def test_read_segment(self):
"""
Tests if signals are correctly stored in a segment.
"""
filename = get_test_file_full_path(
ioclass=NestIO,
filename='0gid-1time-2gex-1262-0.dat',
directory=self.local_test_dir, clean=False)
r = NestIO(filenames=filename)
id_list_to_test = range(1, 10)
seg = r.read_segment(gid_list=id_list_to_test,
t_stop=1000. * pq.ms,
sampling_period=pq.ms, lazy=False,
id_column_dat=0, time_column_dat=1,
value_columns_dat=2, value_types='V_m')
self.assertTrue(len(seg.analogsignals) == len(id_list_to_test))
id_list_to_test = []
seg = r.read_segment(gid_list=id_list_to_test,
t_stop=1000. * pq.ms,
sampling_period=pq.ms, lazy=False,
id_column_dat=0, time_column_dat=1,
value_columns_dat=2, value_types='V_m')
self.assertEqual(len(seg.analogsignals), 50)
def test_read_segment(self):
"""
Tests if spiketrains are correctly stored in a segment.
"""
filename = get_test_file_full_path(ioclass=NestIO,
filename='0gid-1time-1256-0.gdf',
directory=self.local_test_dir,
clean=False)
r = NestIO(filenames=filename)
id_list_to_test = range(1, 10)
seg = r.read_segment(gid_list=id_list_to_test,
t_start=400. * pq.ms,
t_stop=500. * pq.ms,
lazy=False,
id_column_gdf=0,
time_column_gdf=1)
self.assertTrue(len(seg.spiketrains) == len(id_list_to_test))
id_list_to_test = []
seg = r.read_segment(gid_list=id_list_to_test,
t_start=400. * pq.ms,
t_stop=500. * pq.ms,
lazy=False,
id_column_gdf=0,
time_column_gdf=1)
self.assertTrue(len(seg.spiketrains) == 50)
def test_read_segment_range_is_reasonable(self):
"""
Tests if error is thrown correctly, when second entry is smaller than
the first one of the range.
"""
filename = get_test_file_full_path(ioclass=NestIO,
filename='0gid-1time-1256-0.gdf',
directory=self.local_test_dir,
clean=False)
r = NestIO(filenames=filename)
seg = r.read_segment(gid_list=(10, 10),
t_start=400. * pq.ms,
t_stop=500. * pq.ms,
lazy=False,
id_column_gdf=0,
time_column_gdf=1)
self.assertEqual(len(seg.spiketrains), 1)
with self.assertRaises(ValueError):
r.read_segment(gid_list=(10, 9),
t_start=400. * pq.ms,
t_stop=500. * pq.ms,
lazy=False,
id_column_gdf=0,
time_column_gdf=1)
def test_read_integer(self):
"""
Tests if spike times are actually stored as integers if they are stored
in time steps in the file.
"""
filename = self.get_local_path('nest/0time_in_steps-1257-0.gdf')
r = NestIO(filenames=filename)
st = r.read_spiketrain(gdf_id=None, t_start=400. * pq.ms,
t_stop=500. * pq.ms,
time_unit=pq.CompoundUnit('0.1*ms'),
lazy=False, id_column=None, time_column=0)
self.assertTrue(st.magnitude.dtype == np.int32)
seg = r.read_segment(gid_list=[None], t_start=400. * pq.ms,
t_stop=500. * pq.ms,
time_unit=pq.CompoundUnit('0.1*ms'),
lazy=False, id_column_gdf=None, time_column_gdf=0)
sts = seg.spiketrains
self.assertTrue(all([st.magnitude.dtype == np.int32 for st in sts]))
filename = self.get_local_path('nest/0gid-1time_in_steps-1258-0.gdf')
r = NestIO(
filenames=filename)
st = r.read_spiketrain(gdf_id=1, t_start=400. * pq.ms,
t_stop=500. * pq.ms,
time_unit=pq.CompoundUnit('0.1*ms'),
lazy=False, id_column=0, time_column=1)
self.assertTrue(st.magnitude.dtype == np.int32)
seg = r.read_segment(gid_list=[1], t_start=400. * pq.ms,
t_stop=500. * pq.ms,
time_unit=pq.CompoundUnit('0.1*ms'),
lazy=False, id_column_gdf=0, time_column_gdf=1)
sts = seg.spiketrains
self.assertTrue(all([st.magnitude.dtype == np.int32 for st in sts]))
def test_read_segment(self):
"""
Tests if signals are correctly stored in a segment.
"""
filename = get_test_file_full_path(
ioclass=NestIO,
filename='0gid-1time-2gex-1262-0.dat',
directory=self.local_test_dir, clean=False)
r = NestIO(filenames=filename)
id_list_to_test = range(1, 10)
seg = r.read_segment(gid_list=id_list_to_test,
t_stop=1000. * pq.ms,
sampling_period=pq.ms, lazy=False,
id_column_dat=0, time_column_dat=1,
value_columns_dat=2, value_types='V_m')
self.assertTrue(len(seg.analogsignals) == len(id_list_to_test))
id_list_to_test = []
seg = r.read_segment(gid_list=id_list_to_test,
t_stop=1000. * pq.ms,
sampling_period=pq.ms, lazy=False,
id_column_dat=0, time_column_dat=1,
value_columns_dat=2, value_types='V_m')
self.assertEqual(len(seg.analogsignals), 50)
def test_t_stop_undefined_raises_error(self):
"""
Tests if undefined t_stop, i.e., t_stop=None raises error.
