def test_predict_batched(engine):
if not has_jax:
pytest.skip("Jax not installed")
# Allows mix of valid Stimulus types
stims = [{
'A5': BiphasicPulseTrain(25, 4, 0.45),
'C7': BiphasicPulseTrain(50, 2.5, 0.75)
}, {
'B4': BiphasicPulseTrain(3, 1, 0.32)
},
Stimulus({'F3': BiphasicPulseTrain(12, 3, 1.2)})]
implant = ArgusII()
model = BiphasicAxonMapModel(engine=engine, xystep=2)
model.build()
# Import error if we dont have jax
if engine != 'jax':
with pytest.raises(ImportError):
model.predict_percept_batched(implant, stims)
return
percepts_batched = model.predict_percept_batched(implant, stims)
percepts_serial = []
for stim in stims:
implant.stim = stim
percepts_serial.append(model.predict_percept(implant))
npt.assert_equal(len(percepts_serial), len(percepts_batched))
for p1, p2 in zip(percepts_batched, percepts_serial):
npt.assert_almost_equal(p1.data, p2.data)
def test_predict_spatial_jax():
# ensure jax predict spatial is equal to normal
if not has_jax:
pytest.skip("Jax not installed")
model1 = BiphasicAxonMapModel(engine='jax', xystep=2)
model2 = BiphasicAxonMapModel(engine='cython', xystep=2)
model1.build()
model2.build()
implant = ArgusII()
implant.stim = {
'A5': BiphasicPulseTrain(25, 4, 0.45),
'C7': BiphasicPulseTrain(50, 2.5, 0.75)
}
p1 = model1.predict_percept(implant)
p2 = model2.predict_percept(implant)
npt.assert_almost_equal(p1.data, p2.data, decimal=4)
# test changing model parameters, make sure jax is clearing cache on build
model1.axlambda = 800
model2.axlambda = 800
model1.rho = 50
model2.rho = 50
model1.build()
model2.build()
p1 = model1.predict_percept(implant)
p2 = model2.predict_percept(implant)
npt.assert_almost_equal(p1.data, p2.data, decimal=4)
def test_BiphasicTripletTrain(amp, interphase_dur, interpulse_dur, delay_dur,
cathodic_first):
freq = 23.456
stim_dur = 657.456
phase_dur = 2
window_dur = 1000.0 / freq
n_pulses = int(freq * stim_dur / 1000.0)
mid_first_pulse = delay_dur + phase_dur / 2.0
mid_interphase = delay_dur + phase_dur + interphase_dur / 2.0
mid_second_pulse = delay_dur + interphase_dur + 1.5 * phase_dur
mid_interpulse = delay_dur + 2.0*phase_dur + \
interphase_dur + interpulse_dur / 2.0
first_amp = -np.abs(amp) if cathodic_first else np.abs(amp)
second_amp = -first_amp
# Basic usage:
pt = BiphasicTripletTrain(freq,
amp,
phase_dur,
interphase_dur=interphase_dur,
interpulse_dur=interpulse_dur,
delay_dur=delay_dur,
stim_dur=stim_dur,
cathodic_first=cathodic_first)
for i in range(n_pulses):
t_win = i * window_dur
npt.assert_almost_equal(pt[0, np.floor(t_win)], 0)
npt.assert_almost_equal(pt[0, t_win + mid_first_pulse], first_amp)
if interphase_dur > 0:
npt.assert_almost_equal(pt[0, t_win + mid_interphase], 0)
npt.assert_almost_equal(pt[0, t_win + mid_second_pulse], second_amp)
if interpulse_dur > 0:
npt.assert_almost_equal(pt[0, mid_interpulse], 0)
npt.assert_almost_equal(pt.time[0], 0)
npt.assert_almost_equal(pt.time[-1], stim_dur, decimal=2)
npt.assert_equal(pt.cathodic_first, cathodic_first)
npt.assert_equal(pt.is_charge_balanced,
np.isclose(np.trapz(pt.data, pt.time)[0], 0, atol=1e-5))
# Zero frequency:
pt = BiphasicPulseTrain(0, amp, phase_dur)
npt.assert_almost_equal(pt.time, [0, 1000])
npt.assert_almost_equal(pt.data, 0)
# Zero amp:
pt = BiphasicPulseTrain(freq, 0, phase_dur)
npt.assert_almost_equal(pt.data, 0)
# Pulse can fill the entire window (no "unique time points" error):
pt = BiphasicTripletTrain(10, 20, 100 / 6.001, stim_dur=500)
npt.assert_almost_equal(pt.time[-1], 500)
npt.assert_equal(np.round(np.trapz(np.abs(pt.data), pt.time)[0]), 9998)
# Specific number of pulses
for n_pulses in [2, 4, 5]:
