def test_plot_ica_sources():
"""Test plotting of ICA panel."""
raw = read_raw_fif(raw_fname).crop(0, 1).load_data()
picks = _get_picks(raw)
epochs = _get_epochs()
raw.pick_channels([raw.ch_names[k] for k in picks])
ica_picks = pick_types(raw.info,
meg=True,
eeg=False,
stim=False,
ecg=False,
eog=False,
exclude='bads')
ica = ICA(n_components=2, max_pca_components=3, n_pca_components=3)
ica.fit(raw, picks=ica_picks)
ica.exclude = [1]
fig = ica.plot_sources(raw)
fig.canvas.key_press_event('escape')
# Sadly close_event isn't called on Agg backend and the test always passes.
assert_array_equal(ica.exclude, [1])
plt.close('all')
# dtype can change int->np.int after load, test it explicitly
ica.n_components_ = np.int64(ica.n_components_)
fig = ica.plot_sources(raw)
# also test mouse clicks
data_ax = fig.axes[0]
assert len(plt.get_fignums()) == 1
_fake_click(fig, data_ax, [-0.1, 0.9]) # click on y-label
assert len(plt.get_fignums()) == 2
ica.exclude = [1]
ica.plot_sources(raw)
raw.info['bads'] = ['MEG 0113']
with pytest.raises(RuntimeError, match="Raw doesn't match fitted data"):
ica.plot_sources(inst=raw)
ica.plot_sources(epochs)
epochs.info['bads'] = ['MEG 0113']
with pytest.raises(RuntimeError, match="Epochs don't match fitted data"):
ica.plot_sources(inst=epochs)
epochs.info['bads'] = []
ica.plot_sources(epochs.average())
evoked = epochs.average()
fig = ica.plot_sources(evoked)
# Test a click
ax = fig.get_axes()[0]
line = ax.lines[0]
_fake_click(fig, ax, [line.get_xdata()[0], line.get_ydata()[0]], 'data')
_fake_click(fig, ax, [ax.get_xlim()[0], ax.get_ylim()[1]], 'data')
# plot with bad channels excluded
ica.exclude = [0]
ica.plot_sources(evoked)
ica.labels_ = dict(eog=[0])
ica.labels_['eog/0/crazy-channel'] = [0]
ica.plot_sources(evoked) # now with labels
with pytest.raises(ValueError, match='must be of Raw or Epochs type'):
ica.plot_sources('meeow')
plt.close('all')
def inscapesMEG_PP(fname, DATA_FOLDER, SAVE_FOLDER):
fpath = DATA_FOLDER + fname
raw = read_raw_ctf(fpath, preload=True)
picks = mne.pick_types(raw.info, meg=True, eog=True, exclude='bads')
raw.plot()
raw.plot_psd(average=False, picks=picks)
## Filtering
high_cutoff = 200
low_cutoff = 0.5
raw.filter(low_cutoff, high_cutoff, fir_design="firwin")
raw.notch_filter(np.arange(60, high_cutoff + 1, 60),
picks=picks,
filter_length='auto',
phase='zero',
fir_design="firwin")
raw.plot_psd(average=False, picks=picks)
## ICA
ica = ICA(n_components=20, random_state=0).fit(raw, decim=3)
ica.plot_sources(raw)
fmax = 40. ## correlation threshold for ICA components (maybe increase to 40. ?)
## FIND ECG COMPONENTS
ecg_epochs = create_ecg_epochs(raw, ch_name='EEG059')
ecg_inds, ecg_scores = ica.find_bads_ecg(ecg_epochs, ch_name='EEG059')
ica.plot_scores(ecg_scores, ecg_inds)
ica.plot_properties(ecg_epochs,
picks=ecg_inds,
psd_args={'fmax': fmax},
image_args={'sigma': 1.})
## FIND EOG COMPONENTS
eog_epochs = create_eog_epochs(raw, ch_name='EEG057')
eog_inds, eog_scores = ica.find_bads_eog(eog_epochs, ch_name='EEG057')
ica.plot_scores(eog_scores, eog_inds)
ica.plot_properties(eog_epochs,
picks=eog_inds,
psd_args={'fmax': fmax},
image_args={'sigma': 1.})
## EXCLUDE COMPONENTS
ica.exclude = ecg_inds
ica.apply(raw)
ica.exclude = eog_inds
ica.apply(raw)
raw.plot()
# Plot the clean signal.
## SAVE PREPROCESSED FILE
time.sleep(60)
raw.save(SAVE_FOLDER + fname + '_preprocessed.fif.gz', overwrite=True)
time.sleep(30)
filename = SAVE_FOLDER + fname + '_log.html'
#!jupyter nbconvert inscapesMEG_preproc.ipynb --output $filename
clear_output()
def test_plot_ica_sources():
"""Test plotting of ICA panel."""
import matplotlib.pyplot as plt
raw = read_raw_fif(raw_fname).crop(0, 1).load_data()
picks = _get_picks(raw)
epochs = _get_epochs()
raw.pick_channels([raw.ch_names[k] for k in picks])
ica_picks = pick_types(raw.info,
meg=True,
eeg=False,
stim=False,
ecg=False,
eog=False,
exclude='bads')
ica = ICA(n_components=2, max_pca_components=3, n_pca_components=3)
ica.fit(raw, picks=ica_picks)
ica.exclude = [1]
fig = ica.plot_sources(raw)
fig.canvas.key_press_event('escape')
# Sadly close_event isn't called on Agg backend and the test always passes.
assert_array_equal(ica.exclude, [1])
fig = ica.plot_sources(raw, [1])
# test mouse clicks
data_ax = fig.axes[0]
_fake_click(fig, data_ax, [-0.1, 0.9]) # click on y-label
raw.info['bads'] = ['MEG 0113']
assert_raises(RuntimeError, ica.plot_sources, inst=raw)
ica.plot_sources(epochs)
epochs.info['bads'] = ['MEG 0113']
assert_raises(RuntimeError, ica.plot_sources, inst=epochs)
epochs.info['bads'] = []
with warnings.catch_warnings(record=True): # no labeled objects mpl
ica.plot_sources(epochs.average())
evoked = epochs.average()
fig = ica.plot_sources(evoked)
# Test a click
ax = fig.get_axes()[0]
line = ax.lines[0]
_fake_click(
fig, ax,
[line.get_xdata()[0], line.get_ydata()[0]], 'data')
_fake_click(fig, ax, [ax.get_xlim()[0], ax.get_ylim()[1]], 'data')
# plot with bad channels excluded
ica.plot_sources(evoked, exclude=[0])
ica.exclude = [0]
ica.plot_sources(evoked) # does the same thing
ica.labels_ = dict(eog=[0])
ica.labels_['eog/0/crazy-channel'] = [0]
ica.plot_sources(evoked) # now with labels
assert_raises(ValueError, ica.plot_sources, 'meeow')
plt.close('all')
def test_plot_ica_sources():
"""Test plotting of ICA panel."""
raw = read_raw_fif(raw_fname).crop(0, 1).load_data()
picks = _get_picks(raw)
epochs = _get_epochs()
raw.pick_channels([raw.ch_names[k] for k in picks])
ica_picks = pick_types(raw.info, meg=True, eeg=False, stim=False,
ecg=False, eog=False, exclude='bads')
ica = ICA(n_components=2, max_pca_components=3, n_pca_components=3)
ica.fit(raw, picks=ica_picks)
ica.exclude = [1]
fig = ica.plot_sources(raw)
fig.canvas.key_press_event('escape')
# Sadly close_event isn't called on Agg backend and the test always passes.
assert_array_equal(ica.exclude, [1])
plt.close('all')
# dtype can change int->np.int after load, test it explicitly
ica.n_components_ = np.int64(ica.n_components_)
fig = ica.plot_sources(raw, [1])
# also test mouse clicks
data_ax = fig.axes[0]
_fake_click(fig, data_ax, [-0.1, 0.9]) # click on y-label
raw.info['bads'] = ['MEG 0113']
pytest.raises(RuntimeError, ica.plot_sources, inst=raw)
ica.plot_sources(epochs)
epochs.info['bads'] = ['MEG 0113']
pytest.raises(RuntimeError, ica.plot_sources, inst=epochs)
epochs.info['bads'] = []
ica.plot_sources(epochs.average())
evoked = epochs.average()
fig = ica.plot_sources(evoked)
# Test a click
ax = fig.get_axes()[0]
line = ax.lines[0]
_fake_click(fig, ax,
[line.get_xdata()[0], line.get_ydata()[0]], 'data')
_fake_click(fig, ax,
[ax.get_xlim()[0], ax.get_ylim()[1]], 'data')
# plot with bad channels excluded
ica.plot_sources(evoked, exclude=[0])
ica.exclude = [0]
ica.plot_sources(evoked) # does the same thing
ica.labels_ = dict(eog=[0])
ica.labels_['eog/0/crazy-channel'] = [0]
ica.plot_sources(evoked) # now with labels
pytest.raises(ValueError, ica.plot_sources, 'meeow')
plt.close('all')
def run_ica(method, fit_params=None):
chn=['AF3','F7','F3','FC5','T7','P7','O1','O2','P8','T8','FC6','F4','F8','AF4']
ica = ICA(n_components=14, method=method, fit_params=fit_params,
random_state=75)
filt_raw = raw.copy()
filt_raw.load_data().filter(l_freq=2.5, h_freq=None)
t0 = time()
ica.fit(filt_raw)
fit_time = time() - t0
title = ('ICA decomposition using %s (took %.1fs)' % (method, fit_time))
ica.plot_sources(raw)
ica.plot_components(title=title)
ica.exclude = []
# find which ICs match the EOG pattern
eog_indices, eog_scores = ica.find_bads_eog(raw,ch_name='AF4')
ica.exclude = eog_indices
# barplot of ICA component "EOG match" scores
ica.plot_scores(eog_scores)
print(eog_indices)
inpre=input("está de acuerdo con los indices?: (y/n)")
if(inpre=='y'):
print('ok, sigamos')
else:
eog_indices=[]
n=int(input("elija el numero de indices a incluir: "))
for i in range(0,n):
print("introduzca el indice ")
eog_indices.append(int(input(": ")))
ica.plot_properties(raw, picks=eog_indices)
ica.exclude = eog_indices # indices chosen based on various plots above
# plot ICs applied to raw data, with EOG matches highlighted
ica.plot_sources(raw)
# plot ICs applied to the averaged EOG epochs, with EOG matches highlighted
ica.plot_overlay(raw,exclude=eog_indices)
# ica.apply() changes the Raw object in-place, so let's make a copy first:
print('copiando el original')
reconst_raw = raw.copy()
print('aplicando ICA')
ica.apply(reconst_raw)
raw.plot(events=events,event_color=mapcol)
print('muestra reconstruida')
reconst_raw.plot(events=events,event_color=mapcol)
plt.show()
return reconst_raw
def ica_pipe(sample_raw_bandpass):
clf = joblib.load("./models/eog_classifier_v2.joblib")
sample_raw_train = sample_raw_bandpass.copy()
sample_raw_corrected = sample_raw_bandpass.copy()
# Fitting ICA
ica = ICA(method="extended-infomax", random_state=1)
ica.fit(sample_raw_corrected)
maps = _get_ica_map(ica).T
scalings = np.linalg.norm(maps, axis=0)
maps /= scalings[None, :]
X = maps.T
# Predict EOG
eog_preds = clf.predict(X)
list_of_eog = np.where(eog_preds == 1)[0]
# ica.plot_sources(inst=sample_raw_train)
# ica.plot_components(inst=sample_raw_train)
ica.exclude = list_of_eog
ica.apply(sample_raw_corrected)
return ica, sample_raw_train, sample_raw_corrected
def test_plot_instance_components(browser_backend):
"""Test plotting of components as instances of raw and epochs."""
