def instantiate_BG(params={}, antagInjectionSite='none', antag=''):
nest.ResetKernel()
dataPath='log/'
if 'nbcpu' in params:
nest.SetKernelStatus({'local_num_threads': params['nbcpu']})
nstrand.set_seed(params['nestSeed'], params['pythonSeed']) # sets the seed for the BG construction
nest.SetKernelStatus({"data_path": dataPath})
initNeurons()
print '/!\ Using the following LG14 parameterization',params['LG14modelID']
loadLG14params(params['LG14modelID'])
loadThetaFromCustomparams(params)
# We check that all the necessary parameters have been defined. They should be in the modelParams.py file.
# If one of them misses, we exit the program.
necessaryParams=['nbCh','nbMSN','nbFSI','nbSTN','nbGPe','nbGPi','nbCSN','nbPTN','nbCMPf','IeMSN','IeFSI','IeSTN','IeGPe','IeGPi','GMSN','GFSI','GSTN','GGPe','GGPi','inDegCSNMSN','inDegPTNMSN','inDegCMPfMSN','inDegMSNMSN','inDegFSIMSN','inDegSTNMSN','inDegGPeMSN','inDegCSNFSI','inDegPTNFSI','inDegSTNFSI','inDegGPeFSI','inDegCMPfFSI','inDegFSIFSI','inDegPTNSTN','inDegCMPfSTN','inDegGPeSTN','inDegCMPfGPe','inDegSTNGPe','inDegMSNGPe','inDegGPeGPe','inDegMSNGPi','inDegSTNGPi','inDegGPeGPi','inDegCMPfGPi',]
for np in necessaryParams:
if np not in params:
raise KeyError('Missing parameter: '+np)
#------------------------
# creation and connection of the neural populations
#------------------------
createBG()
connectBG(antagInjectionSite,antag)
def instantiate_BG(params={}, antagInjectionSite='none', antag=''):
nest.ResetKernel()
dataPath = 'log/'
if 'nbcpu' in params:
nest.SetKernelStatus({'local_num_threads': params['nbcpu']})
nstrand.set_seed(
params['nestSeed'],
params['pythonSeed']) # sets the seed for the BG construction
nest.SetKernelStatus({"data_path": dataPath})
#nest.SetKernelStatus({"resolution": 0.005}) # simulates with a higher precision
initNeurons()
print '/!\ Using the following LG14 parameterization', params[
'LG14modelID']
loadLG14params(params['LG14modelID'])
loadThetaFromCustomparams(params)
# We check that all the necessary parameters have been defined. They should be in the modelParams.py file.
# If one of them misses, we exit the program.
if params['splitGPe']:
necessaryParams = [
'nbCh',
'nbMSN',
'nbFSI',
'nbSTN',
'nbGPe',
'nbArky',
'nbProt',
'nbGPi',
'nbCSN',
'nbPTN',
'nbCMPf',
'IeMSN',
'IeFSI',
'IeSTN',
'IeGPe',
'IeArky',
'IeProt',
'IeGPi',
'GCSNMSN',
'GPTNMSN',
'GCMPfMSN',
'GMSNMSN',
'GFSIMSN',
'GSTNMSN',
'GGPeMSN',
'GArkyMSN',
'GCSNFSI',
'GPTNFSI',
'GSTNFSI',
'GGPeFSI',
'GArkyFSI',
'GCMPfFSI',
'GFSIFSI',
'GPTNSTN',
'GCMPfSTN',
'GGPeSTN',
'GProtSTN',
'GCMPfGPe',
'GSTNGPe',
'GMSNGPe',
'GGPeGPe',
'GCMPfArky',
'GSTNArky',
'GMSNArky',
'GArkyArky',
'GProtArky',
'GCMPfProt',
'GSTNProt',
'GMSNProt',
'GProtProt',
'GArkyProt',
'GMSNGPi',
'GSTNGPi',
'GGPeGPi',
'GProtGPi',
'GCMPfGPi',
'redundancyCSNMSN',
'redundancyPTNMSN',
'redundancyCMPfMSN',
'redundancyMSNMSN',
'redundancyFSIMSN',
'redundancySTNMSN',
'redundancyGPeMSN',
'redundancyArkyMSN',
'redundancyCSNFSI',
'redundancyPTNFSI',
'redundancySTNFSI',
'redundancyGPeFSI',
'redundancyArkyFSI',
'redundancyCMPfFSI',
'redundancyFSIFSI',
'redundancyPTNSTN',
'redundancyCMPfSTN',
'redundancyGPeSTN',
'redundancyProtSTN',
'redundancyCMPfGPe',
'redundancySTNGPe',
'redundancyMSNGPe',
'redundancyGPeGPe',
'redundancyCMPfArky',
'redundancySTNArky',
'redundancyMSNArky',
'redundancyArkyArky',
'redundancyProtArky',
'redundancyCMPfProt',
'redundancySTNProt',
'redundancyMSNProt',
'redundancyProtProt',
'redundancyArkyProt',
'redundancyMSNGPi',
'redundancySTNGPi',
'redundancyGPeGPi',
'redundancyProtGPi',
