def test_AxonMapModel_find_closest_axon(engine):
model = AxonMapModel(xystep=1,
engine=engine,
n_axons=5,
xrange=(-20, 20),
yrange=(-15, 15),
axons_range=(-45, 45))
model.build()
# Pretend there is an axon close to each point on the grid:
bundles = [
np.array([x + 0.001, y - 0.001], dtype=np.float32).reshape((1, 2))
for x, y in zip(model.spatial.grid.xret.ravel(),
model.spatial.grid.yret.ravel())
]
closest = model.spatial.find_closest_axon(bundles)
for ax1, ax2 in zip(bundles, closest):
npt.assert_almost_equal(ax1[0, 0], ax2[0, 0])
npt.assert_almost_equal(ax1[0, 1], ax2[0, 1])
# Looking up just one point does not return a list of axons:
axon = bundles[0]
closest = model.spatial.find_closest_axon(bundles,
xret=axon[0, 0],
yret=axon[0, 1])
npt.assert_almost_equal(closest, axon)
# Return the index as well:
closest, closest_idx = model.spatial.find_closest_axon(bundles,
xret=axon[0, 0],
yret=axon[0, 1],
return_index=True)
npt.assert_almost_equal(closest, axon)
npt.assert_equal(closest_idx, 0)
def test_AxonMapModel_find_closest_axon(engine):
model = AxonMapModel(xystep=1, engine=engine, n_axons=5,
xrange=(-20, 20), yrange=(-15, 15),
axons_range=(-45, 45))
model.build()
# Pretend there is an axon close to each point on the grid:
bundles = [np.array([x + 0.001, y - 0.001],
dtype=np.float32).reshape((1, 2))
for x, y in zip(model.spatial.grid.xret.ravel(),
model.spatial.grid.yret.ravel())]
closest = model.spatial.find_closest_axon(bundles)
for ax1, ax2 in zip(bundles, closest):
npt.assert_almost_equal(ax1[0, 0], ax2[0, 0])
npt.assert_almost_equal(ax1[0, 1], ax2[0, 1])
def test_AxonMapModel_grow_axon_bundles(engine):
for n_axons in [1, 2, 3, 5, 10]:
model = AxonMapModel(xystep=2, engine=engine, n_axons=n_axons,
axons_range=(-20, 20), xrange=(-20, 20),
yrange=(-15, 15))
bundles = model.spatial.grow_axon_bundles()
npt.assert_equal(len(bundles), n_axons)
def plot_on_axon_map(self,
annotate_implant=False,
annotate_quadrants=True,
ax=None):
if ax is None:
_, ax = plt.subplots(figsize=(10, 10))
AxonMapModel().plot(annotate=annotate_quadrants, ax=ax)
self.earray.plot(annotate=annotate_implant, ax=ax)
def test_AxonMapModel__jansonius2009(eye, loc_od, sign, engine):
# With `rho` starting at 0, all axons should originate in the optic disc
# center
model = AxonMapModel(loc_od=loc_od,
xystep=2,
engine=engine,
ax_segments_range=(0, 45),
n_ax_segments=100)
for phi0 in [-135.0, 66.0, 128.0]:
ax_pos = model.spatial._jansonius2009(phi0)
npt.assert_almost_equal(ax_pos[0, 0], loc_od[0])
npt.assert_almost_equal(ax_pos[0, 1], loc_od[1])
# These axons should all end at the meridian
for phi0 in [110.0, 135.0, 160.0]:
model = AxonMapModel(loc_od=(15, 2),
xystep=2,
engine=engine,
n_ax_segments=801,
ax_segments_range=(0, 45))
ax_pos = model.spatial._jansonius2009(sign * phi0)
npt.assert_almost_equal(ax_pos[-1, 1], 0.0, decimal=1)
# `phi0` must be within [-180, 180]
for phi0 in [-200.0, 181.0]:
with pytest.raises(ValueError):
failed = AxonMapModel(xystep=2, engine=engine)
failed.spatial._jansonius2009(phi0)
# `n_rho` must be >= 1
for n_rho in [-1, 0]:
with pytest.raises(ValueError):
model = AxonMapModel(n_ax_segments=n_rho, xystep=2, engine=engine)
