def run(Vm, Rm, rates_exc, duration=300, interval=0, configFile='cv.xml'):
current = [[0.5,1,0,0,0,0,0,0,0,0,0,1],
[0.01,1,-300,0,0,0,0,0,0,0,0,1],
[0.5,1,0,0,0,0,0,0,0,0,0,1],
[0.6,1,-100,0,0,0,0,0,0,0,0,1],
[1,1,0,0,0,0,0,0,0,0,0,1],
[0,1,0,0,0,0,0,0,0,0,0,1]]
preamble = np.sum(current,0)[0]
current[-1][0] = duration-preamble
writeStimFile('current.stim',current)
conductance = [[preamble,1,0,0,0,0,0,0,0,0,0,1],
[duration-preamble,2,0,0,0,0,0,1,0,0,0,1]]
taus = {'exc': 5, 'inh': 10}
for rate in rates_exc:
for V in Vm:
ratio = lcg.computeRatesRatio(Vm=V, Rin=Rm)
Gm_exc,Gm_inh,Gs_exc,Gs_inh = lcg.computeSynapticBackgroundCoefficients(ratio, rate, Rin=Rm)
print('Vm = %g, rates = %g Hz (exc) %g Hz (inh).' % (V, rate, rate/ratio))
conductance[1][2] = Gm_exc
conductance[1][3] = Gs_exc
conductance[1][4] = taus['exc']
writeStimFile('gexc.stim', conductance)
conductance[1][2] = Gm_inh
conductance[1][3] = Gs_inh
conductance[1][4] = taus['inh']
writeStimFile('ginh.stim', conductance)
sub.call(lcg.common.prog_name + ' -V 3 -c ' + configFile, shell=True)
sub.call('sleep ' + str(interval), shell=True)
def frequency_error(Vbal, target, Rm, R_inh, ai=0, ao=0, duration=10, interval=1, sampling_rate=20000):
ratio = lcg.computeRatesRatio(Vm=Vbal, Rin=Rm)
R_exc = R_inh * ratio[0]
G0_exc,G0_inh,sigma_exc,sigma_inh = lcg.computeSynapticBackgroundCoefficients(ratio[0], R_exc, Rin=Rm)
lcg.writeSpontaneousConfig(0, G0_exc, sigma_exc, G0_inh, sigma_inh, ai, ao, duration, sampling_rate, outfile='spontaneous.xml')
if interval > 0:
sub.call(['sleep', str(interval)])
sub.call(lcg.common.prog_name + ' -c spontaneous.xml -V 4', shell=True)
files = glob.glob('*.h5')
files.sort()
files = files[-1]
entities,info = lcg.loadH5Trace(files)
for ntt in entities:
if ntt['name'] == 'RealNeuron':
V = ntt['data']
break
if max(V) < -40: # no spike in the presynaptic
print('Balanced voltage: %.2f mV.' % Vbal)
print('Spontaneous firing frequency: 0 Hz (0 spikes).')
print('Error = %g Hz^2.' % target**2)
return target**2
t = np.arange(0, len(V)) * info['dt']
spks = lcg.findSpikes(t,V,-20)
freq = float(len(spks)) / duration
print('Balanced voltage: %.2f mV.' % Vbal)
print('Spontaneous firing frequency: %.3f Hz (%d spikes).' % (freq, len(spks)))
print('Error = %g Hz^2.' % (freq-target)**2)
return (freq - target)**2
def main():
mode = None
if len(sys.argv) < 2 or sys.argv[1] in ('-h','--help','help'):
usage()
sys.exit(0)
mode = sys.argv[1]
if mode != 'current' and mode != 'conductance':
print('Unknown working mode: [%s].' % sys.argv[1])
sys.exit(1)
opts = parseGlobalArgs()
if mode == 'current':
opts = dict(parseCurrentModeArgs(), **opts)
tot = len(opts['correlation_coefficients']) * opts['reps']
stim = [[opts['before'], 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1],
[opts['duration'], -2, opts['current_mean'], 0, opts['current_tau'], 0, 0, 1, 0, 2, 0, 1], # indipendent part
[0, -2, 0, 0, opts['current_tau'], 0, 0, 1, 0, 2, 1, 1], # common part
[opts['after'], 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1]]
I = {'m': 0, 's': 0, 'mc': 0, 'sc': 0}
np.random.seed(5061983)
I_seeds = map(int, np.random.uniform(low=0, high=10000, size=opts['reps']))
else:
opts = dict(parseConductanceModeArgs(), **opts)
writeConfigFile(opts)
tot = len(opts['balanced_voltages']) * len(opts['correlation_coefficients']) * opts['reps']
