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...	...	@@ -1,8 +1,8 @@
1		-== Introduction (path and modules) ==
	1	+== Introduction (path and modules): ==
2	2
3	3	First of all we check the path and import the necessary modules .
4	4
5		-=== Check where I am and place myself in the right folder : ===
	5	+=== Check where I am and place myself in the right folder: ===
6	6
7	7	{{code language="python"}}
8	8	# Import the os module
...	...	@@ -18,7 +18,7 @@
18	18	print("Current working directory: {0}".format(os.getcwd()))
19	19	{{/code}}
20	20
21		-=== import the modules necessary for the simulation ===
	21	+=== Import the modules necessary for the simulation: ===
22	22
23	23	{{code language="python"}}
24	24	import nest
...	...	@@ -34,6 +34,211 @@
34	34
35	35	=== ===
36	36
37		-==== Results ====
	37	+=== Define necessary classes to import the Initialization Files: ===
38	38
	39	+
	40	+{{code language="python"}}
	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
	200	+{{/code}}
	201	+
	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	+
39	39	==== ====