def __init__(self, n, seed, modelses, datagenhoc):
self.n = n
h.load_file(modelses)
mrflist = h.List("MulRunFitter")
mrf = mrflist.o(int(mrflist.count()) - 1)
self.N = mrf.p.pf.generatorlist.o(0).gen.po
h('objref nb')
h.nb = mrf.p.pf.generatorlist.o(0).gen.po
cvodewrap.fs.panel()
self.trueParm = self.N.getParm()
self.modelses = modelses
self.seed = seed
if n == 0:
G = noisegen.Gen(self.N)
G.reseed(seed)
self.seed = seed
self.Data = G.datasim()
else:
h.load_file(datagenhoc)
tvec = h.Vector(self.N.Eve.collectionTimes)
vec = h.ch3ssdata(n, seed, tvec, self.trueParm,
self.N.rf.fitnesslist.o(0))
self.Data = []
for i in range(len(vec)):
self.Data.append(numpy.matrix(vec[i]))
if fitglobals.verbose: h.topology()
ss = h.Vector()
cvodewrap.states(ss)
if fitglobals.verbose: ss.printf()
self.N.overwrite(self.Data)
self.H = numpy.matrix(self.Hessian())
def paramPanel(self):
self.box = h.VBox()
self.box.intercept(1)
h.xpanel('')
h.xlabel('Likelihood numerical parameters')
h.xlabel(' Measurement noise')
c = self.Eve.Obs.C
for o in c:
h.xvalue('sigma: ' + o.hpt.s(), (o, 'sigma'), 1)
h.xlabel(' Process noise')
h.xvalue('Injection interval', (self, 'inj_invl'), 1,
self.inj_invl_changed)
s = h.Vector()
cvodewrap.states(s)
sref = h.ref('')
for i in range(len(s)):
cvodewrap.statename(i, sref, 1)
h.xvalue('Diffusion Coeff[%d,%d]: ' % (i, i) + sref[0],
(self.processNoise[i], 'x'), 1, (self.fillPB, i))
h.xcheckbox('Fox & Lu Diffusion (for Hodgkin-Huxley)?', (self, 'hhB'),
self.hhBButton)
h.xvalue(' Fox & Lu: Number Na Channels', (self, 'nNa'), 1,
self.hhBButton)
h.xvalue(' Fox & Lu: Number K Channels', (self, 'nK'), 1,
self.hhBButton)
h.xlabel(' Initial Uncertainty')
for i in range(len(s)):
print i
cvodewrap.statename(i, sref, 1)
h.xvalue('Initial Stand Dev[%d]: ' % i + sref[0],
(self.Sdiag[i], 'x'), 1, (self.fillS, i))
h.xbutton('Show state funnels', self.show_state_funnels)
h.xpanel()
self.box.intercept(0)
self.box.map('Likelihood parameters')
def measJac():
x = h.Vector()
cvodewrap.states(x)
return [
numpy.matrix(x.x[0]),
numpy.matrix([1, 0, 0, 0]),
numpy.matrix(sigm)
]
def flow(self, x0, t1, x1):
self.ss.restore(1)
cvodewrap.yscatter(x0)
cvodewrap.re_init()
h.initPlot()
h.continuerun(t1) # or cvodewrap.solve(t1)
cvodewrap.states(x1)
return x1
def inc_nsums(self):
self.nsums += 1
s = h.Vector()
cvodewrap.states(s)
nstates = len(s)
new = []
for i in range(nstates):
new.append(xstruct())
self.sumto1.append(new)
print 'nsums', self.nsums
print 'sumto1', self.sumto1
def mean(self, time, state): # the observable (under zero noise, ie mean)
ss = h.Vector() #save
cvodewrap.states(ss)
ds = h.Vector()
cvodewrap.f(time, h.Vector(state), ds)
#measurement goes here
x = self.hpt.val
# print 'ss[3]', ss[3]
# print 'x', x
cvodewrap.yscatter(ss) #restore
return x
def noiseJac(self, injectionTimes):
inject0 = injectionTimes[0]
tFinal = injectionTimes[-1]
if self.hhB:
cvodewrap.states(self.states)
h.rates_hh(self.states[0])
alpha_m = h.mtau_hh * h.minf_hh
beta_m = h.mtau_hh * (1.0 - h.minf_hh)
alpha_h = h.htau_hh * h.hinf_hh
beta_h = h.htau_hh * (1.0 - h.hinf_hh)
alpha_n = h.ntau_hh * h.ninf_hh
beta_n = h.ntau_hh * (1.0 - h.ninf_hh)
state_m = copy.deepcopy(self.states[1])
