def test_inputs_V21(self):
"""
Test various inputs to BlackrockIO.read_block with version 2.3 file
to check for parsing errors.
"""
filename = self.get_local_path('blackrock/blackrock_2_1/l101210-001')
reader = BlackrockIO(filename=filename, verbose=False, nsx_to_load=5)
# Assert IOError is raised when no Blackrock files are available
with self.assertRaises(IOError):
reader2 = BlackrockIO(filename='nonexistent')
# with self.assertRaises(IOError):
# reader2 = BlackrockIO(filename=filename, nev_override='nonexistent')
# Load data to maximum extent, one None is not given as list
block = reader.read_block(load_waveforms=False,
signal_group_mode='split-all')
lena = len(block.segments[0].analogsignals[0])
numspa = len(block.segments[0].spiketrains[0])
# Load data using a negative time and a time exceeding the end of the
# recording
too_large_tstop = block.segments[0].analogsignals[0].t_stop + 1 * pq.s
buggy_slice = (-100 * pq.ms, too_large_tstop)
# This is valid in read_segment
seg = reader.read_segment(seg_index=0,
time_slice=buggy_slice,
strict_slicing=False)
# this raise error
with self.assertRaises(AssertionError):
seg = reader.read_segment(seg_index=0,
time_slice=buggy_slice,
strict_slicing=True)
lenb = len(seg.analogsignals[0])
numspb = len(seg.spiketrains[0])
# Same length of analog signal?
# Both should have read the complete data set!
self.assertEqual(lena, lenb)
# Same length of spike train?
# Both should have read the complete data set!
self.assertEqual(numspa, numspb)
# test 4 Units
block = reader.read_block(
load_waveforms=True,
signal_group_mode='split-all',
) #units_group_mode='all-in-one')
self.assertEqual(len(block.segments[0].analogsignals), 96)
#self.assertEqual(len(block.channel_indexes[-1].units), 218)
#self.assertEqual(len(block.channel_indexes[-1].units),
# len(block.segments[0].spiketrains))
anasig = block.segments[0].analogsignals[0]
self.assertIsNotNone(anasig.file_origin)
def test_inputs_V21(self):
"""
Test various inputs to BlackrockIO.read_block with version 2.3 file
to check for parsing errors.
"""
filename = self.get_filename_path('blackrock_2_1/l101210-001')
reader = BlackrockIO(filename=filename, verbose=False, nsx_to_load=5)
# Assert IOError is raised when no Blackrock files are available
with self.assertRaises(IOError):
reader2 = BlackrockIO(filename='nonexistent')
# with self.assertRaises(IOError):
# reader2 = BlackrockIO(filename=filename, nev_override='nonexistent')
# Load data to maximum extent, one None is not given as list
block = reader.read_block(load_waveforms=False, signal_group_mode='split-all')
lena = len(block.segments[0].analogsignals[0])
numspa = len(block.segments[0].spiketrains[0])
# Load data using a negative time and a time exceeding the end of the
# recording
too_large_tstop = block.segments[0].analogsignals[0].t_stop + 1 * pq.s
buggy_slice = (-100 * pq.ms, too_large_tstop)
# This is valid in read_segment
seg = reader.read_segment(seg_index=0, time_slice=buggy_slice, strict_slicing=False)
# this raise error
with self.assertRaises(AssertionError):
seg = reader.read_segment(seg_index=0, time_slice=buggy_slice, strict_slicing=True)
lenb = len(seg.analogsignals[0])
numspb = len(seg.spiketrains[0])
# Same length of analog signal?
# Both should have read the complete data set!
self.assertEqual(lena, lenb)
# Same length of spike train?
# Both should have read the complete data set!
self.assertEqual(numspa, numspb)
# test 4 Units
block = reader.read_block(load_waveforms=True,
signal_group_mode='split-all',
units_group_mode='all-in-one')
self.assertEqual(len(block.segments[0].analogsignals), 96)
self.assertEqual(len(block.channel_indexes[-1].units), 218)
self.assertEqual(len(block.channel_indexes[-1].units),
len(block.segments[0].spiketrains))
anasig = block.segments[0].analogsignals[0]
self.assertIsNotNone(anasig.file_origin)
def test_inputs_V23(self):
"""
Test various inputs to BlackrockIO.read_block with version 2.3 file
to check for parsing errors.
