#cp findppicoeffs.py coding.py
from neuron import h
import matplotlib
matplotlib.use('Agg')
import numpy
from pylab import *
import mytools
import pickle
import time
import sys
import random
from setparams import *
from os.path import exists
import itertools
random.seed(1)
v0 = -62
ca0 = 0.0001
proximalpoint = 400
distalpoint = 620
fs = 8
ITERS = 30
tstop = 11000.0
import mutation_stuff
MT = mutation_stuff.getMT()
defVals = mutation_stuff.getdefvals()
keyList = defVals.keys()
mySuffixes = mutation_stuff.getsuffixes()
mySuffixExceptions = mutation_stuff.getsuffixexceptions()
unpicklefile = open('scalings_cs.sav', 'r')
unpickledlist = pickle.load(unpicklefile)
unpicklefile.close()
theseCoeffsAllAll = unpickledlist[0]
theseMutValsAllAll = unpickledlist[2]
paramdicts = []
paramdicts.append({'transvec.x(31)': 1.0, 'transvec.x(32)': 1.0, 'transvec.x(20)': 1.0, 'transvec.x(21)': 1.0, 'transvec.x(25)': 1.0, 'transvec.x(26)': 1.0}) # 4-6 spikes per burst, control
paramdicts.append({'transvec.x(31)': 1.25, 'transvec.x(32)': 1.25}) # 4-5 spikes per burst
paramdicts.append({'transvec.x(31)': 1.5, 'transvec.x(32)': 1.5}) # 3-4 spikes per burst
paramdicts.append({'transvec.x(31)': 2.0, 'transvec.x(32)': 2.0}) # 3-4 spikes per burst
paramdicts.append({'transvec.x(31)': 4.0, 'transvec.x(32)': 4.0}) # 2-3 spikes per burst
paramdicts.append({'transvec.x(31)': 4.0, 'transvec.x(32)': 4.0, 'transvec.x(20)': 1.3, 'transvec.x(21)': 1.3, 'transvec.x(25)': 1.3, 'transvec.x(26)': 1.3}) # 2 spikes per burst
paramdicts.append({'transvec.x(31)': 4.0, 'transvec.x(32)': 4.0, 'transvec.x(20)': 1.6, 'transvec.x(21)': 1.6, 'transvec.x(25)': 1.6, 'transvec.x(26)': 1.6}) # 1-2 spikes per burst
#lensToStart = [100.0 + x*50 for x in range(0,16)]
lensToStart = [0.0 + x*200 for x in range(0,6)]
lensToEnd = [200.0 + x*200 for x in range(0,5)]+[1325.]
lenToStartBasal = 0.0
lenToEndBasal = 356.0
currCoeff = 0.5
if len(sys.argv) > 2:
currCoeff = float(sys.argv[2])
for icell in range(0,7):
gCoeffsAllAll = []
synlocsAllAll = []
Nsyns_all = []
theseCoeffsAll = theseCoeffsAllAll[icell]
for istartdist in range(0,len(lensToStart)):
lenToStart = lensToStart[istartdist]
lenToEnd = lensToEnd[istartdist]
unpicklefile = open('synlocs'+str(lenToStart)+'-'+str(lenToEnd)+'.sav', 'r')
unpickledlist = pickle.load(unpicklefile)
unpicklefile.close()
Nsyns = unpickledlist[0]
synlocsAll = unpickledlist[3]
lenToStart = int(lenToStart)
lenToEnd = int(lenToEnd)
unpicklefile = open('thresholddistalamp'+str(lenToStart)+'-'+str(lenToEnd)+'_cs'+str(icell)+'_0.sav', 'r')
unpickledlist = pickle.load(unpicklefile)
unpicklefile.close()
gsAll = unpickledlist[1]
