def showplots(name):
"""
Show traces from sound stimulation - without current injection
"""
f = open(name, 'r')
d = pickle.load(f)
f.close()
ncells = len(d['results'])
stiminfo = d['stim']
dur = stiminfo['rundur'] * 1000.
print 'dur: ', dur
print 'stim info: '
print ' fmod: ', stiminfo['fmod']
print ' dmod: ', stiminfo['dmod']
print ' f0: ', stiminfo['f0']
print ' cf: ', stiminfo['cf']
varsg = np.linspace(0.25, 2.0,
int((2.0 - 0.25) / 0.25) + 1) # was not stored...
fig, ax = mpl.subplots(ncells + 1, 2, figsize=(8.5, 11.))
spikelists = [[]] * ncells
prespikes = [[]] * ncells
xmin = 50.
for i in range(ncells):
vdat = d['results'][i]['v']
idat = d['results'][i]['i']
tdat = d['results'][i]['t']
pdat = d['results'][i]['pre']
PH.noaxes(ax[i, 0])
# if i == 0:
# PH.calbar(ax[0, 0], calbar=[120., -120., 25., 20.], axesoff=True, orient='left',
# unitNames={'x': 'ms', 'y': 'mV'}, fontsize=9, weight='normal', font='Arial')
for j in range(len(vdat)):
if j == 2:
ax[i, 0].plot(tdat - xmin, vdat[j], 'k', linewidth=0.5)
if j == 0:
ax[i, 0].annotate('%.2f' % varsg[i], (180., 20.))
ax[i, 0].set_xlim([0, dur - xmin])
ax[i, 0].set_ylim([-75, 50])
PH.referenceline(ax[i, 0],
reference=-62.0,
limits=None,
color='0.33',
linestyle='--',
linewidth=0.5,
dashes=[3, 3])
for j in range(len(vdat)):
detected = PU.findspikes(tdat, vdat[j], -20.)
detected = clean_spiketimes(detected)
spikelists[i].extend(detected)
if j == 0:
n, bins = np.histogram(detected,
np.linspace(0., dur, 201),
density=False)
else:
m, bins = np.histogram(detected,
np.linspace(0., dur, 201),
density=False)
n += m
prespikes[i].extend(pdat)
if j == 0:
n, bins = np.histogram(pdat,
np.linspace(0., dur, 201),
density=False)
else:
m, bins = np.histogram(pdat,
np.linspace(0., dur, 201),
density=False)
n += m
ax[i, 1].bar(bins[:-1] - xmin,
n,
width=bins[1],
facecolor='k',
alpha=0.75)
ax[i, 1].set_xlim([0, dur - xmin])
ax[i, 1].set_ylim([0, 30])
vs = PU.vector_strength(spikelists[i], stiminfo['fmod'])
pre_vs = PU.vector_strength(prespikes[i], stiminfo['fmod'])
# print 'pre: ', pre_vs
# print 'post: ', vs
# apos = ax[i,1].get_position()
# ax[i, 1].set_title('VS = %4.3f' % pre_vs['r'])
# # vector_plot(fig, vs['ph'], np.ones(len(vs['ph'])), yp = apos)
# phase_hist(fig, vs['ph'], yp=apos)
# phase_hist(fig, pre_vs['ph'], yp=apos)
prot = Variations(runtype, runname)
# stim_info = {'nreps': nrep, 'cf': cf, 'f0': f0, 'rundur': rundur, 'pipdur': pipdur, 'dbspl': dbspl, 'fmod': fmod, 'dmod': dmod}
if stiminfo['dmod'] > 0:
stimulus = 'SAM'
else:
stimulus = 'tone'
prot.make_stimulus(stimulus=stimulus,
cf=stiminfo['cf'],
f0=stiminfo['f0'],
simulator=None,
rundur=stiminfo['rundur'],
pipdur=stiminfo['pipdur'],
dbspl=stiminfo['dbspl'],
fmod=stiminfo['fmod'],
dmod=stiminfo['dmod'])
ax[-1, 1].plot(prot.stim.time * 1000. - xmin,
prot.stim.sound,
'k-',
linewidth=0.75)
ax[-1, 1].set_xlim([0, (dur - xmin)])
