def test_RecMEAElectrode_00(self):
"""test RecMEAElectrode implementation,
method='pointsource' with same conductivity in all layers"""
cell = get_cell(n_seg=1)
sigma = 0.3
r = np.array([[0.],
[0.],
[0.]])
mea = lfp.RecMEAElectrode(cell=cell,
x=r[0], y=r[1, ], z=r[2, ],
sigma_T=sigma, sigma_S=sigma, sigma_G=sigma,
method='pointsource')
M = mea.get_transformation_matrix()
imem = np.array([[0., 1., -1.]]) * (4 * np.pi * sigma * cell.z.mean())
V_ex = M @ imem
V_gt = np.array([[0., 1., -1.]])
np.testing.assert_allclose(V_ex, V_gt)
def test_RecMEAElectrode_03(self):
'''test_position_shifted_slice'''
electrodeParams = {
'sigma_T': 0.3,
'sigma_S': 1.5,
'sigma_G': 0.0,
'h': 200,
'z_shift': -200,
'x': np.linspace(0, 1000, 11),
'y': np.zeros(11),
'z': np.zeros(11) - 100,
'method': "pointsource",
'squeeze_cell_factor': None,
}
stick = lfp.CellGeometry(x=np.array([[-17.5, 17.5], [0., 23.],
[23., 46.], [46.,
69.], [69., 92.],
[92., 115.], [115., 125.],
[125., 135.], [135., 145.],
[145., 155.], [155., 165.],
[115., 118.33333333],
[118.33333333, 121.66666667],
[121.66666667, 125.]]),
y=np.array([[0., 0.], [0., 0.], [0., 0.],
[0., 0.], [0., 0.], [0., 0.],
[0., 4.], [4., 8.], [8., 12.],
[12., 16.], [16., 20.], [0., 0.],
[0., 0.], [0., 0.]]),
z=np.array([[0, 0], [0, 0], [0, 0], [0, 0],
[0, 0], [0, 0], [0, 0], [10, 20],
[20, 30], [30, 40], [40, 50],
[0, -10], [-10, -20], [-20,
-30]]),
d=np.zeros(14))
stick.z = stick.z - 100
MEA = lfp.RecMEAElectrode(stick, **electrodeParams)
MEA._test_cell_extent()
def test_RecMEAElectrode_02(self):
'''test return_comp_outside_slice'''
electrodeParams = {
'sigma_T': 0.3,
'sigma_S': 1.5,
'sigma_G': 0.0,
'h': 200,
'x': np.linspace(0, 1000, 11),
'y': np.zeros(11),
'z': np.zeros(11),
'method': "pointsource",
'squeeze_cell_factor': None,
}
stick = lfp.CellGeometry(x=np.array([[-17.5, 17.5], [0., 23.],
[23., 46.], [46.,
69.], [69., 92.],
[92., 115.], [115., 125.],
[125., 135.], [135., 145.],
[145., 155.], [155., 165.],
[115., 118.33333333],
[118.33333333, 121.66666667],
[121.66666667, 125.]]),
y=np.array([[0., 0.], [0., 0.], [0., 0.],
[0., 0.], [0., 0.], [0., 0.],
[0., 4.], [4., 8.], [8., 12.],
[12., 16.], [16., 20.], [0., 0.],
[0., 0.], [0., 0.]]),
z=np.array([[0, 0], [0, 0], [0, 0], [0, 0],
[0, 0], [0, 0], [0, 0], [10, 20],
[20, 30], [30, 40], [40, 50],
[0, -10], [-10, -20], [-20,
-30]]),
d=np.zeros(14))
stick.z = stick.z + 100
MEA = lfp.RecMEAElectrode(stick, **electrodeParams)
np.testing.assert_raises(RuntimeError, MEA._return_comp_outside_slice)
true_bad_comp = np.array([2, 3, 6])
stick.z[true_bad_comp, 0] = 1000
bad_comp, reason = MEA._return_comp_outside_slice()
np.testing.assert_equal(reason, "zstart above")
np.testing.assert_equal(true_bad_comp,
np.arange(stick.totnsegs)[bad_comp])
stick.z[true_bad_comp, 0] = 100
stick.z[true_bad_comp, 0] = -1000
bad_comp, reason = MEA._return_comp_outside_slice()
np.testing.assert_equal(reason, "zstart below")
np.testing.assert_equal(true_bad_comp,
np.arange(stick.totnsegs)[bad_comp])
stick.z[true_bad_comp, 0] = 100
stick.z[true_bad_comp, -1] = 1000
bad_comp, reason = MEA._return_comp_outside_slice()
np.testing.assert_equal(reason, "zend above")
np.testing.assert_equal(true_bad_comp,
np.arange(stick.totnsegs)[bad_comp])
stick.z[true_bad_comp, -1] = 100
stick.z[true_bad_comp, -1] = -1000
bad_comp, reason = MEA._return_comp_outside_slice()
np.testing.assert_equal(reason, "zend below")
np.testing.assert_equal(true_bad_comp,
np.arange(stick.totnsegs)[bad_comp])
stick.z[true_bad_comp, -1] = 100
def test_RecMEAElectrode_01(self):
'''test _test_cell_extent method w/wo. squeeze along z-axis'''
electrodeParams = {
'sigma_T': 0.3,
'sigma_S': 1.5,
'sigma_G': 0.0,
'h': 200,
'x': np.linspace(0, 1000, 11),
'y': np.zeros(11),
'z': np.zeros(11),
'method': "pointsource",
'squeeze_cell_factor': None,
'verbose': False
}
stick = lfp.CellGeometry(x=np.array([[-17.5, 17.5], [0., 23.],
[23., 46.], [46.,
69.], [69., 92.],
[92., 115.], [115., 125.],
[125., 135.], [135., 145.],
[145., 155.], [155., 165.],
[115., 118.33333333],
[118.33333333, 121.66666667],
[121.66666667, 125.]]),
y=np.array([[0., 0.], [0., 0.], [0., 0.],
[0., 0.], [0., 0.], [0., 0.],
[0., 4.], [4., 8.], [8., 12.],
[12., 16.], [16., 20.], [0., 0.],
[0., 0.], [0., 0.]]),
z=np.array([[0, 0], [0, 0], [0, 0], [0, 0],
[0, 0], [0, 0], [0, 0], [10, 20],
[20, 30], [30, 40], [40, 50],
[0, -10], [-10, -20], [-20,
-30]]),
d=np.zeros(14))
stick.z = stick.z + 1
MEA = lfp.RecMEAElectrode(stick, **electrodeParams)
np.testing.assert_raises(RuntimeError, MEA._test_cell_extent)
stick.z = stick.z + 198.
MEA = lfp.RecMEAElectrode(stick, **electrodeParams)
np.testing.assert_raises(RuntimeError, MEA._test_cell_extent)
electrodeParams = {
'sigma_T': 0.3,
'sigma_S': 1.5,
'sigma_G': 0.0,
'h': 200,
'x': np.linspace(0, 1000, 11),
'y': np.zeros(11),
'z': np.zeros(11),
'method': "pointsource",
'squeeze_cell_factor': 0.1,
}
stick.z = stick.z - 200
MEA = lfp.RecMEAElectrode(stick, **electrodeParams)
np.testing.assert_raises(RuntimeError, MEA._test_cell_extent)
stick.z = np.zeros_like(stick.z) + 202
MEA = lfp.RecMEAElectrode(stick, **electrodeParams)
np.testing.assert_raises(RuntimeError, MEA._test_cell_extent)