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Last modified by galluzziandrea on 2022/06/20 12:33

From 2.1 to 1.1 From 8.1 to 7.1

From version 7.1

edited by galluzziandrea
on 2021/12/09 14:49

Change comment: There is no comment for this version

To version 2.1

edited by galluzziandrea
on 2021/12/09 12:34

Change comment: There is no comment for this version

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@@ -1,243 +1,30 @@
--== Introduction (path and modules): ==
++== Code Description ==
--First of all we check the path and import the necessary modules .
--=== Check where I am and place myself in the right folder: ===
++Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat. Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu fugiat nulla pariatur. Excepteur sint occaecat cupidatat non proident, sunt in culpa qui officia deserunt mollit anim id est laborum.
--{{code language="python"}}
--# Import the os module
--import os
++>This is a quote. You can add a quote by selecting some text and clicking the quote button in the editor.
--#Print the current working directory
--print("Current working directory: {0}".format(os.getcwd()))
++Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat. Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu fugiat nulla pariatur. Excepteur sint occaecat cupidatat non proident, sunt in culpa qui officia deserunt mollit anim id est laborum.
--# Change the current working directory
--os.chdir('/mnt/user/shared/Slow waves in fading anesthesia/Nest3Python3')
++=== Results ===
--# Print the current working directory
--print("Current working directory: {0}".format(os.getcwd()))
--{{/code}}
++==== You can also add images ====
--=== Import the modules necessary for the simulation: ===
++[[image:Collaboratory.Apps.Article.Code.ArticleSheet@placeholder.jpg]]
--{{code language="python"}}
--import nest
--import time
--from numpy import exp
--import numpy
--import math
--import random
--import multiprocessing
--Inizio=time.time()
--print('tempo di Inizio:',Inizio)
--{{/code}}
++Photo by David Clode
--===  ===
++==== Or code ====
--=== Define necessary classes to import the Initialization Files: ===
++Code blocks can be added by using the code macro:
--{{code language="python" title=" "}}
--class ImportIniLIFCA():
--    #initialize the information to look for in perseo.ini
--    inf=["NeuronType",               #still fixed value
--         "DelayDistribType",         #still fixed value
--         "SynapticExtractionType",   #still fixed value
--         "Life"]
--
--    def __init__(self,files):
--        self.files=files
--
--    def FilesControllo(self):
--        import sys
--        for i in range(0,len(self.files)):
--            if self.FileControllo(self.files[i]):
--                sys.exit(0)
--
--    def FileControllo(self,file1):
--        try:
--            f1=open(file1,"r")
--            f1.close()
--            return 0
--        except ValueError:
--            print("ValueError")
--            return 1
--        except IOError as err:
--            print("OS error: {0}".format(err))
--            return 1
--        except:
--            print("Unexpected error:", sys.exc_info()[0])
--            return 1
--
--    def Estrai_inf(self,stampa=0):
--
--        InfoPerseo=self.EstraiInfoPerseo()                   #extract info from  perseo.ini
--        AppoggioTempM=self.EstraiInfoModuli()                #extract info from   modules.ini
--        AppoggioTempC=self.EstraiInfoConnectivity()          #extract info from  connectivity.ini
--        AppoggioTempP=self.EstraiProtocol()                  #extract info from  protocol.ini
--
--        def getKey(item):
--            return item[0]
--        InfoProtocol=AppoggioTempP
--        # I convert the extracted information into a suitable format from tuple to list
--
--        InfoBuildT=[AppoggioTempM[0]]
--        for i in range(0,AppoggioTempM[0]):
--            app1=[int(AppoggioTempM[2][i][0])]
--            app=(app1+list(AppoggioTempM[2][i][3:9])+list(AppoggioTempM[2][i][12])+list(AppoggioTempM[2][i][9:12]))
--            InfoBuildT.append(app)
--        del app
--
--        InfoBuild=[float(InfoBuildT[0])]
--        for i in range(0,int(InfoBuildT[0])):
--            app=[]
--            for j in range(0,11):
--                app.append(float(InfoBuildT[i+1][j]))
--            InfoBuild=InfoBuild+[app]
--        del app
--
--        InfoConnectPop=[AppoggioTempM[0]]
--        for i in range(0,len(AppoggioTempC[1][:])):