pt = BiphasicPulseTrain(500, 30, 0.05, n_pulses=n_pulses, stim_dur=19)
npt.assert_almost_equal(np.sum(np.isclose(pt.data, 30)), 2 * n_pulses)
npt.assert_almost_equal(pt.time[-1], 19)
def test_Nanduri2012Temporal():
model = Nanduri2012Temporal()
# 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(ArgusI().stim), None)
# Zero in = zero out:
implant = ArgusI(stim=np.zeros((16, 100)))
percept = model.predict_percept(implant.stim, t_percept=[0, 1, 2])
npt.assert_equal(isinstance(percept, Percept), True)
npt.assert_equal(percept.shape, (16, 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):
implant.stim = np.ones((16, 100))
model.predict_percept(implant.stim, t_percept=[0.2, 0.2])
# Brightness scales differently with amplitude vs frequency:
model = Nanduri2012Temporal(dt=5e-3)
model.build()
sdur = 1000.0 # stimulus duration (ms)
pdur = 0.45 # (ms)
t_percept = np.arange(0, sdur, 5)
implant = ProsthesisSystem(ElectrodeArray(DiskElectrode(0, 0, 0, 260)))
bright_amp = []
for amp in np.linspace(0, 50, 5):
# implant.stim = PulseTrain(model.dt, freq=20, amp=amp, dur=sdur,
# pulse_dur=pdur, interphase_dur=pdur)
implant.stim = BiphasicPulseTrain(20, amp, pdur, interphase_dur=pdur,
stim_dur=sdur)
percept = model.predict_percept(implant.stim, t_percept=t_percept)
bright_amp.append(percept.data.max())
bright_amp_ref = [0.0, 0.00890, 0.0657, 0.1500, 0.1691]
npt.assert_almost_equal(bright_amp, bright_amp_ref, decimal=3)
bright_freq = []
for freq in np.linspace(0, 100, 5):
# implant.stim = PulseTrain(model.dt, freq=freq, amp=20, dur=sdur,
# pulse_dur=pdur, interphase_dur=pdur)
implant.stim = BiphasicPulseTrain(freq, 20, pdur, interphase_dur=pdur,
stim_dur=sdur)
percept = model.predict_percept(implant.stim, t_percept=t_percept)
bright_freq.append(percept.data.max())
bright_freq_ref = [0.0, 0.0394, 0.0741, 0.1073, 0.1385]
npt.assert_almost_equal(bright_freq, bright_freq_ref, decimal=3)
def test_BiphasicTripletTrain(amp, interphase_dur, delay_dur, cathodic_first):
freq = 23.456
stim_dur = 657.456
phase_dur = 2
window_dur = 1000.0 / freq
n_pulses = int(freq * stim_dur / 1000.0)
dt = 1e-6
mid_first_pulse = delay_dur + phase_dur / 2.0
mid_interphase = delay_dur + phase_dur + interphase_dur / 2.0
mid_second_pulse = delay_dur + interphase_dur + 1.5 * phase_dur
first_amp = -np.abs(amp) if cathodic_first else np.abs(amp)
second_amp = -first_amp
# Basic usage:
pt = BiphasicTripletTrain(freq,
amp,
phase_dur,
interphase_dur=interphase_dur,
delay_dur=delay_dur,
stim_dur=stim_dur,
cathodic_first=cathodic_first,
dt=dt)
for i in range(n_pulses):
t_win = i * window_dur
npt.assert_almost_equal(pt[0, t_win], 0)
npt.assert_almost_equal(pt[0, t_win + mid_first_pulse], first_amp)
if interphase_dur > 0:
npt.assert_almost_equal(pt[0, t_win + mid_interphase], 0)
npt.assert_almost_equal(pt[0, t_win + mid_second_pulse], second_amp)
npt.assert_almost_equal(pt.time[0], 0)
npt.assert_almost_equal(pt.time[-1], stim_dur, decimal=2)
npt.assert_equal(pt.cathodic_first, cathodic_first)
npt.assert_equal(pt.charge_balanced,
np.isclose(np.trapz(pt.data, pt.time)[0], 0, atol=1e-5))
# Zero frequency:
pt = BiphasicPulseTrain(0, amp, phase_dur)
npt.assert_almost_equal(pt.time, [0, 1000])
npt.assert_almost_equal(pt.data, 0)
# Zero amp:
pt = BiphasicPulseTrain(freq, 0, phase_dur)
npt.assert_almost_equal(pt.data, 0)
# Specific number of pulses
for n_pulses in [2, 4, 5]:
pt = BiphasicPulseTrain(500,
30,
0.05,
n_pulses=n_pulses,
stim_dur=19,
dt=0.05)
npt.assert_almost_equal(np.sum(np.isclose(pt.data, 30)), n_pulses)
npt.assert_almost_equal(pt.time[-1], 19)
def test_merge_time_axes_merge_tolerance():
