import math
import copy
import pylab
def spike_times(time,vrec,V_min_peak=-20,V_max_valley=0):
valley_reached = 1
sptime = []
for j in range(1,len(time)-1):
if valley_reached and vrec[j] >= V_min_peak and vrec[j] > vrec[j-1] and vrec[j] >= vrec[j+1]:
valley_reached = 0
sptime.append(time[j])
elif valley_reached==False and vrec[j] <= V_max_valley:
valley_reached = 1
return sptime
#membpotderivs(time,vrec): Given the membrane potentials (vrec) at time points time[0],time[1],...,time[N-1],
#return the derivatives at time points time[1],time[2],...,time[N-3]
def membpotderivs(time,vrec):
N = len(time)
tdiff = [x-y for x,y in zip(time[1:N-1],time[0:N-2])]
vdiff = [x-y for x,y in zip(vrec[1:N-1],vrec[0:N-2])]
mderiv = [x/y for x,y in zip(vdiff,tdiff)]
return [0.5*(x+y) for x,y in zip(mderiv[1:N-2],mderiv[0:N-3])]
#limitcyclescaledv(v1,dv1,v2,dv2): Give the coefficient for memb. pot. derivative that one has to use in order to make
#the difference on the derivative axis as significant as the difference on the memb. pot. axis
def limitcyclescaledv(v1,dv1,v2,dv2):
maxv = max(max(v1),max(v2))
minv = min(min(v1),min(v2))
maxdv = max(max(dv1),max(dv2))
mindv = min(min(dv1),min(dv2))
return 1.0*(maxv-minv)/(maxdv-mindv)
def limitcyclediff(v1,dv1,v2,dv2,dvcoeff=0.1):
N1 = len(v1)
N2 = len(v2)
dv1 = [dvcoeff*x for x in dv1]
dv2 = [dvcoeff*x for x in dv2]
Dmin = N1*[0]
for i in range(0,N1):
Dmin[i] = math.sqrt(min([(x-v1[i])**2+(y-dv1[i])**2 for x,y in zip(v2,dv2)]))
vdiff = [x-y for x,y in zip(v1[1:N1],v1[0:N1-1])]
dvdiff = [x-y for x,y in zip(dv1[1:N1],dv1[0:N1-1])]
h = [math.sqrt(x**2+y**2) for x,y in zip(vdiff,dvdiff)]
#use the trapezoid rule for integration:
Dminmean = [(x+y)/2.0 for x,y in zip(Dmin[1:N1],Dmin[0:N1-1])]
print "hsum="+str(sum(h))
return sum([x*y for x,y in zip(Dminmean,h)])
def interpolate(tref,vref,tint): #Assumes that the trefs come sorted!
vint = len(tint)*[0.0]
addedOne = False
#print tref
#print tint
#if tref[len(tref)-1] == tint[len(tint)-1]:
# tref.append(tref[len(tref)-1]+0.0001)
# vref.append(vref[len(tref)-1])
# addedOne = True
if tref[0] > tint[0] or tref[len(tref)-1] < tint[len(tint)-1]:
print "Extrapolation needed!"
return len(tint)*[-1]
indvrecnow = 0
for j in range(0,len(tint)):
while tref[indvrecnow+1] <= tint[j]:
indvrecnow = indvrecnow + 1
if indvrecnow == len(tref)-1: # It must be the last index if this happens
vint[j:len(tint)] = [vref[indvrecnow]]*(len(tint)-j)
return vint
vint[j] = vref[indvrecnow] + 1.0*(tint[j]-tref[indvrecnow])/(tref[indvrecnow+1]-tref[indvrecnow])*(vref[indvrecnow+1]-vref[indvrecnow])
return vint
def interpolate_extrapolate_constant(tref,vref,tint): #Assumes that the trefs come sorted!
