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 get_word_events(sub, task, montage=0):
from ptsa.data.readers import BaseEventReader
from ptsa.data.events import Events
from ptsa.data.readers.IndexReader import JsonIndexReader
reader = JsonIndexReader('/protocols/r1.json')
#Get events
evfiles = list(
reader.aggregate_values('task_events',
subject=sub,
experiment=task,
montage=montage))
evs_on = np.array([])
for ef in evfiles:
try:
base_e_reader = BaseEventReader(filename=ef,
eliminate_events_with_no_eeg=True)
base_events = base_e_reader.read()
if len(evs_on) == 0:
evs_on = base_events[base_events.type == 'WORD']
else:
evs_on = np.concatenate(
(evs_on, base_events[base_events.type == 'WORD']), axis=0)
except:
continue
evs = Events(evs_on)
return evs
def run(self):
events = None
if self.params.include_fr1:
try:
e_path = os.path.join(self.pipeline.mount_point , 'data/events/RAM_FR1', self.pipeline.subject + '_events.mat')
e_reader = BaseEventReader(filename=e_path, eliminate_events_with_no_eeg=True)
events = e_reader.read()
ev_order = np.argsort(events, order=('session','list','mstime'))
events = events[ev_order]
except IOError:
pass
if self.params.include_catfr1:
try:
e_path = os.path.join(self.pipeline.mount_point , 'data/events/RAM_CatFR1', self.pipeline.subject + '_events.mat')
e_reader = BaseEventReader(filename=e_path, eliminate_events_with_no_eeg=True)
catfr1_events = e_reader.read()
ev_order = np.argsort(catfr1_events, order=('session','list','mstime'))
catfr1_events = catfr1_events[ev_order]
if events is None:
events = catfr1_events
else:
catfr1_events.session += 100
fields = list(set(events.dtype.names).intersection(catfr1_events.dtype.names))
events = np.hstack((events[fields],catfr1_events[fields])).view(np.recarray)
except IOError:
pass
events = events[events.type == 'WORD']
print len(events), 'WORD events'
self.pass_object('FR_events', events)
def read_events(self, task, subject):
e_path = join(self.prefix, 'data/events/%s/%s_events.mat' % (task, subject))
base_e_reader = BaseEventReader(filename=e_path, eliminate_events_with_no_eeg=True)
base_events = base_e_reader.read()
return base_events
def test_2_old():
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(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']
# 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(tal_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.experimental.TimeSeriesEEGReader import TimeSeriesEEGReader
time_series_reader = TimeSeriesEEGReader(events=base_events, start_time=0.0,
end_time=1.6, buffer_time=1.0, keep_buffer=True)
base_eegs = time_series_reader.read(channels=monopolar_channels)
# base_eegs = base_eegs[:, 0:10, :]
# bipolar_pairs = bipolar_pairs[0:10]
wf = MorletWaveletFilter(time_series=base_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 '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 test_missing_data_read(self):
self.e_path = '/Volumes/rhino_root/data/events/RAM_PS/R1104D_events.mat'
if sys.platform.startswith('win'):
self.e_path = 'D:/data/events/RAM_PS/R1104D_events.mat'
base_e_reader = BaseEventReader(filename=self.e_path)
base_events = base_e_reader.read()
print('base_events=',base_events)
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 run(self):
task = self.pipeline.task
e_path = os.path.join(self.pipeline.mount_point, 'data', 'events',
task, self.pipeline.subject + '_events.mat')
e_reader = BaseEventReader(filename=e_path,
eliminate_events_with_no_eeg=True)
events = e_reader.read()
ev_order = np.argsort(events, order=('session', 'list', 'mstime'))
events = events[ev_order]
self.pass_object(self.pipeline.task + '_all_events', events)
intr_events = events[(events.intrusion != -999)
& (events.intrusion != 0)]
rec_events = events[events.type == 'REC_WORD']
events = events[events.type == 'WORD']
print len(events), task, 'WORD events'
self.pass_object(task + '_events', events)
self.pass_object(self.pipeline.task + '_intr_events', intr_events)
self.pass_object(self.pipeline.task + '_rec_events', rec_events)
def test_as_dataframe(self):
ber = BaseEventReader(filename=self.filename)
events = ber.as_dataframe()
assert isinstance(events, pd.DataFrame)
with open(self.filename) as f:
assert len(events) == len(json.loads(f.read()))
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 test_read_json(self):
ber = BaseEventReader(filename=self.filename)
events = ber.read_json()
assert isinstance(events, np.recarray)
with open(self.filename) as f:
assert len(events) == len(json.loads(f.read()))
def test_as_dataframe(self):
ber = BaseEventReader(filename=self.filename)
events = ber.as_dataframe()
assert isinstance(events, pd.DataFrame)
with open(self.filename) as f:
assert len(events) == len(json.loads(f.read()))
def get_ltp_subject_sessions_by_experiment(experiment):
events_dir = os.path.join(paths.data_root, 'scalp', 'ltp', experiment, 'behavioral', 'events')
events_files = sorted(glob.glob(os.path.join(events_dir, 'events_all_LTP*.mat')),
key=lambda f: f.split('_')[:-1])
seen_experiments = defaultdict(list)
for events_file in events_files:
print(events_file)
subject = os.path.basename(events_file)[11:-4] # Subject number is the basename with events_all_, .mat removed
subject_no_year = subject.split('_')[0]
if '_' in subject:
continue
mat_events_reader = BaseEventReader(filename=events_file, common_root=paths.data_root)
logger.debug('Loading matlab events {exp}: {subj}'.format(exp=experiment, subj=subject))
try:
mat_events = mat_events_reader.read()
sessions = np.unique(mat_events['session']) - 1 # MATLAB events start counting sessions at 1 instead of 0
version = 0.
