def forwardTest():
spikeTimes = spt = [26, 50, 84, 128, 199, 247, 355]
P = setupSimData(spt = spikeTimes )
S = smc.forward(P.V, P)
pylab.figure()
pylab.plot(P.V.F)
pylab.title('Simulated Fluorescence')
cbar = numpy.zeros(P.V.T)
nbar = numpy.zeros(P.V.T)
for t in xrange(P.V.T):
for i in xrange(P.V.Nparticles):
weight = S.w_f[i,t]
cbar[t] += weight * S.C[i,t]
nbar[t] += weight * S.n[i,t]
#cbar /= P.V.Nparticles
#nbar /= P.V.Nparticles
pylab.figure()
pylab.hold(True)
pylab.title('expected Ca vs arbitrary particles')
pylab.plot(S.C[3,:], label='particle 3')
pylab.plot(S.C[10,:], label='particle 10')
pylab.plot(S.C[20,:], label='particle 20')
pylab.plot(cbar, label='E[C]')
pylab.plot(spikeTimes, 6+numpy.ones(len(spikeTimes)), 'k.', label='simulated spike times')
pylab.legend()
#print(nbar.shape)
pylab.figure()
pylab.hold(True)
pylab.plot(nbar, label='expected spikes')
pylab.plot(spikeTimes, 0.5*numpy.ones(len(spikeTimes)), 'k.', label='simulated spike times')
pylab.legend()
pylab.title('spike detection')
#pylab.figure()
pylab.matshow(S.w_f)
pylab.title('min s.w_f %f , max s.w_f: %f'%(numpy.min(S.w_f), numpy.max(S.w_f)))
pylab.figure()
pylab.hold(True)
pylab.plot(S.w_f[3,:], label='particle 3')
pylab.plot(S.w_f[10,:], label='particle 10')
pylab.plot(S.w_f[20,:], label='particle 20')
pylab.legend()
pylab.title('individual particle weights')
pylab.show()
def paramWalkHelper(spikeTimes, P):
S = smc.forward(P.V, P)
trueSpikes = numpy.zeros(P.V.T,dtype=bool)
trueSpikes[spikeTimes] = True
posterior = 0.0
positivePosterior = 0.0
spikeCount = 0
for t in xrange(P.V.T):
nbar = 0.0
for i in xrange(P.V.Nparticles):
nbar += S.w_f[i,t] * S.n[i,t]
if(trueSpikes[t]):
positivePosterior += nbar
posterior += nbar
spikeCount += 1
else:
posterior += (1-nbar)
print('posterior: %f post/V.T: %f'%(posterior, posterior/P.V.T))
return positivePosterior/spikeCount#posterior/P.V.T
