def run_batch(repetitions, interval, stim_dur, stim_amp, hyperpolarizing_pulse, pre, post,
ai, ao, pairing=False, offset=None):
try:
template_config_file = os.environ['CONFIGURATIONS_PATH'] + '/' + config_file
except:
template_config_file = os.environ['HOME'] + '/configurations/' + config_file
lcg.substituteStrings(template_config_file, config_file, {'TEND': pre+post,
'AI': ai,
'AO_INTRA': ao['intra'],
'AO_EXTRA': ao['extra']})
extra_stim = [[pre,1,0,0,0,0,0,0,0,0,0,1],
[stim_dur['extra'],1,stim_amp['extra'],0,0,0,0,0,0,0,0,1],
[post-stim_dur['extra'],1,0,0,0,0,0,0,0,0,0,1]]
lcg.writeStimFile(extracellular_stim_file, extra_stim, False)
if pairing:
intra_stim = [[pre+offset,1,0,0,0,0,0,0,0,0,0,1],
[stim_dur['intra'],1,stim_amp['intra'],0,0,0,0,0,0,0,0,1],
[post-offset-stim_dur['intra']-hyperpolarizing_pulse['dur']-0.1,1,0,0,0,0,0,0,0,0,0,1],
[hyperpolarizing_pulse['dur'],1,hyperpolarizing_pulse['amp'],0,0,0,0,0,0,0,0,1],
[0.1,1,0,0,0,0,0,0,0,0,0,1]]
else:
intra_stim = [[pre+post-hyperpolarizing_pulse['dur']-0.1,1,0,0,0,0,0,0,0,0,0,1],
[hyperpolarizing_pulse['dur'],1,hyperpolarizing_pulse['amp'],0,0,0,0,0,0,0,0,1],
[0.1,1,0,0,0,0,0,0,0,0,0,1]]
lcg.writeStimFile(intracellular_stim_file, intra_stim, False)
sub.call('lcg kernel -I ' + str(ai) + ' -O ' + str(ao['intra']), shell=True)
sub.call(lcg.common.prog_name + ' -c '+ config_file + ' -n ' + str(repetitions) +
' -i ' + str(interval-(pre+post)), shell=True)
def deflection_error(weight,
target,
templateFile,
trials=10,
window=30e-3,
ai=int(os.environ['AI_CHANNEL']),
ao=int(os.environ['AO_CHANNEL'])):
try:
w = weight[0]
except:
w = weight
lcg.substituteStrings(
templateFile, 'psp.xml', {
'<weight>0</weight>': '<weight>' + str(w) + '</weight>',
'AI': str(ai),
'AO': str(ao)
})
sub.call(lcg.common.prog_name + ' -c psp.xml -V 4 -n ' + str(trials),
shell=True)
# get the file list
files = glob.glob('*.h5')
files.sort()
files = files[-trials:]
# read the first file to allocate memory
entities, info = lcg.loadH5Trace(files[0])
for ntt in entities:
if ntt['name'] == 'RealNeuron' or ntt['id'] == 4:
post = ntt
elif ntt['name'] == 'LIFNeuron':
pre = ntt
elif ntt['name'] == 'Waveform':
t0 = ntt['metadata'][0][0]
#if max(pre['data']) < -50: # no spike in the presynaptic
# print('>>> No spike in the presynaptic neuron. <<<')
# sys.exit(1)
# allocate memory
t = np.arange(0, info['dt'] * len(post['data']), info['dt'])
idx = np.nonzero(t < t0)[0]
dV = np.zeros((trials, len(post['data'])))
dV[0, :] = post['data'] - np.mean(post['data'][idx])
for k in range(1, trials):
entities, info = lcg.loadH5Trace(files[k])
for ntt in entities:
if ntt['name'] == 'RealNeuron' or ntt['id'] == 4:
dV[k, :] = ntt['data'] - np.mean(ntt['data'][idx])
break
dV = np.mean(dV, 0)
idx = np.intersect1d(np.nonzero(t > t0)[0], np.nonzero(t < t0 + window)[0])
deflection = np.max(np.abs(dV[idx]))
print('weight = %.3f -> deflection = %.3f mV' % (weight, deflection))
return (deflection - target)**2
def deflection_error(weight, target, templateFile, trials=10, window=30e-3, ai=int(os.environ['AI_CHANNEL']), ao=int(os.environ['AO_CHANNEL'])):
try:
w = weight[0]
except:
w = weight
lcg.substituteStrings(templateFile, 'psp.xml',
{'<weight>0</weight>': '<weight>' + str(w) + '</weight>',
'AI': str(ai), 'AO': str(ao)})
sub.call(lcg.common.prog_name + ' -c psp.xml -V 4 -n ' + str(trials), shell=True)
# get the file list
files = glob.glob('*.h5')
files.sort()
files = files[-trials:]
# read the first file to allocate memory
entities,info = lcg.loadH5Trace(files[0])
for ntt in entities:
if ntt['name'] == 'RealNeuron' or ntt['id'] == 4:
post = ntt
elif ntt['name'] == 'LIFNeuron':
pre = ntt
elif ntt['name'] == 'Waveform':
t0 = ntt['metadata'][0][0]
