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Last modified by galluzziandrea on 2022/06/20 12:33
From version 15.1
edited by galluzziandrea
on 2022/01/27 17:01
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To version 5.1
edited by galluzziandrea
on 2021/12/09 14:46
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... ... @@ -36,7 +36,8 @@
36 36  
37 37  === Define necessary classes to import the Initialization Files: ===
38 38  
39 -{{code language="python" title=" "}}
39 +
40 +{{code language="python"}}
40 40  class ImportIniLIFCA():
41 41   #initialize the information to look for in perseo.ini
42 42   inf=["NeuronType", #still fixed value
... ... @@ -235,290 +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  
242 +=== Results ===
250 250  
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 -(% class="wikigeneratedid" %)
327 -=== [[image:image-20220127165908-2.png||height="659" width="1149"]] ===
328 -
329 -=== Connecting the network nodes: neuronal populations, Poisson processes and spike detectors ===
330 -
331 -{{code language="python"}}
332 -#############################------------------------------------------------------------------------
333 -print("Connecting ")
334 -#############################------------------------------------------------------------------------
335 -
336 -startconnect = time.time()
337 -Connessioni=[]
338 -Medie=[]
339 -
340 -#create and define the connections between the populations of neurons and the poisson generators
341 -#and between the populations of neurons and the spike detectors with the parameters extracted from the.ini files
342 -
343 -for i in range(0,int(InfoBuild[0])):
344 - nest.Connect(NoisePop[i], NeuronPop[i], syn_spec={'synapse_model': 'static_synapse_hpc',
345 - 'delay': dt,
346 - 'weight': nest.math.redraw(nest.random.normal(mean=float(InfoConnectNoise[i+1][0]),
347 - std=(float(InfoConnectNoise[i+1][1])*float(InfoConnectNoise[i+1][0]))),
348 - min=0., max=float('Inf'))
349 - })
350 - nest.Connect(NeuronPop[i][:int(InfoBuild[i+1][0])], DetectorPop[i], syn_spec={"weight": 1.0, "delay": dt})
351 -
352 -#create and define the connections between the populations of neurons with the parameters extracted from the.ini files
353 -
354 -for i in range(0,len(InfoConnectPop[1:])):
355 -
356 - conn=nest.Connect(NeuronPop[int(InfoConnectPop[i+1][1])], NeuronPop[int(InfoConnectPop[i+1][0])],
357 - {'rule': 'pairwise_bernoulli',
358 - 'p':float(InfoConnectPop[i+1][2]) },
359 - syn_spec={'synapse_model': 'static_synapse_hpc',
360 - 'delay':nest.math.redraw(nest.random.exponential(beta=float(1./(2.99573227355/(float(InfoConnectPop[i+1][4])-float(InfoConnectPop[i+1][3]))))),
361 - min= numpy.max([dt,float(1./float(InfoConnectPop[i+1][4]))]),
362 - max= float(1./(float(InfoConnectPop[i+1][3])-dt/2))),
363 -
364 - 'weight':nest.random.normal(mean=float(InfoConnectPop[i+1][6]),
365 - std=math.fabs(float(InfoConnectPop[i+1][6])*float(InfoConnectPop[i+1][7])))})
366 -
367 -
368 -endconnect = time.time()
369 -{{/code}}
370 -
371 -=== ===
372 -
373 -=== ===
374 -
375 -=== Simulating: neuronal time evolution. ===
376 -
377 -=== ===
378 -
379 -{{code language="python"}}
380 - #############################------------------------------------------------------------------------
381 - print("Simulating")
382 - #############################------------------------------------------------------------------------
383 - ###################################################################################################################################################################
384 - if Salva:
385 - print("I m going to save the data")
386 - #x=str(iterazioni)
387 - f = open(FileName,"w")
388 - if len(InfoProtocol):
389 - print("I m going to split the simulation")
390 - tempo=0
391 - for contatore in range(0,len(InfoProtocol)):
392 - appoggio1=int((tempo+InfoProtocol[contatore][0])/1000.)
393 - appoggio2=int(tempo/1000.)
394 - appoggio3=tempo+InfoProtocol[contatore][0]
395 - if (appoggio1-appoggio2)>=1:
396 - T1=(1+appoggio2)*1000-tempo
397 - nest.Simulate(T1)
398 - #Save the Data!!!!
399 - ###########################################################
400 - Equilibri=[]
401 - for i in range(0,int(InfoBuild[0])):
402 - Equilibri.append([])
403 - a=nest.GetStatus(DetectorPop[i])[0]["events"]["times"]
404 - if len(a)>0:
405 - Trange=(1000*int(numpy.min(a)/1000.),1000*int(numpy.min(a)/1000.)+1000)
406 - hist,Tbin=numpy.histogram(a,200,(Trange[0],Trange[1]))
407 - Equilibri[i]=hist*1000./(5.*int(InfoBuild[i+1][0]))
408 - else:
409 - Trange=(1000*int(tempo/1000.),1000*int(tempo/1000.)+1000)
410 - hist=numpy.zeros(200)
411 - Tbin=numpy.linspace(Trange[0],Trange[1],num=201)
412 - Equilibri[i]=hist
413 - nest.SetStatus(DetectorPop[i],{'n_events':0})
414 - for j in range(0,len(hist)):
415 - f.write(str(Tbin[j])+" ")
416 - for i in range(0,int(InfoBuild[0])):
417 - f.write(str(Equilibri[i][j])+" ")
418 - f.write("\n ")
419 - ###########################################################
420 - tempo=tempo+T1
421 - for contatore2 in range(1,(appoggio1-appoggio2)):
422 - nest.Simulate(1000.)
