def setUp(self):
self.start_time = -0.5
self.end_time = 1.6
self.buffer_time = 0.5
self.event_range = range(0, 30, 1)
# here = osp.abspath(osp.dirname(__file__))
here = get_rhino_root()
self.e_path = osp.join(here, 'data', 'events', 'RAM_FR1', 'R1060M_events.mat')
tal_path = osp.join(here, 'data', 'eeg', 'R1060M', 'tal', 'R1060M_talLocs_database_bipol.mat')
tal_reader = TalReader(filename=tal_path)
self.monopolar_channels = tal_reader.get_monopolar_channels()
self.bipolar_pairs = tal_reader.get_bipolar_pairs()
base_e_reader = BaseEventReader(filename=self.e_path, eliminate_events_with_no_eeg=True)
base_events = base_e_reader.read()
base_events = base_events[base_events.type == 'WORD']
base_ev_order = np.argsort(base_events, order=('session', 'list', 'mstime'))
self.base_events = base_events[base_ev_order]
# retaining first session
dataroot = self.base_events[0].eegfile
self.base_events = self.base_events[self.base_events.eegfile == dataroot]
self.base_events = self.base_events[self.event_range]
eeg_reader = EEGReader(events=self.base_events, channels=self.monopolar_channels,
start_time=self.start_time, end_time=self.end_time, buffer_time=self.buffer_time)
self.base_eegs = eeg_reader.read()
session_reader = EEGReader(session_dataroot=dataroot, channels=self.monopolar_channels)
self.session_eegs = session_reader.read()
def read_session(subject, root, experiment, rhino_root):
jr = JsonIndexReader(rhino_root + '/protocols/r1.json') # Build JSON reader
pairs_path = jr.get_value('pairs', subject=subject, experiment=experiment)
tal_reader = TalReader(filename=pairs_path)
monopolar_channels = tal_reader.get_monopolar_channels()
bipolar_channels = tal_reader.get_bipolar_pairs()
jr = JsonIndexReader(rhino_root + '/protocols/r1.json') # Build JSON reader
pairs_path = jr.get_value('pairs', subject=subject, experiment=experiment)
tal_reader = TalReader(filename=pairs_path)
monopolar_channels = tal_reader.get_monopolar_channels()
p_reader = ParamsReader(dataroot=root)
params = p_reader.read()
samplerate = params['samplerate']
print samplerate
try:
raw_eeg = EEGReader(session_dataroot=root, channels = monopolar_channels)
raw_eeg = raw_eeg.read()
print raw_eeg.shape
except:
with h5py.File(root, 'r') as hfile:
raw_eeg = H5RawReader.H5RawReader.read_h5file(hfile, monopolar_channels,[0])[0]
print raw_eeg.shape
raw_eeg = TimeSeriesX.TimeSeriesX(raw_eeg,
dims=['channels', 'start_offsets', 'time'],
coords={
'channels': monopolar_channels,
'start_offsets': [0],
'time': np.arange(raw_eeg.shape[2])*1000/samplerate,
'offsets': ('time',np.arange(raw_eeg.shape[2])),
'samplerate': samplerate})
return raw_eeg
def setUp(self):
root = get_rhino_root()
self.e_path = osp.join(root, 'data', 'events', 'RAM_FR1',
'R1060M_events.mat')
tal_path = osp.join(root, 'data', 'eeg', 'R1060M', 'tal',
'R1060M_talLocs_database_bipol.mat')
base_e_reader = BaseEventReader(filename=self.e_path,
eliminate_events_with_no_eeg=True)
self.base_events = base_e_reader.read()
tal_reader = TalReader(filename=tal_path)
self.monopolar_channels = tal_reader.get_monopolar_channels()
self.bipolar_pairs = tal_reader.get_bipolar_pairs()
self.base_events = self.base_events[self.base_events.type == 'WORD']
# retaining first session
dataroot = self.base_events[0].eegfile
self.base_events = self.base_events[self.base_events.eegfile == dataroot]
eeg_reader = EEGReader(events=self.base_events, channels=self.monopolar_channels,
start_time=0.0, end_time=1.6, buffer_time=1.0)
self.base_eegs = eeg_reader.read()
def get_bp_data(evs):
eeg_reader = EEGReader(events=evs, channels=monopolar_channels,
start_time=start_time, end_time=end_time, buffer_time=buffer_time)
base_eegs = eeg_reader.read()
m2b = MonopolarToBipolarMapper(time_series=base_eegs, bipolar_pairs=bipolar_pairs)
bp_eegs = m2b.filter()
return bp_eegs
def test_1():
import time
start = time.time()
e_path = '/Users/m/data/events/RAM_FR1/R1060M_events.mat'
from ptsa.data.readers import BaseEventReader
base_e_reader = BaseEventReader(filename=e_path,
eliminate_events_with_no_eeg=True,
use_ptsa_events_class=False)
base_events = base_e_reader.read()
base_events = base_events[base_events.type == 'WORD']
# selecting only one session
base_events = base_events[base_events.eegfile == base_events[0].eegfile]
from ptsa.data.readers.TalReader import TalReader
tal_path = '/Users/m/data/eeg/R1060M/tal/R1060M_talLocs_database_bipol.mat'
tal_reader = TalReader(filename=tal_path)
monopolar_channels = tal_reader.get_monopolar_channels()
bipolar_pairs = tal_reader.get_bipolar_pairs()
dataroot = base_events[0].eegfile
from ptsa.data.readers import EEGReader
session_reader = EEGReader(session_dataroot=dataroot,
channels=monopolar_channels)
session_eegs = session_reader.read()
wavelet_start = time.time()
wf = MorletWaveletFilterSimple(
time_series=session_eegs,
freqs=np.logspace(np.log10(3), np.log10(180), 2),
# freqs=np.array([3.]),
output='power',
# resamplerate=50.0
)
pow_wavelet, phase_wavelet = wf.filter()
print('wavelet total time = ', time.time() - wavelet_start)
# return pow_wavelet
from ptsa.data.filters import EventDataChopper
sedc = EventDataChopper(events=base_events,
session_data=pow_wavelet,
start_time=0.0,
end_time=1.6,
buffer_time=1.0)
chopped_wavelets = sedc.filter()
print('total time = ', time.time() - start)
return chopped_wavelets
def test_R1070T_read(self):
e_path = '/Volumes/rhino_root/data/events/RAM_FR1/R1070T_events.mat'
base_event_reader = BaseEventReader(filename=e_path)
start_time = 0.0
end_time = 1.366
buffer_time = 1.365
base_events = base_event_reader.read()
eeg_reader = EEGReader(events=base_events, channels=np.array(['042', '043']),
start_time=start_time, end_time=end_time, buffer_time=buffer_time)
base_eegs = eeg_reader.read()
def test_1():
import time
start = time.time()
e_path = "/Users/m/data/events/RAM_FR1/R1060M_events.mat"
from ptsa.data.readers import BaseEventReader
base_e_reader = BaseEventReader(filename=e_path, eliminate_events_with_no_eeg=True, use_ptsa_events_class=False)
base_events = base_e_reader.read()
base_events = base_events[base_events.type == "WORD"]
# selecting only one session
base_events = base_events[base_events.eegfile == base_events[0].eegfile]
from ptsa.data.readers.TalReader import TalReader
tal_path = "/Users/m/data/eeg/R1060M/tal/R1060M_talLocs_database_bipol.mat"
tal_reader = TalReader(filename=tal_path)
monopolar_channels = tal_reader.get_monopolar_channels()
bipolar_pairs = tal_reader.get_bipolar_pairs()
dataroot = base_events[0].eegfile
from ptsa.data.readers import EEGReader
session_reader = EEGReader(session_dataroot=dataroot, channels=monopolar_channels)
session_eegs = session_reader.read()
wavelet_start = time.time()
wf = MorletWaveletFilterSimple(
time_series=session_eegs,
