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Last modified by galluzziandrea on 2022/06/20 12:33
From version 16.1
edited by galluzziandrea
on 2022/01/27 17:03
Change comment: There is no comment for this version
To version 4.1
edited by galluzziandrea
on 2021/12/09 14:38
Change comment: There is no comment for this version

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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
... ... @@ -34,502 +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 -(% class="wikigeneratedid" %)
375 -=== [[image:image-20220127170104-1.png||height="630" width="1430"]] ===
376 -
377 -(% class="wikigeneratedid" %)
378 -=== ===
379 -
380 -(% class="wikigeneratedid" %)
381 -=== ===
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 -(% class="wikigeneratedid" %)
524 -=== [[image:image-20220127170155-2.png||height="682" width="1439"]] ===
525 -
526 -=== Results: ===
527 -
528 -the output of this simulationo is...
529 -
530 -
531 -
532 -
533 -
534 -
535 535  ==== ====
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