def mkgap(i):
if rank == i:
gap = h.HalfGap(cell.soma(0.5))
halfgaps.append(gap)
pc.source_var(cell.soma(0.5)._ref_v, i, sec=cell.soma)
gap = pc.target_var(gap, gap._ref_vgap, i + 1)
if rank == (i + 1) % nhost:
gap = h.HalfGap(cell.soma(0.5))
halfgaps.append(gap)
pc.source_var(cell.soma(0.5)._ref_v, i + 1, sec=cell.soma)
gap = pc.target_var(gap, gap._ref_vgap, i)
def mkhalfgap(sid, vseg, gapseg, g):
if vseg != None: pc.source_var(vseg._ref_v, sid, sec=vseg.sec)
if gapseg != None:
hg = h.HalfGap(gapseg)
pc.target_var(hg, hg._ref_vgap, sid)
hg.g = g
hglist.append(hg)
def __init__(self, target, section, conductance=0, record_all=0, Dt=0.1):
self.record_all = record_all
if record_all:
print "Recording all in Gapj"
# Decide what kind of connection to create based on the source and target types
if target.whatami == 'goc':
self.whatami = "gapj_goc2goc"
elif target.whatami == 'stl':
self.whatami = "gapj_stl2stl"
else:
print "What the hell are you doing?!?"
self.gapj = h.HalfGap(.5, sec=section)
self.gapj.g = conductance # nanoSiemens
self.d = 1e9 # distance set by default to infinite
self.CC = 1e9 # expected coupling coefficient
if record_all:
self.record = {}
self.record['v_local'] = h.Vector()
self.record['v_remote'] = h.Vector()
self.record['i_local'] = h.Vector()
self.record['v_remote'].record(self.gapj._ref_vgap, Dt)
self.record['v_local'].record(section(.5)._ref_v, Dt, sec=section)
self.record['i_local'].record(self.gapj._ref_i, Dt)
def mk_halfgap(self, sid_tar, sid_src, seg):
# target exists
settings.pc.source_var(seg._ref_v, sid_tar, sec=seg.sec)
hg = h.HalfGap(seg)
settings.pc.target_var(hg, hg._ref_vgap, sid_src)
hg.g = 0.04 # do not randomize as must be same for other side of gap
self.halfgap_list.append(hg)
def create_halfgaps(self, conduct_range):
self.gaps = [0, 0]
(pre_soma_dx, pre_axon_dx) = self.pre.give_dxs()
(post_soma_dx, post_axon_dx) = self.post.give_dxs()
# Create HalfGap Objects
self.gaps[0] = h.HalfGap(self.pre.axon(1 - (pre_axon_dx / 2)))
self.gaps[1] = h.HalfGap(self.post.soma(0 + (post_soma_dx / 2)))
# Identify cathode vs anode
self.gaps[0].isanode = 1
self.gaps[1].isanode = -1
# Set voltage pointers
h.setpointer(
self.post.soma(0 + (post_soma_dx) / 2)._ref_v, 'vgap',
self.gaps[0])
h.setpointer(
self.pre.axon(1 - (pre_axon_dx) / 2)._ref_v, 'vgap', self.gaps[1])
# Set conductance min and max
self.gaps[0].gmin = conduct_range[0]
self.gaps[1].gmin = conduct_range[0]
self.gaps[0].gmax = conduct_range[1]
self.gaps[1].gmax = conduct_range[1]
if (rank == 0):
stim = h.IClamp(.5)
stim.amp = 0.5
stim.dur = 0.1
soma.gnabar_hh = 0
soma.gkbar_hh = 0
soma.el_hh = -65
soma.gl_hh = .001
soma2.gnabar_hh = 0
soma2.gkbar_hh = 0
soma2.el_hh = -65
soma2.gl_hh = .001
gap = h.HalfGap(.5, sec=soma)
gap.g = .01 # nS
gap2 = h.HalfGap(.5, sec=soma2)
gap2.g = .01 # nS
pc.source_var(soma(.5)._ref_v, rank)
pc.source_var(soma2(.5)._ref_v, rank)
vvec = h.Vector()
print gap.vgap
pc.target_var(gap2._ref_vgap, (rank + 1) % 2)
vvec.record(gap._ref_i)
pc.setup_transfer()
def mkhgap(sid, seg, g):
hg = h.HalfGap(seg)
hg.g = g
pc.target_var(hg, hg._ref_vgap, sid)
hglist.append(hg)