raw = _get_raw()
picks = _get_picks(raw)
ica = ICA(noise_cov=read_cov(cov_fname), n_components=2)
with pytest.warns(RuntimeWarning, match='projection'):
ica.fit(raw, picks=picks)
ica.exclude = [0]
fig = ica.plot_sources(raw, title='Components')
keys = ('home', 'home', 'end', 'down', 'up', 'right', 'left', '-', '+',
'=', 'd', 'd', 'pageup', 'pagedown', 'z', 'z', 's', 's', 'b')
for key in keys:
fig._fake_keypress(key)
x = fig.mne.traces[0].get_xdata()[0]
y = fig.mne.traces[0].get_ydata()[0]
fig._fake_click((x, y), xform='data')
fig._click_ch_name(ch_index=0, button=1)
fig._fake_keypress('escape')
browser_backend._close_all()
epochs = _get_epochs()
fig = ica.plot_sources(epochs, title='Components')
for key in keys:
fig._fake_keypress(key)
# Test a click
x = fig.mne.traces[0].get_xdata()[0]
y = fig.mne.traces[0].get_ydata()[0]
fig._fake_click((x, y), xform='data')
fig._click_ch_name(ch_index=0, button=1)
fig._fake_keypress('escape')
def test_plot_instance_components():
"""Test plotting of components as instances of raw and epochs."""
raw = _get_raw()
picks = _get_picks(raw)
ica = ICA(noise_cov=read_cov(cov_fname), n_components=2)
with pytest.warns(RuntimeWarning, match='projection'):
ica.fit(raw, picks=picks)
ica.exclude = [0]
fig = ica.plot_sources(raw, title='Components')
keys = ('home', 'home', 'end', 'down', 'up', 'right', 'left', '-', '+',
'=', 'd', 'd', 'pageup', 'pagedown', 'z', 'z', 's', 's', 'f11',
'b')
for key in keys:
fig.canvas.key_press_event(key)
ax = fig.mne.ax_main
line = ax.lines[0]
_fake_click(fig, ax, [line.get_xdata()[0], line.get_ydata()[0]], 'data')
_fake_click(fig, ax, [-0.1, 0.9]) # click on y-label
fig.canvas.key_press_event('escape')
plt.close('all')
epochs = _get_epochs()
fig = ica.plot_sources(epochs, title='Components')
for key in keys:
fig.canvas.key_press_event(key)
# Test a click
ax = fig.get_axes()[0]
line = ax.lines[0]
_fake_click(fig, ax, [line.get_xdata()[0], line.get_ydata()[0]], 'data')
_fake_click(fig, ax, [-0.1, 0.9]) # click on y-label
fig.canvas.key_press_event('escape')
def test_plot_ica_sources():
"""Test plotting of ICA panel
"""
import matplotlib.pyplot as plt
raw = io.read_raw_fif(raw_fname,
preload=False).crop(0, 1, copy=False).load_data()
picks = _get_picks(raw)
epochs = _get_epochs()
raw.pick_channels([raw.ch_names[k] for k in picks])
ica_picks = pick_types(raw.info, meg=True, eeg=False, stim=False,
ecg=False, eog=False, exclude='bads')
ica = ICA(n_components=2, max_pca_components=3, n_pca_components=3)
ica.fit(raw, picks=ica_picks)
ica.exclude = [1]
fig = ica.plot_sources(raw)
fig.canvas.key_press_event('escape')
# Sadly close_event isn't called on Agg backend and the test always passes.
assert_array_equal(ica.exclude, [1])
raw.info['bads'] = ['MEG 0113']
assert_raises(RuntimeError, ica.plot_sources, inst=raw)
ica.plot_sources(epochs)
epochs.info['bads'] = ['MEG 0113']
assert_raises(RuntimeError, ica.plot_sources, inst=epochs)
epochs.info['bads'] = []
with warnings.catch_warnings(record=True): # no labeled objects mpl
ica.plot_sources(epochs.average())
evoked = epochs.average()
fig = ica.plot_sources(evoked)
# Test a click
ax = fig.get_axes()[0]
line = ax.lines[0]
_fake_click(fig, ax,
[line.get_xdata()[0], line.get_ydata()[0]], 'data')
_fake_click(fig, ax,
[ax.get_xlim()[0], ax.get_ylim()[1]], 'data')
# plot with bad channels excluded
ica.plot_sources(evoked, exclude=[0])
ica.exclude = [0]
ica.plot_sources(evoked) # does the same thing
ica.labels_ = dict(eog=[0])
ica.labels_['eog/0/crazy-channel'] = [0]
ica.plot_sources(evoked) # now with labels
assert_raises(ValueError, ica.plot_sources, 'meeow')
plt.close('all')
def run_ica(method, fit_params=None):
ica = ICA(n_components=14,
method=method,
fit_params=fit_params,
random_state=95)
filt_raw = raw.copy()
filt_raw.load_data().filter(l_freq=1., h_freq=None)
t0 = time()
ica.fit(filt_raw)
fit_time = time() - t0
title = ('ICA decomposition using %s (took %.1fs)' % (method, fit_time))
ica.plot_sources(raw)
#ica.plot_components(title=title)
ica.exclude = []
# find which ICs match the EOG pattern
eog_indices, eog_scores = ica.find_bads_eog(raw, ch_name='F4')
ica.exclude = eog_indices
# barplot of ICA component "EOG match" scores
ica.plot_scores(eog_scores)
eog_indices, eog_scores = ica.find_bads_eog(raw, ch_name='AF4')
ica.exclude = eog_indices
# barplot of ICA component "EOG match" scores
ica.plot_scores(eog_scores)
# plot diagnostics
ica.plot_properties(raw, picks=eog_indices)
# plot ICs applied to raw data, with EOG matches highlighted
ica.plot_sources(raw)
# plot ICs applied to the averaged EOG epochs, with EOG matches highlighted
#ica.plot_sources(eog_evoked)
ica.plot_overlay(raw)
ica.exclude = [1, 2] # indices chosen based on various plots above
# ica.apply() changes the Raw object in-place, so let's make a copy first:
print('copiando el original')
reconst_raw = raw.copy()
print('aplicando ICA')
ica.apply(reconst_raw)
raw.plot()
print('muestra reconstruida')
reconst_raw.plot()
plt.show()
def run_events(subject_id):
subject = "sub_%03d" % subject_id
print("processing subject: %s" % subject)
in_path = op.join(
data_path, "EEG_Process") #make map yourself in cwd called 'Subjects'
process_path = op.join(
data_path,
"EEG_Process") #make map yourself in cwd called 'EEG_Process'
raw_list = list()
events_list = list()
for run in range(1, 2):
fname = op.join(in_path, 'sub_%03d_raw.fif' % (subject_id, ))
raw = mne.io.read_raw_fif(fname, preload=True)
print(" S %s - R %s" % (subject, run))
#import events and reorganize
delay = int(round(0.0345 * raw.info['sfreq']))
events = mne.read_events(
op.join(in_path, 'events_%03d-eve.fif' % (subject_id, )))
events[:, 0] = events[:, 0] + delay
events_list.append(events)
raw_list.append(raw)
raw, events = mne.concatenate_raws(raw_list, events_list=events_list)
###some visualizations on the blinks in the raw data file###
eog_events = mne.preprocessing.find_eog_events(raw)
onsets = eog_events[:, 0] / raw.info['sfreq'] - 0.25
durations = [0.5] * len(eog_events)
descriptions = ['bad blink'] * len(eog_events)
blink_annot = mne.Annotations(onsets,
durations,
descriptions,
orig_time=raw.info['meas_date'])
raw.set_annotations(blink_annot)
eeg_picks = mne.pick_types(raw.info, eeg=True)
raw.plot(events=eog_events, order=eeg_picks)
###CONCLUSION: NOT THE BEST ALGORITHM
#####ICA#####
ica = ICA(random_state=97, n_components=15)
picks = mne.pick_types(raw.info,
eeg=True,
eog=True,
stim=False,
exclude='bads')
ica.fit(raw, picks=picks)
raw.load_data()
ica.plot_sources(raw)
ica.plot_components()
ica.plot_overlay(raw, exclude=[6], picks='eeg')
#visualize the difference
raw2 = raw.copy()
ica.exclude = [6]
ica.apply(raw2)
raw2.plot()
ica.plot_properties(raw, picks=[6])
def test_plot_ica_sources():
"""Test plotting of ICA panel
"""
import matplotlib.pyplot as plt
raw = io.Raw(raw_fname, preload=False)
raw.crop(0, 1, copy=False)
raw.load_data()
picks = _get_picks(raw)
epochs = _get_epochs()
raw.pick_channels([raw.ch_names[k] for k in picks])
ica_picks = pick_types(raw.info,
meg=True,
eeg=False,
stim=False,
ecg=False,
eog=False,
exclude='bads')
ica = ICA(n_components=2, max_pca_components=3, n_pca_components=3)
ica.fit(raw, picks=ica_picks)
raw.info['bads'] = ['MEG 0113']
assert_raises(RuntimeError, ica.plot_sources, inst=raw)
ica.plot_sources(epochs)
epochs.info['bads'] = ['MEG 0113']
assert_raises(RuntimeError, ica.plot_sources, inst=epochs)
epochs.info['bads'] = []
with warnings.catch_warnings(record=True): # no labeled objects mpl
ica.plot_sources(epochs.average())
evoked = epochs.average()
fig = ica.plot_sources(evoked)
# Test a click
ax = fig.get_axes()[0]
line = ax.lines[0]
_fake_click(
fig, ax,
[line.get_xdata()[0], line.get_ydata()[0]], 'data')
_fake_click(fig, ax, [ax.get_xlim()[0], ax.get_ylim()[1]], 'data')
# plot with bad channels excluded
ica.plot_sources(evoked, exclude=[0])
ica.exclude = [0]
ica.plot_sources(evoked) # does the same thing
ica.labels_ = dict(eog=[0])
ica.labels_['eog/0/crazy-channel'] = [0]
ica.plot_sources(evoked) # now with labels
assert_raises(ValueError, ica.plot_sources, 'meeow')
plt.close('all')
def drop_artefacts(self, n_components, raw, a, b):
"""
Use the ICA to eliminate windows contaminated with blinking
"""
ica = ICA(n_components=n_components)
ica.fit(raw)
picks = pick_types(raw.info,
meg=False,
eeg=True,
stim=False,
eog=False,
exclude='bads')
raw.load_data()
ica.plot_sources(raw)
ica.plot_components(layout=read_layout('eeg1005'))
ica.exclude = [a, b]
reconst_raw = raw.copy()
ica.apply(reconst_raw)
return reconst_raw
def remove_eog_ica(raw, n_components, ch_name, threshold):
"""Remove EOG artifacts by ICA.
