def proto_avgRange(theABF, m1=1.0, m2=1.1):
"""experiment: generic VC time course experiment."""
abf = ABF(theABF)
abf.log.info("analyzing as a fast IV")
plot = ABFplot(abf)
plt.figure(figsize=(SQUARESIZE * 2, SQUARESIZE / 2))
plt.subplot(121)
plot.title = "first sweep"
plot.figure_sweep()
plt.axvspan(m1, m2, color='r', ec=None, alpha=.1)
plt.subplot(122)
plt.grid(alpha=.5)
Ts = np.arange(abf.sweeps) * abf.sweepInterval
Ys = np.empty(abf.sweeps) * np.nan
for sweep in range(abf.sweeps):
Ys[sweep] = abf.average(m1, m2, setsweep=sweep)
for i, t in enumerate(abf.comment_times):
plt.axvline(t / 60, color='r', alpha=.5, lw=2, ls='--')
plt.plot(Ts / 60, Ys, '.')
plt.title(str(abf.comment_tags))
plt.ylabel(abf.units2)
plt.xlabel("minutes")
plt.tight_layout()
frameAndSave(abf, "sweep vs average", "experiment")
plt.close('all')
def proto_avgRange(theABF, m1=None, m2=None):
"""experiment: generic VC time course experiment."""
abf = ABF(theABF)
abf.log.info("analyzing as a fast IV")
if m1 is None:
m1 = abf.sweepLength
if m2 is None:
m2 = abf.sweepLength
I1 = int(abf.pointsPerSec * m1)
I2 = int(abf.pointsPerSec * m2)
Ts = np.arange(abf.sweeps) * abf.sweepInterval
Yav = np.empty(abf.sweeps) * np.nan # average
Ysd = np.empty(abf.sweeps) * np.nan # standard deviation
#Yar=np.empty(abf.sweeps)*np.nan # area
for sweep in abf.setsweeps():
Yav[sweep] = np.average(abf.sweepY[I1:I2])
Ysd[sweep] = np.std(abf.sweepY[I1:I2])
#Yar[sweep]=np.sum(abf.sweepY[I1:I2])/(I2*I1)-Yav[sweep]
plot = ABFplot(abf)
plt.figure(figsize=(SQUARESIZE * 2, SQUARESIZE / 2))
plt.subplot(131)
plot.title = "first sweep"
plot.figure_sweep(0)
plt.title("First Sweep\n(shaded measurement range)")
plt.axvspan(m1, m2, color='r', ec=None, alpha=.1)
plt.subplot(132)
plt.grid(alpha=.5)
for i, t in enumerate(abf.comment_times):
plt.axvline(t / 60, color='r', alpha=.5, lw=2, ls='--')
plt.plot(Ts / 60, Yav, '.', alpha=.75)
plt.title("Range Average\nTAGS: %s" % (", ".join(abf.comment_tags)))
plt.ylabel(abf.units2)
plt.xlabel("minutes")
plt.margins(0, .1)
plt.subplot(133)
plt.grid(alpha=.5)
for i, t in enumerate(abf.comment_times):
plt.axvline(t / 60, color='r', alpha=.5, lw=2, ls='--')
plt.plot(Ts / 60, Ysd, '.', alpha=.5, color='g', ms=15, mew=0)
#plt.fill_between(Ts/60,Ysd*0,Ysd,lw=0,alpha=.5,color='g')
plt.title("Range Standard Deviation\nTAGS: %s" %
(", ".join(abf.comment_tags)))
plt.ylabel(abf.units2)
plt.xlabel("minutes")
plt.margins(0, .1)
plt.axis([None, None, 0, np.percentile(Ysd, 99) * 1.25])
plt.tight_layout()
frameAndSave(abf, "sweep vs average", "experiment")
plt.close('all')