#if max(pre['data']) < -50: # no spike in the presynaptic
# print('>>> No spike in the presynaptic neuron. <<<')
# sys.exit(1)
# allocate memory
t = np.arange(0, info['dt']*len(post['data']), info['dt'])
idx = np.nonzero(t < t0)[0]
dV = np.zeros((trials,len(post['data'])))
dV[0,:] = post['data'] - np.mean(post['data'][idx])
for k in range(1,trials):
entities,info = lcg.loadH5Trace(files[k])
for ntt in entities:
if ntt['name'] == 'RealNeuron' or ntt['id'] == 4:
dV[k,:] = ntt['data'] - np.mean(ntt['data'][idx])
break
dV = np.mean(dV,0)
idx = np.intersect1d(np.nonzero(t>t0)[0], np.nonzero(t<t0+window)[0])
deflection = np.max(np.abs(dV[idx]))
print('weight = %.3f -> deflection = %.3f mV' % (weight,deflection))
return (deflection - target)**2
if config_file == None:
try:
template_file = os.environ[
'CONFIGURATIONS_PATH'] + '/reliability_disynaptic_current.xml'
except:
template_file = os.environ[
'HOME'] + '/configurations/reliability_disynaptic_current.xml'
if os.path.isfile(template_file):
config_file = 'reliability_disynaptic.xml'
lcg.substituteStrings(
template_file, config_file, {
'<weight>0</weight>':
'<weight>' + str(weight) + '</weight>',
'<E>-80</E>':
'<E>' + str(E) + '</E>',
'<tauRise>0</tauRise>':
'<tauRise>' + str(tau_r) + '</tauRise>',
'<tauDecay>0</tauDecay>':
'<tauDecay>' + str(tau_d) + '</tauDecay>',
'<tend>0</tend>':
'<tend>' + str(np.sum(stimulus, 0)[0]) + '</tend>'
})
else:
print('Default configuration file [%s] missing.' % template_file)
usage()
sys.exit(2)
writeStimFile('current.stim', stimulus)
sub.call('lcg kernel -I ' + str(ai) + ' -O ' + str(ao), shell=True)
sub.call(lcg.common.prog_name + ' -V 3 -c ' + config_file + ' -n ' +
str(trials) + ' -i ' + str(interval),
print('Vmin must be smaller than Vmax.')
usage()
sys.exit(1)
if configFile == None:
try:
templateFile = os.environ[
'CONFIGURATIONS_PATH'] + '/in_vivo_like.xml'
except:
templateFile = os.environ[
'HOME'] + '/configurations/in_vivo_like.xml'
if os.path.isfile(templateFile):
configFile = 'cv.xml'
lcg.substituteStrings(
templateFile, configFile, {
'<maxCount>0</maxCount>':
'<maxCount>' + str(nspikes) + '</maxCount>',
'<tend>0</tend>': '<tend>' + str(duration) + '</tend>'
})
else:
print('Default configuration file [%s] missing.' % templateFile)
usage()
sys.exit(2)
Vm = np.arange(Vmin, Vmax + Vstep / 2, Vstep)
rates_exc = np.array([rate])
for i in range(repetitions):
np.random.shuffle(Vm)
sub.call('lcg kernel -I ' + str(ai) + ' -O ' + str(ao), shell=True)
run(Vm, Rm, rates_exc, duration, interval, configFile)
[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],
[duration,2,I_mean,I_std,I_tau,0,0,1,seed,0,0,1],
[1,1,0,0,0,0,0,0,0,0,0,1]]
if config_file == None:
try:
template_file = os.environ['CONFIGURATIONS_PATH'] + '/reliability_disynaptic_current.xml'
except:
template_file = os.environ['HOME'] + '/configurations/reliability_disynaptic_current.xml'
if os.path.isfile(template_file):
config_file = 'reliability_disynaptic.xml'
lcg.substituteStrings(template_file, config_file,
{'<weight>0</weight>': '<weight>'+str(weight)+'</weight>',
'<E>-80</E>': '<E>'+str(E)+'</E>',
'<tauRise>0</tauRise>': '<tauRise>'+str(tau_r)+'</tauRise>',
'<tauDecay>0</tauDecay>': '<tauDecay>'+str(tau_d)+'</tauDecay>',
'<tend>0</tend>': '<tend>'+str(np.sum(stimulus,0)[0])+'</tend>'})
else:
print('Default configuration file [%s] missing.' % template_file)
usage()
sys.exit(2)
writeStimFile('current.stim',stimulus)
sub.call('lcg kernel -I ' + str(ai) + ' -O ' + str(ao), shell=True)
sub.call(lcg.common.prog_name + ' -V 3 -c ' + config_file + ' -n ' + str(trials) + ' -i ' + str(interval), shell=True)
if __name__ == '__main__':
main()
sys.exit(1)
if Vmin >= Vmax:
print('Vmin must be smaller than Vmax.')
