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1		-== H2 Headings Will Appear in Table of Content ==
	1	+== Introduction (path and modules): ==
2	2
	3	+First of all we check the path and import the necessary modules .
3	3
4		-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.
	5	+=== Check where I am and place myself in the right folder: ===
5	5
6		->This is a quote. You can add a quote by selecting some text and clicking the quote button in the editor.
	7	+{{code language="python"}}
	8	+# Import the os module
	9	+import os
7	7
8		-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.
	11	+#Print the current working directory
	12	+print("Current working directory: {0}".format(os.getcwd()))
9	9
10		-=== H3 Headings Will Appear In The Table of Content ===
	14	+# Change the current working directory
	15	+os.chdir('/mnt/user/shared/Slow waves in fading anesthesia/Nest3Python3')
11	11
12		-==== You can also add images ====
	17	+# Print the current working directory
	18	+print("Current working directory: {0}".format(os.getcwd()))
	19	+{{/code}}
13	13
14		-[[image:Collaboratory.Apps.Article.Code.ArticleSheet@placeholder.jpg]]
	21	+=== Import the modules necessary for the simulation: ===
15	15
16		-Photo by David Clode
	23	+{{code language="python"}}
	24	+import nest
	25	+import time
	26	+from numpy import exp
	27	+import numpy
	28	+import math
	29	+import random
	30	+import multiprocessing
	31	+Inizio=time.time()
	32	+print('tempo di Inizio:',Inizio)
	33	+{{/code}}
17	17
18		-==== Or code ====
	35	+=== ===
19	19
20		-Code blocks can be added by using the code macro:
	37	+=== Define necessary classes to import the Initialization Files: ===
21	21
	39	+
22	22	{{code language="python"}}
23		-x = 1
24		-if x == 1:
25		- # indented four spaces
26		- print("x is 1.")
	41	+class ImportIniLIFCA():
	42	+ #initialize the information to look for in perseo.ini
	43	+ inf=["NeuronType", #still fixed value
	44	+ "DelayDistribType", #still fixed value
	45	+ "SynapticExtractionType", #still fixed value
	46	+ "Life"]
	47	+
	48	+ def __init__(self,files):
	49	+ self.files=files
	50	+
	51	+ def FilesControllo(self):
	52	+ import sys
	53	+ for i in range(0,len(self.files)):
	54	+ if self.FileControllo(self.files[i]):
	55	+ sys.exit(0)
	56	+
	57	+ def FileControllo(self,file1):
	58	+ try:
	59	+ f1=open(file1,"r")
	60	+ f1.close()
	61	+ return 0
	62	+ except ValueError:
	63	+ print("ValueError")
	64	+ return 1
	65	+ except IOError as err:
	66	+ print("OS error: {0}".format(err))
	67	+ return 1
	68	+ except:
	69	+ print("Unexpected error:", sys.exc_info()[0])
	70	+ return 1
	71	+
	72	+ def Estrai_inf(self,stampa=0):
	73	+
	74	+ InfoPerseo=self.EstraiInfoPerseo() #extract info from perseo.ini
	75	+ AppoggioTempM=self.EstraiInfoModuli() #extract info from modules.ini
	76	+ AppoggioTempC=self.EstraiInfoConnectivity() #extract info from connectivity.ini
	77	+ AppoggioTempP=self.EstraiProtocol() #extract info from protocol.ini
	78	+
	79	+ def getKey(item):
	80	+ return item[0]
	81	+ InfoProtocol=AppoggioTempP
	82	+ # I convert the extracted information into a suitable format from tuple to list
	83	+
	84	+ InfoBuildT=[AppoggioTempM[0]]
	85	+ for i in range(0,AppoggioTempM[0]):
	86	+ app1=[int(AppoggioTempM[2][i][0])]
	87	+ app=(app1+list(AppoggioTempM[2][i][3:9])+list(AppoggioTempM[2][i][12])+list(AppoggioTempM[2][i][9:12]))
	88	+ InfoBuildT.append(app)
	89	+ del app
	90	+
	91	+ InfoBuild=[float(InfoBuildT[0])]
	92	+ for i in range(0,int(InfoBuildT[0])):
	93	+ app=[]
	94	+ for j in range(0,11):
	95	+ app.append(float(InfoBuildT[i+1][j]))
	96	+ InfoBuild=InfoBuild+[app]
	97	+ del app
	98	+
	99	+ InfoConnectPop=[AppoggioTempM[0]]
	100	+ for i in range(0,len(AppoggioTempC[1][:])):
	101	+ app=list(AppoggioTempC[1][i])
	102	+ InfoConnectPop.append(app)
	103	+ del app
	104	+
	105	+ InfoConnectNoise=[AppoggioTempM[0]]
	106	+ for i in range(0,AppoggioTempM[0]):
	107	+ app=list(AppoggioTempM[2][i][1:3])
	108	+ InfoConnectNoise.append(app)
	109	+
	110	+
	111	+ if stampa==1: #Print on screen of saved data
