def test_neo_rawio_sources():
#~ from neo.rawio.tdtrawio import TdtRawIO
#~ local_tdt_folder = get_tdt_test_files()
#~ neorawio = TdtRawIO(dirname=local_tdt_folder)
#~ neorawio.parse_header()
#~ print(neorawio)
from neo.rawio.blackrockrawio import BlackrockRawIO
filename = get_blackrock_files()
neorawio = BlackrockRawIO(filename=filename)
neorawio.parse_header()
print(neorawio)
sources = ephyviewer.get_sources_from_neo_rawio(neorawio)
#~ print(sources)
for s in sources['signal']:
print(s.t_start, s.nb_channel, s.sample_rate)
print(s.get_chunk(i_start=0, i_stop=1024).shape)
for s in sources['epoch']:
print(s.t_start, s.nb_channel)
#~ print(s.get_chunk(i_start=0, i_stop=1024).shape)
print(s.get_chunk_by_time(chan=0, t_start=None, t_stop=None))
for s in sources['spike']:
print(s.t_start, s.nb_channel)
print(s.get_chunk_by_time(chan=0, t_start=None, t_stop=None))
def test_neoviewer(interactive=False):
#~ from neo.rawio.tdtrawio import TdtRawIO
#~ local_tdt_folder = get_tdt_test_files()
#~ neorawio = TdtRawIO(dirname=local_tdt_folder)
#~ neorawio.parse_header()
#~ print(neorawio)
from neo.rawio.blackrockrawio import BlackrockRawIO
filename = get_blackrock_files()
neorawio = BlackrockRawIO(filename=filename)
neorawio.parse_header()
print(neorawio)
sources = ephyviewer.get_sources_from_neo_rawio(neorawio)
print(sources)
app = ephyviewer.mkQApp()
win = ephyviewer.MainViewer(debug=True, show_auto_scale=True)
for i, sig_source in enumerate(sources['signal']):
view = ephyviewer.TraceViewer(source=sig_source,
name='signal {}'.format(i))
win.add_view(view)
for i, ep_source in enumerate(sources['epoch']):
view = ephyviewer.EpochViewer(source=ep_source, name='epochs')
win.add_view(view)
if interactive:
win.show()
app.exec_()
else:
# close thread properly
win.close()
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
stream_index = 0
self.assertGreater(reader.signal_channels_count(stream_index), 0)
for c in range(0, 8):
raw_sigs = reader.get_analogsignal_chunk(channel_indexes=[c],
stream_index=stream_index)
raw_sigs = raw_sigs.flatten()
assert_equal(raw_sigs[:-1], lfp_ml[c, :])
# Check if spikes in channels are equal
nb_unit = reader.spike_channels_count()
for spike_channel_index in range(nb_unit):
unit_name = reader.header['spike_channels'][spike_channel_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(
spike_channel_index=spike_channel_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(
spike_channel_index=spike_channel_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
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
stream_index = 0
self.assertGreater(reader.signal_channels_count(stream_index), 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.spike_channels_count()
for spike_channel_index in range(nb_unit):
unit_name = reader.header['spike_channels'][
spike_channel_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(
spike_channel_index=spike_channel_index)
assert_equal(io_spikes, matlab_spikes)
# Check all waveforms
io_waveforms = reader.get_spike_raw_waveforms(
spike_channel_index=spike_channel_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)
def __init__(self, filename, **kargs):
BlackrockRawIO.__init__(self, filename=filename, **kargs)
BaseFromRaw.__init__(self, filename)
def __init__(self, filename, nsx_to_load=None, **kargs):
BlackrockRawIO.__init__(self,
filename=filename,
nsx_to_load=nsx_to_load,
**kargs)
BaseFromRaw.__init__(self, filename)
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)
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)