def test_ElectrodeArray():
with pytest.raises(TypeError):
ElectrodeArray("foo")
with pytest.raises(TypeError):
ElectrodeArray(OrderedDict({'A1': 0}))
with pytest.raises(TypeError):
ElectrodeArray([0])
# Empty array:
earray = ElectrodeArray([])
npt.assert_equal(earray.n_electrodes, 0)
# npt.assert_equal(earray[0], None)
npt.assert_equal(earray['A01'], None)
with pytest.raises(TypeError):
earray[PointSource(0, 0, 0)]
ElectrodeArray([])
# A single electrode:
earray = ElectrodeArray(PointSource(0, 1, 2))
npt.assert_equal(earray.n_electrodes, 1)
npt.assert_equal(isinstance(earray[0], PointSource), True)
npt.assert_equal(isinstance(earray[[0]], list), True)
npt.assert_equal(isinstance(earray[[0]][0], PointSource), True)
npt.assert_almost_equal(earray[0].x, 0)
npt.assert_almost_equal(earray[0].y, 1)
npt.assert_almost_equal(earray[0].z, 2)
# Indexing:
ps1, ps2 = PointSource(0, 0, 0), PointSource(1, 1, 1)
earray = ElectrodeArray({'A01': ps1, 'D07': ps2})
npt.assert_equal(earray['A01'], ps1)
npt.assert_equal(earray['D07'], ps2)
# Slots:
npt.assert_equal(hasattr(earray, '__slots__'), True)
npt.assert_equal(hasattr(earray, '__dict__'), False)
def test_ProsthesisSystem():
# Invalid instantiations:
with pytest.raises(ValueError):
ProsthesisSystem(ElectrodeArray(PointSource(0, 0, 0)), eye='both')
# Iterating over the electrode array:
implant = ProsthesisSystem(PointSource(0, 0, 0))
npt.assert_equal(implant.n_electrodes, 1)
npt.assert_equal(implant[0], implant.earray[0])
npt.assert_equal(implant.keys(), implant.earray.keys())
# Set a stimulus after the constructor:
npt.assert_equal(implant.stim, None)
implant.stim = 3
npt.assert_equal(isinstance(implant.stim, Stimulus), True)
npt.assert_equal(implant.stim.shape, (1, 1))
npt.assert_equal(implant.stim.time, None)
npt.assert_equal(implant.stim.electrodes, [0])
with pytest.raises(ValueError):
# Wrong number of stimuli
implant.stim = [1, 2]
with pytest.raises(TypeError):
# Invalid stim type:
implant.stim = "stim"
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_ElectrodeArray_remove_electrode():
earray1 = ElectrodeArray([])
earray2 = ElectrodeArray([])
npt.assert_equal(earray1.n_electrodes, 0)
# Can't remove electrodes from empty electrodeArray
with pytest.raises(ValueError):
earray1.remove_electrode(None)
with pytest.raises(ValueError):
earray1.remove_electrode("foo")
key = [0] * 4
key[0] = 'D03'
key[1] = 'A02'
key[2] = 'F10'
key[3] = 'E12'
earray1.add_electrode(key[0], PointSource(0, 1, 2))
earray1.add_electrode(key[1], PointSource(3, 4, 5))
earray1.add_electrode(key[2], PointSource(6, 7, 8))
earray1.add_electrode(key[3], PointSource(9, 10, 11))
npt.assert_equal(earray1.n_electrodes, 4)
earray2.add_electrode(key[0], PointSource(0, 1, 2))
earray2.add_electrode(key[1], PointSource(3, 4, 5))
earray2.add_electrode(key[2], PointSource(6, 7, 8))
earray2.add_electrode(key[3], PointSource(9, 10, 11))
npt.assert_equal(earray2.n_electrodes, 4)
# Remove one electrode key[1] from the electrodeArray
earray1.remove_electrode(key[0])
npt.assert_equal(earray1.n_electrodes, 3)
# Can't remove an electrode that has been removed
with pytest.raises(ValueError):
earray1.remove_electrode(key[0])
# List keeps order:
npt.assert_equal(earray1[0], earray1[key[1]])
npt.assert_equal(earray1[1], earray1[key[2]])
npt.assert_equal(earray1[2], earray1[key[3]])
# Other electrodes stay the same
for k in [key[1], key[2], key[3]]:
npt.assert_equal(earray1[k].x, earray2[k].x)
npt.assert_equal(earray1[k].y, earray2[k].y)
npt.assert_equal(earray1[k].z, earray2[k].z)
# Remove two more electrodes from the electrodeArray
# List keeps order
earray1.remove_electrode(key[1])
earray1.remove_electrode(key[2])
npt.assert_equal(earray1.n_electrodes, 1)
npt.assert_equal(earray1[0], earray1[key[3]])
# The last electrode stays the same
for key in [key[3]]:
npt.assert_equal(earray1[key].x, earray2[key].x)
npt.assert_equal(earray1[key].y, earray2[key].y)
npt.assert_equal(earray1[key].z, earray2[key].z)
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_ProsthesisSystem():
# Invalid instantiations:
with pytest.raises(ValueError):
ProsthesisSystem(ElectrodeArray(PointSource(0, 0, 0)),
eye='both')