state_h = copy.deepcopy(self.states[2])
state_n = copy.deepcopy(self.states[3])
#if state_m < 0.0:
# state_m = 0.0
#if state_h < 0.0:
# state_h = 0.0
#if state_n < 0.0:
# state_n = 0.0
#if state_m > 1.0:
# state_m = 1.0
#if state_h > 1.0:
# state_h = 1.0
#if state_n > 1.0:
# state_n = 1.0
print 'alpha_h', alpha_h, 'beta_h', beta_h, 'state_h', state_h, 'nNa', self.nNa
self.B[0, 0] = 0.0
self.B[1, 1] = math.sqrt(
(alpha_m * (1.0 - state_m) + beta_m * state_m) / self.nNa)
print 'Inside Sqrt', ((alpha_h *
(1.0 - state_h) + beta_h * state_h) /
self.nNa)
self.B[2, 2] = math.sqrt(
(alpha_h * (1.0 - state_h) + beta_h * state_h) / self.nNa)
self.B[3, 3] = math.sqrt(
(alpha_n * (1.0 - state_n) + beta_n * state_n) / self.nK)
return self.scale * self.B * math.sqrt(tFinal - inject0)
else:
assert (tFinal - inject0 >= 0.0)
assert (not numpy.isnan(self.scale))
R = self.scale * self.B * math.sqrt(tFinal - inject0)
assert (not numpy.isnan(R).any())
return R
def sim(self):
tMax = self.gettMax()
tData = 0
tNoise = 0
h.stdinit()
x = h.Vector()
Data = []
while tData < tMax:
noiseTimes = []
tData += self.Mdt
if tData > tMax:
tData = tMax
while tNoise < min(tMax,tData):
tNoise += self.Ndt
noiseTimes.append(tNoise)
if tNoise > tMax:
tNoise = tMax
h.continuerun(tNoise)
cvodewrap.states(x)
x.x[0] += self.sp*(self.evalW(tNoise) - self.evalW(tNoise-self.Ndt))
cvodewrap.yscatter(x)
cvodewrap.re_init()
Data.append([noiseTimes, x.x[0] + self.sm*self.evalM(tData)])
return Data
def constraintsPanel(self):
self.box = h.HBox()
self.box.intercept(1)
self.box.ref(self)
s = h.Vector()
cvodewrap.states(s)
nstates = len(s)
sref = h.ref('')
h.xpanel("")
h.xlabel('0<=')
for i in range(nstates):
h.xcheckbox('', (self.geq0[i], 'x'), self.constraintsButton)
h.xpanel()
h.xpanel("")
h.xlabel('>=1')
for i in range(nstates):
cvodewrap.statename(i, sref, 1)
h.xcheckbox(sref[0], (self.leq1[i], 'x'), self.constraintsButton)
h.xpanel()
for j in range(self.nsums):
h.xpanel("")
h.xlabel("S%d" % j)
for i in range(nstates):
h.xcheckbox('', (self.sumto1[j][i], 'x'),
self.constraintsButton)
h.xpanel()
h.xpanel("")
h.xbutton("Add Sum-to-1", self.constraintsButton)
h.xbutton("Remove Empty", self.constraintsButton)
h.xbutton("Close", self.constraintsButton)
h.xlabel('QP Solver:')
h.xstatebutton('cvxopt', (self, 'cvxopt_sel'), self.constraintsButton)
h.xstatebutton('custom', (self, 'custom_sel'), self.constraintsButton)
h.xpanel()
self.box.intercept(0)
self.box.map("Constraints")
def printSomeInfo():
if fitglobals.verbose: h.topology()
ss = h.Vector()
cvodewrap.states(ss)
if fitglobals.verbose: ss.printf()
def flowJac(noiseTimes):
cvodewrap.states(x)
t0 = h.t
print 't0'
print t0
ss = [None] * (len(noiseTimes) + 1)
k = 0
ss[0] = h.SaveState()
ss[0].save()
cvodewrap.re_init()
while k < len(noiseTimes):
print noiseTimes[k]
h.continuerun(noiseTimes[k])
ss[k + 1] = h.SaveState()
ss[k + 1].save()
cvodewrap.re_init()
k += 1
cvodewrap.states(value)
# Derivative with respect to state
DFx = pylab.zeros((len(value), len(x)))
k = 0
while k < len(x):
ss[0].restore(1)
cvodewrap.re_init()
cvodewrap.states(x)
temp = x[k]
if abs(temp) > 1:
dx = sqrtEps * abs(temp)
else:
dx = sqrtEps
x.x[k] = temp + dx