"""
filename = self.get_local_path('nest/0gid-1time-1256-0.gdf')
r = NestIO(filenames=filename)
with self.assertRaises(ValueError):
r.read_spiketrain(gdf_id=1, t_start=400. * pq.ms, lazy=False,
id_column=0, time_column=1)
with self.assertRaises(ValueError):
r.read_segment(gid_list=[1, 2, 3], t_start=400. * pq.ms, lazy=False,
id_column_gdf=0, time_column_gdf=1)
def test_wrong_input(self):
"""
Tests two cases of wrong user input, namely
- User does not specify a value column
- User does not make any specifications
- User does not define sampling_period as a unit
- User specifies a non-default value type without
specifying a value_unit
- User specifies t_start < 1.*sampling_period
"""
filename = get_test_file_full_path(
ioclass=NestIO,
filename='0gid-1time-2gex-1262-0.dat',
directory=self.local_test_dir, clean=False)
r = NestIO(filenames=filename)
with self.assertRaises(ValueError):
r.read_segment(t_stop=1000. * pq.ms, lazy=False,
id_column_dat=0, time_column_dat=1)
with self.assertRaises(ValueError):
r.read_segment()
with self.assertRaises(ValueError):
r.read_segment(gid_list=[1], t_stop=1000. * pq.ms,
sampling_period=1. * pq.ms, lazy=False,
id_column_dat=0, time_column_dat=1,
value_columns_dat=2, value_types='V_m')
with self.assertRaises(ValueError):
r.read_segment(gid_list=[1], t_stop=1000. * pq.ms,
sampling_period=pq.ms, lazy=False,
id_column_dat=0, time_column_dat=1,
value_columns_dat=2, value_types='U_mem')
def test_wrong_input(self):
"""
Tests two cases of wrong user input, namely
- User does not specify a value column
- User does not make any specifications
- User does not define sampling_period as a unit
- User specifies a non-default value type without
specifying a value_unit
- User specifies t_start < 1.*sampling_period
"""
filename = get_test_file_full_path(
ioclass=NestIO,
filename='0gid-1time-2gex-1262-0.dat',
directory=self.local_test_dir, clean=False)
r = NestIO(filenames=filename)
with self.assertRaises(ValueError):
r.read_segment(t_stop=1000. * pq.ms, lazy=False,
id_column_dat=0, time_column_dat=1)
with self.assertRaises(ValueError):
r.read_segment()
with self.assertRaises(ValueError):
r.read_segment(gid_list=[1], t_stop=1000. * pq.ms,
sampling_period=1. * pq.ms, lazy=False,
id_column_dat=0, time_column_dat=1,
value_columns_dat=2, value_types='V_m')
with self.assertRaises(ValueError):
r.read_segment(gid_list=[1], t_stop=1000. * pq.ms,
sampling_period=pq.ms, lazy=False,
id_column_dat=0, time_column_dat=1,
value_columns_dat=2, value_types='U_mem')
def test_wrong_input(self):
"""
Tests two cases of wrong user input, namely
- User does not specify neuron IDs although the file contains IDs.
- User does not make any specifications.
"""
filename = self.get_local_path('nest/0gid-1time-1256-0.gdf')
r = NestIO(filenames=filename)
with self.assertRaises(ValueError):
r.read_segment(t_start=400. * pq.ms, t_stop=500. * pq.ms,
lazy=False,
id_column_gdf=0, time_column_gdf=1)
with self.assertRaises(ValueError):
r.read_segment()
def test_t_stop_undefined_raises_error(self):
"""
Tests if undefined t_stop, i.e., t_stop=None raises error.
"""
filename = get_test_file_full_path(
ioclass=NestIO,
filename='0gid-1time-1256-0.gdf',
directory=self.local_test_dir, clean=False)
r = NestIO(filenames=filename)
with self.assertRaises(ValueError):
r.read_spiketrain(gdf_id=1, t_start=400. * pq.ms, lazy=False,
id_column=0, time_column=1)
with self.assertRaises(ValueError):
r.read_segment(gid_list=[1, 2, 3], t_start=400. * pq.ms, lazy=False,
id_column_gdf=0, time_column_gdf=1)
def test_t_stop_undefined_raises_error(self):
"""
Tests if undefined t_stop, i.e., t_stop=None raises error.
"""
filename = get_test_file_full_path(
ioclass=NestIO,
filename='0gid-1time-1256-0.gdf',
directory=self.local_test_dir, clean=False)
r = NestIO(filenames=filename)
with self.assertRaises(ValueError):
r.read_spiketrain(gdf_id=1, t_start=400. * pq.ms, lazy=False,
id_column=0, time_column=1)
with self.assertRaises(ValueError):
r.read_segment(gid_list=[1, 2, 3], t_start=400. * pq.ms, lazy=False,
id_column_gdf=0, time_column_gdf=1)
def test_notimeid(self):
"""
Test for warning, when no time column id was provided.
"""
filename = get_test_file_full_path(
ioclass=NestIO,
filename='0gid-1time-2gex-1262-0.dat',
directory=self.local_test_dir, clean=False)
r = NestIO(filenames=filename)
t_start_targ = 450. * pq.ms
t_stop_targ = 460. * pq.ms
sampling_period = pq.CompoundUnit('5*ms')
with warnings.catch_warnings(record=True) as w:
# Cause all warnings to always be triggered.
warnings.simplefilter("always")
seg = r.read_segment(gid_list=[], t_start=t_start_targ,
sampling_period=sampling_period,
t_stop=t_stop_targ, lazy=False,
id_column_dat=0, time_column_dat=None,
value_columns_dat=2, value_types='V_m')
# Verify number and content of warning
self.assertEqual(len(w), 1)
self.assertIn("no time column id", str(w[0].message))
sts = seg.analogsignals
for st in sts:
self.assertTrue(st.t_start == 1 * 5 * pq.ms)
self.assertTrue(
st.t_stop == len(st) * sampling_period + 1 * 5 * pq.ms)
def test_id_column_none_multiple_neurons(self):
"""
Tests if function correctly raises an error if the user tries to read
from a file which does not contain unit IDs, but data for multiple
units.
