def plot_bifurc(gkbar_list, indir, color_li):
for i, gkbar in enumerate(gkbar_list):
gkdir = labeldir.gkbar_dir(gkbar)
subdir = os.path.join(indir, gkdir)
curtvec = np.load(os.path.join(subdir, 'curtvec.npy'))
fpli = np.load(os.path.join(subdir, 'fpli.npy'))
lab = labeldir.gkbar_lab(gkbar)
color = color_li[i]
plot_bifdiag(curtvec,
fpli,
label=lab,
newfig=False,
color=color,
ms=2.,
alpha=0.7)
plt.xlabel('$I_{inpq}$ (nA)')
# plt.xlim((0, 0.2))
plt.ylabel('Membrane voltage at AIS (mV)')
# plt.ylim((0, 80))
plt.legend(loc=4, fancybox=True, framealpha=0.5)
plt.minorticks_on()
plt.tight_layout()
plt.savefig('%s/bifurc.pdf' % indir)
plt.show()
def varygk_sta(gkbarli, indir_base):
for gkbar in gkbarli:
gkdir = labeldir.gkbar_dir(gkbar)
indir = os.path.join(indir_base, gkdir)
if not os.path.exists(indir):
raise OSError('No such directory: {}'.format(indir))
submit_to_cluster('sta', '../../run/run_sta.py', [indir])
def plot_gains(gkbarli,
indir,
figpath,
normalized=False,
cutoff=False,
statlab=False):
plt.figure()
for gkbar in gkbarli:
gkdir = labeldir.gkbar_dir(gkbar)
subdir = os.path.join(indir, gkdir)
transfdir = os.path.join(subdir, 'transfer')
lab = labeldir.gkbar_lab(gkbar)
if statlab:
lab = lab + plotgain.get_statlab(indir)
plotgain.plot_gain(transfdir, normalized, cutoff, label=lab)
plt.xlabel('Frequency (Hz)')
if normalized:
plt.ylabel('Normalized gain')
plt.ylim(bottom=0.01)
if cutoff:
plt.axhline(1 / np.sqrt(2),
color='black',
linewidth=3,
linestyle='dashed',
alpha=0.4)
else:
plt.ylabel('Gain (Hz/nA)')
plt.ylim(bottom=100)
if cutoff:
plotgain.plot_cutoff(transfdir)
plt.legend(loc=1, prop={'size': 12}, fancybox=True, framealpha=0.5)
plt.tight_layout()
plt.savefig(figpath)
def varygk_sta(gkbarli, indir_base):
for gkbar in gkbarli:
gkdir = labeldir.gkbar_dir(gkbar)
indir = os.path.join(indir_base, gkdir)
if not os.path.exists(indir):
raise OSError('No such directory: {}'.format(indir))
sbmj.run_sta(qname, indir)
def plot_varygk_vthr(gkbarli,
indir,
vname='v_ais',
iname='icap_ais',
figpath=None,
binwidth=None):
print vname
plt.figure()
for gkbar in gkbarli:
gklab = labeldir.gkbar_lab(gkbar)
gkdir = labeldir.gkbar_dir(gkbar)
subdir = os.path.join(indir, gkdir)
with open(os.path.join(subdir, 'fifos.p')) as f:
fifos = pickle.load(f)
vthrli = get_vthr_list(fifos, vname, iname)
print np.mean(vthrli)
if binwidth:
bins = np.arange(min(vthrli), max(vthrli) + binwidth, binwidth)
plt.hist(vthrli, label=gklab, alpha=0.7, bins=bins)
else:
plt.hist(vthrli, label=gklab, alpha=0.7)
plt.xlabel('Voltage at threshold (mV)')
plt.ylabel('# spikes')
plt.legend(prop={'size': 12}, fancybox=True, framealpha=0.5)
plt.tight_layout()
if figpath:
plt.savefig(figpath)
def varygk_spkstat(gkbarli, indir_base):
for gkbar in gkbarli:
gkdir = labeldir.gkbar_dir(gkbar)
indir = os.path.join(indir_base, gkdir)
if not os.path.exists(indir):
raise OSError('No such directory: {}'.format(indir))