model.spatial._jansonius2009(0.0)
# `ax_segments_range` must have min <= max
for lorho in [-200.0, 90.0]:
with pytest.raises(ValueError):
model = AxonMapModel(ax_segments_range=(lorho, 45),
xystep=2,
engine=engine)
model.spatial._jansonius2009(0)
for hirho in [-200.0, 40.0]:
with pytest.raises(ValueError):
model = AxonMapModel(ax_segments_range=(45, hirho),
xystep=2,
engine=engine)
model.spatial._jansonius2009(0)
# A single axon fiber with `phi0`=0 should return a single pixel location
# that corresponds to the optic disc
model = AxonMapModel(loc_od=loc_od,
xystep=2,
engine=engine,
eye=eye,
ax_segments_range=(0, 0),
n_ax_segments=1)
single_fiber = model.spatial._jansonius2009(0)
npt.assert_equal(len(single_fiber), 1)
npt.assert_almost_equal(single_fiber[0], loc_od)
def test_AxonMapModel_calc_axon_contribution(engine):
model = AxonMapModel(xystep=2, engine=engine, n_axons=10,
xrange=(-20, 20), yrange=(-15, 15),
axons_range=(-30, 30))
model.build()
xyret = np.column_stack((model.spatial.grid.xret.ravel(),
model.spatial.grid.yret.ravel()))
bundles = model.spatial.grow_axon_bundles()
axons = model.spatial.find_closest_axon(bundles)
contrib = model.spatial.calc_axon_contribution(axons)
# Check lambda math:
for ax, xy in zip(contrib, xyret):
axon = np.insert(ax, 0, list(xy) + [0], axis=0)
d2 = np.cumsum(np.diff(axon[:, 0], axis=0) ** 2 +
np.diff(axon[:, 1], axis=0) ** 2)
sensitivity = np.exp(-d2 / (2.0 * model.spatial.axlambda ** 2))
npt.assert_almost_equal(sensitivity, ax[:, 2])
def test_plot_argus_simulated_phosphenes(implant):
implant.stim = {'A1': [1, 0, 0], 'B2': [0, 1, 0], 'C3': [0, 0, 1]}
percepts = ScoreboardModel().build().predict_percept(implant)
plot_argus_simulated_phosphenes(percepts, implant)
# Add axon map:
_, ax = plt.subplots()
plot_argus_simulated_phosphenes(percepts,
implant,
ax=ax,
axon_map=AxonMapModel())
def test_AxonMapModel_calc_bundle_tangent(engine):
model = AxonMapModel(xystep=5, engine=engine, n_axons=500,
xrange=(-20, 20), yrange=(-15, 15),
n_ax_segments=500, axons_range=(-180, 180),
ax_segments_range=(3, 50))
npt.assert_almost_equal(model.spatial.calc_bundle_tangent(0, 0), 0.4819,
decimal=3)
npt.assert_almost_equal(model.spatial.calc_bundle_tangent(0, 1000),
-0.5532, decimal=3)
with pytest.raises(TypeError):
model.spatial.calc_bundle_tangent([0], 1000)
with pytest.raises(TypeError):
model.spatial.calc_bundle_tangent(0, [1000])
def test_plot_argus_phosphenes():
df = pd.DataFrame([
{
'subject': 'S1',
'electrode': 'A1',
'image': np.random.rand(10, 10),
'xrange': (-10, 10),
'yrange': (-10, 10)
},
{
'subject': 'S1',
'electrode': 'B2',
'image': np.random.rand(10, 10),
'xrange': (-10, 10),
'yrange': (-10, 10)
},
])
_, ax = plt.subplots()
plot_argus_phosphenes(df, ArgusI(), ax=ax)
plot_argus_phosphenes(df, ArgusII(), ax=ax)
# Add axon map:
_, ax = plt.subplots()
plot_argus_phosphenes(df, ArgusI(), ax=ax, axon_map=AxonMapModel())
# Data must be a DataFrame:
with pytest.raises(TypeError):
plot_argus_phosphenes(np.ones(10), ArgusI())
# DataFrame must have the required columns:
with pytest.raises(ValueError):
plot_argus_phosphenes(pd.DataFrame(), ArgusI())
# Subjects must all be the same:
with pytest.raises(ValueError):