"""
filename = self.get_local_path('nest/0time-1255-0.gdf')
r = NestIO(filenames=filename)
with self.assertRaises(ValueError):
r.read_analogsignal(t_stop=1000. * pq.ms, lazy=False,
sampling_period=pq.ms,
id_column=None, time_column=0,
value_column=1)
r.read_segment(t_stop=1000. * pq.ms, lazy=False,
sampling_period=pq.ms, id_column_gdf=None,
time_column_gdf=0)
def test_notimeid(self):
"""
Test for warning, when no time column id was provided.
"""
filename = get_test_file_full_path(
ioclass=NestIO,
filename='0gid-1time-2gex-1262-0.dat',
directory=self.local_test_dir, clean=False)
r = NestIO(filenames=filename)
t_start_targ = 450. * pq.ms
t_stop_targ = 460. * pq.ms
sampling_period = pq.CompoundUnit('5*ms')
with warnings.catch_warnings(record=True) as w:
# Cause all warnings to always be triggered.
warnings.simplefilter("always")
seg = r.read_segment(gid_list=[], t_start=t_start_targ,
sampling_period=sampling_period,
t_stop=t_stop_targ, lazy=False,
id_column_dat=0, time_column_dat=None,
value_columns_dat=2, value_types='V_m')
# Verify number and content of warning
self.assertEqual(len(w), 1)
self.assertIn("no time column id", str(w[0].message))
sts = seg.analogsignals
for st in sts:
self.assertTrue(st.t_start == 1 * 5 * pq.ms)
self.assertTrue(
st.t_stop == len(st) * sampling_period + 1 * 5 * pq.ms)
def test_values(self):
"""
Tests if the function returns the correct values.
"""
filename = get_test_file_full_path(
ioclass=NestIO,
filename='0gid-1time-2gex-3Vm-1261-0.dat',
directory=self.local_test_dir,
clean=False)
id_to_test = 1
r = NestIO(filenames=filename)
seg = r.read_segment(gid_list=[id_to_test],
t_stop=1000. * pq.ms,
sampling_period=pq.ms,
lazy=False,
id_column_dat=0,
time_column_dat=1,
value_columns_dat=2,
value_types='V_m')
dat = np.loadtxt(filename)
target_data = dat[:, 2][np.where(dat[:, 0] == id_to_test)]
target_data = target_data[:, None]
st = seg.analogsignals[0]
np.testing.assert_array_equal(st.magnitude, target_data)
def test_t_start_t_stop(self):
"""
Test for correct t_start and t_stop values of AnalogSignalArrays.
"""
filename = get_test_file_full_path(
ioclass=NestIO,
filename='0gid-1time-2gex-1262-0.dat',
directory=self.local_test_dir,
clean=False)
r = NestIO(filenames=filename)
t_start_targ = 450. * pq.ms
t_stop_targ = 480. * pq.ms
seg = r.read_segment(gid_list=[],
t_start=t_start_targ,
t_stop=t_stop_targ,
lazy=False,
id_column_dat=0,
time_column_dat=1,
value_columns_dat=2,
value_types='V_m')
anasigs = seg.analogsignals
for anasig in anasigs:
self.assertTrue(anasig.t_start == t_start_targ)
self.assertTrue(anasig.t_stop == t_stop_targ)
def test_read_float(self):
"""
Tests if spike times are stored as floats if they
are stored as floats in the file.
"""
filename = get_test_file_full_path(ioclass=NestIO,
filename='0gid-1time-1256-0.gdf',
directory=self.local_test_dir,
clean=False)
r = NestIO(filenames=filename)
st = r.read_spiketrain(gdf_id=1,
t_start=400. * pq.ms,
t_stop=500. * pq.ms,
lazy=False,
id_column=0,
time_column=1)
self.assertTrue(st.magnitude.dtype == np.float)
seg = r.read_segment(gid_list=[1],
t_start=400. * pq.ms,
t_stop=500. * pq.ms,
lazy=False,
id_column_gdf=0,
time_column_gdf=1)
sts = seg.spiketrains
self.assertTrue(all([s.magnitude.dtype == np.float for s in sts]))
def test_t_start_t_stop(self):
"""
Tests if the t_start and t_stop arguments are correctly processed.
