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1		-== Introduction (path and modules): ==
	1	+== Code Description ==
2	2
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: ===
6	6
7	7	{{code language="python"}}
8		-# Import the os module
9		-import os
10		-
11		-#Print the current working directory
12		-print("Current working directory: {0}".format(os.getcwd()))
13		-
14		-# Change the current working directory
15		-os.chdir('/mnt/user/shared/Slow waves in fading anesthesia/Nest3Python3')
16		-
17		-# Print the current working directory
18		-print("Current working directory: {0}".format(os.getcwd()))
	6	+x = 1
	7	+if x == 1:
	8	+ # indented four spaces
	9	+ print("x is 1.")
19	19	{{/code}}
20	20
21		-=== Import the modules necessary for the simulation: ===
	12	+(% class="wikigeneratedid" %)
	13	+=== ===
22	22
23	23	{{code language="python"}}
24		-import nest
25		-import time
26		-from numpy import exp
27		-import numpy
28		-import math
29		-import random
30		-import multiprocessing
31		-Inizio=time.time()
32		-print('tempo di Inizio:',Inizio)
	16	+x = 1
	17	+if x == 1:
	18	+ # indented four spaces
	19	+ print("x is 1.")
33	33	{{/code}}
34	34
35		-=== ===
	22	+(% class="wikigeneratedid" %)
	23	+=== ===
36	36
37		-=== Define necessary classes to import the Initialization Files: ===
	25	+=== 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		-=== 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		-
521		-==== ====
	27	+==== ====