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_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')
def proto_0222(theABF):
"""protocol: VC sine sweep."""
abf = ABF(theABF)
abf.log.info("analyzing as VC sine sweep")
plot = ABFplot(abf)
plot.figure_height, plot.figure_width = SQUARESIZE / 2, SQUARESIZE / 2
plot.figure_sweeps()
plt.tight_layout()
frameAndSave(abf, "VC sine sweep")
plt.close('all')
def proto_0201(theABF):
"""protocol: membrane test."""
abf = ABF(theABF)
abf.log.info("analyzing as a membrane test")
plot = ABFplot(abf)
plot.figure_height, plot.figure_width = SQUARESIZE / 2, SQUARESIZE / 2
plot.figure_sweeps()
# save it
plt.tight_layout()
frameAndSave(abf, "membrane test")
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_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')