for i, session in enumerate(sessions):
if 'experiment' in mat_events.dtype.names:
experiments = np.unique(mat_events[mat_events['session'] == session]['experiment'])
else:
experiments = [experiment]
for this_experiment in experiments:
n_sessions = seen_experiments[subject_no_year].count(this_experiment)
yield subject_no_year, subject, n_sessions, session, this_experiment, version
seen_experiments[subject_no_year].append(this_experiment)
except IndexError or AttributeError:
traceback.print_exc()
logger.error('Could not get session from {}'.format(events_file))
def run(self):
events = None
if self.params.include_fr1:
try:
e_path = os.path.join(self.pipeline.mount_point , 'data/events/RAM_FR1', self.pipeline.subject + '_math.mat')
e_reader = BaseEventReader(filename=e_path, eliminate_events_with_no_eeg=True)
events = e_reader.read()
print "Got FR1 events"
except IOError:
pass
if self.params.include_catfr1:
try:
e_path = os.path.join(self.pipeline.mount_point , 'data/events/RAM_CatFR1', self.pipeline.subject + '_math.mat')
e_reader = BaseEventReader(filename=e_path, eliminate_events_with_no_eeg=True)
catfr1_events = e_reader.read()
print "Got CatFR1 events"
if events is None:
events = catfr1_events
else:
print "Joining FR1 and CatFR1"
catfr1_events.session = -catfr1_events.session-1
fields = list(set(events.dtype.names).intersection(catfr1_events.dtype.names))
events = np.hstack((events[fields],catfr1_events[fields])).view(np.recarray)
except IOError:
pass
events = events[events.type == 'PROB']
print len(events), 'PROB events'
self.pass_object('control_events', events)
def test_read_json(self):
ber = BaseEventReader(filename=self.filename)
events = ber.read_json()
assert isinstance(events, np.recarray)
with open(self.filename) as f:
assert len(events) == len(json.loads(f.read()))
def test_missing_data_read(self):
self.e_path = '/Volumes/rhino_root/data/events/RAM_PS/R1104D_events.mat'
if sys.platform.startswith('win'):
self.e_path = 'D:/data/events/RAM_PS/R1104D_events.mat'
base_e_reader = BaseEventReader(filename=self.e_path)
base_events = base_e_reader.read()
print('base_events=', base_events)
def get_events():
# ---------------- 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 == 'WORD']
return base_events
def get_stim_events(sub, task, montage=0):
from ptsa.data.readers import BaseEventReader
from ptsa.data.events import Events
from ptsa.data.readers.IndexReader import JsonIndexReader
reader = JsonIndexReader('/protocols/r1.json')
#Get events
evfiles = list(
reader.aggregate_values(
'task_events', subject=sub, experiment=task,
montage=montage)) #This is supposed to work but often does not
if len(evfiles) < 1:
from glob import glob
sessions = [
s.split('/')[-1]
for s in glob('/protocols/r1/subjects/' + sub + '/experiments/' +
task + '/sessions/*')
]
evfiles = []
for sess in sessions:
evfiles.append('/protocols/r1/subjects/' + sub + '/experiments/' +
task + '/sessions/' + sess +
'/behavioral/current_processed/task_events.json')
evs_on = np.array([])
for ef in evfiles:
try:
base_e_reader = BaseEventReader(filename=ef,
eliminate_events_with_no_eeg=True)
base_events = base_e_reader.read()
if len(evs_on) == 0:
evs_on = base_events[base_events.type == 'STIM_ON']
else:
evs_on = np.concatenate(
(evs_on, base_events[base_events.type == 'STIM_ON']),
axis=0)
except:
continue
evs_on = Events(evs_on)
#Reorganize sessions around stim sites
sessions = reader.sessions(subject=sub, experiment=task, montage=montage)
sess_tags = []
for i in range(len(evs_on)):
stimtag = str(evs_on[i]['stim_params']['anode_number']) + '-' + str(
evs_on[i]['stim_params']['cathode_number'])
sess_tags.append(stimtag)
sess_tags = np.array(sess_tags)
if len(np.unique(sess_tags)) <= len(sessions):
session_array = evs_on['session']
else:
session_array = np.empty(len(evs_on))
for idx, s in enumerate(np.unique(sess_tags)):
session_array[sess_tags == s] = int(idx)
sessions = np.unique(session_array)
return evs_on, session_array
def test_2():
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.experimental.TimeSeriesEEGReader import TimeSeriesEEGReader
time_series_reader = TimeSeriesEEGReader(events=base_events,