'redundancyCMPfGPi',
]
else:
necessaryParams = [
'nbCh',
'nbMSN',
'nbFSI',
'nbSTN',
'nbGPe',
'nbGPi',
'nbCSN',
'nbPTN',
'nbCMPf',
'IeMSN',
'IeFSI',
'IeSTN',
'IeGPe',
'IeGPi',
'GCSNMSN',
'GPTNMSN',
'GCMPfMSN',
'GMSNMSN',
'GFSIMSN',
'GSTNMSN',
'GGPeMSN',
'GCSNFSI',
'GPTNFSI',
'GSTNFSI',
'GGPeFSI',
'GCMPfFSI',
'GFSIFSI',
'GPTNSTN',
'GCMPfSTN',
'GGPeSTN',
'GCMPfGPe',
'GSTNGPe',
'GMSNGPe',
'GGPeGPe',
'GMSNGPi',
'GSTNGPi',
'GGPeGPi',
'GCMPfGPi',
'redundancyCSNMSN',
'redundancyPTNMSN',
'redundancyCMPfMSN',
'redundancyMSNMSN',
'redundancyFSIMSN',
'redundancySTNMSN',
'redundancyGPeMSN',
'redundancyCSNFSI',
'redundancyPTNFSI',
'redundancySTNFSI',
'redundancyGPeFSI',
'redundancyCMPfFSI',
'redundancyFSIFSI',
'redundancyPTNSTN',
'redundancyCMPfSTN',
'redundancyGPeSTN',
'redundancyCMPfGPe',
'redundancySTNGPe',
'redundancyMSNGPe',
'redundancyGPeGPe',
'redundancyMSNGPi',
'redundancySTNGPi',
'redundancyGPeGPi',
'redundancyCMPfGPi',
]
for np in necessaryParams:
if np not in params:
raise KeyError('Missing parameter: ' + np)
#------------------------
# creation and connection of the neural populations
#------------------------
createBG()
return connectBG(antagInjectionSite, antag)
def checkAvgFR(showRasters=False,
params={},
antagInjectionSite='none',
antag='',
logFileName=''):
nest.ResetNetwork()
initNeurons(
) # sets the default params of iaf_alpha_psc_mutisynapse neurons to CommonParams
showPotential = False # Switch to True to graph neurons' membrane potentials - does not handle well restarted simulations
dataPath = 'log/'
nest.SetKernelStatus(
{"overwrite_files":
True}) # when we redo the simulation, we erase the previous traces
nstrand.set_seed(params['nestSeed'],
params['pythonSeed']) # sets the seed for the simulation
simulationOffset = nest.GetKernelStatus('time')
print('Simulation Offset: ' + str(simulationOffset))
offsetDuration = 1000.
simDuration = 5000. # ms
#-------------------------
# measures
#-------------------------
spkDetect = {} # spike detectors used to record the experiment
multimeters = {
} # multimeters used to record one neuron in each population
expeRate = {}
antagStr = ''
if antagInjectionSite != 'none':
antagStr = antagInjectionSite + '_' + antag + '_'
# storeGDFdissociated = storeGDF # avoid an error
# if antagStr != '':
# storeGDFdissociated = False # gdf files are not required for antagonist simulation
for N in NUCLEI:
# 1000ms offset period for network stabilization
spkDetect[N] = nest.Create("spike_detector",
params={
"withgid":
True,
"withtime":
True,
"label":
antagStr + N,
"to_memory":
False,
"to_file":
storeGDF,
'start':
offsetDuration + simulationOffset,
'stop':
offsetDuration + simDuration +
simulationOffset
})
nest.Connect(Pop[N], spkDetect[N])
if showPotential:
# multimeter records only the last 200ms in one neuron in each population
multimeters[N] = nest.Create(
'multimeter',
params={
"withgid": True,
'withtime': True,
'interval': 0.1,
'record_from': ['V_m'],
"label": antagStr + N,
"to_file": False,
'start':
offsetDuration + simulationOffset + simDuration - 200.,
'stop': offsetDuration + simDuration + simulationOffset
})
nest.Connect(multimeters[N], [Pop[N][0]])
#-------------------------
# Simulation
#-------------------------
nest.Simulate(simDuration + offsetDuration)
score = 0
text = []
frstr = "#" + str(
params['LG14modelID']) + " , " + antagInjectionSite + ', '
s = '----- RESULTS -----'
print s
text.append(s + '\n')
if antagInjectionSite == 'none':
validationStr = "\n#" + str(params['LG14modelID']) + " , "
frstr += "none , "
for N in NUCLEI:
strTestPassed = 'NO!'
