def main():
fs = 100e3
cf = 1e3
dbspl = 50
tone_duration = 50e-3
sound = wv.ramped_tone(
fs=fs,
freq=cf,
duration=tone_duration,
dbspl=dbspl,
)
anf_trains = cochlea.run_zilany2014(
sound,
fs,
anf_num=(200,0,0),
cf=cf,
seed=0,
species='cat',
)
anf_trains.to_pickle("anf_zilany2014.pkl")
th.plot_raster(anf_trains)
th.show()
def main():
fs = 100e3
cf = 1e3
dbspl = 50
tone_duration = 50e-3
sound = wv.ramped_tone(
fs=fs,
freq=cf,
duration=tone_duration,
dbspl=dbspl,
)
anf_trains = cochlea.run_zilany2014(
sound,
fs,
anf_num=(200, 0, 0),
cf=cf,
seed=0,
species='cat',
)
anf_trains.to_pickle("anf_zilany2014.pkl")
th.plot_raster(anf_trains)
th.show()
def _run_model(model, dbspl, cf, model_pars, tone_duration):
onset = 10e-3
assert tone_duration > onset
fs = model_pars.setdefault('fs', 100e3)
model_pars.setdefault('anf_num', (250,250,250))
model_pars.setdefault('seed', 0)
sound = wv.ramped_tone(
fs=fs,
freq=cf,
duration=tone_duration,
pad=0,
dbspl=dbspl
)
anf = model(
sound=sound,
cf=cf,
**model_pars
)
rates = {}
for typ,trains in anf.groupby('type'):
trimmed = th.trim(trains, onset, None)
rate = th.firing_rate(trimmed)
rates[typ] = rate
return rates
def _run_model(model, dbspl, cf, model_pars):
duration = 100e-3
onset = 10e-3
fs = model_pars.setdefault('fs', 100e3)
model_pars.setdefault('anf_num', (250, 250, 250))
model_pars.setdefault('seed', 0)
sound = wv.ramped_tone(fs=fs,
freq=cf,
duration=duration,
pad=0,
dbspl=dbspl)
anf = model(sound=sound, cf=cf, **model_pars)
# th.plot_raster(anf)
# th.show()
# We want to make sure the the output CF is equal to the desired
# CF.
real_cf, = np.unique(anf['cf'])
assert real_cf == cf
vss = {}
for typ, group in anf.groupby('type'):
trimmed = th.trim(group, onset, None)
vs = th.vector_strength(trimmed, cf)
vss[typ] = vs
return vss
def main():
fs = 48e3
cf = cochlea.get_nearest_cf_holmberg2007(1e3)
### Make sound
sound = wv.ramped_tone(
fs=fs,
freq=cf,
duration=150e-3,
pad=10e-3,
dbspl=70,
)
### Run model
anf_trains = sg.run_holmberg2007_sg(
sound,
fs,
cf=cf,
anf_num=(10, 0, 0),
seed=0,
)
print(th.firing_rate(anf_trains))
### Plot auditory nerve response
fig, ax = plt.subplots(2, 1)
th.plot_signal(signal=sound, fs=fs, ax=ax[0])
th.plot_raster(anf_trains, ax=ax[1])
plt.show()
def create_sound(fs=100e3, freq=500, duration=0.4, dbspl=60):
"""
Create stimulus
"""
import thorns.waves as wv
S = wv.ramped_tone(fs=fs, freq=freq, duration=duration, dbspl=dbspl)
return S
def _run_model(model, dbspl, cf, model_pars):
duration = 100e-3
onset = 10e-3
fs = model_pars.setdefault('fs', 100e3)
model_pars.setdefault('anf_num', (250,250,250))
model_pars.setdefault('seed', 0)
sound = wv.ramped_tone(
fs=fs,
freq=cf,
duration=duration,
pad=0,
dbspl=dbspl
)
anf = model(
sound=sound,
cf=cf,
**model_pars
)
