def __init__(self, n_electrodes, radius, x_center, y_center):
"""Electrodes arranged in a circle
Electrodes will be named 'A0', 'A1', ...
Parameters
----------
n_electrodes : int
how many electrodes to arrange in a circle
radius : float
the radius of the circle (microns)
x_center, y_center : float
the x,y coordinates of the center of the circle (microns),
where (0,0) is the center of the fovea
"""
# The job of the constructor is to create the electrodes. We start
# with an empty collection:
self.electrodes = coll.OrderedDict()
# We then generate a number `n_electrodes` of electrodes, arranged on
# the circumference of a circle:
for n in range(n_electrodes):
# Angular position of the electrode:
ang = 2.0 * np.pi / n_electrodes * n
# Create the disk electrode:
electrode = DiskElectrode(x_center + np.cos(ang) * radius,
y_center + np.sin(ang) * radius, 0, 100)
# Add the electrode to the collection:
self.add_electrode('A' + str(n), electrode)
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_Nanduri2012Spatial():
# Nanduri2012Spatial automatically sets `atten_a`:
model = Nanduri2012Spatial(engine='serial', xystep=5)
# User can set `atten_a`:
model.atten_a = 12345
npt.assert_equal(model.atten_a, 12345)
model.build(atten_a=987)
npt.assert_equal(model.atten_a, 987)
# 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)
# 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)
# Multiple frames are processed independently:
model = Nanduri2012Spatial(engine='serial',
atten_a=14000,
xystep=5,
xrange=(-20, 20),
yrange=(-15, 15))
model.build()
percept = model.predict_percept(ArgusI(stim={'A1': [1, 2]}))
npt.assert_equal(percept.shape, list(model.grid.x.shape) + [2])
pmax = percept.data.max(axis=(0, 1))
npt.assert_almost_equal(percept.data[2, 3, :], pmax)
npt.assert_almost_equal(pmax[1] / pmax[0], 2.0)
# Nanduri model uses a linear dva2ret conversion factor:
for factor in [0.0, 1.0, 2.0]:
npt.assert_almost_equal(model.retinotopy.dva2ret(factor, factor),
(280.0 * factor, 280.0 * factor))
for factor in [0.0, 1.0, 2.0]:
npt.assert_almost_equal(
model.retinotopy.ret2dva(280.0 * factor, 280.0 * factor),
(factor, factor))
def test_plot_implant_on_axon_map():
ax = plot_implant_on_axon_map(ArgusII())
npt.assert_equal(isinstance(ax, Subplot), True)
# Check axis limits:
for xlim, ylim in zip([None, (-2000, 1500)], [(-3000, 1300), None]):
ax = plot_implant_on_axon_map(ArgusII(), xlim=xlim, ylim=ylim)
if xlim is None:
xlim = (-4000, 4500)
if ylim is None:
ylim = (-2500, 3000)
npt.assert_almost_equal(ax.get_xlim(), xlim)
npt.assert_almost_equal(ax.get_ylim(), ylim)
# Check optic disc center in both eyes:
model = AxonMapSpatial()
for eye in ['RE', 'LE']:
for loc_od in [(15.5, 1.5), (17.9, -0.01)]:
od = (-loc_od[0], loc_od[1]) if eye == 'LE' else loc_od
ax = plot_implant_on_axon_map(ArgusII(eye=eye), loc_od=od)
npt.assert_equal(len(ax.patches), 1)
npt.assert_almost_equal(ax.patches[0].center, model.dva2ret(od))
close(ax.figure)
# Electrodes and quadrants can be annotated:
for ann_el, n_el in [(True, 60), (False, 0)]:
for ann_q, n_q in [(True, 4), (False, 0)]:
ax = plot_implant_on_axon_map(ArgusII(),
annotate_implant=ann_el,
annotate_quadrants=ann_q)
npt.assert_equal(len(ax.texts), n_el + n_q)
npt.assert_equal(len(ax.collections[0]._paths), 60)
close(ax.figure)
# Stimulating electrodes are marked:
ax = plot_implant_on_axon_map(ArgusII(stim=np.ones(60)))
# Setting upside_down flips y axis:
ax = plot_implant_on_axon_map(ArgusII(), upside_down=True)
npt.assert_almost_equal(ax.get_xlim(), (-4000, 4500))
npt.assert_almost_equal(ax.get_ylim(), (3000, -2500))
with pytest.raises(TypeError):
plot_implant_on_axon_map(DiskElectrode(0, 0, 0, 100))
with pytest.raises(ValueError):
plot_implant_on_axon_map(ArgusII(), n_bundles=0)
def test_ElectrodeArray_add_electrode():
earray = ElectrodeArray([])