Parameters
----------
raw : instance of Raw.
The raw data.
n_components : int
Number of principal components for ICA.
ch_name : str
The name of the channel to use for EOG peak detection.
threshold : int
The value above which a feature is classified as outlier.
Returns
-------
raw : instance of Raw.
The raw data.
Notes
-----
"""
ica = ICA(n_components=n_components, max_iter='auto')
ica.fit(raw, verbose=0)
while threshold > 1:
eog_inds, _ = ica.find_bads_eog(raw,
ch_name=ch_name,
threshold=threshold,
verbose=0)
if eog_inds:
break
threshold -= 0.3
if not eog_inds:
raise RuntimeError('Didn\'t find a EOG component.')
ica.plot_properties(raw, eog_inds)
ica.exclude = eog_inds
ica.apply(raw, verbose=0)
return raw
def preprocess(eeg_rawdata):
"""
:param eeg_rawdata: numpy array with the shape of (n_channels, n_samples)
:return: filtered EEG raw data
"""
assert eeg_rawdata.shape[0] == 62
eeg_rawdata = np.array(eeg_rawdata)
temp = 0 - (eeg_rawdata.shape[1] % 5)
if temp != 0:
eeg_rawdata = eeg_rawdata[:, :temp]
ch_names = [
'FP1', 'FPZ', 'FP2', 'AF3', 'AF4', 'F7', 'F5', 'F3', 'F1', 'FZ', 'F2',
'F4', 'F6', 'F8', 'FT7', 'FC5', 'FC3', 'FC1', 'FCZ', 'FC2', 'FC4',
'FC6', 'FT8', 'T7', 'C5', 'C3', 'C1', 'CZ', 'C2', 'C4', 'C6', 'T8',
'TP7', 'CP5', 'CP3', 'CP1', 'CPZ', 'CP2', 'CP4', 'CP6', 'TP8', 'P7',
'P5', 'P3', 'P1', 'PZ', 'P2', 'P4', 'P6', 'P8', 'PO7', 'PO5', 'PO3',
'POZ', 'PO4', 'PO6', 'PO8', 'CB1', 'O1', 'OZ', 'O2', 'CB2'
]
info = mne.create_info(
# 通道名
ch_names=ch_names,
# 通道类型
ch_types=['eeg' for _ in range(62)],
# 采样频率
sfreq=1000)
raw_data = mne.io.RawArray(eeg_rawdata, info)
raw_data.load_data().filter(l_freq=1., h_freq=75)
raw_data.resample(200)
ica = ICA(n_components=5, random_state=97)
ica.fit(raw_data)
eog_indices, eog_scores = ica.find_bads_eog(raw_data, ch_name='FP1')
a = abs(eog_scores).tolist()
ica.exclude = [a.index(max(a))]
ica.apply(raw_data)
filted_eeg_rawdata = np.array(raw_data.get_data())
return filted_eeg_rawdata
def run_ica(epochs: Epochs, fit_params: dict = None) -> ICA:
"""
Runs ICA decomposition on Epochs instance.
If there are no EOG channels found, it tries to use 'Fp1' and 'Fp2' as EOG
channels; if they are not found either, it chooses the first two channels
to identify EOG components with mne.preprocessing.ica.find_bads_eog().
Parameters
----------
epochs: the instance to be used for ICA decomposition
fit_params: parameters to be passed to ICA fit (e.g. orthogonal picard, extended infomax)
Returns
-------
ICA instance
"""
ica = ICA(
n_components=settings["ica"]["n_components"],
random_state=42,
method=settings["ica"]["method"],
fit_params=fit_params,
)
ica_epochs = epochs.copy()
ica.fit(ica_epochs, decim=settings["ica"]["decim"])
if "eog" not in epochs.get_channel_types():
if "Fp1" and "Fp2" in epochs.get_montage().ch_names:
eog_channels = ["Fp1", "Fp2"]
else:
eog_channels = epochs.get_montage().ch_names[:2]
logger.info("EOG channels are not found. Attempting to use "
f'{",".join(eog_channels)} channels as EOG channels.')
ica_epochs.set_channel_types({ch: "eog" for ch in eog_channels})
eog_indices, _ = ica.find_bads_eog(ica_epochs)
ica.exclude = eog_indices
return ica
def test_plot_ica_sources():
"""Test plotting of ICA panel
"""
import matplotlib.pyplot as plt
raw = io.Raw(raw_fname, preload=False)
raw.crop(0, 1, copy=False)
raw.preload_data()
picks = _get_picks(raw)
epochs = _get_epochs()
raw.pick_channels([raw.ch_names[k] for k in picks])
ica_picks = pick_types(raw.info, meg=True, eeg=False, stim=False,
ecg=False, eog=False, exclude='bads')
ica = ICA(n_components=2, max_pca_components=3, n_pca_components=3)
ica.fit(raw, picks=ica_picks)
raw.info['bads'] = ['MEG 0113']
assert_raises(RuntimeError, ica.plot_sources, inst=raw)
ica.plot_sources(epochs)
epochs.info['bads'] = ['MEG 0113']
assert_raises(RuntimeError, ica.plot_sources, inst=epochs)
epochs.info['bads'] = []
with warnings.catch_warnings(record=True): # no labeled objects mpl
ica.plot_sources(epochs.average())
evoked = epochs.average()
fig = ica.plot_sources(evoked)
# Test a click
ax = fig.get_axes()[0]
line = ax.lines[0]
_fake_click(fig, ax,
[line.get_xdata()[0], line.get_ydata()[0]], 'data')
_fake_click(fig, ax,
[ax.get_xlim()[0], ax.get_ylim()[1]], 'data')
# plot with bad channels excluded
ica.plot_sources(evoked, exclude=[0])
ica.exclude = [0]
ica.plot_sources(evoked) # does the same thing
assert_raises(ValueError, ica.plot_sources, 'meeow')
plt.close('all')
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)
#
#
# Selecting ICA components manually
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#
# Once we're certain which components we want to exclude, we can specify that
# manually by setting the ``ica.exclude`` attribute. Similar to marking bad
# channels, merely setting ``ica.exclude`` doesn't do anything immediately (it
# just adds the excluded ICs to a list that will get used later when it's
# needed). Once the exclusions have been set, ICA methods like
# :meth:`~mne.preprocessing.ICA.plot_overlay` will exclude those component(s)
# even if no ``exclude`` parameter is passed, and the list of excluded
# components will be preserved when using :meth:`mne.preprocessing.ICA.save`
# and :func:`mne.preprocessing.read_ica`.
ica.exclude = [0, 1] # indices chosen based on various plots above
###############################################################################
# Now that the exclusions have been set, we can reconstruct the sensor signals
# with artifacts removed using the :meth:`~mne.preprocessing.ICA.apply` method
# (remember, we're applying the ICA solution from the *filtered* data to the
# original *unfiltered* signal). Plotting the original raw data alongside the
# reconstructed data shows that the heartbeat and blink artifacts are repaired.
# ica.apply() changes the Raw object in-place, so let's make a copy first:
reconst_raw = raw.copy()
ica.apply(reconst_raw)
raw.plot(order=artifact_picks, n_channels=len(artifact_picks),
show_scrollbars=False)
reconst_raw.plot(order=artifact_picks, n_channels=len(artifact_picks),
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(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 remove_eyeblinks_and_heartbeat(raw, subject, figdir, events, eventid, rng):
"""
Find and repair eyeblink and heartbeat artifacts in the data.
Data should be filtered.
