def __init__(self, post_cell, info):
"""
info is a dict
"""
pre_cells = []
synapses = []
j = 0
xmtr = {}
for nsgc, sgc in enumerate(range(info['n_sgc'])):
pre_cells.append(cells.DummySGC(cf=info['cf'], sr=info['sr']))
if synapseType == 'simple':
synapses.append(pre_cells[-1].connect(post_cell, type=synapseType))
synapses[-1].terminal.netcon.weight[0] =info['gmax']*2.0
elif synapseType == 'multisite':
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
pre_cells[-1].set_sound_stim(info['stim'], seed = info['seed'] + nsgc, simulator=info['simulator'])
Vm = h.Vector()
Vm.record(post_cell.soma(0.5)._ref_v)
rtime = h.Vector()
rtime.record(h._ref_t)
h.tstop = 1e3*info['run_duration'] # duration of a run
h.celsius = info['temp']
h.dt = info['dt']
post_cell.cell_initialize()
info['init']()
h.t = 0.
h.run()
return {'time': np.array(rtime), 'vm': Vm.to_python(), 'xmtr': xmtr, 'pre_cells': pre_cells, 'post_cell': post_cell, 'synapses': synapses}
def run(self, temp=34.0, dt=0.025, seed=575982035, simulator=None):
preCell = cells.DummySGC(cf=4000, sr=2)
postCell = cells.Bushy.create()
synapse = preCell.connect(postCell)
self.pre_cell = preCell
self.post_cell = postCell
self.synapse = synapse
self.stim = sound.TonePip(rate=100e3,
duration=0.1,
f0=4000,
dbspl=80,
ramp_duration=2.5e-3,
pip_duration=0.04,
pip_start=[0.02])
preCell.set_sound_stim(self.stim, seed=seed, simulator=simulator)
self['vm'] = postCell.soma(0.5)._ref_v
#self['prevm'] = preCell.soma(0.5)._ref_v
for i in range(30):
self['xmtr%d' % i] = synapse.terminal.relsite._ref_XMTR[i]
synapse.terminal.relsite.Dep_Flag = False
self['t'] = h._ref_t
h.tstop = 100.0 # duration of a run
h.celsius = temp
h.dt = dt
custom_init()
h.run()
def make_cells(self, cf=16e3, temp=34.0, dt=0.025):
self.pre_cells = []
for n in range(self.npre):
self.pre_cells.append(cells.DummySGC(cf=cf, sr=3))
self.post_cells = []
for n in range(self.npost):
self.post_cell = cells.Bushy.create(species=species)
self.post_cells.append(self.post_cell)
for n in range(self.npre):
for m in range(self.npost):
synapse = self.pre_cells[n].connect(self.post_cells[m])
self.synapse = synapse
synapse.terminal.relsite.Dep_Flag = False
# make variations in the postsynaptic cells
varsg = [0.5, 0.75, 1.0, 1.5, 2.0]
for i, m in enumerate(range(self.npost)):
refgbar_klt = self.post_cells[m].soma().klt.gbar
refgbar_ih = self.post_cells[m].soma().ihvcn.gbar
self.post_cells[m].soma().klt.gbar = refgbar_klt * varsg[i]
self.post_cells[m].soma().ihvcn.gbar = refgbar_ih * varsg[i]
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, temp=34.0, dt=0.025, seed=575982035, stimulus='tone', species='mouse'):
assert stimulus in ['tone', 'SAM', 'clicks'] # cases available
if self.cell == 'bushy':
postCell = cells.Bushy.create(species=species)
elif self.cell == 'tstellate':
postCell = cells.TStellate.create(species=species)
elif self.cell == 'octopus':
postCell = cells.Octopus.create(species=species)
elif self.cell == 'dstellate':
postCell = cells.DStellate.create(species=species)
else:
raise ValueError('cell %s is not yet implemented for phaselocking' % self.cell)
self.post_cell = postCell
self.stimulus = stimulus
self.run_duration = 1. # in seconds
self.pip_duration = 0.8 # in seconds
self.pip_start = [0.02] # in seconds
self.Fs = 100e3 # in Hz
self.f0 = 4000. # stimulus in Hz
self.cf = 4000. # SGCs in Hz
self.fMod = 100. # mod freq, Hz
self.dMod = 50. # % mod depth, Hz
self.dbspl = 60.
if self.stimulus == 'SAM':
self.stim = sound.SAMTone(rate=self.Fs, duration=self.run_duration, f0=self.f0,
fmod=self.fMod, dmod=self.dMod, dbspl=self.dbspl,
ramp_duration=2.5e-3, pip_duration=self.pip_duration,
pip_start=self.pip_start)
if self.stimulus == 'tone':
self.f0 = 1000.
self.cf = 1000.
