def test_vargap():
"""Test fast vs slow variable-gap protocol."""
from cgp.virtexp.elphys.examples import Bond
b = Bond()
protocol = [(100, -80), (50, 0), (np.arange(2, 78, 15), (-90, -80, -70)), (100, 0)]
p1, gap, p2 = b.vargap(protocol) # 4 s
np.testing.assert_equal([len(i) for i in p1, gap, p2], [1, 3, 18])
L = b.vecvclamp(protocol) # 9 s
np.testing.assert_equal([len(i) for i in zip(*[traj for _proto, traj in L])], [18, 18, 18, 18])
def test_bond_protocols(plot=False):
"""Run all Bondarenko protocols."""
from cgp.virtexp.elphys.examples import Bond
b = Bond(chunksize=10000)
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))
bp = b.bond_protocols()
for i, (varnames, protocol, limits, _url) in bp.items():
if len(protocol[0]) == 2: # (duration, voltage), so clamping
# List of (proto, traj), where traj is list of Trajectory
L = b.vecvclamp(protocol)
else: # (n, period, duration, amplitude), so pacing
# List of (proto, paces), where paces is list of Pace
L = b.vecpace(protocol)
if plot:
plotprot(i, varnames, limits, L)
def test_mmfits():
"""
Michaelis-Menten fit of peak i_CaL current vs gap duration.
This uses a reduced version of the variable-gap protocol of Bondarenko's
figure 7. The full version is available as b.bond_protocols()[7].protocol.
"""
from cgp.virtexp.elphys.examples import Bond
b = Bond()
protocol = (1000, -80), (250, 0), (np.linspace(2, 202, 5), -80), (100, 0)
with b.autorestore():
L = b.vecvclamp(protocol)
np.testing.assert_allclose(mmfits(L, k="i_CaL"), (6.44, 18.14), rtol=1e-3)
# Verify improvement of error message in case k is list rather than string.
try:
mmfits(L, 2, ["i_Na"])
except AssertionError, exc:
msg = "k must be a single field name of y or a, not <type 'list'>"
assert msg in str(exc)
# pylint:disable=W0621,C0111,W0102,W0631,C0301
import numpy as np
from matplotlib import pyplot as plt
from matplotlib.pyplot import (plot, ylabel, title,
tick_params, xlim, axis, box, setp, getp)
import os
from joblib import Memory
from cgp.virtexp.elphys.examples import Bond
from cgp.virtexp.elphys.clampable import catrec, markovplot, listify
from cgp.virtexp.elphys.clampable import Bond_protocol
from cgp.utils.splom import spij
### Options, model and protocols
cell = Bond()
protocols = cell.bond_protocols()
# Pacing parameters
nprepace = 10
npace = 4
# P1-P2 double-pulse protocol to study voltage-dependence of ion channel
varnames, protocol, limits, url = listify(protocols[3])
protocol[1][1] = protocol[1][1][::3]
p1p2 = Bond_protocol(varnames, protocol, limits, url)
# Variable-gap protocol to study the rate of recovery from inactivation
varnames, protocol, limits, url = listify(protocols[7])
protocol[2][0] = protocol[2][0][6::3] # don't need so many gap lengths
protocol[2][1] = protocol[2][1][1] # don't vary gap voltage
protocol[3][0] = 300 # make shortest run last until the longest gap is done
vargap = Bond_protocol(varnames, protocol, limits, url)