dff = pd.DataFrame([{'subject': 'S1'}, {'subject': 'S2'}])
plot_argus_phosphenes(dff, ArgusI())
# Works only for Argus:
with pytest.raises(TypeError):
plot_argus_phosphenes(df, AlphaAMS())
# Works only for axon maps:
with pytest.raises(TypeError):
plot_argus_phosphenes(df, ArgusI(), ax=ax, axon_map=ScoreboardModel())
# Manual subject selection
plot_argus_phosphenes(df[df.electrode == 'B2'], ArgusI(), ax=ax)
# If no implant given, dataframe must have additional columns:
with pytest.raises(ValueError):
plot_argus_phosphenes(df, ax=ax)
df['implant_type_str'] = 'ArgusII'
df['implant_x'] = 0
df['implant_y'] = 0
df['implant_rot'] = 0
plot_argus_phosphenes(df, ax=ax)
def test_AxonMapModel_calc_axon_sensitivity(engine):
model = AxonMapModel(xystep=2,
engine=engine,
n_axons=10,
xrange=(-20, 20),
yrange=(-15, 15),
axons_range=(-30, 30))
model.build()
xyret = np.column_stack(
(model.spatial.grid.xret.ravel(), model.spatial.grid.yret.ravel()))
bundles = model.spatial.grow_axon_bundles()
axons = model.spatial.find_closest_axon(bundles)
# Need two separate contribs, one to get cut off axons from, and another
# to actually test against (with/without padding)
contrib = model.spatial.calc_axon_sensitivity(axons, pad=False)
pad = engine == 'jax'
axon_contrib = model.spatial.calc_axon_sensitivity(axons, pad=pad)
# Check lambda math:
max_axon_length = max([len(ax) for ax in contrib])
for ax, xy, model_ax in zip(contrib, xyret, axon_contrib):
axon = np.insert(ax, 0, list(xy) + [0], axis=0)
d2 = np.cumsum(
np.sqrt(
np.diff(axon[:, 0], axis=0)**2 +
np.diff(axon[:, 1], axis=0)**2))**2
max_d2 = -2.0 * model.axlambda**2 * np.log(model.min_ax_sensitivity)
idx_d2 = d2 < max_d2
sensitivity = np.exp(-d2[idx_d2] / (2.0 * model.spatial.axlambda**2))
# Axons need to be padded for jax
if engine == 'jax':
s = np.zeros((max_axon_length))
s[:len(sensitivity)] = sensitivity
if len(sensitivity) > 0:
s[len(sensitivity):] = sensitivity[-1]
sensitivity = s.astype(np.float32)
npt.assert_almost_equal(sensitivity, model_ax[:, 2])
def test_deepcopy_AxonMapModel():
original = AxonMapModel()
copied = copy.deepcopy(original)
# Assert these are two different objects
npt.assert_equal(id(original) != id(copied), True)
# Assert the objects are equivalent
npt.assert_equal(original.__dict__ == copied.__dict__, True)
# Assert that __eq__ works
npt.assert_equal(original == copied, True)
# Assert they do not share the same AxonMapSpatial Object
npt.assert_equal(original.spatial == copied.spatial, True)
npt.assert_equal(id(original.spatial) != id(copied.spatial), True)
# Assert changing copied doesn't change original
copied.spatial.xrange = (-10, 10)
npt.assert_equal(original.spatial != copied.spatial, True)
def test_plot_argus_phosphenes():
df = pd.DataFrame([
{
'subject': 'S1',
'electrode': 'A1',
'image': np.random.rand(10, 10),
'img_x_dva': (-10, 10),
'img_y_dva': (-10, 10)
},
{
'subject': 'S1',
'electrode': 'B2',
'image': np.random.rand(10, 10),
'img_x_dva': (-10, 10),
'img_y_dva': (-10, 10)
},
])
_, ax = plt.subplots()
plot_argus_phosphenes(df, ArgusI(), ax=ax)
plot_argus_phosphenes(df, ArgusII(), ax=ax)
# Add axon map:
_, ax = plt.subplots()
