def runSound(self, parallelize=False):
self.civ = {}
self.iiv = []
if not parallelize:
pass
if parallelize:
nworker = 16
varsg = np.linspace(
0.25, 2.0,
int((2.0 - 0.25) / 0.25) + 1
) #[0.5, 0.75, 1.0, 1.5, 2.0] # covary Ih and gklt in constant ratio
self.npost = len(varsg)
nrep = 25
tasks = range(self.npost)
results = [None] * len(tasks)
ivc = [None] * len(tasks)
gklts = np.zeros(len(varsg))
ghs = np.zeros(len(varsg))
start = time.time()
seed = 0
cf = 16000.
f0 = 16000.
rundur = 0.25 # seconds
pipdur = 0.1 # seconds
dbspl = 50.
fmod = 40.
dmod = 0.
stimulus = 'tone'
# with mp.Parallelize(enumerate(tasks), results=results, workers=nworker, progressDialog='processing in parallel..') as tasker:
with mp.Parallelize(enumerate(tasks),
results=results,
workers=nworker) as tasker:
for i, x in tasker:
post_cell = cells.Bushy.create(species=species)
h.celsius = 34
self.temp = h.celsius
refgbar_klt = post_cell.soma().klt.gbar
refgbar_ih = post_cell.soma().ihvcn.gbar
gklts[i] = refgbar_klt * varsg[i]
ghs[i] = refgbar_ih * varsg[i]
post_cell.soma().klt.gbar = gklts[i]
post_cell.soma().ihvcn.gbar = ghs[i]
post_cell.initial_mechanisms = None # forget the mechanisms we set up initially
post_cell.save_all_mechs(
) # and save new ones because we are explicitely varying them
self.make_stimulus(stimulus=stimulus,
cf=cf,
f0=f0,
rundur=rundur,
pipdur=pipdur,
dbspl=50.,
simulator=None,
fmod=fmod,
dmod=dmod)
pre_cells = []
synapses = []
for n in range(self.npre):
pre_cells.append(cells.DummySGC(cf=cf, sr=2))
synapses.append(pre_cells[n].connect(post_cell,
type=synapseType))
v_reps = []
i_reps = []
p_reps = [] # pre spike on 0'th sgc
for j in range(nrep):
for prec in range(len(pre_cells)):
pre_cells[prec].set_sound_stim(self.stim,
seed=seed)
seed += 1
# for i in range(synapses[-1].terminal.n_rzones):
# xmtr['xmtr%04d'%j] = h.Vector()
# xmtr['xmtr%04d'%j].record(synapses[-1].terminal.relsite._ref_XMTR[i])
# j = j + 1
#synapses[-1].terminal.relsite.Dep_Flag = False # no depression in these simulations
#
# Run simulation
#
post_cell.vm0 = None
post_cell.cell_initialize()
# set starting voltage...
post_cell.soma(0.5).v = post_cell.vm0
h.dt = 0.02
h.t = 0 # run a bit to find true stable rmp
h.tstop = 20.
h.batch_save()
h.batch_run(h.tstop, h.dt, 'v.dat')
self['t'] = h._ref_t
# set up recordings
self['v_post%02d' % j] = post_cell.soma(0.5)._ref_v
h.finitialize() # init and instantiate recordings
print 'running %d' % i
h.t = 0.
h.tstop = rundur * 1000. # rundur is in seconds.
post_cell.check_all_mechs(
) # make sure no further changes were introduced before run.