Nsyns_all.append(Nsyns)
gCoeffsAllAll.append(gsAll[:])
synlocsAllAll.append(synlocsAll[:])
unpicklefile = open('basalsynlocs'+str(lenToStartBasal)+'-'+str(lenToEndBasal)+'.sav', 'r')
unpickledlist = pickle.load(unpicklefile)
unpicklefile.close()
Nsyns = unpickledlist[0]
synlocsAll = unpickledlist[3]
unpicklefile = open('thresholdbasalamp0.0-356.0_cs'+str(icell)+'_0.sav', 'r')
unpickledlist = pickle.load(unpicklefile)
unpicklefile.close()
gsAll = unpickledlist[1]
Nsyns_all.append(Nsyns)
gCoeffsAllAll.append(gsAll[:])
synlocsAllAll.append(synlocsAll[:])
coding_inputs = list(itertools.product([0, 1], repeat=7))
if len(sys.argv) > 3 and int(float(sys.argv[3])) != icell:
continue
h("""
load_file("myrun.hoc")
objref cvode, sl
cvode = new CVode()
cvode.active(1)
cvode.atol(0.001)
access a_soma
double siteVec[2]
sl = new List()
sl=locateSites("apic",620)
maxdiam = 0
for(i=0;i<sl.count();i+=1){
dd1 = sl.o[i].x[1]
dd = apic[sl.o[i].x[0]].diam(dd1)
if (dd > maxdiam) {
j = i
maxdiam = dd
}
}
siteVec[0] = sl.o[j].x[0]
siteVec[1] = sl.o[j].x[1]
objref vsoma, vdend, tvec, recSite, vdends, cadends, casoma
vsoma = new Vector()
casoma = new Vector()
vdend = new Vector()
tvec = new Vector()
cadends = new List()
vdends = new List()
objref ns, syns["""+str(7*Nsyns)+"""]
a_soma cvode.record(&v(0.5),vsoma,tvec)
apic[siteVec[0]] cvode.record(&v(siteVec[1]),vdend,tvec)
v_init = -62
dt = 0.025
""")
paramdict = paramdicts[icell]
setparams(paramdict)
for idist in range(0,6):
h("""
cadends.append(new Vector())
vdends.append(new Vector())
sl = locateSites("apic","""+str((lensToStart[idist]+lensToEnd[idist])*0.5)+""")
maxdiam = 0
for(i=0;i<sl.count();i+=1){
dd1 = sl.o[i].x[1]
dd = apic[sl.o[i].x[0]].diam(dd1)
if (dd > maxdiam) {
j = i
maxdiam = dd
}
}
siteVec[0] = sl.o[j].x[0]
siteVec[1] = sl.o[j].x[1]
apic[siteVec[0]] cvode.record(&cai(siteVec[1]),cadends.o[cadends.count()-1],tvec)
apic[siteVec[0]] cvode.record(&cai(siteVec[1]),vdends.o[vdends.count()-1],tvec)
""")
for istim in range(0,Nsyns):
h("""
siteVec[0] = """+str(synlocsAllAll[idist][istim][0])+"""
siteVec[1] = """+str(synlocsAllAll[idist][istim][1])+"""
apic[siteVec[0]] {
syns["""+str(Nsyns*idist+istim)+"""] = new AlphaSynapse(siteVec[1])
syns["""+str(Nsyns*idist+istim)+"""].e = 0
syns["""+str(Nsyns*idist+istim)+"""].tau = 5
syns["""+str(Nsyns*idist+istim)+"""].onset = 10000
syns["""+str(Nsyns*idist+istim)+"""].gmax = """+str(gCoeffsAllAll[idist][0]*currCoeff)+"""
}
""")
h("""
cadends.append(new Vector())
vdends.append(new Vector())
sl = locateSites("dend","""+str((lenToStartBasal+lenToEndBasal)*0.5)+""")
maxdiam = 0
for(i=0;i<sl.count();i+=1){
dd1 = sl.o[i].x[1]
