def proto_0101(theABF):
abf = ABF(theABF)
abf.log.info("analyzing as an IC tau")
#plot=ABFplot(abf)
plt.figure(figsize=(SQUARESIZE / 2, SQUARESIZE / 2))
plt.grid()
plt.ylabel("relative potential (mV)")
plt.xlabel("time (sec)")
m1, m2 = [.05, .1]
for sweep in range(abf.sweeps):
abf.setsweep(sweep)
plt.plot(abf.sweepX2,
abf.sweepY - abf.average(m1, m2),
alpha=.2,
color='#AAAAFF')
average = abf.averageSweep()
average -= np.average(
average[int(m1**abf.pointsPerSec):int(m2 * abf.pointsPerSec)])
plt.plot(abf.sweepX2, average, color='b', lw=2, alpha=.5)
plt.axvspan(m1, m2, color='r', ec=None, alpha=.1)
plt.axhline(0, color='r', ls="--", alpha=.5, lw=2)
plt.margins(0, .1)
# save it
plt.tight_layout()
frameAndSave(abf, "IC tau")
plt.close('all')
def proto_0203(theABF):
"""protocol: vast IV."""
abf = ABF(theABF)
abf.log.info("analyzing as a fast IV")
plot = ABFplot(abf)
plot.title = ""
m1, m2 = .7, 1
plt.figure(figsize=(SQUARESIZE, SQUARESIZE / 2))
plt.subplot(121)
plot.figure_sweeps()
plt.axvspan(m1, m2, color='r', ec=None, alpha=.1)
plt.subplot(122)
plt.grid(alpha=.5)
Xs = np.arange(abf.sweeps) * 5 - 110
Ys = []
for sweep in range(abf.sweeps):
abf.setsweep(sweep)
Ys.append(abf.average(m1, m2))
plt.plot(Xs, Ys, '.-', ms=10)
plt.axvline(-70, color='r', ls='--', lw=2, alpha=.5)
plt.axhline(0, color='r', ls='--', lw=2, alpha=.5)
plt.margins(.1, .1)
plt.xlabel("membrane potential (mV)")
# save it
plt.tight_layout()
frameAndSave(abf, "fast IV")
plt.close('all')
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_0202(theABF):
"""protocol: MTIV."""
abf = ABF(theABF)
abf.log.info("analyzing as MTIV")
plot = ABFplot(abf)
plot.figure_height, plot.figure_width = SQUARESIZE, SQUARESIZE
plot.title = ""
plot.kwargs["alpha"] = .6
plot.figure_sweeps()
# frame to uppwer/lower bounds, ignoring peaks from capacitive transients
abf.setsweep(0)
plt.axis([None, None, abf.average(.9, 1) - 100, None])
abf.setsweep(-1)
plt.axis([None, None, None, abf.average(.9, 1) + 100])
# save it
plt.tight_layout()
frameAndSave(abf, "MTIV")
plt.close('all')
def proto_0304(theABF):
"""protocol: repeated IC steps."""
abf = ABF(theABF)
abf.log.info("analyzing as repeated current-clamp step")
# prepare for AP analysis
ap = AP(abf)
# calculate rest potential
avgVoltagePerSweep = []
times = []
for sweep in abf.setsweeps():
avgVoltagePerSweep.append(abf.average(0, 3))
times.append(abf.sweepStart / 60)
# detect only step APs
M1, M2 = 3.15, 4.15
ap.detect_time1, ap.detect_time2 = M1, M2
ap.detect()
apsPerSweepCos = [len(x) for x in ap.get_bySweep()]
# detect all APs
M1, M2 = 0, 10
ap.detect_time1, ap.detect_time2 = M1, M2
ap.detect()
apsPerSweepRamp = [len(x) for x in ap.get_bySweep()]
# make the plot of APs and stuff
plt.figure(figsize=(8, 8))
plt.subplot(311)
plt.grid(ls='--', alpha=.5)
plt.plot(times, avgVoltagePerSweep, '.-')
plt.ylabel("Rest Potential (mV)")
comment_lines(abf)
plt.subplot(312)
plt.grid(ls='--', alpha=.5)
plt.plot(times, apsPerSweepCos, '.-')
plt.ylabel("APs in Step (#)")
comment_lines(abf)
plt.subplot(313)
plt.grid(ls='--', alpha=.5)
plt.plot(times, apsPerSweepRamp, '.-')
plt.ylabel("APs in Sweep (#)")
comment_lines(abf)
plt.tight_layout()
frameAndSave(abf, "cos ramp")
plt.close('all')
def proto_0314(theABF):
abf = ABF(theABF)
abf.log.info("analyzing a cosine + ramp protocol")
if len(abf.comment_sweeps > 0):
# comments exist, so graph the average sweep before/after the first comment
sweepsToAverage = 10
baselineSweep1 = max(0, abf.comment_sweeps[0] - sweepsToAverage)
baselineSweep2 = abf.comment_sweeps[0]
drugSweep1 = abf.comment_sweeps[0] + 1
drugSweep2 = min(abf.sweeps - 1,
abf.comment_sweeps[0] + 1 + sweepsToAverage)
plt.figure(figsize=(16, 4))
plt.grid(ls='--', alpha=.5)
plt.plot(abf.sweepX2,
abf.averageSweep(baselineSweep1, baselineSweep2),
label="baseline (%d-%d)" % (baselineSweep1, baselineSweep2),
alpha=.8)
plt.plot(abf.sweepX2,
abf.averageSweep(drugSweep1, drugSweep2),
label="drug (%d-%d)" % (drugSweep1, drugSweep2),
alpha=.8)
plt.margins(0, .05)
plt.legend()
plt.tight_layout()
frameAndSave(abf, "cos ramp avg", closeWhenDone=False)
plt.axis([2.25, 4.5, None, None])
frameAndSave(abf, "cos ramp avgSine", closeWhenDone=False)
plt.axis([9, 12.5, None, None])
frameAndSave(abf, "cos ramp avgRamp")
# prepare for AP analysis
ap = AP(abf)
# calculate rest potential
avgVoltagePerSweep = []
times = []
for sweep in abf.setsweeps():
avgVoltagePerSweep.append(abf.average(0, 2.25))
times.append(abf.sweepStart / 60)
# detect only cos APs
M1, M2 = 2.25, 4.5
ap.detect_time1, ap.detect_time2 = M1, M2
ap.detect()
apsPerSweepCos = [len(x) for x in ap.get_bySweep()]
# detect only ramp APs
M1, M2 = 9, 12.5
ap.detect_time1, ap.detect_time2 = M1, M2
ap.detect()
apsPerSweepRamp = [len(x) for x in ap.get_bySweep()]
# make the plot of APs and stuff
plt.figure(figsize=(8, 8))
plt.subplot(311)
plt.grid(ls='--', alpha=.5)
plt.plot(times, avgVoltagePerSweep, '.-')
plt.ylabel("Rest Potential (mV)")
comment_lines(abf)
plt.subplot(312)
plt.grid(ls='--', alpha=.5)
plt.plot(times, apsPerSweepCos, '.-')
plt.ylabel("APs in Cos (#)")
comment_lines(abf)
plt.subplot(313)
plt.grid(ls='--', alpha=.5)
plt.plot(times, apsPerSweepRamp, '.-')
plt.ylabel("APs in Ramp (#)")
comment_lines(abf)
plt.tight_layout()
frameAndSave(abf, "cos ramp")
plt.close('all')