# Test issue where not enough unique points were collected
# Leading to interpolation to corrupt stimuli data.
# See: https://github.com/pulse2percept/pulse2percept/issues/392
a = BiphasicPulseTrain(20, 1, 0.45)
b = BiphasicPulseTrain(30, 1, 0.45)
stim = Stimulus({"A2": a, "A10": b})
unique_points = np.unique(stim.data)
# Assert no value goes close to 1/3 or -1/3, i.e. a corrupted data point
npt.assert_equal(np.isclose(1 / 3, unique_points, atol=0.1).any(), False)
npt.assert_equal(np.isclose(-1 / 3, unique_points, atol=0.1).any(), False)
def test_Horsager2009Model():
model = Horsager2009Model()
npt.assert_equal(hasattr(model, 'has_space'), True)
npt.assert_equal(model.has_space, False)
npt.assert_equal(hasattr(model, 'has_time'), True)
npt.assert_equal(model.has_time, True)
# User can set `dt`:
model.temporal.dt = 1e-5
npt.assert_almost_equal(model.dt, 1e-5)
npt.assert_almost_equal(model.temporal.dt, 1e-5)
model.build(dt=3e-4)
npt.assert_almost_equal(model.dt, 3e-4)
npt.assert_almost_equal(model.temporal.dt, 3e-4)
# User cannot add more model parameters:
with pytest.raises(FreezeError):
model.rho = 100
# Model and TemporalModel give the same result
for amp, freq in zip([136.02, 120.35, 57.71], [5, 15, 225]):
stim = BiphasicPulseTrain(freq, amp, 0.075, interphase_dur=0.075,
stim_dur=200, cathodic_first=True)
model1 = Horsager2009Model().build()
model2 = Horsager2009Temporal().build()
implant = ProsthesisSystem(PointSource(0, 0, 0), stim=stim)
npt.assert_almost_equal(model1.predict_percept(implant).data,
model2.predict_percept(stim).data)
def test_metadata():
stim = BiphasicPulseTrain(10, 10, 1, metadata='userdata')
npt.assert_equal(stim.metadata['user'], 'userdata')
npt.assert_equal(stim.metadata['freq'], 10)
npt.assert_equal(stim.metadata['amp'], 10)
npt.assert_equal(stim.metadata['phase_dur'], 1)
npt.assert_equal(stim.metadata['delay_dur'], 0)
stim = Stimulus(
{
'A2': BiphasicPulseTrain(10, 10, 1, metadata='userdataA2'),
'B1': BiphasicPulseTrain(11, 9, 2, metadata='userdataB1'),
'C3': BiphasicPulseTrain(12, 8, 3, metadata='userdataC3')
},
metadata='stimulus_userdata')
npt.assert_equal(stim.metadata['user'], 'stimulus_userdata')
npt.assert_equal(stim.metadata['electrodes']['A2']['type'],
BiphasicPulseTrain)
npt.assert_equal(stim.metadata['electrodes']['B1']['metadata']['freq'], 11)
npt.assert_equal(stim.metadata['electrodes']['C3']['metadata']['user'],
'userdataC3')
def test_Horsager2009Temporal():
model = Horsager2009Temporal()
# 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:
implant = ProsthesisSystem(PointSource(0, 0, 0))
npt.assert_equal(model.predict_percept(implant.stim), None)
# Zero in = zero out:
implant.stim = np.zeros((1, 6))
percept = model.predict_percept(implant.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):
implant.stim = np.ones((1, 100))
model.predict_percept(implant.stim, t_percept=[0.2, 0.2])
# Single-pulse brightness from Fig.3:
model = Horsager2009Temporal().build()
for amp, pdur in zip([188.077, 89.74, 10.55], [0.075, 0.15, 4.0]):
stim = BiphasicPulse(amp,
pdur,
interphase_dur=pdur,
stim_dur=200,
cathodic_first=True)
t_percept = np.arange(0, stim.time[-1] + model.dt / 2, model.dt)
percept = model.predict_percept(stim, t_percept=t_percept)
npt.assert_almost_equal(percept.data.max(), 110.3, decimal=2)
# Fixed-duration brightness from Fig.4:
model = Horsager2009Temporal().build()
for amp, freq in zip([136.02, 120.35, 57.71], [5, 15, 225]):
stim = BiphasicPulseTrain(freq,
amp,
0.075,
interphase_dur=0.075,
stim_dur=200,
cathodic_first=True)
t_percept = np.arange(0, stim.time[-1] + model.dt / 2, model.dt)
percept = model.predict_percept(stim, t_percept=t_percept)
npt.assert_almost_equal(percept.data.max(), 36.3, decimal=2)
Generating a pulse train
------------------------
The first step is to build a pulse train using the
:py:class:`~pulse2percept.stimuli.PulseTrain` class.