PH.noaxes(ax[-1, 0])
ax[-1, 0].set_xlim([0, dur - xmin])
ax[-1, 0].set_ylim([-75, 50])
# PH.referenceline(ax[-1, 0], reference=-62.0, limits=None, color='0.33', linestyle='--' ,linewidth=0.5, dashes=[3, 3])
PH.calbar(ax[-1, 0],
calbar=[20., 0., 25., 20.],
axesoff=True,
orient='left',
unitNames={
'x': 'ms',
'y': 'mV'
},
fontsize=9,
weight='normal',
font='Arial')
PH.cleanAxes(ax.ravel().tolist())
mpl.show()
def plotResults(self, res, runInfo, somasite=['postsynapticV', 'postsynapticI', 'dendriteV']):
clist={'axon': 'r', 'heminode': 'g', 'stalk':'y', 'branch': 'g', 'neck': 'b',
'swelling': 'm', 'tip': 'k', 'parentaxon': '', r'synapse': 'c', 'Soma': 'k',
'dendrite': 'c', 'dend': 'c'}
dx = np.array([x for k,x in res['distanceMap'].items()])
dlen = res['monitor']['postsynapticV'].shape[0]
dxmax = np.max(dx)
if self.plotmode == 'pg':
self.plots['Soma'].setLabel('left', 'V')
self.plots['Soma'].plot(res['monitor']['time'][:dlen], res['monitor']['postsynapticV'],
pen=pg.mkPen(clist['Soma'], width=0.5), )
if 'dendriteV' in somasite and self.plots['Dendrite'] is not None and len(res['monitor']['dendriteV']) > 0:
self.plots['Dendrite'].plot(res['monitor']['time'][:dlen],
res['monitor']['dendriteV'], pen=pg.mkPen(clist['dendrite'], width=0.5), )
self.plots['Dendrite'].setLabel('left', 'V (mV)')
if 'vec' in res.keys()and self.plots['p4'] is not None:
for v in res['vec']:
self.plots['p4'].plot(res['monitor']['time'], res['vec'][v],
pen=pg.mkPen(pg.intColor(int(255.*res['distanceMap'][v]/dxmax))),
width=1.5)
if 'postsynapticI' in somasite and self.plots['Iinj'] is not None:
vlen = len(res['monitor']['postsynapticI'])
self.plots['Iinj'].plot(res['monitor']['time'][0:vlen], res['monitor']['postsynapticI'],
pen = pg.mkPen('b', width=0.5))
self.plots['Iinj'].setLabel('left', 'I (inj, nA)')
if 'vec' in res.keys() and self.plots['p4'] is not None:
for v in res['vec']:
self.plots['p4'].plot(res['monitor']['time'], res['vec'][v],
pen=pg.mkPen(pg.intColor(int(255.*res['distanceMap'][v]/dxmax))),
width=0.5)
#for c in res['ICa']:
# self.plots['Dendrite'].plot(res['monitor']['time'], res['ICa'][c]*1e12, pen=pg.mkPen('b', width=1.5))
# self.plots['Iinj'].plot(res['vec']['time'], res['Cai'][c]*1e6, pen=pg.mkPen('g', width=1.5))
#p2.set_ylim(-5e-12, 1e-12)
self.plots['Soma'].setXRange(0., 120., padding=0.2)
self.plots['Dendrite'].setXRange(0., 120., padding=0.2)
if self.plots['Iinj'] is not None:
self.plots['Iinj'].setXRange(0., 120., padding=0.2)
pgPH.cleanAxes([self.plots['Soma'], self.plots['Dendrite'], self.plots['Iinj'], self.plots['p4']])
pgPH.nice_plot(self.plots['Soma'])
pgPH.calbar(self.plots['Soma'], [110, -50, 20, 50])
# pgPH.nice_plot(self.plots['Dendrite'])
# pgPH.calbar(self.plots['Dendrite'], [110, 0.1, 20, 1])
if self.plots['Iinj'] is not None:
pgPH.nice_plot(self.plots['Iinj'])
pgPH.calbar(self.plots['Iinj'], [110, -0.1, 20, 1])
