def proto_0303(theABF):
m1 = 4.15625
abf = ABF(theABF)
abf.log.info("analyzing as a halorhodopsin (2s pulse)")
plt.figure(figsize=(8, 8))
for sweep in abf.setsweeps():
plt.plot(abf.sweepX2, abf.sweepY + 100 * sweep, color='b', alpha=.5)
if abf.ID.startswith("17717"):
plt.axvspan(m1, m1 + 2, alpha=.2, color='g')
else:
plt.axvspan(m1, m1 + 1, alpha=.2, color='g')
plt.margins(0, .01)
plt.tight_layout()
frameAndSave(abf, "halo")
plt.close('all')
plt.figure(figsize=(8, 8))
for sweep in abf.setsweeps():
plt.plot(abf.sweepX2, abf.sweepY, color='b', alpha=.2)
if abf.ID.startswith("17717"):
plt.axvspan(m1, m1 + 2, alpha=.2, color='g')
else:
plt.axvspan(m1, m1 + 1, alpha=.2, color='g')
plt.margins(0, .01)
plt.tight_layout()
frameAndSave(abf, "halo2")
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')
def BLS_average_stack(theABF):
abf = ABF(theABF)
T1, T2 = abf.epochTimes(2)
padding = .1
if abf.units == "mV":
padding = .25
Tdiff = max([T2 - T1, padding])
Tdiff = min([T1, padding])
X1, X2 = T1 - Tdiff, T2 + Tdiff
I1, I2 = X1 * abf.pointsPerSec, X2 * abf.pointsPerSec
plt.figure(figsize=(10, 10))
chunks = np.empty((int(abf.sweeps), int(I2 - I1)))
Xs = np.array(abf.sweepX2[int(I1):int(I2)])
for sweep in abf.setsweeps():
chunks[sweep] = abf.sweepY[int(I1):int(I2)]
plt.subplot(211)
plt.plot(Xs, chunks[sweep], alpha=.2, color='.5', lw=2)
plt.subplot(212)
if abf.units == 'pA':
plt.plot(Xs,
chunks[sweep] + 100 * (abf.sweeps - sweep),
alpha=.5,
color='b',
lw=2) # if VC, focus on BLS
else:
plt.plot(abf.sweepX2,
abf.sweepY + 100 * (abf.sweeps - sweep),
alpha=.5,
color='b',
lw=2) # if IC, show full sweep
plt.subplot(211)
plt.plot(Xs, np.average(chunks, axis=0), alpha=.5, lw=2)
plt.title("%s.abf - BLS - average of %d sweeps" % (abf.ID, abf.sweeps))
plt.ylabel(abf.units2)
plt.axvspan(T1, T2, alpha=.2, color='y', lw=0)
plt.margins(0, .1)
plt.subplot(212)
plt.xlabel("time (sec)")
plt.ylabel("stacked sweeps")
plt.axvspan(T1, T2, alpha=.2, color='y', lw=0)
if abf.units == 'mV':
plt.axvline(T1, color='r', alpha=.2, lw=3)
# plt.axvline(T2,color='r',alpha=.2,lw=3)
plt.margins(0, .1)
plt.tight_layout()
frameAndSave(abf, "BLS", "experiment")
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_gain(theABF, stepSize=25, startAt=-100):
"""protocol: gain function of some sort. step size and start at are pA."""
