def test_FadingTemporal():
model = FadingTemporal()
# User can set their own params:
model.dt = 0.1
npt.assert_equal(model.dt, 0.1)
model.build(dt=1e-4)
npt.assert_equal(model.dt, 1e-4)
# User cannot add more model parameters:
with pytest.raises(FreezeError):
model.rho = 100
# Nothing in, None out:
npt.assert_equal(model.predict_percept(None), None)
# Zero in = zero out:
stim = BiphasicPulse(0, 1)
percept = model.predict_percept(stim, t_percept=[0, 1, 2])
npt.assert_equal(isinstance(percept, Percept), True)
npt.assert_equal(percept.shape, (1, 1, 3))
npt.assert_almost_equal(percept.data, 0)
# Can't request the same time more than once (this would break the Cython
# loop, because `idx_frame` is incremented after a write; also doesn't
# make much sense):
with pytest.raises(ValueError):
stim = Stimulus(np.ones((1, 100)))
model.predict_percept(stim, t_percept=[0.2, 0.2])
# Simple decay for single cathodic pulse:
model = FadingTemporal(tau=1).build()
stim = MonophasicPulse(-1, 1, stim_dur=10)
percept = model.predict_percept(stim, np.arange(stim.duration))
npt.assert_almost_equal(percept.data.ravel()[:3], [0, 0.633, 0.232],
decimal=3)
npt.assert_almost_equal(percept.data.ravel()[-1], 0, decimal=3)
# But all zeros for anodic pulse:
stim = MonophasicPulse(1, 1, stim_dur=10)
percept = model.predict_percept(stim, np.arange(stim.duration))
npt.assert_almost_equal(percept.data, 0)
# tau cannot be negative:
with pytest.raises(ValueError):
FadingTemporal(tau=-1).build()
def test_MonophasicPulse(amp, delay_dur):
phase_dur = 3.456
# Basic usage:
pulse = MonophasicPulse(amp, phase_dur, delay_dur=delay_dur)
npt.assert_almost_equal(pulse[0, 0], 0)
npt.assert_almost_equal(pulse[0, delay_dur + phase_dur / 2.0], amp)
npt.assert_almost_equal(pulse.time[0], 0)
npt.assert_almost_equal(pulse.time[-1], phase_dur + delay_dur)
npt.assert_equal(pulse.cathodic, amp <= 0)
npt.assert_equal(pulse.charge_balanced, False)
# Custom stim dur:
pulse = MonophasicPulse(amp, phase_dur, delay_dur=delay_dur, stim_dur=100)
npt.assert_almost_equal(pulse[0, 0], 0)
npt.assert_almost_equal(pulse[0, delay_dur + phase_dur / 2.0], amp)
npt.assert_almost_equal(pulse.time[0], 0)
npt.assert_almost_equal(pulse.time[-1], 100)
# Zero amplitude:
pulse = MonophasicPulse(0, phase_dur, delay_dur=delay_dur, electrode='A1')
npt.assert_almost_equal(pulse.data, 0)
npt.assert_almost_equal(pulse.time[0], 0)
npt.assert_almost_equal(pulse.time[-1], phase_dur + delay_dur)
npt.assert_equal(pulse.charge_balanced, True)
npt.assert_equal(pulse.electrodes, 'A1')
# You can wrap a pulse in a Stimulus to overwrite attributes:
stim = Stimulus(pulse, electrodes='AA1')
npt.assert_equal(stim.electrodes, 'AA1')
# Or concatenate:
stim = Stimulus([pulse, pulse])
npt.assert_equal(stim.shape[0], 2)
npt.assert_almost_equal(stim.data[0, :], stim.data[1, :])
npt.assert_almost_equal(stim.time, pulse.time)
npt.assert_equal(stim.electrodes, ['A1', 1])
# Concatenate and rename:
stim = Stimulus([pulse, pulse], electrodes=['C1', 'D2'])
npt.assert_equal(stim.electrodes, ['C1', 'D2'])
# Invalid calls:
with pytest.raises(ValueError):
MonophasicPulse(amp, 0)
with pytest.raises(ValueError):
MonophasicPulse(amp, phase_dur, delay_dur=-1)
with pytest.raises(ValueError):