stim = [[opts['before'], 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1],
[opts['duration'], 2, 0, 0, 0, 0, 0, 1, 0, 0, 0, 1],
[opts['after'], 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1]]
gampa = {'m': 0, 's': 0, 'mc': 0, 'sc': 0}
ggaba = {'m': 0, 's': 0, 'mc': 0, 'sc': 0}
np.random.seed(5061983)
ampa_seeds = map(int, np.random.uniform(low=0, high=10000, size=opts['reps']))
np.random.seed(7051983)
gaba_seeds = map(int, np.random.uniform(low=0, high=10000, size=opts['reps']))
if opts['with_nmda']:
np.random.seed(723587)
nmda_seeds = map(int, np.random.uniform(low=0, high=10000, size=opts['reps']))
np.random.seed(int(time.time()))
np.random.shuffle(opts['correlation_coefficients'])
cnt = 0
for c in opts['correlation_coefficients']:
if mode == 'current':
stim[1][3] = np.sqrt(1-c)*opts['current_std']
stim[2][3] = np.sqrt(c)*opts['current_std']
for k in range(opts['reps']):
if cnt%opts['kernel_frequency'] == 0:
sub.call('lcg kernel -I ' + str(opts['ai']) + ' -O ' + str(opts['ao']), shell=True)
stim[1][8] = int(np.random.uniform(low=0, high=100*opts['reps']))
stim[2][8] = I_seeds[k]
lcg.writeStimFile(stim_files['current'], stim, False)
sub.call('lcg vcclamp -V 4 -f ' + stim_files['current'], shell=True)
sub.call(['sleep', str(opts['interval'])])
cnt = cnt+1
if cnt%10 == 0:
print('[%02d/%02d]' % (cnt,tot))
else:
np.random.shuffle(opts['balanced_voltages'])
for v in opts['balanced_voltages']:
ratio = lcg.computeRatesRatio(Vm=v, Rin=opts['input_resistance'])
gampa['m'],ggaba['m'],gampa['s'],ggaba['s'] = lcg.computeSynapticBackgroundCoefficients(
ratio,R_exc=ratio*(1-c)*opts['R_inh'],Rin=opts['input_resistance'])
gampa['mc'],ggaba['mc'],gampa['sc'],ggaba['sc'] = lcg.computeSynapticBackgroundCoefficients(
ratio,R_exc=ratio*c*opts['R_inh'],Rin=opts['input_resistance'])
for k in range(opts['reps']):
current_ampa_seed = int(np.random.uniform(low=0, high=100*opts['reps']))
stim[1][2] = gampa['m']
stim[1][3] = gampa['s']
stim[1][4] = 5
stim[1][8] = current_ampa_seed
lcg.writeStimFile(stim_files['gampa'], stim, False)
stim[1][2] = ggaba['m']
stim[1][3] = ggaba['s']
stim[1][4] = 10
stim[1][8] = int(np.random.uniform(low=0, high=100*opts['reps']))
lcg.writeStimFile(stim_files['ggaba'], stim, False)
stim[1][2] = gampa['mc']
stim[1][3] = gampa['sc']
stim[1][4] = 5
stim[1][8] = ampa_seeds[k]
lcg.writeStimFile(stim_files['gampa_common'], stim, False)
stim[1][2] = ggaba['mc']
stim[1][3] = ggaba['sc']
stim[1][4] = 10
stim[1][8] = gaba_seeds[k]
lcg.writeStimFile(stim_files['ggaba_common'], stim, False)
if opts['with_nmda']:
stim[1][2] = gampa['m']
stim[1][3] = gampa['s']
stim[1][4] = opts['nmda_tau']
stim[1][8] = current_ampa_seed
lcg.writeStimFile(stim_files['gnmda'], stim, False)
stim[1][2] = gampa['m']
stim[1][3] = gampa['s']
stim[1][4] = opts['nmda_tau']
stim[1][8] = ampa_seeds[k]
lcg.writeStimFile(stim_files['gnmda_common'], stim, False)
if cnt%opts['kernel_frequency'] == 0:
sub.call('lcg kernel -I ' + str(opts['ai']) + ' -O ' + str(opts['ao']), shell=True)
cnt = cnt+1
sub.call(lcg.common.prog_name + ' -V 4 -c ' + config_file, shell=True)
sub.call(['sleep', str(opts['interval'])])
if cnt%10 == 0:
print('[%02d/%02d]' % (cnt,tot))
options['gp'] = float(a)
elif o == '-i':
options['gi'] = float(a)
elif o == '-d':
options['gd'] = float(a)
if options['target'] is None:
print('You must specify specify the target frequency (-f switch).')
