def test_calc_lfp_linesource_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_linesource_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_linesource_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_almost_equal(with_saline, without_saline)
def test_calc_lfp_linesource_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_linesource_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_linesource_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_almost_equal(with_saline, without_saline)
def test_calc_lfp_linesource_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_linesource_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_linesource_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_linesource_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_linesource_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_linesource_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_linesource_moi_20steps(self):
"""
Test that the calc_lfp_linesource_moi reproduces previously known
nummerical value
"""
sigma_T = 0.3
sigma_G = 0.0
sigma_S = 1.5
h = 200
steps = 20
correct = 0.00246539
cell = TestCell()
cell.zstart[0] = 0
cell.zend[0] = 110
cell.xstart[0] = -100
cell.xend[0] = 50
calculated = lfpcalc.calc_lfp_linesource_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_linesource_moi_doubling(self):
"""
Test that slice with zero conductivity in 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_linesource(cell,
x=50., y=0, z=0, sigma=sigma_T,
r_limit=cell.diam/2)
in_vitro = lfpcalc.calc_lfp_linesource_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_linesource_moi_20steps(self):
"""
Test that the calc_lfp_linesource_moi reproduces previously known
nummerical value
"""
sigma_T = 0.3
sigma_G = 0.0
sigma_S = 1.5
h = 200
steps = 20
correct = 0.00246539
cell = DummyCell()
cell.zstart[0] = 0
cell.zend[0] = 110
cell.xstart[0] = -100
cell.xend[0] = 50
calculated = lfpcalc.calc_lfp_linesource_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_linesource_moi_doubling(self):
"""
Test that slice with zero conductivity in 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_linesource(cell,
x=50., y=0, z=0, sigma=sigma_T,
r_limit=cell.diam/2)
in_vitro = lfpcalc.calc_lfp_linesource_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_linesource_moi_20steps(self):
"""
Test that the calc_lfp_linesource_moi reproduces previously known
nummerical value
"""
sigma_T = 0.3
sigma_G = 0.0
sigma_S = 1.5
h = 200
steps = 20
correct = 0.00246539
cell = DummyCell(x=np.array([[-100, 50]]), z=np.array([[0, 110]]))
calculated = lfpcalc.calc_lfp_linesource_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_linesource_moi_00(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 = 0.3
h = 200
steps = 20
cell = DummyCell()
in_vivo = lfpcalc.calc_lfp_linesource(cell,
x=0.5,
y=0,
z=0,
sigma=sigma_T,
r_limit=cell.d / 2)
in_vitro = lfpcalc.calc_lfp_linesource_moi(cell,
x=0.5,
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(2 * in_vivo, in_vitro, 4)
def test_calc_lfp_linesource_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 = 0.3
h = 200
steps = 20
cell = TestCell()
cell.zstart[0] = 0.0
cell.zend[0] = 0.0
in_vivo = lfpcalc.calc_lfp_linesource(cell,
x=0.5, y=0, z=0, sigma=sigma_T,
r_limit=cell.diam/2)
in_vitro = lfpcalc.calc_lfp_linesource_moi(cell,
x=0.5, 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, 4)
