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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 +34,488 @@
34	34
35	35	=== ===
36	36
37		-==== Results ====
	37	+=== Define necessary classes to import the Initialization Files: ===
38	38
	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	+
	205	+{{code language="python"}}
	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	+# [.....],[],...]
	236	+{{/code}}
	237	+
	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	+=== Connecting the network nodes: neuronal populations, Poisson processes and spike detectors ===
	327	+
	328	+{{code language="python"}}
	329	+#############################------------------------------------------------------------------------
	330	+print("Connecting ")
	331	+#############################------------------------------------------------------------------------
	332	+
	333	+startconnect = time.time()
	334	+Connessioni=[]
	335	+Medie=[]
	336	+
	337	+#create and define the connections between the populations of neurons and the poisson generators
	338	+#and between the populations of neurons and the spike detectors with the parameters extracted from the.ini files
	339	+
	340	+for i in range(0,int(InfoBuild[0])):
	341	+ nest.Connect(NoisePop[i], NeuronPop[i], syn_spec={'synapse_model': 'static_synapse_hpc',
	342	+ 'delay': dt,
	343	+ 'weight': nest.math.redraw(nest.random.normal(mean=float(InfoConnectNoise[i+1][0]),
	344	+ std=(float(InfoConnectNoise[i+1][1])*float(InfoConnectNoise[i+1][0]))),
	345	+ min=0., max=float('Inf'))
	346	+ })
	347	+ nest.Connect(NeuronPop[i][:int(InfoBuild[i+1][0])], DetectorPop[i], syn_spec={"weight": 1.0, "delay": dt})
	348	+
	349	+#create and define the connections between the populations of neurons with the parameters extracted from the.ini files
	350	+
	351	+for i in range(0,len(InfoConnectPop[1:])):
	352	+
	353	+ conn=nest.Connect(NeuronPop[int(InfoConnectPop[i+1][1])], NeuronPop[int(InfoConnectPop[i+1][0])],
	354	+ {'rule': 'pairwise_bernoulli',
	355	+ 'p':float(InfoConnectPop[i+1][2]) },
	356	+ syn_spec={'synapse_model': 'static_synapse_hpc',
	357	+ 'delay':nest.math.redraw(nest.random.exponential(beta=float(1./(2.99573227355/(float(InfoConnectPop[i+1][4])-float(InfoConnectPop[i+1][3]))))),
	358	+ min= numpy.max([dt,float(1./float(InfoConnectPop[i+1][4]))]),
	359	+ max= float(1./(float(InfoConnectPop[i+1][3])-dt/2))),
	360	+
	361	+ 'weight':nest.random.normal(mean=float(InfoConnectPop[i+1][6]),
	362	+ std=math.fabs(float(InfoConnectPop[i+1][6])*float(InfoConnectPop[i+1][7])))})
	363	+
	364	+
	365	+endconnect = time.time()
	366	+{{/code}}
	367	+
	368	+=== ===
	369	+
	370	+=== ===
	371	+
	372	+=== Simulating: neuronal time evolution. ===
	373	+
	374	+=== ===
	375	+
	376	+{{code language="python"}}
	377	+ #############################------------------------------------------------------------------------
	378	+ print("Simulating")
	379	+ #############################------------------------------------------------------------------------
	380	+ ###################################################################################################################################################################
	381	+ if Salva:
	382	+ print("I m going to save the data")
	383	+ #x=str(iterazioni)
	384	+ f = open(FileName,"w")
	385	+ if len(InfoProtocol):
	386	+ print("I m going to split the simulation")
	387	+ tempo=0
	388	+ for contatore in range(0,len(InfoProtocol)):
	389	+ appoggio1=int((tempo+InfoProtocol[contatore][0])/1000.)
	390	+ appoggio2=int(tempo/1000.)
	391	+ appoggio3=tempo+InfoProtocol[contatore][0]
	392	+ if (appoggio1-appoggio2)>=1:
	393	+ T1=(1+appoggio2)*1000-tempo
	394	+ nest.Simulate(T1)
	395	+ #Save the Data!!!!
	396	+ ###########################################################
	397	+ Equilibri=[]
	398	+ for i in range(0,int(InfoBuild[0])):
	399	+ Equilibri.append([])
	400	+ a=nest.GetStatus(DetectorPop[i])[0]["events"]["times"]
	401	+ if len(a)>0:
	402	+ Trange=(1000*int(numpy.min(a)/1000.),1000*int(numpy.min(a)/1000.)+1000)
	403	+ hist,Tbin=numpy.histogram(a,200,(Trange[0],Trange[1]))
	404	+ Equilibri[i]=hist*1000./(5.*int(InfoBuild[i+1][0]))
	405	+ else:
	406	+ Trange=(1000*int(tempo/1000.),1000*int(tempo/1000.)+1000)
	407	+ hist=numpy.zeros(200)
	408	+ Tbin=numpy.linspace(Trange[0],Trange[1],num=201)
	409	+ Equilibri[i]=hist
	410	+ nest.SetStatus(DetectorPop[i],{'n_events':0})
	411	+ for j in range(0,len(hist)):
	412	+ f.write(str(Tbin[j])+" ")
	413	+ for i in range(0,int(InfoBuild[0])):
	414	+ f.write(str(Equilibri[i][j])+" ")
	415	+ f.write("\n ")
	416	+ ###########################################################
	417	+ tempo=tempo+T1
	418	+ for contatore2 in range(1,(appoggio1-appoggio2)):
	419	+ nest.Simulate(1000.)
