def test_regression():
"""Test Ordinary Least Squares Regression
"""
tmin, tmax = -0.2, 0.5
event_id = dict(aud_l=1, aud_r=2)
# Setup for reading the raw data
raw = mne.io.read_raw_fif(raw_fname)
events = mne.read_events(event_fname)[:10]
epochs = mne.Epochs(raw,
events,
event_id,
tmin,
tmax,
proj=True,
baseline=(None, 0))
picks = np.arange(len(epochs.ch_names))
evoked = epochs.average(picks=picks)
design_matrix = epochs.events[:, 1:].astype(np.float64)
# makes the intercept
design_matrix[:, 0] = 1
# creates contrast: aud_l=0, aud_r=1
design_matrix[:, 1] -= 1
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter('always')
lm = linear_regression(epochs, design_matrix, ['intercept', 'aud'])
assert_true(w[0].category == RuntimeWarning)
assert_true('non-data' in '%s' % w[0].message)
for predictor, parameters in lm.items():
for value in parameters:
assert_equal(value.data.shape, evoked.data.shape)
assert_raises(ValueError, linear_regression, [epochs, epochs],
design_matrix)
stc = read_source_estimate(stc_fname).crop(0, 0.02)
stc_list = [stc, stc, stc]
stc_gen = (s for s in stc_list)
with warnings.catch_warnings(record=True): # divide by zero
warnings.simplefilter('always')
lm1 = linear_regression(stc_list, design_matrix[:len(stc_list)])
lm2 = linear_regression(stc_gen, design_matrix[:len(stc_list)])
for val in lm2.values():
# all p values are 0 < p <= 1 to start, but get stored in float32
# data, so can actually be truncated to 0. Thus the mlog10_p_val
# actually maintains better precision for tiny p-values.
assert_true(np.isfinite(val.p_val.data).all())
assert_true((val.p_val.data <= 1).all())
assert_true((val.p_val.data >= 0).all())
# all -log10(p) are non-negative
assert_true(np.isfinite(val.mlog10_p_val.data).all())
assert_true((val.mlog10_p_val.data >= 0).all())
assert_true((val.mlog10_p_val.data >= 0).all())
for k in lm1:
for v1, v2 in zip(lm1[k], lm2[k]):
assert_array_equal(v1.data, v2.data)
def test_regression():
"""Test Ordinary Least Squares Regression
"""
tmin, tmax = -0.2, 0.5
event_id = dict(aud_l=1, aud_r=2)
# Setup for reading the raw data
raw = mne.io.Raw(raw_fname)
events = mne.read_events(event_fname)[:10]
epochs = mne.Epochs(raw, events, event_id, tmin, tmax, proj=True,
baseline=(None, 0))
picks = np.arange(len(epochs.ch_names))
evoked = epochs.average(picks=picks)
design_matrix = epochs.events[:, 1:].astype(np.float64)
# makes the intercept
design_matrix[:, 0] = 1
# creates contrast: aud_l=0, aud_r=1
design_matrix[:, 1] -= 1
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter('always')
lm = linear_regression(epochs, design_matrix, ['intercept', 'aud'])
assert_true(w[0].category == RuntimeWarning)
assert_true('non-data' in '%s' % w[0].message)
for predictor, parameters in lm.items():
for value in parameters:
assert_equal(value.data.shape, evoked.data.shape)
assert_raises(ValueError, linear_regression, [epochs, epochs],
design_matrix)
stc = read_source_estimate(stc_fname).crop(0, 0.02)
stc_list = [stc, stc, stc]
stc_gen = (s for s in stc_list)
with warnings.catch_warnings(record=True): # divide by zero
warnings.simplefilter('always')
lm1 = linear_regression(stc_list, design_matrix[:len(stc_list)])
lm2 = linear_regression(stc_gen, design_matrix[:len(stc_list)])
for val in lm2.values():
# all p values are 0 < p <= 1 to start, but get stored in float32
# data, so can actually be truncated to 0. Thus the mlog10_p_val
# actually maintains better precision for tiny p-values.
assert_true(np.isfinite(val.p_val.data).all())
assert_true((val.p_val.data <= 1).all())
assert_true((val.p_val.data >= 0).all())
# all -log10(p) are non-negative
assert_true(np.isfinite(val.mlog10_p_val.data).all())
assert_true((val.mlog10_p_val.data >= 0).all())
assert_true((val.mlog10_p_val.data >= 0).all())
for k in lm1:
for v1, v2 in zip(lm1[k], lm2[k]):
assert_array_equal(v1.data, v2.data)
def test_regression():
"""Test Ordinary Least Squares Regression
"""
data_path = sample.data_path()
raw_fname = data_path + '/MEG/sample/sample_audvis_filt-0-40_raw.fif'
event_fname = data_path + '/MEG/sample/sample_audvis_filt-0-40_raw-eve.fif'
tmin, tmax = -0.2, 0.5
event_id = dict(aud_l=1, aud_r=2)
# Setup for reading the raw data
raw = mne.io.Raw(raw_fname)
events = mne.read_events(event_fname)[:10]
epochs = mne.Epochs(raw,
events,
event_id,
tmin,
tmax,
proj=True,
baseline=(None, 0))
picks = np.arange(len(epochs.ch_names))
evoked = epochs.average(picks=picks)
design_matrix = epochs.events[:, 1:].astype(np.float64)
# makes the intercept
design_matrix[:, 0] = 1
# creates contrast: aud_l=0, aud_r=1
design_matrix[:, 1] -= 1
with warnings.catch_warnings(record=True) as w:
lm = linear_regression(epochs, design_matrix, ['intercept', 'aud'])
assert_true(w[0].category == UserWarning)
assert_true('non-data' in '%s' % w[0].message)
for predictor, parameters in lm.items():
for value in parameters:
assert_equal(value.data.shape, evoked.data.shape)
assert_raises(ValueError, linear_regression, [epochs, epochs],
design_matrix)
stc = read_source_estimate(stc_fname).crop(0, 0.02)
stc_list = [stc, stc, stc]
stc_gen = (s for s in stc_list)
with warnings.catch_warnings(record=True): # divide by zero
lm1 = linear_regression(stc_list, design_matrix[:len(stc_list)])
lm2 = linear_regression(stc_gen, design_matrix[:len(stc_list)])
for k in lm1:
for v1, v2 in zip(lm1[k], lm2[k]):
assert_array_equal(v1.data, v2.data)
def sensor_least_squares(epochs):
"""This function will process the sensor least squares regression,
outputting a regression coefficient that will denote the efficiency
of each combination of sensor and timepoint. P-values and T statistics
are also computed."""