Importantly, ICA is fitted on artificially epoched data with reject
criteria estimates via the autoreject package - this is done to reject high-
amplitude artifacts to influence the ICA solution.
The ICA fit is then applied to the raw data.
:param raw: Raw data
:param subject: str, subject identifier, e.g., '001'
:param figdir:
:param rng: random state instance
"""
# prior to an ICA, it is recommended to high-pass filter the data
# as low frequency artifacts can alter the ICA solution. We fit the ICA
# to high-pass filtered (1Hz) data, and apply it to non-highpass-filtered
# data
logging.info("Applying a temporary high-pass filtering prior to ICA")
filt_raw = raw.copy()
filt_raw.load_data().filter(l_freq=1., h_freq=None)
# evoked eyeblinks and heartbeats for diagnostic plots
eog_evoked = create_eog_epochs(filt_raw).average()
eog_evoked.apply_baseline(baseline=(None, -0.2))
if subject == '008':
# subject 008's ECG channel is flat. It will not find any heartbeats by
# default. We let it estimate heartbeat from magnetometers. For this,
# we'll drop the ECG channel
filt_raw.drop_channels('ECG003')
ecg_evoked = create_ecg_epochs(filt_raw).average()
ecg_evoked.apply_baseline(baseline=(None, -0.2))
# make sure that we actually found sensible artifacts here
eog_fig = eog_evoked.plot_joint()
for i, fig in enumerate(eog_fig):
fname = _construct_path([
Path(figdir),
f"sub-{subject}",
"meg",
f"evoked-artifact_eog_sub-{subject}_{i}.png",
])
fig.savefig(fname)
ecg_fig = ecg_evoked.plot_joint()
for i, fig in enumerate(ecg_fig):
fname = _construct_path([
Path(figdir),
f"sub-{subject}",
"meg",
f"evoked-artifact_ecg_sub-{subject}_{i}.png",
])
fig.savefig(fname)
# Chunk raw data into epochs to fit the ICA
# No baseline correction as it would interfere with ICA.
logging.info("Epoching filtered data")
epochs = mne.Epochs(filt_raw,
events,
event_id=eventid,
tmin=0,
tmax=3,
picks='meg',
baseline=None)
## First, estimate rejection criteria for high-amplitude artifacts. This is
## done via autoreject
#logging.info('Estimating bad epochs quick-and-dirty, to improve ICA')
#ar = AutoReject(random_state=rng)
# fit on first 200 epochs to save (a bit of) time
#epochs.load_data()
#ar.fit(epochs[:200])
#epochs_ar, reject_log = ar.transform(epochs, return_log=True)
# run an ICA to capture heartbeat and eyeblink artifacts.
# set a seed for reproducibility.
# When left to figure out the component number by itself, it ends up with
# about 80. I'm setting n_components to 45 to have a chance at checking them
# by hand.
# We fit it on a set of epochs excluding the initial bad epochs following
# https://github.com/autoreject/autoreject/blob/dfbc64f49eddeda53c5868290a6792b5233843c6/examples/plot_autoreject_workflow.py
logging.info('Fitting the ICA')
ica = ICA(max_iter='auto', n_components=45, random_state=rng)
ica.fit(epochs) #[~reject_log.bad_epochs])
logging.info("Searching for eyeblink and heartbeat artifacts in the data")
# get ICA components for the given subject
if subject == '008':
eog_indices = [10]
ecg_indices = [29]
#eog_indices = ica_comps[subject]['eog']
#ecg_indices = ica_comps[subject]['ecg']
# An initially manual component detection did not reproduce after a software
# update - for now, we have to do the automatic detection for all but sub 8
else:
eog_indices, eog_scores = ica.find_bads_eog(filt_raw)
ecg_indices, ecg_scores = ica.find_bads_ecg(filt_raw)
logging.info(f"Identified the following EOG components: {eog_indices}")
logging.info(f"Identified the following ECG components: {ecg_indices}")
# visualize the components
components = ica.plot_components()
for i, fig in enumerate(components):
fname = _construct_path([
Path(figdir),
f"sub-{subject}",
"meg",
f"ica-components_sub-{subject}_{i}.png",
])
fig.savefig(fname)
# visualize the time series of components and save it
plt.rcParams['figure.figsize'] = 30, 20
comp_sources = ica.plot_sources(epochs)
fname = _construct_path([
Path(figdir),
f"sub-{subject}",
"meg",
f"ica-components_sources_sub-{subject}.png",
])
comp_sources.savefig(fname)
# reset plotting params
plt.rcParams['figure.figsize'] = plt.rcParamsDefault['figure.figsize']
# plot EOG components
overlay_eog = ica.plot_overlay(eog_evoked,
exclude=ica_comps[subject]['eog'])
fname = _construct_path([
Path(figdir),
f"sub-{subject}",
"meg",
f"ica-eog-components_over-avg-epochs_sub-{subject}.png",
])
overlay_eog.savefig(fname)
# plot ECG components
overlay_ecg = ica.plot_overlay(ecg_evoked,
exclude=ica_comps[subject]['ecg'])
fname = _construct_path([
Path(figdir),
f"sub-{subject}",
"meg",
f"ica-ecg-components_over-avg-epochs_sub-{subject}.png",
])
overlay_ecg.savefig(fname)
# plot EOG component properties
figs = ica.plot_properties(filt_raw, picks=eog_indices)
for i, fig in enumerate(figs):
fname = _construct_path([
Path(figdir),
f"sub-{subject}",
"meg",
f"ica-property{i}_artifact-eog_sub-{subject}.png",
])
fig.savefig(fname)
# plot ECG component properties
figs = ica.plot_properties(filt_raw, picks=ecg_indices)
for i, fig in enumerate(figs):
fname = _construct_path([
Path(figdir),
f"sub-{subject}",
"meg",
f"ica-property{i}_artifact-ecg_sub-{subject}.png",
])
fig.savefig(fname)
# Set the indices to be excluded
ica.exclude = eog_indices
ica.exclude.extend(ecg_indices)
# plot ICs applied to the averaged EOG epochs, with EOG matches highlighted
sources = ica.plot_sources(eog_evoked)
fname = _construct_path([
Path(figdir),
f"sub-{subject}",
"meg",
f"ica-sources_artifact-eog_sub-{subject}.png",
])
sources.savefig(fname)
# plot ICs applied to the averaged ECG epochs, with ECG matches highlighted
sources = ica.plot_sources(ecg_evoked)
fname = _construct_path([
Path(figdir),
f"sub-{subject}",
"meg",
f"ica-sources_artifact-ecg_sub-{subject}.png",
])
sources.savefig(fname)
# apply the ICA to the raw data
logging.info('Applying ICA to the raw data.')
raw.load_data()
ica.apply(raw)
def preprocess_eeg(id_num, random_seed=None):
# Set important variables
bids_path = BIDSPath(id_num, task=task, datatype=datatype, root=bids_root)
plot_path = os.path.join(plotdir, "sub_{0}".format(id_num))
if os.path.exists(plot_path):
shutil.rmtree(plot_path)
os.mkdir(plot_path)
if not random_seed:
random_seed = int(binascii.b2a_hex(os.urandom(4)), 16)
random.seed(random_seed)
id_info = {"id": id_num, "random_seed": random_seed}
### Load and prepare EEG data #############################################
header = "### Processing sub-{0} (seed: {1}) ###".format(
id_num, random_seed)
print("\n" + "#" * len(header))
print(header)
print("#" * len(header) + "\n")
# Load EEG data
raw = read_raw_bids(bids_path, verbose=True)
# Check if recording is complete
complete = len(raw.annotations) >= 600
# Add a montage to the data
montage_kind = "standard_1005"
montage = mne.channels.make_standard_montage(montage_kind)
mne.datasets.eegbci.standardize(raw)
raw.set_montage(montage)
# Extract some info
eeg_index = mne.pick_types(raw.info, eeg=True, eog=False, meg=False)
ch_names = raw.info["ch_names"]
ch_names_eeg = list(np.asarray(ch_names)[eeg_index])
sample_rate = raw.info["sfreq"]
# Make a copy of the data
raw_copy = raw.copy()
raw_copy.load_data()
# Trim duplicated data (only needed for sub-005)
annot = raw_copy.annotations
file_starts = [a for a in annot if a['description'] == "file start"]
if len(file_starts):
duplicate_start = file_starts[0]['onset']
raw_copy.crop(tmax=duplicate_start)
# Make backup of EOG and EMG channels to re-append after PREP
raw_other = raw_copy.copy()
raw_other.pick_types(eog=True, emg=True, stim=False)
# Prepare copy of raw data for PREP
raw_copy.pick_types(eeg=True)
# Plot data prior to any processing
if complete:
save_psd_plot(id_num, "psd_0_raw", plot_path, raw_copy)
save_channel_plot(id_num, "ch_0_raw", plot_path, raw_copy)
### Clean up events #######################################################
print("\n\n=== Processing Event Annotations... ===\n")
event_names = [
"stim_on", "red_on", "trace_start", "trace_end", "accuracy_submit",
"vividness_submit"
]
doubled = []
wrong_label = []
new_onsets = []
new_durations = []
new_descriptions = []
# Find and flag any duplicate triggers
annot = raw_copy.annotations
trigger_count = len(annot)
for i in range(1, trigger_count - 1):
a = annot[i]
on_last = i + 1 == trigger_count
prev_trigger = annot[i - 1]['description']
next_onset = annot[i + 1]['onset'] if not on_last else a['onset'] + 100
# Determine whether duplicates are doubles or mislabeled
if a['description'] == prev_trigger:
if (next_onset - a['onset']) < 0.002:
doubled.append(a)
else:
wrong_label.append(a)
# Rename annotations to have meaningful names & fix duplicates
for a in raw_copy.annotations:
if a in doubled or a['description'] not in event_names:
continue
if a in wrong_label:
index = event_names.index(a['description'])
a['description'] = event_names[index + 1]
new_onsets.append(a['onset'])
new_durations.append(a['duration'])
new_descriptions.append(a['description'])
# Replace old annotations with new fixed ones
if len(annot):
new_annot = mne.Annotations(
new_onsets,
new_durations,
new_descriptions,
orig_time=raw_copy.annotations[0]['orig_time'])
raw_copy.set_annotations(new_annot)
# Check annotations to verify we have equal numbers of each
orig_counts = Counter(annot.description)
counts = Counter(raw_copy.annotations.description)
print("Updated Annotation Counts:")
for a in event_names:
out = " - '{0}': {1} -> {2}"
print(out.format(a, orig_counts[a], counts[a]))
# Get info
id_info['annot_doubled'] = len(doubled)
id_info['annot_wrong'] = len(wrong_label)
count_vals = [
n for n in counts.values() if n != counts['vividness_submit']
