def test_simulate_evoked():
""" Test simulation of evoked data """
raw = Raw(raw_fname)
fwd = read_forward_solution(fwd_fname, force_fixed=True)
fwd = pick_types_forward(fwd, meg=True, eeg=True, exclude=raw.info['bads'])
cov = read_cov(cov_fname)
evoked_template = read_evokeds(ave_fname, condition=0, baseline=None)
evoked_template.pick_types(meg=True, eeg=True, exclude=raw.info['bads'])
snr = 6 # dB
tmin = -0.1
sfreq = 1000. # Hz
tstep = 1. / sfreq
n_samples = 600
times = np.linspace(tmin, tmin + n_samples * tstep, n_samples)
# Generate times series for 2 dipoles
stc = simulate_sparse_stc(fwd['src'], n_dipoles=2, times=times)
stc._data *= 1e-9
# Generate noisy evoked data
iir_filter = [1, -0.9]
evoked = simulate_evoked(fwd, stc, evoked_template.info, cov, snr,
tmin=0.0, tmax=0.2, iir_filter=iir_filter)
assert_array_almost_equal(evoked.times, stc.times)
assert_true(len(evoked.data) == len(fwd['sol']['data']))
# make a vertex that doesn't exist in fwd, should throw error
stc_bad = stc.copy()
mv = np.max(fwd['src'][0]['vertno'][fwd['src'][0]['inuse']])
stc_bad.vertices[0][0] = mv + 1
assert_raises(RuntimeError, simulate_evoked, fwd, stc_bad,
evoked_template.info, cov, snr, tmin=0.0, tmax=0.2)
evoked_1 = simulate_evoked(fwd, stc, evoked_template.info, cov, np.inf,
tmin=0.0, tmax=0.2)
evoked_2 = simulate_evoked(fwd, stc, evoked_template.info, cov, np.inf,
tmin=0.0, tmax=0.2)
assert_array_equal(evoked_1.data, evoked_2.data)
# test snr definition in dB
evoked_noise = simulate_evoked(fwd, stc, evoked_template.info, cov,
snr=snr, tmin=None, tmax=None,
iir_filter=None)
evoked_clean = simulate_evoked(fwd, stc, evoked_template.info, cov,
snr=np.inf, tmin=None, tmax=None,
iir_filter=None)
noise = evoked_noise.data - evoked_clean.data
empirical_snr = 10 * np.log10(np.mean((evoked_clean.data ** 2).ravel()) /
np.mean((noise ** 2).ravel()))
assert_almost_equal(snr, empirical_snr, decimal=5)
cov['names'] = cov.ch_names[:-2] # Error channels are different.
assert_raises(ValueError, simulate_evoked, fwd, stc, evoked_template.info,
cov, snr=3., tmin=None, tmax=None, iir_filter=None)
def _make_stc(raw, src):
"""Helper to make a STC."""
seed = 42
sfreq = raw.info['sfreq'] # Hz
tstep = 1. / sfreq
n_samples = len(raw.times) // 10
times = np.arange(0, n_samples) * tstep
stc = simulate_sparse_stc(src, 10, times, random_state=seed)
return stc
def test_simulate_evoked():
"""Test simulation of evoked data."""
