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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
...	...	@@ -34,501 +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" 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		-=== [[image:image-20220127165908-2.png||height="659" width="1149"]] ===
327		-
328		-=== Connecting the network nodes: neuronal populations, Poisson processes and spike detectors ===
329		-
330		-{{code language="python"}}
331		-#############################------------------------------------------------------------------------
332		-print("Connecting ")
333		-#############################------------------------------------------------------------------------
334		-
335		-startconnect = time.time()
336		-Connessioni=[]
337		-Medie=[]
338		-
339		-#create and define the connections between the populations of neurons and the poisson generators
340		-#and between the populations of neurons and the spike detectors with the parameters extracted from the.ini files
341		-
342		-for i in range(0,int(InfoBuild[0])):
343		- nest.Connect(NoisePop[i], NeuronPop[i], syn_spec={'synapse_model': 'static_synapse_hpc',
344		- 'delay': dt,
345		- 'weight': nest.math.redraw(nest.random.normal(mean=float(InfoConnectNoise[i+1][0]),
346		- std=(float(InfoConnectNoise[i+1][1])*float(InfoConnectNoise[i+1][0]))),
347		- min=0., max=float('Inf'))
348		- })
349		- nest.Connect(NeuronPop[i][:int(InfoBuild[i+1][0])], DetectorPop[i], syn_spec={"weight": 1.0, "delay": dt})
350		-
351		-#create and define the connections between the populations of neurons with the parameters extracted from the.ini files
352		-
353		-for i in range(0,len(InfoConnectPop[1:])):
354		-
355		- conn=nest.Connect(NeuronPop[int(InfoConnectPop[i+1][1])], NeuronPop[int(InfoConnectPop[i+1][0])],
356		- {'rule': 'pairwise_bernoulli',
357		- 'p':float(InfoConnectPop[i+1][2]) },
358		- syn_spec={'synapse_model': 'static_synapse_hpc',
359		- 'delay':nest.math.redraw(nest.random.exponential(beta=float(1./(2.99573227355/(float(InfoConnectPop[i+1][4])-float(InfoConnectPop[i+1][3]))))),
360		- min= numpy.max([dt,float(1./float(InfoConnectPop[i+1][4]))]),
361		- max= float(1./(float(InfoConnectPop[i+1][3])-dt/2))),
362		-
363		- 'weight':nest.random.normal(mean=float(InfoConnectPop[i+1][6]),
364		- std=math.fabs(float(InfoConnectPop[i+1][6])*float(InfoConnectPop[i+1][7])))})
365		-
366		-
367		-endconnect = time.time()
368		-{{/code}}
369		-
370		-=== ===
371		-
372		-=== ===
373		-
374		-=== ===
375		-
376		-=== ===
377		-
378		-=== ===
379		-
380		-(% class="wikigeneratedid" %)
381		-=== [[image:image-20220127170722-1.png]] ===
382		-
383		-=== Simulating: neuronal time evolution. ===
384		-
385		-=== ===
386		-
387		-{{code language="python"}}
388		- #############################------------------------------------------------------------------------
389		- print("Simulating")
390		- #############################------------------------------------------------------------------------
391		- ###################################################################################################################################################################
392		- if Salva:
393		- print("I m going to save the data")
394		- #x=str(iterazioni)
395		- f = open(FileName,"w")
396		- if len(InfoProtocol):
397		- print("I m going to split the simulation")
398		- tempo=0
399		- for contatore in range(0,len(InfoProtocol)):
400		- appoggio1=int((tempo+InfoProtocol[contatore][0])/1000.)
401		- appoggio2=int(tempo/1000.)
402		- appoggio3=tempo+InfoProtocol[contatore][0]
403		- if (appoggio1-appoggio2)>=1:
404		- T1=(1+appoggio2)*1000-tempo
405		- nest.Simulate(T1)
406		- #Save the Data!!!!
407		- ###########################################################
408		- Equilibri=[]
409		- for i in range(0,int(InfoBuild[0])):
410		- Equilibri.append([])
411		- a=nest.GetStatus(DetectorPop[i])[0]["events"]["times"]
412		- if len(a)>0:
413		- Trange=(1000*int(numpy.min(a)/1000.),1000*int(numpy.min(a)/1000.)+1000)
414		- hist,Tbin=numpy.histogram(a,200,(Trange[0],Trange[1]))
415		- Equilibri[i]=hist*1000./(5.*int(InfoBuild[i+1][0]))
416		- else:
417		- Trange=(1000*int(tempo/1000.),1000*int(tempo/1000.)+1000)
418		- hist=numpy.zeros(200)
419		- Tbin=numpy.linspace(Trange[0],Trange[1],num=201)
420		- Equilibri[i]=hist
421		- nest.SetStatus(DetectorPop[i],{'n_events':0})
422		- for j in range(0,len(hist)):
423		- f.write(str(Tbin[j])+" ")
424		- for i in range(0,int(InfoBuild[0])):
425		- f.write(str(Equilibri[i][j])+" ")
426		- f.write("\n ")
427		- ###########################################################
428		- tempo=tempo+T1
429		- for contatore2 in range(1,(appoggio1-appoggio2)):
430		- nest.Simulate(1000.)