"""
filename = self.get_filename_path('FileSpec2.3001')
reader = BlackrockIO(
filename=filename,
verbose=False,
nsx_to_load=5,
)
# Load data to maximum extent, one None is not given as list
block = reader.read_block(load_waveforms=False)
lena = len(block.segments[0].analogsignals[0])
numspa = len(block.segments[0].spiketrains[0])
# Load data using a negative time and a time exceeding the end of the
# recording
too_large_tstop = block.segments[0].analogsignals[0].t_stop + 1 * pq.s
buggy_slice = (-100 * pq.ms, too_large_tstop)
# this is valid in read_segment because seg_index is specified
seg = reader.read_segment(seg_index=0, time_slice=buggy_slice)
lenb = len(seg.analogsignals[0])
numspb = len(seg.spiketrains[0])
# Same length of analog signal?
# Both should have read the complete data set!
self.assertEqual(lena, lenb)
# Same length of spike train?
# Both should have read the complete data set!
self.assertEqual(numspa, numspb)
# test 4 Units
block = reader.read_block(load_waveforms=True,
units_group_mode='all-in-one')
self.assertEqual(len(block.segments[0].analogsignals), 10)
self.assertEqual(len(block.channel_indexes[-1].units), 4)
self.assertEqual(len(block.channel_indexes[-1].units),
len(block.segments[0].spiketrains))
anasig = block.segments[0].analogsignals[0]
self.assertIsNotNone(anasig.file_origin)
def test_load_muliple_nsx(self):
"""
Test if multiple nsx signals can be loaded at the same time.
"""
filename = self.get_filename_path('blackrock_2_1/l101210-001')
reader = BlackrockIO(filename=filename,
verbose=False,
nsx_to_load='all')
# number of different sampling rates corresponds to number of nsx signals, because
# single nsx contains only signals of identical sampling rate
block = reader.read_block(load_waveforms=False)
sampling_rates = np.unique([
a.sampling_rate.rescale('Hz')
for a in block.filter(objects='AnalogSignal')
])
self.assertEqual(len(sampling_rates), 2)
segment = reader.read_segment()
sampling_rates = np.unique([
a.sampling_rate.rescale('Hz')
for a in segment.filter(objects='AnalogSignal')
])
self.assertEqual(len(sampling_rates), 2)
# load only ns5
reader = BlackrockIO(filename=filename, nsx_to_load=5)
seg = reader.read_segment()
self.assertEqual(len(seg.analogsignals), 1)
self.assertEqual(seg.analogsignals[0].shape, (109224, 96))
# load only ns2
reader = BlackrockIO(filename=filename, nsx_to_load=2)
seg = reader.read_segment()
self.assertEqual(len(seg.analogsignals), 1)
self.assertEqual(seg.analogsignals[0].shape, (3640, 6))
# load only ns2
reader = BlackrockIO(filename=filename, nsx_to_load=[2])
seg = reader.read_segment()
self.assertEqual(len(seg.analogsignals), 1)
# load ns2 + ns5
reader = BlackrockIO(filename=filename, nsx_to_load=[2, 5])
seg = reader.read_segment()
self.assertEqual(len(seg.analogsignals), 2)
self.assertEqual(seg.analogsignals[0].shape, (3640, 6))
self.assertEqual(seg.analogsignals[1].shape, (109224, 96))
# load only ns5
reader = BlackrockIO(filename=filename, nsx_to_load='max')
seg = reader.read_segment()
self.assertEqual(len(seg.analogsignals), 1)
self.assertEqual(seg.analogsignals[0].shape, (109224, 96))
def test_load_muliple_nsx(self):
"""
Test if multiple nsx signals can be loaded at the same time.
