def test_AxonMapSpatial_plot():
model = AxonMapSpatial()
for use_dva, xlim in zip([True, False], [(-18, 18), (-5000, 5000)]):
ax = model.plot(use_dva=use_dva)
npt.assert_equal(isinstance(ax, Subplot), True)
npt.assert_equal(ax.get_xlim(), xlim)
# Simulated area might be larger than that:
model = AxonMapSpatial(xrange=(-20.5, 20.5), yrange=(-16.1, 16.1))
ax = model.plot(use_dva=True)
npt.assert_almost_equal(ax.get_xlim(), (-21, 21))
npt.assert_almost_equal(ax.get_ylim(), (-18, 18))
ax = model.plot(use_dva=False)
npt.assert_almost_equal(ax.get_xlim(), (-6000, 6000))
npt.assert_almost_equal(ax.get_ylim(), (-5000, 5000))
# Figure size can be changed:
ax = model.plot(figsize=(8, 7))
npt.assert_almost_equal(ax.figure.get_size_inches(), (8, 7))
# Quadrants can be annotated:
for ann_q, n_q in [(True, 6), (False, 0)]:
fig, ax = plt.subplots()
model.plot(annotate=ann_q, ax=ax)
npt.assert_equal(len(ax.child_axes), int(n_q > 0))
if len(ax.child_axes) > 0:
npt.assert_equal(len(ax.child_axes[0].texts), n_q)
plt.close(fig)
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
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), 32)
# Overall only a few bright pixels:
npt.assert_almost_equal(np.sum(percept.data), 3.31321, 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)
spatial.build()
spatial_percept = model.predict_percept(ArgusII(stim=np.ones(60)))
npt.assert_almost_equal(percept.data, spatial_percept.data)
npt.assert_equal(percept.time, None)
def test_AxonMapSpatial_plot():
model = AxonMapSpatial()
for use_dva, xlim in zip([True, False], [(-18, 18), (-5000, 5000)]):
ax = model.plot(use_dva=use_dva)
npt.assert_equal(isinstance(ax, Subplot), True)
npt.assert_equal(ax.get_xlim(), xlim)
# Quadrants can be annotated:
for ann_q, n_q in [(True, 6), (False, 0)]:
fig, ax = plt.subplots()
model.plot(annotate=ann_q, ax=ax)
npt.assert_equal(len(ax.child_axes), int(n_q > 0))
if len(ax.child_axes) > 0:
npt.assert_equal(len(ax.child_axes[0].texts), n_q)
plt.close(fig)
def test_AxonMapSpatial_plot():
model = AxonMapSpatial()
ax = model.plot()
npt.assert_equal(isinstance(ax, Subplot), True)
# Electrodes and quadrants can be annotated:
for ann_q, n_q in [(True, 4), (False, 0)]:
ax = model.plot(annotate=ann_q)
npt.assert_equal(len(ax.texts), n_q)
close(ax.figure)
# Setting upside_down flips y axis:
ax = model.plot(upside_down=True, autoscale=True)
npt.assert_equal(ax.get_xlim(), (-5000, 5000))
npt.assert_equal(ax.get_ylim(), (4000, -4000))
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_plot_axon_map():
ax = plot_axon_map()
npt.assert_equal(isinstance(ax, Subplot), True)
# Check axis limits:
for xlim, ylim in zip([None, (-2000, 1500)], [(-3000, 1300), None]):
ax = plot_axon_map(xlim=xlim, ylim=ylim)
if xlim is None:
xlim = (-5000, 5000)
if ylim is None:
ylim = (-4000, 4000)
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)]:
ax = plot_axon_map(eye=eye, loc_od=loc_od)
npt.assert_equal(len(ax.patches), 1)
# Wrong sign for x-coord is automatically corrected:
if eye == 'RE':
od = (np.abs(loc_od[0]), loc_od[1])
else:
od = (-np.abs(loc_od[0]), loc_od[1])
npt.assert_almost_equal(ax.patches[0].center, model.dva2ret(od))
close(ax.figure)
# Electrodes and quadrants can be annotated:
for ann_q, n_q in [(True, 4), (False, 0)]:
ax = plot_axon_map(annotate_quadrants=ann_q)
