def test_calc_lfp_pointsource_moi_infinite_slice(self):
"""
Test that infinitely thick slice does not affect potential.
"""
sigma_T = 0.3
sigma_G = 0.0
sigma_S = 1.5
h = 1e10
steps = 20
cell = TestCell()
cell.zstart[0] = 100
cell.zmid[0] = 100
cell.zend[0] = 100
with_saline = lfpcalc.calc_lfp_pointsource_moi(cell,
x=0, y=0, z=50, sigma_T=sigma_T,
sigma_G=sigma_G, sigma_S=sigma_S,
r_limit=cell.diam/2, h=h, steps=steps)
without_saline = lfpcalc.calc_lfp_pointsource_moi(cell,
x=0, y=0, z=50, sigma_T=sigma_T,
sigma_G=sigma_G, sigma_S=sigma_T,
r_limit=cell.diam/2, h=h, steps=steps)
np.testing.assert_almost_equal(with_saline, without_saline)
def test_calc_lfp_pointsource_moi_saline_effect(self):
"""
Test that the saline bath decreases signal as expected
"""
sigma_T = 0.3
sigma_G = 0.0
sigma_S = 1.5
h = 200
steps = 20
cell = TestCell()
cell.zstart[0] = 100
cell.zmid[0] = 100
cell.zend[0] = 100
with_saline = lfpcalc.calc_lfp_pointsource_moi(cell,
x=0, y=0, z=0, sigma_T=sigma_T,
sigma_G=sigma_G, sigma_S=sigma_S,
r_limit=cell.diam/2, h=h, steps=steps)
without_saline = lfpcalc.calc_lfp_pointsource_moi(cell,
x=0, y=0, z=0, sigma_T=sigma_T,
sigma_G=sigma_G, sigma_S=sigma_T,
r_limit=cell.diam/2, h=h, steps=steps)
np.testing.assert_array_less(with_saline, without_saline)
def test_calc_lfp_pointsource_moi_saline_effect(self):
"""
Test that the saline bath decreases signal as expected
"""
sigma_T = 0.3
sigma_G = 0.0
sigma_S = 1.5
h = 200
steps = 20
cell = DummyCell()
cell.zstart[0] = 100
cell.zmid[0] = 100
cell.zend[0] = 100
with_saline = lfpcalc.calc_lfp_pointsource_moi(cell,
x=0, y=0, z=0, sigma_T=sigma_T,
sigma_G=sigma_G, sigma_S=sigma_S,
r_limit=cell.diam/2, h=h, steps=steps)
without_saline = lfpcalc.calc_lfp_pointsource_moi(cell,
x=0, y=0, z=0, sigma_T=sigma_T,
sigma_G=sigma_G, sigma_S=sigma_T,
r_limit=cell.diam/2, h=h, steps=steps)
np.testing.assert_array_less(with_saline, without_saline)
def test_calc_lfp_pointsource_moi_infinite_slice(self):
"""
Test that infinitely thick slice does not affect potential.
"""
sigma_T = 0.3
sigma_G = 0.0
sigma_S = 1.5
h = 1e10
steps = 20
cell = DummyCell()
cell.zstart[0] = 100
cell.zmid[0] = 100
cell.zend[0] = 100
with_saline = lfpcalc.calc_lfp_pointsource_moi(cell,
x=0, y=0, z=50, sigma_T=sigma_T,
sigma_G=sigma_G, sigma_S=sigma_S,
r_limit=cell.diam/2, h=h, steps=steps)
without_saline = lfpcalc.calc_lfp_pointsource_moi(cell,
x=0, y=0, z=50, sigma_T=sigma_T,
sigma_G=sigma_G, sigma_S=sigma_T,
r_limit=cell.diam/2, h=h, steps=steps)
np.testing.assert_almost_equal(with_saline, without_saline)
def test_calc_lfp_pointsource_moi_doubling(self):
"""
Test that slice with zero-conductivity MEA region (z<0) has twice
the potential as in vivo case at MEA electrode plane
"""
sigma_T = 0.3
sigma_G = 0.0
sigma_S = 0.3
h = 200
steps = 3
cell = TestCell()
cell.zstart[0] = 50
cell.zmid[0] = 50
cell.zend[0] = 50
in_vivo = lfpcalc.calc_lfp_pointsource(cell,
x=50., y=0, z=0, sigma=sigma_T,
r_limit=cell.diam/2)
in_vitro = lfpcalc.calc_lfp_pointsource_moi(cell,
x=50, y=0, z=0, sigma_T=sigma_T,