]
id_info['equal_triggers'] = all(x == count_vals[0] for x in count_vals)
id_info['stim_on'] = counts['stim_on']
id_info['red_on'] = counts['red_on']
id_info['trace_start'] = counts['trace_start']
id_info['trace_end'] = counts['trace_end']
id_info['acc_submit'] = counts['accuracy_submit']
id_info['vivid_submit'] = counts['vividness_submit']
if not complete:
remaining_info = {
'initial_bad': "NA",
'num_initial_bad': "NA",
'interpolated': "NA",
'num_interpolated': "NA",
'remaining_bad': "NA",
'num_remaining_bad': "NA"
}
id_info.update(remaining_info)
e = "\n\n### Incomplete recording for sub-{0}, skipping... ###\n\n"
print(e.format(id_num))
return id_info
### Run components of PREP manually #######################################
print("\n\n=== Performing CleanLine... ===")
# Try to remove line noise using CleanLine approach
linenoise = np.arange(60, sample_rate / 2, 60)
EEG_raw = raw_copy.get_data() * 1e6
EEG_new = removeTrend(EEG_raw, sample_rate=raw.info["sfreq"])
EEG_clean = mne.filter.notch_filter(
EEG_new,
Fs=raw.info["sfreq"],
freqs=linenoise,
filter_length="10s",
method="spectrum_fit",
mt_bandwidth=2,
p_value=0.01,
)
EEG_final = EEG_raw - EEG_new + EEG_clean
raw_copy._data = EEG_final * 1e-6
del linenoise, EEG_raw, EEG_new, EEG_clean, EEG_final
# Plot data following cleanline
save_psd_plot(id_num, "psd_1_cleanline", plot_path, raw_copy)
save_channel_plot(id_num, "ch_1_cleanline", plot_path, raw_copy)
# Perform robust re-referencing
prep_params = {"ref_chs": ch_names_eeg, "reref_chs": ch_names_eeg}
reference = Reference(raw_copy,
prep_params,
ransac=True,
random_state=random_seed)
print("\n\n=== Performing Robust Re-referencing... ===\n")
reference.perform_reference()
# If not interpolating bad channels, use pre-interpolation channel data
if not interpolate_bads:
reference.raw._data = reference.EEG_before_interpolation * 1e-6
reference.interpolated_channels = []
reference.still_noisy_channels = reference.bad_before_interpolation
reference.raw.info["bads"] = reference.bad_before_interpolation
# Plot data following robust re-reference
save_psd_plot(id_num, "psd_2_reref", plot_path, reference.raw)
save_channel_plot(id_num, "ch_2_reref", plot_path, reference.raw)
# Re-append removed EMG/EOG/trigger channels
raw_prepped = reference.raw.add_channels([raw_other])
# Get info
initial_bad = reference.noisy_channels_original["bad_all"]
id_info['initial_bad'] = " ".join(initial_bad)
id_info['num_initial_bad'] = len(initial_bad)
interpolated = reference.interpolated_channels
id_info['interpolated'] = " ".join(interpolated)
id_info['num_interpolated'] = len(interpolated)
remaining_bad = reference.still_noisy_channels
id_info['remaining_bad'] = " ".join(remaining_bad)
id_info['num_remaining_bad'] = len(remaining_bad)
# Print re-referencing info
print("\nRe-Referencing Info:")
print(" - Bad channels original: {0}".format(initial_bad))
if interpolate_bads:
print(" - Bad channels after re-referencing: {0}".format(interpolated))
print(" - Bad channels after interpolation: {0}".format(remaining_bad))
else:
print(
" - Bad channels after re-referencing: {0}".format(remaining_bad))
# Check if too many channels were interpolated for the participant
prop_interpolated = len(
reference.interpolated_channels) / len(ch_names_eeg)
e = "### NOTE: Too many interpolated channels for sub-{0} ({1}) ###"
if max_interpolated < prop_interpolated:
print("\n")
print(e.format(id_num, len(reference.interpolated_channels)))
print("\n")
### Filter data and apply ICA to remove blinks ############################
# Apply highpass & lowpass filters
print("\n\n=== Applying Highpass & Lowpass Filters... ===")
raw_prepped.filter(1.0, 50.0, fir_design='firwin')
# Plot data following frequency filters
save_psd_plot(id_num, "psd_3_filtered", plot_path, raw_prepped)
save_channel_plot(id_num, "ch_3_filtered", plot_path, raw_prepped)
# Perform ICA using EOG data on eye blinks
print("\n\n=== Removing Blinks Using ICA... ===\n")
ica = ICA(n_components=20, random_state=random_seed, method='picard')
ica.fit(raw_prepped, decim=5)
eog_indices, eog_scores = ica.find_bads_eog(raw_prepped)
ica.exclude = eog_indices
if not len(ica.exclude):
err = " - Encountered an ICA error for sub-{0}, skipping for now..."
print("\n")
print(err.format(id_num))
print("\n")
save_bad_fif(raw_prepped, id_num, ica_err_dir)
return id_info
# Plot ICA info & diagnostics before removing from signal
save_ica_plots(id_num, plot_path, raw_prepped, ica, eog_scores)
# Remove eye blink independent components based on ICA
ica.apply(raw_prepped)
# Plot data following ICA
save_psd_plot(id_num, "psd_4_ica", plot_path, raw_prepped)
save_channel_plot(id_num, "ch_4_ica", plot_path, raw_prepped)
### Compute Current Source Density (CSD) estimates ########################
if perform_csd:
print("\n")
print("=== Computing Current Source Density (CSD) Estimates... ===\n")
raw_prepped = mne.preprocessing.compute_current_source_density(
raw_prepped.drop_channels(remaining_bad))
# Plot data following CSD
save_psd_plot(id_num, "psd_5_csd", plot_path, raw_prepped)
save_channel_plot(id_num, "ch_5_csd", plot_path, raw_prepped)
### Write preprocessed data to new EDF ####################################
if max_interpolated < prop_interpolated:
if not os.path.isdir(noisy_bad_dir):
os.makedirs(noisy_bad_dir)
outpath = os.path.join(noisy_bad_dir, outfile_fmt.format(id_num))
else:
outpath = os.path.join(outdir, outfile_fmt.format(id_num))
write_mne_edf(outpath, raw_prepped)
print("\n\n### sub-{0} complete! ###\n\n".format(id_num))
return id_info
def run(self):
eog = self.info['channel_info']['EOG']
misc = self.info['channel_info']['Misc']
stim = self.info['channel_info']['Stim']
try:
ext_files = glob.glob(self.info['ext_file_folder'] + '/' +
self.participant + '/*axis0.dat')
except:
pass
tmin = self.t_epoch[0]
tmax = self.t_epoch[1]
raw = read_raw_edf(self.file, eog=eog, misc=misc)
self.raw = cp.deepcopy(raw)
raw.load_data()
# marker detection (one marker continous trial)
if self.info['marker_detection'] == True:
starts = find_trialstart(raw,
stim_channel=raw.ch_names[stim[0]],
new_samplin_rate=self.sr_new)
try:
starts[1] = starts[0] + 30 * 200
except:
starts = np.r_[starts, (starts[0] + 30 * 200)]
events = np.zeros((len(starts), 3))
events[:, 0] = starts
events[:, 2] = list(self.info['event_dict'].values())
events = events.astype(np.int)
# event detection (one marker regular events)
if self.info['event_detection'] == True:
starts = find_trialstart(raw,
stim_channel=raw.ch_names[stim[0]],
new_samplin_rate=self.sr_new)
events = force_events(ext_files, self.info['event_dict'],
self.sr_new, self.info['trial_length'],
self.info['trials'],
starts[:len(self.info['event_dict'])])
if self.info['ICA'] == True:
ica = ICA(method='fastica')
if self.info['Autoreject'] == True:
ar = AutoReject()
## EEG preprocessing options will applied if parameters are set in object
#read montage
try:
montage = make_standard_montage(self.montage)
raw.set_montage(montage)
except:
pass
#resampling
try:
raw.resample(sfreq=self.sr_new)
except:
pass
#rereferencing
try:
raw, _ = mne.set_eeg_reference(raw, ref_channels=['EXG5', 'EXG6'])
except:
pass
#filter
try:
low = self.filter_freqs[0]
high = self.filter_freqs[1]
raw.filter(low, high, fir_design='firwin')
except:
pass
# occular correction
try:
ica.fit(raw)
ica.exclude = []
eog_indices, eog_scores = ica.find_bads_eog(raw)
ica.exclude = eog_indices
ica.apply(raw)
self.ica = ica
except:
pass
picks = mne.pick_types(raw.info,
meg=False,
eeg=True,
stim=False,
eog=False,
exclude='bads')
event_id = self.info['event_dict']
epochs = mne.Epochs(raw,
events,
event_id,
tmin,
tmax,
proj=True,
baseline=None,
preload=True,
picks=picks)
#epoch rejection
try:
epochs = epochs.drop(indices=self.bads)
except:
pass
try:
epochs, self.autoreject_log = ar.fit_transform(epochs,
return_log=True)
except:
pass
bads = np.asarray(
[l == ['USER'] or l == ['AUTOREJECT'] for l in epochs.drop_log])
self.bads = np.where(bads == True)
self.epochs = epochs
return (self)
# estimate average artifact ecg_evoked = ecg_epochs.average() fig = ica.plot_sources(ecg_evoked, exclude=ecg_inds) # plot ECG sources + selection fig.savefig(img_folder + '/ica_ecg_evoked_sources.png') fig = ica.plot_overlay(ecg_evoked, exclude=ecg_inds) # plot ECG cleaning fig.savefig(img_folder + '/ica_ecg_evoked_overlay.png') #eog_evoked = create_eog_epochs(raw, tmin=-.5, tmax=.5, picks=picks).average() #fig = ica.plot_sources(eog_evoked, exclude=eog_inds) # plot EOG sources + selection #fig.savefig(img_folder + '/ica_eog_evoked_sources.png') #fig = ica.plot_overlay(eog_evoked, exclude=eog_inds) # plot EOG cleaning #fig.savefig(img_folder + '/ica_eog_evoked_overlay.png') tmp=ica.exclude ica.exclude = [] veog_evoked = create_eog_epochs(raw, ch_name='EOG001', tmin=-.5, tmax=.5, picks=picks).average() fig = ica.plot_sources(veog_evoked, exclude=veog_inds) # plot EOG sources + selection fig.savefig(img_folder + '/ica_veog_evoked_sources_veog_inds.png') fig = ica.plot_overlay(veog_evoked, exclude=veog_inds) # plot EOG cleaning fig.savefig(img_folder + '/ica_veog_evoked_overlay_veog_inds.png') fig = ica.plot_sources(veog_evoked, exclude=heog_inds) # plot EOG sources + selection fig.savefig(img_folder + '/ica_veog_evoked_sources_heog_inds.png') fig = ica.plot_overlay(veog_evoked, exclude=heog_inds) # plot EOG cleaning fig.savefig(img_folder + '/ica_veog_evoked_overlay_heog_inds.png') fig = ica.plot_sources(veog_evoked, exclude=eog_inds) # plot EOG sources + selection fig.savefig(img_folder + '/ica_veog_evoked_sources_eog_inds.png') fig = ica.plot_overlay(veog_evoked, exclude=eog_inds) # plot EOG cleaning fig.savefig(img_folder + '/ica_veog_evoked_overlay_eog_inds.png') heog_evoked = create_eog_epochs(raw, ch_name='EOG003', tmin=-.5, tmax=.5, picks=picks).average()
json.dump(json_info, outfile, indent=4)
