def test_eeg_read_keep_buffer(self): # OLD READERS events = self.read_ptsa_events() # 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=0.0, end_time=1.6, buffer_time=1.0, eoffset='eegoffset', keep_buffer=True, eoffset_in_time=False, verbose=True) # NEW READERS base_events = self.read_base_events() 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) time_series_reader.read(channels=['002', '003']) base_eegs = time_series_reader.get_output() # testing assert_array_equal(eegs, base_eegs.data)
def test_eeg_read_keep_buffer_butterworth_filtered(self): # old readers events = self.read_ptsa_events() # in case fancy indexing looses Eventness of events we need to create Events object explicitely if not isinstance(events, Events): events = Events(events) base_events = self.read_base_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) # filtering eegs_filtered = eegs.filtered([58, 62], filt_type='stop', order=4) # New style reading 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) time_series_reader.read(channels=['002', '003']) base_eegs = time_series_reader.get_output() from ptsa.data.filters.ButterworthFilter import ButterworthFilter b_filter = ButterworthFilter(time_series=base_eegs, samplerate=base_eegs.attrs['samplerate'], freq_range=[58, 62], filt_type='stop', order=4) base_eegs_filtered = b_filter.filter() # testing assert_array_equal(eegs_filtered, base_eegs_filtered.data) assert_array_equal(eegs, base_eegs.data)
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_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 test_eeg_resample(self): # old readers events = self.read_ptsa_events() # in case fancy indexing looses Eventness of events we need to create Events object explicitely if not isinstance(events, Events): events = Events(events) base_events = self.read_base_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) # filtering eegs_resampled = eegs.resampled(50.0) # New style reading 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) time_series_reader.read(channels=['002', '003']) base_eegs = time_series_reader.get_output() from ptsa.data.filters.ResampleFilter import ResampleFilter resample_filter = ResampleFilter(time_series=base_eegs, resamplerate=50.0) base_eegs_resampled = resample_filter.filter() # testing assert_array_equal(eegs_resampled, base_eegs_resampled.data)
ts_dict = time_series_session_reader.read() print ts_dict ts=ts_dict.items()[0][1] resample_filter_rounded = ResampleFilter(time_series=ts, resamplerate=50.0,round_to_original_timepoints=True) # resample_filter_rounded = ResampleFilter(time_series=ts, resamplerate=50.0) base_eegs_resampled_rounded = resample_filter_rounded.filter() ###################################### 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=['003', '004']) resample_filter = ResampleFilter(time_series=base_eegs, resamplerate=50.0) base_eegs_resampled = resample_filter.filter() resample_filter_rounded = ResampleFilter(time_series=base_eegs, resamplerate=50.0, round_to_original_timepoints=True) base_eegs_resampled_rounded = resample_filter_rounded.filter() print
resample_filter_rounded = ResampleFilter(time_series=ts, resamplerate=50.0, round_to_original_timepoints=True) # resample_filter_rounded = ResampleFilter(time_series=ts, resamplerate=50.0) base_eegs_resampled_rounded = resample_filter_rounded.filter() ###################################### 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=['003', '004']) resample_filter = ResampleFilter(time_series=base_eegs, resamplerate=50.0) base_eegs_resampled = resample_filter.filter() resample_filter_rounded = ResampleFilter(time_series=base_eegs, resamplerate=50.0, round_to_original_timepoints=True) base_eegs_resampled_rounded = resample_filter_rounded.filter() print