def plotprot(i, varnames, limits, L):
"""Plot one protocol."""
from pylab import figure, subplot, plot, savefig, legend, axis
figure()
proto0, _ = L[0]
isclamped = len(proto0[0]) == 2
for j, (n, lim) in enumerate(zip(varnames, limits)):
subplot(len(varnames), 1, j + 1)
leg = set()
for k in n.split():
if isclamped: # clamp protocol
# For each protocol, traj is a list with a Trajectory
# for each pulse.
for _proto, traj in L:
t, y, _dy, a = catrec(*traj[1:])
plot(t, y[k] if k in y.dtype.names else a[k], label=k if (k not in leg) else None)
leg.add(k)
else: # pacing protocol
# For each protocol, paces is a list of Pace
for _proto, paces in L:
t, y, _dy, a, _stats = catrec(*paces)
plot(t, y[k] if k in y.dtype.names else a[k], label=k if (k not in leg) else None)
leg.add(k)
legend()
if lim:
axis(lim)
savefig("fig%s%s.png" % (i, b.name))
def pacing_output():
# Prepacing
for _t, _y, _stats in cell.aps(n=nprepace):
pass
# A few paces
t, y, _stats = catrec(*cell.aps(n=npace), globalize_time=False)
dy, a = cell.rates_and_algebraic(t, y)
return t, y, dy, a
def exp_vargap(L=L):
h = []
for proto, traj in L:
t, y, _dy, _a = catrec(*traj)
h.extend(plot(t, y["V"], **lineplotopt))
setp(h, color="gray")
hi = h[len(h) // 2]
setp(hi, color="black", zorder=10)
title("Variable-gap clamping")
ylabel("Voltage")
tweak()
xmin = proto[0][0] - 300
xmax = getp(hi, "xdata")[-1]
# from IPython.core.debugger import Tracer; Tracer()()
xlim(xmin, xmax)
def exp_p1p2(L=L):
h = []
for proto, traj in L:
t, y, dy, a = catrec(*traj)
h.extend(plot(t, y["V"], **lineplotopt))
setp(h, color="gray")
hi = h[len(h) // 2]
setp(hi, color="black", zorder=10)
# from IPython.core.debugger import Tracer; Tracer()()
title("Double-pulse clamping")
ylabel("Voltage")
tweak()
xmin = proto[0][0] - 300
xmax = t[-1]
xlim(xmin, xmax)
def cycle(self, index=0, tmax=None, tol=1e-4, n=None):
"""
Find limit cycle (integrate until successive extrema are almost equal).
:param str_or_int index: Index of state variable to base search on.
:param float tmax: Time limit for aborting search for limit cycle.
:param float tol: Tolerance for weighted root-mean-square norm of
change in state vector between successive extrema.
:param int n: Keep history of up to n extrema while searching for
limit cycle.
.. plot::
:include-source:
>>> from matplotlib import pyplot as plt
>>> from cgp.cvodeint.namedcvodeint import Namedcvodeint
>>> from cgp.utils.unstruct import unstruct
>>> from cgp.phenotyping.attractor import AttractorMixin
>>> class Test(Namedcvodeint, AttractorMixin):
... '''Inherits van der Pol equations as default example.'''
... pass
>>> test = Test(t=[0, 10000])
>>> t, y, period = test.cycle()
>>> period
6.663...
>>> h = plt.plot(t, unstruct(y), '-')
"""
if tmax is None:
tmax = self.t[-1]
extrema = deque([self.next_extremum(tmax, index)], maxlen=n)
while True:
t, y, (te, ye) = tup = self.next_extremum(tmax, index)
extrema.appendleft(tup)
# pylint:disable=W0612,C0301
for lag, (t_, y_, (te_, ye_)) in enumerate(extrema): #@UnusedVariable
if lag == 0:
continue
diff = unstruct(ye_) - unstruct(ye)
if self.weighted_rms(diff) < tol:
L = reversed(list(extrema)[:lag])
t, y, _ = catrec(*L, globalize_time=False)
period = te - te_
return t, y.squeeze(), period
tweak()
xlim(pacelim)
def vis_ct(t=t, y=y):
plot(t, y["Cai"], **lineplotopt)
title("Calcium transient")
ylabel("[Ca]")
tweak()
xlim(pacelim)
### Double-pulse protocol
L = vecvclamp(p1p2.protocol)
proto, traj = L[3]
t, y, dy, a = catrec(*traj)
def exp_p1p2(L=L):
h = []
for proto, traj in L:
t, y, _dy, _a = catrec(*traj)
h.extend(plot(t, y["V"], **lineplotopt))
setp(h, color="gray")
hi = h[len(h) // 2]
setp(hi, color="black", zorder=10)
# from IPython.core.debugger import Tracer; Tracer()()
title("Double-pulse clamping")
ylabel("Voltage")
tweak()
xmin = proto[0][0] - 300