raw = read_raw_fif(raw_fname)
fwd = read_forward_solution(fwd_fname)
fwd = convert_forward_solution(fwd, force_fixed=True, use_cps=False)
fwd = pick_types_forward(fwd, meg=True, eeg=True, exclude=raw.info['bads'])
cov = read_cov(cov_fname)
evoked_template = read_evokeds(ave_fname, condition=0, baseline=None)
evoked_template.pick_types(meg=True, eeg=True, exclude=raw.info['bads'])
cov = regularize(cov, evoked_template.info)
nave = evoked_template.nave
tmin = -0.1
sfreq = 1000. # Hz
tstep = 1. / sfreq
n_samples = 600
times = np.linspace(tmin, tmin + n_samples * tstep, n_samples)
# Generate times series for 2 dipoles
stc = simulate_sparse_stc(fwd['src'], n_dipoles=2, times=times,
random_state=42)
# Generate noisy evoked data
iir_filter = [1, -0.9]
evoked = simulate_evoked(fwd, stc, evoked_template.info, cov,
iir_filter=iir_filter, nave=nave)
assert_array_almost_equal(evoked.times, stc.times)
assert_true(len(evoked.data) == len(fwd['sol']['data']))
assert_equal(evoked.nave, nave)
# make a vertex that doesn't exist in fwd, should throw error
stc_bad = stc.copy()
mv = np.max(fwd['src'][0]['vertno'][fwd['src'][0]['inuse']])
stc_bad.vertices[0][0] = mv + 1
assert_raises(RuntimeError, simulate_evoked, fwd, stc_bad,
evoked_template.info, cov)
evoked_1 = simulate_evoked(fwd, stc, evoked_template.info, cov,
nave=np.inf)
evoked_2 = simulate_evoked(fwd, stc, evoked_template.info, cov,
nave=np.inf)
assert_array_equal(evoked_1.data, evoked_2.data)
# Test the equivalence snr to nave
with warnings.catch_warnings(record=True): # deprecation
evoked = simulate_evoked(fwd, stc, evoked_template.info, cov,
snr=6, random_state=42)
assert_allclose(np.linalg.norm(evoked.data, ord='fro'),
0.00078346820226502716)
cov['names'] = cov.ch_names[:-2] # Error channels are different.
assert_raises(ValueError, simulate_evoked, fwd, stc, evoked_template.info,
cov, nave=nave, iir_filter=None)
def test_simulate_evoked():
"""Test simulation of evoked data."""
raw = read_raw_fif(raw_fname)
fwd = read_forward_solution(fwd_fname)
fwd = convert_forward_solution(fwd, force_fixed=True, use_cps=False)
fwd = pick_types_forward(fwd, meg=True, eeg=True, exclude=raw.info['bads'])
cov = read_cov(cov_fname)
evoked_template = read_evokeds(ave_fname, condition=0, baseline=None)
evoked_template.pick_types(meg=True, eeg=True, exclude=raw.info['bads'])
cov = regularize(cov, evoked_template.info)
nave = evoked_template.nave
tmin = -0.1
sfreq = 1000. # Hz
tstep = 1. / sfreq
n_samples = 600
times = np.linspace(tmin, tmin + n_samples * tstep, n_samples)
# Generate times series for 2 dipoles
stc = simulate_sparse_stc(fwd['src'], n_dipoles=2, times=times,
random_state=42)
# Generate noisy evoked data
iir_filter = [1, -0.9]
evoked = simulate_evoked(fwd, stc, evoked_template.info, cov,
iir_filter=iir_filter, nave=nave)
assert_array_almost_equal(evoked.times, stc.times)
assert len(evoked.data) == len(fwd['sol']['data'])
assert_equal(evoked.nave, nave)
assert len(evoked.info['projs']) == len(cov['projs'])
evoked_white = whiten_evoked(evoked, cov)
assert abs(evoked_white.data[:, 0].std() - 1.) < 0.1
# make a vertex that doesn't exist in fwd, should throw error
stc_bad = stc.copy()
mv = np.max(fwd['src'][0]['vertno'][fwd['src'][0]['inuse']])
stc_bad.vertices[0][0] = mv + 1
pytest.raises(RuntimeError, simulate_evoked, fwd, stc_bad,
evoked_template.info, cov)
evoked_1 = simulate_evoked(fwd, stc, evoked_template.info, cov,
nave=np.inf)
evoked_2 = simulate_evoked(fwd, stc, evoked_template.info, cov,
nave=np.inf)
assert_array_equal(evoked_1.data, evoked_2.data)
cov['names'] = cov.ch_names[:-2] # Error channels are different.
with pytest.raises(RuntimeError, match='Not all channels present'):
simulate_evoked(fwd, stc, evoked_template.info, cov)
def test_metrics():
"""Test simulation metrics"""
src = read_source_spaces(src_fname)
times = np.arange(600) / 1000.
