def measure_passive (gid, pop_name, v_init, env, prelength=1000.0, mainlength=2000.0, stimdur=500.0, cell_dict={}):
biophys_cell = init_biophys_cell(env, pop_name, gid, register_cell=False, cell_dict=cell_dict)
hoc_cell = biophys_cell.hoc_cell
h.dt = env.dt
tstop = prelength+mainlength
soma = list(hoc_cell.soma)[0]
stim1 = h.IClamp(soma(0.5))
stim1.delay = prelength
stim1.dur = stimdur
stim1.amp = -0.1
h('objref tlog, Vlog')
h.tlog = h.Vector()
h.tlog.record (h._ref_t)
h.Vlog = h.Vector()
h.Vlog.record (soma(0.5)._ref_v)
h.tstop = tstop
Rin = h.rn(hoc_cell)
neuron_utils.simulate(v_init, prelength, mainlength)
## compute membrane time constant
vrest = h.Vlog.x[int(h.tlog.indwhere(">=",prelength-1))]
vmin = h.Vlog.min()
vmax = vrest
## the time it takes the system's step response to reach 1-1/e (or
## 63.2%) of the peak value
amp23 = 0.632 * abs (vmax - vmin)
vtau0 = vrest - amp23
tau0 = h.tlog.x[int(h.Vlog.indwhere ("<=", vtau0))] - prelength
results = {'Rin': np.asarray([Rin], dtype=np.float32),
'vmin': np.asarray([vmin], dtype=np.float32),
'vmax': np.asarray([vmax], dtype=np.float32),
'vtau0': np.asarray([vtau0], dtype=np.float32),
'tau0': np.asarray([tau0], dtype=np.float32)
}
env.synapse_attributes.del_syn_id_attr_dict(gid)
if gid in env.biophys_cells[pop_name]:
del env.biophys_cells[pop_name][gid]
return results
def passive_test(template_class, tree, v_init):
cell = cells.make_neurotree_cell(template_class, neurotree_dict=tree)
h.topology()
h.dt = 0.025
prelength = 1000
mainlength = 2000
tstop = prelength + mainlength
stimdur = 500.0
soma = list(cell.soma)[0]
stim1 = h.IClamp(soma(0.5))
stim1.delay = prelength
stim1.dur = stimdur
stim1.amp = -0.1
h.tlog = h.Vector()
h.tlog.record(h._ref_t)
h.Vlog = h.Vector()
h.Vlog.record(soma(0.5)._ref_v)
h.tstop = tstop
neuron_utils.simulate(v_init, prelength, mainlength)
## compute membrane time constant
vrest = h.Vlog.x[int(h.tlog.indwhere(">=", prelength - 1))]
vmin = h.Vlog.min()
vmax = vrest
## the time it takes the system's step response to reach 1-1/e (or
## 63.2%) of the peak value
amp23 = 0.632 * abs(vmax - vmin)
vtau0 = vrest - amp23
tau0 = h.tlog.x[int(h.Vlog.indwhere("<=", vtau0))] - prelength
f = open("HIPPCell_passive_results.dat", 'w')
f.write("DC input resistance: %g MOhm\n" % h.rn(cell))
f.write("vmin: %g mV\n" % vmin)
f.write("vtau0: %g mV\n" % vtau0)
f.write("tau0: %g ms\n" % tau0)
f.close()