h.batch_run(h.tstop, h.dt, 'v.dat')
v_reps.append(self['v_post%02d' % j])
i_reps.append(0. * self['v_post%02d' % j])
p_reps.append(pre_cells[0]._stvec.to_python())
tasker.results[i] = {
'v': v_reps,
'i': i_reps,
't': self['t'],
'pre': pre_cells[0]._stvec.to_python()
}
print("\nParallel time: %d workers, %0.2f sec" %
(nworker, time.time() - start))
cell_info = {'gklt': gklts, 'gh': ghs}
stim_info = {
'nreps': nrep,
'cf': cf,
'f0': f0,
'rundur': rundur,
'pipdur': pipdur,
'dbspl': dbspl,
'fmod': fmod,
'dmod': dmod
}
res = {'cells': cell_info, 'stim': stim_info, 'results': results}
if runname is not None:
f = open(runname, 'w')
pickle.dump(res, f)
f.close()
def run(self,
mode='IV',
cf=16e3,
temp=34.0,
dt=0.025,
stimamp=0,
iinj=[1.0]):
self.dt = dt
self.temp = temp
self.make_cells(cf, temp, dt)
print dir(self.pre_cells[0])
seed = 0
j = 0
if mode == 'sound':
self.make_stimulus(stimulus='tone')
for np in range(len(self.pre_cells)):
self.pre_cells[np].set_sound_stim(self.stim, seed=seed)
seed += 1
synapses.append(pre_cells[-1].connect(post_cell,
post_opts={
'AMPAScale': 2.0,
'NMDAScale': 2.0
},
type=synapseType))
for i in range(synapses[-1].terminal.n_rzones):
xmtr['xmtr%04d' % j] = h.Vector()
xmtr['xmtr%04d' % j].record(
synapses[-1].terminal.relsite._ref_XMTR[i])
j = j + 1
synapses[
-1].terminal.relsite.Dep_Flag = False # no depression in these simulations
print 'setup to run'
self.stim_params = []
self.istim = []
self.istims = []
if mode == 'pulses':
for i, pre_cell in enumerate(self.pre_cells):
stim = {}
stim['NP'] = 10
stim['Sfreq'] = 100.0 # stimulus frequency
stim['delay'] = 10.0
stim['dur'] = 0.5
stim['amp'] = stimamp
stim['PT'] = 0.0
stim['dt'] = dt
(secmd, maxt, tstims) = make_pulse(stim)
self.stim_params.append(stim)
stim['amp'] = 0.
(secmd2, maxt2, tstims2) = make_pulse(stim)
# istim current pulse train
istim = h.iStim(0.5, sec=pre_cell.soma)
i_stim_vec = h.Vector(secmd)
self.istim.append((istim, i_stim_vec))
self['istim%02d' % i] = istim._ref_i
self.postpars = []
self.poststims = []
if mode == 'IV':
for i, post_cell in enumerate(self.post_cells):
pstim = {}
pstim['NP'] = 1
pstim['Sfreq'] = 100.0 # stimulus frequency
pstim['delay'] = 10.0
pstim['dur'] = 100
pstim['amp'] = iinj[0]
pstim['PT'] = 0.0
pstim['dt'] = dt
(secmd, maxt, tstims) = make_pulse(pstim)
self.postpars.append(pstim)
# istim current pulse train
pistim = h.iStim(0.5, sec=post_cell.soma)
pi_stim_vec = h.Vector(secmd)
self.poststims.append((pistim, pi_stim_vec))
self['poststim%02d' % i] = pistim._ref_i
#
# Run simulation
#
h.celsius = temp
self.temp = temp
# first find rmp for each cell
for m in range(self.npost):
self.post_cells[m].vm0 = None
self.post_cells[m].cell_initialize()
# set starting voltage...
self.post_cells[m].soma(0.5).v = self.post_cells[m].vm0
h.dt = 0.02
h.t = 0 # run a bit to find true stable rmp
h.tstop = 20.
h.batch_save()
h.batch_run(h.tstop, h.dt, 'v.dat')
# order matters: don't set these up until we need to
self['t'] = h._ref_t
# set up recordings
if mode == 'pulses':
for i in range(self.npre):
self.istim[i][1].play(self.istim[i][0]._ref_i, dt, 0)
self['v_pre%02d' % i] = self.pre_cells[i].soma(0.5)._ref_v
for m in range(self.npost):
if mode == 'IV':
self.poststims[m][1].play(self.poststims[m][0]._ref_i, dt, 0)
self['v_post%02d' % m] = self.post_cells[m].soma(0.5)._ref_v
h.finitialize() # init and instantiate recordings
print 'running'
h.t = 0.
h.tstop = 200.
h.batch_run(h.tstop, h.dt, 'v.dat')