def test_AxonMapModel():
set_params = {'xystep': 2, 'engine': 'serial', '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 = models.AxonMapModel()
for param in set_params:
npt.assert_equal(hasattr(model, param), True)
# User can override default values
for key, value in set_params.items():
setattr(model, key, value)
npt.assert_equal(getattr(model, key), value)
model = models.AxonMapModel(**set_params)
model.build(**set_params)
for key, value in set_params.items():
npt.assert_equal(getattr(model, key), value)
# Zeros in, zeros out:
implant = implants.ArgusII(stim=np.zeros(60))
npt.assert_almost_equal(model.predict_percept(implant), 0)
implant.stim = np.zeros(60)
npt.assert_almost_equal(model.predict_percept(implant), 0)
# Implant and model must be built for same eye:
with pytest.raises(ValueError):
implant = implants.ArgusII(eye='LE', stim=np.zeros(60))
model.predict_percept(implant)
def test_AxonMapModel_predict_percept():
model = models.AxonMapModel(xystep=1, axlambda=100, thresh_percept=0)
model.build()
# Single-electrode stim:
img_stim = np.zeros(60)
img_stim[47] = 1
percept = model.predict_percept(implants.ArgusII(stim=img_stim))
# Single bright pixel, rest of arc is less bright:
npt.assert_equal(np.sum(percept > 0.9), 1)
npt.assert_equal(np.sum(percept > 0.5), 2)
npt.assert_equal(np.sum(percept > 0.1), 8)
npt.assert_equal(np.sum(percept > 0.0001), 28)
# Overall only a few bright pixels:
npt.assert_almost_equal(np.sum(percept), 3.207, decimal=3)
# Brightest pixel is in lower right:
npt.assert_almost_equal(percept[18, 25], np.max(percept))
# Top half is empty:
npt.assert_almost_equal(np.sum(percept[:15, :]), 0)
# Same for lower band:
npt.assert_almost_equal(np.sum(percept[21:, :]), 0)
# Full Argus II with small lambda: 60 bright spots
model = models.AxonMapModel(engine='serial', xystep=1, rho=100,
axlambda=40)
model.build()
percept = model.predict_percept(implants.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 > 0.5), 58)
npt.assert_equal(np.sum(percept > 0.275), 60)
def test_BaseModel_predict_percept():
img_stim = np.zeros(60)
model = ValidBaseModel(engine='serial',
xystep=5,
xrange=(-30, 30),
yrange=(-20, 20))
# Model must be built first:
with pytest.raises(models.NotBuiltError):
model.predict_percept(implants.ArgusII())
# But then must pass through ``predict_percept`` just fine
model.build()
percept = model.predict_percept(implants.ArgusII(stim=img_stim))
npt.assert_equal(percept.shape, (9, 13))
npt.assert_almost_equal(percept, 0)
# Requires ProsthesisSystem object:
with pytest.raises(TypeError):
model.predict_percept(img_stim)
# None in, None out:
npt.assert_equal(model.predict_percept(implants.ArgusII(stim=None)), None)
# `img_stim` must have right size:
for shape in [(2, 60), (59, ), (2, 3, 4)]:
with pytest.raises(ValueError):
model.predict_percept(implants.ArgusII(stim=np.zeros(shape)))
# Single-pixel percept:
model = ValidBaseModel(engine='serial', xrange=(0.45, 0.45), yrange=(0, 0))
model.build()
percept = model.predict_percept(implants.ArgusII(stim=np.zeros(60)))
npt.assert_equal(percept.shape, (1, 1))
npt.assert_almost_equal(percept, 0)
def test_BaseModel_fit():
# Create a valid DataFrame
X = get_dummy_data(nrows=3)
# Model must be fitted first thing
model = ValidBaseModel(engine='serial')
npt.assert_equal(model._is_fitted, False)
model.fit(X)
npt.assert_equal(model._is_fitted, True)
npt.assert_equal(hasattr(model, 'implant'), True)
npt.assert_equal(hasattr(model, 'implant_type'), True)
npt.assert_equal(isinstance(model.implant, model.implant_type), True)
# `fit` only accepts DataFrame
for XX in [42, [3.3, 1.1], np.array([[0]]), {'img': [[2]]}]:
with pytest.raises(TypeError):
model.fit(XX)
yy = pd.DataFrame([{'img': [[2]]}, {'img': [[4]]}], index=[0, 1])
for XX in [42, [3.3, 1.1], {'img': [[2]]}]:
with pytest.raises(TypeError):
model.fit(XX, y=yy)
for yy in [42, [3.3, 1.1], {'img': [[2]]}]:
with pytest.raises(TypeError):
model.fit(X, y=yy)
# We must pass an implant type, not an implant instance
with pytest.raises(TypeError):
model = ValidBaseModel(engine='serial', implant_type=p2pi.ArgusII())
model.fit(X)
with pytest.raises(TypeError):
model = ValidBaseModel(engine='serial')
model.set_params(implant_type=p2pi.ArgusII())
model.fit(X)
with pytest.raises(TypeError):
model = ValidBaseModel(engine='serial')