spkstat.get_spkstat_from_file(indir)
def varygk_simulation(gkbarli, ttime, pardir_base, outdir_base):
for gkbar in gkbarli:
gkdir = labeldir.gkbar_dir(gkbar)
pardir = os.path.join(pardir_base, gkdir)
outdir = os.path.join(outdir_base, gkdir)
if not os.path.exists(outdir):
os.makedirs(outdir)
run_simulation(ttime, outdir, pardir)
def plot_operpoint(gkbar, spdir, frtli, colorli, cv=1, rad=0.005):
gkdir = labeldir.gkbar_dir(gkbar)
for i, frt in enumerate(frtli):
targsdir = labeldir.targs_dir(frt, cv)
indir = os.path.join(spdir, targsdir, gkdir)
stimpar = jspar.load(os.path.join(indir, 'stimpar.json'))
yrad = 2 * rad
color = colorli[i]
ell = patches.Ellipse((stimpar['mean'], stimpar['std']), rad, yrad, color=color, alpha=0.5)
ax = plt.gca()
ax.add_artist(ell)
def varygk_contours(gkbarli, bracketli, outdir, *args, **kwargs):
for i, gkbar in enumerate(gkbarli):
gkdir = labeldir.gkbar_dir(gkbar)
subdir = os.path.join(outdir, gkdir)
if not os.path.exists(subdir):
os.mkdir(subdir)
ncellpar = {'gkbar': gkbar}
cellpar = copy.copy(deflt_cellpar)
cellpar.update(ncellpar)
bracket = bracketli[i]
run_contours(subdir, cellpar, spkthr, bracket, *args, **kwargs)
def plot_gains(gkbarli, indir, figpath, normalized=False, statlab=False):
plt.figure(figsize=(8, 4))
for gkbar in gkbarli:
gkdir = labeldir.gkbar_dir(gkbar)
subdir = os.path.join(indir, gkdir)
transfdir = os.path.join(subdir, 'transfer')
transf = np.load(os.path.join(transfdir, 'transf.npy'))
fvec = np.load(os.path.join(transfdir, 'fvec.npy'))
gain = np.absolute(transf)
phase = np.angle(transf)
phase = np.negative(
phase
) ## this is used before changing phase to negative in transfer.py
lab = labeldir.gkbar_lab(gkbar)
if statlab:
statfile = os.path.join(subdir, 'spkstat.json')
if not os.path.isfile(statfile):
spkstat.get_spkstat_from_file(subdir)
stat = jspar.load(statfile)
stat_lab = '(frt:%.1f cv:%.2f lv:%.2f)' % (stat['frt'], stat['cv'],
stat['lv'])
lab = lab + ' ' + stat_lab
if normalized:
gain = gain / gain[1]
plt.subplot(121)
plt.semilogx(fvec, gain, label=lab)
plt.subplot(122)
plt.semilogx(fvec, phase, label=lab)
plt.subplot(121)
plt.xlabel('Frequency (Hz)')
if normalized:
plt.ylabel('Gain')
else:
plt.ylabel('Gain (Hz/nA)')
# plt.ylim(5e5, 2e6)
plt.legend(loc=1, prop={'size': 8}, fancybox=True, framealpha=0.5)
plt.subplot(122)
plt.xlabel('Frequency (Hz)')
plt.ylabel('Phase')
# plt.legend(prop={'size':8}, loc=4)
plt.legend(loc=1, prop={'size': 8}, fancybox=True, framealpha=0.5)
plt.tight_layout()
if figpath:
plt.savefig(figpath)
def varygk_ficurve(gkbarli, curtvec, outdir, noise=0, tau=0):
if not os.path.exists(outdir):
raise OSError('No such output directory: {}'.format(outdir))
for gkbar in gkbarli:
gkdir = labeldir.gkbar_dir(gkbar)
subdir = os.path.join(outdir, gkdir)
if not os.path.exists(subdir):
os.mkdir(subdir)
ncellpar = {'gkbar': gkbar}
cellpar = copy.copy(deflt_cellpar)
cellpar.update(ncellpar)
run_ficurve(curtvec, cellpar, subdir, noise, tau)