freqs=np.logspace(np.log10(3), np.log10(180), 2),
# freqs=np.array([3.]),
output="power",
# resamplerate=50.0
)
pow_wavelet, phase_wavelet = wf.filter()
print "wavelet total time = ", time.time() - wavelet_start
# return pow_wavelet
from ptsa.data.filters import EventDataChopper
sedc = EventDataChopper(events=base_events, session_data=pow_wavelet, start_time=0.0, end_time=1.6, buffer_time=1.0)
chopped_wavelets = sedc.filter()
print "total time = ", time.time() - start
return chopped_wavelets
def test_event_data_chopper(self):
dataroot = self.base_events[0].eegfile
session_reader = EEGReader(session_dataroot=dataroot, channels=self.monopolar_channels)
session_eegs = session_reader.read()
sedc = DataChopper(events=self.base_events, session_data=session_eegs,
start_time=self.start_time, end_time=self.end_time, buffer_time=self.buffer_time)
chopped_session = sedc.filter()
assert_array_equal(chopped_session, self.base_eegs)
sedc = DataChopper(start_offsets=self.base_events.eegoffset, session_data=session_eegs,
start_time=self.start_time, end_time=self.end_time, buffer_time=self.buffer_time)
chopped_session = sedc.filter()
assert_array_equal(chopped_session, self.base_eegs)
def _test_eeg_with_tal_struct(self, subject, experiment, session, struct_type='mono'):
from ptsa.data.readers import JsonIndexReader,TalReader,EEGReader,BaseEventReader
import os
tal_file = 'contacts' if struct_type=='mono' else 'pairs'
jr = JsonIndexReader(os.path.join(get_rhino_root(),'protocols','r1.json'))
events = BaseEventReader(filename=jr.get_value('task_events',subject=subject,experiment=experiment,session=session)).read()
tal_struct = TalReader(filename=jr.get_value(tal_file,subject=subject),struct_type=struct_type).read()
eeg_reader = EEGReader(events=events[:10],channels=tal_struct[:10],start_time=0.0,end_time=0.1)
eeg = eeg_reader.read()
print(eeg)
channel_name = eeg_reader.channel_name
for col in tal_struct.dtype.names:
if col != 'atlases': # Because I don't want to deal with NaNs at the moment
assert_array_equal(eeg[channel_name].data[col],tal_struct[:10][col])
def compute_continuous_wavelets(dataroot):
session_reader = EEGReader(session_dataroot=dataroot, channels=monopolar_channels)
session_eegs = session_reader.read()
m2b = MonopolarToBipolarMapper(time_series=session_eegs, bipolar_pairs=bipolar_pairs)
session_bp_eegs = m2b.filter()
wf = MorletWaveletFilter(time_series=session_bp_eegs,
freqs=np.logspace(np.log10(3), np.log10(180), 8),
output='power',
frequency_dim_pos=0,
verbose=True
)
pow_wavelet_session, phase_wavelet_session = wf.filter()
return pow_wavelet_session
def test_eeg_read_incomplete_data(self):
e_path_incomplete = '/Volumes/rhino_root/data/events/RAM_PS/R1104D_events.mat'
if sys.platform.startswith('win'):
e_path_incomplete = 'D:/data/events/RAM_PS/R1104D_events.mat'
base_event_reader = BaseEventReader(filename=e_path_incomplete)
base_events = base_event_reader.read()
sess_1 = base_events[base_events.session == 1]
sess_3 = base_events[base_events.session == 3]
sess_5 = base_events[base_events.session == 5]
sess_7 = base_events[base_events.session == 7]
sess_1[440].eegoffset = 2000000000000
sess_1[444].eegoffset = 2000000000000
sess_1[434].eegoffset = 2000000000000
shuffled_sess_events = np.hstack((sess_3, sess_7, sess_1, sess_5)).view(np.recarray)
eeg_reader = EEGReader(events=shuffled_sess_events, channels=np.array(['002', '003']),
start_time=self.start_time, end_time=self.end_time, buffer_time=self.buffer_time)
base_eegs = eeg_reader.read()
if eeg_reader.removed_bad_data():
print('REMOVED BAD DATA !!!!!!!!!!!!!')
events = base_eegs['events'].data.view(np.recarray)
if not isinstance(events, Events):
events = Events(events)
from ptsa.data.rawbinwrapper import RawBinWrapper
events = events.add_fields(esrc=np.dtype(RawBinWrapper))
# ------------- using PTSAevent reader functions to prepare events for reading old-ptsa-style
ptsa_event_reader = PTSAEventReader()
ptsa_event_reader.attach_rawbinwrapper_groupped(events)
eegs = events.get_data(channels=['002', '003'], start_time=self.start_time, end_time=self.end_time,
buffer_time=self.buffer_time, eoffset='eegoffset', keep_buffer=True,
eoffset_in_time=False, verbose=True)
npt.assert_array_equal(eegs[:, :, :-1], base_eegs.data)
def test_h5reader_full_session(self):
dataroot = self.dataroot_template.format(
subject='R1354E',
experiment='FR1',
session=0,
filename='R1354E_FR1_0_26Oct17_2006.h5'
)
EEGReader(session_dataroot=dataroot,channels=np.array([])).read()
def test_base_raw_reader(self):
e_path = '/Users/m/data/events/RAM_FR1/R1060M_events.mat'
base_e_reader = BaseEventReader(filename=e_path, eliminate_events_with_no_eeg=True)
base_events = base_e_reader.read()
base_events = base_events[base_events.type == 'WORD']
dataroot = base_events[0].eegfile
brr_session = BaseRawReader(dataroot=dataroot, channels=np.array(['002', '003']))
array_session, read_ok_mask = brr_session.read()
eeg_reader = EEGReader(events=base_events, channels=np.array(['002', '003']),
start_time=self.start_time, end_time=self.end_time, buffer_time=0.0)
base_eegs = eeg_reader.read()
for i in xrange(100):
offset = base_events[i].eegoffset
npt.assert_array_equal(array_session[:, 0, offset:offset + 100], base_eegs[:, i, :100])
def test_monopolar_to_bipolar_filter_and_data_chopper(self):
dataroot = self.base_events[0].eegfile
session_reader = EEGReader(session_dataroot=dataroot, channels=self.monopolar_channels)
session_eegs = session_reader.read()
m2b = MonopolarToBipolarMapper(time_series=session_eegs, bipolar_pairs=self.bipolar_pairs)
bp_session_eegs = m2b.filter()
sedc = DataChopper(events=self.base_events, session_data=bp_session_eegs, start_time=self.start_time,
end_time=self.end_time, buffer_time=self.buffer_time)
bp_session_eegs_chopped = sedc.filter()
m2b = MonopolarToBipolarMapper(time_series=self.base_eegs, bipolar_pairs=self.bipolar_pairs)
bp_base_eegs = m2b.filter()
assert_array_equal(bp_session_eegs_chopped, bp_base_eegs)
def test_with_events(self):
dataroot_format = osp.join(get_rhino_root(), 'scratch', 'ptsa_test',
'R1308T', 'experiments', 'FR1', 'sessions',
'3', 'behavioral', 'current_processed',
'task_events.json')
events = CMLEventReader(filename=dataroot_format).read()[:20]
EEGReader(events=events,
channels=np.array(['%.03d' % i for i in range(1, 10)]),
start_time=0.0,
end_time=0.5).read()
def test_h5reader_empty_channels(self):
dataroot = self.task_events_template.format(
subject='R1358T',
experiment='FR1',
session=0
)
events = CMLEventReader(filename=dataroot).read()[:20]
eeg = EEGReader(events=events, channels=np.array([]),
start_time=0.0, end_time=0.5).read()
assert len(eeg['channels']) > 0
def test_h5reader_empty_channels(self):
dataroot_format = osp.join(get_rhino_root(), 'scratch', 'ptsa_test',
'R1308T', 'experiments', 'FR1', 'sessions',
