def locate_and_create(pair, positions):
""" For a pair of cables and a set of resistor positions,
locate, create and connect those resistors to the cables """
# Pair indices
i, j = pair
# Get resistors' lengths
rl = get_rl(pair, positions)
# Iterate over resistors positions
for zr, l in zip(positions, rl):
# For each cable, see where this falls
# On cable i:
i_sec, z_on_i = anatomy.locate(ws.seclens[i], zr)
seci = ws.sections[i][i_sec]
sgi = seci(z_on_i)
# On cable j:
j_sec, z_on_j = anatomy.locate(ws.seclens[j], zr)
secj = ws.sections[j][j_sec]
sgj = secj(z_on_j)
# Value of the resistor (MOhm)
ephres = res / l
# Create the resistor
create_eph(ephres, sgi, sgj, seci, secj, i, j, zr)
def locate_pads_on_nerve(self):
""" Find the locations in the nerve corresponding
to the pads """
# Iterate over the ring's pads
self.contact_points = []
for i_pad in range(self.npads):
# The pad's angular position determines which cable cell(s)
# is (are) stimulated
# Select which of the targets is in contact
# with a pad 'i_pad' according to its angular position
angdiff = np.abs(ws.contour_angles - self.thts[i_pad])
which_cables = np.where(angdiff == angdiff.min())[0]
# Iterate over possible cables
ncables_here = len(which_cables)
for i_cable in which_cables:
# For cable_cell i, see where this is
try:
i_sec, zpos = anatomy.locate(ws.seclens[i_cable], self.z)
except TypeError:
msg = 'ERROR: A ring of an electrode could not be placed on the nerve'
ws.log(msg)
ws.terminate()
# Add the point
point = {'cable': i_cable, 'section': i_sec, 'z': zpos}
try:
self.contact_points[i_pad].append(point)
except IndexError:
self.contact_points.append([point])
def __init__(self, name, index=0):
PointElectrode.__init__(self, name, index)
settings = self.settings
try:
self.xyz = settings['point']
except KeyError:
self.xyz = settings['points'][self.index]
self.x, self.y, self.z = self.xyz
# Find the cable this corresponds to
dists = geo.dist((self.x, self.y), (ws.nvt.x, ws.nvt.y))
these = np.where(dists == dists.min())[0]
# print('Points:', these)
# Choose only one cable
cable_i = these[0]
# print('Cable:', ws.nvt.cables[cable_i])
# Locate the section and segment (z value) of the cable
j_sec, z_on_j = anatomy.locate(ws.seclens[cable_i], self.z)
# print('Section and segment:', j_sec, z_on_j)
# Cable and point of the cable to work on
self.point = {'cable': cable_i, 'section': j_sec, 'z': z_on_j}
self.set_stim_info()
def set_stimulation(self):
""" Connect grounds """
# Go straigth to connect the wanted points to ground
for (x, y, z) in ws.electrodes_settings[self.name]["points"]:
# Find the cable this corresponds to
dists = geo.dist((x, y), (ws.nvt.x, ws.nvt.y))
these = np.where(dists == dists.min())[0]
# print('Points:', these)
# Choose only one cable
cable_i = these[0]
# print('Cable:', ws.nvt.cables[cable_i])
# Locate the section and segment (z value) of the cable
j_sec, z_on_j = anatomy.locate(ws.seclens[cable_i], z)
# Cable and point of the cable to work on
point = {'cable': cable_i, 'section': j_sec, 'z': z_on_j}
# Ground it
ground_segment(point)
def connect_resistors(self):
""" Connect the transverse resistors with ephapses in NEURON """
def locate_and_create(pair, positions):
""" For a pair of cables and a set of resistor positions,
locate, create and connect those resistors to the cables """
# Pair indices
i, j = pair
# Get resistors' lengths
rl = get_rl(pair, positions)
# Iterate over resistors positions
for zr, l in zip(positions, rl):
# For each cable, see where this falls
# On cable i:
i_sec, z_on_i = anatomy.locate(ws.seclens[i], zr)
seci = ws.sections[i][i_sec]
sgi = seci(z_on_i)
# On cable j:
j_sec, z_on_j = anatomy.locate(ws.seclens[j], zr)
secj = ws.sections[j][j_sec]
sgj = secj(z_on_j)
# Value of the resistor (MOhm)
ephres = res / l
# Create the resistor
create_eph(ephres, sgi, sgj, seci, secj, i, j, zr)
# ws.log("Created a transverse resistor at z = %f um with value %f MOhm"%(zr, ephres))
ws.eph_counter = 0
ws.nrn_res = {}
for pair, res in self.resistors.items():
i, j = pair
# Cable
cable_cell_i = ws.cables_hoc[i]
cable_cell_j = ws.cables_hoc[j]
# I have to connect the cables in a staggered manner
# If I am only taking the nodes of Ranvier into account
# and the connection is to be set between two axons:
if ws.EC["resistor network"][
"transverse resistor locations"] == "regular":
# Separation between transverse resistors
sep = float(ws.EC["resistor network"]["resistors separation"])
# Positions of the resistors
# res_positions = np.arange(0, ws.length, sep)
res_positions = np.arange(0.5, ws.length, sep)
# Create and connect the resistors
locate_and_create(pair, res_positions)
elif ws.EC["resistor network"]["transverse resistor locations"] == "only nodes of Ranvier" and \
('xon' in ws.cables[i].cabletype and 'xon' in ws.cables[j].cabletype):
# Get resistors' positions and lengths (um)
# Merge the ws.zprofs_RN of the two axons
# This array will contain the postions of the resistors
# over the z-axis
zp_pair = np.append(ws.zprofs_RN[i], ws.zprofs_RN[j])
zp_pair.sort()
# Remove repeated values (can --will, actually, happen if
# there's aligned nodes)
zp_pair = np.unique(zp_pair)
# Create and connect the resistors
locate_and_create(pair, zp_pair)
else:
# If I am taking all nodes into account, the compartments of only one
# of the two cables (arbitrarily chosen; cable 'i' by default)
# are plugged to transverse resistors. These are then connected
# to the second cable wherever they must, regardless of the
# topology of this second cable.
# Get resistors' lengths (um)
# From what is explained above, in this case the z-profile of one
# of the cables only is used as zp_pair
rl = get_rl(pair, ws.zprofs[i])
# Iterate over segments
for ii, sgi in enumerate(ws.segments[i]):
# Get the section and segment of cable j which sgi lies against
zi = ws.zprofs[i][ii]
j_sec, z_ioverj = anatomy.locate(ws.seclens[j], zi)
seci = sgi.sec
secj = ws.sections[j][j_sec]
sgj = secj(z_ioverj)
# Value of the resistor (MOhm)
ephres = res / rl[ii]
# Create the resistor
create_eph(ephres, sgi, sgj, seci, secj, i, j, zi)