def plot_hists(indir, figpath, gkbarli, nbin=20):
plt.figure()
for gkbar in gkbarli:
gkdir = labeldir.gkbar_dir(gkbar)
subdir = os.path.join(indir, gkdir)
spktimes = np.load(os.path.join(subdir, 'spktimes.npy'))
gklab = labeldir.gkbar_lab(gkbar)
ssg.plot_hist(spktimes, nbin, log=True, label=gklab)
plt.xlabel('ISI (ms)')
plt.ylabel('# ISI / total # ISI')
plt.legend(loc=1, prop={'size': 14}, fancybox=True, framealpha=0.5)
plt.savefig(figpath)
def plot_gains(tauli, indir, gkbar, frttarg, cvtarg, figpath, normalized=False, statlab=False):
plt.figure(figsize=(8, 4))
gkdir = labeldir.gkbar_dir(gkbar)
firgain = 0
for i, tau in enumerate(tauli):
optsubdir = labeldir.opt_subdir(tau, frttarg, cvtarg)
subdir = os.path.join(indir, optsubdir, gkdir)
transfdir = os.path.join(subdir, 'transfer')
transf = np.load(os.path.join(transfdir, 'transf.npy'))
fvec = np.load(os.path.join(transfdir, 'fvec.npy'))
gain = np.absolute(transf)
phase = np.angle(transf)
if normalized:
gain = gain / gain[1]
lab = labeldir.tau_lab(tau)
if statlab:
statfile = os.path.join(subdir, 'stat.json')
if not os.path.isfile(statfile):
spkstat.get_stat_from_file(subdir)
stat = jspar.load(statfile)
stat_lab = '(frt:%.1f cv:%.2f lv:%.2f)' % (stat['frt'], stat['cv'], stat['lv'])
lab = lab + ' ' + stat_lab
plt.subplot(121)
plt.semilogx(fvec, gain, label=lab)
plt.subplot(122)
plt.semilogx(fvec, phase, label=lab)
plt.subplot(121)
plt.xlabel('$f$ (Hz)')
if normalized:
plt.ylabel('Gain')
else:
plt.ylabel('Gain (Hz/nA)')
# plt.ylim(5e5, 2e6)
plt.legend(loc=1, prop={'size': 8}, fancybox=True, framealpha=0.5)
plt.subplot(122)
plt.xlabel('$f$ (Hz)')
plt.ylabel('Phase')
# plt.legend(prop={'size':8}, loc=4)
plt.legend(loc=1, prop={'size': 8}, fancybox=True, framealpha=0.5)
plt.tight_layout()
if figpath:
plt.savefig(figpath)
def plot_thresh_hists(gkbarli, figpath):
plt.figure(figsize=(23, 5))
for gkbar in gkbarli:
gklab = labeldir.gkbar_lab(gkbar)
vthrli, ivslopeli, mvslopeli, indli = varygk_ivslope(gkbar, ppsubdir)
gkdir = labeldir.gkbar_dir(gkbar)
indir = os.path.join(ppsubdir, gkdir)
with open(os.path.join(indir, 'fifos.p')) as f:
fifos = pickle.load(f)
mtslopeli = get_slope_list(fifos, 'time', 'nav_m', 'icap_ais')
print gkbar
print 'nspk', len(vthrli)
print 'v', np.mean(vthrli)
print 'didv', np.mean(ivslopeli)
print 'dmdv', np.mean(mvslopeli)
print 'dmdt', np.mean(mtslopeli)
print 't2spk', 40 - np.mean(indli) * 0.025
plt.subplot(141)
plt.hist(vthrli, alpha=0.7, label=gklab)
plt.subplot(142)
plt.hist(ivslopeli, alpha=0.7, label=gklab)
plt.subplot(143)
plt.hist(mvslopeli, alpha=0.7, label=gklab)
plt.subplot(144)
plt.hist(mtslopeli, alpha=0.7, label=gklab)
plt.subplot(141)
plt.xlabel('Voltage at threshold (mV)')
plt.ylabel('# spikes')
plt.legend(prop={'size': 12}, fancybox=True, framealpha=0.5)
plt.subplot(142)
plt.xlabel('dI/dV (nA/mV)')
plt.ylabel('# spikes')
plt.legend(prop={'size': 12}, fancybox=True, framealpha=0.5)