'3', 'behavioral', 'current_processed',
'task_events.json')
events = CMLEventReader(filename=dataroot_format).read()[:20]
eeg = EEGReader(events=events,
channels=np.array([]),
start_time=0.0,
end_time=0.5).read()
assert len(eeg.bipolar_pairs) > 0
def test_with_events(self):
dataroot = self.task_events_template.format(
subject='R1358T',
experiment='FR1',
session=0
)
events = CMLEventReader(filename=dataroot).read()[:20]
EEGReader(events=events,
channels=np.array(['{:03d}'.format(i).encode() for i in range(1, 10)]),
start_time=0.0,
end_time=0.5).read()
def test_event_data_chopper(self):
dataroot = self.base_events[0].eegfile
session_reader = EEGReader(session_dataroot=dataroot,
channels=self.monopolar_channels)
session_eegs = session_reader.read()
sedc = DataChopper(events=self.base_events,
timeseries=session_eegs,
start_time=self.start_time,
end_time=self.end_time,
buffer_time=self.buffer_time)
chopped_session = sedc.filter()
assert_array_equal(chopped_session, self.base_eegs)
sedc = DataChopper(start_offsets=self.base_events.eegoffset,
timeseries=session_eegs,
start_time=self.start_time,
end_time=self.end_time,
buffer_time=self.buffer_time)
chopped_session = sedc.filter()
assert_array_equal(chopped_session, self.base_eegs)
def get_stim_eeg(evs_on,
tal_struct,
bipolar_pairs,
monopolar_channels,
chans=np.array([]),
start_time=-1.0,
end_time=1.5):
from ptsa.data.readers import EEGReader
from ptsa.data.filters import MonopolarToBipolarMapper
#Get EEG clips
eeg_reader = EEGReader(events=evs_on,
channels=chans,
start_time=start_time,
end_time=end_time,
buffer_time=0.0)
eegs = eeg_reader.read()
eegs = eegs.baseline_corrected((-1.0, 2.5))
if tal_struct is np.nan:
return eegs, np.nan
if ('bipolar_pairs'
in list(eegs.coords)): #Gotta do this for bipolar ENS subjects
bps_eeg = [list(i) for i in np.array(eegs['bipolar_pairs'])]
bps_tal = [list(i) for i in np.array(tal_struct['channel'])]
bps_eeg_good = []
bps_tal_good = []
for iidx, i in enumerate(bps_eeg):
for jidx, j in enumerate(bps_tal):
if i == j:
bps_eeg_good.append(iidx)
bps_tal_good.append(jidx)
bps_eeg_good = np.array(bps_eeg_good)
bps_tal_good = np.array(bps_tal_good)
eegs_raw = eegs[bps_eeg_good]
tal_struct = tal_struct[bps_tal_good]
else:
try:
m2b = MonopolarToBipolarMapper(time_series=eegs,
bipolar_pairs=bipolar_pairs)
eegs_raw = m2b.filter()
except KeyError: #we've got to do this subject with specified channels
eeg_reader = EEGReader(events=evs_on,
channels=monopolar_channels,
start_time=start_time,
end_time=end_time,
buffer_time=0.0)
eegs = eeg_reader.read()
eegs = eegs.baseline_corrected((-1.0, 2.5))
#Bipolar rereference
m2b = MonopolarToBipolarMapper(time_series=eegs,
bipolar_pairs=bipolar_pairs)
eegs_raw = m2b.filter()
return eegs_raw, tal_struct
def test_scalp_eeg_readers(self):
subject_list = ['LTP001', 'LTP002', 'LTP040']
task = 'catFR'
monopolar_channels = np.array(map(lambda x: str(x).zfill(3), range(1,129)))
for subject in subject_list:
e_path = e_path_matlab_scalp(self.prefix, subject, task)
cml_evs = read_events(e_path=e_path,
reader_class=CMLEventReader,
common_root='data/scalp_events',
normalize_eeg_path=True
)
eeg_reader = EEGReader(events=cml_evs[:30], channels = monopolar_channels,
start_time=self.start_time, end_time=self.end_time, buffer_time=self.buffer_time)
eegs = eeg_reader.read()
print eegs
def test_monopolar_to_bipolar_filter_and_data_chopper(self):
dataroot = self.base_events[0].eegfile
session_reader = EEGReader(session_dataroot=dataroot,
channels=self.monopolar_channels)
session_eegs = session_reader.read()
m2b = MonopolarToBipolarMapper(timeseries=session_eegs,
bipolar_pairs=self.bipolar_pairs)
bp_session_eegs = m2b.filter()
sedc = DataChopper(events=self.base_events,
timeseries=bp_session_eegs,
start_time=self.start_time,
end_time=self.end_time,
buffer_time=self.buffer_time)
bp_session_eegs_chopped = sedc.filter()
m2b = MonopolarToBipolarMapper(timeseries=self.base_eegs,
bipolar_pairs=self.bipolar_pairs)
bp_base_eegs = m2b.filter()
assert_array_equal(bp_session_eegs_chopped, bp_base_eegs)
def test_eeg_read(self):
ptsa_reader = PTSAEventReader(filename=self.e_path)
events = ptsa_reader.read()
# in case fancy indexing looses Eventness of events we need to create Events object explicitely
if not isinstance(events, Events):
events = Events(events)
eegs = events.get_data(channels=['002', '003'], start_time=self.start_time, end_time=self.end_time,
buffer_time=self.buffer_time, eoffset='eegoffset', keep_buffer=True,
eoffset_in_time=False, verbose=True)
base_event_reader = BaseEventReader(filename=self.e_path)
base_events = base_event_reader.read()
eeg_reader = EEGReader(events=base_events, channels=np.array(['002', '003']),
start_time=self.start_time, end_time=self.end_time, buffer_time=self.buffer_time)
base_eegs = eeg_reader.read()
npt.assert_array_equal(eegs[:, :, :-1], base_eegs.data)
def test_eeg_reader(self, subject, session):
jr = JsonIndexReader(
osp.join(get_rhino_root(), 'protocols', 'ltp.json'))
events = BaseEventReader(filename=jr.get_value(
'task_events', subject=subject, session=session)).read()
# hack to make the scalp events work with Rhino mounted
events['eegfile'] = get_rhino_root() + events[0]['eegfile']
channels = np.array([0, 1])
eeg = EEGReader(events=events[:10],
channels=channels,
start_time=0.0,
end_time=0.1).read()
assert (eeg['channels'].values['index'] == channels).all()
assert (eeg['channels'].values['label'] == np.array(
['A1', 'A2'], dtype=bytes)).all()
def setUp(self):
self.start_time = -0.5
self.end_time = 1.6
self.buffer_time = 0.5
self.event_range = range(0, 30, 1)
# here = osp.abspath(osp.dirname(__file__))
here = get_rhino_root()
self.e_path = osp.join(here, 'data', 'events', 'RAM_FR1',
'R1060M_events.mat')
tal_path = osp.join(here, 'data', 'eeg', 'R1060M', 'tal',
'R1060M_talLocs_database_bipol.mat')
tal_reader = TalReader(filename=tal_path)
self.monopolar_channels = tal_reader.get_monopolar_channels()
self.bipolar_pairs = tal_reader.get_bipolar_pairs()
base_e_reader = BaseEventReader(filename=self.e_path,
eliminate_events_with_no_eeg=True)
base_events = base_e_reader.read()
base_events = base_events[base_events.type == 'WORD']
base_ev_order = np.argsort(base_events,
order=('session', 'list', 'mstime'))
self.base_events = base_events[base_ev_order]
# retaining first session
dataroot = self.base_events[0].eegfile
self.base_events = self.base_events[self.base_events.eegfile ==
dataroot]
self.base_events = self.base_events[self.event_range]
eeg_reader = EEGReader(events=self.base_events,
channels=self.monopolar_channels,
start_time=self.start_time,
end_time=self.end_time,
buffer_time=self.buffer_time)
self.base_eegs = eeg_reader.read()
session_reader = EEGReader(session_dataroot=dataroot,