plot_argus_phosphenes(df, ArgusI(), ax=ax, axon_map=AxonMapModel())
# Data must be a DataFrame:
with pytest.raises(TypeError):
plot_argus_phosphenes(np.ones(10), ArgusI())
# DataFrame must have the required columns:
with pytest.raises(ValueError):
plot_argus_phosphenes(pd.DataFrame(), ArgusI())
# Subjects must all be the same:
with pytest.raises(ValueError):
dff = pd.DataFrame([{'subject': 'S1'}, {'subject': 'S2'}])
plot_argus_phosphenes(dff, ArgusI())
# Works only for Argus:
with pytest.raises(TypeError):
plot_argus_phosphenes(df, AlphaAMS())
def test_AxonMapModel_predict_percept(engine):
model = AxonMapModel(xystep=0.55,
axlambda=100,
thresh_percept=0,
engine=engine)
model.build()
# Single-electrode stim:
img_stim = np.zeros(60)
img_stim[47] = 1
percept = model.predict_percept(ArgusII(stim=img_stim))
# Single bright pixel, rest of arc is less bright:
npt.assert_equal(np.sum(percept.data > 0.9), 1)
npt.assert_equal(np.sum(percept.data > 0.7), 2)
npt.assert_equal(np.sum(percept.data > 0.1), 28)
npt.assert_equal(np.sum(percept.data > 0.0001), 96)
# Overall only a few bright pixels:
npt.assert_almost_equal(np.sum(percept.data), 10.0812, decimal=3)
# Brightest pixel is in lower right:
npt.assert_almost_equal(percept.data[34, 47, 0], np.max(percept.data))
# Top half is empty:
npt.assert_almost_equal(np.sum(percept.data[:27, :, 0]), 0)
# Same for lower band:
npt.assert_almost_equal(np.sum(percept.data[39:, :, 0]), 0)
# Full Argus II with small lambda: 60 bright spots
model = AxonMapModel(engine='serial', xystep=1, rho=100, axlambda=40)
model.build()
percept = model.predict_percept(ArgusII(stim=np.ones(60)))
# Most spots are pretty bright, but there are 2 dimmer ones (due to their
# location on the retina):
npt.assert_equal(np.sum(percept.data > 0.5), 33)
npt.assert_equal(np.sum(percept.data > 0.275), 62)
# Model gives same outcome as Spatial:
spatial = AxonMapSpatial(engine='serial', xystep=1, rho=100, axlambda=40)
spatial.build()
spatial_percept = model.predict_percept(ArgusII(stim=np.ones(60)))
npt.assert_almost_equal(percept.data, spatial_percept.data)
def test_AxonMapModel(engine):
set_params = {
'xystep': 2,
'engine': engine,
'rho': 432,
'axlambda': 2,
'n_axons': 9,
'n_ax_segments': 50,
'xrange': (-30, 30),
'yrange': (-20, 20),
'loc_od_x': 5,
'loc_od_y': 6
}
model = AxonMapModel()
for param in set_params:
npt.assert_equal(hasattr(model.spatial, param), True)
# User can override default values
for key, value in set_params.items():
setattr(model.spatial, key, value)
npt.assert_equal(getattr(model.spatial, key), value)
model = AxonMapModel(**set_params)
model.build(**set_params)
for key, value in set_params.items():
npt.assert_equal(getattr(model.spatial, key), value)
# Zeros in, zeros out:
implant = ArgusII(stim=np.zeros(60))
npt.assert_almost_equal(model.predict_percept(implant).data, 0)
implant.stim = np.zeros(60)
npt.assert_almost_equal(model.predict_percept(implant).data, 0)
# Implant and model must be built for same eye:
with pytest.raises(ValueError):
implant = ArgusII(eye='LE', stim=np.zeros(60))
model.predict_percept(implant)
with pytest.raises(ValueError):
AxonMapModel(eye='invalid').build()
with pytest.raises(ValueError):
AxonMapModel(xystep=5).build(eye='invalid')