--            app=list(AppoggioTempC[1][i])
--            InfoConnectPop.append(app)
--        del app
--
--        InfoConnectNoise=[AppoggioTempM[0]]
--        for i in range(0,AppoggioTempM[0]):
--            app=list(AppoggioTempM[2][i][1:3])
--            InfoConnectNoise.append(app)
--
--
--        if stampa==1: #Print on screen of saved data
--            for i,j in enumerate(InfoPerseo):
--                print(self.inf[i],"=",j)
--            print("\n")
--            print("the network consists of ", AppoggioTempM[0], " neuronal population" )
--            print(AppoggioTempM[1])
--            for i in range(0,AppoggioTempM[0]):
--                print(AppoggioTempM[2][i])
--            print("\n")
--            print(AppoggioTempC[0])
--            for i in range(0,AppoggioTempM[0]**2):
--                print(AppoggioTempC[1][i])
--            print("\n")
--            for i in InfoProtocol:
--                print("SET_PARAM"+str(i))
--
--
--        return InfoPerseo,InfoBuild,InfoConnectPop,InfoConnectNoise,InfoProtocol
--
--    def EstraiProtocol(self):
--        import string
--        f1=open(self.files[3],"r")
--        ProtocolList= []
--        for x in f1.readlines():
--            y=x.split()
--            if len(y):
--                if x[0]!="#" and y[0]=="SET_PARAM":
--                    try:
--                        ProtocolList.append([float(y[1]),int(y[2]),float(y[3]),float(y[4])])
--                    except ValueError:
--                        pass
--        f1.close()
--        return ProtocolList
--
--    def EstraiInfoPerseo(self):
--        import string
--        f1=open(self.files[0],"r")
--        InfList= []
--        for x in f1.readlines():
--            y=x.split()
--            if len(y):
--                if x[0]!="#":
--                    for findinf in self.inf:
--                        try:
--                            temp=y.index(findinf)
--                            InfList.append(y[temp+2])
--                        except ValueError:
--                            pass
--        f1.close()
--        return InfList
--
--    def EstraiInfoModuli(self):
--        import string
--        f1=open(self.files[2],"r")
--        NumPop=0
--        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):
--                    ParamList.append(y[j])
--        f1.close()
--        PopsParamList=[]
--        f1=open(self.files[2],"r")
--        x=f1.readlines()
--        for j in range(0,NumPop):
--            appo=x[4+j];
--            PopsParamList.append(appo.split())
--        f1.close()
--        return NumPop,ParamList,PopsParamList
--
--    def EstraiInfoConnectivity(self):
--        import string
--        f1=open(self.files[1],"r")
--        PopConParamList=[]
--        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])
--        f1.close()
--        return ParamList,PopConParamList
--{{/code}}
--
--=== Import the initialization files: ===
--
--in this section we...
--
  {{code language="python"}}
--Salva=1
--file1="perseo35.ini"
--file2="c_cortsurf_Pot1.43PotStr148v3.ini"
--file3="m_cortsurf_Pot1.43.ini"
--file4="ProtocolExploration36.ini"
--files=[file1,file2,file3,file4]
--#define the name of the Output file
--FileName="dati/Rates_Nest_Run_Milano_Test36_13x13_"+str(nest.Rank())+"_Pot1.43PotStr148v3Long3.dat"
--#check the existence of the files being read
--ImpFil=ImportIniLIFCA(files);
--ImpFil.FilesControllo()
--
--#extract the information of interest from the files.ini and transfer them to the files:
--#InfoPerseo,InfoBuild,InfoConnectPop,InfoConnectNoise
--
--stampa=0;  #stampa=1 print  output simulation data on screen stampa=0 dont
--InfoPerseo,InfoBuild,InfoConnectPop,InfoConnectNoise,InfoProtocol=ImpFil.Estrai_inf(stampa)
--
--# InfoPerseo=["NeuronType","DelayDistribType","SynapticExtractionType","Life" ]
--# InfoBuild=[numero di popolazioni,
--#             [N,C_ext,\nu_ext,\tau,\tetha,H,\tau_arp,NeuronInitType,\alpha_c,\tau_c,g_c],
--#             [.....],[],...]
--# InfoConnectPop=[numero di popolazioni,
--#             [post,pre,c,Dmin,Dmax,syn typ,J,DJ],
--#             [.....],[],...]
--# InfoConnectNoise=[numero di popolazioni,
--#             [J_ext,DJ_ext],
--#             [.....],[],...]
--# InfoProtocol=[[time,population,param_num,value],
--#             [.....],[],...]
++x = 1
++if x == 1:
++    # indented four spaces
++    print("x is 1.")
  {{/code}}
--
--
--
--=== Results ===
--
--====  ====
++(% class="wikigeneratedid" id="HH4Won27tAppearinToC" %)
++