.ch_names.index(e) for e in ica_raw.info['bads']]) ica.n_pca_components = 2 ica.save(test_ica_fname) ica_read = read_ica(test_ica_fname) assert_true(ica.n_pca_components == ica_read.n_pca_components) ica.n_pca_components = 4 ica_read.n_pca_components = 4 ica.exclude = [] ica.save(test_ica_fname) ica_read = read_ica(test_ica_fname) assert_true(ica.ch_names == ica_read.ch_names) assert_true(np.allclose(ica.mixing_matrix_, ica_read.mixing_matrix_, rtol=1e-16, atol=1e-32)) assert_array_equal(ica.pca_components_, ica_read.pca_components_) assert_array_equal(ica.pca_mean_, ica_read.pca_mean_) assert_array_equal(ica.pca_explained_variance_, ica_read.pca_explained_variance_) assert_array_equal(ica._pre_whitener, ica_read._pre_whitener) # assert_raises(RuntimeError, ica_read.decompose_raw, raw) sources = ica.get_sources_raw(raw) sources2 = ica_read.get_sources_raw(raw) assert_array_almost_equal(sources, sources2) _raw1 = ica.pick_sources_raw(raw, exclude=[1]) _raw2 = ica_read.pick_sources_raw(raw, exclude=[1]) assert_array_almost_equal(_raw1[:, :][0], _raw2[:, :][0]) os.remove(test_ica_fname) # score funcs raw, with catch since "ties preclude exact" warning # XXX this should be fixed by a future PR... with warnings.catch_warnings(True) as w: sfunc_test = [ica.find_sources_raw(raw, target='EOG 061', score_func=n, start=0, stop=10) for n, f in score_funcs.items()] # score funcs raw # check lenght of scores [assert_true(ica.n_components_ == len(scores)) for scores in sfunc_test] # check univariate stats scores = ica.find_sources_raw(raw, score_func=stats.skew) # check exception handling assert_raises(ValueError, ica.find_sources_raw, raw, target=np.arange(1)) ## score funcs epochs ## # check lenght of scores # XXX this needs to be fixed, some of the score funcs don't seem to be # suited for the testing data. with warnings.catch_warnings(True) as w: sfunc_test = [ica.find_sources_epochs(epochs_eog, target='EOG 061', score_func=n) for n, f in score_funcs.items()] # check lenght of scores [assert_true(ica.n_components_ == len(scores)) for scores in sfunc_test] # check univariat stats scores = ica.find_sources_epochs(epochs, score_func=stats.skew) # check exception handling assert_raises(ValueError, ica.find_sources_epochs, epochs, target=np.arange(1)) # ecg functionality ecg_scores = ica.find_sources_raw(raw, target='MEG 1531', score_func='pearsonr') ecg_events = ica_find_ecg_events(raw, sources[np.abs(ecg_scores).argmax()]) assert_true(ecg_events.ndim == 2) # eog functionality eog_scores = ica.find_sources_raw(raw, target='EOG 061', score_func='pearsonr') eog_events = ica_find_eog_events(raw, sources[np.abs(eog_scores).argmax()]) assert_true(eog_events.ndim == 2) # Test ica fiff export ica_raw = ica.sources_as_raw(raw, start=0, stop=100) assert_true(ica_raw.last_samp - ica_raw.first_samp == 100) ica_chans = [ch for ch in ica_raw.ch_names if 'ICA' in ch] assert_true(ica.n_components_ == len(ica_chans)) test_ica_fname = op.join(op.abspath(op.curdir), 'test_ica.fif') ica_raw.save(test_ica_fname) ica_raw2 = fiff.Raw(test_ica_fname, preload=True) assert_array_almost_equal(ica_raw._data, ica_raw2._data) ica_raw2.close() os.remove(test_ica_fname) # regression test for plot method assert_raises(ValueError, ica.plot_sources_raw, raw, order=np.arange(50)) assert_raises(ValueError, ica.plot_sources_epochs, epochs, order=np.arange(50))
