def test_auto_trigger_selection_text(caplog):
"""Test auto_trigger_selection."""
test_time = np.array([0, 1, 2, 3, 4])
test_trigger = np.array([0, 1, 2, 3, 4])
test_half = np.array([0, 1, 2])
test_twice = np.array([0, 1, 2, 3, 4, 5, 6, 7, 8, 9])
test_timeseries = [
test_time, test_trigger, test_half, test_twice, test_twice, test_twice
]
test_freq = [1, 1, 0.5, 2, 2, 2]
test_chn_name = ['time', 'trigger', 'half', 'CO2', 'CO 2', 'strigose']
test_units = ['s', 'V', 'V', 'V', 'V', 'V']
# test when trigger is not the name of the channel
test_chtrig = 2
phys_in = po.BlueprintInput(test_timeseries, test_freq, test_chn_name,
test_units, test_chtrig)
assert 'Trigger channel name is not' in caplog.text
# test when trigger is 0 and that the trigger channel is recognized by name:
test_chtrig = 0
phys_in = po.BlueprintInput(test_timeseries, test_freq, test_chn_name,
test_units, test_chtrig)
assert phys_in.trigger_idx == 1
# test when no trigger is found
test_chn_name = ['time', 'trigger', 'TRIGGER', 'CO2', 'CO 2', 'strigose']
with raises(Exception) as errorinfo:
phys_in = po.BlueprintInput(test_timeseries, test_freq, test_chn_name,
test_units, test_chtrig)
assert 'More than one possible trigger channel' in str(errorinfo.value)
def test_BlueprintInput():
test_time = np.array([0, 1, 1, 2, 3, 5, 8, 13])
test_trigger = np.array([0, 1, 0, 0, 0, 0, 0, 0])
test_chocolate = np.array([1, 0, 0, 1, 0, 0, 1, 0])
test_timeseries = [test_time, test_trigger, test_chocolate]
test_freq = [42.0, 3.14, 20.0]
test_chn_name = ['time', 'trigger', 'chocolate']
test_units = ['s', 's', 'sweetness']
num_channnels = len(test_timeseries)
blueprint_in = po.BlueprintInput(test_timeseries, test_freq, test_chn_name,
test_units)
# Tests rename_channels
new_names = ['trigger', 'time', 'lindt']
blueprint_in.rename_channels(new_names.copy())
assert blueprint_in.ch_name == ['time', 'trigger', 'lindt']
# Tests return_index
test_index = blueprint_in.return_index(1)
assert (test_index[0] == test_trigger).all()
assert test_index[1] == len(test_timeseries)
assert test_index[2] == test_freq[1]
assert test_index[3] == test_chn_name[1]
assert test_index[4] == test_units[1]
# Tests delete_at_index
blueprint_in.delete_at_index(2)
assert blueprint_in.ch_amount == num_channnels - 1
# Tests check_trigger_amount
blueprint_in.check_trigger_amount(thr=0.9, num_timepoints_expected=1)
assert blueprint_in.num_timepoints_found == 1
def test_auto_trigger_selection_time():
"""Test auto_trigger_selection in time domain."""
# Simulate 10 s of a trigger, O2 and ECG
T = 10
nSamp = 100
fs = nSamp / T
test_time = np.linspace(0, T, nSamp)
test_freq = [fs, fs, fs, fs]
# O2 as a sinusoidal of 0.5 Hz
test_O2 = np.sin(2 * np.pi * 0.5 * test_time)
# ECG as a sinusoidal with 1.5 Hz
test_ecg = np.sin(2 * np.pi * 1.5 * test_time)
# Trigger as a binary signal
test_trigger = np.zeros(nSamp)
test_trigger[1:nSamp:4] = 1
test_timeseries = [test_time, test_O2, test_ecg, test_trigger]
test_chn_name = ['time', 'O2', 'ecg', 'tiger']
test_units = ['s', 'V', 'V', 'V']
# test when chtrig is 0 and the trigger is not recognized by text matching:
test_chtrig = 0
phys_in = po.BlueprintInput(test_timeseries, test_freq, test_chn_name,
test_units, test_chtrig)
assert phys_in.trigger_idx == 3
def test_BlueprintInput_slice():
"""Test BlueprintInput_slice.__getitem__ ."""
