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1		-== Code Description ==
	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
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	11	+#Print the current working directory
	12	+print("Current working directory: {0}".format(os.getcwd()))
9	9
10		-=== Results ===
	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	+{{code language="python" title=" "}}
	40	+class ImportIniLIFCA():
	41	+ #initialize the information to look for in perseo.ini
	42	+ inf=["NeuronType", #still fixed value
	43	+ "DelayDistribType", #still fixed value
	44	+ "SynapticExtractionType", #still fixed value
	45	+ "Life"]
	46	+
	47	+ def __init__(self,files):
	48	+ self.files=files
	49	+
	50	+ def FilesControllo(self):
	51	+ import sys
	52	+ for i in range(0,len(self.files)):
	53	+ if self.FileControllo(self.files[i]):
	54	+ sys.exit(0)
	55	+
	56	+ def FileControllo(self,file1):
	57	+ try:
	58	+ f1=open(file1,"r")
	59	+ f1.close()
	60	+ return 0
	61	+ except ValueError:
	62	+ print("ValueError")
	63	+ return 1
	64	+ except IOError as err:
	65	+ print("OS error: {0}".format(err))
	66	+ return 1
	67	+ except:
	68	+ print("Unexpected error:", sys.exc_info()[0])
	69	+ return 1
	70	+
	71	+ def Estrai_inf(self,stampa=0):
	72	+
	73	+ InfoPerseo=self.EstraiInfoPerseo() #extract info from perseo.ini
	74	+ AppoggioTempM=self.EstraiInfoModuli() #extract info from modules.ini
	75	+ AppoggioTempC=self.EstraiInfoConnectivity() #extract info from connectivity.ini
	76	+ AppoggioTempP=self.EstraiProtocol() #extract info from protocol.ini
	77	+
	78	+ def getKey(item):
	79	+ return item[0]
	80	+ InfoProtocol=AppoggioTempP
	81	+ # I convert the extracted information into a suitable format from tuple to list
	82	+
	83	+ InfoBuildT=[AppoggioTempM[0]]
	84	+ for i in range(0,AppoggioTempM[0]):
	85	+ app1=[int(AppoggioTempM[2][i][0])]
	86	+ app=(app1+list(AppoggioTempM[2][i][3:9])+list(AppoggioTempM[2][i][12])+list(AppoggioTempM[2][i][9:12]))
	87	+ InfoBuildT.append(app)
	88	+ del app
	89	+
	90	+ InfoBuild=[float(InfoBuildT[0])]
	91	+ for i in range(0,int(InfoBuildT[0])):
	92	+ app=[]
	93	+ for j in range(0,11):
	94	+ app.append(float(InfoBuildT[i+1][j]))
	95	+ InfoBuild=InfoBuild+[app]
	96	+ del app
	97	+
	98	+ InfoConnectPop=[AppoggioTempM[0]]
	99	+ for i in range(0,len(AppoggioTempC[1][:])):
	100	+ app=list(AppoggioTempC[1][i])
	101	+ InfoConnectPop.append(app)
	102	+ del app
	103	+
	104	+ InfoConnectNoise=[AppoggioTempM[0]]
	105	+ for i in range(0,AppoggioTempM[0]):
	106	+ app=list(AppoggioTempM[2][i][1:3])
	107	+ InfoConnectNoise.append(app)
	108	+
	109	+
	110	+ if stampa==1: #Print on screen of saved data
	111	+ for i,j in enumerate(InfoPerseo):
	112	+ print(self.inf[i],"=",j)
	113	+ print("\n")
	114	+ print("the network consists of ", AppoggioTempM[0], " neuronal population" )
	115	+ print(AppoggioTempM[1])
	116	+ for i in range(0,AppoggioTempM[0]):
	117	+ print(AppoggioTempM[2][i])
	118	+ print("\n")
	119	+ print(AppoggioTempC[0])
	120	+ for i in range(0,AppoggioTempM[0]**2):
	121	+ print(AppoggioTempC[1][i])
	122	+ print("\n")
	123	+ for i in InfoProtocol:
	124	+ print("SET_PARAM"+str(i))
	125	+
	126	+
	127	+ return InfoPerseo,InfoBuild,InfoConnectPop,InfoConnectNoise,InfoProtocol
	128	+
	129	+ def EstraiProtocol(self):
	130	+ import string