"""
filename = get_test_file_full_path(ioclass=NestIO,
filename='0gid-1time-1256-0.gdf',
directory=self.local_test_dir,
clean=False)
r = NestIO(filenames=filename)
t_stop_targ = 490. * pq.ms
t_start_targ = 410. * pq.ms
seg = r.read_segment(gid_list=[],
t_start=t_start_targ,
t_stop=t_stop_targ,
lazy=False,
id_column_gdf=0,
time_column_gdf=1)
sts = seg.spiketrains
self.assertTrue(
np.max([np.max(st.magnitude) for st in sts if len(st) > 0]) <
t_stop_targ.rescale(sts[0].times.units).magnitude)
self.assertTrue(
np.min([np.min(st.magnitude) for st in sts if len(st) > 0]) >=
t_start_targ.rescale(sts[0].times.units).magnitude)
def test_read_analogsignal_and_spiketrain(self):
"""
Test if spiketrains and analogsignals can be read simultaneously
using read_segment
"""
files = [
'0gid-1time-2gex-3Vm-1261-0.dat', '0gid-1time_in_steps-1258-0.gdf'
]
filenames = [
get_test_file_full_path(ioclass=NestIO,
filename=file,
directory=self.local_test_dir,
clean=False) for file in files
]
r = NestIO(filenames=filenames)
seg = r.read_segment(gid_list=[],
t_start=400 * pq.ms,
t_stop=600 * pq.ms,
id_column_gdf=0,
time_column_gdf=1,
id_column_dat=0,
time_column_dat=1,
value_columns_dat=2)
self.assertEqual(len(seg.spiketrains), 50)
self.assertEqual(len(seg.analogsignals), 50)
def test_wrong_input(self):
"""
Tests two cases of wrong user input, namely
- User does not specify neuron IDs although the file contains IDs.
- User does not make any specifications.
"""
filename = get_test_file_full_path(
ioclass=NestIO,
filename='0gid-1time-1256-0.gdf',
directory=self.local_test_dir, clean=False)
r = NestIO(filenames=filename)
with self.assertRaises(ValueError):
r.read_segment(t_start=400. * pq.ms, t_stop=500. * pq.ms,
lazy=False,
id_column_gdf=0, time_column_gdf=1)
with self.assertRaises(ValueError):
r.read_segment()
def test_read_segment_range_is_reasonable(self):
"""
Tests if error is thrown correctly, when second entry is smaller than
the first one of the range.
"""
filename = get_test_file_full_path(
ioclass=NestIO,
filename='0gid-1time-1256-0.gdf',
directory=self.local_test_dir, clean=False)
r = NestIO(filenames=filename)
seg = r.read_segment(gid_list=(10, 10), t_start=400. * pq.ms,
t_stop=500. * pq.ms, lazy=False,
id_column_gdf=0, time_column_gdf=1)
self.assertEqual(len(seg.spiketrains), 1)
with self.assertRaises(ValueError):
r.read_segment(gid_list=(10, 9), t_start=400. * pq.ms,
t_stop=500. * pq.ms, lazy=False,
id_column_gdf=0, time_column_gdf=1)
def test_read_segment_accepts_range(self):
"""
Tests if spiketrains can be retrieved by specifying a range of GDF IDs.
"""
filename = self.get_local_path('nest/0gid-1time-1256-0.gdf')
r = NestIO(filenames=filename)
seg = r.read_segment(gid_list=(10, 39), t_start=400. * pq.ms,
t_stop=500. * pq.ms, lazy=False,
id_column_gdf=0, time_column_gdf=1)
self.assertEqual(len(seg.spiketrains), 30)
def test_read_segment_annotates(self):
"""
Tests if correct annotation is added when reading a segment.
"""
filename = self.get_local_path('nest/0gid-1time-1256-0.gdf')
r = NestIO(filenames=filename)
IDs = (5, 11)
sts = r.read_segment(gid_list=(5, 11), t_start=400. * pq.ms,
t_stop=500. * pq.ms)
for ID in np.arange(5, 12):
self.assertEqual(ID, sts.spiketrains[ID - 5].annotations['id'])
def test_read_segment_can_return_empty_spiketrains(self):
"""
Tests if read_segment makes sure that only non-zero spike trains are
returned.
"""
filename = self.get_local_path('nest/0gid-1time-1256-0.gdf')
r = NestIO(filenames=filename)
seg = r.read_segment(gid_list=[], t_start=400.4 * pq.ms,
t_stop=400.5 * pq.ms)
for st in seg.spiketrains:
self.assertEqual(st.size, 0)
def test_id_column_none_multiple_neurons(self):
"""
Tests if function correctly raises an error if the user tries to read
from a file which does not contain unit IDs, but data for multiple
units.