channels=self.monopolar_channels)
self.session_eegs = session_reader.read()
if __name__ == '__main__':
for subject in bipolar_subjects:
logger.set_subject(subject, 'R1')
sucess, _ = make_bipolar_montage(subject)
if sucess:
tal = TalReader(filename=pairs_path_template.format(
protocols_root=test_index_root, subject=subject))
new_bipolar_pairs = tal.get_bipolar_pairs()
jr = JsonIndexReader(
osp.join(reference_index_root, 'protocols', 'r1.json'))
task_event_files = list(
jr.aggregate_values('task_events', subject=subject, montage=0))
events = CMLEventReader(filename=task_event_files[0]).read()
eeg = EEGReader(events=events[:1],
channels=np.array([]),
start_time=0.0,
end_time=0.1).read()
hdf_bipolar_pairs = eeg.bipolar_pairs.values
new_bipolar_pairs = new_bipolar_pairs.astype(
hdf_bipolar_pairs.dtype)
if not np.in1d(hdf_bipolar_pairs, new_bipolar_pairs).all():
logger.info(
'\n\n%s missing from new_bipolar_pairs\n\n' %
str(hdf_bipolar_pairs[
~np.in1d(hdf_bipolar_pairs, new_bipolar_pairs)]))
if not np.in1d(new_bipolar_pairs, hdf_bipolar_pairs).all():
logger.info(
'\n\n%s missing from new_bipolar_pairs\n\n' %
str(new_bipolar_pairs[
~np.in1d(new_bipolar_pairs, hdf_bipolar_pairs)]))
def compute_ps_powers(self, events, sessions, monopolar_channels, bipolar_pairs, experiment):
n_freqs = len(self.params.freqs)
n_bps = len(bipolar_pairs)
pow_mat_pre = pow_mat_post = None
pow_ev = None
samplerate = winsize = bufsize = None
monopolar_channels_list = list(monopolar_channels)
for sess in sessions:
sess_events = events[events.session == sess]
# print type(sess_events)
n_events = len(sess_events)
print 'Loading EEG for', n_events, 'events of session', sess
pre_start_time = self.params.ps_start_time - self.params.ps_offset
pre_end_time = self.params.ps_end_time - self.params.ps_offset
# eegs_pre = Events(sess_events).get_data(channels=channels, start_time=pre_start_time, end_time=pre_end_time,
# buffer_time=self.params.ps_buf, eoffset='eegoffset', keep_buffer=True, eoffset_in_time=False)
eeg_pre_reader = EEGReader(events=sess_events, channels=np.array(monopolar_channels_list),
start_time=pre_start_time,
end_time=pre_end_time, buffer_time=self.params.ps_buf)
eegs_pre = eeg_pre_reader.read()
if samplerate is None:
# samplerate = round(eegs_pre.samplerate)
# samplerate = eegs_pre.attrs['samplerate']
samplerate = float(eegs_pre['samplerate'])
winsize = int(round(samplerate*(pre_end_time-pre_start_time+2*self.params.ps_buf)))
bufsize = int(round(samplerate*self.params.ps_buf))
print 'samplerate =', samplerate, 'winsize =', winsize, 'bufsize =', bufsize
pow_ev = np.empty(shape=n_freqs*winsize, dtype=float)
self.wavelet_transform.init(self.params.width, self.params.freqs[0], self.params.freqs[-1], n_freqs, samplerate, winsize)
# mirroring
nb_ = int(round(samplerate*(self.params.ps_buf)))
eegs_pre[...,-nb_:] = eegs_pre[...,-nb_-2:-2*nb_-2:-1]
dim3_pre = eegs_pre.shape[2] # because post-stim time inreval does not align for all stim events (stims have different duration)
# we have to take care of aligning eegs_post ourselves time dim to dim3
# eegs_post = np.zeros_like(eegs_pre)
from ptsa.data.TimeSeriesX import TimeSeriesX
eegs_post = TimeSeriesX(np.zeros_like(eegs_pre),dims=eegs_pre.dims,coords=eegs_pre.coords)
post_start_time = self.params.ps_offset
post_end_time = self.params.ps_offset + (self.params.ps_end_time - self.params.ps_start_time)
for i_ev in xrange(n_events):
ev_offset = sess_events[i_ev].pulse_duration
if ev_offset > 0:
if experiment == 'PS3' and sess_events[i_ev].nBursts > 0:
ev_offset *= sess_events[i_ev].nBursts + 1
ev_offset *= 0.001
else:
ev_offset = 0.0
# eeg_post = Events(sess_events[i_ev:i_ev+1]).get_data(channels=channels, start_time=post_start_time+ev_offset,
# end_time=post_end_time+ev_offset, buffer_time=self.params.ps_buf,
# eoffset='eegoffset', keep_buffer=True, eoffset_in_time=False)
eeg_post_reader = EEGReader(events=sess_events[i_ev:i_ev+1], channels=np.array(monopolar_channels_list),
start_time=post_start_time+ev_offset,
end_time=post_end_time+ev_offset, buffer_time=self.params.ps_buf)
eeg_post = eeg_post_reader.read()
dim3_post = eeg_post.shape[2]
# here we take care of possible mismatch of time dim length
if dim3_pre == dim3_post:
eegs_post[:,i_ev:i_ev+1,:] = eeg_post
elif dim3_pre < dim3_post:
eegs_post[:,i_ev:i_ev+1,:] = eeg_post[:,:,:-1]
else:
eegs_post[:,i_ev:i_ev+1,:-1] = eeg_post
# mirroring
eegs_post[...,:nb_] = eegs_post[...,2*nb_:nb_:-1]
print 'Computing', experiment, 'powers'
sess_pow_mat_pre = np.empty(shape=(n_events, n_bps, n_freqs), dtype=np.float)
sess_pow_mat_post = np.empty_like(sess_pow_mat_pre)
for i,ti in enumerate(bipolar_pairs):
bp = ti['channel_str']
print 'Computing powers for bipolar pair', bp
elec1 = np.where(monopolar_channels == bp[0])[0][0]
elec2 = np.where(monopolar_channels == bp[1])[0][0]
#
# for i,ti in enumerate(tal_info):
# bp = ti['channel_str']
# print 'Computing powers for bipolar pair', bp
# elec1 = np.where(channels == bp[0])[0][0]
# elec2 = np.where(channels == bp[1])[0][0]
bp_data_pre = eegs_pre[elec1] - eegs_pre[elec2]
# bp_data_pre.attrs['samplerate'] = samplerate
bp_data_pre = bp_data_pre.filtered([58,62], filt_type='stop', order=self.params.filt_order)
for ev in xrange(n_events):
#pow_pre_ev = phase_pow_multi(self.params.freqs, bp_data_pre[ev], to_return='power')
self.wavelet_transform.multiphasevec(bp_data_pre[ev][0:winsize], pow_ev)
#sess_pow_mat_pre[ev,i,:] = np.mean(pow_pre_ev[:,nb_:-nb_], axis=1)
pow_ev_stripped = np.reshape(pow_ev, (n_freqs,winsize))[:,bufsize:winsize-bufsize]
if self.params.log_powers:
np.log10(pow_ev_stripped, out=pow_ev_stripped)
sess_pow_mat_pre[ev,i,:] = np.nanmean(pow_ev_stripped, axis=1)
bp_data_post = eegs_post[elec1] - eegs_post[elec2]
# bp_data_post.attrs['samplerate'] = samplerate
bp_data_post = bp_data_post.filtered([58,62], filt_type='stop', order=self.params.filt_order)
for ev in xrange(n_events):
#pow_post_ev = phase_pow_multi(self.params.freqs, bp_data_post[ev], to_return='power')
self.wavelet_transform.multiphasevec(bp_data_post[ev][0:winsize], pow_ev)
#sess_pow_mat_post[ev,i,:] = np.mean(pow_post_ev[:,nb_:-nb_], axis=1)
pow_ev_stripped = np.reshape(pow_ev, (n_freqs,winsize))[:,bufsize:winsize-bufsize]
if self.params.log_powers:
np.log10(pow_ev_stripped, out=pow_ev_stripped)
sess_pow_mat_post[ev,i,:] = np.nanmean(pow_ev_stripped, axis=1)
sess_pow_mat_pre = sess_pow_mat_pre.reshape((n_events, n_bps*n_freqs))
#sess_pow_mat_pre = zscore(sess_pow_mat_pre, axis=0, ddof=1)
sess_pow_mat_post = sess_pow_mat_post.reshape((n_events, n_bps*n_freqs))
#sess_pow_mat_post = zscore(sess_pow_mat_post, axis=0, ddof=1)
sess_pow_mat_joint = zscore(np.vstack((sess_pow_mat_pre,sess_pow_mat_post)), axis=0, ddof=1)
sess_pow_mat_pre = sess_pow_mat_joint[:n_events,...]
