Wiki source code of Code description

Version 5.1 by galluzziandrea on 2021/12/09 14:46
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1 == Introduction (path and modules): ==
2
3 First of all we check the path and import the necessary modules .
4
5 === Check where I am and place myself in the right folder: ===
6
7 {{code language="python"}}
8 # Import the os module
9 import os
10
11 #Print the current working directory
12 print("Current working directory: {0}".format(os.getcwd()))
13
14 # Change the current working directory
15 os.chdir('/mnt/user/shared/Slow waves in fading anesthesia/Nest3Python3')
16
17 # Print the current working directory
18 print("Current working directory: {0}".format(os.getcwd()))
19 {{/code}}
20
21 === Import the modules necessary for the simulation: ===
22
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}}
34
35 === ===
36
37 === Define necessary classes to import the Initialization Files: ===
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
244 ==== ====