vint = len(tint)*[0.0]
addedOne = False
#print tref
#print tint
#if tref[len(tref)-1] == tint[len(tint)-1]:
# tref.append(tref[len(tref)-1]+0.0001)
# vref.append(vref[len(tref)-1])
# addedOne = True
indvrecnow = 0
for j in range(0,len(tint)):
if tint[j] < tref[0]:
vint[j] = vref[0]
continue
if indvrecnow >= len(tref) - 1:
vint[j] = vref[-1]
while tref[indvrecnow+1] <= tint[j]:
indvrecnow = indvrecnow + 1
if indvrecnow == len(tref)-1: # It must be the last index if this happens
vint[j:len(tint)] = [vref[indvrecnow]]*(len(tint)-j)
return vint
vint[j] = vref[indvrecnow] + 1.0*(tint[j]-tref[indvrecnow])/(tref[indvrecnow+1]-tref[indvrecnow])*(vref[indvrecnow+1]-vref[indvrecnow])
return vint
#kronecker product of list A and list B
def kron(A,B):
C = []
if type(B[0]) is int or type(B[0]) is float:
for i in range(0,len(A)):
for j in range(0,len(B)):
print "asdf"
print B[j]
C.append(A[i]*B[j])
elif type(B[0][0]) is int or type(B[0][0]) is float:
for i in range(0,len(A)):
for j in range(0,len(B)):
C.append([x*A[i] for x in B[j]])
return C
def cumprod(A):
B = len(A)*[0]; B[0]=A[0]
for j in range(1,len(A)):
B[j] = B[j-1]*A[j]
return B
def oscillatorypoissontimeseries(N, minfreq, maxfreq, oscfreq, phase, T, isprinted=0):
a = 0.5*(minfreq + maxfreq)
b = 0.5*(maxfreq - minfreq)
meanT = 1.0/a
omega = 2*pylab.pi*oscfreq
sptime = pylab.zeros([int(0.001*2*T*N/meanT)+100,2],dtype='d')
#sptime = []
Nplaced = 0
for iN in range(0,N):
t = 0
while t < T:
e = pylab.log(1-pylab.rand())
Ttrial = meanT #Ttrial in sec, t and T in msec
# Newton's method:
for iter in range(0,50):
Ttrialold = Ttrial
Ttrial = Ttrial - (e + a*Ttrial - b/omega*(pylab.cos(omega*(0.001*t+Ttrial)+phase)-pylab.cos(omega*0.001*t+phase))) / (a + b*pylab.sin(omega*(0.001*t+Ttrial)+phase))
myerr = abs(e + a*Ttrial - b/omega*(pylab.cos(omega*(0.001*t+Ttrial)+phase)-pylab.cos(omega*0.001*t+phase)))
if Ttrial < 0 or myerr > 0.0001:
Ttrial = meanT
# If Newton's method didn't give good result, try fixed point method: Find T such that -aT+b/omega(pylab.cos(omega*t+phase)-pylab.cos(phase)) = pylab.log(1-x):
for iter in range(0,30000):
Ttrial = (b/omega*(pylab.cos(omega*(0.001*t+Ttrial)+phase)-pylab.cos(omega*0.001*t+phase)) - e)/a
Ttrialold = Ttrial
Ttrial = (b/omega*(pylab.cos(omega*(0.001*t+Ttrial)+phase)-pylab.cos(omega*0.001*t+phase)) - e)/a
if isprinted > 1:
print('iN='+str(iN)+', Err(Ttrial) = '+str(abs(Ttrial-Ttrialold))+', Ttrial = '+str(Ttrial)+', t = '+str(t)+', newPhase='+str(omega*(t/1000+Ttrial)+phase)+', myerr='+str(myerr))
t = t+Ttrial*1000
sptime[Nplaced,:] = [iN,t]
#sptime.append([iN,t])
Nplaced = Nplaced + 1
if isprinted > 0:
print('spikes for iN='+str(iN)+' complete')
sptime = sptime[:Nplaced,:]
if isprinted > 0:
print(str(Nplaced)+' spikes in total, '+str(int(0.001*2*T*N/meanT)+100)+' reserved')
return sptime
def printlistlen(A):
#TODO: recursive method might work out but needs some thought...
