def setUp(self):
self.e_path = '/Users/m/data/events/RAM_FR1/R1060M_events.mat'
tal_path = '/Users/m/data/eeg/R1060M/tal/R1060M_talLocs_database_bipol.mat'
# ---------------- NEW STYLE PTSA -------------------
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 main_fcn():
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)
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()
print('bipolar_pairs=', bipolar_pairs)
from ptsa.data.readers.EEGReader import EEGReader
sessions = np.unique(base_events.session)
dataroot = base_events[0].eegfile
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()
time_series_reader = EEGReader(events=base_events, channels=monopolar_channels, start_time=0.0,
end_time=1.6, buffer_time=1.0)
base_eegs = time_series_reader.read()
m2b = MonopolarToBipolarMapper(time_series=base_eegs, bipolar_pairs=bipolar_pairs)
ts_filtered = m2b.filter()
del base_eegs
del time_series_reader
print()
pass
def setUp(self):
self.event_range = range(0, 30, 1)
self.e_path = '/Users/m/data/events/RAM_FR1/R1060M_events.mat'
self.tal_path = '/Users/m/data/eeg/R1060M/tal/R1060M_talLocs_database_bipol.mat'
if sys.platform.startswith('win'):
self.e_path = 'D:/data/events/RAM_FR1/R1060M_events.mat'
self.tal_path = 'D:/data/eeg/R1060M/tal/R1060M_talLocs_database_bipol.mat'
# --------------- TAL STRUCTS READ
tal_reader = TalReader(filename=self.tal_path)
self.monopolar_channels = tal_reader.get_monopolar_channels()
# ---------------- ORIG PTSA -------------------
e_reader = PTSAEventReader(filename=self.e_path, eliminate_events_with_no_eeg=True)
events = e_reader.read()
events = events[events.type == 'WORD']
events = events[self.event_range]
ev_order = np.argsort(events, order=('session','list','mstime'))
self.events = events[ev_order]
# self.events = self.read_ptsa_events()
# in case fancy indexing looses Eventness of events we need to create Events object explicitely
if not isinstance(self.events, Events):
self.events = Events(self.events)
start_time = 0.0
end_time = 1.6
buffer_time = 1.0
self.eegs = self.events.get_data(channels=['002', '003'], start_time=start_time, end_time=end_time,
buffer_time=buffer_time, eoffset='eegoffset', keep_buffer=True,
eoffset_in_time=False, verbose=True)
# ---------------- NEW STYLE PTSA -------------------
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'))
base_events = base_events[base_ev_order]
self.base_events = base_events[self.event_range]
# self.base_events = self.read_base_events()
eeg_reader = EEGReader(events=self.base_events, channels=np.array(['002', '003']),
start_time=start_time, end_time=end_time, buffer_time=buffer_time)
self.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)
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()
print 'bipolar_pairs=', bipolar_pairs
from ptsa.data.readers.EEGReader import EEGReader
time_series_reader = EEGReader(events=base_events, start_time=0.0,channels=monopolar_channels, end_time=1.6, buffer_time=1.0)
base_eegs = time_series_reader.read()
# base_eegs = base_eegs[:, 0:10, :]
# bipolar_pairs = bipolar_pairs[0:10]
from ptsa.data.filters import MorletWaveletFilter
wf = MorletWaveletFilter(time_series=base_eegs,
freqs=np.logspace(np.log10(3), np.log10(180), 8),
# freqs=np.array([3.]),
output='power',
)
pow_wavelet, phase_wavelet = wf.filter()
print 'total time = ', time.time() - start
res_start = time.time()
# from ptsa.data.filters.ResampleFilter import ResampleFilter
# rsf = ResampleFilter (resamplerate=50.0)
# rsf.set_input(pow_wavelet)
# pow_wavelet = rsf.filter()
print 'resample_time=', time.time() - res_start
return pow_wavelet
def setUp(self):
self.event_range = range(0, 30, 1)
self.e_path = '/Users/m/data/events/RAM_FR1/R1060M_events.mat'
self.tal_path = '/Users/m/data/eeg/R1060M/tal/R1060M_talLocs_database_bipol.mat'
# --------------- TAL STRUCTS READ
tal_reader = TalReader(filename=self.tal_path)
self.monopolar_channels = tal_reader.get_monopolar_channels()
# ---------------- ORIG PTSA -------------------
e_reader = PTSAEventReader(filename=self.e_path, eliminate_events_with_no_eeg=True)
events = e_reader.read()
events = events[events.type == 'WORD']
events = events[self.event_range]
ev_order = np.argsort(events, order=('session','list','mstime'))
self.events = events[ev_order]
# self.events = self.read_ptsa_events()
# in case fancy indexing looses Eventness of events we need to create Events object explicitely
if not isinstance(self.events, Events):
self.events = Events(self.events)
start_time = 0.0
end_time = 1.6
buffer_time = 1.0
self.eegs = self.events.get_data(channels=['002', '003'], start_time=start_time, end_time=end_time,
buffer_time=buffer_time, eoffset='eegoffset', keep_buffer=True,
eoffset_in_time=False, verbose=True)
# ---------------- NEW STYLE PTSA -------------------
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'))
base_events = base_events[base_ev_order]
self.base_events = base_events[self.event_range]
# self.base_events = self.read_base_events()
eeg_reader = EEGReader(events=self.base_events, channels=np.array(['002', '003']),
start_time=start_time, end_time=end_time, buffer_time=buffer_time)