plt.subplot(143)
plt.xlabel('dm/dV (/mV)')
plt.ylabel('# spikes')
plt.legend(prop={'size': 12}, fancybox=True, framealpha=0.5)
plt.subplot(144)
plt.xlabel('dm/dt (/ms)')
plt.ylabel('# spikes')
plt.legend(prop={'size': 12}, fancybox=True, framealpha=0.5)
plt.tight_layout()
plt.savefig(figpath)
def varygk_cutoff(indir, gkbarli):
cofreqli = []
for gkbar in gkbarli:
gkdir = labeldir.gkbar_dir(gkbar)
subdir = os.path.join(indir, gkdir)
transfdir = os.path.join(subdir, 'transfer')
transf = np.load(os.path.join(transfdir, 'transf.npy'))
fvec = np.load(os.path.join(transfdir, 'fvec.npy'))
gain = np.absolute(transf)
cofreq = transfer.get_cutoff_freq(fvec, gain)
cofreqli.append(cofreq)
return np.array(cofreqli)
def plot_srcrs(indir, figpath, gkbarli, norder=10):
plt.figure()
for gkbar in gkbarli:
gkdir = labeldir.gkbar_dir(gkbar)
subdir = os.path.join(indir, gkdir)
spktimes = np.load(os.path.join(subdir, 'spktimes.npy'))
gklab = labeldir.gkbar_lab(gkbar)
ssg.plot_srcr(spktimes, norder, label=gklab)
plt.xlabel('Order')
plt.ylabel('Spearman Rank Coefficient')
plt.ylim((-0.025, 0.15))
plt.legend(loc=1, prop={'size': 14}, fancybox=True, framealpha=0.5)
plt.tight_layout()
plt.savefig(figpath)
def plot_ficurves(gkbarli,
indir,
marker='o-',
labapd='',
colorli=None,
**kwargs):
for i, gkbar in enumerate(gkbarli):
gkdir = labeldir.gkbar_dir(gkbar)
lab = labeldir.gkbar_lab(gkbar)
if labapd:
lab = lab + labapd
subdir = os.path.join(indir, gkdir)
if colorli:
color = colorli[i]
kwargs['color'] = color
plotficurve.plot_ficurve(subdir, marker, label=lab, **kwargs)
def plot_ficurve(gkbarli, indir):
for gkbar in gkbarli:
gkdir = labeldir.gkbar_dir(gkbar)
subdir = os.path.join(indir, gkdir)
curtvec = np.load(os.path.join(subdir, 'curtvec.npy'))
frtvec = np.load(os.path.join(subdir, 'frtvec.npy'))
lab = labeldir.gkbar_lab(gkbar)
plt.plot(curtvec, frtvec, 'o-', label=lab, ms=2., alpha=0.7)
plt.xlabel('I (nA)')
# plt.xlim((0, 0.2))
plt.ylabel('Firing rate (Hz)')
# plt.ylim((0, 80))
plt.legend(loc=4, prop={'size': 7}, fancybox=True, framealpha=0.5)
plt.minorticks_on()
plt.savefig(os.path.join(indir, 'fi_curve.pdf'))
plt.show()
def plot_transfs(gkbarli, indir, figpath, statlab=False):
plt.figure(figsize=(8, 4))
for gkbar in gkbarli:
gkdir = labeldir.gkbar_dir(gkbar)
subdir = os.path.join(indir, gkdir)
transfdir = os.path.join(subdir, 'transfer')
lab = labeldir.gkbar_lab(gkbar)
if statlab:
lab = lab + plotgain.get_statlab(indir)
plotgain.plot_transf(transfdir, label=lab)
plt.subplot(121)
plt.xlabel('Frequency (Hz)')
plt.ylabel('Gain (Hz/nA)')
plt.legend(loc=1, prop={'size': 12}, fancybox=True, framealpha=0.5)
plt.subplot(122)
plt.xlabel('Frequency (Hz)')
plt.ylabel('Phase')
plt.legend(loc=1, prop={'size': 12}, fancybox=True, framealpha=0.5)
plt.tight_layout()
plt.savefig(figpath)
def varygk_optstimpar(gkbarli, xzeroli, ttime, tau, frttarg, cvtarg,
outdir_base):
print 'Start to optimize stimpar ...'
