def test_RecExtElectrode_04(self):
"""test RecExcElectrode implementation,
method='root_as_point' and rootinds parameter"""
cell = get_cell(n_seg=4)
sigma = 0.3
r = np.array([1, 0, 2])
# all point sources
el0 = lfp.PointSourcePotential(cell=cell,
x=np.array([r[0]]),
y=np.array([r[1]]),
z=np.array([r[2]]),
sigma=sigma)
M0 = el0.get_transformation_matrix()
# all line sources
el1 = lfp.LineSourcePotential(cell=cell,
x=np.array([r[0]]),
y=np.array([r[1]]),
z=np.array([r[2]]),
sigma=sigma)
M1 = el1.get_transformation_matrix()
# vary which index is treated as point
ids = np.arange(cell.totnsegs)
for i in range(cell.totnsegs):
el = lfp.RecExtElectrode(cell=cell,
x=r[0],
y=r[1],
z=r[2],
sigma=sigma,
method='root_as_point',
rootinds=np.array([i]))
M = el.get_transformation_matrix()
np.testing.assert_almost_equal(M0[0, i], M[0, i])
np.testing.assert_equal(M1[0, ids != i], M[0, ids != i])
# multiple roots
for i in range(cell.totnsegs - 1):
rootinds = np.array([i, i + 1])
notroots = np.ones(cell.totnsegs, dtype=bool)
notroots[rootinds] = False
el = lfp.RecExtElectrode(cell=cell,
x=r[0],
y=r[1],
z=r[2],
sigma=sigma,
method='root_as_point',
rootinds=rootinds)
M = el.get_transformation_matrix()
np.testing.assert_allclose(M0[0, rootinds], M[0, rootinds])
np.testing.assert_equal(M1[0, notroots], M[0, notroots])
def test_RecExtElectrode_03(self):
"""test RecExcElectrode implementation,
method='pointsource' with anisotropy"""
cell = get_cell(n_seg=1)
cell.x = np.array([[0., 2.4]])
cell.y = np.array([[0., 2.4]])
cell.z = np.array([[0., 2.4]])
sigma = [0.6, 0.3, 0.45]
r = np.array([[0.], [0.], [0.]])
el = lfp.RecExtElectrode(cell=cell,
x=r[0],
y=r[1],
z=r[2],
sigma=sigma,
method='pointsource')
M = el.get_transformation_matrix()
imem = np.array([[0., 1., -1.]])
V_ex = M @ imem
sigma_r = np.sqrt(sigma[1] * sigma[2] * 1.2**2 +
sigma[0] * sigma[2] * 1.2**2 +
sigma[0] * sigma[1] * 1.2**2)
V_gt = np.array([[0., 1., -1.]]) / (4 * np.pi * sigma_r)
np.testing.assert_allclose(V_ex, V_gt)
def test_RecExtElectrode_01(self):
"""test LineSourcePotential implementation,
method='linesource'"""
cell = get_cell(n_seg=1)
cell.z = cell.z * 10
el = lfp.RecExtElectrode(cell=cell,
x=np.array([2.]),
y=np.array([0.]),
z=np.array([5.]),
sigma=0.3,
method='linesource')
M = el.get_transformation_matrix()
imem = np.array([[0., 1., -1.]])
V_ex = M @ imem
Deltas_n = 10.
h_n = -5.
r_n = 2.
l_n = Deltas_n + h_n
# Use Eq. C.13 case II (h<0, l>0) from Gary Holt's 1998 thesis
V_gt = imem / (4 * np.pi * el.sigma * Deltas_n) * np.log(
(np.sqrt(h_n**2 + r_n**2) - h_n) *
(np.sqrt(l_n**2 + r_n**2) + l_n) / r_n**2)
np.testing.assert_allclose(V_ex, V_gt)
def test_RecExtElectrode_02(self):
"""test RecExcElectrode implementation,
method='root_as_point'"""
cell = get_cell(n_seg=1)
sigma = 0.3
r = np.array([[cell.d[0]], [0.], [cell.z.mean()]])
el = lfp.RecExtElectrode(cell=cell,
x=r[0],
y=r[1, ],
z=r[2, ],
sigma=sigma,
method='root_as_point')
M = el.get_transformation_matrix()
imem = np.array([[0., 1., -1.]]) * (4 * np.pi * sigma * cell.d[0])
V_ex = M @ imem
V_gt = np.array([[0., 1., -1.]])
np.testing.assert_allclose(V_ex, V_gt)