def main(argv):
i0 = 40.0
nMin = -0.1
nMax = 0.7
iPulseStrength = 0.0
resultsFilenamePattern = 'results/integrationINapIKFig4-yyPulseStrength%d.npz'
phaseFigFilename = 'figures/fig4-yyPhaseSpace.eps'
voltageFigFilename = 'figures/fig4-yyVoltage.eps'
plt.figure()
plotLowThresholdINapIKVectorField(I=i0, nMin=nMin, nMax=nMax)
resultsFilename = resultsFilenamePattern % iPulseStrength
results = np.load(resultsFilename)
ys = results["ys"]
plt.plot(ys[0, :], ys[1, :], label="p=%d"%iPulseStrength)
plt.grid()
plt.legend()
plt.xlabel('Voltage (mv)')
plt.ylabel('K activation variable, n')
plt.savefig(phaseFigFilename)
times = results["times"]
plt.figure()
plt.plot(times, ys[0, :], label="p=%d"%iPulseStrength)
results.close()
plt.grid()
plt.legend()
plt.xlabel('Time (secs)')
plt.ylabel('Voltage (mv)')
plt.savefig(voltageFigFilename)
pdb.set_trace()
def main(argv):
phaseFigFilename = 'figures/fig4-4bPhaseSpace.eps'
voltageFigFilename = 'figures/fig4-4bVoltage.eps'
resultsFilenamePattern = 'results/integrationINapIKStepsize%d.npz'
i0 = 40
resultsFilename = resultsFilenamePattern % i0
results = np.load(resultsFilename)
plt.figure()
plotLowThresholdINapIKVectorField()
plt.plot(results['ys'][0, :], results['ys'][1, :], label="%d" % i0)
plt.grid()
plt.legend()
plt.xlabel('Voltage (mv)')
plt.ylabel('K activation variable, n')
plt.savefig(phaseFigFilename)
plt.figure()
plt.plot(results['times'], results['ys'][0, :], label="%d" % i0)
plt.grid()
plt.legend()
plt.xlabel('Time (secs)')
plt.ylabel('Voltage (mv)')
plt.savefig(voltageFigFilename)
pdb.set_trace()
def main(argv):
i0 = 35
numberOfPhaseMarks = 8
annotationGap = 0.02
initialTransientLength = 10
resultsFilename = 'results/integrationINapIKFig10_1_INapIKLowThreshold.npz'
aFigFilename = 'figures/fig10_1b_INapIKLowThreshold.eps'
results = np.load(resultsFilename)
times = results['times']
ys = results['ys']
transientIndices = np.nonzero(times < initialTransientLength)[0]
pdb.set_trace()
times = np.delete(arr=times, obj=transientIndices)
ys = np.delete(arr=ys, obj=transientIndices, axis=1)
spikeIndices = getPeakIndices(v=ys[0, :])
spikeTimes = times[spikeIndices]
times = np.delete(times, np.arange(0, spikeIndices[0]))
times = times - times[0]
ys = np.delete(ys, np.arange(0, spikeIndices[0]), axis=1)
spikeIndices = spikeIndices - spikeIndices[0]
spikeTimes = spikeTimes - spikeTimes[0]
period = spikeTimes[1] - spikeTimes[0]
phases = times % period
phasesToPlot = np.arange(0, period, period / numberOfPhaseMarks)
indicesBtwFirstAndSecondSpike = np.arange(0, spikeIndices[1])
phasesToSearch = phases[indicesBtwFirstAndSecondSpike]
indicesPhasesToPlot = np.empty(len(phasesToPlot), dtype=np.int64)
for i in xrange(len(phasesToPlot)):
phaseToPlot = phasesToPlot[i]
indicesPhasesToPlot[i] = np.argmin(np.abs(phasesToSearch -
phaseToPlot))
plt.figure()
plotLowThresholdINapIKVectorField(i=i0)
plt.plot(ys[0, :], ys[1, :], label="limit cycle attractor")
plt.plot(ys[0, indicesPhasesToPlot], ys[1, indicesPhasesToPlot], 'ro')
plt.annotate("0,T",
xy=ys[:, 0],
xytext=ys[:, indicesPhasesToPlot[0]] + annotationGap,