def test_AxonMapModel(engine):
set_params = {
'xystep': 2,
'engine': engine,
'rho': 432,
'axlambda': 20,
'n_axons': 9,
'n_ax_segments': 50,
'xrange': (-30, 30),
'yrange': (-20, 20),
'loc_od': (5, 6)
}
model = AxonMapModel()
for param in set_params:
npt.assert_equal(hasattr(model.spatial, param), True)
# User can override default values
for key, value in set_params.items():
setattr(model.spatial, key, value)
npt.assert_equal(getattr(model.spatial, key), value)
model = AxonMapModel(**set_params)
model.build(**set_params)
for key, value in set_params.items():
npt.assert_equal(getattr(model.spatial, key), value)
# Converting ret <=> dva
npt.assert_equal(isinstance(model.retinotopy, Watson2014Map), True)
npt.assert_almost_equal(model.retinotopy.ret2dva(0, 0), (0, 0))
npt.assert_almost_equal(model.retinotopy.dva2ret(0, 0), (0, 0))
model2 = AxonMapModel(retinotopy=Watson2014DisplaceMap())
npt.assert_equal(isinstance(model2.retinotopy, Watson2014DisplaceMap),
True)
# Zeros in, zeros out:
implant = ArgusII(stim=np.zeros(60))
npt.assert_almost_equal(model.predict_percept(implant).data, 0)
implant.stim = np.zeros(60)
npt.assert_almost_equal(model.predict_percept(implant).data, 0)
# Implant and model must be built for same eye:
with pytest.raises(ValueError):
implant = ArgusII(eye='LE', stim=np.zeros(60))
model.predict_percept(implant)
with pytest.raises(ValueError):
AxonMapModel(eye='invalid').build()
with pytest.raises(ValueError):
AxonMapModel(xystep=5).build(eye='invalid')
# Lambda cannot be too small:
with pytest.raises(ValueError):
AxonMapModel(axlambda=9).build()
Creating the model ------------------ The first step is to instantiate the :py:class:`~pulse2percept.models.AxonMapModel` class by calling its constructor method. The two most important parameters to set are ``rho`` and ``axlambda`` from the equation above (here set to 200 micrometers and 500 micrometers, respectively): """ # sphinx_gallery_thumbnail_number = 2 from pulse2percept.models import AxonMapModel model = AxonMapModel(rho=200, axlambda=500) ############################################################################## # Parameters you don't specify will take on default values. You can inspect # all current model parameters as follows: print(model) ############################################################################## # This reveals a number of other parameters to set, such as: # # * ``xrange``, ``yrange``: the extent of the visual field to be simulated, # specified as a range of x and y coordinates (in degrees of visual angle, # or dva). For example, we are currently sampling x values between -20 dva # and +20dva, and y values between -15 dva and +15 dva. # * ``xystep``: The resolution (in dva) at which to sample the visual field.
hex_grid.plot()
##############################################################################
# The following example centers the grid on (x,y) = (-600um, 200 um),
# z=150um away from the retinal surface, and rotates it clockwise by 45 degrees
# (note the minus sign):
from numpy import pi
offset_grid = ElectrodeGrid((11, 13),
500,
type='hex',
x=-600,
y=200,
z=150,
rot=-pi / 4,
etype=DiskElectrode,
r=100)