npt.assert_equal(earray.n_electrodes, 0)
with pytest.raises(TypeError):
earray.add_electrode('A01', ElectrodeArray([]))
# Add an electrode:
key0 = 'A04'
earray.add_electrode(key0, PointSource(0, 1, 2))
npt.assert_equal(earray.n_electrodes, 1)
# Both numeric and string index should work:
for key in [key0, 0]:
npt.assert_equal(isinstance(earray[key], PointSource), True)
npt.assert_almost_equal(earray[key].x, 0)
npt.assert_almost_equal(earray[key].y, 1)
npt.assert_almost_equal(earray[key].z, 2)
with pytest.raises(ValueError):
# Can't add the same electrode twice:
earray.add_electrode(key0, PointSource(0, 1, 2))
# Add another electrode:
key1 = 'A01'
earray.add_electrode(key1, DiskElectrode(4, 5, 6, 7))
npt.assert_equal(earray.n_electrodes, 2)
# Both numeric and string index should work:
for key in [key1, 1]:
npt.assert_equal(isinstance(earray[key], DiskElectrode), True)
npt.assert_almost_equal(earray[key].x, 4)
npt.assert_almost_equal(earray[key].y, 5)
npt.assert_almost_equal(earray[key].z, 6)
npt.assert_almost_equal(earray[key].r, 7)
# We can also get a list of electrodes:
for keys in [[key0, key1], [0, key1], [key0, 1], [0, 1]]:
selected = earray[keys]
npt.assert_equal(isinstance(selected, list), True)
npt.assert_equal(isinstance(selected[0], PointSource), True)
npt.assert_equal(isinstance(selected[1], DiskElectrode), True)
def test_plot_implant_on_axon_map():
fig, ax = plot_implant_on_axon_map(ArgusII())
npt.assert_equal(isinstance(fig, Figure), True)
npt.assert_equal(isinstance(ax, Subplot), True)
# Check axis limits:
xmin, xmax, ymin, ymax = dva2ret([-20, 20, -15, 15])
npt.assert_equal(ax.get_xlim(), (xmin, xmax))
npt.assert_equal(ax.get_ylim(), (ymin, ymax))
# Check optic disc center in both eyes:
for eye in ['RE', 'LE']:
for loc_od in [(15.5, 1.5), (17.9, -0.01)]:
od = (-loc_od[0], loc_od[1]) if eye == 'LE' else loc_od
_, ax = plot_implant_on_axon_map(ArgusII(eye=eye), loc_od=od)
npt.assert_equal(len(ax.patches), 1)
npt.assert_almost_equal(ax.patches[0].center, dva2ret(od))
# Electrodes and quadrants can be annotated:
for ann_el, n_el in [(True, 60), (False, 0)]:
for ann_q, n_q in [(True, 4), (False, 0)]:
_, ax = plot_implant_on_axon_map(ArgusII(),
annotate_implant=ann_el,
annotate_quadrants=ann_q)
npt.assert_equal(len(ax.texts), n_el + n_q)
# Stimulating electrodes are marked:
fig, ax = plot_implant_on_axon_map(ArgusII(stim=np.ones(60)))
# Setting upside_down flips y axis:
_, ax = plot_implant_on_axon_map(ArgusII(), upside_down=True)
npt.assert_equal(ax.get_xlim(), (xmin, xmax))
npt.assert_equal(ax.get_ylim(), (ymax, ymin))
with pytest.raises(TypeError):
plot_implant_on_axon_map(DiskElectrode(0, 0, 0, 100))
with pytest.raises(ValueError):
plot_implant_on_axon_map(ArgusII(), n_bundles=0)
stim.plot(time=(0, 60)) ############################################################################### # Creating an implant # ------------------- # # Before we can run the Nanduri model, we need to create a retinal implant to # which we can assign the above pulse train. # # For the purpose of this exercise, we will create an # :py:class:`~pulse2percept.implants.ElectrodeArray` consisting of a single # :py:class:`~pulse2percept.implants.DiskElectrode` with radius=260um centered # at (x,y) = (0,0); i.e., centered over the fovea: from pulse2percept.implants import DiskElectrode, ElectrodeArray earray = ElectrodeArray(DiskElectrode(0, 0, 0, 260)) ############################################################################### # Usually we would use a predefined retinal implant such as # :py:class:`~pulse2percept.implants.ArgusII` or # :py:class:`~pulse2percept.implants.AlphaIMS`. Alternatively, we can wrap the # electrode array created above with a # :py:class:`~pulse2percept.implants.ProsthesisSystem` to create our own # retinal implant. We will also assign the above created stimulus to it: from pulse2percept.implants import ProsthesisSystem implant = ProsthesisSystem(earray, stim=stim) ############################################################################### # Running the model # -----------------