start_time=0.0,
end_time=1.6,
buffer_time=1.0,
keep_buffer=True)
base_eegs = time_series_reader.read(channels=monopolar_channels)
# base_eegs = base_eegs[:, 0:10, :]
# bipolar_pairs = bipolar_pairs[0:10]
wf = MorletWaveletFilter(
time_series=base_eegs,
freqs=np.logspace(np.log10(3), np.log10(180), 2),
# 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'
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 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 __init__(self, **kwds):
BaseEventReader.__init__(self, **kwds)
if self.eeg_fname_search_pattern != '' and self.eeg_fname_replace_pattern != '':
self.alter_eeg_path_flag = True
else:
self.alter_eeg_path_flag = False
def __init__(self, **kwds):
BaseEventReader.__init__(self, **kwds)
if self.eeg_fname_search_pattern != '' and self.eeg_fname_replace_pattern != '':
self.alter_eeg_path_flag = True
else:
self.alter_eeg_path_flag = False
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 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 get_suffixes(subject):
events_file= os.path.join(DATA_ROOT, '..', 'events', 'RAM_PS', '{}_events.mat'.format(subject))
mat_events_reader = BaseEventReader(filename=events_file, common_root=DATA_ROOT)
mat_events = mat_events_reader.read()
sessions = np.unique(mat_events.session)
suffixes = {}
for session in sessions:
sess_events = mat_events[mat_events.session == session]
eegfile = sess_events[10].eegfile
suffixes[session] = '_'.join(eegfile.split('_')[-2:])
return suffixes
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_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 read_base_events(self):
base_e_reader = BaseEventReader(event_file=self.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[self.event_range]
return base_events
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 get_suffixes(subject):
events_file = os.path.join(DATA_ROOT, '..', 'events', 'RAM_PS',
'{}_events.mat'.format(subject))
mat_events_reader = BaseEventReader(filename=events_file,
common_root=DATA_ROOT)
mat_events = mat_events_reader.read()
sessions = np.unique(mat_events.session)
suffixes = {}
for session in sessions:
sess_events = mat_events[mat_events.session == session]
eegfile = sess_events[10].eegfile
suffixes[session] = '_'.join(eegfile.split('_')[-2:])
return suffixes
def run(self):
task = self.pipeline.task
from ptsa.data.readers import BaseEventReader
e_path = os.path.join(self.pipeline.mount_point , 'data', 'events', task, self.pipeline.subject + '_events.mat')
e_reader = BaseEventReader(filename=e_path, eliminate_events_with_no_eeg=True)
events = e_reader.read()
events = events[events.type == 'WORD']
print len(events), task, 'WORD events'
self.pass_object(task+'_events', events)
def read_base_events(self):
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]
base_events = base_events[self.event_range]
return base_events
def run(self):
subject = self.pipeline.subject
experiment = self.pipeline.experiment
from ptsa.data.readers import BaseEventReader
e_path = os.path.join(self.pipeline.mount_point , 'data', 'events', 'RAM_PS', self.pipeline.subject + '_events.mat')
e_reader = BaseEventReader(filename=e_path, eliminate_events_with_no_eeg=True)
events = e_reader.read()
ev_order = np.argsort(events, order=('session','mstime'))
events = events[ev_order]
# try:
# events = Events(get_events(subject=subject, task='RAM_PS', path_prefix=self.pipeline.mount_point))
# except IOError:
# raise Exception('No parameter search for subject %s' % subject)
#
events = events[events.experiment == experiment]
if len(events) == 0:
raise Exception('No %s events for subject %s' % (experiment,subject))
sessions = np.unique(events.session)
print experiment, 'sessions:', sessions
events = pd.DataFrame.from_records(events)
events = compute_isi(events)
is_stim_event_type_vec = np.vectorize(is_stim_event_type)
stim_mask = is_stim_event_type_vec(events.type)
if experiment == 'PS3':
stim_inds = np.where(stim_mask)[0]
stim_events = pd.DataFrame(events[stim_mask])
last_burst_inds = stim_inds + stim_events['nBursts'].values
last_bursts = events.ix[last_burst_inds]
events = stim_events