test_time = np.array([0, 1, 2, 3, 4])
test_trigger = np.array([0, 1, 2, 3, 4])
test_half = np.array([0, 1, 2])
test_twice = np.array([0, 1, 2, 3, 4, 5, 6, 7, 8, 9])
test_timeseries = [test_time, test_trigger, test_half, test_twice]
test_freq = [1, 1, 0.5, 2]
test_chn_name = ['time', 'trigger', 'half', 'twice']
test_units = ['s', 'V', 'V', 'V']
test_chtrig = 1
phys_in = po.BlueprintInput(test_timeseries, test_freq, test_chn_name,
test_units, test_chtrig)
phys_dict = {'timeseries': test_timeseries,
'freq': test_freq,
'ch_name': ['time', 'trigger', 'half', 'twice'],
'units': ['s', 'V', 'V', 'V'],
'trigger_idx': 1,
'num_timepoints_found': None,
'thr': None,
'time_offset': 0}
# Test all-comprehensive slice
assert phys_in[0:len(test_trigger)] == phys_dict
# Test instantaneous slice first and last
phys_dict['timeseries'] = [np.array([test_time[0]]),
np.array([test_trigger[0]]),
np.array([test_half[0]]),
np.array([test_twice[0]])]
assert phys_in[0] == phys_dict
phys_dict['timeseries'] = [np.array([test_time[-1]]),
np.array([test_trigger[-1]]),
np.array([test_half[-1]]),
np.array([test_twice[-2]])]
assert phys_in[-1] == phys_dict
# Test slice in the middle
phys_dict['timeseries'] = [np.array(test_time[2:4]),
np.array(test_trigger[2:4]),
np.array(test_half[1:2]),
np.array(test_twice[4:8])]
assert phys_in[2:4] == phys_dict
# Test slice in the middle with steps
phys_dict['timeseries'] = [np.array(test_time[1:4:2]),
np.array(test_trigger[1:4:2]),
np.array(test_half[0:2:1]),
np.array(test_twice[4:8:4])]
assert phys_in[1:4:2] == phys_dict
def test_are_equal():
"""Test are_equal ."""
test_string = 'So Long, and Thanks for All the Fish'
test_time = np.array([0, 1, 1, 2, 3, 5, 8, 13])
test_trigger = np.array([0, 1, 0, 0, 0, 0, 0, 0])
class C(object):
c = 'c'
c1 = C()
c1.ts = [test_time, test_trigger]
c2 = C()
c2.ts = [test_time]
test_half = np.array([0, 1, 2])
test_twice = np.array([0, 1, 2, 3, 4, 5, 6, 7, 8, 9])
test_timeseries = [test_time, test_trigger, test_half, test_twice]
test_freq = [1, 1, 0.5, 2]
test_chn_name = ['time', 'trigger', 'half', 'twice']
test_units = ['s', 'V', 'V', 'V']
test_chtrig = 1
phys_in = po.BlueprintInput(test_timeseries, test_freq, test_chn_name,
test_units, test_chtrig)
phys_out = po.BlueprintInput([test_trigger, test_half, test_twice],
test_freq, test_chn_name,
test_units, test_chtrig)
assert po.are_equal(test_string, test_string)
assert po.are_equal(c1, c1)
assert po.are_equal(phys_in, phys_in)
assert po.are_equal(c1, c1.__dict__)
assert po.are_equal(c1.__dict__, c1)
assert not po.are_equal(c1, c2)
assert not po.are_equal(c1, phys_in)
assert not po.are_equal(phys_out, phys_in)
assert not po.are_equal(phys_in, c2)
assert not po.are_equal(c1, c2.__dict__)
assert not po.are_equal(test_string, c1)
def test_BlueprintInput():
test_time = np.array([0, 1, 1, 2, 3, 5, 8, 13])
test_trigger = np.array([0, 1, 0, 0, 0, 0, 0, 0])
test_chocolate = np.array([1, 0, 0, 1, 0, 0, 1, 0])
test_timeseries = [test_time, test_trigger, test_chocolate]
test_freq = [42.0, 3.14, 20.0]
test_chn_name = ['time', 'trigger', 'chocolate']
test_units = ['s', 's', 'sweetness']
test_chtrig = 1
num_channnels = len(test_timeseries)
blueprint_in = po.BlueprintInput(test_timeseries, test_freq, test_chn_name,
test_units, test_chtrig)
# Tests rename_channels
new_names = ['trigger', 'time', 'lindt']
blueprint_in.rename_channels(new_names)
assert blueprint_in.ch_name == ['time', 'trigger', 'lindt']
# Tests return_index
test_index = blueprint_in.return_index(1)
