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Last modified by galluzziandrea on 2022/06/20 12:33
From version 9.1
edited by galluzziandrea
on 2021/12/09 15:04
Change comment: There is no comment for this version
To version 7.1
edited by galluzziandrea
on 2021/12/09 14:49
Change comment: There is no comment for this version

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... ... @@ -235,285 +235,9 @@
235 235  # [.....],[],...]
236 236  {{/code}}
237 237  
238 -=== Defining general and nest.kernel parameters ===
239 239  
240 -{{code language="python"}}
241 -#############################------------------------------------------------------------------------
242 -#Clean the Network
243 -#############################------------------------------------------------------------------------
244 -nest.ResetKernel()
245 245  
246 -#############################------------------------------------------------------------------------
247 -#insert the introductory parameters of the simulation
248 -#############################------------------------------------------------------------------------
249 249  
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 -
512 512  === Results ===
513 513  
514 -
515 -
516 -
517 -
518 -
519 519  ==== ====