sigma_G=sigma_G, sigma_S=sigma_S,
r_limit=cell.diam/2, h=h, steps=steps)
np.testing.assert_almost_equal(2 * in_vivo, in_vitro, decimal=9)
def test_calc_lfp_moi_ecog(self):
"""
Test that LFPy ECoG scenario gives expected analytical result
"""
sigma_T = 0.3
sigma_G = 0.3
sigma_S = 1.5
h = 5000
steps = 20
cell = DummyCell()
cell.zmid[0] = h - 50
cell.zstart[0] = h - 50
cell.zend[0] = h - 50
cell.xmid[0] = 0
cell.xstart[0] = 0
cell.xend[0] = 0
source_scaling = (sigma_T - sigma_S) / (sigma_S + sigma_T)
z = h - 20 # Recording position z <= h, z != cell.zmid[0]
analytic = cell.imem[0] / (4 * np.pi * sigma_T) * (
1 / np.abs(z - cell.zmid[0]) + # real source
source_scaling / np.abs(z - (2 * h - cell.zmid[0])) # image source
)
moi_method_lfpy = lfpcalc.calc_lfp_pointsource_moi(cell,
x=0., y=0, z=z, sigma_T=sigma_T,
sigma_G=sigma_G, sigma_S=sigma_S,
r_limit=cell.diam/2, h=h, steps=steps)
np.testing.assert_equal(analytic, moi_method_lfpy)
def test_calc_lfp_pointsource_moi_homogeneous(self):
"""
Test that slice where all layers have same conductivity reproduces
in vivo results.
"""
sigma_T = 0.3
sigma_G = 0.3
sigma_S = 0.3
h = 300
steps = 20
cell = TestCell()
cell.zmid[0] = h / 2
cell.zstart[0] = h / 2
cell.zend[0] = h / 2
in_vivo = lfpcalc.calc_lfp_pointsource(cell,
x=0.5,
y=0,
z=1,
sigma=sigma_T,
r_limit=cell.diam / 2)
in_vitro = lfpcalc.calc_lfp_pointsource_moi(cell,
x=0.5,
y=0,
z=1,
sigma_T=sigma_T,
sigma_G=sigma_G,
sigma_S=sigma_S,
r_limit=cell.diam / 2,
h=h,
steps=steps)
np.testing.assert_equal(in_vivo, in_vitro)
def test_calc_lfp_pointsource_moi_doubling(self):
"""
Test that slice with zero-conductivity MEA region (z<0) has twice
the potential as in vivo case at MEA electrode plane
"""
sigma_T = 0.3
sigma_G = 0.0
sigma_S = 0.3
h = 200
steps = 3
cell = DummyCell()
cell.zstart[0] = 50
cell.zmid[0] = 50
cell.zend[0] = 50
in_vivo = lfpcalc.calc_lfp_pointsource(cell,
x=50., y=0, z=0, sigma=sigma_T,
r_limit=cell.diam/2)
in_vitro = lfpcalc.calc_lfp_pointsource_moi(cell,
x=50, y=0, z=0, sigma_T=sigma_T,
sigma_G=sigma_G, sigma_S=sigma_S,
r_limit=cell.diam/2, h=h, steps=steps)
np.testing.assert_almost_equal(2 * in_vivo, in_vitro, decimal=9)
def test_lfpcalc_calc_lfp_pointsource_moi_01(self):
"""
Test that ECoG scenario gives expected analytical result
"""
sigma_T = 0.3
sigma_G = 0.3
sigma_S = 1.5
h = 5000
steps = 20
cell = DummyCell(x=np.array([[0, 0]]), z=np.array([[h - 50, h - 50]]))
source_scaling = (sigma_T - sigma_S) / (sigma_S + sigma_T)
z = h - 20 # Recording position z <= h, z != cell.z.mean(axis=-1)[0]
analytic = cell.imem[0] / (4 * np.pi * sigma_T) * (
1 / np.abs(z - cell.z.mean(axis=-1)[0]) + # real source
# image source
source_scaling / np.abs(z - (2 * h - cell.z.mean(axis=-1)[0])))
moi_method_lfpy = lfpcalc.calc_lfp_pointsource_moi(cell,
x=0.,
y=0,
z=z,
sigma_T=sigma_T,
sigma_G=sigma_G,
sigma_S=sigma_S,
r_limit=cell.d / 2,
h=h,
steps=steps)
np.testing.assert_equal(analytic, moi_method_lfpy)
def test_lfpcalc_calc_lfp_pointsource_moi_00(self):
"""
Test slice where all layers have same conductivity reproduces
isotropic case.
