def runsim():
t0 = time.time() # clock start time
pc.set_maxstep(
10) # sets the default max solver step in ms (purposefully large)
for elec in lelec:
elec.setup()
elec.LFPinit()
h.finitialize(
) # initialize cells to -65 mV, after all the NetCon delays have been specified
if pcID == 0:
for tt in range(0, int(h.tstop), printdt):
h.cvode.event(tt, prsimtime) # print time callbacks
h.fcurrent()
h.frecord_init(
) # set state variables if they have been changed since h.finitialize
pc.psolve(h.tstop) # actual simulation - run the solver
pc.barrier()
# these calls aggregate data across procs/nodes
pc.allreduce(dp_rec_L2, 1)
pc.allreduce(
dp_rec_L5,
1) # combine dp_rec on every node, 1=add contributions together
for elec in lelec:
elec.lfp_final()
net.aggregate_currents(
) # aggregate the currents independently on each proc
# combine net.current{} variables on each proc
pc.allreduce(net.current['L5Pyr_soma'], 1)
pc.allreduce(net.current['L2Pyr_soma'], 1)
pc.barrier()
# write time and calculated dipole to data file only if on the first proc
# only execute this statement on one proc
savedat(p, pcID, t_vec, dp_rec_L2, dp_rec_L5, net)
for elec in lelec:
print('end; t_vec.size()', t_vec.size(), 'elec.lfp_t.size()',
elec.lfp_t.size())
if pcID == 0:
if debug: print("Simulation run time: %4.4f s" % (time.time() - t0))
if debug: print("Simulation directory is: %s" % ddir.dsim)
if paramrw.find_param(doutf['file_param'],
'save_spec_data') or usingOngoingInputs(
doutf['file_param']):
runanalysis(p, doutf['file_param'], doutf['file_dpl_norm'],
doutf['file_spec']) # run spectral analysis
if paramrw.find_param(doutf['file_param'], 'save_figs'):
savefigs(ddir, p, p_exp) # save output figures
pc.barrier() # make sure all done in case multiple trials
def getInputs (self):
""" get a dictionary of input types used in simulation
with distal/proximal specificity for evoked,ongoing inputs
"""
dinty = {'Evoked':False,'Ongoing':False,'Poisson':False,'Tonic':False,'EvokedDist':False,\
'EvokedProx':False,'OngoingDist':False,'OngoingProx':False}
try:
dinty['Evoked'] = usingEvokedInputs(dfile['outparam'])
dinty['EvokedDist'] = usingEvokedInputs(dfile['outparam'], lsuffty = ['_evdist_'])
dinty['EvokedProx'] = usingEvokedInputs(dfile['outparam'], lsuffty = ['_evprox_'])
dinty['Ongoing'] = usingOngoingInputs(dfile['outparam'])
dinty['OngoingDist'] = usingOngoingInputs(dfile['outparam'], lty = ['_dist'])
dinty['OngoingProx'] = usingOngoingInputs(dfile['outparam'], lty = ['_prox'])
dinty['Poisson'] = usingPoissonInputs(dfile['outparam'])
dinty['Tonic'] = usingTonicInputs(dfile['outparam'])
except:
pass
return dinty
dclr = {'L2_pyramidal' : 'g',
'L5_pyramidal' : 'r',
'L2_basket' : 'w',
'L5_basket' : 'b'}
ntrial = 1; tstop = -1; outparamf = spkpath = paramf = ''; EvokedInputs = OngoingInputs = PoissonInputs = False;
for i in range(len(sys.argv)):
if sys.argv[i].endswith('.txt'):
spkpath = sys.argv[i]
elif sys.argv[i].endswith('.param'):
paramf = sys.argv[i]
tstop = paramrw.quickgetprm(paramf,'tstop',float)
ntrial = paramrw.quickgetprm(paramf,'N_trials',int)
EvokedInputs = paramrw.usingEvokedInputs(paramf)
OngoingInputs = paramrw.usingOngoingInputs(paramf)
PoissonInputs = paramrw.usingPoissonInputs(paramf)
outparamf = os.path.join(dconf['datdir'],paramf.split('.param')[0].split(os.path.sep)[-1],'param.txt')
try:
extinputs = spikefn.ExtInputs(spkpath, outparamf)
except ValueError:
print("Error: could not load spike timings from %s" % spkpath)
extinputs.add_delay_times()
alldat = {}
ncell = len(net.cells)
binsz = 5.0