def add_original(self, P):
"""
P : array
Parameter map of the statistic of interest.
"""
self.clusters = []
# find clusters
clusters, n = self._find_clusters(P)
clusters_v = scipy.ndimage.measurements.sum(P, clusters, xrange(1, n + 1))
for i in xrange(n):
v = clusters_v[i]
p = 1 - percentileofscore(self.dist, np.abs(v), 'mean') / 100
if p <= self.pmax:
im = P * (clusters == i + 1)
name = 'p=%.3f' % p
threshold = self.t_upper if (v > 0) else self.t_lower
properties = {'p': p, 'unit': self.unit, 'threshold': threshold}
ndv = ndvar(im, dims=self.dims, name=name, properties=properties)
self.clusters.append(ndv)
props = {'unit': self.unit, 'cs': self.cs,
'threshold_lower': self.t_lower,
'threshold_upper': self.t_upper}
self.P = ndvar(P, dims=self.dims, name=self.name, properties=props)
def __init__(self, Y='MEG', X='condition', sub=None, ds=None,
p=.05, contours={.01: '.5', .001: '0'}):
"""
uses scipy.stats.f_oneway
"""
Y = asndvar(Y, sub=sub, ds=ds)
X = ascategorial(X, sub=sub, ds=ds)
Ys = [Y[X == c] for c in X.cells]
Ys = [y.x.reshape((y.x.shape[0], -1)) for y in Ys]
N = Ys[0].shape[1]
Ps = []
for i in xrange(N):
groups = (y[:, i] for y in Ys)
F, p = scipy.stats.f_oneway(*groups)
Ps.append(p)
test_name = 'One-way ANOVA'
dims = Y.dims[1:]
Ps = np.reshape(Ps, tuple(len(dim) for dim in dims))
properties = Y.properties.copy()
properties['colorspace'] = _cs.get_sig(p=p, contours=contours)
properties['test'] = test_name
p = ndvar(Ps, dims, properties=properties, name=X.name)
# store results
self.name = "anova"
self.p = p
self.all = p
def fiff_mne(ds, fwd='{fif}*fwd.fif', cov='{fif}*cov.fif', label=None, name=None,
tstart= -0.1, tstop=0.6, baseline=(None, 0)):
"""
adds data from one label as
"""
if name is None:
if label:
_, lbl = os.path.split(label)
lbl, _ = os.path.splitext(lbl)
name = lbl.replace('-', '_')
else:
name = 'stc'
info = ds.info['info']
raw = ds.info['raw']
fif_name = raw.info['filename']
fif_name, _ = os.path.splitext(fif_name)
if fif_name.endswith('raw'):
fif_name = fif_name[:-3]
fwd = fwd.format(fif=fif_name)
if '*' in fwd:
d, n = os.path.split(fwd)
names = fnmatch.filter(os.listdir(d), n)
if len(names) == 1:
fwd = os.path.join(d, names[0])
else:
raise IOError("No unique fwd file matching %r" % fwd)
cov = cov.format(fif=fif_name)
if '*' in cov:
d, n = os.path.split(cov)
names = fnmatch.filter(os.listdir(d), n)
if len(names) == 1:
cov = os.path.join(d, names[0])
else:
raise IOError("No unique cov file matching %r" % cov)
fwd = mne.read_forward_solution(fwd, force_fixed=False, surf_ori=True)
cov = mne.Covariance(cov)
inv = _mn.make_inverse_operator(info, fwd, cov, loose=0.2, depth=0.8)
epochs = mne_Epochs(ds, tstart=tstart, tstop=tstop, baseline=baseline)
# mne example:
snr = 3.0
lambda2 = 1.0 / snr ** 2
if label is not None:
label = mne.read_label(label)
stcs = _mn.apply_inverse_epochs(epochs, inv, lambda2, dSPM=False, label=label)
x = np.vstack(s.data.mean(0) for s in stcs)
s = stcs[0]
dims = ('case', var(s.times, 'time'),)
ds[name] = ndvar(x, dims, properties=None, info='')
return stcs
def _get_vessel_for_Y(self, Ydata):
Ydata = np.array([self._cfunc(data, axis=0) for data in Ydata])
T = np.arange(self._tw.tstart, self._tw.tend, 1 / self._samplingrate)
time = _vsl.var(T, name='time')
dims = ('case', time)
properties = {'samplingrate': self._samplingrate}
Y = _vsl.ndvar(Ydata, dims, properties=properties, name=self._name)
return Y
def evoked_ndvar(evoked, name='MEG'):
"Convert an mne Evoked object of a list thereof to an ndvar"
if isinstance(evoked, mne.fiff.Evoked):
x = evoked.data
dims = ()
else:
x = np.array([e.data for e in evoked])
dims = ('case',)
evoked = evoked[0]
sensor = sensor_net(evoked)
time = var(evoked.times, name='time')
properties = {'colorspace': _cs.get_MEG(2e-13)}
return ndvar(x, dims + (sensor, time), properties=properties, name=name)
def __init__(self, Y='MEG', X='condition', sub=None, ds=None,
p=.05, contours={.01: '.5', .001: '0'}):
self.name = "anova"
Y = self.Y = asndvar(Y, sub=sub, ds=ds)
X = self.X = asmodel(X, sub=sub, ds=ds)
fitter = _glm.lm_fitter(X)
properties = Y.properties.copy()
properties['colorspace'] = _cs.get_sig(p=p, contours=contours)
kwargs = dict(dims=Y.dims[1:], properties=properties)
self.all = []
self.p_maps = {}
for e, _, Ps in fitter.map(Y.x):
name = e.name
P = ndvar(Ps, name=name, **kwargs)
self.all.append(P)
self.p_maps[e] = P
def stc_ndvar(stc, subject='fsaverage', name=None, check=True):
"""
create an ndvar object from an mne SourceEstimate object
stc : SourceEstimate | list of SourceEstimates
The source estimate object(s).
subject : str
MRI subject (used for loading MRI in PySurfer plotting)
name : str | None
Ndvar name.
check : bool
If multiple stcs are provided, check if all stcs have the same times
and vertices.
