Code description - HBP Wiki

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== Introduction (path and modules): ==

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First of all we check the path and import the necessary modules .

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=== Check where I am and place myself in the right folder: ===

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# Import the os module

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import os

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#Print the current working directory

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print("Current working directory: {0}".format(os.getcwd()))

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# Change the current working directory

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os.chdir('/mnt/user/shared/Slow waves in fading anesthesia/Nest3Python3')

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# Print the current working directory

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print("Current working directory: {0}".format(os.getcwd()))

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=== Import the modules necessary for the simulation: ===

import nest

import time

from numpy import exp

import numpy

import math

import random

import multiprocessing

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Inizio=time.time()

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print('tempo di Inizio:',Inizio)

=== ===

=== Define necessary classes to import the Initialization Files: ===

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{{code language="python" width="90%" title="

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120%"}}

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class ImportIniLIFCA():

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#initialize the information to look for in perseo.ini

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inf=["NeuronType", #still fixed value

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"DelayDistribType", #still fixed value

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"SynapticExtractionType", #still fixed value

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"Life"]

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def __init__(self,files):

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self.files=files

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def FilesControllo(self):

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import sys

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for i in range(0,len(self.files)):

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if self.FileControllo(self.files[i]):

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sys.exit(0)

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def FileControllo(self,file1):

try:

f1=open(file1,"r")

f1.close()

return 0

except ValueError:

print("ValueError")

return 1

except IOError as err:

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print("OS error: {0}".format(err))

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return 1

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except:

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print("Unexpected error:", sys.exc_info()[0])

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return 1

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def Estrai_inf(self,stampa=0):

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InfoPerseo=self.EstraiInfoPerseo() #extract info from perseo.ini

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AppoggioTempM=self.EstraiInfoModuli() #extract info from modules.ini

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AppoggioTempC=self.EstraiInfoConnectivity() #extract info from connectivity.ini

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AppoggioTempP=self.EstraiProtocol() #extract info from protocol.ini

def getKey(item):

return item[0]

InfoProtocol=AppoggioTempP

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# I convert the extracted information into a suitable format from tuple to list

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InfoBuildT=[AppoggioTempM[0]]

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for i in range(0,AppoggioTempM[0]):

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app1=[int(AppoggioTempM[2][i][0])]

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app=(app1+list(AppoggioTempM[2][i][3:9])+list(AppoggioTempM[2][i][12])+list(AppoggioTempM[2][i][9:12]))

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InfoBuildT.append(app)

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del app

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InfoBuild=[float(InfoBuildT[0])]

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for i in range(0,int(InfoBuildT[0])):

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app=[]

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for j in range(0,11):

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app.append(float(InfoBuildT[i+1][j]))

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InfoBuild=InfoBuild+[app]

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del app

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InfoConnectPop=[AppoggioTempM[0]]

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for i in range(0,len(AppoggioTempC[1][:])):

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app=list(AppoggioTempC[1][i])

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InfoConnectPop.append(app)

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del app

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InfoConnectNoise=[AppoggioTempM[0]]

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for i in range(0,AppoggioTempM[0]):

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app=list(AppoggioTempM[2][i][1:3])

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InfoConnectNoise.append(app)

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if stampa==1: #Print on screen of saved data

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for i,j in enumerate(InfoPerseo):

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print(self.inf[i],"=",j)

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print("\n")

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print("the network consists of ", AppoggioTempM[0], " neuronal population" )

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print(AppoggioTempM[1])

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for i in range(0,AppoggioTempM[0]):

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print(AppoggioTempM[2][i])

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print("\n")

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print(AppoggioTempC[0])

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for i in range(0,AppoggioTempM[0]**2):

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print(AppoggioTempC[1][i])

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print("\n")

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for i in InfoProtocol:

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print("SET_PARAM"+str(i))

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return InfoPerseo,InfoBuild,InfoConnectPop,InfoConnectNoise,InfoProtocol

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def EstraiProtocol(self):

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import string

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f1=open(self.files[3],"r")

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ProtocolList= []

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for x in f1.readlines():

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y=x.split()

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if len(y):

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if x[0]!="#" and y[0]=="SET_PARAM":

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try:

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ProtocolList.append([float(y[1]),int(y[2]),float(y[3]),float(y[4])])

except ValueError:

pass

f1.close()

return ProtocolList

def EstraiInfoPerseo(self):

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import string

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f1=open(self.files[0],"r")

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InfList= []

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for x in f1.readlines():

y=x.split()

if len(y):

if x[0]!="#":

for findinf in self.inf:

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try:

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temp=y.index(findinf)

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InfList.append(y[temp+2])

except ValueError:

pass

f1.close()

return InfList

def EstraiInfoModuli(self):

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import string

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f1=open(self.files[2],"r")

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NumPop=0

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for i,x in enumerate(f1.readlines()):

y=x.split()

if len(y):

if x[0]!="#":

NumPop=NumPop+1

if i==2:

ParamList=[]

for j in range(1,14):

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ParamList.append(y[j])

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f1.close()

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PopsParamList=[]

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f1=open(self.files[2],"r")

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x=f1.readlines()

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for j in range(0,NumPop):

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appo=x[4+j];

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PopsParamList.append(appo.split())

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f1.close()

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return NumPop,ParamList,PopsParamList

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def EstraiInfoConnectivity(self):

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import string

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f1=open(self.files[1],"r")

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PopConParamList=[]

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for i,x in enumerate(f1.readlines()):

y=x.split()

if len(y):

if x[0]!="#":

PopConParamList.append(y)

if i==1:

ParamList=[]

for j in range(1,9):

ParamList.append(y[j])

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f1.close()

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return ParamList,PopConParamList

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=== Import the initialization files: ===

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in this section we...

Salva=1

file1="perseo35.ini"

file2="c_cortsurf_Pot1.43PotStr148v3.ini"

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file3="m_cortsurf_Pot1.43.ini"

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file4="ProtocolExploration36.ini"

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files=[file1,file2,file3,file4]

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#define the name of the Output file

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FileName="dati/Rates_Nest_Run_Milano_Test36_13x13_"+str(nest.Rank())+"_Pot1.43PotStr148v3Long3.dat"

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#check the existence of the files being read

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ImpFil=ImportIniLIFCA(files);

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ImpFil.FilesControllo()

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#extract the information of interest from the files.ini and transfer them to the files:

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#InfoPerseo,InfoBuild,InfoConnectPop,InfoConnectNoise

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stampa=0; #stampa=1 print output simulation data on screen stampa=0 dont

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InfoPerseo,InfoBuild,InfoConnectPop,InfoConnectNoise,InfoProtocol=ImpFil.Estrai_inf(stampa)

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# InfoPerseo=["NeuronType","DelayDistribType","SynapticExtractionType","Life" ]

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# InfoBuild=[numero di popolazioni,

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# [N,C_ext,\nu_ext,\tau,\tetha,H,\tau_arp,NeuronInitType,\alpha_c,\tau_c,g_c],

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# [.....],[],...]

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# InfoConnectPop=[numero di popolazioni,

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# [post,pre,c,Dmin,Dmax,syn typ,J,DJ],

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# [.....],[],...]

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# InfoConnectNoise=[numero di popolazioni,

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# [J_ext,DJ_ext],

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# [.....],[],...]

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# InfoProtocol=[[time,population,param_num,value],

# [.....],[],...]

=== Results ===

==== ====

Wiki source code of Code description

Slow waves in fading anesthesia