"""
filename = get_test_file_full_path(
ioclass=NestIO,
filename='0time-1255-0.gdf',
directory=self.local_test_dir, clean=False)
r = NestIO(filenames=filename)
with self.assertRaises(ValueError):
r.read_analogsignal(t_stop=1000. * pq.ms, lazy=False,
sampling_period=pq.ms,
id_column=None, time_column=0,
value_column=1)
r.read_segment(t_stop=1000. * pq.ms, lazy=False,
sampling_period=pq.ms, id_column_gdf=None,
time_column_gdf=0)
def test_read_spiketrain(self):
"""
Tests reading files in the 4 different formats:
- without GIDs, with times as floats
- without GIDs, with times as integers in time steps
- with GIDs, with times as floats
- with GIDs, with times as integers in time steps
"""
filename = get_test_file_full_path(
ioclass=NestIO,
filename='0time-1255-0.gdf',
directory=self.local_test_dir, clean=False)
r = NestIO(filenames=filename)
r.read_spiketrain(t_start=400. * pq.ms, t_stop=500. * pq.ms, lazy=False,
id_column=None, time_column=0)
r.read_segment(t_start=400. * pq.ms, t_stop=500. * pq.ms, lazy=False,
id_column_gdf=None, time_column_gdf=0)
filename = get_test_file_full_path(
ioclass=NestIO,
filename='0time_in_steps-1257-0.gdf',
directory=self.local_test_dir, clean=False)
r = NestIO(filenames=filename)
r.read_spiketrain(t_start=400. * pq.ms, t_stop=500. * pq.ms,
time_unit=pq.CompoundUnit('0.1*ms'), lazy=False,
id_column=None, time_column=0)
r.read_segment(t_start=400. * pq.ms, t_stop=500. * pq.ms,
time_unit=pq.CompoundUnit('0.1*ms'), lazy=False,
id_column_gdf=None, time_column_gdf=0)
filename = get_test_file_full_path(
ioclass=NestIO,
filename='0gid-1time-1256-0.gdf',
directory=self.local_test_dir, clean=False)
r = NestIO(filenames=filename)
r.read_spiketrain(gdf_id=1, t_start=400. * pq.ms, t_stop=500. * pq.ms,
lazy=False, id_column_gdf=0, time_column_gdf=1)
r.read_segment(gid_list=[1], t_start=400. * pq.ms, t_stop=500. * pq.ms,
lazy=False, id_column_gdf=0, time_column_gdf=1)
filename = get_test_file_full_path(
ioclass=NestIO,
filename='0gid-1time_in_steps-1258-0.gdf',
directory=self.local_test_dir, clean=False)
r = NestIO(filenames=filename)
r.read_spiketrain(gdf_id=1, t_start=400. * pq.ms, t_stop=500. * pq.ms,
time_unit=pq.CompoundUnit('0.1*ms'), lazy=False,
id_column=0, time_column=1)
r.read_segment(gid_list=[1], t_start=400. * pq.ms, t_stop=500. * pq.ms,
time_unit=pq.CompoundUnit('0.1*ms'), lazy=False,
id_column_gdf=0, time_column_gdf=1)
def test_read_spiketrain(self):
"""
Tests reading files in the 4 different formats:
- without GIDs, with times as floats
- without GIDs, with times as integers in time steps
- with GIDs, with times as floats
- with GIDs, with times as integers in time steps
"""
filename = get_test_file_full_path(
ioclass=NestIO,
filename='0time-1255-0.gdf',
directory=self.local_test_dir, clean=False)
r = NestIO(filenames=filename)
r.read_spiketrain(t_start=400. * pq.ms, t_stop=500. * pq.ms, lazy=False,
id_column=None, time_column=0)
r.read_segment(t_start=400. * pq.ms, t_stop=500. * pq.ms, lazy=False,
id_column_gdf=None, time_column_gdf=0)
filename = get_test_file_full_path(
ioclass=NestIO,
filename='0time_in_steps-1257-0.gdf',
directory=self.local_test_dir, clean=False)
r = NestIO(filenames=filename)
r.read_spiketrain(t_start=400. * pq.ms, t_stop=500. * pq.ms,
time_unit=pq.CompoundUnit('0.1*ms'), lazy=False,
id_column=None, time_column=0)
r.read_segment(t_start=400. * pq.ms, t_stop=500. * pq.ms,
time_unit=pq.CompoundUnit('0.1*ms'), lazy=False,
id_column_gdf=None, time_column_gdf=0)
filename = get_test_file_full_path(
ioclass=NestIO,
filename='0gid-1time-1256-0.gdf',
directory=self.local_test_dir, clean=False)
r = NestIO(filenames=filename)
r.read_spiketrain(gdf_id=1, t_start=400. * pq.ms, t_stop=500. * pq.ms,
lazy=False, id_column_gdf=0, time_column_gdf=1)
r.read_segment(gid_list=[1], t_start=400. * pq.ms, t_stop=500. * pq.ms,
lazy=False, id_column_gdf=0, time_column_gdf=1)
filename = get_test_file_full_path(
ioclass=NestIO,
filename='0gid-1time_in_steps-1258-0.gdf',
directory=self.local_test_dir, clean=False)
r = NestIO(filenames=filename)
r.read_spiketrain(gdf_id=1, t_start=400. * pq.ms, t_stop=500. * pq.ms,
time_unit=pq.CompoundUnit('0.1*ms'), lazy=False,
id_column=0, time_column=1)
r.read_segment(gid_list=[1], t_start=400. * pq.ms, t_stop=500. * pq.ms,
time_unit=pq.CompoundUnit('0.1*ms'), lazy=False,
id_column_gdf=0, time_column_gdf=1)
def test_read_segment(self):
"""
Tests if spiketrains are correctly stored in a segment.
"""
filename = get_test_file_full_path(
ioclass=NestIO,
filename='0gid-1time-1256-0.gdf',
directory=self.local_test_dir, clean=False)
r = NestIO(filenames=filename)
id_list_to_test = range(1, 10)
seg = r.read_segment(gid_list=id_list_to_test, t_start=400. * pq.ms,
t_stop=500. * pq.ms, lazy=False,
id_column_gdf=0, time_column_gdf=1)
self.assertTrue(len(seg.spiketrains) == len(id_list_to_test))
id_list_to_test = []
seg = r.read_segment(gid_list=id_list_to_test, t_start=400. * pq.ms,
t_stop=500. * pq.ms, lazy=False,
id_column_gdf=0, time_column_gdf=1)
self.assertTrue(len(seg.spiketrains) == 50)
def test_read_integer(self):
"""
Tests if spike times are actually stored as integers if they are stored
in time steps in the file.