del json_info, json_file
# Estimate ICA
ica = ICA(method='picard', max_iter=1000, random_state=97,
fit_params=dict(ortho=True, extended=True),
verbose=True)
ica.fit(epochs)
# Save ICA
ica_file = deriv_path / f'{sub}_task-{task}_ref-FCz_desc-ica_ica.fif.gz'
ica.save(ica_file)
# Find EOG artifacts
eog_inds, eog_scores = ica.find_bads_eog(raw)
ica.exclude = eog_inds
eog_ica_plot = ica.plot_scores(eog_scores, labels=['VEOG', 'HEOG'])
eog_ica_file = fig_path / f'{sub}_task-{task}_ic_eog_scores.png'
eog_ica_plot.savefig(eog_ica_file, dpi=600)
plt.close(eog_ica_plot)
# Plot all component properties
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}')
# Make a JSON
json_info = {
'Description': 'ICA components',
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 compute_ica(raw, subject, n_components=0.99, picks=None, decim=None,
reject=None, ecg_tmin=-0.5, ecg_tmax=0.5, eog_tmin=-0.5,
eog_tmax=0.5, n_max_ecg=3, n_max_eog=1,
n_max_ecg_epochs=200, show=True, img_scale=1.0,
random_state=None, report=None, artifact_stats=None):
"""Run ICA in raw data
Parameters
----------,
raw : instance of Raw
Raw measurements to be decomposed.
subject : str
The name of the subject.
picks : array-like of int, shape(n_channels, ) | None
Channels to be included. This selection remains throughout the
initialized ICA solution. If None only good data channels are used.
Defaults to None.
n_components : int | float | None | 'rank'
The number of components used for ICA decomposition. If int, it must be
smaller then max_pca_components. If None, all PCA components will be
used. If float between 0 and 1 components can will be selected by the
cumulative percentage of explained variance.
If 'rank', the number of components equals the rank estimate.
Defaults to 0.99.
decim : int | None
Increment for selecting each nth time slice. If None, all samples
within ``start`` and ``stop`` are used. Defalts to None.
reject : dict | None
Rejection parameters based on peak to peak amplitude.
Valid keys are 'grad' | 'mag' | 'eeg' | 'eog' | 'ecg'.
If reject is None then no rejection is done. You should
use such parameters to reject big measurement artifacts
and not EOG for example. It only applies if `inst` is of type Raw.
Defaults to {'mag': 5e-12}
ecg_tmin : float
Start time before ECG event. Defaults to -0.5.
ecg_tmax : float
End time after ECG event. Defaults to 0.5.
eog_tmin : float
Start time before rog event. Defaults to -0.5.
eog_tmax : float
End time after rog event. Defaults to 0.5.
n_max_ecg : int | None
The maximum number of ECG components to exclude. Defaults to 3.
n_max_eog : int | None
The maximum number of EOG components to exclude. Defaults to 1.
n_max_ecg_epochs : int
The maximum number of ECG epochs to use for phase-consistency
estimation. Defaults to 200.
show : bool
Show figure if True
scale_img : float
The scaling factor for the report. Defaults to 1.0.
random_state : None | int | instance of np.random.RandomState
np.random.RandomState to initialize the FastICA estimation.
As the estimation is non-deterministic it can be useful to
fix the seed to have reproducible results. Defaults to None.
report : instance of Report | None
The report object. If None, a new report will be generated.
artifact_stats : None | dict
A dict that contains info on amplitude ranges of artifacts and
numbers of events, etc. by channel type.
Returns
-------
ica : instance of ICA
The ICA solution.
report : dict
A dict with an html report ('html') and artifact statistics ('stats').
"""
if report is None:
report = Report(subject=subject, title='ICA preprocessing')
if n_components == 'rank':
n_components = raw.estimate_rank(picks=picks)
ica = ICA(n_components=n_components, max_pca_components=None,
random_state=random_state, max_iter=256)
ica.fit(raw, picks=picks, decim=decim, reject=reject)
comment = []
for ch in ('mag', 'grad', 'eeg'):
if ch in ica:
comment += [ch.upper()]
if len(comment) > 0:
comment = '+'.join(comment) + ' '
else:
comment = ''
topo_ch_type = 'mag'
if 'GRAD' in comment and 'MAG' not in comment:
topo_ch_type = 'grad'
elif 'EEG' in comment:
topo_ch_type = 'eeg'
###########################################################################
# 2) identify bad components by analyzing latent sources.
title = '%s related to %s artifacts (red) ({})'.format(subject)
# generate ECG epochs use detection via phase statistics
reject_ = {'mag': 5e-12, 'grad': 5000e-13, 'eeg': 300e-6}
if reject is not None:
reject_.update(reject)
for ch_type in ['mag', 'grad', 'eeg']:
if ch_type not in ica:
reject_.pop(ch_type)
picks_ = np.array([raw.ch_names.index(k) for k in ica.ch_names])
if 'eeg' in ica:
if 'ecg' in raw:
picks_ = np.append(picks_,
pick_types(raw.info, meg=False, ecg=True)[0])
else:
logger.info('There is no ECG channel, trying to guess ECG from '
'magnetormeters')
if artifact_stats is None:
artifact_stats = dict()
ecg_epochs = create_ecg_epochs(raw, tmin=ecg_tmin, tmax=ecg_tmax,
keep_ecg=True, picks=picks_, reject=reject_)
n_ecg_epochs_found = len(ecg_epochs.events)
artifact_stats['ecg_n_events'] = n_ecg_epochs_found
n_max_ecg_epochs = min(n_max_ecg_epochs, n_ecg_epochs_found)
artifact_stats['ecg_n_used'] = n_max_ecg_epochs
sel_ecg_epochs = np.arange(n_ecg_epochs_found)
rng = np.random.RandomState(42)
rng.shuffle(sel_ecg_epochs)
ecg_ave = ecg_epochs.average()
report.add_figs_to_section(ecg_ave.plot(), 'ECG-full', 'artifacts')
ecg_epochs = ecg_epochs[sel_ecg_epochs[:n_max_ecg_epochs]]
ecg_ave = ecg_epochs.average()
report.add_figs_to_section(ecg_ave.plot(), 'ECG-used', 'artifacts')
_put_artifact_range(artifact_stats, ecg_ave, kind='ecg')
ecg_inds, scores = ica.find_bads_ecg(ecg_epochs, method='ctps')
if len(ecg_inds) > 0:
ecg_evoked = ecg_epochs.average()
del ecg_epochs
fig = ica.plot_scores(scores, exclude=ecg_inds, labels='ecg',
title='', show=show)
report.add_figs_to_section(fig, 'scores ({})'.format(subject),
section=comment + 'ECG',
scale=img_scale)
current_exclude = [e for e in ica.exclude] # issue #2608 MNE
fig = ica.plot_sources(raw, ecg_inds, exclude=ecg_inds,
title=title % ('components', 'ecg'), show=show)
report.add_figs_to_section(fig, 'sources ({})'.format(subject),
section=comment + 'ECG',
scale=img_scale)
ica.exclude = current_exclude
fig = ica.plot_components(ecg_inds, ch_type=topo_ch_type,
title='', colorbar=True, show=show)
report.add_figs_to_section(fig, title % ('sources', 'ecg'),
section=comment + 'ECG', scale=img_scale)
ica.exclude = current_exclude
ecg_inds = ecg_inds[:n_max_ecg]
ica.exclude += ecg_inds
fig = ica.plot_sources(ecg_evoked, exclude=ecg_inds, show=show)
report.add_figs_to_section(fig, 'evoked sources ({})'.format(subject),
section=comment + 'ECG',
scale=img_scale)
fig = ica.plot_overlay(ecg_evoked, exclude=ecg_inds, show=show)
report.add_figs_to_section(fig,
'rejection overlay ({})'.format(subject),
section=comment + 'ECG',
scale=img_scale)
# detect EOG by correlation
picks_eog = np.concatenate(
[picks_, pick_types(raw.info, meg=False, eeg=False, ecg=False,
eog=True)])
eog_epochs = create_eog_epochs(raw, tmin=eog_tmin, tmax=eog_tmax,
picks=picks_eog, reject=reject_)
artifact_stats['eog_n_events'] = len(eog_epochs.events)
artifact_stats['eog_n_used'] = artifact_stats['eog_n_events']
eog_ave = eog_epochs.average()
report.add_figs_to_section(eog_ave.plot(), 'EOG-used', 'artifacts')
_put_artifact_range(artifact_stats, eog_ave, kind='eog')
eog_inds = None
if len(eog_epochs.events) > 0:
eog_inds, scores = ica.find_bads_eog(eog_epochs)
if eog_inds is not None and len(eog_epochs.events) > 0:
fig = ica.plot_scores(scores, exclude=eog_inds, labels='eog',
show=show, title='')
report.add_figs_to_section(fig, 'scores ({})'.format(subject),
section=comment + 'EOG',
scale=img_scale)
current_exclude = [e for e in ica.exclude] # issue #2608 MNE
fig = ica.plot_sources(raw, eog_inds, exclude=ecg_inds,
title=title % ('sources', 'eog'), show=show)
report.add_figs_to_section(fig, 'sources', section=comment + 'EOG',
scale=img_scale)
ica.exclude = current_exclude
fig = ica.plot_components(eog_inds, ch_type=topo_ch_type,
title='', colorbar=True, show=show)
report.add_figs_to_section(fig, title % ('components', 'eog'),
section=comment + 'EOG', scale=img_scale)
ica.exclude = current_exclude
eog_inds = eog_inds[:n_max_eog]
ica.exclude += eog_inds
eog_evoked = eog_epochs.average()
fig = ica.plot_sources(eog_evoked, exclude=eog_inds, show=show)
report.add_figs_to_section(
fig, 'evoked sources ({})'.format(subject),
section=comment + 'EOG', scale=img_scale)
fig = ica.plot_overlay(eog_evoked, exclude=eog_inds, show=show)
report.add_figs_to_section(
fig, 'rejection overlay({})'.format(subject),
section=comment + 'EOG', scale=img_scale)
else:
del eog_epochs
# check the amplitudes do not change
if len(ica.exclude) > 0:
fig = ica.plot_overlay(raw, show=show) # EOG artifacts remain
html = _render_components_table(ica)
report.add_htmls_to_section(
html, captions='excluded components',
section='ICA rejection summary (%s)' % ch_type)
report.add_figs_to_section(
fig, 'rejection overlay({})'.format(subject),
section=comment + 'RAW', scale=img_scale)
return ica, dict(html=report, stats=artifact_stats)
def ICA_pipeline(mne_array,
regions,
chans_to_plot=20,
base_name="",
exclude=None,
skip_plots=False):
"""This is example code using mne."""