sys.exit(1)
if options['input_resistance'] is not None or options['R_exc'] is not None or options['balanced_voltage'] is not None:
if options['input_resistance'] is None or options['R_exc'] is None or options['balanced_voltage'] is None:
print('To inject a noisy background input, you must specify:')
print(' 1. The input resistance of the cell (-R switch).')
print(' 2. The firing frequency of the background excitatory population (-F switch).')
print(' 3. The balanced voltage (-v switch).')
sys.exit(1)
ratio = lcg.computeRatesRatio(options['balanced_voltage'], options['input_resistance'])
options['Gm_exc'],options['Gm_inh'],options['Gs_exc'],options['Gs_inh'] = \
lcg.computeSynapticBackgroundCoefficients(ratio, options['R_exc'], options['input_resistance'])
writeFiles(options)
sub.call('lcg kernel -I ' + str(options['ai']) + ' -O ' + str(options['ao']), shell=True)
sub.call(lcg.common.prog_name + ' -c ' + config_file + ' -n ' + str(nreps) + ' -i ' + str(interval), shell=True)
if __name__ == '__main__':
main()
with_preamble = True
elif o == '--no-shuffle':
shuffle = False
elif o == '--no-kernel':
kernel = False
if input_resistance is None:
print('You must specify the input resistance of the cell (-R switch).')
sys.exit(1)
if R_exc is None and R_inh is None:
print('You must specify at least one between excitatory or inhibitory presynaptic rate (--R-exc or --R-inh switches).')
sys.exit(1)
if R_inh is None and not V_bal is None:
ratio = lcg.computeRatesRatio(Vm=V_bal, Rin=input_resistance)
R_inh = R_exc / ratio
elif R_exc is None and not V_bal is None:
ratio = lcg.computeRatesRatio(Vm=V_bal, Rin=input_resistance)
R_exc = R_inh * ratio
elif R_exc is None or R_inh is None:
print('You must specify the balanced voltage (--V-bal switch).')
sys.exit(1)
if duration is None:
print('You must specify the duration of the stimulation (-d switch).')
sys.exit(1)
if len(stim_ampl) == 1:
stim_ampl.append(stim_ampl[0])
stim_ampl.append(1)
'AO_PRE': str(ao[0]),
'AO_POST': str(ao[1]),
'KERNEL_PRE':
'kernel-' + str(ai[0]) + '-' + str(ao[0]) + '.dat',
'KERNEL_POST':
'kernel-' + str(ai[1]) + '-' + str(ao[1]) + '.dat',
'TEND': str(stim_dur)
})
else:
os.remove('pulses.stim')
print('Default configuration file [%s] missing.' % template_file)
usage()
sys.exit(1)
if with_bg:
ratio = lcg.computeRatesRatio(Vm=balanced_voltage,
Rin=input_resistance)
Gm_exc, Gm_inh, Gs_exc, Gs_inh = lcg.computeSynapticBackgroundCoefficients(
ratio, R_exc=bg_freq, Rin=input_resistance)
lcg.writeGStimFiles(
{
'm': Gm_exc,
's': Gs_exc,
'tau': 5,
'seed': 5061983
}, {
'm': Gm_inh,
's': Gs_inh,
'tau': 10,
'seed': 7051983
}, stim_dur, 0, 0)
def main():
mode = None
if len(sys.argv) < 2 or sys.argv[1] in ('-h','--help','help'):
usage()
sys.exit(0)
mode = sys.argv[1]
if mode != 'current' and mode != 'conductance':
print('Unknown working mode: [%s].' % sys.argv[1])
sys.exit(1)
opts = parseGlobalArgs()
if mode == 'current':
opts = dict(parseCurrentModeArgs(), **opts)
if opts['separate'] and (type(opts['ao']) == int or type(opts['ai']) == int or \
len(opts['ao']) == 1 or len(opts['ai']) == 1):
print('When using the --separate options, two channels must be specified (use the -I and -O options).')