events['train_duration'] = last_bursts['mstime'].values - events['mstime'].values + last_bursts['pulse_duration'].values
else:
events = events[stim_mask]
events = events.to_records(index=False)
print len(events), 'stim', experiment, 'events'
# events = Events(events.to_records(index=False))
#
# joblib.dump(events, self.get_path_to_resource_in_workspace(subject+'-'+experiment+'-ps_events.pkl'))
self.pass_object(experiment+'_events', events)
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 run(self):
task = self.pipeline.task
from ptsa.data.readers import BaseEventReader
e_path = os.path.join(self.pipeline.mount_point, 'data', 'events',
task, self.pipeline.subject + '_events.mat')
e_reader = BaseEventReader(filename=e_path,
eliminate_events_with_no_eeg=True)
events = e_reader.read()
events = events[events.type == 'WORD']
print len(events), task, 'WORD events'
self.pass_object(task + '_events', events)
def run(self):
try:
e_path = os.path.join(self.pipeline.mount_point, 'data/events', self.pipeline.task, self.pipeline.subject+'_math.mat')
e_reader = BaseEventReader(filename=e_path, eliminate_events_with_no_eeg=False)
events = e_reader.read()
ev_order = np.argsort(events, order=('session','mstime'))
events = events[ev_order]
events = events[events.type == 'PROB']
self.pass_object(self.pipeline.task+'_math_events', events)
except IOError:
self.pass_object(self.pipeline.task+'_math_events', None)
def read_base_events(self):
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]
base_events = base_events[self.event_range]
return base_events
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 read_events_debug(self):
# event_files = ['/Users/m/data/dboy_ev.mat']
event_files = [
'/Volumes/rhino_root/data/eeg/FR438/behavioral/session_0/events.mat'
]
for event_file in event_files:
e_path = event_file
base_e_reader = BaseEventReader(filename=e_path,
eliminate_events_with_no_eeg=False,
normalize_eeg_path=False)
base_events = base_e_reader.read()
print base_events['store'][447]
return base_events
def read_base_events(self):
base_e_reader = BaseEventReader(event_file=self.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[self.event_range]
return base_events
def run(self):
subject = self.pipeline.subject
experiment = self.pipeline.experiment
from ptsa.data.readers import BaseEventReader
e_path = os.path.join(self.pipeline.mount_point, 'data', 'events',
'RAM_PS', self.pipeline.subject + '_events.mat')
e_reader = BaseEventReader(filename=e_path,
eliminate_events_with_no_eeg=True)
events = e_reader.read()
# try:
# events = Events(get_events(subject=subject, task='RAM_PS', path_prefix=self.pipeline.mount_point))
# except IOError:
# raise Exception('No parameter search for subject %s' % subject)
#
events = events[events.experiment == experiment]
if len(events) == 0:
raise Exception('No %s events for subject %s' %
(experiment, subject))
#
# events = correct_eegfile_field(events)
# events = self.attach_raw_bin_wrappers(events)
sessions = np.unique(events.session)
print experiment, 'sessions:', sessions
events = pd.DataFrame.from_records(events)
events = compute_isi(events)
is_stim_event_type_vec = np.vectorize(is_stim_event_type)
events = events[is_stim_event_type_vec(events.type)]
print len(events), 'stim', experiment, 'events'
events = events.to_records(index=False)
# events = Events(events.to_records(index=False))
#
# joblib.dump(events, self.get_path_to_resource_in_workspace(subject+'-'+experiment+'-ps_events.pkl'))
self.pass_object(experiment + '_events', events)
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 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 run(self):
subject = self.pipeline.subject
experiment = self.pipeline.experiment
from ptsa.data.readers import BaseEventReader
e_path = os.path.join(self.pipeline.mount_point , 'data', 'events', 'RAM_PS', self.pipeline.subject + '_events.mat')
e_reader = BaseEventReader(filename=e_path, eliminate_events_with_no_eeg=True)
events = e_reader.read()
# try:
# events = Events(get_events(subject=subject, task='RAM_PS', path_prefix=self.pipeline.mount_point))
# except IOError:
# raise Exception('No parameter search for subject %s' % subject)
#
events = events[events.experiment == experiment]