#toCheck = A
#lens = [len(x) for x in A]
#levels = [0 for x in A]
#while type(toCheck) is list and len(toCheck) > 0:
# while type(toCheck[0]) is list and len(toCheck[0]) > 0:
# toCheck.append(toCheck[0][0])
# lens.append[len
# toCheck[0].pop(0)
nan = -1
if type(A) is list:
B = copy.deepcopy(A)
listFound0 = False
for i0 in range(0,len(B)):
if type(B[i0]) is list:
listFound0 = True
listFound1 = False
for i1 in range(0,len(B[i0])):
if type(B[i0][i1]) is list:
listFound1 = True
listFound2 = False
for i2 in range(0,len(B[i0][i1])):
if type(B[i0][i1][i2]) is list:
listFound2 = True
listFound3 = False
for i3 in range(0,len(B[i0][i1][i2])):
if type(B[i0][i1][i2][i3]) is list:
listFound3 = True
listFound4 = False
for i4 in range(0,len(B[i0][i1][i2][i3])):
if type(B[i0][i1][i2][i3][i4]) is list:
listFound4 = True
listFound5 = False
for i5 in range(0,len(B[i0][i1][i2][i3][i4])):
if type(B[i0][i1][i2][i3][i4][i5]) is list:
listFound5 = True
listFound6 = False
for i6 in range(0,len(B[i0][i1][i2][i3][i4][i5])):
if type(B[i0][i1][i2][i3][i4][i5][i6]) is list:
listFound6 = True
B[i0][i1][i2][i3][i4][i5][i6] = len(B[i0][i1][i2][i3][i4][i5][i6])
else:
B[i0][i1][i2][i3][i4][i5][i6] = nan
if not listFound6:
B[i0][i1][i2][i3][i4][i5] = len(B[i0][i1][i2][i3][i4][i5])
else:
B[i0][i1][i2][i3][i4][i5] = nan
if not listFound5:
B[i0][i1][i2][i3][i4] = len(B[i0][i1][i2][i3][i4])
else:
B[i0][i1][i2][i3][i4] = nan
if not listFound4:
B[i0][i1][i2][i3] = len(B[i0][i1][i2][i3])
else:
B[i0][i1][i2][i3] = nan
if not listFound3:
B[i0][i1][i2] = len(B[i0][i1][i2])
else:
B[i0][i1][i2] = nan
if not listFound2:
B[i0][i1] = len(B[i0][i1])
else:
B[i0][i1] = nan
if not listFound1:
B[i0] = len(B[i0])
else:
B[i0] = nan
if not listFound0:
B = len(B)
else:
B = nan
print B
def drawarrow(ax,x,y,acoeff=1,prc=0.9,lw=1,lc='#000000'):
d = [x[1]-x[0], y[1]-y[0]];
k = pylab.sqrt(d[0]**2 + d[1]**2)
d = d/k
dperp = [acoeff*z for z in [-d[1], d[0]]];
lens = k-k*(1-prc);
perplen = 0.5*k*(1-prc);
px = [x[0],x[1],x[0]+lens*d[0]+perplen*dperp[0],x[0]+lens*d[0]-perplen*dperp[0]];
py = [y[0],y[1],y[0]+lens*d[1]+perplen*dperp[1],y[0]+lens*d[1]-perplen*dperp[1]];
px = [px[0],px[1],px[2],px[1],px[3]]
py = [py[0],py[1],py[2],py[1],py[3]]
#px = reshape([px(:,[1 2 3 2 4]) nan(size(x,1),1)]',size(x,1)*6,1);
#py = reshape([py(:,[1 2 3 2 4]) nan(size(x,1),1)]',size(x,1)*6,1);
ax.plot(px,py,'k-',linewidth=lw,color=lc)
def timeseriesmean(times,x):
return 1.0*sum([(t2-t1)*(x1+x2)/2 for t1,t2,x1,x2 in zip(times[0:-1],times[1:],x[0:-1],x[1:])])/(times[-1]-times[0])
def timeseriessecondmoment(times,x):
return 1.0*sum([(t2-t1)*(x1**2+x2**2)/2 for t1,t2,x1,x2 in zip(times[0:-1],times[1:],x[0:-1],x[1:])])
def timeseriesstd(times,x,xmean=pylab.nan):
if pylab.isnan(xmean):
xmean = timeseriesmean(times,x)