sess_pow_mat_post = sess_pow_mat_joint[n_events:,...]
pow_mat_pre = np.vstack((pow_mat_pre,sess_pow_mat_pre)) if pow_mat_pre is not None else sess_pow_mat_pre
pow_mat_post = np.vstack((pow_mat_post,sess_pow_mat_post)) if pow_mat_post is not None else sess_pow_mat_post
return pow_mat_pre, pow_mat_post
def compute_powers(self, events, sessions, monopolar_channels, bipolar_pairs, start_time, end_time, mirror_front, mirror_back):
n_freqs = len(self.params.freqs)
n_bps = len(bipolar_pairs)
self.pow_mat = None
pow_ev = None
winsize = bufsize = None
for sess in sessions:
sess_events = events[events.session == sess]
n_events = len(sess_events)
print 'Loading EEG for', n_events, 'events of session', sess
# eegs = Events(sess_events).get_data(channels=channels, start_time=self.params.control_start_time, end_time=self.params.control_end_time,
# buffer_time=self.params.control_buf, eoffset='eegoffset', keep_buffer=True, eoffset_in_time=False)
# from ptsa.data.readers import TimeSeriesEEGReader
# time_series_reader = TimeSeriesEEGReader(events=sess_events, start_time=self.params.control_start_time,
# end_time=self.params.control_end_time, buffer_time=self.params.control_buf, keep_buffer=True)
#
# eegs = time_series_reader.read(monopolar_channels)
eeg_reader = EEGReader(events=sess_events, channels = monopolar_channels,
start_time=start_time, end_time=end_time, buffer_time=self.params.control_buf)
eegs = eeg_reader.read()
# print 'eegs=',eegs.values[0,0,:2],eegs.values[0,0,-2:]
# sys.exit()
#
# a = eegs[0]-eegs[1]
#eegs[...,:1365] = eegs[...,2730:1365:-1]
#eegs[...,2731:4096] = eegs[...,2729:1364:-1]
if self.samplerate is None:
self.samplerate = float(eegs.samplerate)
winsize = int(round(self.samplerate*(self.params.control_end_time-self.params.control_start_time+2*self.params.control_buf)))
bufsize = int(round(self.samplerate*self.params.control_buf))
print 'samplerate =', self.samplerate, 'winsize =', winsize, 'bufsize =', bufsize
pow_ev = np.empty(shape=n_freqs*winsize, dtype=float)
self.wavelet_transform.init(self.params.width, self.params.freqs[0], self.params.freqs[-1], n_freqs, self.samplerate, winsize)
# mirroring
nb_ = int(round(self.samplerate*(self.params.control_buf)))
if mirror_front:
eegs[...,:nb_] = eegs[...,2*nb_-1:nb_-1:-1]
if mirror_back:
eegs[...,-nb_:] = eegs[...,-nb_-1:-2*nb_-1:-1]
print 'Computing control powers'
sess_pow_mat = np.empty(shape=(n_events, n_bps, n_freqs), dtype=np.float)
#monopolar_channels_np = np.array(monopolar_channels)
for i,ti in enumerate(bipolar_pairs):
# print bp
# print monopolar_channels
# print np.where(monopolar_channels == bp[0])
# print np.where(monopolar_channels == bp[1])
bp = ti['channel_str']
print 'Computing powers for bipolar pair', bp
elec1 = np.where(monopolar_channels == bp[0])[0][0]
elec2 = np.where(monopolar_channels == bp[1])[0][0]
# print 'elec1=',elec1
# print 'elec2=',elec2
# eegs_elec1 = eegs[elec1]
# eegs_elec2 = eegs[elec2]
# print 'eegs_elec1=',eegs_elec1
# print 'eegs_elec2=',eegs_elec2
# eegs_elec1.reset_coords('channels')
# eegs_elec2.reset_coords('channels')
bp_data = eegs[elec1] - eegs[elec2]
bp_data.attrs['samplerate'] = self.samplerate
# bp_data = eegs[elec1] - eegs[elec2]
# bp_data = eegs[elec1] - eegs[elec2]
# bp_data = eegs.values[elec1] - eegs.values[elec2]
bp_data = bp_data.filtered([58,62], filt_type='stop', order=self.params.filt_order)
for ev in xrange(n_events):
self.wavelet_transform.multiphasevec(bp_data[ev][0:winsize], pow_ev)
#if np.min(pow_ev) < 0.0:
# print ev, events[ev]
# joblib.dump(bp_data[ev], 'bad_bp_ev%d'%ev)
# joblib.dump(eegs[elec1][ev], 'bad_elec1_ev%d'%ev)
# joblib.dump(eegs[elec2][ev], 'bad_elec2_ev%d'%ev)
# print 'Negative powers detected'
# import sys
# sys.exit(1)
pow_ev_stripped = np.reshape(pow_ev, (n_freqs,winsize))[:,bufsize:winsize-bufsize]
if self.params.log_powers:
np.log10(pow_ev_stripped, out=pow_ev_stripped)
sess_pow_mat[ev,i,:] = np.nanmean(pow_ev_stripped, axis=1)
sess_pow_mat = zscore(sess_pow_mat, axis=0, ddof=1)
self.pow_mat = np.concatenate((self.pow_mat,sess_pow_mat), axis=0) if self.pow_mat is not None else sess_pow_mat
self.pow_mat = np.reshape(self.pow_mat, (len(events), n_bps*n_freqs))
filename=rhino_root +
'/data/eeg/scalp/ltp/ltpFR2/behavioral/events/events_all_LTP377.mat',
use_reref_eeg=True,
common_root='data').read()
words = events[events.type == 'WORD']
