def dipole_insert(self, yscale):
# insert dipole into each section of this cell
# dends must have already been created!!
# it's easier to use wholetree here, this includes soma
seclist = h.SectionList()
seclist.wholetree(sec=self.soma)
# create a python section list list_all
self.list_all = [sec for sec in seclist]
for sect in self.list_all:
sect.insert('dipole')
# Dipole is defined in dipole_pp.mod
self.dipole_pp = [h.Dipole(1, sec=sect) for sect in self.list_all]
# setting pointers and ztan values
for sect, dpp in zip(self.list_all, self.dipole_pp):
# assign internal resistance values to dipole point process (dpp)
dpp.ri = h.ri(1, sec=sect)
# sets pointers in dipole mod file to the correct locations
# h.setpointer(ref, ptr, obj)
h.setpointer(sect(0.99)._ref_v, 'pv', dpp)
if self.celltype.startswith('L2'):
h.setpointer(h._ref_dp_total_L2, 'Qtotal', dpp)
elif self.celltype.startswith('L5'):
h.setpointer(h._ref_dp_total_L5, 'Qtotal', dpp)
# gives INTERNAL segments of the section, non-endpoints
# creating this because need multiple values simultaneously
loc = np.array([seg.x for seg in sect])
# these are the positions, including 0 but not L
pos = np.array([seg.x for seg in sect.allseg()])
# diff in yvals, scaled against the pos np.array. y_long as in longitudinal
y_scale = (yscale[sect.name()] * sect.L) * pos
# y_long = (h.y3d(1, sec=sect) - h.y3d(0, sec=sect)) * pos
# diff values calculate length between successive section points
y_diff = np.diff(y_scale)
# y_diff = np.diff(y_long)
# doing range to index multiple values of the same np.array simultaneously
for i in range(len(loc)):
# assign the ri value to the dipole
sect(loc[i]).dipole.ri = h.ri(loc[i], sec=sect)
# range variable 'dipole'
# set pointers to previous segment's voltage, with boundary condition
if i:
h.setpointer(
sect(loc[i - 1])._ref_v, 'pv',
sect(loc[i]).dipole)
else:
h.setpointer(sect(0)._ref_v, 'pv', sect(loc[i]).dipole)
# set aggregate pointers
h.setpointer(dpp._ref_Qsum, 'Qsum', sect(loc[i]).dipole)
if self.celltype.startswith('L2'):
h.setpointer(h._ref_dp_total_L2, 'Qtotal',
sect(loc[i]).dipole)
elif self.celltype.startswith('L5'):
h.setpointer(h._ref_dp_total_L5, 'Qtotal',
sect(loc[i]).dipole)
# add ztan values
sect(loc[i]).dipole.ztan = y_diff[i]
# set the pp dipole's ztan value to the last value from y_diff
dpp.ztan = y_diff[-1]
def insert_dipole(self, yscale):
"""Insert dipole into each section of this cell.
Parameters
----------
yscale : dict
Dictionary of length scales to calculate dipole without
3d shape.
"""
self.dpl_vec = h.Vector(1)
self.dpl_ref = self.dpl_vec._ref_x[0]
# dends must have already been created!!
# it's easier to use wholetree here, this includes soma
sec_list = h.SectionList()
sec_list.wholetree(sec=self.soma)
sec_list = [sec for sec in sec_list]
for sect in sec_list:
sect.insert('dipole')
# Dipole is defined in dipole_pp.mod
self.dipole_pp = [h.Dipole(1, sec=sect) for sect in sec_list]
# setting pointers and ztan values
for sect, dpp in zip(sec_list, self.dipole_pp):
dpp.ri = h.ri(1, sec=sect) # assign internal resistance
# sets pointers in dipole mod file to the correct locations
dpp._ref_pv = sect(0.99)._ref_v
dpp._ref_Qtotal = self.dpl_ref
# gives INTERNAL segments of the section, non-endpoints
# creating this because need multiple values simultaneously
pos_all = np.array([seg.x for seg in sect.allseg()])
# diff in yvals, scaled against the pos np.array. y_long as
# in longitudinal
sect_name = sect.name().split('_', 1)[1]
y_scale = (yscale[sect_name] * sect.L) * pos_all
# y_long = (h.y3d(1, sec=sect) - h.y3d(0, sec=sect)) * pos
# diff values calculate length between successive section points
y_diff = np.diff(y_scale)
# y_diff = np.diff(y_long)
# doing range to index multiple values of the same
# np.array simultaneously
for idx, pos in enumerate(pos_all[1:-1]):
# assign the ri value to the dipole
# ri not defined at 0 and L
sect(pos).dipole.ri = h.ri(pos, sec=sect)
# range variable 'dipole'
# set pointers to previous segment's voltage, with
# boundary condition
sect(pos).dipole._ref_pv = sect(pos_all[idx])._ref_v
# set aggregate pointers
sect(pos).dipole._ref_Qsum = dpp._ref_Qsum
sect(pos).dipole._ref_Qtotal = self.dpl_ref
# add ztan values
sect(pos).dipole.ztan = y_diff[idx]
# set the pp dipole's ztan value to the last value from y_diff
dpp.ztan = y_diff[-1]
self.dipole = h.Vector().record(self.dpl_ref)
def _insert_dipole(self, sec_name_apical):
"""Insert dipole into each section of this cell.
Parameters
----------
sec_name_apical : str
The name of the section along which dipole moment is calculated.
"""
self.dpl_vec = h.Vector(1)
self.dpl_ref = self.dpl_vec._ref_x[0]
cos_thetas = _get_cos_theta(self.sections, 'apical_trunk')
# setting pointers and ztan values
for sect_name in self.sections:
sect = self._nrn_sections[sect_name]
sect.insert('dipole')
dpp = h.Dipole(1, sec=sect) # defined in dipole_pp.mod
self.dipole_pp.append(dpp)
dpp.ri = h.ri(1, sec=sect) # assign internal resistance
# sets pointers in dipole mod file to the correct locations
dpp._ref_pv = sect(0.99)._ref_v
dpp._ref_Qtotal = self.dpl_ref
# gives INTERNAL segments of the section, non-endpoints
# creating this because need multiple values simultaneously
pos_all = np.array([seg.x for seg in sect.allseg()])
seg_lens = np.diff(pos_all) * sect.L
seg_lens_z = seg_lens * cos_thetas[sect_name]
# alternative procedure below with y_long(itudinal)
# y_long = (h.y3d(1, sec=sect) - h.y3d(0, sec=sect)) * pos
# y_diff = np.diff(y_long)
# doing range to index multiple values of the same
# np.array simultaneously
for idx, pos in enumerate(pos_all[1:-1]):
# assign the ri value to the dipole
# ri not defined at 0 and L
sect(pos).dipole.ri = h.ri(pos, sec=sect)
# range variable 'dipole'
# set pointers to previous segment's voltage, with
# boundary condition
sect(pos).dipole._ref_pv = sect(pos_all[idx])._ref_v
# set aggregate pointers
sect(pos).dipole._ref_Qsum = dpp._ref_Qsum
sect(pos).dipole._ref_Qtotal = self.dpl_ref
# add ztan values
sect(pos).dipole.ztan = seg_lens_z[idx]
# set the pp dipole's ztan value to the last value from seg_lens_z
dpp.ztan = seg_lens_z[-1]
self.dipole = h.Vector().record(self.dpl_ref)