"""
sigma_T = 0.3
sigma_G = 0.3
sigma_S = 0.3
h = 300
steps = 20
cell = DummyCell(np.array([[h / 2, h / 2]]))
in_vivo = lfpcalc.calc_lfp_pointsource(cell,
x=0.5,
y=0,
z=1,
sigma=sigma_T,
r_limit=cell.d / 2)
in_vitro = lfpcalc.calc_lfp_pointsource_moi(cell,
x=0.5,
y=0,
z=1,
sigma_T=sigma_T,
sigma_G=sigma_G,
sigma_S=sigma_S,
r_limit=cell.d / 2,
h=h,
steps=steps)
np.testing.assert_equal(in_vivo, in_vitro)
def test_lfpcalc_calc_lfp_pointsource_moi_20steps(self):
"""
Test that the calc_lfp_pointsource_moi reproduces previously known
nummerical value
"""
sigma_T = 0.3
sigma_G = 0.0
sigma_S = 1.5
h = 200
steps = 20
correct = 0.00108189
cell = DummyCell(x=np.array([[0., -200.]]), z=np.array(([[0., 220.]])))
calculated = lfpcalc.calc_lfp_pointsource_moi(cell,
x=100,
y=0,
z=0,
sigma_T=sigma_T,
sigma_G=sigma_G,
sigma_S=sigma_S,
r_limit=cell.d / 2,
h=h,
steps=steps)
np.testing.assert_almost_equal(correct, calculated, 5)
def test_lfpcalc_calc_lfp_pointsource_moi_02(self):
"""
Very close to point source, in vivo and in vitro have similar results,
e.g., the positions should be adjusted similarly.
"""
sigma_T = 0.3
sigma_G = 0.0
sigma_S = 1.5
h = 2000
steps = 20
cell = DummyCell(z=np.array([[h / 2, h / 2]]))
in_vivo = lfpcalc.calc_lfp_pointsource(cell,
x=0.5,
y=0,
z=h / 2,
sigma=sigma_T,
r_limit=cell.d / 2)
in_vitro = lfpcalc.calc_lfp_pointsource_moi(cell,
x=0.5,
y=0,
z=h / 2,
sigma_T=sigma_T,
sigma_G=sigma_G,
sigma_S=sigma_S,
r_limit=cell.d / 2,
h=h,
steps=steps)
np.testing.assert_almost_equal(in_vivo, in_vitro, 4)
def test_calc_lfp_pointsource_moi_too_close(self):
"""
Very close to point source, in vivo and in vitro have similar results,
e.g., the positions should be adjusted similarly.