"""
filename = get_test_file_full_path(
ioclass=NestIO,
filename='0time_in_steps-1257-0.gdf',
directory=self.local_test_dir, clean=False)
r = NestIO(filenames=filename)
st = r.read_spiketrain(gdf_id=None, t_start=400. * pq.ms,
t_stop=500. * pq.ms,
time_unit=pq.CompoundUnit('0.1*ms'),
lazy=False, id_column=None, time_column=0)
self.assertTrue(st.magnitude.dtype == np.int32)
seg = r.read_segment(gid_list=[None], t_start=400. * pq.ms,
t_stop=500. * pq.ms,
time_unit=pq.CompoundUnit('0.1*ms'),
lazy=False, id_column_gdf=None, time_column_gdf=0)
sts = seg.spiketrains
self.assertTrue(all([st.magnitude.dtype == np.int32 for st in sts]))
filename = get_test_file_full_path(
ioclass=NestIO,
filename='0gid-1time_in_steps-1258-0.gdf',
directory=self.local_test_dir, clean=False)
r = NestIO(
filenames=filename)
st = r.read_spiketrain(gdf_id=1, t_start=400. * pq.ms,
t_stop=500. * pq.ms,
time_unit=pq.CompoundUnit('0.1*ms'),
lazy=False, id_column=0, time_column=1)
self.assertTrue(st.magnitude.dtype == np.int32)
seg = r.read_segment(gid_list=[1], t_start=400. * pq.ms,
t_stop=500. * pq.ms,
time_unit=pq.CompoundUnit('0.1*ms'),
lazy=False, id_column_gdf=0, time_column_gdf=1)
sts = seg.spiketrains
self.assertTrue(all([st.magnitude.dtype == np.int32 for st in sts]))
def test_multiple_value_columns(self):
"""
Test for simultaneous loading of multiple columns from dat file.
"""
filename = self.get_local_path('nest/0gid-1time-2Vm-3Iex-4Iin-1264-0.dat')
r = NestIO(filenames=filename)
sampling_period = pq.CompoundUnit('5*ms')
seg = r.read_segment(gid_list=[1001],
value_columns_dat=[2, 3],
sampling_period=sampling_period)
anasigs = seg.analogsignals
self.assertEqual(len(anasigs), 2)
def test_read_segment_accepts_range(self):
"""
Tests if spiketrains can be retrieved by specifying a range of GDF IDs.
"""
filename = get_test_file_full_path(
ioclass=NestIO,
filename='0gid-1time-1256-0.gdf',
directory=self.local_test_dir, clean=False)
r = NestIO(filenames=filename)
seg = r.read_segment(gid_list=(10, 39), t_start=400. * pq.ms,
t_stop=500. * pq.ms, lazy=False,
id_column_gdf=0, time_column_gdf=1)
self.assertEqual(len(seg.spiketrains), 30)
def test_read_segment_accepts_range(self):
"""
Tests if spiketrains can be retrieved by specifying a range of GDF IDs.
"""
filename = get_test_file_full_path(
ioclass=NestIO,
filename='0gid-1time-1256-0.gdf',
directory=self.local_test_dir, clean=False)
r = NestIO(filenames=filename)
seg = r.read_segment(gid_list=(10, 39), t_start=400. * pq.ms,
t_stop=500. * pq.ms, lazy=False,
id_column_gdf=0, time_column_gdf=1)
self.assertEqual(len(seg.spiketrains), 30)
def test_read_segment_annotates(self):
"""
Tests if correct annotation is added when reading a segment.
"""
filename = get_test_file_full_path(
ioclass=NestIO,
filename='0gid-1time-1256-0.gdf',
directory=self.local_test_dir, clean=False)
r = NestIO(filenames=filename)
IDs = (5, 11)
sts = r.read_segment(gid_list=(5, 11), t_start=400. * pq.ms,
t_stop=500. * pq.ms)
for ID in np.arange(5, 12):
self.assertEqual(ID, sts.spiketrains[ID - 5].annotations['id'])
def test_read_segment_annotates(self):
"""
Tests if correct annotation is added when reading a segment.
"""
filename = get_test_file_full_path(
ioclass=NestIO,
filename='0gid-1time-1256-0.gdf',
directory=self.local_test_dir, clean=False)
r = NestIO(filenames=filename)
IDs = (5, 11)
sts = r.read_segment(gid_list=(5, 11), t_start=400. * pq.ms,
t_stop=500. * pq.ms)
for ID in np.arange(5, 12):
self.assertEqual(ID, sts.spiketrains[ID - 5].annotations['id'])
def test_read_segment_can_return_empty_spiketrains(self):
"""
Tests if read_segment makes sure that only non-zero spike trains are
returned.
"""
filename = get_test_file_full_path(
ioclass=NestIO,
filename='0gid-1time-1256-0.gdf',
directory=self.local_test_dir, clean=False)
r = NestIO(filenames=filename)
seg = r.read_segment(gid_list=[], t_start=400. * pq.ms,
t_stop=1. * pq.ms)
for st in seg.spiketrains:
self.assertEqual(st.size, 0)
def test_read_segment_can_return_empty_spiketrains(self):
"""
Tests if read_segment makes sure that only non-zero spike trains are
returned.
"""
filename = get_test_file_full_path(
ioclass=NestIO,
filename='0gid-1time-1256-0.gdf',
directory=self.local_test_dir, clean=False)
r = NestIO(filenames=filename)
seg = r.read_segment(gid_list=[], t_start=400.4 * pq.ms,
t_stop=400.5 * pq.ms)
for st in seg.spiketrains:
self.assertEqual(st.size, 0)
def test_multiple_value_columns(self):
"""
Test for simultaneous loading of multiple columns from dat file.
