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)
def test_direct_memory_transfer():
#h('''create soma''')
cell = h.rinzelnrn()
#h.psection()
#dir(h)
#h.soma.L=5.6419
#h.soma.diam=5.6419
#h.soma.insert("rinzelnrn")
gc = 2.1
pp = 0.5
cell.soma.Ra = 1
cell.dend.Ra = 1
global_Ra = (1e-6 / (gc / pp *
(h.area(0.5) * 1e-8) * 1e-3)) / (2 * h.ri(0.5))
cell.soma.Ra = global_Ra
cell.soma.cm = 3
cell.dend.Ra = global_Ra
cell.dend.cm = 3
# soma
cell.soma.insert("pas")
cell.soma.insert("kdr")
cell.soma.insert("nafPR")
cell.soma.gmax_nafPR = 30e-3
cell.soma.gmax_kdr = 15e-3
cell.soma.g_pas = 0.1e-3
cell.soma.e_pas = -60
# dend
cell.dend.insert("pas")
cell.dend.insert("rcadecay")
cell.dend.insert("cal")
cell.dend.insert("kcRT03")
cell.dend.insert("rkq")
cell.dend.g_pas = 0.1e-3
cell.dend.e_pas = -60
cell.dend.phi_rcadecay = 130
cell.dend.gmax_cal = 00010e-3
cell.dend.erev_cal = 80
cell.dend.gmax_kcRT03 = 00015e-3
cell.dend.gmax_rkq = 0000.8e-3
cell.dend.ek = -75
ic = h.IClamp(cell.soma(.5))
ic.delay = .5
ic.dur = 0.1
ic.amp = 0.3
#for testing external mod file
#h.soma.insert("hh")
h.cvode.use_fast_imem(1)
h.cvode.cache_efficient(1)
h.tstop = 50
h.celsius = 37.0
h.v_init = -60
v = h.Vector()
v.record(cell.soma(.5)._ref_v, sec=cell.soma)
i_mem = h.Vector()
i_mem.record(cell.soma(.5)._ref_i_membrane_, sec=cell.soma)
tv = h.Vector()
tv.record(h._ref_t, sec=cell.soma)
h.run()
vstd = v.cl()
tvstd = tv.cl()
i_memstd = i_mem.cl()
# Save current (after run) value to compare with transfer back from coreneuron
#tran_std = [h.t, cell.soma(.5).v, cell.soma(.5).hh.m]
from neuron import coreneuron
coreneuron.enable = True
pc = h.ParallelContext()
pc.set_maxstep(10)
h.stdinit()
pc.psolve(h.tstop)
#tran = [h.t, cell.soma(.5).v, cell.soma(.5).hh.m]
assert (tv.eq(tvstd))
#assert(v.cl().sub(vstd).abs().max() < 1e-10)
assert (i_mem.cl().sub(i_memstd).abs().max() < 1e-10)
#assert(h.Vector(tran_std).sub(h.Vector(tran)).abs().max() < 1e-10)
f = open('v.dat', 'w')
for i in range(tv.size()):
print('{} {}'.format(tv[i], v[i]), file=open("v.dat", "a"))
h.quit()
def make_rec(recid,
population,
gid,
cell,
sec=None,
loc=None,
ps=None,
param='v',
label=None,
dt=None,
description=''):
"""
Makes a recording vector for the specified quantity in the specified section and location.
:param recid: str
:param population: str
:param gid: integer
:param cell: :class:'BiophysCell'
:param sec: :class:'HocObject'
:param loc: float
:param ps: :class:'HocObject'
:param param: str
:param dt: float
:param ylabel: str
:param description: str
"""
vec = h.Vector()
if (sec is None) and (loc is None) and (ps is not None):
hocobj = ps
seg = ps.get_segment()
if seg is not None:
loc = seg.x
sec = seg.sec
origin = list(cell.soma)[0]
distance = h.distance(origin(0.5), seg)
ri = h.ri(loc, sec=sec)
else:
distance = None
ri = None
elif (sec is not None) and (loc is not None):
hocobj = sec(loc)
if cell.soma.__class__.__name__.lower() == "section":
origin = cell.soma
else:
origin = list(cell.soma)[0]
h.distance(sec=origin)
distance = h.distance(origin(0.5), sec(loc))
ri = h.ri(loc, sec=sec)
else:
raise RuntimeError(
'make_rec: either sec and loc or ps must be specified')
section_index = None
if sec is not None:
for i, this_section in enumerate(cell.sections):
if this_section == sec:
section_index = i
break
if label is None:
label = param
if dt is None:
vec.record(getattr(hocobj, f'_ref_{param}'))
else:
vec.record(getattr(hocobj, f'_ref_{param}'), dt)
rec_dict = {
'name': recid,
'gid': gid,
'cell': cell,
'population': population,
'loc': loc,
'section': section_index,
'distance': distance,
'ri': ri,
'description': description,
'vec': vec,
'label': label
}
return rec_dict
def pr(sec):
for seg in sec.allseg():
print sec.name(), seg.x, h.area(seg.x, sec=sec), h.ri(seg.x, sec=sec)