raw = mne_array
if not skip_plots:
# Plot raw signal
raw.plot(n_channels=chans_to_plot,
block=True,
duration=25,
show=True,
clipping="transparent",
title="Raw LFP Data from {}".format(base_name),
remove_dc=False,
scalings=dict(eeg=350e-6))
# Perform ICA using mne
from mne.preprocessing import ICA
filt_raw = raw.copy()
filt_raw.load_data().filter(l_freq=1., h_freq=None)
ica = ICA(method='fastica', random_state=97)
# ica = ICA(method='picard', random_state=97)
ica.fit(filt_raw)
# ica.exclude = [4, 6, 12]
raw.load_data()
if exclude is None:
# Plot raw ICAs
print('Select channels to exclude using this plot...')
ica.plot_sources(raw,
block=False,
stop=25,
title='ICA from {}'.format(base_name))
print('Click topo to get more ICA properties')
ica.plot_components(inst=raw)
# Overlay ICA cleaned signal over raw. Seperate plot for each region.
# TODO Add scroll bar or include window selection option.
# cont = input("Plot region overlay? (y|n) \n")
# if cont.strip().lower() == "y":
# reg_grps = []
# for reg in set(regions):
# temp_grp = []
# for ch in raw.info.ch_names:
# if reg in ch:
# temp_grp.append(ch)
# reg_grps.append(temp_grp)
# for grps in reg_grps:
# ica.plot_overlay(raw, stop=int(30 * 250), title='{}'.format(
# grps[0][:3]), picks=grps)
else:
# ICAs to exclude
ica.exclude = exclude
if not skip_plots:
ica.plot_sources(raw,
block=False,
stop=25,
title='ICA from {}'.format(base_name))
ica.plot_components(inst=raw)
# Apply ICA exclusion
reconst_raw = raw.copy()
exclude_raw = raw.copy()
print("ICAs excluded: ", ica.exclude)
ica.apply(reconst_raw)
if not skip_plots:
# change exclude to all except chosen ICs
all_ICs = list(range(ica.n_components_))
for i in ica.exclude:
all_ICs.remove(i)
ica.exclude = all_ICs
ica.apply(exclude_raw)
# Plot excluded ICAs
exclude_raw.plot(block=True,
show=True,
clipping="transparent",
duration=25,
title="Excluded ICs from {}".format(base_name),
remove_dc=False,
scalings=dict(eeg=350e-6))
# Plot reconstructed signals w/o excluded ICAs
reconst_raw.plot(
block=True,
show=True,
clipping="transparent",
duration=25,
title="Reconstructed LFP Data from {}".format(base_name),
remove_dc=False,
scalings=dict(eeg=350e-6))
return reconst_raw
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 test_plot_ica_sources(raw_orig, mpl_backend):
"""Test plotting of ICA panel."""
raw = raw_orig.copy().crop(0, 1)
picks = _get_picks(raw)
epochs = _get_epochs()
raw.pick_channels([raw.ch_names[k] for k in picks])
ica_picks = pick_types(raw.info,
meg=True,
eeg=False,
stim=False,
ecg=False,
eog=False,
exclude='bads')
ica = ICA(n_components=2)
ica.fit(raw, picks=ica_picks)
ica.exclude = [1]
fig = ica.plot_sources(raw)
assert mpl_backend._get_n_figs() == 1
# change which component is in ICA.exclude (click data trace to remove
# current one; click name to add other one)
fig._redraw()
# ToDo: This will be different methods in pyqtgraph
x = fig.mne.traces[1].get_xdata()[5]
y = fig.mne.traces[1].get_ydata()[5]
fig._fake_click((x, y), xform='data') # exclude = []
_click_ch_name(fig, ch_index=0, button=1) # exclude = [0]
fig._fake_keypress(fig.mne.close_key)
fig._close_event()
assert mpl_backend._get_n_figs() == 0
assert_array_equal(ica.exclude, [0])
# test when picks does not include ica.exclude.
fig = ica.plot_sources(raw, picks=[1])
assert len(plt.get_fignums()) == 1
mpl_backend._close_all()
# dtype can change int->np.int64 after load, test it explicitly
ica.n_components_ = np.int64(ica.n_components_)
# test clicks on y-label (need >2 secs for plot_properties() to work)
long_raw = raw_orig.crop(0, 5)
fig = ica.plot_sources(long_raw)
assert len(plt.get_fignums()) == 1
fig._redraw()
_click_ch_name(fig, ch_index=0, button=3)
assert len(fig.mne.child_figs) == 1
assert len(plt.get_fignums()) == 2
# close child fig directly (workaround for mpl issue #18609)
fig._fake_keypress('escape', fig=fig.mne.child_figs[0])
assert len(plt.get_fignums()) == 1
fig._fake_keypress(fig.mne.close_key)
assert len(plt.get_fignums()) == 0
del long_raw
# test with annotations
orig_annot = raw.annotations
raw.set_annotations(Annotations([0.2], [0.1], 'Test'))
fig = ica.plot_sources(raw)
assert len(fig.mne.ax_main.collections) == 1
assert len(fig.mne.ax_hscroll.collections) == 1
raw.set_annotations(orig_annot)
# test error handling
raw_ = raw.copy().load_data()
raw_.drop_channels('MEG 0113')
with pytest.raises(RuntimeError, match="Raw doesn't match fitted data"), \
pytest.warns(RuntimeWarning, match='could not be picked'):
ica.plot_sources(inst=raw_)
epochs_ = epochs.copy().load_data()
epochs_.drop_channels('MEG 0113')
with pytest.raises(RuntimeError, match="Epochs don't match fitted data"), \
pytest.warns(RuntimeWarning, match='could not be picked'):
ica.plot_sources(inst=epochs_)
del raw_
del epochs_
# test w/ epochs and evokeds
ica.plot_sources(epochs)
ica.plot_sources(epochs.average())
evoked = epochs.average()
fig = ica.plot_sources(evoked)
# Test a click
ax = fig.get_axes()[0]
line = ax.lines[0]
_fake_click(fig, ax, [line.get_xdata()[0], line.get_ydata()[0]], 'data')
_fake_click(fig, ax, [ax.get_xlim()[0], ax.get_ylim()[1]], 'data')
# plot with bad channels excluded
ica.exclude = [0]
ica.plot_sources(evoked)
# pretend find_bads_eog() yielded some results
ica.labels_ = {'eog': [0], 'eog/0/crazy-channel': [0]}
ica.plot_sources(evoked) # now with labels
# pass an invalid inst
with pytest.raises(ValueError, match='must be of Raw or Epochs type'):
ica.plot_sources('meeow')
def run_preprocessing_eog(raw_eeg,
tmin=0,
tmax=60,
remove_artefact=True,
show=True):
'''Function to remove occular artefact by removing the ICA component(s) that are closest to a reference channel (here Fp2)
Parameters
----------
raw_eeg : Raw file
tmin : default 0
tmax : default 60
remove_artefact : wether to remove the ICA component from raw (default True)
show : show scores (default : true)
Return
------
Return cleaned raw or original raw if remove_artefact = True or no matching components were found.