We want to generate a 20Hz pulse train (0.45ms pulse duration, cathodic-first)
at 30uA that lasts for a second:
"""
# sphinx_gallery_thumbnail_number = 4
from pulse2percept.stimuli import BiphasicPulseTrain, Stimulus
tsample = 0.005 # sampling time step (ms)
phase_dur = 0.45 # duration of the cathodic/anodic phase (ms)
stim_dur = 1000 # stimulus duration (ms)
amp_th = 30 # threshold current (uA)
stim = BiphasicPulseTrain(20, amp_th, phase_dur, interphase_dur=phase_dur,
stim_dur=stim_dur)
# Configure Matplotlib:
import matplotlib.pyplot as plt
plt.style.use('ggplot')
from matplotlib import rc
rc('font', size=12)
# Plot the stimulus in the range t=[0, 60] ms:
stim.plot(time=(0, 60))
###############################################################################
# Creating an implant
# -------------------
#
# Before we can run the Nanduri model, we need to create a retinal implant to
def test_Nanduri2012Model_predict_percept():
# Nothing in = nothing out:
model = Nanduri2012Model(xrange=(0, 0), yrange=(0, 0), engine='serial')
model.build()
implant = ArgusI(stim=None)
npt.assert_equal(model.predict_percept(implant), None)
implant.stim = np.zeros(16)
npt.assert_almost_equal(model.predict_percept(implant).data, 0)
# Single-pixel model same as TemporalModel:
implant = ProsthesisSystem(DiskElectrode(0, 0, 0, 100))
# implant.stim = PulseTrain(5e-6)
implant.stim = BiphasicPulseTrain(20, 20, 0.45, interphase_dur=0.45)
t_percept = [0, 0.01, 1.0]
percept = model.predict_percept(implant, t_percept=t_percept)
temp = Nanduri2012Temporal().build()
temp = temp.predict_percept(implant.stim, t_percept=t_percept)
npt.assert_almost_equal(percept.data, temp.data, decimal=4)
# Only works for DiskElectrode arrays:
with pytest.raises(TypeError):
implant = ProsthesisSystem(ElectrodeArray(PointSource(0, 0, 0)))
implant.stim = 1
model.predict_percept(implant)
with pytest.raises(TypeError):
implant = ProsthesisSystem(
ElectrodeArray(
[DiskElectrode(0, 0, 0, 100),
PointSource(100, 100, 0)]))
implant.stim = [1, 1]
model.predict_percept(implant)
# Requested times must be multiples of model.dt:
implant = ProsthesisSystem(ElectrodeArray(DiskElectrode(0, 0, 0, 260)))
# implant.stim = PulseTrain(tsample)
implant.stim = BiphasicPulseTrain(20, 20, 0.45)
model.temporal.dt = 0.1
with pytest.raises(ValueError):
model.predict_percept(implant, t_percept=[0.01])
with pytest.raises(ValueError):
model.predict_percept(implant, t_percept=[0.01, 1.0])
with pytest.raises(ValueError):
model.predict_percept(implant, t_percept=np.arange(0, 0.5, 0.101))
model.predict_percept(implant, t_percept=np.arange(0, 0.5, 1.0000001))
# 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):
model.predict_percept(implant, t_percept=[0.2, 0.2])