### We want to make sure the the output CF is equal to the desired
### CF.
real_cf, = np.unique(anf['cf'])
assert real_cf == cf
hsr = anf[anf['type']=='hsr']
hsr = th.trim(hsr, onset, None)
si_hsr = th.vector_strength(hsr, cf)
msr = anf[anf['type']=='msr']
msr = th.trim(msr, onset, None)
si_msr = th.vector_strength(msr, cf)
lsr = anf[anf['type']=='lsr']
lsr = th.trim(lsr, onset, None)
si_lsr = th.vector_strength(lsr, cf)
# print(si_hsr)
# th.plot_raster(anf)
# th.show()
vss = {
'hsr': si_hsr,
'msr': si_msr,
'lsr': si_lsr,
}
return vss
def error_func(
dbspl,
model,
cf,
spont_rate,
model_pars,
asr_filter=False,
freq=None
):
pars = dict(model_pars)
fs = pars.setdefault('fs', 100e3)
pars.setdefault('seed', 0)
pars.setdefault('anf_num', (1000, 0, 0))
if freq is None:
freq = cf
tone_duration = 250e-3
onset = 15e-3
sound = wv.ramped_tone(
fs,
freq,
duration=tone_duration,
ramp=2.5e-3,
pad=0,
dbspl=dbspl
)
if asr_filter:
sound = adjust_to_human_thresholds(sound, fs, model)
anf = model(
sound=sound,
cf=cf,
**pars
)
trains = th.trim(anf, onset, None)
rate = th.firing_rate(trains)
error = rate - spont_rate
logging.debug("{} {} {}".format(dbspl, rate, error))
return error
def _run_model(model, dbspl, cf, model_pars, tone_duration):
onset = 10e-3
assert tone_duration > onset
fs = model_pars.setdefault('fs', 100e3)
model_pars.setdefault('anf_num', (250,250,250))
model_pars.setdefault('seed', 0)
sound = wv.ramped_tone(
fs=fs,
freq=cf,
duration=tone_duration,
pad=0,
dbspl=dbspl
)
anf = model(
sound=sound,
cf=cf,
**model_pars
)
### TODO: try to use DataFrame.groupby instead
hsr = anf.query("type == 'hsr'")
hsr = th.trim(hsr, onset, None)
rate_hsr = th.firing_rate(hsr)
msr = anf.query("type == 'msr'")
msr = th.trim(msr, onset, None)
rate_msr = th.firing_rate(msr)
lsr = anf.query("type == 'lsr'")
lsr = th.trim(lsr, onset, None)
rate_lsr = th.firing_rate(lsr)
rates = {
'hsr': rate_hsr,
'msr': rate_msr,
'lsr': rate_lsr,
}
return rates
def main():
fs = 100e3
cf = 500
convergence = (35, 0, 0)
# Generate sound
sound = wv.ramped_tone(fs=fs, freq=cf, duration=50e-3, pad=30e-3, dbspl=50)
# Run inner ear model
anf_trains = cochlea.run_zilany2014(sound=sound,
fs=fs,
cf=cf,
anf_num=convergence,
species='cat',
seed=0)
# Run GBC
cn.set_celsius(37)
cn.set_fs(fs)
gbc = cn.GBC_Point(convergence=convergence,
cf=cf,
endbulb_class='tonic',
record_voltages=True)
gbc.load_anf_trains(anf_trains, seed=0)
cn.run(duration=len(sound) / fs, objects=[gbc])
# Collect the results
gbc_trains = gbc.get_trains()
voltages = gbc.get_voltages()
# Present the results
print(gbc_trains)
fig, ax = plt.subplots(2, 1)
th.plot_raster(anf_trains, ax=ax[0])
ax[0].set_title("ANF input")
th.plot_signal(voltages, fs=fs, ax=ax[1])
th.show()
def _run_model(model, dbspl, cf, model_pars):
duration = 100e-3
onset = 10e-3
fs = model_pars.setdefault('fs', 100e3)
model_pars.setdefault('anf_num', (250,250,250))
model_pars.setdefault('seed', 0)
sound = wv.ramped_tone(
fs=fs,
freq=cf,
duration=duration,
pad=0,
dbspl=dbspl
)
anf = model(
sound=sound,
cf=cf,
**model_pars
)
hsr = anf[anf['type']=='hsr']
hsr = th.trim(hsr, onset, None)
rate_hsr = th.firing_rate(hsr)
msr = anf[anf['type']=='msr']
msr = th.trim(msr, onset, None)
rate_msr = th.firing_rate(msr)
lsr = anf[anf['type']=='lsr']
lsr = th.trim(lsr, onset, None)
rate_lsr = th.firing_rate(lsr)
rates = {
'hsr': rate_hsr,
'msr': rate_msr,
'lsr': rate_lsr,
}
return rates
def main():
fs = 100e3
cf = 1e3
tmax = 50e-3
sound = wv.ramped_tone(
fs=fs,
freq=cf,
duration=tmax,
pad=30e-3,
dbspl=50,
)
anf_trains = cochlea.run_zilany2014(
sound=sound,
fs=fs,
cf=cf,