self.base_eegs = eeg_reader.read()
def test_full_session_read(self):
# ---------------- ORIG PTSA -------------------
e_reader = PTSAEventReader(filename=self.e_path,
eliminate_events_with_no_eeg=True)
events = e_reader.read()
events = events[events.type == 'WORD']
events = events[self.event_range]
ev_order = np.argsort(events, order=('session', 'list', 'mstime'))
self.events = events[ev_order]
# self.events = self.read_ptsa_events()
# in case fancy indexing looses Eventness of events we need to create Events object explicitely
if not isinstance(self.events, Events):
self.events = Events(self.events)
eegs = self.events.get_data(channels=self.monopolar_channels,
start_time=0.0,
end_time=1.6,
buffer_time=1.0,
eoffset='eegoffset',
keep_buffer=True,
eoffset_in_time=False,
verbose=True)
# removing last entry to match dimensions - ptsa adds one extra element at the end of time axis
eegs = eegs[:, :, :-1]
eeg_reader = EEGReader(events=self.base_events,
channels=self.monopolar_channels,
start_time=0.0,
end_time=1.6,
buffer_time=1.0)
base_eegs = eeg_reader.read()
assert_array_equal(x=eegs, y=base_eegs)
# checking if axes match
assert_array_equal(np.array(eegs['channels']['name']),
base_eegs['channels'].data)
assert_array_almost_equal(np.array(eegs['time']),
base_eegs['time'].data,
decimal=3)
assert_array_equal(np.array(eegs['events']['item']),
base_eegs['events'].data['item'])
print()
def test_event_data_chopper(self):
dataroot=self.base_events[0].eegfile
from ptsa.data.readers import EEGReader
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=0.0, end_time=1.6, buffer_time=1.0)
chopped_session = sedc.filter()
sedc_so = DataChopper(start_offsets=self.base_events.eegoffset, session_data=session_eegs, start_time=0.0, end_time=1.6, buffer_time=1.0)
chopped_session_so = sedc_so.filter()
assert_array_equal(chopped_session,chopped_session_so)
def test_event_data_chopper(self):
dataroot=self.base_events[0].eegfile
from ptsa.data.readers import EEGReader
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=0.0, end_time=1.6, buffer_time=1.0)
chopped_session = sedc.filter()
sedc_so = DataChopper(start_offsets=self.base_events.eegoffset, session_data=session_eegs, start_time=0.0, end_time=1.6, buffer_time=1.0)
chopped_session_so = sedc_so.filter()
assert_array_equal(chopped_session,chopped_session_so)
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_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_full_session_read(self):
# ---------------- ORIG PTSA -------------------
e_reader = PTSAEventReader(filename=self.e_path, eliminate_events_with_no_eeg=True)
events = e_reader.read()
events = events[events.type == 'WORD']
events = events[self.event_range]
ev_order = np.argsort(events, order=('session','list','mstime'))
self.events = events[ev_order]
# self.events = self.read_ptsa_events()
# in case fancy indexing looses Eventness of events we need to create Events object explicitely
if not isinstance(self.events, Events):
self.events = Events(self.events)
eegs = self.events.get_data(channels=self.monopolar_channels, start_time=0.0, end_time=1.6,
buffer_time=1.0, eoffset='eegoffset', keep_buffer=True,
eoffset_in_time=False, verbose=True)
# removing last entry to match dimensions - ptsa adds one extra element at the end of time axis
eegs = eegs[:,:,:-1]
eeg_reader = EEGReader(events=self.base_events, channels=self.monopolar_channels,
start_time=0.0, end_time=1.6, buffer_time=1.0)
base_eegs = eeg_reader.read()
assert_array_equal(x=eegs, y=base_eegs)
# checking if axes match
assert_array_equal(np.array(eegs['channels']['name']), base_eegs['channels'].data)
assert_array_almost_equal(np.array(eegs['time']), base_eegs['time'].data, decimal=3)
assert_array_equal(np.array(eegs['events']['item']), base_eegs['events'].data['item'])
print
def main_fcn():
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)
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()
print 'bipolar_pairs=', bipolar_pairs
from ptsa.data.readers.EEGReader import EEGReader
sessions = np.unique(base_events.session)
dataroot = base_events[0].eegfile
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()
time_series_reader = EEGReader(events=base_events,
channels=monopolar_channels,
start_time=0.0,
end_time=1.6,
buffer_time=1.0)
base_eegs = time_series_reader.read()
m2b = MonopolarToBipolarMapper(time_series=base_eegs,
bipolar_pairs=bipolar_pairs)
ts_filtered = m2b.filter()
del base_eegs
del time_series_reader
print
pass
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)
self.e_path = '/Users/m/data/events/RAM_FR1/R1060M_events.mat'
tal_path = '/Users/m/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()
# ---------------- NEW STYLE PTSA -------------------
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]
# self.base_events = base_events[self.event_range]
# self.base_events = self.read_base_events()
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_eegs(self, events, channels):
eeg_reader = EEGReader(events=events, channels=channels,
start_time=self.start_time, end_time=self.end_time, buffer_time=self.buffer_time)
self.base_eegs = eeg_reader.read()