expeRate[N] = nest.GetStatus(spkDetect[N], 'n_events')[0] / float(
nbSim[N] * simDuration) * 1000
if expeRate[N] <= FRRNormal[N][1] and expeRate[N] >= FRRNormal[N][
0]:
# if the measured rate is within acceptable values
strTestPassed = 'OK'
score += 1
validationStr += N + "=OK , "
else:
# out of the ranges
if expeRate[N] > FRRNormal[N][1]:
difference = expeRate[N] - FRRNormal[N][1]
validationStr += N + "=+%.2f , " % difference
else:
difference = expeRate[N] - FRRNormal[N][0]
validationStr += N + "=%.2f , " % difference
frstr += '%f , ' % (expeRate[N])
s = '* ' + N + ' - Rate: ' + str(
expeRate[N]) + ' Hz -> ' + strTestPassed + ' (' + str(
FRRNormal[N][0]) + ' , ' + str(FRRNormal[N][1]) + ')'
print s
text.append(s + '\n')
else:
validationStr = ""
frstr += str(antag) + " , "
for N in NUCLEI:
expeRate[N] = nest.GetStatus(spkDetect[N], 'n_events')[0] / float(
nbSim[N] * simDuration) * 1000
if N == antagInjectionSite:
strTestPassed = 'NO!'
if expeRate[N] <= FRRAnt[N][antag][1] and expeRate[
N] >= FRRAnt[N][antag][0]:
# if the measured rate is within acceptable values
strTestPassed = 'OK'
score += 1
validationStr += N + "_" + antag + "=OK , "
else:
# out of the ranges
if expeRate[N] > FRRNormal[N][1]:
difference = expeRate[N] - FRRNormal[N][1]
validationStr += N + "_" + antag + "=+%.2f , " % difference
else:
difference = expeRate[N] - FRRNormal[N][0]
validationStr += N + "_" + antag + "=%.2f , " % difference
s = '* ' + N + ' with ' + antag + ' antagonist(s): ' + str(
expeRate[N]) + ' Hz -> ' + strTestPassed + ' (' + str(
FRRAnt[N][antag][0]) + ' , ' + str(
FRRAnt[N][antag][1]) + ')'
print s
text.append(s + '\n')
else:
s = '* ' + N + ' - Rate: ' + str(expeRate[N]) + ' Hz'
print s
text.append(s + '\n')
frstr += '%f , ' % (expeRate[N])
s = '-------------------'
print s
text.append(s + '\n')
frstr += '\n'
firingRatesFile = open(dataPath + 'firingRates.csv', 'a')
firingRatesFile.writelines(frstr)
firingRatesFile.close()
#print "************************************** file writing",text
#res = open(dataPath+'OutSummary_'+logFileName+'.txt','a')
res = open(dataPath + 'OutSummary.txt', 'a')
res.writelines(text)
res.close()
validationFile = open("validationArray.csv", 'a')
validationFile.write(validationStr)
validationFile.close()
#-------------------------
# Displays
#-------------------------
if showRasters and interactive:
displayStr = ' (' + antagStr[:-1] + ')' if (
antagInjectionSite != 'none') else ''
for N in NUCLEI:
nest.raster_plot.from_device(spkDetect[N],
hist=True,
title=N + displayStr)
if showPotential:
pl.figure()
nsub = 231
for N in NUCLEI:
pl.subplot(nsub)
nest.voltage_trace.from_device(multimeters[N],
title=N + displayStr + ' #0')
nest.Disconnect(Pop[N], multimeters[N])
pl.axhline(y=BGparams[N]['V_th'], color='r', linestyle='-')
nsub += 1
pl.show()
return score, 5 if antagInjectionSite == 'none' else 1