	131	+ f1=open(self.files[3],"r")
	132	+ ProtocolList= []
	133	+ for x in f1.readlines():
	134	+ y=x.split()
	135	+ if len(y):
	136	+ if x[0]!="#" and y[0]=="SET_PARAM":
	137	+ try:
	138	+ ProtocolList.append([float(y[1]),int(y[2]),float(y[3]),float(y[4])])
	139	+ except ValueError:
	140	+ pass
	141	+ f1.close()
	142	+ return ProtocolList
	143	+
	144	+ def EstraiInfoPerseo(self):
	145	+ import string
	146	+ f1=open(self.files[0],"r")
	147	+ InfList= []
	148	+ for x in f1.readlines():
	149	+ y=x.split()
	150	+ if len(y):
	151	+ if x[0]!="#":
	152	+ for findinf in self.inf:
	153	+ try:
	154	+ temp=y.index(findinf)
	155	+ InfList.append(y[temp+2])
	156	+ except ValueError:
	157	+ pass
	158	+ f1.close()
	159	+ return InfList
	160	+
	161	+ def EstraiInfoModuli(self):
	162	+ import string
	163	+ f1=open(self.files[2],"r")
	164	+ NumPop=0
	165	+ for i,x in enumerate(f1.readlines()):
	166	+ y=x.split()
	167	+ if len(y):
	168	+ if x[0]!="#":
	169	+ NumPop=NumPop+1
	170	+ if i==2:
	171	+ ParamList=[]
	172	+ for j in range(1,14):
	173	+ ParamList.append(y[j])
	174	+ f1.close()
	175	+ PopsParamList=[]
	176	+ f1=open(self.files[2],"r")
	177	+ x=f1.readlines()
	178	+ for j in range(0,NumPop):
	179	+ appo=x[4+j];
	180	+ PopsParamList.append(appo.split())
	181	+ f1.close()
	182	+ return NumPop,ParamList,PopsParamList
	183	+
	184	+ def EstraiInfoConnectivity(self):
	185	+ import string
	186	+ f1=open(self.files[1],"r")
	187	+ PopConParamList=[]
	188	+ for i,x in enumerate(f1.readlines()):
	189	+ y=x.split()
	190	+ if len(y):
	191	+ if x[0]!="#":
	192	+ PopConParamList.append(y)
	193	+ if i==1:
	194	+ ParamList=[]
	195	+ for j in range(1,9):
	196	+ ParamList.append(y[j])
	197	+ f1.close()
	198	+ return ParamList,PopConParamList
	199	+{{/code}}
	200	+
	201	+=== Import the initialization files: ===
	202	+
	203	+in this section we...
	204	+
22	22	{{code language="python"}}
23		-x = 1
24		-if x == 1:
25		- # indented four spaces
26		- print("x is 1.")
	206	+Salva=1
	207	+file1="perseo35.ini"
	208	+file2="c_cortsurf_Pot1.43PotStr148v3.ini"
	209	+file3="m_cortsurf_Pot1.43.ini"
	210	+file4="ProtocolExploration36.ini"
	211	+files=[file1,file2,file3,file4]
	212	+#define the name of the Output file
	213	+FileName="dati/Rates_Nest_Run_Milano_Test36_13x13_"+str(nest.Rank())+"_Pot1.43PotStr148v3Long3.dat"
	214	+#check the existence of the files being read
	215	+ImpFil=ImportIniLIFCA(files);
	216	+ImpFil.FilesControllo()
	217	+
	218	+#extract the information of interest from the files.ini and transfer them to the files:
	219	+#InfoPerseo,InfoBuild,InfoConnectPop,InfoConnectNoise
	220	+
	221	+stampa=0; #stampa=1 print output simulation data on screen stampa=0 dont
	222	+InfoPerseo,InfoBuild,InfoConnectPop,InfoConnectNoise,InfoProtocol=ImpFil.Estrai_inf(stampa)
	223	+
	224	+# InfoPerseo=["NeuronType","DelayDistribType","SynapticExtractionType","Life" ]
	225	+# InfoBuild=[numero di popolazioni,
	226	+# [N,C_ext,\nu_ext,\tau,\tetha,H,\tau_arp,NeuronInitType,\alpha_c,\tau_c,g_c],
	227	+# [.....],[],...]
	228	+# InfoConnectPop=[numero di popolazioni,
	229	+# [post,pre,c,Dmin,Dmax,syn typ,J,DJ],
	230	+# [.....],[],...]
	231	+# InfoConnectNoise=[numero di popolazioni,
	232	+# [J_ext,DJ_ext],
	233	+# [.....],[],...]
	234	+# InfoProtocol=[[time,population,param_num,value],
	235	+# [.....],[],...]