model.fit(X, implant_type=p2pi.ArgusII())
# Implant rotation must be in radians:
with pytest.raises(ValueError):
model = ValidBaseModel(implant_rot=180)
model.fit(X)
# `fit_params` must take effect
model = ValidBaseModel(engine='serial')
model_params = model.get_params()
for key, value in six.iteritems(model_params):
npt.assert_equal(getattr(model, key), value)
if isinstance(value, (int, float)):
set_param = {key: 0.1234}
elif isinstance(value, (list, set, tuple, np.ndarray)):
set_param = {key: np.array([0, 0])}
else:
continue
model.fit(X, **set_param)
npt.assert_equal(getattr(model, key), set_param[key])
def test_ScoreboardModel_predict_percept():
model = models.ScoreboardModel(xystep=1, rho=100, thresh_percept=0)
model.build()
# Single-electrode stim:
img_stim = np.zeros(60)
img_stim[47] = 1
percept = model.predict_percept(implants.ArgusII(stim=img_stim))
# Single bright pixel, very small Gaussian kernel:
npt.assert_equal(np.sum(percept > 0.9), 1)
npt.assert_equal(np.sum(percept > 0.5), 1)
npt.assert_equal(np.sum(percept > 0.1), 1)
npt.assert_equal(np.sum(percept > 0.00001), 9)
# Brightest pixel is in lower right:
npt.assert_almost_equal(percept[18, 25], np.max(percept))
# Full Argus II: 60 bright spots
model = models.ScoreboardModel(engine='serial', xystep=1, rho=100)
model.build()
percept = model.predict_percept(implants.ArgusII(stim=np.ones(60)))
npt.assert_equal(np.sum(np.isclose(percept, 0.9, rtol=0.1, atol=0.1)), 60)
def test_ArgusII(ztype, x, y, rot):
# Create an ArgusII and make sure location is correct
# Height `h` can either be a float or a list
z = 100 if ztype == 'float' else np.ones(60) * 20
argus = implants.ArgusII(x=x, y=y, z=z, rot=rot)
# Slots:
npt.assert_equal(hasattr(argus, '__slots__'), True)
npt.assert_equal(hasattr(argus, '__dict__'), False)
# Coordinates of first electrode
xy = np.array([-2587.5, -1437.5]).T
# Rotate
rot_rad = np.deg2rad(rot)
R = np.array(
[np.cos(rot_rad), -np.sin(rot_rad),
np.sin(rot_rad),
np.cos(rot_rad)]).reshape((2, 2))
xy = np.matmul(R, xy)
# Then off-set: Make sure first electrode is placed
# correctly
npt.assert_almost_equal(argus['A1'].x, xy[0] + x)
npt.assert_almost_equal(argus['A1'].y, xy[1] + y)
# Make sure array center is still (x,y)
y_center = argus['F1'].y + (argus['A10'].y - argus['F1'].y) / 2
npt.assert_almost_equal(y_center, y)
x_center = argus['A1'].x + (argus['F10'].x - argus['A1'].x) / 2
npt.assert_almost_equal(x_center, x)
# Make sure radius is correct
for e in ['A1', 'B3', 'C5', 'D7', 'E9', 'F10']:
npt.assert_almost_equal(argus[e].r, 112.5)
# `h` must have the right dimensions
with pytest.raises(ValueError):
implants.ArgusII(x=-100, y=10, z=np.zeros(5))
with pytest.raises(ValueError):
implants.ArgusII(x=-100, y=100, z=[1, 2, 3])
# Indexing must work for both integers and electrode names
argus = implants.ArgusII()
for idx, (name, electrode) in enumerate(argus.electrodes.items()):
npt.assert_equal(electrode, argus[idx])
npt.assert_equal(electrode, argus[name])
npt.assert_equal(argus["unlikely name for an electrode"], None)
# Right-eye implant:
xc, yc = 500, -500
argus_re = implants.ArgusII(eye='RE', x=xc, y=yc)
npt.assert_equal(argus_re['A10'].x > argus_re['A1'].x, True)
npt.assert_almost_equal(argus_re['A10'].y, argus_re['A1'].y)
# Left-eye implant:
argus_le = implants.ArgusII(eye='LE', x=xc, y=yc)
npt.assert_equal(argus_le['A1'].x > argus_le['A10'].x, True)
npt.assert_almost_equal(argus_le['A10'].y, argus_le['A1'].y)
# In both left and right eyes, rotation with positive angle should be
# counter-clock-wise (CCW): for (x>0,y>0), decreasing x and increasing y
for eye, el in zip(['LE', 'RE'], ['F2', 'F10']):
# By default, electrode 'F1' in a left eye has the same coordinates as
# 'F10' in a right eye (because the columns are reversed). Thus both
# cases are testing an electrode with x>0, y>0:
before = implants.ArgusII(eye=eye)
after = implants.ArgusII(eye=eye, rot=20)
npt.assert_equal(after[el].x < before[el].x, True)
npt.assert_equal(after[el].y > before[el].y, True)
# Set a stimulus via dict:
argus = implants.ArgusII(stim={'B7': 13})
npt.assert_equal(argus.stim.shape, (1, 1))
npt.assert_equal(argus.stim.electrodes, ['B7'])
# Set a stimulus via array:
argus = implants.ArgusII(stim=np.ones(60))
npt.assert_equal(argus.stim.shape, (60, 1))
npt.assert_almost_equal(argus.stim.data, 1)