'''
raw_inter = raw_eeg.copy().crop(tmin=tmin, tmax=tmax)
filtered_raw = raw_inter.filter(l_freq=1., h_freq=40.)
ica = ICA(n_components=raw_eeg.info.get('nchan') - 2, random_state=9)
print(raw_eeg.info)
ica.fit(filtered_raw, verbose=False)
ica.exclude = []
# find which ICs match the EOG pattern
eog_indices, eog_scores = ica.find_bads_eog(raw_inter,
ch_name='Fp2',
threshold=1.4,
verbose=False)
ica.exclude = eog_indices
if show == True:
ica.plot_sources(filtered_raw)
ica.plot_components()
# barplot of ICA component "EOG match" scores
ica.plot_scores(eog_scores)
#ica.plot_overlay(raw_inter)
#ica.plot_properties(raw_inter)
if eog_indices != []:
print('matching ICA component found')
# plot diagnostics
#ica.plot_properties(filtered_raw, picks=eog_indices)
# plot ICs applied to raw data, with EOG matches highlighted
if show == True:
ica.plot_sources(raw_inter)
if remove_artefact == True:
reconst_raw = filtered_raw.copy()
ica.apply(reconst_raw)
return reconst_raw
else:
return filtered_raw
else:
print('No matching ICA component')
return filtered_raw
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))
def test_plot_ica_sources():
"""Test plotting of ICA panel."""
raw = read_raw_fif(raw_fname).crop(0, 1).load_data()
picks = _get_picks(raw)
epochs = _get_epochs()
raw.pick_channels([raw.ch_names[k] for k in picks])
ica_picks = pick_types(raw.info,
meg=True,
eeg=False,
stim=False,
ecg=False,
eog=False,
exclude='bads')
ica = ICA(n_components=2)
ica.fit(raw, picks=ica_picks)
ica.exclude = [1]
fig = ica.plot_sources(raw)
assert len(plt.get_fignums()) == 1
# change which component is in ICA.exclude (click data trace to remove
# current one; click name to add other one)
fig.canvas.draw()
x = fig.mne.traces[1].get_xdata()[5]
y = fig.mne.traces[1].get_ydata()[5]
_fake_click(fig, fig.mne.ax_main, (x, y), xform='data') # exclude = []
_click_ch_name(fig, ch_index=0, button=1) # exclude = [0]
fig.canvas.key_press_event(fig.mne.close_key)
_close_event(fig)
assert len(plt.get_fignums()) == 0
assert_array_equal(ica.exclude, [0])
# test when picks does not include ica.exclude.
fig = ica.plot_sources(raw, picks=[1])
assert len(plt.get_fignums()) == 1
plt.close('all')
# dtype can change int->np.int64 after load, test it explicitly
ica.n_components_ = np.int64(ica.n_components_)
# test clicks on y-label (need >2 secs for plot_properties() to work)
long_raw = read_raw_fif(raw_fname).crop(0, 5).load_data()
fig = ica.plot_sources(long_raw)
assert len(plt.get_fignums()) == 1
fig.canvas.draw()
_fake_click(fig, fig.mne.ax_main, (-0.1, 0), xform='data', button=3)
assert len(fig.mne.child_figs) == 1
assert len(plt.get_fignums()) == 2
# close child fig directly (workaround for mpl issue #18609)
fig.mne.child_figs[0].canvas.key_press_event('escape')
assert len(plt.get_fignums()) == 1
fig.canvas.key_press_event(fig.mne.close_key)
assert len(plt.get_fignums()) == 0
del long_raw
# test with annotations
orig_annot = raw.annotations
raw.set_annotations(Annotations([0.2], [0.1], 'Test'))
fig = ica.plot_sources(raw)
assert len(fig.mne.ax_main.collections) == 1
assert len(fig.mne.ax_hscroll.collections) == 1
raw.set_annotations(orig_annot)
# test error handling
raw.info['bads'] = ['MEG 0113']
with pytest.raises(RuntimeError, match="Raw doesn't match fitted data"):
ica.plot_sources(inst=raw)
epochs.info['bads'] = ['MEG 0113']
with pytest.raises(RuntimeError, match="Epochs don't match fitted data"):
ica.plot_sources(inst=epochs)
epochs.info['bads'] = []
# test w/ epochs and evokeds
ica.plot_sources(epochs)
ica.plot_sources(epochs.average())
evoked = epochs.average()
fig = ica.plot_sources(evoked)
# Test a click
ax = fig.get_axes()[0]
line = ax.lines[0]
_fake_click(fig, ax, [line.get_xdata()[0], line.get_ydata()[0]], 'data')
_fake_click(fig, ax, [ax.get_xlim()[0], ax.get_ylim()[1]], 'data')
# plot with bad channels excluded
ica.exclude = [0]
ica.plot_sources(evoked)
ica.labels_ = dict(eog=[0])
ica.labels_['eog/0/crazy-channel'] = [0]
ica.plot_sources(evoked) # now with labels
with pytest.raises(ValueError, match='must be of Raw or Epochs type'):
ica.plot_sources('meeow')
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 run_preprocessing_eog(raw_eeg, tmin=0, remove_artefact=True, show=False):
'''
Remove EOG artefacts
Parameters
----------
raw_eeg : mne raw file
tmin : minimum time to consider (default = 0)
remove_artefact : whether to remove artefacts once found (default = True)
show : Whether to show plots (components, signal before and after ... )
Return
------
Clean raw file if remove artefact is true, original raw file otherwise
'''
raw_inter = raw_eeg.copy().crop(tmin=tmin)
filtered_raw = raw_inter.filter(l_freq=3., h_freq=40.)
print(filtered_raw.annotations)
ica = ICA(n_components=raw_eeg.info.get('nchan'), random_state=9)
ica.fit(filtered_raw, verbose=False)
ica.exclude = []
# find which ICs match the EOG pattern
eog_indices, eog_scores = ica.find_bads_eog(raw_inter,
threshold=1.6,
ch_name='Fpz',
verbose=False)
eog_indices.append(3)
#eog_indices.append(4)
ica.exclude = eog_indices
if show == True:
ica.plot_sources(filtered_raw)
ica.plot_components()
# barplot of ICA component "EOG match" scores
#ica.plot_scores(eog_scores)
ica.plot_overlay(raw_inter)
#ica.plot_properties(raw_inter)
if eog_indices != []:
print('matching ICA component found')
# plot diagnostics
#ica.plot_properties(filtered_raw, picks=eog_indices)
# plot ICs applied to raw data, with EOG matches highlighted
if show == True:
ica.plot_sources(raw_inter)
if remove_artefact == True:
reconst_raw = filtered_raw.copy()
ica.apply(reconst_raw)
return reconst_raw.filter(3, 40)
else:
return filtered_raw
else:
print('No matching ICA component')
return filtered_raw
raw = raw.filter(filt_l, filt_h)
print("Finding events...")
events = find_events(raw) # the output of this is a 3 x n_trial np array
print("Epoching data...")
epochs = Epochs(raw, events, tmin=tmin, tmax=tmax, decim=5, baseline=None)
print("Creating ICA object...")
# apply ICA to the conjoint data
picks = pick_types(raw.info, meg=True, exclude='bads')
ica = ICA(n_components=0.9, method='fastica', max_iter=300)
print("Fitting epochs...")
# get ica components
ica.exclude = []
ica.fit(epochs, picks=picks)
print("Saving ICA solution...")
ica.save(ica_fname) # save solution
#__________________________________________________________
subject = 'A0307'
meg_dir = '/Users/ea84/Dropbox/shepard_sourceloc/%s/' % (subject)
raw_fname = meg_dir + subject + '_shepard-raw.fif'
ica_fname = meg_dir + subject + '_shepard_ica1-ica.fif'
ica_raw_fname = meg_dir + subject + '_ica_shepard-raw.fif' # applied ica to raw
# params
filt_l = 1 # same as aquisition
ica.plot_sources(raw)
ica.plot_components()
# notify when done
os.system('say "... I am ready for you Neil."')
#%% Select components to exclude and zero them out
rm_select = [0, 3, 8]
# blinks
ica.plot_overlay(raw, exclude=rm_select, picks='eeg')
# indices chosen based on various plots above
ica.exclude = rm_select
# apply ICA
# ica.apply() changes the Raw object in-place:
ica.apply(raw)
# plot raw data excluding ocular artifacts for quality check
raw.plot()
#%% Fit autoreject
events = mne.make_fixed_length_events(raw, duration=tstep)
epochs = mne.Epochs(raw,
events,
tmin=0.0,
tmax=tstep,
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)
print('Fit %d components (explaining at least %0.1f%% of the variance)'
% (ica.n_components_, 100 * n_components))
# Find onsets of heart beats and blinks. Create epochs around them
ecg_epochs = create_ecg_epochs(raw, tmin=-.3, tmax=.3, preload=False)
eog_epochs = create_eog_epochs(raw, tmin=-.5, tmax=.5, preload=False)
# Find ICA components that correlate with heart beats.
ecg_epochs.decimate(5)
ecg_epochs.load_data()
ecg_epochs.apply_baseline((None, None))
ecg_inds, ecg_scores = ica.find_bads_ecg(ecg_epochs, method='ctps')
ecg_scores = np.abs(ecg_scores)
rank = np.argsort(ecg_scores)[::-1]
rank = [r for r in rank if ecg_scores[r] > 0.05]
ica.exclude = rank[:n_ecg_components]
print(' Found %d ECG indices' % (len(ecg_inds),))
# Find ICA components that correlate with eye blinks
eog_epochs.decimate(5)
eog_epochs.load_data()
eog_epochs.apply_baseline((None, None))
eog_inds, eog_scores = ica.find_bads_eog(eog_epochs)
eog_scores = np.max(np.abs(eog_scores), axis=0)
# Remove all components with a correlation > 0.1 to the EOG channels and that
# have not already been flagged as ECG components
rank = np.argsort(eog_scores)[::-1]
rank = [r for r in rank if eog_scores[r] > 0.1 and r not in ecg_inds]
ica.exclude += rank[:n_eog_components]
print(' Found %d EOG indices' % (len(eog_inds),))