def test_ica_additional(): """Test additional ICA functionality""" tempdir = _TempDir() stop2 = 500 raw = Raw(raw_fname).crop(1.5, stop, False) raw.load_data() picks = pick_types(raw.info, meg=True, stim=False, ecg=False, eog=False, exclude='bads') test_cov = read_cov(test_cov_name) events = read_events(event_name) picks = pick_types(raw.info, meg=True, stim=False, ecg=False, eog=False, exclude='bads') epochs = Epochs(raw, events[:4], event_id, tmin, tmax, picks=picks, baseline=(None, 0), preload=True) # test if n_components=None works with warnings.catch_warnings(record=True): ica = ICA(n_components=None, max_pca_components=None, n_pca_components=None, random_state=0) ica.fit(epochs, picks=picks, decim=3) # for testing eog functionality picks2 = pick_types(raw.info, meg=True, stim=False, ecg=False, eog=True, exclude='bads') epochs_eog = Epochs(raw, events[:4], event_id, tmin, tmax, picks=picks2, baseline=(None, 0), preload=True) test_cov2 = test_cov.copy() ica = ICA(noise_cov=test_cov2, n_components=3, max_pca_components=4, n_pca_components=4) assert_true(ica.info is None) with warnings.catch_warnings(record=True): ica.fit(raw, picks[:5]) assert_true(isinstance(ica.info, Info)) assert_true(ica.n_components_ < 5) ica = ICA(n_components=3, max_pca_components=4, n_pca_components=4) assert_raises(RuntimeError, ica.save, '') with warnings.catch_warnings(record=True): ica.fit(raw, picks=[1, 2, 3, 4, 5], start=start, stop=stop2) # test corrmap ica2 = ica.copy() corrmap([ica, ica2], (0, 0), threshold='auto', label='blinks', plot=True, ch_type="mag") corrmap([ica, ica2], (0, 0), threshold=2, plot=False, show=False) assert_true(ica.labels_["blinks"] == ica2.labels_["blinks"]) assert_true(0 in ica.labels_["blinks"]) plt.close('all') # test warnings on bad filenames with warnings.catch_warnings(record=True) as w: warnings.simplefilter('always') ica_badname = op.join(op.dirname(tempdir), 'test-bad-name.fif.gz') ica.save(ica_badname) read_ica(ica_badname) assert_naming(w, 'test_ica.py', 2) # test decim ica = ICA(n_components=3, max_pca_components=4, n_pca_components=4) raw_ = raw.copy() for _ in range(3): raw_.append(raw_) n_samples = raw_._data.shape[1] with warnings.catch_warnings(record=True): ica.fit(raw, picks=None, decim=3) assert_true(raw_._data.shape[1], n_samples) # test expl var ica = ICA(n_components=1.0, max_pca_components=4, n_pca_components=4) with warnings.catch_warnings(record=True): ica.fit(raw, picks=None, decim=3) assert_true(ica.n_components_ == 4) # epochs extraction from raw fit assert_raises(RuntimeError, ica.get_sources, epochs) # test reading and writing test_ica_fname = op.join(op.dirname(tempdir), 'test-ica.fif') for cov in (None, test_cov): ica = ICA(noise_cov=cov, n_components=2, max_pca_components=4, n_pca_components=4) with warnings.catch_warnings(record=True): # ICA does not converge ica.fit(raw, picks=picks, start=start, stop=stop2) sources = ica.get_sources(epochs).get_data() assert_true(ica.mixing_matrix_.shape == (2, 2)) assert_true(ica.unmixing_matrix_.shape == (2, 2)) assert_true(ica.pca_components_.shape == (4, len(picks))) assert_true(sources.shape[1] == ica.n_components_) for exclude in [[], [0]]: ica.exclude = [0] ica.labels_ = {'foo': [0]} ica.save(test_ica_fname) ica_read = read_ica(test_ica_fname) assert_true(ica.exclude == ica_read.exclude) assert_equal(ica.labels_, ica_read.labels_) ica.exclude = [] ica.apply(raw, exclude=[1]) assert_true(ica.exclude == []) ica.exclude = [0, 1] ica.apply(raw, exclude=[1]) assert_true(ica.exclude == [0, 1]) ica_raw = ica.get_sources(raw) assert_true(ica.exclude == [ica_raw.ch_names.index(e) for e in ica_raw.info['bads']]) # test filtering d1 = ica_raw._data[0].copy() with warnings.catch_warnings(record=True): # dB warning ica_raw.filter(4, 20) assert_true((d1 != ica_raw._data[0]).any()) d1 = ica_raw._data[0].copy() with warnings.catch_warnings(record=True): # dB warning ica_raw.notch_filter([10]) assert_true((d1 != ica_raw._data[0]).any()) ica.n_pca_components = 2 ica.save(test_ica_fname) ica_read = read_ica(test_ica_fname) assert_true(ica.n_pca_components == ica_read.n_pca_components) # check type consistency attrs = ('mixing_matrix_ unmixing_matrix_ pca_components_ ' 'pca_explained_variance_ _pre_whitener') def f(x, y): return getattr(x, y).dtype for attr in attrs.split(): assert_equal(f(ica_read, attr), f(ica, attr)) ica.n_pca_components = 4 ica_read.n_pca_components = 4 ica.exclude = [] ica.save(test_ica_fname) ica_read = read_ica(test_ica_fname) for attr in ['mixing_matrix_', 'unmixing_matrix_', 'pca_components_', 'pca_mean_', 'pca_explained_variance_', '_pre_whitener']: assert_array_almost_equal(getattr(ica, attr), getattr(ica_read, attr)) assert_true(ica.ch_names == ica_read.ch_names) assert_true(isinstance(ica_read.info, Info)) sources = ica.get_sources(raw)[:, :][0] sources2 = ica_read.get_sources(raw)[:, :][0] assert_array_almost_equal(sources, sources2) _raw1 = ica.apply(raw, exclude=[1]) _raw2 = ica_read.apply(raw, exclude=[1]) assert_array_almost_equal(_raw1[:, :][0], _raw2[:, :][0]) os.remove(test_ica_fname) # check scrore funcs for name, func in get_score_funcs().items(): if name in score_funcs_unsuited: continue scores = ica.score_sources(raw, target='EOG 061', score_func=func, start=0, stop=10) assert_true(ica.n_components_ == len(scores)) # check univariate stats scores = ica.score_sources(raw, score_func=stats.skew) # check exception handling assert_raises(ValueError, ica.score_sources, raw, target=np.arange(1)) params = [] params += [(None, -1, slice(2), [0, 1])] # varicance, kurtosis idx params params += [(None, 'MEG 1531')] # ECG / EOG channel params for idx, ch_name in product(*params): ica.detect_artifacts(raw, start_find=0, stop_find=50, ecg_ch=ch_name, eog_ch=ch_name, skew_criterion=idx, var_criterion=idx, kurt_criterion=idx) with warnings.catch_warnings(record=True): idx, scores = ica.find_bads_ecg(raw, method='ctps') assert_equal(len(scores), ica.n_components_) idx, scores = ica.find_bads_ecg(raw, method='correlation') assert_equal(len(scores), ica.n_components_) idx, scores = ica.find_bads_ecg(epochs, method='ctps') assert_equal(len(scores), ica.n_components_) assert_raises(ValueError, ica.find_bads_ecg, epochs.average(), method='ctps') assert_raises(ValueError, ica.find_bads_ecg, raw, method='crazy-coupling') idx, scores = ica.find_bads_eog(raw) assert_equal(len(scores), ica.n_components_) raw.info['chs'][raw.ch_names.index('EOG 061') - 