""" Tests of neo.rawio.examplerawio """ import unittest from neo.rawio.blackrockrawio import BlackrockRawIO from neo.test.rawiotest.common_rawio_test import BaseTestRawIO import numpy as np from numpy.testing import assert_equal try: import scipy.io HAVE_SCIPY = True except ImportError: HAVE_SCIPY = False class TestBlackrockRawIO(BaseTestRawIO, unittest.TestCase, ): rawioclass = BlackrockRawIO entities_to_test = ['FileSpec2.3001', 'blackrock_2_1/l101210-001'] files_to_download = [ 'FileSpec2.3001.nev', 'FileSpec2.3001.ns5', 'FileSpec2.3001.ccf', 'FileSpec2.3001.mat', 'blackrock_2_1/l101210-001.mat', 'blackrock_2_1/l101210-001_nev-02_ns5.mat', 'blackrock_2_1/l101210-001.ns2', 'blackrock_2_1/l101210-001.ns5', 'blackrock_2_1/l101210-001.nev', 'blackrock_2_1/l101210-001-02.nev'] @unittest.skipUnless(HAVE_SCIPY, "requires scipy") def test_compare_blackrockio_with_matlabloader(self): """ This test compares the output of ReachGraspIO.read_block() with the output generated by a Matlab implementation of a Blackrock file reader provided by the company. The output for comparison is provided in a .mat file created by the script create_data_matlab_blackrock.m. The function tests LFPs, spike times, and digital events on channels 80-83 and spike waveforms on channel 82, unit 1. For details on the file contents, refer to FileSpec2.3.txt Ported to the rawio API by Samuel Garcia. """ # Load data from Matlab generated files ml = scipy.io.loadmat(self.get_filename_path('FileSpec2.3001.mat')) lfp_ml = ml['lfp'] # (channel x time) LFP matrix ts_ml = ml['ts'] # spike time stamps elec_ml = ml['el'] # spike electrodes unit_ml = ml['un'] # spike unit IDs wf_ml = ml['wf'] # waveform unit 1 channel 1 mts_ml = ml['mts'] # marker time stamps mid_ml = ml['mid'] # marker IDs # Load data in channels 1-3 from original data files using the Neo # BlackrockIO reader = BlackrockRawIO(filename=self.get_filename_path('FileSpec2.3001')) reader.parse_header() # Check if analog data on channels 1-8 are equal self.assertGreater(reader.signal_channels_count(), 0) for c in range(0, 8): raw_sigs = reader.get_analogsignal_chunk(channel_indexes=[c]) raw_sigs = raw_sigs.flatten() assert_equal(raw_sigs[:-1], lfp_ml[c, :]) # Check if spikes in channels are equal nb_unit = reader.unit_channels_count() for unit_index in range(nb_unit): unit_name = reader.header['unit_channels'][unit_index]['name'] # name is chXX#YY where XX is channel_id and YY is unit_id channel_id, unit_id = unit_name.split('#') channel_id = int(channel_id.replace('ch', '')) unit_id = int(unit_id) matlab_spikes = ts_ml[(elec_ml == channel_id) & (unit_ml == unit_id)] io_spikes = reader.get_spike_timestamps(unit_index=unit_index) assert_equal(io_spikes, matlab_spikes) # Check waveforms of channel 1, unit 0 if channel_id == 1 and unit_id == 0: io_waveforms = reader.get_spike_raw_waveforms(unit_index=unit_index) io_waveforms = io_waveforms[:, 0, :] # remove dim 1 assert_equal(io_waveforms, wf_ml) # Check if digital input port events are equal nb_ev_chan = reader.event_channels_count() # ~ print(reader.header['event_channels']) for ev_chan in range(nb_ev_chan): name = reader.header['event_channels']['name'][ev_chan] # ~ print(name) all_timestamps, _, labels = reader.get_event_timestamps( event_channel_index=ev_chan) if name == 'digital_input_port': for label in np.unique(labels): python_digievents = all_timestamps[labels == label] matlab_digievents = mts_ml[mid_ml == int(label)] assert_equal(python_digievents, matlab_digievents) elif name == 'comments': pass # TODO: Save comments to Matlab file. @unittest.skipUnless(HAVE_SCIPY, "requires scipy") def test_compare_blackrockio_with_matlabloader_v21(self): """ This test compares the output of ReachGraspIO.read_block() with the output generated by a Matlab implementation of a Blackrock file reader provided by the company. The output for comparison is provided in a .mat file created by the script create_data_matlab_blackrock.m. The function tests LFPs, spike times, and digital events. Ported to the rawio API by Samuel Garcia. """ dirname = self.get_filename_path('blackrock_2_1/l101210-001') # First run with parameters for ns5, then run with correct parameters for ns2 parameters = [('blackrock_2_1/l101210-001_nev-02_ns5.mat', {'nsx_to_load': 5, 'nev_override': '-'.join([dirname, '02'])}, 96), ('blackrock_2_1/l101210-001.mat', {'nsx_to_load': 2}, 6)] for param in parameters: # Load data from Matlab generated files ml = scipy.io.loadmat(self.get_filename_path(filename=param[0])) lfp_ml = ml['lfp'] # (channel x time) LFP matrix ts_ml = ml['ts'] # spike time stamps elec_ml = ml['el'] # spike electrodes unit_ml = ml['un'] # spike unit IDs wf_ml = ml['wf'] # waveforms mts_ml = ml['mts'] # marker time stamps mid_ml = ml['mid'] # marker IDs # Load data from original data files using the Neo BlackrockIO reader = BlackrockRawIO(dirname, **param[1]) reader.parse_header() # Check if analog data are equal self.assertGreater(reader.signal_channels_count(), 0) for c in range(0, param[2]): raw_sigs = reader.get_analogsignal_chunk(channel_indexes=[c]) raw_sigs = raw_sigs.flatten() assert_equal(raw_sigs[:], lfp_ml[c, :]) # Check if spikes in channels are equal nb_unit = reader.unit_channels_count() for unit_index in range(nb_unit): unit_name = reader.header['unit_channels'][unit_index]['name'] # name is chXX#YY where XX is channel_id and YY is unit_id channel_id, unit_id = unit_name.split('#') channel_id = int(channel_id.replace('ch', '')) unit_id = int(unit_id) matlab_spikes = ts_ml[(elec_ml == channel_id) & (unit_ml == unit_id)] io_spikes = reader.get_spike_timestamps(unit_index=unit_index) assert_equal(io_spikes, matlab_spikes) # Check all waveforms io_waveforms = reader.get_spike_raw_waveforms(unit_index=unit_index) io_waveforms = io_waveforms[:, 0, :] # remove dim 1 matlab_wf = wf_ml[np.nonzero( np.logical_and(elec_ml == channel_id, unit_ml == unit_id)), :][0] assert_equal(io_waveforms, matlab_wf) # Check if digital input port events are equal nb_ev_chan = reader.event_channels_count() # ~ print(reader.header['event_channels']) for ev_chan in range(nb_ev_chan): name = reader.header['event_channels']['name'][ev_chan] # ~ print(name) if name == 'digital_input_port': all_timestamps, _, labels = reader.get_event_timestamps( event_channel_index=ev_chan) for label in np.unique(labels): python_digievents = all_timestamps[labels == label] matlab_digievents = mts_ml[mid_ml == int(label)] assert_equal(python_digievents, matlab_digievents) if __name__ == '__main__': unittest.main()