def test_ptsa_event_ordering(self):
# --------------------OROG PTSA - one raw bin wrapper per event
e_reader = PTSAEventReader(filename=self.e_path,
eliminate_events_with_no_eeg=True,
use_groupped_rawbinwrapper=False)
events = e_reader.read()
events = events[events.type == 'WORD']
events = events[self.event_range]
if not isinstance(events, Events):
events = Events(events)
eegs = events.get_data(channels=['002', '003'],
start_time=0.0,
end_time=1.6,
buffer_time=1.0,
eoffset='eegoffset',
keep_buffer=True,
eoffset_in_time=False,
verbose=True)
eegs = eegs[:, :, :-1]
words_ptsa = eegs['events']['item']
print('words_ptsa=', words_ptsa)
words = self.base_eegs['events'].data['item']
print(words)
assert_array_equal(np.array(words_ptsa), words)
assert_array_equal(eegs, self.base_eegs)
def test_ptsa_event_ordering(self):
# --------------------OROG PTSA - one raw bin wrapper per event
e_reader = PTSAEventReader(filename=self.e_path, eliminate_events_with_no_eeg=True, use_groupped_rawbinwrapper=False)
events = e_reader.read()
events = events[events.type == 'WORD']
events = events[self.event_range]
if not isinstance(events, Events):
events = Events(events)
eegs = events.get_data(channels=['002', '003'], start_time=0.0, end_time=1.6,
buffer_time=1.0, eoffset='eegoffset', keep_buffer=True,
eoffset_in_time=False, verbose=True)
eegs = eegs[:,:,:-1]
words_ptsa = eegs['events']['item']
print 'words_ptsa=',words_ptsa
words = self.base_eegs['events'].data['item']
print words
assert_array_equal(np.array(words_ptsa),words)
assert_array_equal(eegs, self.base_eegs)
def test_eventness(self):
events = self.read_ptsa_events()
ptsa_reader = PTSAEventReader(filename=self.e_path)
events = ptsa_reader.read()
self.assertIsInstance(events, Events, "WARNING:Warning Fancy Indexing Causes Events to be recarray")
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 read_ptsa_events(self):
e_reader = PTSAEventReader(event_file=self.e_path,
eliminate_events_with_no_eeg=True)
e_reader.read()
events = e_reader.get_output()
events = events[events.type == 'WORD']
events = events[self.event_range]
ev_order = np.argsort(events, order=('session', 'list', 'mstime'))
events = events[ev_order]
return events
def read_ptsa_events(self):
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'))
events = events[ev_order]
return events
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_read(self):
ptsa_reader = PTSAEventReader(filename=self.e_path)
events = ptsa_reader.read()
base_event_reader = BaseEventReader(filename=self.e_path)
base_events = base_event_reader.read()
for base_event, event in zip(base_events, events):
self.assertEqual(base_event['item'], event['item'])
for base_event, event in zip(base_events, events):
self.assertEqual(base_event.eegoffset, event.eegoffset)
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_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_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 run(self):
# PTSA EVENT READER
# e_path = join(self.pipeline.mount_point, 'data/events', self.pipeline.task,self.pipeline.subject+'_events.mat')
e_path = '/Users/m/data/events/RAM_FR1/R1060M_events.mat'
# e_path = '/Users/m/data/events/RAM_FR1/R1056M_events.mat'
e_reader = PTSAEventReader(event_file=e_path, eliminate_events_with_no_eeg=True)
e_reader.read()
events = e_reader.get_output()
events = events[events.type == 'WORD']
events = events[0:30]
ev_order = np.argsort(events, order=('session','list','mstime'))
events = events[ev_order]
events = Events(events) # necessary workaround for new numpy
print 'events=',events
eegs= events.get_data(channels=['002','003'], start_time=0.0, end_time=1.6,
buffer_time=1.0, eoffset='eegoffset', keep_buffer=False, eoffset_in_time=False,verbose=True)
print eegs
# BASE READER
base_e_reader = BaseEventReader(event_file=e_path, eliminate_events_with_no_eeg=True, use_ptsa_events_class=False)
base_e_reader.read()
base_events = base_e_reader.get_output()
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]
base_events = base_events[0:30]
print 'base_events=',base_events
from ptsa.data.readers.TimeSeriesEEGReader import TimeSeriesEEGReader
time_series_reader = TimeSeriesEEGReader(base_events)
time_series_reader.start_time = 0.0
time_series_reader.end_time = 1.6
time_series_reader.buffer_time = 1.0
time_series_reader.keep_buffer = False
time_series_reader.read(channels=['002','003'])
base_eegs = time_series_reader.get_output()
print
def run(self):
# PTSA EVENT READER
# e_path = join(self.pipeline.mount_point, 'data/events', self.pipeline.task,self.pipeline.subject+'_events.mat')
e_path = '/Users/m/data/events/RAM_FR1/R1060M_events.mat'
# e_path = '/Users/m/data/events/RAM_FR1/R1056M_events.mat'
e_reader = PTSAEventReader(event_file=e_path,
eliminate_events_with_no_eeg=True)
e_reader.read()
events = e_reader.get_output()
events = events[events.type == 'WORD']
events = events[0:30]
ev_order = np.argsort(events, order=('session', 'list', 'mstime'))
events = events[ev_order]
events = Events(events) # necessary workaround for new numpy
print 'events=', events
eegs = events.get_data(channels=['002', '003'],
start_time=0.0,
end_time=1.6,
buffer_time=1.0,
eoffset='eegoffset',
keep_buffer=False,
eoffset_in_time=False,
verbose=True)
print eegs
# BASE READER
base_e_reader = BaseEventReader(event_file=e_path,
eliminate_events_with_no_eeg=True,
use_ptsa_events_class=False)
base_e_reader.read()
base_events = base_e_reader.get_output()
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]
base_events = base_events[0:30]
print 'base_events=', base_events
from ptsa.data.readers.TimeSeriesEEGReader import TimeSeriesEEGReader
time_series_reader = TimeSeriesEEGReader(base_events)
time_series_reader.start_time = 0.0
time_series_reader.end_time = 1.6
time_series_reader.buffer_time = 1.0
time_series_reader.keep_buffer = False
time_series_reader.read(channels=['002', '003'])
base_eegs = time_series_reader.get_output()
print