1]['kind'] = 202 idx, scores = ica.find_bads_eog(raw) assert_true(isinstance(scores, list)) assert_equal(len(scores[0]), ica.n_components_) # check score funcs for name, func in get_score_funcs().items(): if name in score_funcs_unsuited: continue scores = ica.score_sources(epochs_eog, target='EOG 061', score_func=func) assert_true(ica.n_components_ == len(scores)) # check univariate stats scores = ica.score_sources(epochs, score_func=stats.skew) # check exception handling assert_raises(ValueError, ica.score_sources, epochs, target=np.arange(1)) # ecg functionality ecg_scores = ica.score_sources(raw, target='MEG 1531', score_func='pearsonr') with warnings.catch_warnings(record=True): # filter attenuation warning ecg_events = ica_find_ecg_events(raw, sources[np.abs(ecg_scores).argmax()]) assert_true(ecg_events.ndim == 2) # eog functionality eog_scores = ica.score_sources(raw, target='EOG 061', score_func='pearsonr') with warnings.catch_warnings(record=True): # filter attenuation warning eog_events = ica_find_eog_events(raw, sources[np.abs(eog_scores).argmax()]) assert_true(eog_events.ndim == 2) # Test ica fiff export ica_raw = ica.get_sources(raw, start=0, stop=100) assert_true(ica_raw.last_samp - ica_raw.first_samp == 100) assert_true(len(ica_raw._filenames) == 0) # API consistency ica_chans = [ch for ch in ica_raw.ch_names if 'ICA' in ch] assert_true(ica.n_components_ == len(ica_chans)) test_ica_fname = op.join(op.abspath(op.curdir), 'test-ica_raw.fif') ica.n_components = np.int32(ica.n_components) ica_raw.save(test_ica_fname, overwrite=True) ica_raw2 = Raw(test_ica_fname, preload=True) assert_allclose(ica_raw._data, ica_raw2._data, rtol=1e-5, atol=1e-4) ica_raw2.close() os.remove(test_ica_fname) # Test ica epochs export ica_epochs = ica.get_sources(epochs) assert_true(ica_epochs.events.shape == epochs.events.shape) ica_chans = [ch for ch in ica_epochs.ch_names if 'ICA' in ch] assert_true(ica.n_components_ == len(ica_chans)) assert_true(ica.n_components_ == ica_epochs.get_data().shape[1]) assert_true(ica_epochs._raw is None) assert_true(ica_epochs.preload is True) # test float n pca components ica.pca_explained_variance_ = np.array([0.2] * 5) ica.n_components_ = 0 for ncomps, expected in [[0.3, 1], [0.9, 4], [1, 1]]: ncomps_ = ica._check_n_pca_components(ncomps) assert_true(ncomps_ == expected)
def run_evoked(subject): print("Processing subject: %s" % subject) meg_subject_dir = op.join(config.meg_dir, subject) # load epochs to reject ICA components extension = '-epo' fname_in = op.join(meg_subject_dir, config.base_fname.format(**locals())) epochs = mne.read_epochs(fname_in, preload=True) extension = 'cleaned-epo' fname_out = op.join(meg_subject_dir, config.base_fname.format(**locals())) print("Input: ", fname_in) print("Output: ", fname_out) # load first run of raw data for ecg /eog epochs raw_list = list() print(" Loading one run from raw data") extension = config.runs[0] + '_sss_raw' raw_fname_in = op.join(meg_subject_dir, config.base_fname.format(**locals())) raw = mne.io.read_raw_fif(raw_fname_in, preload=True) # run ICA on MEG and EEG picks_meg = mne.pick_types(raw.info, meg=True, eeg=False, eog=False, stim=False, exclude='bads') picks_eeg = mne.pick_types(raw.info, meg=False, eeg=True, eog=False, stim=False, exclude='bads') all_picks = {'meg': picks_meg, 'eeg': picks_eeg} if config.eeg: ch_types = ['meg', 'eeg'] else: ch_types = ['meg'] for ch_type in ch_types: print(ch_type) picks = all_picks[ch_type] # Load ICA fname_ica = op.join( meg_subject_dir, '{0}_{1}_{2}-ica.fif'.format(subject, config.study_name, ch_type)) print('Reading ICA: ' + fname_ica) ica = read_ica(fname=fname_ica) pick_ecg = mne.pick_types(raw.info, meg=False, eeg=False, ecg=True, eog=False) # ECG # either needs an ecg channel, or avg of the mags (i.e. MEG data) if pick_ecg or ch_type == 'meg': picks_ecg = np.concatenate([picks, pick_ecg]) # Create ecg epochs if ch_type == 'meg': reject = { 'mag': config.reject['mag'], 'grad': config.reject['grad'] } elif ch_type == 'eeg': reject = {'eeg': config.reject['eeg']} ecg_epochs = create_ecg_epochs(raw, picks=picks_ecg, reject=reject, baseline=(None, 0), tmin=-0.5, tmax=0.5) ecg_average = ecg_epochs.average() # XXX I had to lower the threshold for ctps (default 0.25), otherwise it does not # find any components # check how this behaves on other data ecg_inds, scores = ica.find_bads_ecg(ecg_epochs, method='ctps', threshold=0.1) del ecg_epochs report_name = op.join( meg_subject_dir, '{0}_{1}_{2}-reject_ica.html'.format(subject, config.study_name, ch_type)) report = Report(report_name, verbose=False) # Plot r score report.add_figs_to_section(ica.plot_scores(scores, exclude=ecg_inds), captions=ch_type.upper() + ' - ECG - ' + 'R scores') # Plot source time course report.add_figs_to_section(ica.plot_sources(ecg_average, exclude=ecg_inds), captions=ch_type.upper() + ' - ECG - ' + 'Sources time course') # Plot source time course report.add_figs_to_section(ica.plot_overlay(ecg_average, exclude=ecg_inds), captions=ch_type.upper() + ' - ECG - ' + 'Corrections') else: print('no ECG channel!') # EOG pick_eog = mne.pick_types(raw.info, meg=False, eeg=False, ecg=False, eog=True) if pick_eog.any(): print('using EOG channel') picks_eog = np.concatenate([picks, pick_eog]) # Create eog epochs eog_epochs = create_eog_epochs(raw, picks=picks_eog, reject=None, baseline=(None, 0), tmin=-0.5, tmax=0.5) eog_average = eog_epochs.average() eog_inds, scores = ica.find_bads_eog(eog_epochs) del eog_epochs # Plot r score report.add_figs_to_section(ica.plot_scores(scores, exclude=eog_inds), captions=ch_type.upper() + ' - EOG - ' + 'R scores') # Plot source time course report.add_figs_to_section(ica.plot_sources(eog_average, exclude=eog_inds), captions=ch_type.upper() + ' - EOG - ' + 'Sources time course') # Plot source time course report.add_figs_to_section(ica.plot_overlay(eog_average, exclude=eog_inds), captions=ch_type.upper() + ' - EOG - ' + 'Corrections') report.save(report_name, overwrite=True, open_browser=False) else: print('no EOG channel!') ica_reject = (list(ecg_inds) + list(eog_inds) + list(config.rejcomps_man[subject][ch_type])) # now reject the components print('Rejecting from ' + ch_type + ': ' + str(ica_reject)) epochs = ica.apply(epochs, exclude=ica_reject) print('Saving epochs') epochs.save(fname_out) report.add_figs_to_section(ica.plot_overlay(raw.copy(), exclude=ica_reject), captions=ch_type.upper() + ' - ALL(epochs) - ' + 'Corrections') if config.plot: epochs.plot_image(combine='gfp', group_by='type', sigma=2., cmap="YlGnBu_r")