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])
def test_DiskElectrode():
with pytest.raises(TypeError):
DiskElectrode(0, 0, 0, [1, 2])
with pytest.raises(TypeError):
DiskElectrode(0, np.array([0, 1]), 0, 1)
# Invalid radius:
with pytest.raises(ValueError):
DiskElectrode(0, 0, 0, -5)
# Check params:
electrode = DiskElectrode(0, 1, 2, 100)
npt.assert_almost_equal(electrode.x, 0)
npt.assert_almost_equal(electrode.y, 1)
npt.assert_almost_equal(electrode.z, 2)
# On the electrode surface (z=2, x^2+y^2<=100^2)
npt.assert_almost_equal(electrode.electric_potential(0, 1, 2, 1), 1)
npt.assert_almost_equal(electrode.electric_potential(30, -30, 2, 1), 1)
npt.assert_almost_equal(electrode.electric_potential(0, 101, 2, 1), 1)
npt.assert_almost_equal(electrode.electric_potential(0, -99, 2, 1), 1)
npt.assert_almost_equal(electrode.electric_potential(100, 1, 2, 1), 1)
npt.assert_almost_equal(electrode.electric_potential(-100, 1, 2, 1), 1)
# Right off the surface (z=2, x^2+y^2>100^2)
npt.assert_almost_equal(electrode.electric_potential(0, 102, 2, 1),
0.910,
decimal=3)
npt.assert_almost_equal(electrode.electric_potential(0, -100, 2, 1),
0.910,
decimal=3)
# Some distance away from the electrode (z>2):
npt.assert_almost_equal(electrode.electric_potential(0, 1, 38, 1),
0.780,
decimal=3)
# Slots:
npt.assert_equal(hasattr(electrode, '__slots__'), True)
npt.assert_equal(hasattr(electrode, '__dict__'), False)
# Plots:
ax = electrode.plot()
npt.assert_equal(len(ax.texts), 0)
npt.assert_equal(len(ax.patches), 1)
npt.assert_equal(isinstance(ax.patches[0], Circle), True)
def test_DiskElectrode():
with pytest.raises(TypeError):
DiskElectrode(0, 0, 0, [1, 2])
with pytest.raises(TypeError):
DiskElectrode(0, np.array([0, 1]), 0, 1)
# Invalid radius:
with pytest.raises(ValueError):
DiskElectrode(0, 0, 0, -5)
# Check params:
electrode = DiskElectrode(0, 1, 2, 100)
npt.assert_almost_equal(electrode.x, 0)
npt.assert_almost_equal(electrode.y, 1)
npt.assert_almost_equal(electrode.z, 2)
# On the electrode surface (z=2, x^2+y^2<=100^2)
npt.assert_almost_equal(electrode.electric_potential(0, 1, 2, 1), 1)
npt.assert_almost_equal(electrode.electric_potential(30, -30, 2, 1), 1)
npt.assert_almost_equal(electrode.electric_potential(0, 101, 2, 1), 1)
npt.assert_almost_equal(electrode.electric_potential(0, -99, 2, 1), 1)
npt.assert_almost_equal(electrode.electric_potential(100, 1, 2, 1), 1)
npt.assert_almost_equal(electrode.electric_potential(-100, 1, 2, 1), 1)
# Right off the surface (z=2, x^2+y^2>100^2)
npt.assert_almost_equal(electrode.electric_potential(0, 102, 2, 1),
0.910,
decimal=3)
npt.assert_almost_equal(electrode.electric_potential(0, -100, 2, 1),
0.910,
decimal=3)
# Some distance away from the electrode (z>2):
npt.assert_almost_equal(electrode.electric_potential(0, 1, 38, 1),
0.780,
decimal=3)
def _set_grid(self):
"""Private method to build the electrode grid"""
n_elecs = np.prod(self.shape)
rows, cols = self.shape
# The user did not specify a unique naming scheme:
if len(self.names) == 2:
# Create electrode names, using either A-Z or 1-n:
if self.name_rows.isalpha():
rws = [
chr(i) for i in range(ord(self.name_rows),
ord(self.name_rows) + rows + 1)
]
elif self.name_rows.isdigit():
rws = [
str(i) for i in range(int(self.name_rows), rows +
int(self.name_rows))
]
else:
raise ValueError("rows must be alphabetic or numeric")
if self.name_cols.isalpha():
clms = [
chr(i) for i in range(ord(self.name_cols),
ord(self.name_cols) + cols)
]
elif self.name_cols.isdigit():
clms = [
str(i) for i in range(int(self.name_cols), cols +
int(self.name_cols))
]
else:
raise ValueError("Columns must be alphabetic or numeric.")