MonophasicPulse(amp, phase_dur, delay_dur=delay_dur, stim_dur=1)
with pytest.raises(ValueError):
MonophasicPulse(amp,
phase_dur,
delay_dur=delay_dur,
electrode=['A1', 'B2'])
# They are pseudo-monophasic pulse pairs, where the anodic phases were # presented 20 ms after the end of the second cathodic pulse. # # The initial cathodic pulse always has a fixed amplitude of 50% of the single # pulse threshold: from pulse2percept.stimuli import MonophasicPulse # Phase duration: phase_dur = 0.075 # Single-pulse threshold determines this current: amp_th = 20 # Cathodic phase of the standard pulse:: cath_standard = MonophasicPulse(-0.5 * amp_th, phase_dur) ############################################################################### # The delay between the start of the conditioning pulse and the start of the # test pulse was varied systematically (between 0.15 and 12 ms). # The amplitude of the second pulse was varied to determine thresholds. # Delay was varied between 0.15 and 12 ms: delay_dur = 12 # Vary this current to determine threshold: amp_test = 45 # Cathodic phase of the test pulse (delivered after a delay): cath_test = MonophasicPulse(-amp_test, phase_dur, delay_dur=delay_dur)
def test_pulse_append(amp, phase_dur):
# Build a biphasic pulse from two monophasic pulses:
mono = MonophasicPulse(amp, phase_dur)
bi = BiphasicPulse(amp, phase_dur)
npt.assert_equal(mono.append(-mono) == bi, True)
def test_AsymmetricBiphasicPulse(amp1, amp2, interphase_dur, delay_dur,
cathodic_first):
phase_dur1 = 2.1
phase_dur2 = 4.87
mid_first_pulse = delay_dur + phase_dur1 / 2.0
mid_interphase = delay_dur + phase_dur1 + interphase_dur / 2.0
mid_second_pulse = delay_dur + phase_dur1 + interphase_dur + phase_dur2 / 2
first_amp = -np.abs(amp1) if cathodic_first else np.abs(amp1)
second_amp = np.abs(amp2) if cathodic_first else -np.abs(amp2)
min_dur = delay_dur + phase_dur1 + interphase_dur + phase_dur2
# Basic usage:
pulse = AsymmetricBiphasicPulse(amp1,
amp2,
phase_dur1,
phase_dur2,
interphase_dur=interphase_dur,
delay_dur=delay_dur,
cathodic_first=cathodic_first)
npt.assert_almost_equal(pulse[0, 0], 0)
npt.assert_almost_equal(pulse[0, mid_first_pulse], first_amp)
npt.assert_almost_equal(pulse[0, mid_interphase], 0)
npt.assert_almost_equal(pulse[0, mid_second_pulse], second_amp)
npt.assert_almost_equal(pulse.time[0], 0)
npt.assert_almost_equal(pulse.time[-1], min_dur, decimal=3)
npt.assert_equal(pulse.cathodic_first, cathodic_first)
npt.assert_equal(pulse.is_charge_balanced,
np.isclose(np.trapz(pulse.data, pulse.time)[0], 0))
# Custom stim dur:
pulse = AsymmetricBiphasicPulse(amp1,
amp2,
phase_dur1,
phase_dur2,
interphase_dur=interphase_dur,
delay_dur=delay_dur,
cathodic_first=cathodic_first,
stim_dur=100,
electrode='A1')
npt.assert_almost_equal(pulse[0, 0], 0)
npt.assert_almost_equal(pulse[0, mid_first_pulse], first_amp)
npt.assert_almost_equal(pulse[0, mid_interphase], 0)
npt.assert_almost_equal(pulse[0, mid_second_pulse], second_amp)
npt.assert_almost_equal(pulse.time[0], 0)
npt.assert_almost_equal(pulse.time[-1], 100)
npt.assert_equal(pulse.electrodes, 'A1')
# Exact stim dur:
stim_dur = delay_dur + phase_dur1 + interphase_dur + phase_dur2
pulse = AsymmetricBiphasicPulse(amp1,