"""
filename = get_test_file_full_path(
ioclass=NestIO,
filename='0gid-1time-2Vm-3Iex-4Iin-1264-0.dat',
directory=self.local_test_dir, clean=False)
r = NestIO(filenames=filename)
sampling_period = pq.CompoundUnit('5*ms')
seg = r.read_segment(gid_list=[1001],
value_columns_dat=[2, 3],
sampling_period=sampling_period)
anasigs = seg.analogsignals
self.assertEqual(len(anasigs), 2)
def test_read_analogsignal_and_spiketrain(self):
"""
Test if spiketrains and analogsignals can be read simultaneously
using read_segment
"""
files = ['nest/0gid-1time-2gex-3Vm-1261-0.dat',
'nest/0gid-1time_in_steps-1258-0.gdf']
filenames = [self.get_local_path(e) for e in files]
r = NestIO(filenames=filenames)
seg = r.read_segment(gid_list=[], t_start=400 * pq.ms,
t_stop=600 * pq.ms,
id_column_gdf=0, time_column_gdf=1,
id_column_dat=0, time_column_dat=1,
value_columns_dat=2)
self.assertEqual(len(seg.spiketrains), 50)
self.assertEqual(len(seg.analogsignals), 50)
def test_values(self):
"""
Tests if the routine loads the correct numbers from the file.
"""
id_to_test = 1
filename = self.get_local_path('nest/0gid-1time-1256-0.gdf')
r = NestIO(filenames=filename)
seg = r.read_segment(gid_list=[id_to_test],
t_start=400. * pq.ms,
t_stop=500. * pq.ms, lazy=False,
id_column_gdf=0, time_column_gdf=1)
dat = np.loadtxt(filename)
target_data = dat[:, 1][np.where(dat[:, 0] == id_to_test)]
st = seg.spiketrains[0]
np.testing.assert_array_equal(st.magnitude, target_data)
def test_read_analogsignal(self):
"""
Tests reading files in the 2 different formats:
- with GIDs, with times as floats
- with GIDs, with time as integer
"""
filename = get_test_file_full_path(
ioclass=NestIO,
filename='0gid-1time-2gex-3Vm-1261-0.dat',
directory=self.local_test_dir, clean=False)
r = NestIO(filenames=filename)
r.read_analogsignal(gid=1, t_stop=1000. * pq.ms,
sampling_period=pq.ms, lazy=False,
id_column=0, time_column=1,
value_column=2, value_type='V_m')
r.read_segment(gid_list=[1], t_stop=1000. * pq.ms,
sampling_period=pq.ms, lazy=False, id_column_dat=0,
time_column_dat=1, value_columns_dat=2,
value_types='V_m')
filename = get_test_file_full_path(
ioclass=NestIO,
filename='0gid-1time_in_steps-2Vm-1263-0.dat',
directory=self.local_test_dir, clean=False)
r = NestIO(filenames=filename)
r.read_analogsignal(gid=1, t_stop=1000. * pq.ms,
time_unit=pq.CompoundUnit('0.1*ms'),
sampling_period=pq.ms, lazy=False,
id_column=0, time_column=1,
value_column=2, value_type='V_m')
r.read_segment(gid_list=[1], t_stop=1000. * pq.ms,
time_unit=pq.CompoundUnit('0.1*ms'),
sampling_period=pq.ms, lazy=False, id_column_dat=0,
time_column_dat=1, value_columns_dat=2,
value_types='V_m')
filename = get_test_file_full_path(
ioclass=NestIO,
filename='0gid-1time-2Vm-1259-0.dat',
directory=self.local_test_dir, clean=False)
r = NestIO(filenames=filename)
r.read_analogsignal(gid=1, t_stop=1000. * pq.ms,
time_unit=pq.CompoundUnit('0.1*ms'),
sampling_period=pq.ms, lazy=False,
id_column=0, time_column=1,
value_column=2, value_type='V_m')
r.read_segment(gid_list=[1], t_stop=1000. * pq.ms,
time_unit=pq.CompoundUnit('0.1*ms'),
sampling_period=pq.ms, lazy=False, id_column_dat=0,
time_column_dat=1, value_columns_dat=2,
value_types='V_m')
def test_read_analogsignal(self):
"""
Tests reading files in the 2 different formats:
- with GIDs, with times as floats
- with GIDs, with time as integer
"""
filename = get_test_file_full_path(
ioclass=NestIO,
filename='0gid-1time-2gex-3Vm-1261-0.dat',
directory=self.local_test_dir, clean=False)
r = NestIO(filenames=filename)
r.read_analogsignal(gid=1, t_stop=1000. * pq.ms,
sampling_period=pq.ms, lazy=False,
id_column=0, time_column=1,
value_column=2, value_type='V_m')
r.read_segment(gid_list=[1], t_stop=1000. * pq.ms,
sampling_period=pq.ms, lazy=False, id_column_dat=0,
time_column_dat=1, value_columns_dat=2,
value_types='V_m')
filename = get_test_file_full_path(
ioclass=NestIO,
filename='0gid-1time_in_steps-2Vm-1263-0.dat',
directory=self.local_test_dir, clean=False)
r = NestIO(filenames=filename)
r.read_analogsignal(gid=1, t_stop=1000. * pq.ms,
time_unit=pq.CompoundUnit('0.1*ms'),
sampling_period=pq.ms, lazy=False,
id_column=0, time_column=1,
value_column=2, value_type='V_m')
r.read_segment(gid_list=[1], t_stop=1000. * pq.ms,
time_unit=pq.CompoundUnit('0.1*ms'),
sampling_period=pq.ms, lazy=False, id_column_dat=0,
time_column_dat=1, value_columns_dat=2,
value_types='V_m')
filename = get_test_file_full_path(
ioclass=NestIO,
filename='0gid-1time-2Vm-1259-0.dat',
directory=self.local_test_dir, clean=False)
r = NestIO(filenames=filename)
r.read_analogsignal(gid=1, t_stop=1000. * pq.ms,
time_unit=pq.CompoundUnit('0.1*ms'),
sampling_period=pq.ms, lazy=False,
id_column=0, time_column=1,
value_column=2, value_type='V_m')
r.read_segment(gid_list=[1], t_stop=1000. * pq.ms,
time_unit=pq.CompoundUnit('0.1*ms'),
sampling_period=pq.ms, lazy=False, id_column_dat=0,
time_column_dat=1, value_columns_dat=2,
value_types='V_m')
def test_read_analogsignal_and_spiketrain(self):
"""
Test if spiketrains and analogsignals can be read simultaneously
using read_segment
"""
files = ['0gid-1time-2gex-3Vm-1261-0.dat',
'0gid-1time_in_steps-1258-0.gdf']
filenames = [get_test_file_full_path(ioclass=NestIO, filename=file,
directory=self.local_test_dir,
clean=False)
for file in files]
r = NestIO(filenames=filenames)
seg = r.read_segment(gid_list=[], t_start=400 * pq.ms,
t_stop=600 * pq.ms,
id_column_gdf=0, time_column_gdf=1,
id_column_dat=0, time_column_dat=1,
value_columns_dat=2)
self.assertEqual(len(seg.spiketrains), 50)
self.assertEqual(len(seg.analogsignals), 50)
def test_read_float(self):
"""
Tests if spike times are stored as floats if they
are stored as floats in the file.
