def align(trials, window, offsets):
sample_rate = utils.get_samplerate(trials)
w = np.arange(int(window[0]*sample_rate), int(sample_rate))
feat_lab = [ trials.feat_lab[0],
(w / float(sample_rate)).tolist()]
feat_shape = (trials.feat_shape[0], len(w))
data = np.zeros(feat_shape + (trials.ninstances,))
for i,t in enumerate(offsets):
t -= window[0]
data[:,:,i] = trials.data[:,int(t*sample_rate)+w,i]
trials_aligned = DataSet(data=data, feat_lab=feat_lab, default=trials)
return trials_aligned
def slice(d, markers_to_class, offsets):
'''
Slice function, used to extract fixed-length segments (called trials) of
EEG from a recording. Opposite of :func:`psychic.concatenate_trials`.
Segments are sliced based on the onset of some event code.
Given for example an EEG recording which contains two marker codes:
1. Left finger tapping
2. Right finger tapping
Trials can be extracted in the following manner:
>>> import psychic
>>> d = psychic.load_bdf(psychic.find_data_path('priming-short.bdf'))
>>> mdict = {1:'related', 2:'unrelated'}
>>> sample_rate = psychic.get_samplerate(d)
>>> begin = int(-0.2 * sample_rate)
>>> end = int(1.0 * sample_rate)
>>> trials = psychic.slice(d, mdict, (begin, end))
>>> print trials
DataSet with 208 instances, 12280 features [40x307], 2 classes: [104, 104], extras: []
Parameters
----------
markers_to_class : dict
A dictionary containing as keys the event codes to use as onset of the
trial and as values a class label for the resulting trials. For example
``{1:'left finger tapping', 2:'right finger tapping'}``
offsets : tuple
Indicates the time (start, end), relative to the onset of marker, to
extract as trial. Values are given in samples.
Returns
-------
d : :class:`DataSet`
The extracted segments:
- ``d.data``: [channels x samples x trials]
- ``d.labels``: [classes x trials]
- ``d.ids``: Timestamps indicating the marker onsets
- ``d.cl_lab``: The class labels as specified in the
``markers_to_class`` dictionary
- ``d.feat_lab``: Feature labels for the axes [channels (strings),
time in seconds (floats)]
'''
assert len(d.feat_shape) == 1, 'Data must be continuous EEG.'
assert d.labels.shape[0] == 1 and d.labels.dtype == np.int, ('Labels are'
'the wrong format. It must be an integer marker stream.')
start_off, end_off = offsets
data, labels, ids = [], [], []
cl_lab = sorted(set(markers_to_class.values()))
events, events_i, events_d = markers.markers_to_events(d.labels.flat)
for (mark, cl) in markers_to_class.items():
cl_i = cl_lab.index(cl)
for i in events_i[events==mark]: # fails if there is *ONE* event
(start, end) = i + start_off, i + end_off
if start < 0 or end > d.ninstances:
logging.getLogger('psychic.utils.slice').warning(
'Cannot extract slice [%d, %d] for class %s'
% (start, end, cl))
continue
dslice = d[start:end]
data.append(dslice.data)
labels.append(cl_i)
ids.append(d.ids[:,i])
event_time = np.arange(start_off, end_off) / float(utils.get_samplerate(d))
feat_lab = [d.feat_lab[0], event_time.tolist()]
if len(data) == 0:
data = np.zeros(d.feat_shape + (len(event_time),0))
labels = np.zeros((len(cl_lab),0))
ids = np.zeros((1,0))
else:
data = np.concatenate([x[...,np.newaxis] for x in data], axis=2)
labels = helpers.to_one_of_n(labels, class_rows=range(len(cl_lab)))
ids = np.atleast_2d(np.vstack(ids).T)
feat_dim_lab = ['channels', 'time']
d = DataSet(
data=data,
labels=labels,
ids=ids,
cl_lab=cl_lab,
feat_lab=feat_lab,
feat_dim_lab=feat_dim_lab,
default=d
)
return d.sorted()