amp2,
phase_dur1,
phase_dur2,
interphase_dur=interphase_dur,
delay_dur=delay_dur,
cathodic_first=cathodic_first,
stim_dur=stim_dur,
electrode='A1')
npt.assert_almost_equal(pulse.time[0], 0)
npt.assert_almost_equal(pulse.time[-1], stim_dur, decimal=6)
# Zero amplitude:
pulse = AsymmetricBiphasicPulse(0,
0,
phase_dur1,
phase_dur2,
interphase_dur=interphase_dur,
delay_dur=delay_dur,
cathodic_first=cathodic_first)
npt.assert_almost_equal(pulse.data, 0)
npt.assert_almost_equal(pulse.time[0], 0)
npt.assert_almost_equal(pulse.time[-1], min_dur, decimal=3)
npt.assert_equal(pulse.is_charge_balanced,
np.isclose(np.trapz(pulse.data, pulse.time)[0], 0))
# If both phases have the same values, it's basically a symmetric biphasic
# pulse:
abp = AsymmetricBiphasicPulse(amp1,
amp1,
phase_dur1,
phase_dur1,
interphase_dur=interphase_dur,
delay_dur=delay_dur,
cathodic_first=cathodic_first)
bp = BiphasicPulse(amp1,
phase_dur1,
interphase_dur=interphase_dur,
delay_dur=delay_dur,
cathodic_first=cathodic_first)
bp_min_dur = phase_dur1 * 2 + interphase_dur + delay_dur
npt.assert_almost_equal(abp[:, np.linspace(0, bp_min_dur, num=5)],
bp[:, np.linspace(0, bp_min_dur, num=5)])
npt.assert_equal(abp.cathodic_first, bp.cathodic_first)
# If one phase is zero, it's basically a monophasic pulse:
abp = AsymmetricBiphasicPulse(amp1,
0,
phase_dur1,
phase_dur2,
interphase_dur=interphase_dur,
delay_dur=delay_dur,
cathodic_first=cathodic_first)
mono = MonophasicPulse(first_amp,
phase_dur1,
delay_dur=delay_dur,
stim_dur=min_dur)
npt.assert_almost_equal(abp[:, np.linspace(0, min_dur, num=5)],
mono[:, np.linspace(0, min_dur, num=5)])
npt.assert_equal(abp.cathodic_first, mono.cathodic)
# You can wrap a pulse in a Stimulus to overwrite attributes:
stim = Stimulus(pulse, electrodes='AA1')
npt.assert_equal(stim.electrodes, 'AA1')
# Or concatenate:
stim = Stimulus([pulse, pulse])
npt.assert_equal(stim.shape[0], 2)
npt.assert_almost_equal(stim.data[0, :], stim.data[1, :])
npt.assert_almost_equal(stim.time, pulse.time, decimal=2)
npt.assert_equal(stim.electrodes, [0, 1])
# Concatenate and rename:
stim = Stimulus([pulse, pulse], electrodes=['C1', 'D2'])
npt.assert_equal(stim.electrodes, ['C1', 'D2'])
# Invalid calls:
with pytest.raises(ValueError):
AsymmetricBiphasicPulse(amp1, amp2, 0, phase_dur2)
with pytest.raises(ValueError):
AsymmetricBiphasicPulse(amp1, amp2, phase_dur1, 0)
with pytest.raises(ValueError):
AsymmetricBiphasicPulse(amp1,
amp2,
phase_dur1,
phase_dur2,
interphase_dur=-1)
with pytest.raises(ValueError):
AsymmetricBiphasicPulse(amp1,
amp2,
phase_dur1,
phase_dur2,
interphase_dur=interphase_dur,
delay_dur=-1)
with pytest.raises(ValueError):
AsymmetricBiphasicPulse(amp1,
amp2,
phase_dur1,
phase_dur2,
interphase_dur=interphase_dur,
delay_dur=delay_dur,
stim_dur=1)
with pytest.raises(ValueError):
AsymmetricBiphasicPulse(amp1,
amp2,
phase_dur1,
phase_dur2,
interphase_dur=interphase_dur,
delay_dur=delay_dur,
electrode=['A1', 'B2'])