from mne.stats.regression import linear_regression
names = ['intercept', 'trial-count']
intercept = np.ones((len(epochs), ), dtype=np.float)
design_matrix = np.column_stack([
intercept, # intercept
np.linspace(0, 1, len(intercept))
])
# also accepts source estimates
lm = linear_regression(epochs, design_matrix, names)
def plot_topomap(x, unit):
x.plot_topomap(ch_type='eeg',
scale=1,
size=1.5,
vmax=np.max,
unit=unit,
times=np.linspace(0.1, 0.2, 5))
trial_count = lm['trial-count']
plot_topomap(trial_count.beta, unit='z (beta)')
plot_topomap(trial_count.t_val, unit='t')
plot_topomap(trial_count.mlog10_p_val, unit='-log10 p')
plot_topomap(trial_count.stderr, unit='z (error)')
def test_regression():
"""Test Ordinary Least Squares Regression
"""
data_path = sample.data_path()
raw_fname = data_path + '/MEG/sample/sample_audvis_filt-0-40_raw.fif'
event_fname = data_path + '/MEG/sample/sample_audvis_filt-0-40_raw-eve.fif'
tmin, tmax = -0.2, 0.5
event_id = dict(aud_l=1, aud_r=2)
# Setup for reading the raw data
raw = mne.io.Raw(raw_fname)
events = mne.read_events(event_fname)[:10]
epochs = mne.Epochs(raw, events, event_id, tmin, tmax, proj=True,
baseline=(None, 0))
picks = np.arange(len(epochs.ch_names))
evoked = epochs.average(picks=picks)
design_matrix = epochs.events[:, 1:].astype(np.float64)
# makes the intercept
design_matrix[:, 0] = 1
# creates contrast: aud_l=0, aud_r=1
design_matrix[:, 1] -= 1
with warnings.catch_warnings(record=True) as w:
lm = linear_regression(epochs, design_matrix, ['intercept', 'aud'])
assert_true(w[0].category == UserWarning)
assert_true('non-data' in '%s' % w[0].message)
for predictor, parameters in lm.items():
for value in parameters:
assert_equal(value.data.shape, evoked.data.shape)
assert_raises(ValueError, linear_regression, [epochs, epochs],
design_matrix)
stc = read_source_estimate(stc_fname).crop(0, 0.02)
stc_list = [stc, stc, stc]
stc_gen = (s for s in stc_list)
lm1 = linear_regression(stc_list, design_matrix[:len(stc_list)])
lm2 = linear_regression(stc_gen, design_matrix[:len(stc_list)])
for k in lm1:
for v1, v2 in zip(lm1[k], lm2[k]):
assert_array_equal(v1.data, v2.data)
preload=True,
reject=reject)
###############################################################################
# Run regression
names = ['intercept', 'trial-count']
intercept = np.ones((len(epochs), ), dtype=np.float)
design_matrix = np.column_stack([
intercept, # intercept
np.linspace(0, 1, len(intercept))
])
# also accepts source estimates
lm = linear_regression(epochs, design_matrix, names)
def plot_topomap(x, units):
x.plot_topomap(ch_type='mag',
scalings=1.,
size=1.5,
vmax=np.max,
units=units,
times=np.linspace(0.1, 0.2, 5))
trial_count = lm['trial-count']
plot_topomap(trial_count.beta, units='z (beta)')
plot_topomap(trial_count.t_val, units='t')
reject = dict(mag=5e-12)
epochs = mne.Epochs(raw, events, event_id, tmin, tmax, proj=True,
picks=picks, baseline=(None, 0), preload=True,
reject=reject)
###############################################################################
# Run regression
names = ['intercept', 'trial-count']
intercept = np.ones((len(epochs),), dtype=np.float)
design_matrix = np.column_stack([intercept, # intercept
np.linspace(0, 1, len(intercept))])
# also accepts source estimates
lm = linear_regression(epochs, design_matrix, names)
def plot_topomap(x, unit):
x.plot_topomap(ch_type='mag', scale=1, size=1.5, vmax=np.max, unit=unit,
times=np.linspace(0.1, 0.2, 5))
trial_count = lm['trial-count']
plot_topomap(trial_count.beta, unit='z (beta)')
plot_topomap(trial_count.t_val, unit='t')
plot_topomap(trial_count.mlog10_p_val, unit='-log10 p')
plot_topomap(trial_count.stderr, unit='z (error)')