if len(events) == 0:
raise Exception('No %s events for subject %s' % (experiment,subject))
#
# events = correct_eegfile_field(events)
# events = self.attach_raw_bin_wrappers(events)
sessions = np.unique(events.session)
print experiment, 'sessions:', sessions
events = pd.DataFrame.from_records(events)
events = compute_isi(events)
is_stim_event_type_vec = np.vectorize(is_stim_event_type)
events = events[is_stim_event_type_vec(events.type)]
print len(events), 'stim', experiment, 'events'
events = events.to_records(index=False)
# events = Events(events.to_records(index=False))
#
# joblib.dump(events, self.get_path_to_resource_in_workspace(subject+'-'+experiment+'-ps_events.pkl'))
self.pass_object(experiment+'_events', events)
def get_ps4_events(fn):
from ptsa.data.readers import BaseEventReader
from ptsa.data.events import Events
#Get events
evfiles = [fn]
evs_on = np.array([])
for ef in evfiles:
try:
base_e_reader = BaseEventReader(filename=ef,
eliminate_events_with_no_eeg=True)
base_events = base_e_reader.read()
if len(evs_on) == 0:
evs_on = base_events[base_events.type == 'STIM_ON']
else:
evs_on = np.concatenate(
(evs_on, base_events[base_events.type == 'STIM_ON']),
axis=0)
except:
continue
evs_on = Events(evs_on)
#Reorganize sessions around stim sites
sessions = np.unique(evs_on['session'])
sess_tags = []
for i in range(len(evs_on)):
stimtag = str(evs_on[i]['anode_num']) + '-' + str(
evs_on[i]['cathode_num'])
sess_tags.append(stimtag)
sess_tags = np.array(sess_tags)
if len(np.unique(sess_tags)) <= len(sessions):
session_array = evs_on['session']
else:
session_array = np.empty(len(evs_on))
for idx, s in enumerate(np.unique(sess_tags)):
session_array[sess_tags == s] = int(idx)
sessions = np.unique(session_array)
return evs_on, session_array
def run(self):
task = self.pipeline.task
e_path = os.path.join(self.pipeline.mount_point, 'data/events', task, self.pipeline.subject + '_events.mat')
e_reader = BaseEventReader(filename=e_path, eliminate_events_with_no_eeg=False)
events = e_reader.read()
self.pass_object(self.pipeline.task+'_all_events', events)
intr_events = events[(events.intrusion!=-999) & (events.intrusion!=0)]
rec_events = events[events.type == 'REC_WORD']
events = events[events.type == 'WORD']
print len(events), task, 'WORD events'
self.pass_object(task+'_events', events)
self.pass_object(self.pipeline.task+'_intr_events', intr_events)
self.pass_object(self.pipeline.task+'_rec_events', rec_events)
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 run(self):
task = self.pipeline.task
from ptsa.data.readers import BaseEventReader
e_path = os.path.join(self.pipeline.mount_point , 'data', 'events', task, self.pipeline.subject + '_math.mat')
e_reader = BaseEventReader(filename=e_path, eliminate_events_with_no_eeg=True)
events = e_reader.read()
# events = Events(get_events(subject=self.pipeline.subject, task=task, path_prefix=self.pipeline.mount_point))
# events = correct_eegfile_field(events)
# ev_order = np.argsort(events, order=('session','list','mstime'))
# events = events[ev_order]
#
# events = self.attach_raw_bin_wrappers(events)
events = events[events.type == 'PROB']
print len(events), task, 'PROB events'
self.pass_object(task+'_control_events', events)
def run(self):
task = self.pipeline.task
e_path = os.path.join(self.pipeline.mount_point , 'data', 'events', task, self.pipeline.subject + '_events.mat')
e_reader = BaseEventReader(filename=e_path, eliminate_events_with_no_eeg=True)
events = e_reader.read()
ev_order = np.argsort(events, order=('session','list','mstime'))
events = events[ev_order]
self.pass_object(self.pipeline.task+'_all_events', events)
intr_events = events[(events.intrusion!=-999) & (events.intrusion!=0)]
rec_events = events[events.type == 'REC_WORD']
events = events[events.type == 'WORD']
print len(events), task, 'WORD events'
self.pass_object(task+'_events', events)
self.pass_object(self.pipeline.task+'_intr_events', intr_events)
self.pass_object(self.pipeline.task+'_rec_events', rec_events)
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)