assert test_index[0] is not test_trigger
assert (test_index[0] == test_trigger).all()
assert test_index[1] == len(test_timeseries)
assert test_index[2] == test_freq[1]
assert test_index[3] == test_chn_name[1]
assert test_index[4] == test_units[1]
# Tests delete_at_index
blueprint_in.delete_at_index(2)
assert blueprint_in.ch_amount == num_channnels - 1
# Tests check_trigger_amount
blueprint_in.check_trigger_amount(thr=0.9, num_timepoints_expected=1)
assert blueprint_in.num_timepoints_found == 1
assert blueprint_in.time_offset == 1
test_offset_time = test_time - 1
assert np.array_equal(blueprint_in.timeseries[0], test_offset_time)
# Tests delete_at_index with trigger channel
blueprint_in.delete_at_index(test_chtrig)
assert blueprint_in.ch_amount == num_channnels - 2
assert blueprint_in.trigger_idx == 0
# Test __eq__
assert blueprint_in == blueprint_in
with raises(IndexError) as errorinfo:
blueprint_in.__getitem__(1000)
assert 'out of bounds' in str(errorinfo.value)
def test_BlueprintOutput():
test_time = np.array([0, 1, 1, 2, 3, 5, 8, 13])
test_trigger = np.array([0, 1, 0, 0, 0, 0, 0, 0])
test_chocolate = np.array([1, 0, 0, 1, 0, 0, 1, 0])
test_timeseries = [test_time, test_trigger, test_chocolate]
test_freq = [42.0, 3.14, 20.0]
test_chn_name = ['trigger', 'time', 'chocolate']
test_units = ['s', 's', 'sweetness']
test_chtrig = 1
num_channnels = len(test_timeseries)
blueprint_in = po.BlueprintInput(test_timeseries, test_freq, test_chn_name,
test_units, test_chtrig)
# Tests init_from_blueprint
blueprint_out = po.BlueprintOutput.init_from_blueprint(blueprint_in)
start_time = blueprint_out.start_time
assert (blueprint_out.timeseries == np.asarray(test_timeseries).T).all()
assert blueprint_out.freq == test_freq[0]
assert blueprint_out.ch_name == test_chn_name
assert blueprint_out.units == test_units
assert blueprint_out.start_time == 0
# Tests return_index
test_timeseries = np.array([[0, 1, 1, 2, 3, 5, 8, 13],
[0, 1, 0, 0, 0, 0, 0, 0],
[1, 0, 0, 1, 0, 0, 1, 0]]).T
test_freq = 42.0
test_chn_name = ['trigger', 'time', 'chocolate']
test_units = ['s', 's', 'sweetness']
num_channnels = test_timeseries.shape[1]
blueprint_out = po.BlueprintOutput(test_timeseries, test_freq, test_chn_name, test_units,
start_time)
test_index = blueprint_out.return_index(1)
assert (test_index[0] == test_trigger).all()
assert test_index[1] == test_timeseries.shape[1]
assert test_index[3] == test_chn_name[1]
assert test_index[4] == test_units[1]
# Tests delete_at_index
blueprint_out.delete_at_index(1)
assert len(blueprint_out.ch_name) == num_channnels - 1
assert len(blueprint_out.units) == num_channnels - 1
assert blueprint_out.timeseries.shape[1] == num_channnels - 1
assert blueprint_out.ch_amount == num_channnels - 1
# Test __eq__
assert blueprint_out == blueprint_out
def test_cta_time_interp():
"""Test BlueprintInput.check_trigger_amount with time resampling."""
test_time = np.array([0, 7])
test_trigger = np.array([0, 1, 0, 0, 0, 0, 0, 0])
test_timeseries = [test_time, test_trigger]
test_freq = [42.0, 3.14]
test_chn_name = ['time', 'trigger']
test_units = ['s', 's']
test_chtrig = 1
blueprint_in = po.BlueprintInput(test_timeseries, test_freq, test_chn_name,
test_units, test_chtrig)
# Test check_trigger_amount with time resampling
blueprint_in.check_trigger_amount(thr=0.9, num_timepoints_expected=1)
assert blueprint_in.num_timepoints_found == 1
assert blueprint_in.time_offset == 1
test_offset_time = test_time - 1
assert np.array_equal(blueprint_in.timeseries[0], test_offset_time)