# select all available channels
eegfile = words[0].eegfile
eegfile_reref = str.split(str(eegfile), '/')
day = eegfile_reref[-1]
eegfile_reref = '/'.join(eegfile_reref[0:-1])
channels = glob.glob(eegfile_reref + '/' + day + "*.[0-9]*")
channels = np.array([str.split(x, '.')[-1] for x in channels])
#channels = np.array(['{:03}'.format(x) for x in range(0,132)])
eeg = EEGReader(events=words, channels=channels, start_time=0.3,
end_time=1.6).read()
b_filter = ButterworthFilter(time_series=eeg, order=4, freq_range=[58, 62])
eeg_filtered = b_filter.filter()
eeg_buffered = eeg_filtered.add_mirror_buffer(1.3)
eeg_buffered.data = np.ascontiguousarray(eeg_buffered.data)
import time
pt = time.time()
freqs = np.logspace(np.log10(3), np.log10(180), 50)
pow_ev, _ = MorletWaveletFilterCpp(time_series=eeg_buffered,
freqs=freqs[0:1],
output='power',
cpus=20,
verbose=False).filter()
run_time = time.time() - pt
monopolar_channels = tal_reader.get_monopolar_channels()
bipolar_pairs = tal_reader.get_bipolar_pairs()
# ---------------- NEW STYLE PTSA -------------------
base_e_reader = BaseEventReader(filename=e_path,
eliminate_events_with_no_eeg=True)
base_events = base_e_reader.read()
base_events = base_events[(base_events.type == 'STIMULATING')]
base_events = base_events[base_events.session == 2]
from ptsa.data.readers.EEGReader import EEGReader
eeg_reader = EEGReader(events=base_events,
channels=monopolar_channels[0:3],
start_time=-1.1,
end_time=-0.1,
buffer_time=1.0)
base_eegs = eeg_reader.read()
bw_base_eegs = base_eegs.filtered(freq_range=[58., 62.],
filt_type='stop',
order=4)
b, a = butter_bandpass(58., 62., float(base_eegs['samplerate']), 4)
y_in = base_eegs[0, 0, :].data
y_out = butter_bandpass_filter(y_in, 58., 62.,
float(base_eegs['samplerate']), 4)
try:
return str(''.join(c for c in unicodedata.normalize('NFD', unicode(s))
if unicodedata.category(c) != 'Mn'))
except UnicodeError: # If accents can't be converted, just remove them
return str(re.sub(r'[^A-Za-z0-9 -_.]', '', s))
if __name__ == '__main__':
e_path = '/Volumes/db_root/protocols/r1/subjects/R1001P/experiments/FR1/sessions/0/behavioral/current_processed/task_events.json'
e_reader = BaseEventReader(filename=e_path)
events = e_reader.read()
from ptsa.data.readers import EEGReader
eeg_reader = EEGReader(events=events, channels=np.array(['006']), start_time = 0., end_time=1.6, buffer_time=1.0)
base_eeg = eeg_reader.read()
print base_eeg
#
# from ptsa.data.MatlabIO import *
#
# # d = deserialize_objects_from_matlab_format('/Volumes/rhino_root/home2/yezzyat/R1108J_1_sess2_rawEEG_chans1_2.mat', 'ye')
# d = deserialize_objects_from_matlab_format('/Volumes/rhino_root/home2/yezzyat/R1060M_FR1_sess0_rawEEG_chans2_3.mat', 'ye')
#
# print d
#
# from BaseEventReader import BaseEventReader
# # e_path = join('/Volumes/rhino_root', 'data/events/RAM_FR1/R1060M_math.mat')
# e_path = '/Volumes/rhino_root/data/events/RAM_PS/R1108J_1_events.mat'
# e_path = '/Volumes/rhino_root/data/events/RAM_PS/R1108J_1_events.mat'
def compute_powers(self, events, sessions,monopolar_channels , bipolar_pairs ):
n_freqs = len(self.params.freqs)
n_bps = len(bipolar_pairs)
self.pow_mat = None
pow_ev = None
winsize = bufsize = None
for sess in sessions:
sess_events = events[events.session == sess]
n_events = len(sess_events)
print 'Loading EEG for', n_events, 'events of session', sess
# eegs = Events(sess_events).get_data(channels=channels, start_time=self.params.fr1_start_time, end_time=self.params.fr1_end_time,
# buffer_time=self.params.fr1_buf, eoffset='eegoffset', keep_buffer=True, eoffset_in_time=False)
# from ptsa.data.readers import TimeSeriesEEGReader
# time_series_reader = TimeSeriesEEGReader(events=sess_events, start_time=self.params.fr1_start_time,
# end_time=self.params.fr1_end_time, buffer_time=self.params.fr1_buf, keep_buffer=True)
#
# eegs = time_series_reader.read(monopolar_channels)
# VERSION 2/22/2016
# eeg_reader = EEGReader(events=sess_events, channels=monopolar_channels,
# start_time=self.params.fr1_start_time,
# end_time=self.params.fr1_end_time, buffer_time=self.params.fr1_buf)
# VERSION WITH MIRRORING
eeg_reader = EEGReader(events=sess_events, channels=monopolar_channels,
start_time=self.params.fr1_start_time,
end_time=self.params.fr1_end_time, buffer_time=0.0)
eegs = eeg_reader.read()
if eeg_reader.removed_bad_data():
print 'REMOVED SOME BAD EVENTS !!!'