27	27	{{/code}}
28	28
29		-(% class="wikigeneratedid" id="HH4Won27tAppearinToC" %)
30		-
	238	+=== Defining general and nest.kernel parameters ===
	239	+
	240	+{{code language="python"}}
	241	+#############################------------------------------------------------------------------------
	242	+#Clean the Network
	243	+#############################------------------------------------------------------------------------
	244	+nest.ResetKernel()
	245	+
	246	+#############################------------------------------------------------------------------------
	247	+#insert the introductory parameters of the simulation
	248	+#############################------------------------------------------------------------------------
	249	+
	250	+
	251	+dt = 0.1 # the resolution in ms
	252	+StartMisure=0. # start time of measurements
	253	+simtime = int(float(InfoPerseo[3])) # Simulation time in ms (200 s)
	254	+if simtime<=StartMisure: # If the simulation time is less than StartMisure, it is increased by StartMisure
	255	+ simtime=simtime+StartMisure
	256	+start=0.0 # start time of poissonian processes
	257	+origin=0.0 # temporal origin
	258	+
	259	+#############################------------------------------------------------------------------------
	260	+# Kernel parameters
	261	+#############################------------------------------------------------------------------------
	262	+LNT=multiprocessing.cpu_count();
	263	+nest.SetKernelStatus({"local_num_threads": LNT})
	264	+nest.SetKernelStatus({"resolution": dt, "print_time": True,
	265	+ "overwrite_files": True})
	266	+
	267	+#############################------------------------------------------------------------------------
	268	+#"randomize" the seeds of the random generators
	269	+#############################------------------------------------------------------------------------
	270	+
	271	+#msd = int(math.fabs(time.process_time()*1000))
	272	+#N_vp = nest.GetKernelStatus(['total_num_virtual_procs'])[0]
	273	+#pyrngs = [numpy.random.RandomState(s) for s in range(msd, msd+N_vp)]
	274	+#nest.SetKernelStatus({"grng_seed" : msd+N_vp})
	275	+#nest.SetKernelStatus({"rng_seeds" : list(range(msd+N_vp+1, msd+2*N_vp+1))})
	276	+{{/code}}
	277	+
	278	+=== Building the network: neuronal populations , Poisson processes and spike detectors ===
	279	+
	280	+{{code language="python"}}
	281	+#############################------------------------------------------------------------------------
	282	+print("Building network")
	283	+#############################------------------------------------------------------------------------
	284	+
	285	+startbuild = time.time() #initialize the calculation of the time used to simulate
	286	+
	287	+NeuronPop=[]
	288	+NoisePop=[]
	289	+DetectorPop=[]
	290	+
	291	+#define and initialize the populations of neurons with the parameters extracted from the.ini files
	292	+for i in range(1,int(InfoBuild[0])+1):
	293	+ if int(InfoBuild[i][7])==0:
	294	+ app=float(InfoBuild[i][5])
	295	+ else:
	296	+ app=0.
	297	+ app2= nest.Create("aeif_psc_exp", int(InfoBuild[i][0]),params={"C_m": 1.0,
	298	+ "g_L": 1.0/float(InfoBuild[i][3]),
	299	+ "t_ref": float(InfoBuild[i][6]),
	300	+ "E_L": 0.0,
	301	+ "V_reset": float(InfoBuild[i][5]),
	302	+ "V_m": app,
	303	+ "V_th": float(InfoBuild[i][4]),
	304	+ "Delta_T": 0.,
	305	+ "tau_syn_ex": 1.0,
	306	+ "tau_syn_in": 1.0,
	307	+ "a": 0.0,
	308	+ "b": float(InfoBuild[i][10]),
	309	+ "tau_w": float(InfoBuild[i][9]),
	310	+ "V_peak":float(InfoBuild[i][4])+10.0})
	311	+ NeuronPop.append(app2)
	312	+
	313	+#define and initialize the poisson generators and the spike detectors with the parameters extracted from the.ini files
	314	+
	315	+for i in range(1,int(InfoBuild[0])+1):
	316	+ app3= nest.Create("poisson_generator",params={"rate": float(InfoBuild[i][1]*InfoBuild[i][2]),
	317	+ 'origin':0.,
	318	+ 'start':start})
	319	+ NoisePop.append(app3)
	320	+ app4 = nest.Create("spike_recorder",params={ "start":StartMisure})
	321	+ DetectorPop.append(app4)
	322	+
	323	+endbuild = time.time()
	324	+{{/code}}
	325	+
	326	+=== Results ===
	327	+
	328	+==== ====