anf_num=(300, 0, 0),
seed=0,
species='cat',
)
anfs = cochlea.make_brian_group(anf_trains)
print(anfs)
brainstem = make_brainstem_group(100)
print(brainstem)
monitor = brian.SpikeMonitor(brainstem)
net = brian.Network([brainstem, monitor])
net.run(tmax*second)
brian.raster_plot(monitor)
brian.show()
def error_func(dbspl,
model,
cf,
spont_rate,
model_pars,
asr_filter=False,
freq=None):
pars = dict(model_pars)
fs = pars.setdefault('fs', 100e3)
pars.setdefault('seed', 0)
pars.setdefault('anf_num', (1000, 0, 0))
if freq is None:
freq = cf
tone_duration = 250e-3
onset = 15e-3
sound = wv.ramped_tone(fs,
freq,
duration=tone_duration,
ramp=2.5e-3,
pad=0,
dbspl=dbspl)
if asr_filter:
sound = adjust_to_human_thresholds(sound, fs, model)
anf = model(sound=sound, cf=cf, **pars)
trains = th.trim(anf, onset, None)
rate = th.firing_rate(trains)
error = rate - spont_rate
logging.debug("{} {} {}".format(dbspl, rate, error))
return error
def _run_model(model, dbspl, cf, model_pars):
duration = 100e-3
onset = 10e-3
fs = model_pars.setdefault('fs', 100e3)
model_pars.setdefault('anf_num', (250,250,250))
model_pars.setdefault('seed', 0)
sound = wv.ramped_tone(
fs=fs,
freq=cf,
duration=duration,
pad=0,
dbspl=dbspl
)
anf = model(
sound=sound,
cf=cf,
**model_pars
)
# th.plot_raster(anf)
# th.show()
### We want to make sure the the output CF is equal to the desired
### CF.
real_cf, = np.unique(anf['cf'])
assert real_cf == cf
vss = {}
for typ,group in anf.groupby('type'):
trimmed = th.trim(group, onset, None)
vs = th.vector_strength(trimmed, cf)
vss[typ] = vs
return vss
def main():
fs = 100e3
cf = 1e3
tmax = 50e-3
sound = wv.ramped_tone(
fs=fs,
freq=cf,
duration=tmax,
pad=30e-3,
dbspl=50,
)
anf_trains = cochlea.run_zilany2014(
sound=sound,
fs=fs,
cf=cf,
anf_num=(300, 0, 0),
seed=0,
species='cat',
)
anfs = cochlea.make_brian_group(anf_trains)
print(anfs)
brainstem = make_brainstem_group(100)
print(brainstem)
monitor = brian.SpikeMonitor(brainstem)
net = brian.Network([brainstem, monitor])
net.run(tmax * second)
brian.raster_plot(monitor)
brian.show()
def _run_model(model, dbspl, cf, model_pars, tone_duration):
onset = 10e-3
assert tone_duration > onset
fs = model_pars.setdefault('fs', 100e3)
model_pars.setdefault('anf_num', (250, 250, 250))
model_pars.setdefault('seed', 0)
sound = wv.ramped_tone(fs=fs,
freq=cf,
duration=tone_duration,
pad=0,
dbspl=dbspl)
anf = model(sound=sound, cf=cf, **model_pars)
rates = {}
for typ, trains in anf.groupby('type'):
trimmed = th.trim(trains, onset, None)
rate = th.firing_rate(trimmed)
rates[typ] = rate
return rates
def main():
fs = 100e3 # s
cf = 600 # Hz
duration = 50e-3 # s
# Simulation sampling frequency
cn.set_fs(40e3) # Hz
# Generate sound
sound = wv.ramped_tone(
fs=fs,
freq=cf,
duration=duration,
dbspl=30,
)
# Generate ANF trains
anf_trains = cochlea.run_zilany2014(
sound=sound,
fs=fs,
anf_num=(300, 0, 0), # (HSR, MSR, LSR)
cf=cf,
species='cat',
seed=0,
)
# Generate ANF and GBC groups
anfs = cn.make_anf_group(anf_trains)
gbcs = cn.make_gbc_group(100)
# Connect ANFs and GBCs
synapses = brian.Connection(
anfs,
gbcs,
'ge_syn',
)
convergence = 20
weight = cn.synaptic_weight(pre='anf', post='gbc', convergence=convergence)
synapses.connect_random(anfs,
gbcs,
p=convergence / len(anfs),
fixed=True,
weight=weight)
# Monitors for the GBCs
spikes = brian.SpikeMonitor(gbcs)
# Run the simulation
cn.run(duration=len(sound) / fs, objects=[anfs, gbcs, synapses, spikes])
# Present the results
gbc_trains = th.make_trains(spikes)
fig, ax = plt.subplots(2, 1)
th.plot_raster(anf_trains, ax=ax[0])
th.plot_raster(gbc_trains, ax=ax[1])
plt.show()