print 'gkbar_list: ' + str(gkbarli)
print 'x0_list: ' + str(xzeroli)
print 'tau: %.0f' % tau
print 'frt: %.0f\tcv: %.1f' % (frttarg, cvtarg)
optsubdir = labeldir.opt_subdir(tau, frttarg, cvtarg)
outdir = os.path.join(outdir_base, optsubdir)
if not os.path.exists(outdir):
os.makedirs(outdir)
for gkbar, x0 in zip(gkbarli, xzeroli):
gkdir = labeldir.gkbar_dir(gkbar)
subdir = os.path.join(outdir, gkdir)
if not os.path.exists(subdir):
os.mkdir(subdir)
ncellpar = {'gkbar': gkbar}
cellpar = copy.copy(deflt_cellpar)
cellpar.update(ncellpar)
run_optstimpar(subdir, cellpar, spkthr, x0, tau, ttime, frttarg,
cvtarg)
frttarg = 5
cvtarg = 1.
tfcsubdir = labeldir.opt_subdir(tau, frttarg, cvtarg)
optsubdir = os.path.join(optdir, tfcsubdir)
threxsubdir = os.path.join(threxdir, tfcsubdir)
# gkbar = 0
# gkdir = labeldir.gkbar_dir(gkbar)
# outdir = os.path.join(threxsubdir, gkdir)
# # plot_traj_thresh(outdir, 'time', 'nav_m')
# plot_align_from_file(outdir, 'nav_m')
# plt.show()
gkbarli = [0, 5e-3, 15e-3]
trajcolorli = ['#1f77b4', '#ff7f0e', '#2ca02c']
thrcolorli = ['darkblue', 'chocolate', 'darkgreen']
for i, gkbar in enumerate(gkbarli):
trajcolor = trajcolorli[i]
thrcolor = thrcolorli[i]
gkdir = labeldir.gkbar_dir(gkbar)
outdir = os.path.join(threxsubdir, gkdir)
# plot_traj_thresh(outdir, 'time', 'nav_m')
gklab = labeldir.gkbar_lab(gkbar)
plot_align_thresh(outdir, 'nav_m', trajcolor, thrcolor, label=gklab)
plt.xlabel('time to spike (ms)')
plt.ylabel('Nav gating variable $m$')
plt.legend()
plt.savefig(os.path.join(threxsubdir, 'mt.pdf'))
plt.show()
def varygk_ivslope(gkbar, ppsubdir):
gkdir = labeldir.gkbar_dir(gkbar)
indir = os.path.join(ppsubdir, gkdir)
with open(os.path.join(indir, 'fifos.p')) as f:
fifos = pickle.load(f)
return get_ivslope_list(fifos)
def varygk_transfer(gkbarli, indir_base):
for gkbar in gkbarli:
gkdir = labeldir.gkbar_dir(gkbar)
indir = os.path.join(indir_base, gkdir)
transfer.run_transfer(indir)