cvodewrap.yscatter(x)
cvodewrap.re_init()
dx = x[k] - temp # trick to reduce finite precision error
h.continuerun(noiseTimes[len(noiseTimes) - 1])
cvodewrap.states(df)
df.sub(value)
df.div(dx)
DFx[:, k] = numpy.array(df)
k += 1
# Derivative with respect to noise
DFn = pylab.zeros((len(value), len(noiseTimes)))
noiseTimes.insert(0, t0)
k = 0
while k < len(noiseTimes) - 1:
ss[k + 1].restore(1)
cvodewrap.re_init()
if k < len(noiseTimes) - 2:
dx = sqrtEps
cvodewrap.states(x)
x.x[0] += sigp * math.sqrt(noiseTimes[k + 1] - noiseTimes[k]) * dx
cvodewrap.yscatter(x)
cvodewrap.re_init()
h.continuerun(noiseTimes[len(noiseTimes) - 1])
cvodewrap.states(df)
df.sub(value)
df.div(dx)
DFn[:, k] = numpy.array(df)
else:
DFn[:, k] = numpy.array(
[sigp * math.sqrt(noiseTimes[k + 1] - noiseTimes[k]), 0, 0, 0])
k += 1
return [numpy.matrix(value).T, numpy.matrix(DFx), numpy.matrix(DFn)]
class Flow(object):
def __init__(self):
self.ss = h.SaveState()
self.ss.save()
self.t0 = h.t
def flow(self, x0, t1, x1):
self.ss.restore(1)
cvodewrap.yscatter(x0)
cvodewrap.re_init()
h.initPlot()
h.continuerun(t1) # or cvodewrap.solve(t1)
cvodewrap.states(x1)
return x1
if __name__ == '__main__':
h.load_file('hh.ses')
h.Graph[0].exec_menu('Keep Lines')
h.stdinit()
h.continuerun(1.5)
flow = Flow()
x = h.Vector()
x1 = h.Vector()
cvodewrap.states(x)
for i in range(5):
print i, x
x.x[0] += 5
flow.flow(x, h.tstop, x1)
def __init__(self, ho):
#h.mulfit_after_quad_pycallback = self.after_quad
pc = h.ParallelContext()
nhost = int(pc.nhost_bbs())
if nhost > 1:
fitglobals.verbose = 0
self.xlvec = h.Vector()
self.ylvec = h.Vector()
self.g = None
self.rf = ho
ol = []
vl = self.rf.yvarlist
fl = self.rf.fitnesslist
tlast = 0
self.n_chdat = 0
for i in range(len(vl)):
self.n_chdat += fl.o(i).n_chdat
tl = list(fl.o(i).xdat_)
o = obs.NeuronObservable(vl.o(i), tl)
o.sigma = 0.01
ol.append(o)
if (tlast < tl[-1]):
tlast = tl[-1]
s = h.Vector()
cvodewrap.active(1)
cvodewrap.states(s)
assert (len(s) > 0)
assert (len(vl) > 0)
self.covGrowthTime = 100
self.varTerm = 1
self.processNoise = []
self.Sdiag = []
Sto = sto.StochasticModel(len(s), tlast)
for i in range(len(s)):
self.Sdiag.append(WrappedVal(Sto.InitialCovSqrt[i, i]))
for i in range(len(s)):
self.processNoise.append(WrappedVal(Sto.B[i, i]))
Obs = obs.ObservationModel(ol)
self.Eve = eve.EventTable(Sto, Obs)
self.hhB = self.Eve.Sto.hhB
self.nNa = self.Eve.Sto.nNa
self.nK = self.Eve.Sto.nK
self.Sys = detsys.NeuronModel()
self.inj_invl = 1.0
self.Eve.newInjectionInterval(self.inj_invl)
# self.inj_invl_changed(Sys, P.tstop)
# self.M = models.Model(Sys, Obs, P)
self.Data = self.__data(fl, self.Eve)
self.pf = self.getParmFitness()
self.pf.verbose = fitglobals.verbose
self.dlikedt = h.Vector()
self.likefailed = False
#CONSTRAINTS GUI INIT
s = h.Vector()
cvodewrap.states(s)
nstates = len(s)
self.geq0 = []
self.leq1 = []
self.sumto1 = []
self.cvxopt_sel = True
self.custom_sel = True
self.nsums = 2
for j in range(self.nsums):
self.sumto1.append([])
for i in range(nstates):
self.geq0.append(xstruct())
self.leq1.append(xstruct())
for j in range(self.nsums):
self.sumto1[j].append(xstruct())
EKF.constraintsOn(self.geq0, self.leq1, self.sumto1)