def read(self):
# calling base class read fcn
evs = BaseEventReader.read(self)
evs = self.correct_eegfile_field(evs)
evs = Events(evs).add_fields(esrc=np.dtype(RawBinWrapper))
import pathlib
eegfiles = np.unique(evs.eegfile)
for eegfile in eegfiles:
eeg_file_path = join(self.data_dir_prefix, str(pathlib.Path(str(eegfile)).parts[1:]))
raw_bin_wrapper = RawBinWrapper(eeg_file_path)
inds = np.where(evs.eegfile == eegfile)[0]
for i in inds:
evs[i]['esrc'] = raw_bin_wrapper
# self.subject_path = str(pathlib.Path(eeg_file_path).parts[:-2])
# attaching
# evs.add_fields(esrc=np.dtype(RawBinWrapper))
self.set_output(evs)
return self.get_output()
def read(self):
# calling base class read fcn
evs = BaseEventReader.read(self)
# evs = self.correct_eegfile_field(evs) ################## RESTORE THIS
evs = evs.add_fields(esrc=np.dtype(RawBinWrapper))
import pathlib
for ev in evs:
try:
eeg_file_path = join(self.data_dir_prefix, str(pathlib.Path(str(ev.eegfile)).parts[1:]))
ev.esrc = RawBinWrapper(eeg_file_path)
self.raw_data_root=str(eeg_file_path)
except TypeError:
print 'skipping event with eegfile=',ev.eegfile
pass
# self.subject_path = str(pathlib.Path(eeg_file_path).parts[:-2])
# attaching
# evs.add_fields(esrc=np.dtype(RawBinWrapper))
self.set_output(evs)
return self.get_output()
def run(self):
#if self.pipeline.task != 'RAM_FR1':
# return
try:
e_path = join(self.pipeline.mount_point, 'data/events', self.pipeline.task, self.pipeline.subject+'_math.mat')
e_reader = BaseEventReader(event_file=e_path, eliminate_events_with_no_eeg=False, data_dir_prefix=self.pipeline.mount_point)
events = e_reader.read()
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 __init__(self, **kwds):
'''
Constructor:
:param kwds:allowed values are:
-------------------------------------
:param filename {str} - path to event file
:param eliminate_events_with_no_eeg {bool} - flag to automatically remov events woth no eegfile (default True)
:param use_reref_eeg {bool} - flag that changes eegfiles to point reref eegs. Default is False and eegs read
are nonreref ones
:param attach_rawbinwrapper {bool} - flag signaling whether to attach rawbinwrappers to Event obj or not.
Default is True
:param use_groupped_rawbinwrapper {bool} - flag signaling whether to use groupped rawbinwrappers
(i.e. shared between many events with same eeglile) or not. Default is True. When True data reads are much faster
:return: None
'''
BaseEventReader.__init__(self, **kwds)
def run(self):
#if self.pipeline.task != 'RAM_FR1':
# return
try:
e_path = join(self.pipeline.mount_point, 'data/events',
self.pipeline.task,
self.pipeline.subject + '_math.mat')
e_reader = BaseEventReader(
event_file=e_path,
eliminate_events_with_no_eeg=False,
data_dir_prefix=self.pipeline.mount_point)
events = e_reader.read()
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(self):
'''
Reads Matlab event file , converts it to np.recarray and attaches rawbinwrappers (if appropriate flags indicate so)
:return: Events object. depending on flagg settings the rawbinwrappers may be attached as well
'''
# calling base class read fcn
evs = BaseEventReader.read(self)
# in case evs is simply recarray
if not isinstance(evs, Events):
evs = Events(evs)
if self.attach_rawbinwrapper:
evs = evs.add_fields(esrc=np.dtype(RawBinWrapper))
if self.use_groupped_rawbinwrapper: # this should be default choice - much faster execution
self.attach_rawbinwrapper_groupped(evs)
else: # used for debugging purposes
self.attach_rawbinwrapper_individual(evs)
return evs
def __init__(self, event_file, **kwds):
BaseEventReader.__init__(self,event_file, **kwds)
# 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'
# e_path ='/Users/m/data/events/RAM_FR1/R1056M_events.mat'
e_path = join('/Volumes/rhino_root',
'data/events/RAM_FR1/R1062J_events.mat')
e_reader = BaseEventReader(filename=e_path,
eliminate_events_with_no_eeg=True)
events = e_reader.read()
print
# from ptsa.data.readers.TalReader import TalReader
#
# 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)
#
evs = evs[indicator]
self.__events = evs
return self.__events
def get_subject_path(self):
return self.subject_path
def get_raw_data_root(self):
return self.raw_data_root
def get_output(self):
return self.__events
def set_output(self,evs):
self.__events = evs
if __name__=='__main__':
from BaseEventReader import BaseEventReader
e_path = join('/Volumes/rhino_root', 'data/events/RAM_FR1/R1060M_math.mat')
# e_path = '/Users/m/data/events/RAM_FR1/R1056M_events.mat'
e_reader = BaseEventReader(event_file=e_path, eliminate_events_with_no_eeg=True, data_dir_prefix='/Volumes/rhino_root')
events = e_reader.read()
events = e_reader.get_output()
evs = evs[indicator]
self.__events = evs
return self.__events
def get_subject_path(self):
return self.subject_path
def get_raw_data_root(self):
return self.raw_data_root
def get_output(self):
return self.__events
def set_output(self, evs):
self.__events = evs
if __name__ == '__main__':
from BaseEventReader import BaseEventReader
e_path = join('/Volumes/rhino_root', 'data/events/RAM_FR1/R1060M_math.mat')
# e_path = '/Users/m/data/events/RAM_FR1/R1056M_events.mat'
e_reader = BaseEventReader(event_file=e_path,
eliminate_events_with_no_eeg=True,
data_dir_prefix='/Volumes/rhino_root')
events = e_reader.read()
events = e_reader.get_output()
def __init__(self, event_file, **kwds):
BaseEventReader.__init__(self,event_file, **kwds)
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'
# e_path ='/Users/m/data/events/RAM_FR1/R1056M_events.mat'
e_path = join('/Volumes/rhino_root', 'data/events/RAM_FR1/R1062J_events.mat')
e_reader = BaseEventReader(filename=e_path, eliminate_events_with_no_eeg=True)
events = e_reader.read()
print
# from ptsa.data.readers.TalReader import TalReader
#
# 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)