# They are pseudo-monophasic pulse pairs, where the anodic phases were # presented 20 ms after the end of the second cathodic pulse. # # The initial cathodic pulse always has a fixed amplitude of 50% of the single # pulse threshold: from pulse2percept.stimuli import MonophasicPulse # Phase duration: phase_dur = 0.075 # Single-pulse threshold determines this current: amp_th = 20 # Cathodic phase of the standard pulse:: cath_stand = MonophasicPulse(-0.5 * amp_th, phase_dur) ############################################################################### # The delay between the start of the conditioning pulse and the start of the # test pulse was varied systematically (between 0.15 and 12 ms). # The amplitude of the second pulse was varied to determine thresholds. # Delay was varied between 0.15 and 12 ms: delay_dur = 12 # Vary this current to determine threshold: amp_test = 45 # Cathodic phase of the test pulse (delivered after a delay): cath_test = MonophasicPulse(-amp_test, phase_dur, delay_dur=delay_dur)
pulse_type = 'anodic' # anodic: positive amplitude, cathodic: negative
pulse_dur = 4.6 / 1000 # pulse duration in seconds
delay_dur = 10.0 / 1000 # pulse delivered after delay in seconds
stim_dur = 0.5 # stimulus duration in seconds (pulse padded with zeros)
time_step = 0.1 / 1000 # temporal sampling step in seconds
##############################################################################
# The sampling step ``time_step`` defines at which temporal resolution the
# stimulus is resolved. In the above example, the time step is 0.1 ms.
#
# By calling Stimulus with a ``MonophasicPulse`` source, we can generate a
# single pulse:
monophasic_stim = Stimulus(
MonophasicPulse(ptype=pulse_type,
pdur=pulse_dur,
delay_dur=delay_dur,
stim_dur=stim_dur,
tsample=time_step))
print(monophasic_stim)
##############################################################################
# Here, ``data`` is a 2D NumPy array where rows are electrodes and columns are
# the points in time. Since we did not specify any electrode names in
# ``MonophasicPulse``, the number of electrodes is inferred from the input
# source type. There is only one row in the above example, denoting a single
# electrode.
#
# By default, the :py:class:`~pulse2percept.stimuli.MonophasicPulse` object
# automatically assumes a current amplitude of 1 uA.
##############################################################################
------------------
A :py:class:`~pulse2percept.stimuli.MonophasicPulse` has a single phase and can
be either anodic (by definition: has a positive current amplitude) or cathodic
(negative current amplitude).
Monophasic pulses require an amplitude (in uA) and a phase duration (in ms).
You can also specify the total stimulus duration: zeros will be inserted after
the pulse up to the desired duration:
"""
# sphinx_gallery_thumbnail_number = 6
from pulse2percept.stimuli import MonophasicPulse
mono = MonophasicPulse(-20, 1, stim_dur=50)
mono.plot()
##############################################################################
# .. note ::
#
# The sign of ``amp`` will determine whether the pulse is cathodic
# (negative current) or anodic (positive current).
#
# A (symmetric) biphasic pulse
# ----------------------------
#
# A :py:class:`~pulse2percept.stimuli.BiphasicPulse` consists of a cathodic and
# an anodic phase, optionally separated by an interphase gap.
# Both cathodic and anodic phases will have the same duration ("symmetric").
#
