def ap_test(template_class, tree, v_init):
cell = cells.make_neurotree_cell(template_class, neurotree_dict=tree)
h.dt = 0.025
prelength = 100.0
stimdur = 10.0
soma = list(cell.soma)[0]
initial_amp = 0.05
h.tlog = h.Vector()
h.tlog.record(h._ref_t)
h.Vlog = h.Vector()
h.Vlog.record(soma(0.5)._ref_v)
thr = cells.find_spike_threshold_minimum(cell,
loc=0.5,
sec=soma,
duration=stimdur,
initial_amp=initial_amp)
f = open("HIPPCell_ap_results.dat", 'w')
f.write("## current amplitude: %g\n" % thr)
f.close()
f = open("HIPPCell_voltage_trace.dat", 'w')
for i in range(0, int(h.tlog.size())):
f.write('%g %g\n' % (h.tlog.x[i], h.Vlog.x[i]))
f.close()
def measure_ap (gid, pop_name, v_init, env, 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
prelength = 100.0
stimdur = 10.0
soma = list(hoc_cell.soma)[0]
initial_amp = 0.05
h.tlog = h.Vector()
h.tlog.record (h._ref_t)
h.Vlog = h.Vector()
h.Vlog.record (soma(0.5)._ref_v)
thr = cells.find_spike_threshold_minimum(hoc_cell,loc=0.5,sec=soma,duration=stimdur,initial_amp=initial_amp)
results = { 'spike threshold current': np.asarray([thr], dtype=np.float32),
'spike threshold trace t': np.asarray(h.tlog.to_python(), dtype=np.float32),
'spike threshold trace v': np.asarray(h.Vlog.to_python(), 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