def calc_field(all_params, seg_coords,results_sim):
# run the simulation for t_length
print 'simulate neuron'
grid_size = all_params['grid_size']
external_resistivity = all_params['external_resistivity']
record_x_range = all_params[
'record_x_range'] # the grid with defined cells might be of different size that the one where we calculate
record_y_range = all_params['record_y_range']
# estimates the field in every defined point of the grid
print 'estimate the field'
n_samp = grid_size # grid size will be n_samp x n_samp
xx, yy = field.calc_grid(record_x_range, record_y_range, n_samp) # define grid
v_ext = field.estimate_on_grid(seg_coords, results_sim['I'], xx, yy, eta=external_resistivity)
# find dipole moment for this cell
Q = field.calc_dipole_moment(seg_coords, results_sim['I_axial'])
Q_len = np.sqrt(np.sum(Q ** 2, 0))
results_sim = {'xx': xx, # grid xx
'yy': yy, # grid yy
'Q': Q, # dipole
'Q_len': Q_len, # dipole length
'v_ext': np.array(v_ext), # potential
'seg_coords': seg_coords}
return results_sim
def test_current_dipole_of_single_cylinder():
cylinder_pos = (0, 0, 0)
L = 1
def Q_analytical(L, theta, I0):
return (L*I0*np.cos(theta)*diam**2/4*1e-8,
L*I0*np.sin(theta)*diam**2/4*1e-8, 0)
pi = np.pi
#length, theta, current, expected dipole moment
tests = [(L, 0, 1.),
(L, pi/2., 1.),
(L, pi/4., 1.),
(L, pi, 1.),
(2*L,0, 1.),
(L, 0., 2.)
]
for l, theta, I0 in tests:
coord, I_axial = conf_cylinder(cylinder_pos,
theta=theta,
L=l,
I_0=I0)
Q = field.calc_dipole_moment(coord, I_axial)
Q_expected = Q_analytical(l, theta, I0)
assert_almost_equal(Q, np.array(Q_expected)[:, None],
err_msg='failed for theta=%f, l=%f' % (theta,l))
def test_current_dipole_of_single_cylinder():
cylinder_pos = (0, 0, 0)
L = 1
def Q_analytical(L, theta, I0):
return (L * I0 * np.cos(theta) * diam**2 / 4 * 1e-8,
L * I0 * np.sin(theta) * diam**2 / 4 * 1e-8, 0)
pi = np.pi
#length, theta, current, expected dipole moment
tests = [(L, 0, 1.), (L, pi / 2., 1.), (L, pi / 4., 1.), (L, pi, 1.),
(2 * L, 0, 1.), (L, 0., 2.)]
for l, theta, I0 in tests:
coord, I_axial = conf_cylinder(cylinder_pos, theta=theta, L=l, I_0=I0)
Q = field.calc_dipole_moment(coord, I_axial)
Q_expected = Q_analytical(l, theta, I0)
assert_almost_equal(Q,
np.array(Q_expected)[:, None],
err_msg='failed for theta=%f, l=%f' % (theta, l))
def assert_dipole_equal(cylinders, Q_expected):
coord, I_axial = concat_cylinders(cylinders)
Q = field.calc_dipole_moment(coord, I_axial)
assert_almost_equal(Q,
np.array(Q_expected)[:, None] * 1e-8 / 4 * diam**2)
def assert_dipole_equal(cylinders, Q_expected):
coord, I_axial = concat_cylinders(cylinders)
Q = field.calc_dipole_moment(coord, I_axial)
assert_almost_equal(Q, np.array(Q_expected)[:, None] * 1e-8 / 4 * diam ** 2)