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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
...	...	@@ -34,211 +34,6 @@
34	34
35	35	=== ===
36	36
37		-=== Define necessary classes to import the Initialization Files: ===
	37	+==== Results ====
38	38
39		-{{code language="python" width="90%" title="
40		-120%"}}
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		-
244	244	==== ====