dd = apic[sl.o[i].x[0]].diam(dd1)
if (dd > maxdiam) {
j = i
maxdiam = dd
}
}
siteVec[0] = sl.o[j].x[0]
siteVec[1] = sl.o[j].x[1]
dend[siteVec[0]] cvode.record(&cai(siteVec[1]),cadends.o[cadends.count()-1],tvec)
dend[siteVec[0]] cvode.record(&cai(siteVec[1]),vdends.o[vdends.count()-1],tvec)
""")
for istim in range(0,Nsyns):
h("""
siteVec[0] = """+str(synlocsAllAll[6][istim][0])+"""
siteVec[1] = """+str(synlocsAllAll[6][istim][1])+"""
dend[siteVec[0]] {
syns["""+str(Nsyns*6+istim)+"""] = new AlphaSynapse(siteVec[1])
syns["""+str(Nsyns*6+istim)+"""].e = 0
syns["""+str(Nsyns*6+istim)+"""].tau = 5
syns["""+str(Nsyns*6+istim)+"""].onset = 10000
syns["""+str(Nsyns*6+istim)+"""].gmax = """+str(gCoeffsAllAll[6][0]*currCoeff)+"""
}
""")
coeffCoeffs = [[0.25,0],[0.125,0],[0.5,0],[0.5,1.0/3],[0.5,2.0/3],[0.5,1.0],[-0.25,0],[-0.125,0],[-0.5,0]]
counter = -1
for igene in range(0,len(MT)):
gCoeffsThisGene = []
for imut in range(0,len(MT[igene])):
gCoeffsThisMut = []
nVals = len(MT[igene][imut])*[0]
thesemutvars = []
theseCoeffs = theseCoeffsAll[igene][imut]
for imutvar in range(0,len(MT[igene][imut])):
thesemutvars.append(MT[igene][imut][imutvar][0])
if type(MT[igene][imut][imutvar][1]) is int or type(MT[igene][imut][imutvar][1]) is float:
MT[igene][imut][imutvar][1] = [MT[igene][imut][imutvar][1]]
nVals[imutvar] = len(MT[igene][imut][imutvar][1])
cumprodnVals = cumprod(nVals)
allmutvars = cumprodnVals[len(MT[igene][imut])-1]*[thesemutvars]
allmutvals = []
for iallmutval in range(0,cumprodnVals[len(MT[igene][imut])-1]):
allmutvals.append([0]*len(thesemutvars))
for iallmutval in range(0,cumprodnVals[len(MT[igene][imut])-1]):
for imutvar in range(0,len(MT[igene][imut])):
if imutvar==0:
allmutvals[iallmutval][imutvar] = MT[igene][imut][imutvar][1][iallmutval%nVals[imutvar]]
else:
allmutvals[iallmutval][imutvar] = MT[igene][imut][imutvar][1][(iallmutval/cumprodnVals[imutvar-1])%nVals[imutvar]]
for iallmutval in range(0,cumprodnVals[len(MT[igene][imut])-1]):
counter = counter + 1
if len(sys.argv) > 1 and int(float(sys.argv[1])) != counter:
continue
if exists('codings'+str(currCoeff)+'_cs'+str(icell)+'_'+str(counter)+'.sav'):
continue
gCoeffsThisMutVal = []
close("all")
f, axarr = plt.subplots(2, 2)
iters = [0, 2, 5, 6, 8, -1]
nspsThisVal = []
coding_outputs = []
for iiter in range(0,len(iters)):
nspsThisIter = []
iter = iters[iiter]
gCoeffsThisIter = []
if iter >= 0:
thisCoeff = coeffCoeffs[iter][0]*theseCoeffs[iallmutval] + coeffCoeffs[iter][1]*(1.0 - 0.5*theseCoeffs[iallmutval])
else:
thisCoeff = 0
if iter == -1 and (igene > 0 or imut > 0 or iallmutval > 0):
continue # do the control only once!