color="red",
size=14)
for i in xrange(1, len(indicesPhasesToPlot)):
plt.annotate("%d/%dT" % (i, numberOfPhaseMarks),
xy=ys[:, indicesPhasesToPlot[i]],
xytext=ys[:, indicesPhasesToPlot[i]] + annotationGap,
color="red",
size=14)
plt.grid()
plt.legend(loc="upper left")
plt.xlabel('Voltage (mv)')
plt.ylabel('K activation variable, n')
plt.ylim((-0.1, 0.8))
plt.savefig(aFigFilename)
plt.show()
pdb.set_trace()
def main(argv):
# iPulseStrengths = (1000000, 1200000, 1210000, 1220000, 1230000, 1250000, 1400000)
iPulseStrengths = (1000000, 1220000, 1400000)
resultsFilenamePattern = 'results/integrationINapIKIPulseStrength%d.npz'
phaseFigFilename = 'figures/fig4-7PhaseSpace.eps'
voltageFigFilename = 'figures/fig4-7Voltage.eps'
plt.figure()
plotLowThresholdINapIKVectorField()
'''
plotINapIKVectorField(I=0.0, C=1.0, EL=-78, gL=8, gNa=20, gK=10,
VoneHalf_m=-20, k_m=15,
VoneHalf_n=-45, k_n=5, tauV=1, ENa=60,
EK=-90, nDotScaleFactor=200,
vMin=-90.0, vMax=20.0, nVs=19, nVsDense=100,
nMin=0.0, nMax=0.7, nNs=18,
vNullclineLabel="v nullcline",
nNullclineLabel="n nullcline")a
'''
for iPulseStrength in iPulseStrengths:
resultsFilename = resultsFilenamePattern % iPulseStrength
results = np.load(resultsFilename)
plt.plot(results['ys'][0, :],
results['ys'][1, :],
label="p=%d" % iPulseStrength)
results.close()
plt.grid()
plt.legend()
plt.xlabel('Voltage (mv)')
plt.ylabel('K activation variable, n')
plt.savefig(phaseFigFilename)
plt.figure()
for iPulseStrength in iPulseStrengths:
resultsFilename = resultsFilenamePattern % iPulseStrength
results = np.load(resultsFilename)
plt.plot(results['times'],
results['ys'][0, :],
label="p=%d" % iPulseStrength)
results.close()
plt.grid()
plt.legend()
plt.xlabel('Time (secs)')
plt.ylabel('Voltage (mv)')
plt.savefig(voltageFigFilename)
pdb.set_trace()
def main(argv):
integrationFilename = 'results/integrationINapIKFig10_10_INapIKLowThreshold_aboveUnstable.npz'
figFilename = 'figures/fig10_10b_INapIKLowThreshold_aboveUnstable.eps'
nPhases = 6
ylim = (-.1, .7)
fontsize = 20
integrationRes = np.load(integrationFilename)
plt.plot(integrationRes["ysDCTrainPulses"][0, :],
integrationRes["ysDCTrainPulses"][1, :],
label="train pulses")
plt.plot(integrationRes["ysDC"][0, :],
integrationRes["ysDC"][1, :],
label="DC")
plotLowThresholdINapIKVectorField(i=integrationRes["i0"])
plt.xlabel("Membrane Potential (V)")
plt.ylabel('K activation variable, n')
plt.ylim(ylim)
spikeIndices = getPeakIndices(v=integrationRes["ysDCTrainPulses"][0, :])
spikeTimes = integrationRes["timesDCTrainPulses"][spikeIndices]
pulseTimes = np.arange(start=integrationRes["tPulse"],
stop=spikeTimes[-1],
step=integrationRes["Ts"])
pulseIndices = np.empty(pulseTimes.shape)
for i in range(len(pulseIndices)):
pulseIndices[i] = np.argmin(
np.abs(pulseTimes[i] - integrationRes["timesDCTrainPulses"]))
for i in range(len(pulseIndices)):
annotation = r"$\theta_{%d}$" % (i + 1)
plt.annotate(annotation,
xy=(integrationRes["ysDCTrainPulses"][0, pulseIndices[i]],
integrationRes["ysDCTrainPulses"][1,
pulseIndices[i]]),