##############################################################################
# .. note::
#
# Clockwise/counter-clockwise rotations refer to rotations on the retinal
# surface (that is, as if seen on a fundus photograph).
#
# We can also plot the grid on top of a map of retinal nerve fiber bundles:
from pulse2percept.models import AxonMapModel
AxonMapModel().plot()
offset_grid.plot()
# --------------------- # # Psychophsyics stimuli can be passed to an implant and combined with a model. # To demonstrate, we will pass a ``GratingStimululus`` to an # :py:class:`~pulse2percept.implants.ArgusII` implant and use the # :py:class:`~pulse2percept.models.AxonMapModel` [Beyeler2019]_ to interpret it: # # .. important :: # # Don't forget to build the model before using ``predict_percept`` # from pulse2percept.implants import ArgusII from pulse2percept.models import AxonMapModel model = AxonMapModel() model.build() implant = ArgusII() implant.stim = GratingStimulus((25, 25), temporal_freq=0.1) percept = model.predict_percept(implant) percept.play() ##################################################################################### # As you can see in the above code segment, the stimulus passed to the implant does # not necessarily have to have the same dimensions as the electrode grid. # This is functionality built in to the implant code: The implant will automatically # rescale the stimulus to the appropriate size. # In the case of Argus II, the stimulus would thus be downscaled to a 6x10 image. #
.. _NCT00279500: https://clinicaltrials.gov/ct2/show/NCT00279500
.. _NCT00407602: https://www.clinicaltrials.gov/ct2/show/NCT00407602
"""
# sphinx_gallery_thumbnail_number = 2
import matplotlib.pyplot as plt
from pulse2percept.implants import *
from pulse2percept.models import AxonMapModel
fig, ax = plt.subplots(ncols=2, figsize=(10, 6))
# For illustrative purpose, also show the map of fiber
# bundles in the optic fiber layer:
model = AxonMapModel()
model.plot(ax=ax[0])
# Argus I is typically implanted at a 30-45deg angle:
ArgusI(rot=-0.52).plot(ax=ax[0], annotate=True)
ax[0].set_title('Argus I')
model.plot(ax=ax[1])
# Argus II is typically implanted at a 30-45deg angle:
ArgusII(rot=-0.52).plot(ax=ax[1], annotate=False)
ax[1].set_title('Argus II')
###############################################################################
# PRIMA Bionic Vision System (Pixium Vision SA)
# ----------------------------------------------
#
# :py:class:`~pulse2percept.implants.PRIMA` is a subretinal device developed
###############################################################################
# Great! We have just reproduced a panel from Figure 2 in [Beyeler2019]_.
#
# As [Beyeler2019]_ went on to show, the orientation of these phosphenes is
# well aligned with the map of nerve fiber bundles (NFBs) in each subject's
# eye.
#
# To see how the phosphene drawings line up with the NFBs, we can also pass an
# :py:class:`~pulse2percept.models.AxonMapModel` to the function.
# Of course, we need to make sure that we use the correct dimensions. Subject
# S2 had their optic disc center located 16.2 deg nasally, 1.38 deg superior
# from the fovea:
from pulse2percept.models import AxonMapModel
model = AxonMapModel(loc_od=(16.2, 1.38))
plot_argus_phosphenes(data, argus, axon_map=model)
###############################################################################
# Predicting phosphene shape
# --------------------------
#
# In addition, the :py:class:`~pulse2percept.models.AxonMapModel` is well
# suited to predict the shape of individual phosphenes. Using the values given
# in [Beyeler2019]_, we can tailor the axon map parameters to Subject 2:
import numpy as np
model = AxonMapModel(rho=315,
axlambda=500,
loc_od=(16.2, 1.38),
xrange=(-30, 30),
def test_AxonMapModel_predict_percept(engine):
model = AxonMapModel(xystep=0.55,
axlambda=100,
rho=100,
thresh_percept=0,
engine=engine,
xrange=(-20, 20),
yrange=(-15, 15),
n_axons=500)
model.build()
# Single-electrode stim:
img_stim = np.zeros(60)
img_stim[47] = 1
# Axon map jax predict_percept not implemented yet
if engine == 'jax':
with pytest.raises(NotImplementedError):
percept = model.predict_percept(ArgusII(stim=img_stim))
return
percept = model.predict_percept(ArgusII(stim=img_stim))