# facilitating Argus I naming scheme
if self.name_cols.isalpha() and not self.name_rows.isalpha():
names = [
clms[j] + rws[i] for i in range(len(rws))
for j in range(len(clms))
]
else:
names = [
rws[i] + clms[j] for i in range(len(rws))
for j in range(len(clms))
]
else:
if len(self.names) != n_elecs:
raise ValueError("If `names` specifies more than row/column "
"names, it must have %d entries, not "
"%d)." % (n_elecs, len(self.names)))
names = self.names
if isinstance(self.z, (list, np.ndarray)):
# Specify different height for every electrode in a list:
z_arr = np.asarray(self.z).flatten()
if z_arr.size != n_elecs:
raise ValueError("If `h` is a list, it must have %d entries, "
"not %d." % (n_elecs, len(self.z)))
else:
# If `z` is a scalar, choose same height for all electrodes:
z_arr = np.ones(n_elecs, dtype=float) * self.z
# Make a 2D meshgrid from x, y coordinates:
# For example, cols=3 with spacing=100 should give: [-100, 0, 100]
x_arr_lshift = (np.arange(cols) * self.spacing -
(cols / 2.0 - 0.5) * self.spacing -
self.spacing * 0.25)
x_arr_rshift = (np.arange(cols) * self.spacing -
(cols / 2.0 - 0.5) * self.spacing +
self.spacing * 0.25)
y_arr = (np.arange(rows) * math.sqrt(3) * self.spacing / 2.0 -
(rows / 2.0 - 0.5) * self.spacing)
x_arr_lshift, y_arr_lshift = np.meshgrid(x_arr_lshift,
y_arr,
sparse=False)
x_arr_rshift, y_arr_rshift = np.meshgrid(x_arr_rshift,
y_arr,
sparse=False)
# added code to interleave arrays
x_arr = []
for row in range(0, rows):
if row % 2 == 0:
x_arr.append(x_arr_lshift[row])
else:
x_arr.append(x_arr_rshift[row])
x_arr = np.array(x_arr)
y_arr = y_arr_rshift
# Rotate the grid:
rotmat = np.array([
np.cos(self.rot), -np.sin(self.rot),
np.sin(self.rot),
np.cos(self.rot)
]).reshape((2, 2))
xy = np.matmul(rotmat, np.vstack((x_arr.flatten(), y_arr.flatten())))
x_arr = xy[0, :]
y_arr = xy[1, :]
# Apply offset to make the grid centered at (self.x, self.y):
x_arr += self.x
y_arr += self.y
if issubclass(self.etype, DiskElectrode):
if isinstance(self.r, (list, np.ndarray)):
# Specify different radius for every electrode in a list:
if len(self.r) != n_elecs:
err_s = ("If `r` is a list, it must have %d entries, not "
"%d)." % (n_elecs, len(self.r)))
raise ValueError(err_s)
r_arr = self.r
else:
# If `r` is a scalar, choose same radius for all electrodes:
r_arr = np.ones(n_elecs, dtype=float) * self.r
# Create a grid of DiskElectrode objects:
for x, y, z, r, name in zip(x_arr, y_arr, z_arr, r_arr, names):
self.add_electrode(name, DiskElectrode(x, y, z, r))
elif issubclass(self.etype, PointSource):
# Create a grid of PointSource objects:
for x, y, z, name in zip(x_arr, y_arr, z_arr, names):
self.add_electrode(name, PointSource(x, y, z))
else:
raise NotImplementedError