if iter == 5:
gCoeffsThisIter.append([])
continue
#thisg = gsAllAll[icell][igene][imut][iallmutval][iiter]
#print "iter="+str(iter)+", thisCoeff="+str(thisCoeff)
mutText = ""
for imutvar in range(0,len(MT[igene][imut])):
if imutvar > 0 and imutvar%2==0:
mutText = mutText+"\n"
mutvars = allmutvars[iallmutval][imutvar]
mutvals = allmutvals[iallmutval][imutvar]
if type(mutvars) is str:
mutvars = [mutvars]
mutText = mutText + str(mutvars) + ": "
for kmutvar in range(0,len(mutvars)):
mutvar = mutvars[kmutvar]
if (mutvar.find('off') > -1 and mutvar.find('offc') < 0) or mutvar.find('eh') > -1:
newVal = defVals[mutvar]+mutvals*thisCoeff
if mutvals >= 0 and kmutvar==0:
mutText = mutText + "+" + str(mutvals) +" mV"
elif kmutvar==0:
mutText = mutText + str(mutvals) +" mV"
else:
newVal = defVals[mutvar]*(mutvals**thisCoeff)
if kmutvar==0:
mutText = mutText + "*" + str(mutvals)
if kmutvar < len(mutvars)-1:
mutText = mutText + ", "
mySuffix = mutvars[kmutvar][mutvars[kmutvar].find('_')+1:len(mutvars[kmutvar])]
mySuffixInd = next((i for i,x in enumerate(mySuffixes) if x.find(mySuffix) > -1))
isException = 0
for jsuffe in range(0,len(mySuffixExceptions[mySuffixInd])):
if mySuffixExceptions[mySuffixInd][jsuffe][0].find(mutvars[kmutvar]) > -1:
isException = 1
exceptionInd = jsuffe
if not isException:
print ("""forall if(ismembrane(\""""+mySuffix+"""\")) """+mutvars[kmutvar]+""" = """+str(newVal))
h("""forall if(ismembrane(\""""+mySuffix+"""\")) """+mutvars[kmutvar]+""" = """+str(newVal))
else:
print ("""forall if(ismembrane(\""""+mySuffix+"""\")) """+mySuffixExceptions[isuffix][j][1]+""" = """+str(newVal))
h("""forall if(ismembrane(\""""+mySuffix+"""\")) """+mySuffixExceptions[isuffix][j][1]+""" = """+str(newVal))
print mutText
thisCa = h.a_soma.cainf_cad
h("""
tstop = """+str(tstop)+"""
cai0_ca_ion = """+str(thisCa)+"""
v_init = """+str(v0)+"""
""")
coding_outputs_thisiter = []
for icoding in range(0,len(coding_inputs)):
for idist in range(0,6):
for istim in range(0,Nsyns):
h("syns["+str(Nsyns*idist+istim)+"].gmax = "+str(gCoeffsAllAll[idist][0]*currCoeff*coding_inputs[icoding][idist]))
print "syns["+str(Nsyns*idist)+"+istim].gmax = "+str(gCoeffsAllAll[idist][0]*currCoeff*coding_inputs[icoding][idist])
for istim in range(0,Nsyns):
h("syns["+str(Nsyns*6+istim)+"].gmax = "+str(gCoeffsAllAll[6][0]*currCoeff*coding_inputs[icoding][6]))
print "syns["+str(Nsyns*6)+"+istim].gmax = "+str(gCoeffsAllAll[6][0]*currCoeff*coding_inputs[icoding][6])
timenow = time.time()
h.init()
try:
h.run()
except RuntimeError:
hasErred = 1
print "Too large g!"
times=np.array(h.tvec)
Vsoma=np.array(h.vsoma)
spikes = mytools.spike_times(times,Vsoma,-50,-50)
nSpikes1 = len(spikes)
coding_outputs_thisiter.append([max(array(h.cadends)[i]) for i in range(0,7)]+[nSpikes1]+[max(array(h.vdends)[i]) for i in range(0,7)])
coding_outputs.append(coding_outputs_thisiter[:])
#Restore default values:
for imutvar in range(0,len(MT[igene][imut])):
mutvars = allmutvars[iallmutval][imutvar]
mutvals = allmutvals[iallmutval][imutvar]
if type(mutvars) is str:
mutvars = [mutvars]
for kmutvar in range(0,len(mutvars)):
newVal = defVals[mutvars[kmutvar]]
mySuffix = mutvars[kmutvar][mutvars[kmutvar].find('_')+1:len(mutvars[kmutvar])]
mySuffixInd = next((i for i,x in enumerate(mySuffixes) if x.find(mySuffix) > -1))
isException = 0
for jsuffe in range(0,len(mySuffixExceptions[mySuffixInd])):
if mySuffixExceptions[mySuffixInd][jsuffe][0].find(mutvars[kmutvar]) > -1:
isException = 1
exceptionInd = jsuffe
if not isException:
h("""forall if(ismembrane(\""""+mySuffix+"""\")) """+mutvars[kmutvar]+""" = """+str(defVals[mutvars[kmutvar]]))
else:
h("""forall if(ismembrane(\""""+mySuffix+"""\")) """+mySuffixExceptions[isuffix][j][1]+""" = """+str(defVals[mutvars[kmutvar]]))
picklelist = [theseCoeffsAll,coding_inputs,coding_outputs,MT]
file = open('codings'+str(currCoeff)+'_cs'+str(icell)+'_'+str(counter)+'.sav', 'w')
pickle.dump(picklelist,file)
file.close()