"""
filename = self.get_filename_path('blackrock_2_1/l101210-001')
reader = BlackrockIO(filename=filename, verbose=False, nsx_to_load='all')
# number of different sampling rates corresponds to number of nsx signals, because
# single nsx contains only signals of identical sampling rate
block = reader.read_block(load_waveforms=False)
sampling_rates = np.unique(
[a.sampling_rate.rescale('Hz') for a in block.filter(objects='AnalogSignal')])
self.assertEqual(len(sampling_rates), len(reader._selected_nsx))
segment = reader.read_segment()
sampling_rates = np.unique(
[a.sampling_rate.rescale('Hz') for a in segment.filter(objects='AnalogSignal')])
self.assertEqual(len(sampling_rates), len(reader._selected_nsx))
def test_load_muliple_nsx(self):
"""
Test if multiple nsx signals can be loaded at the same time.
"""
filename = self.get_filename_path('blackrock_2_1/l101210-001')
reader = BlackrockIO(filename=filename, verbose=False, nsx_to_load='all')
# number of different sampling rates corresponds to number of nsx signals, because
# single nsx contains only signals of identical sampling rate
block = reader.read_block(load_waveforms=False)
sampling_rates = np.unique(
[a.sampling_rate.rescale('Hz') for a in block.filter(objects='AnalogSignal')])
self.assertEqual(len(sampling_rates), 2)
segment = reader.read_segment()
sampling_rates = np.unique(
[a.sampling_rate.rescale('Hz') for a in segment.filter(objects='AnalogSignal')])
self.assertEqual(len(sampling_rates), 2)
# load only ns5
reader = BlackrockIO(filename=filename, nsx_to_load=5)
seg = reader.read_segment()
self.assertEqual(len(seg.analogsignals), 1)
self.assertEqual(seg.analogsignals[0].shape, (109224, 96))
# load only ns2
reader = BlackrockIO(filename=filename, nsx_to_load=2)
seg = reader.read_segment()
self.assertEqual(len(seg.analogsignals), 1)
self.assertEqual(seg.analogsignals[0].shape, (3640, 6))
# load only ns2
reader = BlackrockIO(filename=filename, nsx_to_load=[2])
seg = reader.read_segment()
self.assertEqual(len(seg.analogsignals), 1)
# load ns2 + ns5
reader = BlackrockIO(filename=filename, nsx_to_load=[2, 5])
seg = reader.read_segment()
self.assertEqual(len(seg.analogsignals), 2)
self.assertEqual(seg.analogsignals[0].shape, (3640, 6))
self.assertEqual(seg.analogsignals[1].shape, (109224, 96))
# load only ns5
reader = BlackrockIO(filename=filename, nsx_to_load='max')
seg = reader.read_segment()
self.assertEqual(len(seg.analogsignals), 1)
self.assertEqual(seg.analogsignals[0].shape, (109224, 96))
def test_inputs_V23(self):
"""
Test various inputs to BlackrockIO.read_block with version 2.3 file
to check for parsing errors.
"""
filename = self.get_filename_path('FileSpec2.3001')
reader = BlackrockIO(
filename=filename,
verbose=False,
nsx_to_load=5,
)
# Load data to maximum extent, one None is not given as list
block = reader.read_block(time_slices=None, load_waveforms=False)
lena = len(block.segments[0].analogsignals[0])
numspa = len(block.segments[0].spiketrains[0])
# Load data using a negative time and a time exceeding the end of the
# recording raise an error
too_large_tstop = block.segments[0].analogsignals[0].t_stop + 1 * pq.s
buggy_slice = (-100 * pq.ms, too_large_tstop)
#this raise error in read_block
with self.assertRaises(ValueError):
block = reader.read_block(time_slices=[buggy_slice])
#but this is valid in read_segment because seg_index is specified
seg = reader.read_segment(seg_index=0, time_slice=buggy_slice)
lenb = len(seg.analogsignals[0])
numspb = len(seg.spiketrains[0])