423 - #Save the Data!!!!
424 - ###########################################################
425 - Equilibri=[]
426 - for i in range(0,int(InfoBuild[0])):
427 - Equilibri.append([])
428 - a=nest.GetStatus(DetectorPop[i])[0]["events"]["times"]
429 - if len(a)>0:
430 - Trange=(1000*int(numpy.min(a)/1000.),1000*int(numpy.min(a)/1000.)+1000)
431 - hist,Tbin=numpy.histogram(a,200,(Trange[0],Trange[1]))
432 - Equilibri[i]=hist*1000./(5.*int(InfoBuild[i+1][0]))
433 - else:
434 - Trange=(1000*int(tempo/1000.),1000*int(tempo/1000.)+1000)
435 - hist=numpy.zeros(200)
436 - Tbin=numpy.linspace(Trange[0],Trange[1],num=201)
437 - Equilibri[i]=hist
438 - nest.SetStatus(DetectorPop[i],{'n_events':0})
439 - for j in range(0,len(hist)):
440 - f.write(str(Tbin[j])+" ")
441 - for i in range(0,int(InfoBuild[0])):
442 - f.write(str(Equilibri[i][j])+" ")
443 - f.write("\n ")
444 - tempo=tempo+1000.
445 - T2=appoggio3-tempo
446 - nest.Simulate(T2);
447 - tempo=tempo+T2;
448 - else:
449 - nest.Simulate(InfoProtocol[contatore][0])
450 - temp=InfoProtocol[contatore][0]
451 - tempo=tempo+temp
452 - if InfoProtocol[contatore][2]==4:
453 - nest.SetStatus(NoisePop[InfoProtocol[contatore][1]],params={"rate": float(InfoBuild[1+InfoProtocol[contatore][1]][2]*InfoProtocol[contatore][3])})
454 - if InfoProtocol[contatore][2]==12:
455 - nest.SetStatus(NeuronPop[InfoProtocol[contatore][1]], params={"b": float(InfoProtocol[contatore][3])})
456 - else:
457 - nest.Simulate(simtime)
458 - tempo=simtime
459 - if (simtime-tempo)>0.:
460 - nest.Simulate(simtime-tempo)
461 -
462 -
463 - endsimulate = time.time()
464 - f.close()
465 - else:
466 - if len(InfoProtocol):
467 - tempo=0
468 - for contatore in range(0,len(InfoProtocol)):
469 - nest.Simulate(InfoProtocol[contatore][0])
470 - temp=InfoProtocol[contatore][0]
471 - tempo=tempo+temp
472 - if InfoProtocol[contatore][2]==4:
473 - nest.SetStatus(NoisePop[InfoProtocol[contatore][1]],params={"rate": float(InfoBuild[1+InfoProtocol[contatore][1]][2]*InfoProtocol[contatore][3])})
474 - #print "Population:", InfoProtocol[contatore][1] ,";Parameter:", InfoProtocol[contatore][2] ,"; Value: ",InfoProtocol[contatore][3]
475 - if InfoProtocol[contatore][2]==12:
476 - nest.SetStatus(NeuronPop[InfoProtocol[contatore][1]], params={"b": float(InfoProtocol[contatore][3])})
477 - #print "Population:", InfoProtocol[contatore][1] ,";Parameter:", InfoProtocol[contatore][2] ,"; Value: ",InfoProtocol[contatore][3]
478 -
479 - else:
480 - nest.Simulate(simtime)
481 - tempo=simtime
482 - if (simtime-tempo)>0.:
483 - nest.Simulate(simtime-tempo)
484 - endsimulate = time.time()
485 -
486 -
487 - ###################################################################################################################################################################
488 -
489 - #############################------------------------------------------------------------------------
490 - #print some information from the simulation
491 - #############################------------------------------------------------------------------------
492 -
493 - num_synapses = nest.GetDefaults('static_synapse_hpc')["num_connections"]
494 - build_time = endbuild - startbuild
495 - connect_time = endconnect - startconnect
496 - sim_time = endsimulate - endconnect
497 -
498 - N_neurons=0
499 - for i in range(0,int(InfoBuild[0])):
500 - N_neurons=N_neurons+int(InfoBuild[i+1][0])
501 -
502 - print(" Network simulation (Python) neuron type:",InfoPerseo[0])
503 - print("Number of neurons : {0}".format(N_neurons))
504 - print("Number of synapses: {0}".format(num_synapses))
505 - print("Building time : %.2f s" % build_time)
506 - print("Connecting time : %.2f s" % connect_time)
507 - print("Simulation time : %.2f s" % sim_time)
508 -
509 -Fine=time.time()
510 -print ("Total Simulation time : %.2f s" % (Fine-Inizio))
511 -{{/code}}
512 -
513 -=== ===
514 -
515 -=== Results: ===
516 -
517 -the output of this simulationo is...
518 -
519 -
520 -
521 -
522 -
523 -
524 524  ==== ====
image-20220127165822-1.png
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