def make_stimulus(self, stimulus='tone', cf=16000., f0=16000., simulator=None,
rundur=0.2, pipdur=0.05, dbspl=50.,
fmod=100., dmod=0.):
self.stimulus = stimulus
self.run_duration = rundur # in seconds
self.pip_duration = pipdur # in seconds
self.pip_start = [0.1] # in seconds
self.Fs = 100e3 # in Hz
self.f0 = f0 # stimulus in Hz
self.cf = cf # SGCs in Hz
self.fMod = fmod # mod freq, Hz
self.dMod = dmod # % mod depth, Hz
self.dbspl = dbspl
self.simulator = simulator
self.sr = 1 # set SR group
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.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)
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 run_sim(*args):
cf = 1000
sr = 2
seed = 12345678
stim = sound.TonePip(rate=100e3,
duration=0.01,
f0=4000,
dbspl=80,
ramp_duration=0.002,
pip_duration=0.004,
pip_start=[0.001])
spikes = an_model.get_spiketrain(cf=cf, sr=sr, seed=seed, stim=stim)
cf = cache.get_cache_filename(cf, sr, seed, stim)
mtime = os.stat(cf).st_mtime
return cf, mtime, spikes
def test_tonepip():
rate = 100000
dur = 0.1
ps = 0.01
rd = 0.02
pd = 0.08
db = 60
s1 = sound.TonePip(rate=rate,
duration=dur,
f0=5321,
dbspl=db,
pip_duration=pd,
pip_start=[ps],
ramp_duration=rd)
# test array sizes
assert s1.sound.size == s1.time.size == int(dur * rate) + 1
# test for consistency
assert np.allclose(
[s1.sound.min(), s1.sound.mean(),
s1.sound.max()],
[-0.028284253158247834, -1.0954891976168953e-10, 0.028284270354167296])
# test that we got the requested amplitude
assert np.allclose(s1.measure_dbspl(ps + rd, ps + pd - rd),
db,
atol=0.1,
rtol=0.01)
# test for quiet before and after pip
assert np.all(s1.sound[:int(ps * rate) - 1] == 0)
assert np.all(s1.sound[int((ps + pd) * rate) + 1:] == 0)
# test the sound can be recreated from its key
key = s1.key()
s2 = sound.create(**key)
assert np.all(s1.time == s2.time)
assert np.all(s1.sound == s2.sound)
def run(self,
pops,
cf=16e3,
temp=34.0,
dt=0.025,
stim='sound',
simulator='cochlea'):
"""
1. Connect pop1 => pop2
2. Instantiate a single cell in pop2
3. Automatically generate presynaptic cells and synapses from pop1
4. Stimulate presynaptic cells and record postsynaptically
"""
pre_pop, post_pop = pops
pre_pop.connect(post_pop)
self.pre_pop = pre_pop
self.post_pop = post_pop
# start with one cell, selected from the user-selected population, that has
# a cf close to the center CF
post_cell_ind = post_pop.select(1, cf=cf, create=True)[0]
post_cell = post_pop.get_cell(post_cell_ind)
post_pop.resolve_inputs(depth=1)
post_sec = post_cell.soma
self.post_cell_ind = post_cell_ind
self.post_cell = post_cell
pre_cell_inds = post_pop.cell_connections(post_cell_ind)[pre_pop]
pre_cells = [pre_pop.get_cell(i) for i in pre_cell_inds]
pre_secs = [cell.soma for cell in pre_cells]
self.pre_cells = pre_cells
self.pre_cell_inds = pre_cell_inds
self.stim = sound.TonePip(rate=100e3,
duration=0.1,
f0=cf,
dbspl=60,
ramp_duration=2.5e-3,
pip_duration=0.05,
pip_start=[0.02])
##
## voltage clamp the target cell
##
#clampV = 40.0
#vccontrol = h.VClamp(0.5, sec=post_cell.soma)
#vccontrol.dur[0] = 10.0
#vccontrol.amp[0] = clampV
#vccontrol.dur[1] = 100.0
#vccontrol.amp[1] = clampV
#vccontrol.dur[2] = 20.0
#vccontrol.amp[2] = clampV
#
# set up stimulation of the presynaptic cells
#
self.stim_params = []
self.istim = []
for i, pre_cell in enumerate(pre_cells):
if stim == 'sound':
pre_cell.set_sound_stim(self.stim, seed=i, simulator=simulator)
amp = 0.0
else:
amp = 3.0
istim = h.iStim(0.5, sec=pre_cell.soma)
stim = {}
stim['NP'] = 10
stim['Sfreq'] = 100.0 # stimulus frequency
stim['delay'] = 10.0
stim['dur'] = 0.5
stim['amp'] = amp
stim['PT'] = 0.0
stim['dt'] = dt
(secmd, maxt, tstims) = util.make_pulse(stim)
self.stim_params.append(stim)
# istim current pulse train
i_stim_vec = h.Vector(secmd)
i_stim_vec.play(istim._ref_i, dt, 0, pre_cell.soma(0.5))
self.istim.append((istim, i_stim_vec))
self['istim'] = istim._ref_i
# record presynaptic Vm
self['v_pre%d' % i] = pre_cell.soma(0.5)._ref_v
self['t'] = h._ref_t
self['v_post'] = post_cell.soma(0.5)._ref_v
#
# Run simulation
#
h.dt = dt
self.dt = dt
h.celsius = post_cell.status['temperature']
self.temp = h.celsius
post_cell.cell_initialize() # proper initialization.