	420	+ #Save the Data!!!!
	421	+ ###########################################################
	422	+ Equilibri=[]
	423	+ for i in range(0,int(InfoBuild[0])):
	424	+ Equilibri.append([])
	425	+ a=nest.GetStatus(DetectorPop[i])[0]["events"]["times"]
	426	+ if len(a)>0:
	427	+ Trange=(1000*int(numpy.min(a)/1000.),1000*int(numpy.min(a)/1000.)+1000)
	428	+ hist,Tbin=numpy.histogram(a,200,(Trange[0],Trange[1]))
	429	+ Equilibri[i]=hist*1000./(5.*int(InfoBuild[i+1][0]))
	430	+ else:
	431	+ Trange=(1000*int(tempo/1000.),1000*int(tempo/1000.)+1000)
	432	+ hist=numpy.zeros(200)
	433	+ Tbin=numpy.linspace(Trange[0],Trange[1],num=201)
	434	+ Equilibri[i]=hist
	435	+ nest.SetStatus(DetectorPop[i],{'n_events':0})
	436	+ for j in range(0,len(hist)):
	437	+ f.write(str(Tbin[j])+" ")
	438	+ for i in range(0,int(InfoBuild[0])):
	439	+ f.write(str(Equilibri[i][j])+" ")
	440	+ f.write("\n ")
	441	+ tempo=tempo+1000.
	442	+ T2=appoggio3-tempo
	443	+ nest.Simulate(T2);
	444	+ tempo=tempo+T2;
	445	+ else:
	446	+ nest.Simulate(InfoProtocol[contatore][0])
	447	+ temp=InfoProtocol[contatore][0]
	448	+ tempo=tempo+temp
	449	+ if InfoProtocol[contatore][2]==4:
	450	+ nest.SetStatus(NoisePop[InfoProtocol[contatore][1]],params={"rate": float(InfoBuild[1+InfoProtocol[contatore][1]][2]*InfoProtocol[contatore][3])})
	451	+ if InfoProtocol[contatore][2]==12:
	452	+ nest.SetStatus(NeuronPop[InfoProtocol[contatore][1]], params={"b": float(InfoProtocol[contatore][3])})
	453	+ else:
	454	+ nest.Simulate(simtime)
	455	+ tempo=simtime
	456	+ if (simtime-tempo)>0.:
	457	+ nest.Simulate(simtime-tempo)
	458	+
	459	+
	460	+ endsimulate = time.time()
	461	+ f.close()
	462	+ else:
	463	+ if len(InfoProtocol):
	464	+ tempo=0
	465	+ for contatore in range(0,len(InfoProtocol)):
	466	+ nest.Simulate(InfoProtocol[contatore][0])
	467	+ temp=InfoProtocol[contatore][0]
	468	+ tempo=tempo+temp
	469	+ if InfoProtocol[contatore][2]==4:
	470	+ nest.SetStatus(NoisePop[InfoProtocol[contatore][1]],params={"rate": float(InfoBuild[1+InfoProtocol[contatore][1]][2]*InfoProtocol[contatore][3])})
	471	+ #print "Population:", InfoProtocol[contatore][1] ,";Parameter:", InfoProtocol[contatore][2] ,"; Value: ",InfoProtocol[contatore][3]
	472	+ if InfoProtocol[contatore][2]==12:
	473	+ nest.SetStatus(NeuronPop[InfoProtocol[contatore][1]], params={"b": float(InfoProtocol[contatore][3])})
	474	+ #print "Population:", InfoProtocol[contatore][1] ,";Parameter:", InfoProtocol[contatore][2] ,"; Value: ",InfoProtocol[contatore][3]
	475	+
	476	+ else:
	477	+ nest.Simulate(simtime)
	478	+ tempo=simtime
	479	+ if (simtime-tempo)>0.:
	480	+ nest.Simulate(simtime-tempo)
	481	+ endsimulate = time.time()
	482	+
	483	+
	484	+ ###################################################################################################################################################################
	485	+
	486	+ #############################------------------------------------------------------------------------
	487	+ #print some information from the simulation
	488	+ #############################------------------------------------------------------------------------
	489	+
	490	+ num_synapses = nest.GetDefaults('static_synapse_hpc')["num_connections"]
	491	+ build_time = endbuild - startbuild
	492	+ connect_time = endconnect - startconnect
	493	+ sim_time = endsimulate - endconnect
	494	+
	495	+ N_neurons=0
	496	+ for i in range(0,int(InfoBuild[0])):
	497	+ N_neurons=N_neurons+int(InfoBuild[i+1][0])
	498	+
	499	+ print(" Network simulation (Python) neuron type:",InfoPerseo[0])
	500	+ print("Number of neurons : {0}".format(N_neurons))
	501	+ print("Number of synapses: {0}".format(num_synapses))
	502	+ print("Building time : %.2f s" % build_time)
	503	+ print("Connecting time : %.2f s" % connect_time)
	504	+ print("Simulation time : %.2f s" % sim_time)
	505	+
	506	+Fine=time.time()
	507	+print ("Total Simulation time : %.2f s" % (Fine-Inizio))
	508	+{{/code}}
	509	+
	510	+=== ===
	511	+
	512	+=== Results: ===
	513	+
	514	+the output of this simulationo is...
	515	+
	516	+
	517	+
	518	+
	519	+
	520	+
39	39	==== ====