with pytest.raises(TypeError):
ProsthesisSystem(Stimulus)
# Iterating over the electrode array:
implant = ProsthesisSystem(PointSource(0, 0, 0))
npt.assert_equal(implant.n_electrodes, 1)
npt.assert_equal(implant[0], implant.earray[0])
npt.assert_equal(implant.electrode_names, implant.earray.electrode_names)
for i, e in zip(implant, implant.earray):
npt.assert_equal(i, e)
# Set a stimulus after the constructor:
npt.assert_equal(implant.stim, None)
implant.stim = 3
npt.assert_equal(isinstance(implant.stim, Stimulus), True)
npt.assert_equal(implant.stim.shape, (1, 1))
npt.assert_equal(implant.stim.time, None)
npt.assert_equal(implant.stim.electrodes, [0])
ax = implant.plot()
npt.assert_equal(len(ax.texts), 0)
npt.assert_equal(len(ax.collections), 1)
with pytest.raises(ValueError):
# Wrong number of stimuli
implant.stim = [1, 2]
with pytest.raises(TypeError):
# Invalid stim type:
implant.stim = "stim"
# Invalid electrode names:
with pytest.raises(ValueError):
implant.stim = {'A1': 1}
with pytest.raises(ValueError):
implant.stim = Stimulus({'A1': 1})
# Safe mode requires charge-balanced pulses:
with pytest.raises(ValueError):
implant = ProsthesisSystem(PointSource(0, 0, 0), safe_mode=True)
implant.stim = 1
# Slots:
npt.assert_equal(hasattr(implant, '__slots__'), True)
npt.assert_equal(hasattr(implant, '__dict__'), False)
def test_PointSource():
electrode = PointSource(0, 1, 2)
npt.assert_almost_equal(electrode.x, 0)
npt.assert_almost_equal(electrode.y, 1)
npt.assert_almost_equal(electrode.z, 2)
npt.assert_almost_equal(electrode.electric_potential(0, 1, 2, 1, 1), 1)
npt.assert_almost_equal(electrode.electric_potential(0, 0, 0, 1, 1),
0.035,
decimal=3)
def test_PointSource():
electrode = PointSource(0, 1, 2)
npt.assert_almost_equal(electrode.x, 0)
npt.assert_almost_equal(electrode.y, 1)
npt.assert_almost_equal(electrode.z, 2)
npt.assert_almost_equal(electrode.electric_potential(0, 1, 2, 1, 1), 1)
npt.assert_almost_equal(electrode.electric_potential(0, 0, 0, 1, 1),
0.035,
decimal=3)
# Slots:
npt.assert_equal(hasattr(electrode, '__slots__'), True)
npt.assert_equal(hasattr(electrode, '__dict__'), False)
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)
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_PointSource():
electrode = PointSource(0, 1, 2)
npt.assert_almost_equal(electrode.x, 0)
npt.assert_almost_equal(electrode.y, 1)
npt.assert_almost_equal(electrode.z, 2)
npt.assert_almost_equal(electrode.electric_potential(0, 1, 2, 1, 1), 1)
npt.assert_almost_equal(electrode.electric_potential(0, 0, 0, 1, 1),
0.035,
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_ElectrodeArray_add_electrodes():
earray = ElectrodeArray([])
npt.assert_equal(earray.n_electrodes, 0)
with pytest.raises(TypeError):
earray.add_electrodes(None)
with pytest.raises(TypeError):
earray.add_electrodes("foo")
# Add 2 electrodes, keep order:
key = [0] * 6
key[0] = 'D03'
key[1] = 'A02'
earray.add_electrodes({key[0]: PointSource(0, 1, 2)})
earray.add_electrodes({key[1]: PointSource(3, 4, 5)})
npt.assert_equal(earray[0], earray[key[0]])
npt.assert_equal(earray[1], earray[key[1]])
# Can't add the same key twice:
with pytest.raises(ValueError):
earray.add_electrodes({key[0]: PointSource(3, 5, 7)})
# Add 2 more, now keep order:
key[2] = 'F10'
key[3] = 'E12'
earray.add_electrodes({key[2]: PointSource(6, 7, 8)})
earray.add_electrodes({key[3]: PointSource(9, 10, 11)})
npt.assert_equal(earray[0], earray[key[0]])
npt.assert_equal(earray[1], earray[key[1]])
npt.assert_equal(earray[2], earray[key[2]])
npt.assert_equal(earray[3], earray[key[3]])
# List keeps order:
earray.add_electrodes([PointSource(12, 13, 14), PointSource(15, 16, 17)])
npt.assert_equal(earray[0], earray[key[0]])
npt.assert_equal(earray[1], earray[key[1]])
npt.assert_equal(earray[2], earray[key[2]])
npt.assert_equal(earray[3], earray[key[3]])
npt.assert_equal(earray[4].x, 12)
npt.assert_equal(earray[5].x, 15)
# Order is preserved in for loop:
for i, (key, val) in enumerate(earray.items()):
npt.assert_equal(earray[i], earray[key])
npt.assert_equal(earray[i], val)
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 _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