rng = np.random.RandomState(42)
stc1 = simulate_sparse_stc(src, n_dipoles=2, times=times, random_state=rng)
stc2 = simulate_sparse_stc(src, n_dipoles=2, times=times, random_state=rng)
E1_rms = source_estimate_quantification(stc1, stc1, metric='rms')
E2_rms = source_estimate_quantification(stc2, stc2, metric='rms')
E1_cos = source_estimate_quantification(stc1, stc1, metric='cosine')
E2_cos = source_estimate_quantification(stc2, stc2, metric='cosine')
# ### Tests to add
assert_true(E1_rms == 0.)
assert_true(E2_rms == 0.)
assert_almost_equal(E1_cos, 0.)
assert_almost_equal(E2_cos, 0.)
stc_bad = stc2.copy().crop(0, 0.5)
assert_raises(ValueError, source_estimate_quantification, stc1, stc_bad)
stc_bad = stc2.copy()
stc_bad.tmin -= 0.1
assert_raises(ValueError, source_estimate_quantification, stc1, stc_bad)
assert_raises(ValueError, source_estimate_quantification, stc1, stc2,
metric='foo')
def test_simulate_evoked():
""" Test simulation of evoked data """
raw = Raw(raw_fname)
fwd = read_forward_solution(fwd_fname, force_fixed=True)
fwd = pick_types_forward(fwd, meg=True, eeg=True, exclude=raw.info['bads'])
cov = read_cov(cov_fname)
evoked_template = read_evokeds(ave_fname, condition=0, baseline=None)
evoked_template.pick_types(meg=True, eeg=True, exclude=raw.info['bads'])
snr = 6 # dB
tmin = -0.1
sfreq = 1000. # Hz
tstep = 1. / sfreq
n_samples = 600
times = np.linspace(tmin, tmin + n_samples * tstep, n_samples)
# Generate times series for 2 dipoles
stc = simulate_sparse_stc(fwd['src'], n_dipoles=2, times=times)
stc._data *= 1e-9
# Generate noisy evoked data
iir_filter = [1, -0.9]
evoked = simulate_evoked(fwd, stc, evoked_template.info, cov, snr,
tmin=0.0, tmax=0.2, iir_filter=iir_filter)
assert_array_almost_equal(evoked.times, stc.times)
assert_true(len(evoked.data) == len(fwd['sol']['data']))
# make a vertex that doesn't exist in fwd, should throw error
stc_bad = stc.copy()
mv = np.max(fwd['src'][0]['vertno'][fwd['src'][0]['inuse']])
stc_bad.vertices[0][0] = mv + 1
assert_raises(RuntimeError, simulate_evoked, fwd, stc_bad,
evoked_template.info, cov, snr, tmin=0.0, tmax=0.2)
evoked_1 = simulate_evoked(fwd, stc, evoked_template.info, cov, np.inf,
tmin=0.0, tmax=0.2)
evoked_2 = simulate_evoked(fwd, stc, evoked_template.info, cov, np.inf,
tmin=0.0, tmax=0.2)
assert_array_equal(evoked_1.data, evoked_2.data)
labels = [mne.read_label(data_path + '/MEG/sample/labels/%s.label' % ln)
for ln in label_names]
###############################################################################
# Generate source time courses from 2 dipoles and the correspond evoked data
times = np.arange(300, dtype=np.float) / raw.info['sfreq'] - 0.1
rng = np.random.RandomState(42)
def data_fun(times):
"""Function to generate random source time courses"""
return (1e-9 * np.sin(30. * times) *
np.exp(- (times - 0.15 + 0.05 * rng.randn(1)) ** 2 / 0.01))
stc = simulate_sparse_stc(fwd['src'], n_dipoles=2, times=times,
random_state=42, labels=labels, data_fun=data_fun)
###############################################################################
# Generate noisy evoked data
picks = mne.pick_types(raw.info, meg=True, exclude='bads')
iir_filter = fit_iir_model_raw(raw, order=5, picks=picks, tmin=60, tmax=180)[1]
snr = 6. # dB
evoked = simulate_evoked(fwd, stc, info, cov, snr, iir_filter=iir_filter)
###############################################################################
# Plot
plot_sparse_source_estimates(fwd['src'], stc, bgcolor=(1, 1, 1),
opacity=0.5, high_resolution=True)
plt.figure()
plt.psd(evoked.data[0])
"""Generate time-staggered sinusoids at harmonics of 10Hz"""
global n
n_samp = len(times)
window = np.zeros(n_samp)
start, stop = [int(ii * float(n_samp) / (2 * n_dipoles))
for ii in (2 * n, 2 * n + 1)]
window[start:stop] = 1.
