if half_linear:
v_cell_ext[:, :] = utils.half_linear_field(
cell, pulse_start, pulse_start + pulse_duration, n_tsteps,
axis='z') * amp
else:
v_cell_ext[:, :] = utils.linear_field(
cell, pulse_start, pulse_start + pulse_duration, n_tsteps,
axis='z') * amp
cell.insert_v_ext(v_cell_ext, t)
# Run simulation, electrode object argument in cell.simulate
# print("running cell {2} distance from electrode: {0} current intensity: {1}").format(depth, amp, cell_id)
cell.simulate(rec_imem=True, rec_vmem=True)
spike_time_loc = utils.return_first_spike_time_and_idx(cell.vmem)
if spike_time_loc[0] is not None:
print("!!!spike at segment {0} @ t = {1} ms").format(
spike_time_loc[1], spike_time_loc[0] * cell.dt)
c_vext = v_cell_ext[spike_time_loc[1]][spike_time_loc[0]]
# FIGURES
fig = plt.figure(figsize=[12, 8])
initial = spike_time_loc[1]
# ax1 = plt.subplot(111, projection="3d",
# title="t = " + str(spike_time_loc[0] * cell.dt) + "ms", aspect=1, xlabel="x [$\mu$m]",
# ylabel="y [$\mu$m]", zlabel="z [$\mu$m]", xlim=[-600, 600], ylim=[-600, 600], zlim=[-1800, 200])
# # [ax1.plot([cell.xstart[idx], cell.xend[idx]], [cell.ystart[idx], cell.yend[idx]], [cell.zstart[idx], cell.zend[idx]], '-',
# # c='k', clip_on=False) for idx in range(cell.totnsegs)]
# # [plt.plot([cell.xstart[idx], cell.xend[idx]], [cell.zstart[idx], cell.zend[idx]], '-',
# DEBUG
if np.isnan(cell.vmem).any():
print("NaN for cell {}".format(RANK))
utils.dendritic_spike(cell)
# print('rank {}, pulse_start {}, buffer {}'.format(RANK, pulse_start, params.sim['buffer']))
spike_time_loc = utils.spike_soma(
cell,
from_t=(pulse_start - params.sim['buffer']),
to_t=(pulse_start + pulse_duration +
params.sim['buffer']))
if spike_time_loc[0] is not None:
spiked = True
detail_spike = utils.return_first_spike_time_and_idx(
cell.vmem)
print("!spike! at time {0} and position {1}, rank {2}".
format(detail_spike[0],
cell.get_idx_name(detail_spike[1])[1],
RANK))
# print("DEBUG 0 rank {}".format(RANK))
# current[RANK][np.where(amp_spread == amp)[0][0]] = dis
current[RANK][i_amp] = dis
# print("DEBUG 1 rank {}".format(RANK))
# c_vext[RANK][np.where(amp_spread == amp)[0][0]] = v_cell_ext[detail_spike[1]][detail_spike[0]]
c_vext[RANK][i_amp] = v_cell_ext[detail_spike[1]][
detail_spike[0]]
# print("DEBUG 2 rank {}".format(RANK))
# ap_loc[RANK][np.where(amp_spread == amp)[0][0]] = detail_spike[1]
ap_loc[RANK][i_amp] = detail_spike[1]