"""
if isinstance(stc, mne.SourceEstimate):
case = False
x = stc.data
else:
case = True
stcs = stc
stc = stcs[0]
if check:
vert_lh, vert_rh = stc.vertno
times = stc.times
for stc_ in stcs[1:]:
assert np.all(times == stc_.times)
lh, rh = stc_.vertno
assert np.all(vert_lh == lh)
assert np.all(vert_rh == rh)
x = np.array([s.data for s in stcs])
time = var(stc.times, name='time')
ss = source_space(stc.vertno, subject=subject)
if case:
dims = ('case', ss, time)
else:
dims = (ss, time)
return ndvar(x, dims, name=name)
def epochs_ndvar(epochs, name='MEG', meg=True, eeg=False, exclude='bads',
mult=1, unit='T', properties=None, sensors=None):
"""
Convert an mne.Epochs object to an ndvar.
Parameters
----------
epoch : mne.Epochs
The epochs object
name : None | str
Name for the ndvar.
meg : bool or string
MEG channels to include (:func:`mne.fiff.pick_types` kwarg).
If True include all MEG channels. If False include None
If string it can be 'mag' or 'grad' to select only gradiometers
or magnetometers. It can also be 'ref_meg' to get CTF
reference channels.
eeg : bool
If True include EEG channels (:func:`mne.fiff.pick_types` kwarg).
exclude : list of string | str
Channels to exclude (:func:`mne.fiff.pick_types` kwarg).
If 'bads' (default), exclude channels in info['bads'].
If empty do not exclude any.
mult : scalar
multiply all data by a constant. If used, the ``unit`` kwarg should
specify the target unit, not the source unit.
unit : str
Unit of the data (default is 'T').
target : str
name for the new ndvar containing the epoch data
reject : None | scalar
Threshold for rejecting epochs (peak to peak). Requires a for of
mne-python which implements the Epochs.model['index'] variable.
raw : None | mne.fiff.Raw
Raw file providing the data; if ``None``, ``ds.info['raw']`` is used.
sensors : None | eelbrain.vessels.sensors.sensor_net
The default (``None``) reads the sensor locations from the fiff file.
If the fiff file contains incorrect sensor locations, a different
sensor_net can be supplied through this kwarg.
"""
props = {'proj': 'z root',
'unit': unit,
'ylim': 2e-12 * mult,
'summary_ylim': 3.5e-13 * mult,
'colorspace': _cs.get_MEG(2e-12 * mult),
'summary_colorspace': _cs.get_MEG(2e-13 * mult),
'samplingrate': epochs.info['sfreq'],
}
if properties:
props.update(properties)
picks = mne.fiff.pick_types(epochs.info, meg=meg, eeg=eeg, stim=False,
eog=False, include=[], exclude=exclude)
x = epochs.get_data()[:, picks]
if mult != 1:
x *= mult
if sensors is None:
sensor = sensor_net(epochs, picks=picks)
else:
sensor = sensors
time = var(epochs.times, name='time')
return ndvar(x, ('case', sensor, time), properties=props, name=name)
def __init__(self, Y, X, norm=None, sub=None, ds=None,
contours={.05: (.8, .2, .0), .01: (1., .6, .0), .001: (1., 1., .0)}):
"""
Y : ndvar
Dependent variable.
X : continuous | None
The continuous predictor variable.
norm : None | categorial
Categories in which to normalize (z-score) X.
"""
Y = asndvar(Y, sub=sub, ds=ds)
X = asvar(X, sub=sub, ds=ds)
if not Y.has_case:
msg = ("Dependent variable needs case dimension")
raise ValueError(msg)
y = Y.x.reshape((len(Y), -1))
if norm is not None:
y = y.copy()
for cell in norm.cells:
idx = (norm == cell)
y[idx] = scipy.stats.mstats.zscore(y[idx])
n = len(X)
x = X.x.reshape((n, -1))
# covariance
m_x = np.mean(x)
if np.isnan(m_x):
raise ValueError("np.mean(x) is nan")
x -= m_x
y -= np.mean(y, axis=0)
cov = np.sum(x * y, axis=0) / (n - 1)
# correlation
r = cov / (np.std(x, axis=0) * np.std(y, axis=0))
# p-value calculation
# http://en.wikipedia.org/wiki/Pearson_product-moment_correlation_coefficient#Inference
pcont = {}
r_ps = {}
df = n - 2
for p, color in contours.iteritems():
t = scipy.stats.distributions.t.isf(p, df)
r_p = t / np.sqrt(n - 2 + t ** 2)
pcont[r_p] = color
r_ps[r_p] = p
pcont[-r_p] = color
r_ps[-r_p] = p
dims = Y.dims[1:]
shape = Y.x.shape[1:]
properties = Y.properties.copy()
cs = _cs.Colorspace(cmap=_cs.cm_xpolar, vmax=1, vmin= -1, contours=pcont, ps=r_ps)
properties['colorspace'] = cs
r = ndvar(r.reshape(shape), dims=dims, properties=properties)
# store results
self.name = "%s corr %s" % (Y.name, X.name)
self.r = r
self.all = r