n += 1
data = 25e-9 * np.sin(2. * np.pi * 10. * n * times)
data *= window
return data
times = raw.times[:int(raw.info['sfreq'] * epoch_duration)]
src = read_source_spaces(src_fname)
stc = simulate_sparse_stc(src, n_dipoles=n_dipoles, times=times,
data_fun=data_fun, random_state=0)
# look at our source data
fig, ax = plt.subplots(1)
ax.plot(times, 1e9 * stc.data.T)
ax.set(ylabel='Amplitude (nAm)', xlabel='Time (sec)')
mne.viz.utils.plt_show()
##############################################################################
# Simulate raw data
raw_sim = simulate_raw(raw, stc, trans_fname, src, bem_fname, cov='simple',
iir_filter=[0.2, -0.2, 0.04], ecg=True, blink=True,
n_jobs=1, verbose=True)
raw_sim.plot()
##############################################################################
# Plot evoked data
n_samp = len(times)
window = np.zeros(n_samp)
start, stop = [int(ii * float(n_samp) / (2 * n_dipoles))
for ii in (2 * n, 2 * n + 1)]
window[start:stop] = 1.
n += 1
data = 25e-9 * np.sin(2. * np.pi * 10. * n * times)
data *= window
return data
times = raw_nrm.times[:int(raw_nrm.info['sfreq'] * epoch_duration)]
# stc = simulate_sparse_stc(src, n_dipoles=n_dipoles, times=times,
# data_fun=data_fun, random_state=0)
stc = simulate_sparse_stc(src, times=times, n_dipoles=n_dipoles,
data_fun=data_fun,
labels=labels_to_sim,
random_state=0)
print stc.data.max()
# look at our source data
fig, ax = plt.subplots(1)
ax.plot(times, 1e9 * stc.data.T)
ax.set(ylabel='Amplitude (nAm)', xlabel='Time (sec)')
fig.show()
##############################################################################
# Simulate raw data
raw_sim = simulate_raw(raw_nrm, stc, trans_nrm, src, bem_fname, cov='simple',
iir_filter=[0.2, -0.2, 0.04], ecg=True, blink=True,
n_jobs=2, verbose=True)
closes_vertnos = closest_nodes(stim_coords['surf'], surf[0], fwd['src'][0]['vertno'])
stim_vert = surf[0][closes_vertnos]
pulse = 5e-6
def data_fun(times):
data = np.hstack((np.repeat(0, 1000), -pulse, -pulse, pulse, pulse, np.repeat(0, 997)))
return data
times = np.linspace(-0.5, 0.5, 2001)
lab = mne.Label(closes_vertnos, subject=subj,
pos=stim_vert, hemi='lh', name='stim')
stc = simulate_sparse_stc(fwd1['src'], n_dipoles=1, times=times, location='center', subject=subj,
subjects_dir=subjects_dir, random_state=42, labels=[lab], data_fun=data_fun)
plot_sparse_source_estimates(fwd1['src'], stc, high_resolution=True)
fwd['src'].plot(trans=trans, subjects_dir=subjects_dir)
info['sfreq'] = 2000
#iir_filter = fit_iir_model_raw(raw, order=5, picks=picks, tmin=60, tmax=180)[1]
nave = 30 # simulate average of 100 epochs
evoked_sim = simulate_evoked(fwd, stc, info, cov, nave=nave, use_cps=True,
iir_filter=None)
evoked_ds = evoked_sim.copy()
evoked_ds.filter(None, 400, method='iir', iir_params=None)
evoked_ds.resample(1000)