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at each contact
sigma : float * quantity.Quantity
conductivity of tissue in units of S/m or 1/(ohm*m)
sigma_top : float * quantity.Quantity
conductivity on top of tissue in units of S/m or 1/(ohm*m)
tol : float
tolerance of numerical integration
f_type : str
type of spatial filter, must be a scipy.signal filter design method
f_order : list
settings for spatial filter, arg passed to filter design function
num_steps : int
number of data points for the spatially upsampled LFP/CSD data
'''
CSD.__init__(self, lfp, f_type, f_order)
try:
assert(diam.units == coord_electrode.units)
except AssertionError as ae:
print('units of coord_electrode ({}) and diam ({}) differ'.format(coord_electrode.units,
diam.units))
raise
try:
assert(np.all(np.diff(coord_electrode) > 0))
except AssertionError as ae:
print('values of coord_electrode not continously increasing')
raise ae
try:
assert(diam.size == 1 or diam.size == coord_electrode.size)
if diam.size == coord_electrode.size:
at each contact
h : float or np.ndarray * quantity.Quantity
assumed thickness of the source cylinders at all or each contact
sigma : float * quantity.Quantity
conductivity of tissue in units of S/m or 1/(ohm*m)
sigma_top : float * quantity.Quantity
conductivity on top of tissue in units of S/m or 1/(ohm*m)
tol : float
tolerance of numerical integration
f_type : str
type of spatial filter, must be a scipy.signal filter design method
f_order : list
settings for spatial filter, arg passed to filter design function
'''
CSD.__init__(self, lfp, f_type, f_order)
try:
assert(diam.units == coord_electrode.units)
except AssertionError as ae:
print('units of coord_electrode ({}) and diam ({}) differ'.format(coord_electrode.units,
diam.units))
raise ae
try:
assert(np.all(np.diff(coord_electrode) > 0))
except AssertionError as ae:
print('values of coord_electrode not continously increasing')
raise ae
try:
assert(diam.size == 1 or diam.size == coord_electrode.size)
if diam.size == coord_electrode.size:
----------
lfp : np.ndarray * quantity.Quantity
LFP signal of shape (# channels, # time steps) in units of V
coord_electrode : np.ndarray * quantity.Quantity
depth of evenly spaced electrode contact points of shape
(# contacts, ) in units of m, must be monotonously increasing
sigma : float * quantity.Quantity
conductivity of tissue in units of S/m or 1/(ohm*m)
vaknin_el : bool
flag for using method of Vaknin to endpoint electrodes
f_type : str
type of spatial filter, must be a scipy.signal filter design method
f_order : list
settings for spatial filter, arg passed to filter design function
'''
CSD.__init__(self, lfp, f_type, f_order)
self.name = 'Standard CSD method'
self.coord_electrode = coord_electrode
self.sigma = sigma
self.vaknin_el = vaknin_el
try:
assert(np.all(np.diff(np.diff(coord_electrode)))==0)
except AssertionError as ae:
print('coord_electrode not monotonously varying')
raise ae
if vaknin_el:
#extend array of lfps by duplicating potential at endpoint contacts
if lfp.ndim == 1:
self.lfp = np.empty((lfp.shape[0]+2, )) * lfp.units
depth of evenly spaced electrode contact points of shape
(# contacts, ) in units of m
diam : float * quantity.Quantity
diamater of the assumed circular planar current sources centered
at each contact
sigma : float * quantity.Quantity
conductivity of tissue in units of S/m or 1/(ohm*m)
sigma_top : float * quantity.Quantity
conductivity on top of tissue in units of S/m or 1/(ohm*m)
f_type : str
type of spatial filter, must be a scipy.signal filter design method
f_order : list
settings for spatial filter, arg passed to filter design function
'''
CSD.__init__(self, lfp)
try:
assert(diam.units == coord_electrode.units)
except AssertionError as ae:
print('units of coord_electrode ({}) and diam ({}) differ'.format(coord_electrode.units,
diam.units))
raise ae
try:
assert(np.all(np.diff(coord_electrode) > 0))
except AssertionError as ae:
print('values of coord_electrode not continously increasing')
raise ae
try:
assert(diam.size == 1 or diam.size == coord_electrode.size)