h.dt = self.dt
custom_init(v_init=post_cell.vm0)
h.t = 0.
h.tstop = 200.0
while h.t < h.tstop:
h.fadvance()
def run(self,
temp=34.0,
dt=0.025,
seed=575982035,
reps=10,
stimulus='tone',
simulator='cochlea'):
assert stimulus in ['tone', 'SAM', 'clicks'] # cases available
assert self.cell in ['bushy', 'tstellate', 'octopus', 'dstellate']
self.nrep = reps
self.stimulus = stimulus
self.run_duration = 0.20 # in seconds
self.pip_duration = 0.05 # in seconds
self.pip_start = [0.1] # 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 = 0. # % mod depth, Hz
self.dbspl = 50.
self.simulator = simulator
self.sr = 1 # set SR group
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 = 4000.
self.cf = 4000.
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=self.cell,
pre_type='sgc')[0]
self.n_sgc = int(np.round(n_sgc))
# for simple synapses, need this value:
self.AMPA_gmax = data.get(
'sgc_synapse',
species=species,
post_type=self.cell,
field='AMPA_gmax')[0] / 1e3 # convert nS to uS for NEURON
self.vms = [None for n in range(self.nrep)]
self.synapses = [None for n in range(self.nrep)]
self.xmtrs = [None for n in range(self.nrep)]
self.pre_cells = [None for n in range(self.nrep)]
self.time = [None for n in range(self.nrep)]
info = {
'n_sgc': self.n_sgc,
'gmax': self.AMPA_gmax,
'stim': self.stim,
'simulator': self.simulator,
'cf': self.cf,
'sr': self.sr,
'seed': seed,
'run_duration': self.run_duration,
'temp': temp,
'dt': dt,
'init': custom_init
}
if not self.parallelize:
for nr in range(self.nrep):
info['seed'] = seed + 3 * self.n_sgc * nr
res = RunTrial(self.cell, info)
# res contains: {'time': time, 'vm': Vm, 'xmtr': xmtr, 'pre_cells': pre_cells, 'post_cell': post_cell}
self.pre_cells[nr] = res['pre_cells']
self.time[nr] = res['time']
self.xmtr = {k: v.to_python() for k, v in res['xmtr'].items()}
self.vms[nr] = res['vm']
self.synapses[nr] = res['synapses']
self.xmtrs[nr] = self.xmtr
if self.parallelize:
### Use parallelize with multiple workers
tasks = range(len(self.nrep))
results3 = results[:]
start = time.time()
# with mp.Parallelize(enumerate(tasks), results=results, progressDialog='processing in parallel..') as tasker:
with mp.Parallelize(enumerate(tasks), results=results) as tasker:
for i, x in tasker:
tot = 0
for j in xrange(size):
tot += j * x
tasker.results[i] = tot
print("\nParallel time, %d workers: %0.2f" %
(mp.Parallelize.suggestedWorkerCount(), time.time() - start))
print("Results match serial: %s" % str(results3 == results))
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 run(self,
temp=34.0,
dt=0.025,
seed=575982035,
reps=10,
stimulus='tone',
simulator='cochlea',
parallelize=False):
assert stimulus in ['tone', 'SAM', 'clicks'] # cases available
assert self.cell in [
'bushy', 'tstellate', 'octopus', 'dstellate', 'tuberculoventral',
'pyramidal'
]
self.nrep = reps
self.stimulus = stimulus
self.run_duration = 0.20 # in seconds
self.pip_duration = 0.05 # in seconds
self.pip_start = [0.1] # 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 = 0. # % mod depth, Hz
self.dbspl = 50.
self.simulator = simulator
self.sr = 2 # set SR group
if self.stimulus == 'SAM':
self.dMod = 100.
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 = 4000.
self.cf = 4000.