elif self.plotmode == 'mpl':
self.plots['Soma'].set_ylabel('V')
self.plots['Soma'].plot(res['monitor']['time'][:dlen], res['monitor']['postsynapticV'],
color=clist['Soma'], linewidth=0.5)
if 'dendriteV' in somasite and self.plots['Dendrite'] is not None and len(res['monitor']['dendriteV']) > 0:
self.plots['Dendrite'].plot(res['monitor']['time'][:dlen],
res['monitor']['dendriteV'], color=clist['dendrite'], linewidth=0.5)
self.plots['Dendrite'].set_ylabel('V (mV)')
if 'vec' in res.keys()and self.plots['p4'] is not None:
for v in res['vec']:
self.plots['p4'].plot(res['monitor']['time'], res['vec'][v],
color=[[int(255.*res['distanceMap'][v]/dxmax)]*3],
linewidth=0.75)
if 'postsynapticI' in somasite and self.plots['Iinj'] is not None:
vlen = len(res['monitor']['postsynapticI'])
self.plots['Iinj'].plot(res['monitor']['time'][0:vlen], res['monitor']['postsynapticI'],
color='b', linewidth=0.5)
self.plots['Iinj'].set_ylabel('I (inj, nA)')
if 'vec' in res.keys() and self.plots['p4'] is not None:
for v in res['vec']:
self.plots['p4'].plot(res['monitor']['time'], res['vec'][v],
color=[[int(255.*res['distanceMap'][v]/dxmax)]*3],
linewidth=0.75)
#for c in res['ICa']:
# self.plots['Dendrite'].plot(res['monitor']['time'], res['ICa'][c]*1e12, pen=pg.mkPen('b', width=1.5))
# self.plots['Iinj'].plot(res['vec']['time'], res['Cai'][c]*1e6, pen=pg.mkPen('g', width=1.5))
#p2.set_ylim(-5e-12, 1e-12)
self.plots['Soma'].set_xlim(0., 120.)
self.plots['Dendrite'].set_xlim(0., 120.)
if self.plots['Iinj'] is not None:
self.plots['Iinj'].set_xlim(0., 120.)
PH.cleanAxes([self.plots['Soma'], self.plots['Dendrite'], self.plots['Iinj']])
PH.nice_plot(self.plots['Soma'])
PH.calbar(self.plots['Soma'], [110, -50, 20, 50])
PH.nice_plot(self.plots['Dendrite'])
PH.calbar(self.plots['Dendrite'], [110, -50, 20, 50])
# pgPH.nice_plot(self.plots['Dendrite'])
# pgPH.calbar(self.plots['Dendrite'], [110, 0.1, 20, 1])
if self.plots['Iinj'] is not None:
PH.nice_plot(self.plots['Iinj'])
PH.calbar(self.plots['Iinj'], [110, -0.1, 20, 1])
def run_democlamp(cell, dend, vsteps=[-60,-70,-60], tsteps=[10,50,100]):
"""
Does some stuff.
"""
f1 = pylab.figure(1)
gs = GS.GridSpec(2, 2,
width_ratios=[1, 1],
height_ratios=[1, 1])
# note numbering for insets goes from 1 (upper right) to 4 (lower right)
# counterclockwise
pA = f1.add_subplot(gs[0])
pAi = INSETS.inset_axes(pA, width="66%", height="40%", loc=2)
pB = f1.add_subplot(gs[1])
pBi = INSETS.inset_axes(pB, width="66%", height="40%", loc=4)
pC = f1.add_subplot(gs[2])
pCi = INSETS.inset_axes(pC, width="66%", height="40%", loc=2)
pD = f1.add_subplot(gs[3])
pDi = INSETS.inset_axes(pD, width="66%", height="40%", loc=1)
#h.topology()
Ld = 0.5
Ld2 = 1.0
VClamp = h.SEClamp(0.5, cell)
VClamp.dur1 = tsteps[0]
VClamp.amp1 = vsteps[0]
VClamp.dur2 = tsteps[1]
VClamp.amp2 = vsteps[1]
VClamp.dur3 = tsteps[2]
VClamp.amp3 = vsteps[2]
Rs0 = 10.