fontsize=fontsize)
plt.savefig(figFilename)
plt.show()
pdb.set_trace()
def main(argv):
phaseFigFilename = 'figures/fig4-10PhaseSpace.eps'
voltageFigFilename = 'figures/fig4-10Voltage.eps'
resultsFilenamePattern = 'results/integrationINapIKStepsize%d.npz'
i0 = 40.0
plt.figure()
plotLowThresholdINapIKVectorField()
'''
plotINapIKVectorField(I=i0, C=1.0, EL=-78, gL=8, gNa=20, gK=10,
VoneHalf_m=-20, k_m=15,
VoneHalf_n=-45, k_n=5, tauV=1, ENa=60,
EK=-90, nDotScaleFactor=200,
vMin=-90.0, vMax=20.0, nVs=19, nVsDense=100,
nMin=0.0, nMax=0.7, nNs=18,
vNullclineLabel="v nullcline",
nNullclineLabel="n nullcline")
'''
plt.xlabel('Voltage (mv)')
plt.ylabel('K activation variable, n')
resultsFilename = resultsFilenamePattern % i0
results = np.load(resultsFilename)
plt.plot(results['ys'][0, :], results['ys'][1, :], label="%d" % i0)
plt.grid()
plt.legend()
plt.xlabel('Voltage (mv)')
plt.ylabel('K activation variable, n')
plt.savefig(phaseFigFilename)
plt.figure()
plt.plot(results['times'], results['ys'][0, :], label="%d" % i0)
plt.grid()
plt.legend()
plt.xlabel('Time (secs)')
plt.ylabel('Voltage (mv)')
plt.savefig(voltageFigFilename)
pdb.set_trace()
def main(argv):
if len(argv) != 3:
sys.exit("Usage: %s i0 a" % argv[0])
i0 = float(argv[1])
a = float(argv[2])
resultsFilename = 'results/integrationINapIKExampleP172I%.02fa%f.npz' % (
i0, a)
phaseFigFilename = 'figures/figPhaseSpaceExampleINapIKP172I%.02fa%f.eps' % (
i0, a)
voltageFigFilename = 'figures/figVoltageExampleINapIKP172I%.02fa%f.eps' % (
i0, a)
results = np.load(resultsFilename)
plt.figure()
plotLowThresholdINapIKVectorField(i=results['i0'])
plt.plot(results['ys'][0, :], results['ys'][1, :], label="trayectory")
axes = plt.gca()
ylim = axes.get_ylim()
axes.set_ylim((-0.1, ylim[1]))
plt.grid()
plt.legend()
plt.xlabel('Voltage (mv)')
plt.ylabel('K activation variable, n')
plt.savefig(phaseFigFilename)
plt.figure()
plt.plot(results['times'], results['ys'][0, :])
results.close()
plt.grid()
plt.xlabel('Time (msec)')
plt.ylabel('Voltage (mv)')
plt.savefig(voltageFigFilename)
plt.show()
pdb.set_trace()
def main(argv):
if len(argv) != 3:
print("Usage %s <I> <label>" % argv[0])
return
i0 = float(argv[1])
label = argv[2]
nMin = -0.1
nMax = 0.7
resultsFilename = 'results/integrationINapIKFig4-34%s.npz' % label
phaseFigFilename = 'figures/fig4-34%sPhaseSpace.eps' % label
voltageFigFilename = 'figures/fig4-34%sVoltage.eps' % label
plt.figure()
plotLowThresholdINapIKVectorField(I=i0, nMin=nMin, nMax=nMax)
results = np.load(resultsFilename)
ys = results["ys"]
plt.plot(ys[0, :], ys[1, :], label="I=%d" % i0)
plt.grid()
plt.legend()
plt.xlabel('Voltage (mv)')
plt.ylabel('K activation variable, n')
plt.savefig(phaseFigFilename)
times = results["times"]
plt.figure()
plt.plot(times, ys[0, :], label="I=%d" % i0)
results.close()
plt.grid()
plt.legend()
plt.xlabel('Time (secs)')
plt.ylabel('Voltage (mv)')
plt.savefig(voltageFigFilename)
pdb.set_trace()
def main(argv):
figFilename = 'figures/fig4-4.eps'
plotLowThresholdINapIKVectorField()
plt.savefig(figFilename)
pdb.set_trace()