# Single bright pixel, rest of arc is less bright:
npt.assert_equal(np.sum(percept.data > 0.8), 1)
npt.assert_equal(np.sum(percept.data > 0.6), 2)
npt.assert_equal(np.sum(percept.data > 0.1), 7)
npt.assert_equal(np.sum(percept.data > 0.0001), 31)
# Overall only a few bright pixels:
npt.assert_almost_equal(np.sum(percept.data), 3.3087, decimal=3)
# Brightest pixel is in lower right:
npt.assert_almost_equal(percept.data[33, 46, 0], np.max(percept.data))
# Top half is empty:
npt.assert_almost_equal(np.sum(percept.data[:27, :, 0]), 0)
# Same for lower band:
npt.assert_almost_equal(np.sum(percept.data[39:, :, 0]), 0)
# Full Argus II with small lambda: 60 bright spots
model = AxonMapModel(engine='serial',
xystep=1,
rho=100,
axlambda=40,
xrange=(-20, 20),
yrange=(-15, 15),
n_axons=500)
model.build()
percept = model.predict_percept(ArgusII(stim=np.ones(60)))
# Most spots are pretty bright, but there are 2 dimmer ones (due to their
# location on the retina):
npt.assert_equal(np.sum(percept.data > 0.5), 28)
npt.assert_equal(np.sum(percept.data > 0.275), 56)
# Model gives same outcome as Spatial:
spatial = AxonMapSpatial(engine='serial',
xystep=1,
rho=100,
axlambda=40,
xrange=(-20, 20),
yrange=(-15, 15),
n_axons=500)
spatial.build()
spatial_percept = spatial.predict_percept(ArgusII(stim=np.ones(60)))
npt.assert_almost_equal(percept.data, spatial_percept.data)
npt.assert_equal(percept.time, None)
# Warning for nonzero electrode-retina distances
implant = ArgusI(stim=np.ones(16), z=10)
msg = ("Nonzero electrode-retina distances do not have any effect on the "
"model output.")
assert_warns_msg(UserWarning, model.predict_percept, msg, implant)
############################################################################### # Great! We have just reproduced a panel from Figure 2 in [Beyeler2019]_. # # As [Beyeler2019]_ went on to show, the orientation of these phosphenes is # well aligned with the map of nerve fiber bundles (NFBs) in each subject's # eye. # # To see how the phosphene drawings line up with the NFBs, we can also pass an # :py:class:`~pulse2percept.models.AxonMapModel` to the function. # Of course, we need to make sure that we use the correct dimensions. Subject # S2 had their optic disc center located 14 deg nasally, 2.4 deg superior from # the fovea: from pulse2percept.models import AxonMapModel model = AxonMapModel(loc_od=(14, 2.4)) plot_argus_phosphenes(data, argus, axon_map=model) ############################################################################### # Analyzing phosphene shape # ------------------------- # # The phosphene drawings also come annotated with different shape descriptors: # area, orientation, and elongation. # Elongation is also called eccentricity in the computer vision literature, # which is not to be confused with retinal eccentricity. It is simply a number # between 0 and 1, where 0 corresponds to a circle and 1 corresponds to an # infinitesimally thin line (note that the Methods section of [Beyeler2019]_ # got it wrong). # # [Beyeler2019]_ made the point that if each phosphene could be considered a
------------------ The first step is to instantiate the :py:class:`~pulse2percept.models.AxonMapModel` class by calling its constructor method. The two most important parameters to set are ``rho`` and ``axlambda`` from the equation above (here set to 150 micrometers and 500 micrometers, respectively): """ # sphinx_gallery_thumbnail_number = 2 import numpy as np from pulse2percept.implants import ArgusII from pulse2percept.models import AxonMapModel model = AxonMapModel(rho=150, axlambda=500) ############################################################################## # Parameters you don't specify will take on default values. You can inspect # all current model parameters as follows: print(model) ############################################################################## # This reveals a number of other parameters to set, such as: # # * ``xrange``, ``yrange``: the extent of the visual field to be simulated, # specified as a range of x and y coordinates (in degrees of visual angle, # or dva). For example, we are currently sampling x values between -20 dva # and +20dva, and y values between -15 dva and +15 dva. # * ``xystep``: The resolution (in dva) at which to sample the visual field.