"""
filename = get_test_file_full_path(
ioclass=NestIO,
filename='0gid-1time-1256-0.gdf',
directory=self.local_test_dir, clean=False)
r = NestIO(filenames=filename)
st = r.read_spiketrain(gdf_id=1, t_start=400. * pq.ms,
t_stop=500. * pq.ms,
lazy=False, id_column=0, time_column=1)
self.assertTrue(st.magnitude.dtype == np.float)
seg = r.read_segment(gid_list=[1], t_start=400. * pq.ms,
t_stop=500. * pq.ms,
lazy=False, id_column_gdf=0, time_column_gdf=1)
sts = seg.spiketrains
self.assertTrue(all([s.magnitude.dtype == np.float for s in sts]))
def test_values(self):
"""
Tests if the routine loads the correct numbers from the file.
"""
id_to_test = 1
filename = get_test_file_full_path(
ioclass=NestIO,
filename='0gid-1time-1256-0.gdf',
directory=self.local_test_dir, clean=False)
r = NestIO(filenames=filename)
seg = r.read_segment(gid_list=[id_to_test],
t_start=400. * pq.ms,
t_stop=500. * pq.ms, lazy=False,
id_column_gdf=0, time_column_gdf=1)
dat = np.loadtxt(filename)
target_data = dat[:, 1][np.where(dat[:, 0] == id_to_test)]
st = seg.spiketrains[0]
np.testing.assert_array_equal(st.magnitude, target_data)
def test_t_start_t_stop(self):
"""
Test for correct t_start and t_stop values of AnalogSignalArrays.
"""
filename = get_test_file_full_path(
ioclass=NestIO,
filename='0gid-1time-2gex-1262-0.dat',
directory=self.local_test_dir, clean=False)
r = NestIO(filenames=filename)
t_start_targ = 450. * pq.ms
t_stop_targ = 480. * pq.ms
seg = r.read_segment(gid_list=[], t_start=t_start_targ,
t_stop=t_stop_targ, lazy=False,
id_column_dat=0, time_column_dat=1,
value_columns_dat=2, value_types='V_m')
anasigs = seg.analogsignals
for anasig in anasigs:
self.assertTrue(anasig.t_start == t_start_targ)
self.assertTrue(anasig.t_stop == t_stop_targ)
def test_t_start_t_stop(self):
"""
Tests if the t_start and t_stop arguments are correctly processed.
"""
filename = get_test_file_full_path(
ioclass=NestIO,
filename='0gid-1time-1256-0.gdf',
directory=self.local_test_dir, clean=False)
r = NestIO(filenames=filename)
t_stop_targ = 490. * pq.ms
t_start_targ = 410. * pq.ms
seg = r.read_segment(gid_list=[], t_start=t_start_targ,
t_stop=t_stop_targ, lazy=False,
id_column_gdf=0, time_column_gdf=1)
sts = seg.spiketrains
self.assertTrue(np.max([np.max(st.magnitude) for st in sts
if len(st) > 0])
< t_stop_targ.rescale(sts[0].times.units).magnitude)
self.assertTrue(np.min([np.min(st.magnitude) for st in sts
if len(st) > 0])
>= t_start_targ.rescale(sts[0].times.units).magnitude)
def test_values(self):
"""
Tests if the function returns the correct values.
"""
filename = get_test_file_full_path(
ioclass=NestIO,
filename='0gid-1time-2gex-3Vm-1261-0.dat',
directory=self.local_test_dir, clean=False)
id_to_test = 1
r = NestIO(filenames=filename)
seg = r.read_segment(gid_list=[id_to_test],
t_stop=1000. * pq.ms,
sampling_period=pq.ms, lazy=False,
id_column_dat=0, time_column_dat=1,
value_columns_dat=2, value_types='V_m')
dat = np.loadtxt(filename)
target_data = dat[:, 2][np.where(dat[:, 0] == id_to_test)]
target_data = target_data[:, None]
st = seg.analogsignals[0]
np.testing.assert_array_equal(st.magnitude, target_data)