abf = ABF(theABF)
abf.log.info("analyzing as an IC ramp")
plot = ABFplot(abf)
plot.kwargs["lw"] = .5
plot.title = ""
currents = np.arange(abf.sweeps) * stepSize - startAt
# AP detection
ap = AP(abf)
ap.detect_time1 = .1
ap.detect_time2 = .7
ap.detect()
# stacked plot
plt.figure(figsize=(SQUARESIZE, SQUARESIZE))
ax1 = plt.subplot(221)
plot.figure_sweeps()
ax2 = plt.subplot(222)
ax2.get_yaxis().set_visible(False)
plot.figure_sweeps(offsetY=150)
# add vertical marks to graphs:
for ax in [ax1, ax2]:
for limit in [ap.detect_time1, ap.detect_time2]:
ax.axvline(limit, color='r', ls='--', alpha=.5, lw=2)
# make stacked gain function
ax4 = plt.subplot(223)
plt.ylabel("frequency (Hz)")
plt.ylabel("seconds")
plt.grid(alpha=.5)
freqs = ap.get_bySweep("freqs")
times = ap.get_bySweep("times")
for i in range(abf.sweeps):
if len(freqs[i]):
plt.plot(times[i][:-1],
freqs[i],
'-',
alpha=.5,
lw=2,
color=plot.getColor(i / abf.sweeps))
# make gain function graph
ax4 = plt.subplot(224)
ax4.grid(alpha=.5)
plt.plot(currents, ap.get_bySweep("median"), 'b.-', label="median")
plt.plot(currents, ap.get_bySweep("firsts"), 'g.-', label="first")
plt.xlabel("applied current (pA)")
plt.legend(loc=2, fontsize=10)
plt.axhline(40, color='r', alpha=.5, ls="--", lw=2)
plt.margins(.02, .1)
# save it
plt.tight_layout()
frameAndSave(abf, "AP Gain %d_%d" % (startAt, stepSize))
plt.close('all')
# make a second figure that just shows every sweep up to the first AP
plt.figure(figsize=(SQUARESIZE, SQUARESIZE))
plt.grid(alpha=.5)
plt.ylabel("Membrane Potential (mV)")
plt.xlabel("Time (seconds)")
for sweep in abf.setsweeps():
plt.plot(abf.sweepX2, abf.sweepY, color='b', alpha=.5)
if np.max(abf.sweepY > 0):
break
plt.tight_layout()
plt.margins(0, .1)
plt.axis([0, 1, None, None])
plt.title("%d pA Steps from Rest" % stepSize)
frameAndSave(abf, "voltage response fromRest", closeWhenDone=False)
plt.axis([1.5, 2.5, None, None])
plt.title("%d pA Steps from %d pA" % (stepSize, startAt))
frameAndSave(abf, "voltage response hyperpol", closeWhenDone=False)
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')
def proto_0303(theABF):
"""protocol: repeated IC ramps."""
abf = ABF(theABF)
abf.log.info("analyzing as a halorhodopsin (2s pulse)")
# show average voltage
proto_avgRange(theABF, 0.2, 1.2)
plt.close('all')
# show stacked sweeps
plt.figure(figsize=(8, 8))
for sweep in abf.setsweeps():
color = 'b'
if sweep in np.array(abf.comment_sweeps, dtype=int):
color = 'r'
plt.plot(abf.sweepX2, abf.sweepY + 100 * sweep, color=color, alpha=.5)
plt.margins(0, .01)
plt.tight_layout()
frameAndSave(abf, "IC ramps")
plt.close('all')
# do AP event detection
ap = AP(abf)
ap.detect_time1 = 2.3
ap.detect_time2 = 8.3
ap.detect()
apCount = []
apSweepTimes = []
for sweepNumber, times in enumerate(ap.get_bySweep("times")):
apCount.append(len(times))
if len(times):
apSweepTimes.append(times[0])
else:
apSweepTimes.append(0)
# plot AP frequency vs time
plt.figure(figsize=(8, 8))
ax1 = plt.subplot(211)
plt.grid(alpha=.4, ls='--')
plt.plot(np.arange(len(apCount)) * abf.sweepLength / 60,
apCount,
'.-',
ms=15)
comment_lines(abf)
plt.ylabel("AP Count")
plt.subplot(212, sharex=ax1)
plt.grid(alpha=.4, ls='--')
plt.plot(np.arange(len(apCount)) * abf.sweepLength / 60,
apSweepTimes,
'.-',
ms=15)
comment_lines(abf)
plt.ylabel("First AP Time (s)")
plt.xlabel("Experiment Duration (minutes)")
plt.tight_layout()
frameAndSave(abf, "IC ramp freq")
plt.close('all')
