def mark_by_threshold(dataset, DV='MEG', threshold=2e-12, above=False, below=None,
target='accept'):
"""
Marks epochs based on a threshold criterion (any sensor exceeding the
threshold at any time)
above: True, False, None
How to mark segments that exceed the threshold: True->good;
False->bad; None->don't change
below:
Same as ``above`` but for segments that do not exceed the threshold
threshold : float
The threshold value.
1.25e-11: detect saturated channels
2e-12: conservative final rejection
target : factor or str
Factor (or its name) in which the result is stored. If ``var`` is
a string and the dataset does not contain that factor, it is
created.
"""
if isinstance(DV, basestring):
DV = dataset[DV]
# get the factor on which to store results
if _data.isfactor(target) or _data.isvar(target):
assert len(target) == dataset.N
elif isinstance(target, basestring):
if target in dataset:
target = dataset[target]
else:
x = _np.ones(dataset.N, dtype=bool)
target = _data.var(x, name=target)
dataset.add(target)
else:
raise ValueError("target needs to be a factor")
# do the thresholding
if _data.isndvar(DV):
for ID in xrange(dataset.N):
data = DV[ID]
v = _np.max(_np.abs(data.x))
if v > threshold:
if above is not None:
target[ID] = above
elif below is not None:
target[ID] = below
else:
for ID in xrange(dataset.N):
v = DV[ID]
if v > threshold:
if above is not None:
target[ID] = above
elif below is not None:
target[ID] = below
def __init__(self, Y, X, match=None, sub=None, match_func=np.mean):
"""
divides Y into cells defined by X
Y dependent measurement
X factor or interaction
match factor on which cases are matched (i.e. subject for a repeated
measures comparisons). If several data points with the same
case fall into one cell of X, they are combined using
match_func. If match is not None, celltable.groups contains the
{Xcell -> [match values of data points], ...} mapping corres-
ponding to self.data
sub Bool Array of length N specifying which cases to include
match_func: see match
e.g.
>>> c = S.celltable(Y, A%B, match=subject)
"""
if _data.isfactor(Y):
if sub is not None:
Y = Y[sub]
else:
Y = _data.asvar(Y, sub)
X = _data.ascategorial(X, sub)
assert X.N == Y.N
if match:
match = _data.asfactor(match, sub)
assert match.N == Y.N
self.groups = {}
# save args
self.X = X
self.Y = Y
self.sub = sub
self.match = match
# extract cells and cell data
self.data = {}
self.data_indexes = {}
self.cells = X.cells
self.indexes = sorted(X.cells.keys())
for cell in self.indexes:
sub = X==cell
self.data_indexes[cell] = sub
newdata = Y.x[sub]
if match:
# get match ids
group = match.x[sub]
occurring_ids = np.unique(group)
# sort
if len(occurring_ids) < len(group):
newdata = np.array([match_func(newdata[group==ID])
for ID in occurring_ids])
group = occurring_ids
else:
sort_arg = np.argsort(group)
group = group[sort_arg]
newdata = newdata[sort_arg]
self.groups[cell] = group
self.data[cell] = newdata
if match:
# determine which cells compare values for dependent values on
# match_variable
# n_cells = len(self.indexes)
# self.within = np.empty((n_cells, n_cells), dtype=bool)
self.within = {}
for cell1 in self.indexes:
for cell2 in self.indexes:
if cell1==cell2:
self.within[cell1,cell2] = True
else:
v = self.groups[cell1] == self.groups[cell2]
if v is not False:
v = all(v)
self.within[cell1,cell2] = v
self.within[cell2,cell1] = v
self.all_within = np.all(self.within.values())
else:
self.within = self.all_within = False