def test_StandardCSD_03(self):
'''test using non-standard SI units 3'''
# set some parameters for ground truth csd and csd estimates.
# contact point coordinates
z_j = np.arange(21) * 1E-4 * pq.m
# source coordinates
z_i = z_j
# current source density magnitude
C_i = np.zeros(z_i.size) * pq.A / pq.m**2
C_i[7:12:2] += np.array([-.5, 1., -.5]) * pq.A / pq.m**2
# uniform conductivity
sigma = 0.3 * pq.mS / pq.m
# flag for debug plots
plot = False
# get LFP and CSD at contacts
phi_j, C_i = get_lfp_of_planes(z_j, z_i, C_i, sigma, plot)
std_input = {
'lfp': phi_j,
'coord_electrode': z_j,
'sigma': sigma * 1E3 * pq.mS / pq.S,
'f_type': 'gaussian',
'f_order': (3, 1),
}
std_csd = icsd.StandardCSD(**std_input)
csd = std_csd.get_csd()
self.assertEqual(C_i.units, csd.units)
nt.assert_array_almost_equal(C_i, csd)
_icsd = icsd.SplineiCSD(**icsd_input[m])
icsd_output.update(
{'icsd_spline': _icsd.filter_csd(_icsd.get_csd()) * 1E-9})
my_errors['spline'], my_diams['spline'], diam_best['spline'] = \
minimize_icsd_error_brute(m)
icsd_input[m].update({'diam': diam_best['spline'] * pq.m})
print 'best diameter spline: %.5e' % diam_best['spline']
_icsd = icsd.SplineiCSD(**icsd_input[m])
icsd_output.update(
{'icsd_spline': _icsd.filter_csd(_icsd.get_csd()) * 1E-9})
elif m == 'std':
_icsd = icsd.StandardCSD(**icsd_input[m])
icsd_output.update(
{'csd_std': _icsd.filter_csd(_icsd.get_csd()) * 1E-9})
print('Compute correlation coefficients between CSD and estimates')
my_corrcoefs = {}
for m in icsd_input:
if m == 'delta':
my_corrcoefs['delta'], _, _ = maximize_icsd_correlation_brute(m)
elif m == 'step':
my_corrcoefs['step'], _, _ = maximize_icsd_correlation_brute(m)
elif m == 'spline':
my_corrcoefs['spline'], _, _ = maximize_icsd_correlation_brute(m)
print('Compute correlation coefficients between CSD and estimates done')
### Mean EPSP, synapses.i, synapses.v with st.dev. ####