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=self.cell,
pre_type='sgc')[0]
self.n_sgc = int(np.round(n_sgc))
# for simple synapses, need this value:
self.AMPA_gmax = data.get(
'sgc_synapse',
species=species,
post_type=self.cell,
field='AMPA_gmax')[0] / 1e3 # convert nS to uS for NEURON
self.vms = [None for n in range(self.nrep)]
self.synapses = [None for n in range(self.nrep)]
self.xmtrs = [None for n in range(self.nrep)]
self.pre_cells = [None for n in range(self.nrep)]
self.time = [None for n in range(self.nrep)]
info = {
'n_sgc': self.n_sgc,
'gmax': self.AMPA_gmax,
'stim': self.stim,
'simulator': self.simulator,
'cf': self.cf,
'sr': self.sr,
'seed': seed,
'run_duration': self.run_duration,
'temp': temp,
'dt': dt,
'init': custom_init
}
if not parallelize:
for nr in range(self.nrep):
info['seed'] = seed + 3 * self.n_sgc * nr
res = runTrial(self.cell, info)
# res contains: {'time': time, 'vm': Vm, 'xmtr': xmtr, 'pre_cells': pre_cells, 'post_cell': post_cell}
self.pre_cells[nr] = res['pre_cells']
self.time[nr] = res['time']
self.xmtr = {k: v.to_python() for k, v in res['xmtr'].items()}
self.vms[nr] = res['vm']
self.synapses[nr] = res['synapses']
self.xmtrs[nr] = self.xmtr
if parallelize:
pass
def test_an_model():
# model fiber parameters
CF = 1.5e3 # CF in Hz
cohc = 1.0 # normal ohc function
cihc = 1.0 # normal ihc function
species = 1 # 1 for cat (2 for human with Shera et al. tuning 3 for human with Glasberg & Moore tuning)
noiseType = 1 # 1 for variable fGn (0 for fixed fGn)
fiberType = 3 # spontaneous rate (in spikes/s) of the fiber BEFORE refractory effects "1" = Low "2" = Medium "3" = High
implnt = 0 # "0" for approximate or "1" for actual implementation of the power-law functions in the Synapse
# stimulus parameters
F0 = CF # stimulus frequency in Hz
Fs = 100e3 # sampling rate in Hz (must be 100, 200 or 500 kHz)
T = 150e-3 # stimulus duration in seconds
pdur = 0.02 # pip duration
pstart = [0.01, 0.035] # pip start times
rt = 2.5e-3 # rise/fall time in seconds
stimdb = 65 # stimulus intensity in dB SPL
# PSTH parameters
nrep = 1000 # number of stimulus repetitions (e.g., 50)
psthbinwidth = 0.5e-3 # binwidth in seconds
stim = sound.TonePip(rate=Fs,
duration=T,
f0=F0,
dbspl=stimdb,
pip_duration=pdur,
pip_start=pstart,
ramp_duration=rt)
t = stim.time
pin = stim.sound
db = stim.measure_dbspl(rt, T - rt)
an_model.seed_rng(34978)
start = time.time()
vihc = an_model.model_ihc(pin,
CF,
nrep,
1 / Fs,
T + 1e-3,
cohc,
cihc,
species,
_transfer=False)
print "IHC time:", time.time() - start
start = time.time()
m, v, psth = an_model.model_synapse(vihc, CF, nrep, 1 / Fs, fiberType,
noiseType, implnt)
print "Syn time:", time.time() - start
win = pg.GraphicsWindow()
p1 = win.addPlot(title='Input Stimulus (%0.1f dBSPL)' % db)
p1.plot(t, pin)
p2 = win.addPlot(col=0, row=1, title='IHC voltage')
p2.setXLink(p1)
vihc = vihc.get()[0]
vihc = vihc[:len(vihc) // nrep]
t = np.arange(len(vihc)) * 1e-5
p2.plot(t, vihc)
p3 = win.addPlot(col=0, row=2, title='ANF PSTH')
p3.setXLink(p2)
ds = 100
size = psth.size // ds
psth = psth[:size * ds].reshape(size, ds).sum(axis=1)
t = np.arange(len(psth)) * 1e-5 * ds
p3.plot(t, psth[:-1], stepMode=True, fillLevel=0, fillBrush='w')
if sys.flags.interactive == 0:
pg.QtGui.QApplication.exec_()
for i in range(nreps):
tasks.append((f, db, i))
results = {}
workers = 1 if not parallel else None
tot_runs = len(fvals) * len(levels) * nreps
with mp.Parallelize(enumerate(tasks),
results=results,
progressDialog='Running parallel simulation..',
workers=workers) as tasker:
for i, task in tasker:
f, db, iteration = task
stim = sound.TonePip(
rate=100e3,
duration=stimpar['dur'],
f0=f,
dbspl=db, # dura 0.2, pip_start 0.1 pipdur 0.04
ramp_duration=2.5e-3,
pip_duration=stimpar['pip'],
pip_start=stimpar['start'])
print("=== Start run %d/%d ===" % (i + 1, tot_runs))
cachefile = os.path.join(
cachepath, 'seed=%d_f0=%f_dbspl=%f_syntype=%s_iter=%d.pk' %
(seed, f, db, syntype, iteration))
if '--ignore-cache' in sys.argv or not os.path.isfile(cachefile):
result = prot.run(stim, seed=i)
pickle.dump(result, open(cachefile, 'wb'))
else:
print(" (Loading cached results)")
result = pickle.load(open(cachefile, 'rb'))
tasker.results[(f, db, iteration)] = (stim, result)
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()