# It's ok to extrapolate beyond `stim` if the `extrapolate` flag is set:
model.temporal.dt = 1e-2
npt.assert_almost_equal(
model.predict_percept(implant, t_percept=10000).data, 0)
# Output shape must be determined by t_percept:
npt.assert_equal(
model.predict_percept(implant, t_percept=0).shape, (1, 1, 1))
npt.assert_equal(
model.predict_percept(implant, t_percept=[0, 1]).shape, (1, 1, 2))
# Brightness vs. size (use values from Nanduri paper):
model = Nanduri2012Model(xystep=0.5, xrange=(-4, 4), yrange=(-4, 4))
model.build()
implant = ProsthesisSystem(ElectrodeArray(DiskElectrode(0, 0, 0, 260)))
amp_th = 30
bright_th = 0.107
stim_dur = 1000.0
pdur = 0.45
t_percept = np.arange(0, stim_dur, 5)
amp_factors = [1, 6]
frames_amp = []
for amp_f in amp_factors:
implant.stim = BiphasicPulseTrain(20,
amp_f * amp_th,
pdur,
interphase_dur=pdur,
stim_dur=stim_dur)
percept = model.predict_percept(implant, t_percept=t_percept)
idx_frame = np.argmax(np.max(percept.data, axis=(0, 1)))
brightest_frame = percept.data[..., idx_frame]
frames_amp.append(brightest_frame)
npt.assert_equal([np.sum(f > bright_th) for f in frames_amp], [0, 161])
freqs = [20, 120]
frames_freq = []
for freq in freqs:
implant.stim = BiphasicPulseTrain(freq,
1.25 * amp_th,
pdur,
interphase_dur=pdur,
stim_dur=stim_dur)
percept = model.predict_percept(implant, t_percept=t_percept)
idx_frame = np.argmax(np.max(percept.data, axis=(0, 1)))
brightest_frame = percept.data[..., idx_frame]
frames_freq.append(brightest_frame)
npt.assert_equal([np.sum(f > bright_th) for f in frames_freq], [21, 49])
# The same procedure can be repeated for
# :py:class:`~pulse2percept.stimuli.BiphasicPulseTrain` stimuli to reproduce
# Fig. 4.
from pulse2percept.stimuli import BiphasicPulseTrain
# Load the data:
fixed_dur = data[(data.stim_type == 'fixed_duration') & (data.subject == 'S05')
& (data.electrode == 'C3') & (data.pulse_dur == 0.075)]
# Find the threshold:
amp_th = []
for _, row in fixed_dur.iterrows():
stim = BiphasicPulseTrain(row['stim_freq'],
1,
row['pulse_dur'],
interphase_dur=row['interphase_dur'],
stim_dur=row['stim_dur'],
cathodic_first=True)
amp_th.append(
model.find_threshold(stim,
row['theta'],
amp_range=(0, 300),
amp_tol=1,
bright_tol=0.1))
plt.semilogx(fixed_dur.stim_freq, fixed_dur.stim_amp, 's', label='data')
plt.semilogx(fixed_dur.stim_freq, amp_th, 'k-', linewidth=3, label='model')
plt.xticks([5, 15, 75, 225])
plt.xlabel('frequency (Hz)')
plt.ylabel('threshold current (uA)')
plt.legend()
A series of biphasic pulses can be created with the
:py:class:`~pulse2percept.stimuli.BiphasicPulseTrain` class.
You have the same options as when setting up a single
:py:class:`~pulse2percept.stimuli.BiphasicPulse`, in addition to specifying
a pulse train frequency (``freq``) and total stimulus duration (``stim_dur``).