sess_events = eegs['events'].values.view(np.recarray)
n_events = len(sess_events)
events = np.hstack((events[events.session!=sess],sess_events)).view(np.recarray)
ev_order = np.argsort(events, order=('session','list','mstime'))
events = events[ev_order]
self.pass_object(self.pipeline.task+'_events', events)
# mirroring
#eegs[...,:1365] = eegs[...,2730:1365:-1]
#eegs[...,2731:4096] = eegs[...,2729:1364:-1]
eegs = eegs.add_mirror_buffer(duration=self.params.fr1_buf)
if self.samplerate is None:
self.samplerate = float(eegs.samplerate)
winsize = int(round(self.samplerate*(self.params.fr1_end_time-self.params.fr1_start_time+2*self.params.fr1_buf)))
bufsize = int(round(self.samplerate*self.params.fr1_buf))
print 'samplerate =', self.samplerate, 'winsize =', winsize, 'bufsize =', bufsize
pow_ev = np.empty(shape=n_freqs*winsize, dtype=float)
self.wavelet_transform.init(self.params.width, self.params.freqs[0], self.params.freqs[-1], n_freqs, self.samplerate, winsize)
print 'Computing FR1 powers'
sess_pow_mat = np.empty(shape=(n_events, n_bps, n_freqs), dtype=np.float)
#monopolar_channels_np = np.array(monopolar_channels)
for i,ti in enumerate(bipolar_pairs):
# print bp
# print monopolar_channels
# print np.where(monopolar_channels == bp[0])
# print np.where(monopolar_channels == bp[1])
bp = ti['channel_str']
print 'Computing powers for bipolar pair', bp
elec1 = np.where(monopolar_channels == bp[0])[0][0]
elec2 = np.where(monopolar_channels == bp[1])[0][0]
# print 'elec1=',elec1
# print 'elec2=',elec2
# eegs_elec1 = eegs[elec1]
# eegs_elec2 = eegs[elec2]
# print 'eegs_elec1=',eegs_elec1
# print 'eegs_elec2=',eegs_elec2
# eegs_elec1.reset_coords('channels')
# eegs_elec2.reset_coords('channels')
bp_data = eegs[elec1] - eegs[elec2]
bp_data.attrs['samplerate'] = self.samplerate
# bp_data = eegs[elec1] - eegs[elec2]
# bp_data = eegs[elec1] - eegs[elec2]
# bp_data = eegs.values[elec1] - eegs.values[elec2]
bp_data = bp_data.filtered([58,62], filt_type='stop', order=self.params.filt_order)
for ev in xrange(n_events):
self.wavelet_transform.multiphasevec(bp_data[ev][0:winsize], pow_ev)
#if np.min(pow_ev) < 0.0:
# print ev, events[ev]
# joblib.dump(bp_data[ev], 'bad_bp_ev%d'%ev)
# joblib.dump(eegs[elec1][ev], 'bad_elec1_ev%d'%ev)
# joblib.dump(eegs[elec2][ev], 'bad_elec2_ev%d'%ev)
# print 'Negative powers detected'
# import sys
# sys.exit(1)
pow_ev_stripped = np.reshape(pow_ev, (n_freqs,winsize))[:,bufsize:winsize-bufsize]
if self.params.log_powers:
np.log10(pow_ev_stripped, out=pow_ev_stripped)
sess_pow_mat[ev,i,:] = np.nanmean(pow_ev_stripped, axis=1)
self.pow_mat = np.concatenate((self.pow_mat,sess_pow_mat), axis=0) if self.pow_mat is not None else sess_pow_mat
self.pow_mat = np.reshape(self.pow_mat, (len(events), n_bps*n_freqs))
tal_path = '/Volumes/rhino_root/data/eeg/R1108J_1/tal/R1108J_1_talLocs_database_bipol.mat'
tal_reader = TalReader(filename=tal_path)
monopolar_channels = tal_reader.get_monopolar_channels()
bipolar_pairs = tal_reader.get_bipolar_pairs()
# ---------------- NEW STYLE PTSA -------------------
base_e_reader = BaseEventReader(filename=e_path, eliminate_events_with_no_eeg=True)
base_events = base_e_reader.read()
base_events = base_events[(base_events.type == 'STIMULATING') ]
base_events = base_events[base_events.session == 2]
from ptsa.data.readers.EEGReader import EEGReader
eeg_reader = EEGReader(events=base_events, channels=monopolar_channels[0:3],
start_time=-1.1, end_time=-0.1, buffer_time=1.0)
base_eegs = eeg_reader.read()
bw_base_eegs = base_eegs.filtered(freq_range=[58.,62.], filt_type='stop', order=4)
b, a = butter_bandpass(58.,62.,float(base_eegs['samplerate']), 4)
y_in = base_eegs[0,0,:].data
y_out = butter_bandpass_filter(y_in, 58.,62.,float(base_eegs['samplerate']), 4)
import matplotlib;
matplotlib.use('Qt4Agg')
def compute_ps_powers(self, events, sessions, monopolar_channels,
bipolar_pairs, experiment):
n_freqs = len(self.params.freqs)
n_bps = len(bipolar_pairs)
pow_mat_pre = pow_mat_post = None
pow_ev = None
samplerate = winsize = bufsize = None
monopolar_channels_list = list(monopolar_channels)
for sess in sessions:
sess_events = events[events.session == sess]
# print type(sess_events)
n_events = len(sess_events)
print 'Loading EEG for', n_events, 'events of session', sess
pre_start_time = self.params.ps_start_time - self.params.ps_offset
pre_end_time = self.params.ps_end_time - self.params.ps_offset
# eegs_pre = Events(sess_events).get_data(channels=channels, start_time=pre_start_time, end_time=pre_end_time,
# buffer_time=self.params.ps_buf, eoffset='eegoffset', keep_buffer=True, eoffset_in_time=False)
eeg_pre_reader = EEGReader(
events=sess_events,
channels=np.array(monopolar_channels_list),
start_time=pre_start_time,
end_time=pre_end_time,
buffer_time=self.params.ps_buf)
eegs_pre = eeg_pre_reader.read()
if samplerate is None:
# samplerate = round(eegs_pre.samplerate)
# samplerate = eegs_pre.attrs['samplerate']
samplerate = float(eegs_pre['samplerate'])
winsize = int(
round(samplerate * (pre_end_time - pre_start_time +
2 * self.params.ps_buf)))
bufsize = int(round(samplerate * self.params.ps_buf))
print 'samplerate =', samplerate, 'winsize =', winsize, 'bufsize =', bufsize
pow_ev = np.empty(shape=n_freqs * winsize, dtype=float)
self.wavelet_transform.init(self.params.width,
self.params.freqs[0],
self.params.freqs[-1], n_freqs,
samplerate, winsize)
# mirroring
nb_ = int(round(samplerate * (self.params.ps_buf)))
eegs_pre[..., -nb_:] = eegs_pre[..., -nb_ - 2:-2 * nb_ - 2:-1]
dim3_pre = eegs_pre.shape[
2] # because post-stim time inreval does not align for all stim events (stims have different duration)
# we have to take care of aligning eegs_post ourselves time dim to dim3
# eegs_post = np.zeros_like(eegs_pre)
from ptsa.data.TimeSeriesX import TimeSeriesX
eegs_post = TimeSeriesX(np.zeros_like(eegs_pre),
dims=eegs_pre.dims,
coords=eegs_pre.coords)
post_start_time = self.params.ps_offset
post_end_time = self.params.ps_offset + (self.params.ps_end_time -
self.params.ps_start_time)
for i_ev in xrange(n_events):
ev_offset = sess_events[i_ev].pulse_duration
if ev_offset > 0:
if experiment == 'PS3' and sess_events[i_ev].nBursts > 0:
ev_offset *= sess_events[i_ev].nBursts + 1
ev_offset *= 0.001
else:
ev_offset = 0.0
# eeg_post = Events(sess_events[i_ev:i_ev+1]).get_data(channels=channels, start_time=post_start_time+ev_offset,
# end_time=post_end_time+ev_offset, buffer_time=self.params.ps_buf,
# eoffset='eegoffset', keep_buffer=True, eoffset_in_time=False)
eeg_post_reader = EEGReader(
events=sess_events[i_ev:i_ev + 1],
channels=np.array(monopolar_channels_list),
start_time=post_start_time + ev_offset,
end_time=post_end_time + ev_offset,