"""
sigma_T = 0.3
sigma_G = 0.0
sigma_S = 1.5
h = 2000
steps = 20
cell = TestCell()
cell.zmid[0] = h / 2
cell.zstart[0] = h / 2
cell.zend[0] = h / 2
in_vivo = lfpcalc.calc_lfp_pointsource(cell,
x=0.5,
y=0,
z=h / 2,
sigma=sigma_T,
r_limit=cell.diam / 2)
in_vitro = lfpcalc.calc_lfp_pointsource_moi(cell,
x=0.5,
y=0,
z=h / 2,
sigma_T=sigma_T,
sigma_G=sigma_G,
sigma_S=sigma_S,
r_limit=cell.diam / 2,
h=h,
steps=steps)
np.testing.assert_almost_equal(in_vivo, in_vitro, 4)
def test_calc_lfp_moi_ecog(self):
"""
Test that LFPy ECoG scenario gives expected analytical result
"""
sigma_T = 0.3
sigma_G = 0.3
sigma_S = 1.5
h = 5000
steps = 20
cell = TestCell()
cell.zmid[0] = h - 50
cell.zstart[0] = h - 50
cell.zend[0] = h - 50
cell.xmid[0] = 0
cell.xstart[0] = 0
cell.xend[0] = 0
source_scaling = (sigma_T - sigma_S) / (sigma_S + sigma_T)
z = h - 20 # Recording position z <= h, z != cell.zmid[0]
analytic = cell.imem[0] / (4 * np.pi * sigma_T) * (
1 / np.abs(z - cell.zmid[0]) + # real source
source_scaling / np.abs(z - (2 * h - cell.zmid[0])) # image source
)
moi_method_lfpy = lfpcalc.calc_lfp_pointsource_moi(cell,
x=0., y=0, z=z, sigma_T=sigma_T,
sigma_G=sigma_G, sigma_S=sigma_S,
r_limit=cell.diam/2, h=h, steps=steps)
np.testing.assert_equal(analytic, moi_method_lfpy)
def test_calc_lfp_pointsource_moi_20steps(self):
"""
Test that the calc_lfp_pointsource_moi reproduces previously known
nummerical value
"""
sigma_T = 0.3
sigma_G = 0.0
sigma_S = 1.5
h = 200
steps = 20
correct = 0.00108189
cell = TestCell()
cell.zmid[0] = 110
cell.xmid[0] = -100
calculated = lfpcalc.calc_lfp_pointsource_moi(cell,
x=100,
y=0,
z=0,
sigma_T=sigma_T,
sigma_G=sigma_G,
sigma_S=sigma_S,
r_limit=cell.diam / 2,
h=h,
steps=steps)
np.testing.assert_almost_equal(correct, calculated, 5)
def test_calc_lfp_pointsource_moi_20steps(self):
"""
Test that the calc_lfp_pointsource_moi reproduces previously known
nummerical value
"""
sigma_T = 0.3
sigma_G = 0.0
sigma_S = 1.5
h = 200
steps = 20
correct = 0.00108189
cell = TestCell()
cell.zmid[0] = 110
cell.xmid[0] = -100
calculated = lfpcalc.calc_lfp_pointsource_moi(cell,
x=100, y=0, z=0, sigma_T=sigma_T,
sigma_G=sigma_G, sigma_S=sigma_S,
r_limit=cell.diam/2, h=h, steps=steps)
np.testing.assert_almost_equal(correct, calculated, 5)
def test_calc_lfp_pointsource_moi_homogeneous(self):
"""
Test that slice where all layers have same conductivity reproduces
in vivo results.
"""
sigma_T = 0.3
sigma_G = 0.3
sigma_S = 0.3
h = 300
steps = 20
cell = TestCell()
cell.zmid[0] = h/2
cell.zstart[0] = h/2
cell.zend[0] = h/2
in_vivo = lfpcalc.calc_lfp_pointsource(cell,
x=0.5, y=0, z=1, sigma=sigma_T,
r_limit=cell.diam/2)
in_vitro = lfpcalc.calc_lfp_pointsource_moi(cell,
x=0.5, y=0, z=1, sigma_T=sigma_T,
sigma_G=sigma_G, sigma_S=sigma_S,
r_limit=cell.diam/2, h=h, steps=steps)
np.testing.assert_equal(in_vivo, in_vitro)
def test_calc_lfp_pointsource_moi_too_close(self):
"""
Very close to point source, in vivo and in vitro have similar results,
e.g., the positions should be adjusted similarly.
"""
sigma_T = 0.3
sigma_G = 0.0
sigma_S = 1.5
h = 2000
steps = 20
cell = TestCell()
cell.zmid[0] = h/2
cell.zstart[0] = h/2
cell.zend[0] = h/2
in_vivo = lfpcalc.calc_lfp_pointsource(cell,
x=0.5, y=0, z=h/2, sigma=sigma_T,
r_limit=cell.diam/2)
in_vitro = lfpcalc.calc_lfp_pointsource_moi(cell,
x=0.5, y=0, z=h/2, sigma_T=sigma_T,
sigma_G=sigma_G, sigma_S=sigma_S,
r_limit=cell.diam/2, h=h, steps=steps)
np.testing.assert_almost_equal(in_vivo, in_vitro, 4)
