def events(vhdr_path=None):
if vhdr_path is None:
vhdr_path = ui.ask_file("Pick a Brain Vision EEG Header File",
"Pick a Brain Vision EEG Header File",
ext=[('vhdr', 'Brain Vision Header File')])
if not vhdr_path:
return
hdr = vhdr(vhdr_path)
if hdr.markerfile is None:
raise IOError("No marker file referenced in %r" % vhdr_path)
elif hdr.DataType == 'FREQUENCYDOMAIN':
raise NotImplementedError
txt = open(hdr.markerfile).read()
m = marker_re.findall(txt)
m = np.array(m)
name, _ = os.path.split(os.path.basename(hdr.path))
ds = dataset(name=name)
ds['Mk'] = var(np.array(m[:,0], dtype=int))
ds['event_type'] = factor(m[:,1])
ds['event_ID'] = var(np.array(m[:,3], dtype=int))
ds['i_start'] = var(np.array(m[:,4], dtype=int))
ds['points'] = var(np.array(m[:,5], dtype=int))
ds['channel'] = var(np.array(m[:,6], dtype=int))
ds.info['hdr'] = hdr
ds.info['samplingrate'] = hdr.samplingrate
return ds
def get_triggers(self, Id='Id', T='t_edf'):
"""
Returns a dataset with trigger Ids and corresponding Edf time values
"""
ds = dataset()
ds[Id] = var(self.triggers['Id'])
ds[T] = self.get_T(name=T)
return ds
def export_durs(self):
ds = dataset()
idx = self.words == 'sp'
words = self.words[~idx]
durs = self.word_durs[~idx]
ds['words'] = factor([first.lower() + second.lower() for first, second in
zip(words[::2], words[1::2])])
ds['c1_dur'] = var(durs[::2])
ds['c2_dur'] = var(durs[1::2])
return ds
def export_durs(self):
ds = dataset()
idx = self.words == 'sp'
words = self.words[~idx]
durs = self.word_durs[~idx]
ds['words'] = factor([
first.lower() + second.lower()
for first, second in zip(words[::2], words[1::2])
])
ds['c1_dur'] = var(durs[::2])
ds['c2_dur'] = var(durs[1::2])
return ds
def get_dataset(self):
"get a dataframe containing Y and covariates"
Y, covs = self._collect_data()
indexes = Y.keys()
Ydata = [Y[index] for index in indexes]
Y = self._get_vessel_for_Y(Ydata)
ds = _vsl.dataset(Y)
# create _data objects
for var, valdict in covs.iteritems():
X = [valdict[index] for index in indexes]
if var.dict_enabled:
Y = _vsl.factor(X, name=var.name, random=var.random,
labels=var.dictionary, colors=var._color_dict)
else:
Y = _vsl.var(X, name=var.name)
ds.add(Y)
return ds
def events(raw=None, merge= -1, proj=False, name=None,
stim_channel='STI 014',
stim_channel_bl=0, verbose=False):
"""
Read events from a raw fiff file.
Use :func:`fiff_epochs` to load MEG data corresponding to those events.
Parameters
----------
raw : str(path) | None | mne.fiff.Raw
The raw fiff file from which to extract events (if ``None``, a file
dialog will be displayed).
merge : int
use to merge events lying in neighboring samples. The integer value
indicates over how many samples events should be merged, and the sign
indicates in which direction they should be merged (negative means
towards the earlier event, positive towards the later event).
proj : bool | str
Path to the projections file that will be loaded with the raw file.
``'{raw}'`` will be expanded to the raw file's path minus extension.
With ``proj=True``, ``'{raw}_*proj.fif'`` will be used,
looking for any projection file starting with the raw file's name.
If multiple files match the pattern, a ValueError will be raised.
name : str | None
A name for the dataset. If ``None``, the raw filename will be used.
stim_channel : str
Name of the trigger channel.
stim_channel_bl : int
For corrupted event channels:
After kit2fiff conversion of sqd files with unused trigger channels,
the resulting fiff file's event channel can contain a baseline other
than 0. This interferes with normal event extraction. If the baseline
value is provided as parameter, the events can still be extracted.