buffer_time=self.params.ps_buf)
eeg_post = eeg_post_reader.read()
dim3_post = eeg_post.shape[2]
# here we take care of possible mismatch of time dim length
if dim3_pre == dim3_post:
eegs_post[:, i_ev:i_ev + 1, :] = eeg_post
elif dim3_pre < dim3_post:
eegs_post[:, i_ev:i_ev + 1, :] = eeg_post[:, :, :-1]
else:
eegs_post[:, i_ev:i_ev + 1, :-1] = eeg_post
# mirroring
eegs_post[..., :nb_] = eegs_post[..., 2 * nb_:nb_:-1]
print 'Computing', experiment, 'powers'
sess_pow_mat_pre = np.empty(shape=(n_events, n_bps, n_freqs),
dtype=np.float)
sess_pow_mat_post = np.empty_like(sess_pow_mat_pre)
for i, ti in enumerate(bipolar_pairs):
bp = ti['channel_str']
print 'Computing powers for bipolar pair', bp
elec1 = np.where(monopolar_channels == bp[0])[0][0]
elec2 = np.where(monopolar_channels == bp[1])[0][0]
#
# for i,ti in enumerate(tal_info):
# bp = ti['channel_str']
# print 'Computing powers for bipolar pair', bp
# elec1 = np.where(channels == bp[0])[0][0]
# elec2 = np.where(channels == bp[1])[0][0]
bp_data_pre = eegs_pre[elec1] - eegs_pre[elec2]
# bp_data_pre.attrs['samplerate'] = samplerate
bp_data_pre = bp_data_pre.filtered(
[58, 62], filt_type='stop', order=self.params.filt_order)
for ev in xrange(n_events):
#pow_pre_ev = phase_pow_multi(self.params.freqs, bp_data_pre[ev], to_return='power')
self.wavelet_transform.multiphasevec(
bp_data_pre[ev][0:winsize], pow_ev)
#sess_pow_mat_pre[ev,i,:] = np.mean(pow_pre_ev[:,nb_:-nb_], axis=1)
pow_ev_stripped = np.reshape(
pow_ev, (n_freqs, winsize))[:,
bufsize:winsize - bufsize]
if self.params.log_powers:
np.log10(pow_ev_stripped, out=pow_ev_stripped)
sess_pow_mat_pre[ev, i, :] = np.nanmean(pow_ev_stripped,
axis=1)
bp_data_post = eegs_post[elec1] - eegs_post[elec2]
# bp_data_post.attrs['samplerate'] = samplerate
bp_data_post = bp_data_post.filtered(
[58, 62], filt_type='stop', order=self.params.filt_order)
for ev in xrange(n_events):
#pow_post_ev = phase_pow_multi(self.params.freqs, bp_data_post[ev], to_return='power')
self.wavelet_transform.multiphasevec(
bp_data_post[ev][0:winsize], pow_ev)
#sess_pow_mat_post[ev,i,:] = np.mean(pow_post_ev[:,nb_:-nb_], axis=1)
pow_ev_stripped = np.reshape(
pow_ev, (n_freqs, winsize))[:,
bufsize:winsize - bufsize]
if self.params.log_powers:
np.log10(pow_ev_stripped, out=pow_ev_stripped)
sess_pow_mat_post[ev, i, :] = np.nanmean(pow_ev_stripped,
axis=1)
sess_pow_mat_pre = sess_pow_mat_pre.reshape(
(n_events, n_bps * n_freqs))
#sess_pow_mat_pre = zscore(sess_pow_mat_pre, axis=0, ddof=1)
sess_pow_mat_post = sess_pow_mat_post.reshape(
(n_events, n_bps * n_freqs))
#sess_pow_mat_post = zscore(sess_pow_mat_post, axis=0, ddof=1)
sess_pow_mat_joint = zscore(np.vstack(
(sess_pow_mat_pre, sess_pow_mat_post)),
axis=0,
ddof=1)
sess_pow_mat_pre = sess_pow_mat_joint[:n_events, ...]
sess_pow_mat_post = sess_pow_mat_joint[n_events:, ...]
pow_mat_pre = np.vstack(
(pow_mat_pre, sess_pow_mat_pre
)) if pow_mat_pre is not None else sess_pow_mat_pre
pow_mat_post = np.vstack(
(pow_mat_post, sess_pow_mat_post
)) if pow_mat_post is not None else sess_pow_mat_post
return pow_mat_pre, pow_mat_post
def compute_powers(self, events, sessions, monopolar_channels,
bipolar_pairs):
n_freqs = len(self.params.freqs)
n_bps = len(bipolar_pairs)
self.pow_mat = None
pow_ev = None
winsize = bufsize = None
for sess in sessions:
sess_events = events[events.session == sess]
n_events = len(sess_events)
print 'Loading EEG for', n_events, 'events of session', sess
# eegs = Events(sess_events).get_data(channels=channels, start_time=self.params.fr1_start_time, end_time=self.params.fr1_end_time,
# buffer_time=self.params.fr1_buf, eoffset='eegoffset', keep_buffer=True, eoffset_in_time=False)
# from ptsa.data.readers import TimeSeriesEEGReader
# time_series_reader = TimeSeriesEEGReader(events=sess_events, start_time=self.params.fr1_start_time,
# end_time=self.params.fr1_end_time, buffer_time=self.params.fr1_buf, keep_buffer=True)
#
# eegs = time_series_reader.read(monopolar_channels)
eeg_reader = EEGReader(events=sess_events,
channels=monopolar_channels,
start_time=self.params.fr1_start_time,
end_time=self.params.fr1_end_time,
buffer_time=self.params.fr1_buf)
eegs = eeg_reader.read()
# print 'eegs=',eegs.values[0,0,:2],eegs.values[0,0,-2:]
# sys.exit()
#
# a = eegs[0]-eegs[1]
# mirroring
#eegs[...,:1365] = eegs[...,2730:1365:-1]
#eegs[...,2731:4096] = eegs[...,2729:1364:-1]
if self.samplerate is None:
self.samplerate = float(eegs.samplerate)
winsize = int(
round(
self.samplerate *
(self.params.fr1_end_time - self.params.fr1_start_time
+ 2 * self.params.fr1_buf)))
bufsize = int(round(self.samplerate * self.params.fr1_buf))
print 'samplerate =', self.samplerate, 'winsize =', winsize, 'bufsize =', bufsize
pow_ev = np.empty(shape=n_freqs * winsize, dtype=float)
self.wavelet_transform.init(self.params.width,
self.params.freqs[0],
self.params.freqs[-1], n_freqs,
self.samplerate, winsize)
print 'Computing FR1 powers'
sess_pow_mat = np.empty(shape=(n_events, n_bps, n_freqs),
dtype=np.float)
#monopolar_channels_np = np.array(monopolar_channels)
for i, ti in enumerate(bipolar_pairs):
# print bp
# print monopolar_channels
# print np.where(monopolar_channels == bp[0])
# print np.where(monopolar_channels == bp[1])
bp = ti['channel_str']
print 'Computing powers for bipolar pair', bp
elec1 = np.where(monopolar_channels == bp[0])[0][0]
elec2 = np.where(monopolar_channels == bp[1])[0][0]
# print 'elec1=',elec1
# print 'elec2=',elec2
# eegs_elec1 = eegs[elec1]
# eegs_elec2 = eegs[elec2]
# print 'eegs_elec1=',eegs_elec1
# print 'eegs_elec2=',eegs_elec2
# eegs_elec1.reset_coords('channels')
# eegs_elec2.reset_coords('channels')
bp_data = eegs[elec1] - eegs[elec2]
bp_data.attrs['samplerate'] = self.samplerate
# bp_data = eegs[elec1] - eegs[elec2]
# bp_data = eegs[elec1] - eegs[elec2]
# bp_data = eegs.values[elec1] - eegs.values[elec2]
bp_data = bp_data.filtered([58, 62],
filt_type='stop',
order=self.params.filt_order)
for ev in xrange(n_events):
self.wavelet_transform.multiphasevec(
bp_data[ev][0:winsize], pow_ev)
#if np.min(pow_ev) < 0.0:
# print ev, events[ev]
# joblib.dump(bp_data[ev], 'bad_bp_ev%d'%ev)
# joblib.dump(eegs[elec1][ev], 'bad_elec1_ev%d'%ev)
# joblib.dump(eegs[elec2][ev], 'bad_elec2_ev%d'%ev)
# print 'Negative powers detected'
# import sys
# sys.exit(1)
pow_ev_stripped = np.reshape(
pow_ev, (n_freqs, winsize))[:,
bufsize:winsize - bufsize]
if self.params.log_powers:
np.log10(pow_ev_stripped, out=pow_ev_stripped)
sess_pow_mat[ev, i, :] = np.nanmean(pow_ev_stripped,
axis=1)
self.pow_mat = np.concatenate(
(self.pow_mat, sess_pow_mat),
axis=0) if self.pow_mat is not None else sess_pow_mat
self.pow_mat = np.reshape(self.pow_mat, (len(events), n_bps * n_freqs))