return pylab.sqrt(1.0*sum([(t2-t1)*((x1-xmean)**2+(x2-xmean)**2)/2 for t1,t2,x1,x2 in zip(times[0:-1],times[1:],x[0:-1],x[1:])])/(times[-1]-times[0]))
def drawdiscontinuity(ax,y,yoffset,x=0,xoffset=0.1,lw=2.0,lw2=1.0):
thisline = ax.plot([x-xoffset,x+xoffset],[y-yoffset,y],'k-',linewidth=lw2)
thisline[0].set_clip_on(False)
thisline = ax.plot([x-xoffset,x+xoffset],[y,y+yoffset],'k-',linewidth=lw2)
thisline[0].set_clip_on(False)
thisline = ax.plot([x-xoffset,x+xoffset],[y-0.5*yoffset,y+0.5*yoffset],'k-',color='#FFFFFF',zorder=100,linewidth=lw)
thisline[0].set_clip_on(False)
def firingratecurve(spikes,T=[],dt=1.0,gauss_std=5.0):
if type(spikes) is list:
spikes = pylab.array(spikes)
if type(T) is list and len(T) == 0:
T = max(spikes[0,:])
FRs = pylab.zeros([int(T/dt),1])
FRts = [dt*(i+0.5) for i in range(0,len(FRs))]
for iFRt in range(0,len(FRs)):
FRs[iFRt] = sum(pylab.exp(-1/2*(FRts[iFRt]-spikes[0,:])**2/gauss_std**2))
return [FRs,FRts]
#From Pylab:
def find(condition):
"Return the indices where ravel(condition) is true"
res, = numpy.nonzero(numpy.ravel(condition))
return res
import math
#From ../colorsredtolila.py
def colorsredtolila(N):
C = colorsredtolilaint(N)
hexlist = []
for j in range(0,N):
myhex = '#'
for k in range(0,3):
if C[j][k] < 16:
myhex = myhex + '0' + hex(C[j][k])[2]
else:
myhex = myhex + hex(C[j][k])[2:4]
hexlist.append(myhex)
return hexlist
def colorsredtolilaint(N):
linchange = [1.0/(N-1)*x for x in range(0,N)]
linchange_x = [x/0.8 for x in [0.0, 0.36, 0.45, 0.65, 0.7, 0.8]]
linchange_y = [0.0, 0.29, 0.46, 0.65, 0.75, 0.83]
for i in range(0,len(linchange)):
ind = N
for j in range(0,len(linchange_x)):
if linchange[i] >= linchange_x[j]:
ind = j
if ind < len(linchange_x)-1:
linchange[i] = linchange_y[ind]+(linchange_y[ind+1]-linchange_y[ind])*(linchange[i]-linchange_x[ind])/(linchange_x[ind+1]-linchange_x[ind])
C = hsv2rgblist([int(255*x) for x in linchange],[1.0]*N,[1.0]*N);
return C
def hsv2rgblist(h, s, v):
hs = []
ss = []
vs = []
for i in range(0,len(h)):
h1, s1, v1 = hsv2rgb(h[i],s[i],v[i])
hs.append(h1)
ss.append(s1)
vs.append(v1)
return zip(hs,ss,vs)
def hsv2rgb(h, s, v):
h = float(h)
s = float(s)
v = float(v)
h60 = h / 60.0
h60f = math.floor(h60)
hi = int(h60f) % 6
f = h60 - h60f
p = v * (1 - s)
q = v * (1 - f * s)
t = v * (1 - (1 - f) * s)
r, g, b = 0, 0, 0
if hi == 0: r, g, b = v, t, p
elif hi == 1: r, g, b = q, v, p
elif hi == 2: r, g, b = p, v, t
elif hi == 3: r, g, b = p, q, v
elif hi == 4: r, g, b = t, p, v
elif hi == 5: r, g, b = v, p, q
r, g, b = int(r * 255), int(g * 255), int(b * 255)
return r, g, b
def rgb2hsv(r, g, b):
r, g, b = r/255.0, g/255.0, b/255.0
mx = max(r, g, b)
mn = min(r, g, b)
df = mx-mn
if mx == mn:
h = 0
elif mx == r:
h = (60 * ((g-b)/df) + 360) % 360
elif mx == g:
h = (60 * ((b-r)/df) + 120) % 360
elif mx == b:
h = (60 * ((r-g)/df) + 240) % 360
if mx == 0:
s = 0
else:
s = df/mx
v = mx
return h, s, v