sys.exit(1)
else:
opts = dict(parseConductanceModeArgs(), **opts)
if (mode == 'current' and opts['with_bg']) or mode == 'conductance':
ratio = lcg.computeRatesRatio(Vm=opts['balanced_voltage'], Rin=opts['input_resistance'])
Gm_exc,Gm_inh,Gs_exc,Gs_inh = lcg.computeSynapticBackgroundCoefficients(ratio, R_exc=opts['R_exc'], Rin=opts['input_resistance'])
opts['Gm_exc'] = Gm_exc
opts['Gm_inh'] = Gm_inh
else:
# no background conductances, it will be a current-clamp experiment
gexc = None
ginh = None
if mode == 'current':
if opts['with_bg']:
# background conductances only
gexc = [[2.61,1,0,0,0,0,0,0,0,0,0,1],
[opts['duration'],2,Gm_exc,Gs_exc,5,0,0,1,random_seed,0,0,1],
[1,1,0,0,0,0,0,0,0,0,0,1]]
ginh = [[2.61,1,0,0,0,0,0,0,0,0,0,1],
[opts['duration'],2,Gm_inh,Gs_inh,10,0,0,1,random_seed,0,0,1],
[1,1,0,0,0,0,0,0,0,0,0,1]]
if opts['mean'] == 0 and opts['std'] == 0 and opts['tau'] == 0:
# sinusoidal modulating current only
if opts['separate']:
current = [[opts['duration'],1,0,0,0,0,0,1,random_seed,0,0,1], # OU current
[1,1,0,0,0,0,0,0,0,0,0,1]]
modulation = [[opts['duration'],3,opts['I_modul'],frequency_value,0,0,0,0,0,0,0,1],
[1,1,0,0,0,0,0,0,0,0,0,1]]
else:
current = [[opts['duration'],3,opts['I_modul'],frequency_value,0,0,0,0,0,0,0,1],
[1,1,0,0,0,0,0,0,0,0,0,1]]
elif opts['tau'] == 0:
# sinusoid on top of a DC current
if opts['separate']:
current = [[opts['duration'],1,opts['mean'],0,0,0,0,0,random_seed,0,0,1], # OU current
[1,1,0,0,0,0,0,0,0,0,0,1]]
modulation = [[opts['duration'],3,opts['I_modul'],frequency_value,0,0,0,0,0,0,0,1],
[1,1,0,0,0,0,0,0,0,0,0,1]]
else:
current = [[opts['duration'],-2,opts['mean'],0,0,0,0,0,0,1,0,1],
[0,-2,opts['I_modul'],frequency_value,0,0,0,0,0,3,1,1],
[1,1,0,0,0,0,0,0,0,0,0,1]]
else:
# sinusoid on top of a noisy (OU) current
if opts['separate']:
current = [[opts['duration'],2,opts['mean'],opts['std'],opts['tau'],0,0,1,random_seed,0,0,1], # OU current
[1,1,0,0,0,0,0,0,0,0,0,1]]
modulation = [[opts['duration'],3,opts['I_modul'],frequency_value,0,0,0,0,0,0,0,1],
[1,1,0,0,0,0,0,0,0,0,0,1]]
else:
current = [[opts['duration'],-2,opts['mean'],opts['std'],opts['tau'],0,0,1,random_seed,2,0,1], # OU current
[0,-2,opts['I_modul'],frequency_value,0,0,0,0,0,3,1,1],
[1,1,0,0,0,0,0,0,0,0,0,1]]
else:
# current just for the preamble
current = [[opts['duration']+1,1,0,0,0,0,0,0,0,0,0,1]]
# conductances
opts['R_inh'] = opts['R_exc']/ratio
if opts['exc']:
gexc = createSinusoidallyModOU(frequency_value, 'exc', random_seed, opts)
else:
gexc = [{'matrix': [[2.61,1,0,0,0,0,0,0,0,0,0,1],
[opts['duration'],2,Gm_exc,Gs_exc,5,0,0,1,random_seed,0,0,1],
[1,1,0,0,0,0,0,0,0,0,0,1]], 'filename': 'gexc.stim'}]
if opts['inh']:
ginh = createSinusoidallyModOU(frequency_value, 'inh', random_seed, opts)
else:
ginh = [{'matrix': [[2.61,1,0,0,0,0,0,0,0,0,0,1],
[opts['duration'],2,Gm_inh,Gs_inh,10,0,0,1,random_seed,0,0,1],
[1,1,0,0,0,0,0,0,0,0,0,1]], 'filename': 'ginh.stim'}]
if gexc and ginh:
writeConfigurationFile(opts)
cnt = 0
tot = opts['reps']*len(opts['frequencies'])
for i in range(opts['reps']):
np.random.shuffle(opts['frequencies'])
for f in opts['frequencies']:
if opts['compute_kernel'] and cnt%opts['kernel_frequency'] == 0:
