def savedat(p, rank, t_vec, dp_rec_L2, dp_rec_L5, net):
global doutf
# write time and calculated dipole to data file only if on the first proc
# only execute this statement on one proc
if rank == 0:
# write params to the file
paramrw.write(doutf['file_param'], p, net.gid_dict)
# write the raw dipole
with open(doutf['file_dpl'], 'w') as f:
for k in range(int(t_vec.size())):
f.write("%03.3f\t" % t_vec.x[k])
f.write("%5.4f\t" % (dp_rec_L2.x[k] + dp_rec_L5.x[k]))
f.write("%5.4f\t" % dp_rec_L2.x[k])
f.write("%5.4f\n" % dp_rec_L5.x[k])
# renormalize the dipole and save
dpl = Dipole(
doutf['file_dpl']) # fix to allow init from data rather than file
dpl.baseline_renormalize(doutf['file_param'])
dpl.convert_fAm_to_nAm()
dconf['dipole_scalefctr'] = dpl.scale(
paramrw.find_param(doutf['file_param'], 'dipole_scalefctr'))
dpl.smooth(
paramrw.find_param(doutf['file_param'], 'dipole_smooth_win') /
h.dt)
dpl.write(doutf['file_dpl_norm'])
# write the somatic current to the file
# for now does not write the total but just L2 somatic and L5 somatic
with open(doutf['file_current'], 'w') as fc:
for t, i_L2, i_L5 in zip(t_vec.x, net.current['L2Pyr_soma'].x,
net.current['L5Pyr_soma'].x):
fc.write("%03.3f\t" % t)
# fc.write("%5.4f\t" % (i_L2 + i_L5))
fc.write("%5.4f\t" % i_L2)
fc.write("%5.4f\n" % i_L5)
# write output spikes
file_spikes_tmp = fio.file_spike_tmp(dproj)
spikes_write(net, file_spikes_tmp)
# move the spike file to the spike dir
if rank == 0: shutil.move(file_spikes_tmp, doutf['file_spikes'])
if p['save_vsoma']: save_volt()
if p['save_cai']: save_cai()
if p['save_ica']: save_ica()
for i, elec in enumerate(lelec):
elec.lfpout(fn=doutf['file_lfp'].split('.txt')[0] + '_' + str(i) +
'.txt',
tvec=t_vec)
simparams = p = p_exp.return_pdict(
expmt_group, 0) # return the param dict for this simulation
pc.barrier() # get all nodes to this place before continuing
pc.gid_clear()
# global variables, should be node-independent
h("dp_total_L2 = 0.")
h("dp_total_L5 = 0.")
# Set tstop before instantiating any classes
h.tstop = p['tstop']
h.dt = p['dt'] # simulation duration and time-step
h.celsius = p['celsius'] # 37.0 # p['celsius'] # set temperature
# spike file needs to be known by all nodes
file_spikes_tmp = fio.file_spike_tmp(dproj)
net = network.NetworkOnNode(p) # create node-specific network
t_vec = h.Vector()
t_vec.record(h._ref_t) # time recording
dp_rec_L2 = h.Vector()
dp_rec_L2.record(h._ref_dp_total_L2) # L2 dipole recording
dp_rec_L5 = h.Vector()
dp_rec_L5.record(h._ref_dp_total_L5) # L5 dipole recording
net.movecellstopos() # position cells in 2D grid
def expandbbox(boxA, boxB):
return [(min(boxA[i][0], boxB[i][0]), max(boxA[i][1], boxB[i][1]))
for i in range(3)]