Returns
-------
events : dataset
A dataset with the following variables:
- *i_start*: the index of the event in the raw file.
- *eventID*: the event value.
The dataset's info dictionary contains the following values:
- *raw*: the mne Raw object.
- *samplingrate*: the samplingrate of the raw file.
"""
if raw is None or isinstance(raw, basestring):
raw = Raw(raw, proj=proj, verbose=verbose)
if name is None:
raw_file = raw.info['filename']
name = os.path.basename(raw_file)
if stim_channel_bl:
pick = mne.event.pick_channels(raw.info['ch_names'], include=stim_channel)
data, _ = raw[pick, :]
idx = np.where(np.abs(np.diff(data[0])) > 0)[0]
# find baseline NULL-events
values = data[0, idx + 1]
valid_events = np.where(values != stim_channel_bl)[0]
idx = idx[valid_events]
values = values[valid_events]
N = len(values)
events = np.empty((N, 3), dtype=np.int32)
events[:, 0] = idx
events[:, 1] = np.zeros_like(idx)
events[:, 2] = values
else:
events = mne.find_events(raw, verbose=verbose, stim_channel=stim_channel)
if len(events) == 0:
raise ValueError("No events found!")
if merge:
index = np.ones(len(events), dtype=bool)
diff = np.diff(events[:, 0])
where = np.where(diff <= abs(merge))[0]
if merge > 0:
# drop the earlier event
index[where] = False
else:
# drop the later event
index[where + 1] = False
# move the trigger value to the earlier event
for w in reversed(where):
i1 = w
i2 = w + 1
events[i1, 2] = events[i2, 2]
events = events[index]
istart = var(events[:, 0], name='i_start')
event = var(events[:, 2], name='eventID')
info = {'raw': raw,
'samplingrate': raw.info['sfreq'],
'info': raw.info}
return dataset(event, istart, name=name, info=info)
def tsv(path=None, names=True, types='auto', empty='nan', delimiter=None,
skiprows=0):
"""
returns a ``dataset`` with data from a tab-separated values file.
Parameters
----------
names : list of str | bool
* ``['name1', ...]`` use these names
* ``True``: look for names on the first line of the file
* ``False``: use "v1", "v2", ...
types : 'auto' | list of int
* ``'auto'`` -> import as var if all values can be converted float,
otherwise as factor
* list of 0=auto, 1=factor, 2=var. e.g. ``[0,1,1,0]``
empty :
value to substitute for empty cells
delimiter : str
value delimiting cells in the input file (None = any whitespace;
e.g., ``'\\t'``)
skiprows : int
Skip so many rows at the beginning of the file (for tsv files with
headers). Column names (if names==True) are expected to come after
the skipped rows.
"""
if path is None:
path = ui.ask_file("Select file to import as dataframe",
"Select file to import as dataframe")
if not path:
return
with open(path) as f:
for i in xrange(skiprows):
f.readline()
# read / create names
if names == True:
names = f.readline().split(delimiter)
names = [n.strip().strip('"') for n in names]
lines = []
for line in f:
values = []
for v in line.split(delimiter):
v = v.strip()
if not v:
v = empty
values.append(v)
lines.append(values)
n_vars = len(lines[0])
if not names:
names = ['v%i' % i for i in xrange(n_vars)]
n = len(names)
# decide whether to drop first column
if n_vars == n:
start = 0
elif n_vars == n + 1:
start = 1
else:
raise ValueError("number of header different from number of data")
if types in ['auto', None, False, True]:
types = [0] * n
else:
assert len(types) == n
# prepare for reading data
data = []
for _ in xrange(n):
data.append([])
# read rest of the data
for line in lines:
for i, v in enumerate(line[start:]):
for str_del in ["'", '"']:
if v[0] == str_del:
v = v.strip(str_del)
types[i] = 1
data[i].append(v)
ds = _data.dataset(name=os.path.basename(path))
for name, values, force_type in zip(names, data, types):
v = np.array(values)
if force_type in [0, 2]:
try:
v = v.astype(float)
f = _data.var(v, name=name)
except:
f = _data.factor(v, name=name)
else:
f = _data.factor(v, name=name)
ds.add(f)
return ds