if 'separate' in opts and opts['separate']:
# compute a kernel for each channel
sub.call('lcg kernel -I ' + str(opts['ai'][0]) + ' -O ' + str(opts['ao'][0]) +
' -F '+ str(opts['sampling_rate']) + ' --non-rt --append', shell=True)
sub.call('lcg kernel -I ' + str(opts['ai'][1]) + ' -O ' + str(opts['ao'][1]) +
' -F '+ str(opts['sampling_rate']) + ' --non-rt --append', shell=True)
pass
else:
sub.call('lcg kernel -I ' + str(opts['ai']) + ' -O ' + str(opts['ao']) +
' -F '+ str(opts['sampling_rate']), shell=True)
cnt = cnt+1
print('[%02d/%02d] F = %g Hz.' % (cnt,tot,f))
I = copy.deepcopy(current)
replaceValue(I, random_seed)
replaceValue(I, frequency_value, f)
lcg.writeStimFile(current_file, I, preamble=True)
if 'separate' in opts and opts['separate']:
I = copy.deepcopy(modulation)
replaceValue(I, frequency_value, f)
lcg.writeStimFile(modulation_file, I, preamble=[0,0])
if gexc and ginh:
for stimulus in gexc:
G = copy.deepcopy(stimulus['matrix'])
replaceValue(G, random_seed)
replaceValue(G, frequency_value, f)
lcg.writeStimFile(stimulus['filename'], G)
for stimulus in ginh:
G = copy.deepcopy(stimulus['matrix'])
replaceValue(G, random_seed)
replaceValue(G, frequency_value, f)
lcg.writeStimFile(stimulus['filename'], G)
sub.call(lcg.common.prog_name + ' -V 3 -c ' + config_file, shell=True)
else:
if 'separate' in opts and opts['separate']:
channels = [{'type':'input', 'channel':opts['ai'][0]},{'type':'input', 'channel':opts['ai'][1]},
{'type':'output', 'channel':opts['ao'][0], 'stimfile':current_file},
{'type':'output', 'channel':opts['ao'][1], 'stimfile':modulation_file}]
lcg.writeIOConfigurationFile(config_file,opts['sampling_rate'],opts['duration']+3.61,channels)
sub.call(lcg.common.prog_name + ' -c ' + config_file, shell=True)
else:
sub.call('lcg stimulus -s ' + current_file + ' -F '+ str(opts['sampling_rate']), shell=True)
if cnt != tot:
sub.call(['sleep', str(opts['interval'])])
stim_dur = lcg.writePulsesStimFile(f=stim_freq, dur=1, amp=stim_amp, N=15, delay=1, withRecovery=False)
if os.path.isfile(template_file):
lcg.substituteStrings(template_file, config_file,
{'WGT': str(weight),
'AI_PRE': str(ai[0]), 'AI_POST': str(ai[1]),
'AO_PRE': str(ao[0]), 'AO_POST': str(ao[1]),
'KERNEL_PRE': 'kernel-'+str(ai[0])+'-'+str(ao[0])+'.dat',
'KERNEL_POST': 'kernel-'+str(ai[1])+'-'+str(ao[1])+'.dat',
'TEND': str(stim_dur)})
else:
os.remove('pulses.stim')
print('Default configuration file [%s] missing.' % template_file)
usage()
sys.exit(1)
if with_bg:
ratio = lcg.computeRatesRatio(Vm=balanced_voltage, Rin=input_resistance)
Gm_exc,Gm_inh,Gs_exc,Gs_inh = lcg.computeSynapticBackgroundCoefficients(ratio, R_exc=bg_freq, Rin=input_resistance)
lcg.writeGStimFiles({'m': Gm_exc, 's': Gs_exc, 'tau': 5, 'seed': 5061983},
{'m': Gm_inh, 's': Gs_inh, 'tau': 10, 'seed': 7051983},
stim_dur, 0, 0)
sub.call('lcg kernel -a -F 15000 -I ' + str(ai[0]) + ' -O ' + str(ao[0]), shell=True)
sub.call('lcg kernel -a -F 15000 -I ' + str(ai[1]) + ' -O ' + str(ao[1]), shell=True)
sub.call(lcg.common.prog_name + ' -c ' + config_file + ' -n ' + str(trials) + ' -i ' + str(interval), shell=True)
if __name__ == '__main__':
main()