usage()
sys.exit(1)
if configFile == None:
try:
templateFile = os.environ['CONFIGURATIONS_PATH'] + '/in_vivo_like.xml'
except:
templateFile = os.environ['HOME'] + '/configurations/in_vivo_like.xml'
if os.path.isfile(templateFile):
configFile = 'cv.xml'
lcg.substituteStrings(templateFile, configFile,
{'<maxCount>0</maxCount>': '<maxCount>'+str(nspikes)+'</maxCount>',
'<tend>0</tend>': '<tend>'+str(duration)+'</tend>'})
else:
print('Default configuration file [%s] missing.' % templateFile)
usage()
sys.exit(2)
Vm = np.arange(Vmin,Vmax+Vstep/2,Vstep)
rates_exc = np.array([rate])
for i in range(repetitions):
np.random.shuffle(Vm)
sub.call('lcg kernel -I ' + str(ai) + ' -O ' + str(ao), shell=True)
run(Vm, Rm, rates_exc, duration, interval, configFile)
if __name__ == '__main__':
main()
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)
usage()
sys.exit(1)
if with_bg and (not input_resistance or not bg_freq or not balanced_voltage):
print('You need to specify the input resistance, the firing rate of the')
print('excitatory background synaptic activity and the balanced voltage.')
usage()
sys.exit(1)
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)
def run_batch(repetitions,
interval,
stim_dur,
stim_amp,
hyperpolarizing_pulse,
pre,
post,
ai,
ao,
pairing=False,
offset=None):
try:
template_config_file = os.environ[
'CONFIGURATIONS_PATH'] + '/' + config_file
except:
template_config_file = os.environ[
'HOME'] + '/configurations/' + config_file
lcg.substituteStrings(
template_config_file, config_file, {
'TEND': pre + post,
'AI': ai,
'AO_INTRA': ao['intra'],
'AO_EXTRA': ao['extra']
})
extra_stim = [[
pre, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1
], [stim_dur['extra'], 1, stim_amp['extra'], 0, 0, 0, 0, 0, 0, 0, 0, 1],
[post - stim_dur['extra'], 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1]]
lcg.writeStimFile(extracellular_stim_file, extra_stim, False)
if pairing:
intra_stim = [[pre + offset, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1],
[
stim_dur['intra'], 1, stim_amp['intra'], 0, 0, 0, 0,
0, 0, 0, 0, 1
],
[
post - offset - stim_dur['intra'] -
hyperpolarizing_pulse['dur'] - 0.1, 1, 0, 0, 0, 0, 0,
0, 0, 0, 0, 1
],
[
hyperpolarizing_pulse['dur'], 1,
hyperpolarizing_pulse['amp'], 0, 0, 0, 0, 0, 0, 0, 0,
1
], [0.1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1]]
else:
intra_stim = [[
pre + post - hyperpolarizing_pulse['dur'] - 0.1, 1, 0, 0, 0, 0, 0,
0, 0, 0, 0, 1
],
[
hyperpolarizing_pulse['dur'], 1,
hyperpolarizing_pulse['amp'], 0, 0, 0, 0, 0, 0, 0, 0,
1
], [0.1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1]]
lcg.writeStimFile(intracellular_stim_file, intra_stim, False)
sub.call('lcg kernel -I ' + str(ai) + ' -O ' + str(ao['intra']),
shell=True)
sub.call(lcg.common.prog_name + ' -c ' + config_file + ' -n ' +
str(repetitions) + ' -i ' + str(interval - (pre + post)),
shell=True)