self.stim = sound.TonePip(rate=self.Fs, duration=self.run_duration, f0=self.f0, dbspl=self.dbspl,
ramp_duration=2.5e-3, pip_duration=self.pip_duration,
pip_start=self.pip_start)
if self.stimulus == 'clicks':
self.click_rate = 0.020 # msec
self.stim = sound.ClickTrain(rate=self.Fs, duration=self.run_duration,
f0=self.f0, dbspl=self.dbspl, click_start=0.010, click_duration=100.e-6,
click_interval=self.click_rate, nclicks=int((self.run_duration-0.01)/self.click_rate),
ramp_duration=2.5e-3)
n_sgc = data.get('convergence', species=species, post_type=postCell.type, pre_type='sgc')[0]
self.n_sgc = int(np.round(n_sgc))
self.pre_cells = []
self.synapses = []
j = 0
for k in range(self.n_sgc):
seed = seed + k
preCell = cells.DummySGC(cf=self.cf, sr=2)
synapse = preCell.connect(postCell)
for i in range(synapse.terminal.n_rzones):
self['xmtr%03d'%j] = synapse.terminal.relsite._ref_XMTR[i]
j = j + 1
synapse.terminal.relsite.Dep_Flag = False
preCell.set_sound_stim(self.stim, seed=seed)
self.pre_cells.append(preCell)
self.synapses.append(synapse)
self['vm'] = postCell.soma(0.5)._ref_v
#self['prevm'] = preCell.soma(0.5)._ref_v
self['t'] = h._ref_t
postCell.cell_initialize()
h.tstop = 1e3*self.run_duration # duration of a run
h.celsius = temp
h.dt = dt
self.custom_init()
h.run()
def runTrial(cell, info):
"""
info is a dict
"""
if cell == 'bushy':
post_cell = cells.Bushy.create(species=species)
elif cell == 'tstellate':
post_cell = cells.TStellate.create(species=species)
elif cell == 'octopus':
post_cell = cells.Octopus.create(species=species)
elif cell == 'dstellate':
post_cell = cells.DStellate.create(species=species)
elif cell == 'tuberculoventral':
post_cell = cells.DStellate.create(species=species)
elif cell == 'pyramidal':
post_cell = cells.DStellate.create(species=species)
else:
raise ValueError('cell %s is not yet implemented for PSTH testing' %
self.cell)
pre_cells = []
synapses = []
j = 0
xmtr = {}
for nsgc, sgc in enumerate(range(info['n_sgc'])):
pre_cells.append(cells.DummySGC(cf=info['cf'], sr=info['sr']))
if synapseType == 'simple':
synapses.append(pre_cells[-1].connect(post_cell, type=synapseType))
synapses[-1].terminal.netcon.weight[0] = info['gmax']
elif synapseType == 'multisite':
synapses.append(pre_cells[-1].connect(post_cell,
post_opts={
'AMPAScale': 1.0,
'NMDAScale': 1.0
},
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
pre_cells[-1].set_sound_stim(info['stim'],
seed=info['seed'] + nsgc,
simulator=info['simulator'])
Vm = h.Vector()
Vm.record(post_cell.soma(0.5)._ref_v)
rtime = h.Vector()
rtime.record(h._ref_t)
h.tstop = 1e3 * info['run_duration'] # duration of a run
h.celsius = info['temp']
h.dt = info['dt']
post_cell.cell_initialize()
info['init']()
h.t = 0.
h.run()
return {
'time': np.array(rtime),
'vm': Vm.to_python(),
'xmtr': xmtr,
'pre_cells': pre_cells,
'post_cell': post_cell,
'synapses': synapses
}
def run(self, temp=38.0, dt=0.025, seed=575982035, simulator=None):
ears = {'left': [500., 502, 498], 'right': [500., 502., 498]}
self.beatfreq = 0.
self.f0 = 500.
f0 = {'left': self.f0, 'right': self.f0+self.beatfreq}
nsgc = len(ears.keys())
sgcCell = {}
bushyCell = {}
msoCell = {}
synapse = {}
self.stim = {}
self.ears = ears
self.stimdur = 0.2
self.stimdelay = 0.02
self.rundur = self.stimdelay + self.stimdur + 0.02
for i, ear in enumerate(ears.keys()):
nsgc = len(ears[ear]) # how many sgcs are specified for this ear
sgcCell[ear] = [cells.DummySGC(cf=ears[ear][k], sr=2) for k in range(nsgc)]
bushyCell[ear] = [cells.Bushy.create(temperature=temp)]
synapse[ear] = [sgcCell[ear][k].connect(bushyCell[ear][0]) for k in range(nsgc)]
self.stim[ear] = [sound.TonePip(rate=100e3, duration=self.stimdur+0.1, f0=f0[ear], dbspl=80,
ramp_duration=2.5e-3, pip_duration=self.stimdur,
pip_start=[self.stimdelay]) for k in range(nsgc)]
for k in range(len(self.stim[ear])):
sgcCell[ear][k].set_sound_stim(self.stim[ear][k], seed=seed + i*seed + k, simulator=simulator)
self['vm_bu_%s' % ear] = bushyCell[ear][0].soma(0.5)._ref_v
for k in range(30):
self['xmtr%d_%s'%(k, ear)] = synapse[ear][0].terminal.relsite._ref_XMTR[k]
for k in range(len(synapse[ear])):
synapse[ear][k].terminal.relsite.Dep_Flag = False # turn off depression
msoCell = cells.MSO.create(temperature=temp) # one target MSO cell
msosyn = {}
for ear in ears:
msosyn[ear] = bushyCell[ear][0].connect(msoCell)
self.sgc_cells = sgcCell
self.bushy_cells = bushyCell
self.synapses = synapse
self.msyns = msosyn
self.msoCell = msoCell
self.all_cells = [] # hold all "real" cells (DummySGC does not have mechanisms)
for ear in ears.keys():
self.all_cells.append([c for c in self.bushy_cells[ear]])
self.all_cells.append([self.msoCell])
self['vm_mso'] = self.msoCell.soma(0.5)._ref_v
for k, ear in enumerate(ears.keys()):
for i in range(30):
self['mso_xmtr%d_%s'%(i, ear)] = msosyn[ear].terminal.relsite._ref_XMTR[i]
msosyn[ear].terminal.relsite.Dep_Flag = False # turn off depression
self['t'] = h._ref_t
h.tstop = self.rundur*1e3 # duration of a run
h.celsius = temp
h.dt = dt
custom_init()
# confirm that all cells are ok
for cg in self.all_cells:
for c in cg:
c.check_all_mechs()
while h.t < h.tstop:
h.fadvance()