	112	+ for i,j in enumerate(InfoPerseo):
	113	+ print(self.inf[i],"=",j)
	114	+ print("\n")
	115	+ print("the network consists of ", AppoggioTempM[0], " neuronal population" )
	116	+ print(AppoggioTempM[1])
	117	+ for i in range(0,AppoggioTempM[0]):
	118	+ print(AppoggioTempM[2][i])
	119	+ print("\n")
	120	+ print(AppoggioTempC[0])
	121	+ for i in range(0,AppoggioTempM[0]**2):
	122	+ print(AppoggioTempC[1][i])
	123	+ print("\n")
	124	+ for i in InfoProtocol:
	125	+ print("SET_PARAM"+str(i))
	126	+
	127	+
	128	+ return InfoPerseo,InfoBuild,InfoConnectPop,InfoConnectNoise,InfoProtocol
	129	+
	130	+ def EstraiProtocol(self):
	131	+ import string
	132	+ f1=open(self.files[3],"r")
	133	+ ProtocolList= []
	134	+ for x in f1.readlines():
	135	+ y=x.split()
	136	+ if len(y):
	137	+ if x[0]!="#" and y[0]=="SET_PARAM":
	138	+ try:
	139	+ ProtocolList.append([float(y[1]),int(y[2]),float(y[3]),float(y[4])])
	140	+ except ValueError:
	141	+ pass
	142	+ f1.close()
	143	+ return ProtocolList
	144	+
	145	+ def EstraiInfoPerseo(self):
	146	+ import string
	147	+ f1=open(self.files[0],"r")
	148	+ InfList= []
	149	+ for x in f1.readlines():
	150	+ y=x.split()
	151	+ if len(y):
	152	+ if x[0]!="#":
	153	+ for findinf in self.inf:
	154	+ try:
	155	+ temp=y.index(findinf)
	156	+ InfList.append(y[temp+2])
	157	+ except ValueError:
	158	+ pass
	159	+ f1.close()
	160	+ return InfList
	161	+
	162	+ def EstraiInfoModuli(self):
	163	+ import string
	164	+ f1=open(self.files[2],"r")
	165	+ NumPop=0
	166	+ for i,x in enumerate(f1.readlines()):
	167	+ y=x.split()
	168	+ if len(y):
	169	+ if x[0]!="#":
	170	+ NumPop=NumPop+1
	171	+ if i==2:
	172	+ ParamList=[]
	173	+ for j in range(1,14):
	174	+ ParamList.append(y[j])
	175	+ f1.close()
	176	+ PopsParamList=[]
	177	+ f1=open(self.files[2],"r")
	178	+ x=f1.readlines()
	179	+ for j in range(0,NumPop):
	180	+ appo=x[4+j];
	181	+ PopsParamList.append(appo.split())
	182	+ f1.close()
	183	+ return NumPop,ParamList,PopsParamList
	184	+
	185	+ def EstraiInfoConnectivity(self):
	186	+ import string
	187	+ f1=open(self.files[1],"r")
	188	+ PopConParamList=[]
	189	+ for i,x in enumerate(f1.readlines()):
	190	+ y=x.split()
	191	+ if len(y):
	192	+ if x[0]!="#":
	193	+ PopConParamList.append(y)
	194	+ if i==1:
	195	+ ParamList=[]
	196	+ for j in range(1,9):
	197	+ ParamList.append(y[j])
	198	+ f1.close()
	199	+ return ParamList,PopConParamList
27	27	{{/code}}
28	28
29		-(% class="wikigeneratedid" id="HH4Won27tAppearinToC" %)
30		-
	202	+=== Import the initialization files: ===
	203	+
	204	+in this section we...
	205	+
	206	+{{code language="python"}}
	207	+Salva=1
	208	+file1="perseo35.ini"
	209	+file2="c_cortsurf_Pot1.43PotStr148v3.ini"
	210	+file3="m_cortsurf_Pot1.43.ini"
	211	+file4="ProtocolExploration36.ini"
	212	+files=[file1,file2,file3,file4]
	213	+#define the name of the Output file
	214	+FileName="dati/Rates_Nest_Run_Milano_Test36_13x13_"+str(nest.Rank())+"_Pot1.43PotStr148v3Long3.dat"
	215	+#check the existence of the files being read
	216	+ImpFil=ImportIniLIFCA(files);
	217	+ImpFil.FilesControllo()
	218	+
	219	+#extract the information of interest from the files.ini and transfer them to the files:
	220	+#InfoPerseo,InfoBuild,InfoConnectPop,InfoConnectNoise
	221	+
	222	+stampa=0; #stampa=1 print output simulation data on screen stampa=0 dont
	223	+InfoPerseo,InfoBuild,InfoConnectPop,InfoConnectNoise,InfoProtocol=ImpFil.Estrai_inf(stampa)
	224	+
	225	+# InfoPerseo=["NeuronType","DelayDistribType","SynapticExtractionType","Life" ]
	226	+# InfoBuild=[numero di popolazioni,
	227	+# [N,C_ext,\nu_ext,\tau,\tetha,H,\tau_arp,NeuronInitType,\alpha_c,\tau_c,g_c],
	228	+# [.....],[],...]
	229	+# InfoConnectPop=[numero di popolazioni,
	230	+# [post,pre,c,Dmin,Dmax,syn typ,J,DJ],
	231	+# [.....],[],...]
	232	+# InfoConnectNoise=[numero di popolazioni,
	233	+# [J_ext,DJ_ext],
	234	+# [.....],[],...]
	235	+# InfoProtocol=[[time,population,param_num,value],
	236	+# [.....],[],...]
	237	+{{/code}}
	238	+
	239	+
	240	+
	241	+
	242	+=== Results ===
	243	+
	244	+==== ====