For example, a 20 Hz pulse train lasting 200 ms and made from anodic-first
biphasic pulses (30 uA, 2 ms pulse duration, no interphase gap) can be
created as follows:
"""
# sphinx_gallery_thumbnail_number = 4
from pulse2percept.stimuli import BiphasicPulseTrain
pt = BiphasicPulseTrain(20, 30, 2, stim_dur=200, cathodic_first=False)
pt.plot()
###############################################################################
# You can also limit the number of pulses in the train, but still make the
# stimulus last 200 ms:
pt = BiphasicPulseTrain(20,
30,
2,
n_pulses=3,
stim_dur=200,
cathodic_first=False)
pt.plot()
###############################################################################
def test_biphasicAxonMapSpatial(engine):
# Lambda cannot be too small:
with pytest.raises(ValueError):
BiphasicAxonMapSpatial(axlambda=9).build()
model = BiphasicAxonMapModel(engine=engine, xystep=2).build()
# Jax not implemented yet
if engine == 'jax':
with pytest.raises(NotImplementedError):
implant = ArgusII()
implant.stim = Stimulus({'A5': BiphasicPulseTrain(20, 1, 0.45)})
percept = model.predict_percept(implant)
return
# Only accepts biphasic pulse trains with no delay dur
implant = ArgusI(stim=np.ones(16))
with pytest.raises(TypeError):
model.predict_percept(implant)
# Nothing in, None out:
npt.assert_equal(model.predict_percept(ArgusI()), None)
# Zero in = zero out:
implant = ArgusI(stim=np.zeros(16))
percept = model.predict_percept(implant)
npt.assert_equal(isinstance(percept, Percept), True)
npt.assert_equal(percept.shape, list(model.grid.x.shape) + [1])
npt.assert_almost_equal(percept.data, 0)
npt.assert_equal(percept.time, None)
# Should be equal to axon map model if effects models return 1
model = BiphasicAxonMapSpatial(engine=engine, xystep=2)
def bright_model(freq, amp, pdur):
return 1
def size_model(freq, amp, pdur):
return 1
def streak_model(freq, amp, pdur):
return 1
model.bright_model = bright_model
model.size_model = size_model
model.streak_model = streak_model
model.build()
axon_map = AxonMapSpatial(xystep=2).build()
implant = ArgusII()
implant.stim = Stimulus({'A5': BiphasicPulseTrain(20, 1, 0.45)})
percept = model.predict_percept(implant)
percept_axon = axon_map.predict_percept(implant)
npt.assert_almost_equal(percept.data[:, :, 0],
percept_axon.get_brightest_frame())
# Effect models must be callable
model = BiphasicAxonMapSpatial(engine=engine, xystep=2)
model.bright_model = 1.0
with pytest.raises(TypeError):
model.build()
# If t_percept is not specified, there should only be one frame
model = BiphasicAxonMapSpatial(engine=engine, xystep=2)
model.build()
implant = ArgusII()
implant.stim = Stimulus({'A5': BiphasicPulseTrain(20, 1, 0.45)})
percept = model.predict_percept(implant)
npt.assert_equal(percept.time is None, True)
# If t_percept is specified, only first frame should have data
# and the rest should be empty
percept = model.predict_percept(implant, t_percept=[0, 1, 2, 5, 10])
npt.assert_equal(len(percept.time), 5)
npt.assert_equal(np.any(percept.data[:, :, 0]), True)
npt.assert_equal(np.any(percept.data[:, :, 1:]), False)
# Test that default models give expected values
model = BiphasicAxonMapSpatial(engine=engine,
rho=400,
axlambda=600,
xystep=1,
xrange=(-20, 20),
yrange=(-15, 15))
model.build()
implant = ArgusII()
implant.stim = Stimulus({'A4': BiphasicPulseTrain(20, 1, 1)})
percept = model.predict_percept(implant)
npt.assert_equal(np.sum(percept.data > 0.0813), 81)
npt.assert_equal(np.sum(percept.data > 0.1626), 59)
npt.assert_equal(np.sum(percept.data > 0.2439), 44)
npt.assert_equal(np.sum(percept.data > 0.4065), 26)
npt.assert_equal(np.sum(percept.data > 0.5691), 14)
implant.plot()
plt.show()
##############################################################################
# As mentioned above, the Biphasic Axon Map Model only accepts
# :py:class:`~pulse2percept.stimuli.BiphasicPulseTrain`
# stimuli with no :py:attr:`~pulse2percept.stimuli.BiphasicPulseTrain.delay_dur`.
# The amplitude given to the BiphasicPulseTrain
# is interpreted as amplitude as a factor of threshold (i.e. an amp of 1 means
# 1xTh)
#
# You can easily assign BiphasicPulseTrains to electrodes with a dictionary
# The following creates a train with 20Hz frequency, 1xTh amplitude, and 0.45ms
# pulse / phase duration.
implant.stim = {'A4': BiphasicPulseTrain(20, 1, 0.45)}
implant.stim.plot()
##############################################################################
# Finally, you can predict the percept resulting from stimulation
percept = model.predict_percept(implant)
ax = percept.plot()
ax.set_title('Predicted percept')
plt.show()
##############################################################################
# Increasing the frequency will make phosphenes brighter
fig, axes = plt.subplots(1, 2, sharex=True, sharey=True)
implant.stim = {'A4': BiphasicPulseTrain(50, 1, 0.45)}
new_percept = model.predict_percept(implant)
new_percept.plot(ax=axes[1])