431		- #Save the Data!!!!
432		- ###########################################################
433		- Equilibri=[]
434		- for i in range(0,int(InfoBuild[0])):
435		- Equilibri.append([])
436		- a=nest.GetStatus(DetectorPop[i])[0]["events"]["times"]
437		- if len(a)>0:
438		- Trange=(1000*int(numpy.min(a)/1000.),1000*int(numpy.min(a)/1000.)+1000)
439		- hist,Tbin=numpy.histogram(a,200,(Trange[0],Trange[1]))
440		- Equilibri[i]=hist*1000./(5.*int(InfoBuild[i+1][0]))
441		- else:
442		- Trange=(1000*int(tempo/1000.),1000*int(tempo/1000.)+1000)
443		- hist=numpy.zeros(200)
444		- Tbin=numpy.linspace(Trange[0],Trange[1],num=201)
445		- Equilibri[i]=hist
446		- nest.SetStatus(DetectorPop[i],{'n_events':0})
447		- for j in range(0,len(hist)):
448		- f.write(str(Tbin[j])+" ")
449		- for i in range(0,int(InfoBuild[0])):
450		- f.write(str(Equilibri[i][j])+" ")
451		- f.write("\n ")
452		- tempo=tempo+1000.
453		- T2=appoggio3-tempo
454		- nest.Simulate(T2);
455		- tempo=tempo+T2;
456		- else:
457		- nest.Simulate(InfoProtocol[contatore][0])
458		- temp=InfoProtocol[contatore][0]
459		- tempo=tempo+temp
460		- if InfoProtocol[contatore][2]==4:
461		- nest.SetStatus(NoisePop[InfoProtocol[contatore][1]],params={"rate": float(InfoBuild[1+InfoProtocol[contatore][1]][2]*InfoProtocol[contatore][3])})
462		- if InfoProtocol[contatore][2]==12:
463		- nest.SetStatus(NeuronPop[InfoProtocol[contatore][1]], params={"b": float(InfoProtocol[contatore][3])})
464		- else:
465		- nest.Simulate(simtime)
466		- tempo=simtime
467		- if (simtime-tempo)>0.:
468		- nest.Simulate(simtime-tempo)
469		-
470		-
471		- endsimulate = time.time()
472		- f.close()
473		- else:
474		- if len(InfoProtocol):
475		- tempo=0
476		- for contatore in range(0,len(InfoProtocol)):
477		- nest.Simulate(InfoProtocol[contatore][0])
478		- temp=InfoProtocol[contatore][0]
479		- tempo=tempo+temp
480		- if InfoProtocol[contatore][2]==4:
481		- nest.SetStatus(NoisePop[InfoProtocol[contatore][1]],params={"rate": float(InfoBuild[1+InfoProtocol[contatore][1]][2]*InfoProtocol[contatore][3])})
482		- #print "Population:", InfoProtocol[contatore][1] ,";Parameter:", InfoProtocol[contatore][2] ,"; Value: ",InfoProtocol[contatore][3]
483		- if InfoProtocol[contatore][2]==12:
484		- nest.SetStatus(NeuronPop[InfoProtocol[contatore][1]], params={"b": float(InfoProtocol[contatore][3])})
485		- #print "Population:", InfoProtocol[contatore][1] ,";Parameter:", InfoProtocol[contatore][2] ,"; Value: ",InfoProtocol[contatore][3]
486		-
487		- else:
488		- nest.Simulate(simtime)
489		- tempo=simtime
490		- if (simtime-tempo)>0.:
491		- nest.Simulate(simtime-tempo)
492		- endsimulate = time.time()
493		-
494		-
495		- ###################################################################################################################################################################
496		-
497		- #############################------------------------------------------------------------------------
498		- #print some information from the simulation
499		- #############################------------------------------------------------------------------------
500		-
501		- num_synapses = nest.GetDefaults('static_synapse_hpc')["num_connections"]
502		- build_time = endbuild - startbuild
503		- connect_time = endconnect - startconnect
504		- sim_time = endsimulate - endconnect
505		-
506		- N_neurons=0
507		- for i in range(0,int(InfoBuild[0])):
508		- N_neurons=N_neurons+int(InfoBuild[i+1][0])
509		-
510		- print(" Network simulation (Python) neuron type:",InfoPerseo[0])
511		- print("Number of neurons : {0}".format(N_neurons))
512		- print("Number of synapses: {0}".format(num_synapses))
513		- print("Building time : %.2f s" % build_time)
514		- print("Connecting time : %.2f s" % connect_time)
515		- print("Simulation time : %.2f s" % sim_time)
516		-
517		-Fine=time.time()
518		-print ("Total Simulation time : %.2f s" % (Fine-Inizio))
519		-{{/code}}
520		-
521		-=== ===
522		-
523		-=== [[image:image-20220127170155-2.png||height="682" width="1439"]] ===
524		-
525		-=== Results: ===
526		-
527		-the output of this simulationo is...
528		-
529		-
530		-
531		-
532		-
533		-
534	534	==== ====

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