# Same length of analog signal?
# Both should have read the complete data set!
self.assertEqual(lena, lenb)
# Same length of spike train?
# Both should have read the complete data set!
self.assertEqual(numspa, numspb)
# n_starts and n_stops not given as list
# verifies identical length of returned signals given equal durations
# as input
ns5_unit = block.segments[0].analogsignals[0].sampling_period
time_slice = (100 * ns5_unit, 200 * ns5_unit)
block = reader.read_block(time_slices=[time_slice])
lena = len(block.segments[0].analogsignals[0])
time_slice = (100 * ns5_unit, 200 * ns5_unit)
block = reader.read_block(time_slices=[time_slice])
lenb = len(block.segments[0].analogsignals[0])
# Same length?
self.assertEqual(lena, lenb)
# Length should be 100 samples exactly
self.assertEqual(lena, 100)
# test 4 Units
time_slices = [(0, 1000 * pq.ms), (3000 * pq.ms, 4000 * pq.ms)]
block = reader.read_block(time_slices=time_slices,
load_waveforms=True,
units_group_mode='all-in-one')
self.assertEqual(len(block.segments), 2)
self.assertEqual(len(block.segments[0].analogsignals), 10)
self.assertEqual(len(block.channel_indexes[-1].units), 4)
self.assertEqual(len(block.channel_indexes[-1].units),
len(block.segments[0].spiketrains))
anasig = block.segments[0].analogsignals[0]
self.assertIsNotNone(anasig.file_origin)
def test_inputs_V23(self):
"""
Test various inputs to BlackrockIO.read_block with version 2.3 file
to check for parsing errors.
"""
filename = self.get_filename_path('FileSpec2.3001')
reader = BlackrockIO(filename=filename, verbose=False, nsx_to_load=5,)
# Load data to maximum extent, one None is not given as list
block = reader.read_block(time_slices=None, load_waveforms=False)
lena = len(block.segments[0].analogsignals[0])
numspa = len(block.segments[0].spiketrains[0])
# Load data using a negative time and a time exceeding the end of the
# recording raise an error
too_large_tstop = block.segments[0].analogsignals[0].t_stop + 1 * pq.s
buggy_slice = (-100 * pq.ms, too_large_tstop)
#this raise error in read_block
with self.assertRaises(ValueError):
block = reader.read_block(time_slices=[buggy_slice])
#but this is valid in read_segment because seg_index is specified
seg = reader.read_segment(seg_index=0, time_slice=buggy_slice)
lenb = len(seg.analogsignals[0])
numspb = len(seg.spiketrains[0])
# Same length of analog signal?
# Both should have read the complete data set!
self.assertEqual(lena, lenb)
# Same length of spike train?
# Both should have read the complete data set!
self.assertEqual(numspa, numspb)
# n_starts and n_stops not given as list
# verifies identical length of returned signals given equal durations
# as input
ns5_unit = block.segments[0].analogsignals[0].sampling_period
time_slice = (100 * ns5_unit, 200 * ns5_unit)
block = reader.read_block(time_slices=[time_slice])
lena = len(block.segments[0].analogsignals[0])
time_slice = (100 * ns5_unit, 200 * ns5_unit)
block = reader.read_block(time_slices=[time_slice])
lenb = len(block.segments[0].analogsignals[0])
# Same length?
self.assertEqual(lena, lenb)
# Length should be 100 samples exactly
self.assertEqual(lena, 100)
# test 4 Units
time_slices=[(0, 1000*pq.ms), (3000*pq.ms, 4000*pq.ms)]
block = reader.read_block(time_slices=time_slices, load_waveforms=True,
units_group_mode='all-in-one')
self.assertEqual(len(block.segments), 2)
self.assertEqual(len(block.segments[0].analogsignals), 10)
self.assertEqual(len(block.channel_indexes[-1].units), 4)
self.assertEqual(len(block.channel_indexes[-1].units),
len(block.segments[0].spiketrains))
anasig = block.segments[0].analogsignals[0]
self.assertIsNotNone(anasig.file_origin)