npt.assert_equal(len(ax.texts), n_q)
# Setting upside_down flips y axis:
ax = plot_axon_map(upside_down=True)
npt.assert_equal(ax.get_xlim(), (-5000, 5000))
npt.assert_equal(ax.get_ylim(), (4000, -4000))
with pytest.raises(ValueError):
plot_axon_map(loc_od=[3])
with pytest.raises(ValueError):
plot_axon_map(eye='foo')
with pytest.raises(ValueError):
plot_axon_map(n_bundles=0)
def test_deepcopy_AxonMapSpatial():
original = AxonMapSpatial()
copied = copy.deepcopy(original)
# Assert these are two different objects
npt.assert_equal(id(original) != id(copied), True)
# Assert these objects are equivalent
npt.assert_equal(original.__dict__ == copied.__dict__, True)
npt.assert_equal(original == copied, True)
# Assert building one object does not affect the copied
original.build()
npt.assert_equal(copied.is_built, False)
npt.assert_equal(original.__dict__ != copied.__dict__, True)
# Assert destroying the original doesn't affect the copied
original = None
npt.assert_equal(copied is not None, True)
def test_AxonMapSpatial(engine):
# AxonMapSpatial automatically sets `rho`, `axlambda`:
model = AxonMapSpatial(engine=engine, xystep=5)
# User can set `rho`:
model.rho = 123
npt.assert_equal(model.rho, 123)
model.build(rho=987)
npt.assert_equal(model.rho, 987)
# Converting ret <=> dva
npt.assert_almost_equal(model.ret2dva(0), 0)
npt.assert_almost_equal(model.dva2ret(0), 0)
# 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)
# Multiple frames are processed independently:
model = AxonMapSpatial(engine=engine, rho=200, axlambda=100, xystep=5)
model.build()
percept = model.predict_percept(ArgusI(stim={'A1': [1, 0], 'B3': [0, 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, 0], pmax[0])
npt.assert_almost_equal(percept.data[2, 3, 1], 0)
npt.assert_almost_equal(percept.data[3, 4, 0], 0)
npt.assert_almost_equal(percept.data[3, 4, 1], pmax[1])
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)
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)
def test_AxonMapSpatial(engine):
# AxonMapSpatial automatically sets `rho`, `axlambda`:
model = AxonMapSpatial(engine=engine, xystep=5)
# User can set `rho`:
model.rho = 123
npt.assert_equal(model.rho, 123)
model.build(rho=987)
npt.assert_equal(model.rho, 987)
# 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 = AxonMapSpatial(retinotopy=Watson2014DisplaceMap())
npt.assert_equal(isinstance(model2.retinotopy, Watson2014DisplaceMap),
True)
# 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)
# Lambda cannot be too small:
with pytest.raises(ValueError):
AxonMapSpatial(axlambda=9).build()
# Multiple frames are processed independently:
model = AxonMapSpatial(engine=engine,
rho=200,
axlambda=100,
xystep=5,
xrange=(-20, 20),
yrange=(-15, 15))
model.build()
# Axon map jax predict_percept not implemented yet
if engine == 'jax':
with pytest.raises(NotImplementedError):
percept = model.predict_percept(
ArgusII(stim={
'A1': [1, 0],
'B3': [0, 2]
}))
return
percept = model.predict_percept(ArgusI(stim={'A1': [1, 0], 'B3': [0, 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, 0], pmax[0])
npt.assert_almost_equal(percept.data[2, 3, 1], 0)
npt.assert_almost_equal(percept.data[3, 4, 0], 0)
npt.assert_almost_equal(percept.data[3, 4, 1], pmax[1])
npt.assert_almost_equal(percept.time, [0, 1])