VClamp.rs = Rs0
compensation = [0., 70., 95.]
cms = [cell.cm*(100.-c)/100. for c in compensation]
vrec = h.iStim(Ld, sec=dend[0])
vrec.delay = 0
vrec.dur = 1e9 # these actually do not matter...
vrec.iMax = 0.0
vrec2 = h.iStim(Ld2, sec=dend[0])
vrec2.delay = 0
vrec2.dur = 1e9 # these actually do not matter...
vrec2.iMax = 0.0
stim = {}
stim['NP'] = 1
stim['Sfreq'] = 20 # stimulus frequency
stim['delay'] = tsteps[0]
stim['dur'] = tsteps[1]
stim['amp'] = vsteps[1]
stim['PT'] = 0.0
stim['hold'] = vsteps[0]
# (secmd, maxt, tstims) = make_pulse(stim)
tend = 79.5
linetype = ['-', '-', '-']
linethick = [0.5, 0.75, 1.25]
linecolor = [[0.66, 0.66, 0.66], [0.4, 0.4, 0.3], 'k']
n = 0
vcmds = [-70, -20]
vplots = [(pA, pAi, pC, pCi), (pB, pBi, pD, pDi)]
for m, VX in enumerate(vcmds):
stim['amp'] = VX
pl = vplots[m]
print m, VX
(secmd, maxt, tstims) = make_pulse(stim)
for n, rsc in enumerate(compensation):
vec={}
for var in ['VCmd', 'i_inj', 'time', 'Vsoma', 'Vdend',
'Vdend2', 'VCmdR']:
vec[var] = h.Vector()
VClamp.rs = Rs0*(100.-rsc)/100.
cell.cm = cms[n]
# print VClamp.rs, cell.cm, VClamp.rs*cell.cm
vec['VCmd'] = h.Vector(secmd)
vec['Vsoma'].record(cell(0.5)._ref_v, sec=cell)
vec['Vdend'].record(dend[0](Ld)._ref_v, sec=dend[0])
vec['time'].record(h._ref_t)
vec['i_inj'].record(VClamp._ref_i, sec=cell)
vec['VCmdR'].record(VClamp._ref_vc, sec=cell)
VClamp.amp2 = VX
# vec['VCmd'].play(VClamp.amp2, h.dt, 0, sec=cell)
h.tstop = tend
h.init()
h.finitialize(-60)
h.run()
vc = np.asarray(vec['Vsoma'])
tc = np.asarray(vec['time'])
# now plot the data, raw and as insets
for k in [0, 1]:
pl[k].plot(vec['time'], vec['i_inj'], color=linecolor[n], linestyle = linetype[n], linewidth=linethick[n])
yl = pl[k].get_ylim()
if k == 0:
pass
#pl[k].set_ylim([1.5*yl[0], -1.5*yl[1]])
else:
pass
for k in [2,3]:
pl[k].plot(vec['time'], vec['Vsoma'], color=linecolor[n], linestyle = linetype[n], linewidth=linethick[n])
pl[k].plot(vec['time'], vec['VCmdR'], color=linecolor[n], linestyle = '--', linewidth=1, dashes=(1,1))
pl[k].plot(vec['time'], vec['Vdend'], color=linecolor[n], linestyle = linetype[n], linewidth=linethick[n], dashes=(3,3))
if VX < vsteps[0]:
pl[k].set_ylim([-72, -40])
else:
pl[k].set_ylim([-62,VX+30])
ptx = 10.8
pBi.set_xlim([9.8, ptx])
pAi.set_xlim([9.8, ptx])
PH.setX(pAi, pCi)
PH.setX(pBi, pDi)
pD.set_ylim([-65, 10])
# PH.setY(pC, pCi) # match Y limits
PH.cleanAxes([pA, pAi, pB, pBi, pC, pCi, pD, pDi])
PH.formatTicks([pA, pB, pC, pD], axis='x', fmt='%d')
PH.formatTicks([pC, pD], axis='y', fmt='%d')
PH.calbar(pAi, [ptx-1, 0, 0.2, 2.])
PH.calbar(pCi, [ptx-1, -50., 0.2, 10])
PH.calbar(pBi, [ptx-1, 0, 0.2, 10])
PH.calbar(pDi, [ptx-1, -50., 0.2, 20])
pylab.draw()
pylab.show()