def plot_spikes(self):
self.raster_ax.clear()
sp = spikeplot.SpikePlot(fig=self.fig, savefig=False)
sp.set_markercolor('red')
sp.set_markeredgewidth(2.)
sp.plot_spikes(
[self.ref],
label='ref',
draw=False,
)
sp.set_markercolor('blue')
sp.plot_spikes([self.comp + self.t],
label='comp',
cell_offset=1,
draw=False)
coincidences, mask_a, mask_b, ratio = \
spiketrain.get_sync_traits( self.ref, self.comp+self.t, window=5)
idx = 0
for i in mask_a:
if i == 1:
self.raster_ax.plot([self.ref[idx]], [.6],
marker='o',
color='red')
idx += 1
idx = 0
for i in mask_b:
if i == 1:
self.raster_ax.plot([self.comp[idx] + self.t], [2.4],
marker='o',
color='blue')
idx += 1
self.raster_ax.set_yticks([1, 2])
self.raster_ax.set_yticklabels(['', '%+.1f ms' % self.t])
self.raster_ax.set_xlim(self.axlim)
def plot(self):
# spiketrains should be all the times of the spikes in a list separated by neuron, a list of lists
spiketrains = self.get_spiketrains()
sp = spikeplot.SpikePlot()
sp.set_markerscale(0.5)
sp.plot_spikes(spiketrains)
def plot_one_neuron(self, neuron):
if neuron in self.recordings:
spiketrain = self.recordings[neuron]
sp = spikeplot.SpikePlot()
sp.set_markerscale(0.5)
sp.plot_spikes(spiketrain)
def show_plots(time, v_plts, currents, spikes):
plt.figure('A')
plt.plot(time, v_plts[0], 'g-')
plt.plot(time, currents[0], 'r-')
plt.figure('B')
plt.plot(time, v_plts[1], 'b-')
plt.plot(time, currents[1], 'y-')
plt.figure('X')
plt.plot(time, v_plts[2], 'k-')
plt.plot(time, currents[2], 'm-')
plt.figure('All')
plt.plot(time, v_plts[0], 'g-')
plt.plot(time, currents[0], 'r-')
plt.plot(time, v_plts[1], 'b-')
plt.plot(time, currents[1], 'y-')
plt.plot(time, v_plts[2], 'k-')
plt.plot(time, currents[2], 'm-')
sp = spikeplot.SpikePlot()
sp.plot_spikes(spikes)
plt.show()
ax1.legend(field, ['field'])
ax1.set_ylabel('mV')
ax1.set_xlabel('time (ms)')
#----------------------------------------------------------------------------
# Raster plot
#----------------------------------------------------------------------------
labels = ['PY', 'IN', 'TC', 'RE']
y = [50, 150, 250, 350]
fig_handle = pyplot.figure(figsize=(8, 4))
ax = fig_handle.add_subplot(111)
ax.set_title('Raster plot')
ax.set_xlabel('$t$ (ms)') # Note LaTeX
ax.set_yticks([])
sp = spikeplot.SpikePlot(fig=fig_handle)
sp.set_markerscale(2)
sp.set_marker('.')
PYspikes = spiketrain.netconvecs_to_listoflists(PYtimevec, PYidvec)
sp.set_markercolor('black')
sp.plot_spikes(PYspikes, draw=False, label='PY')
INspikes = spiketrain.netconvecs_to_listoflists(INtimevec, INidvec)
sp.set_markercolor('blue')
sp.plot_spikes(INspikes, cell_offset=len(PYspikes), label='IN')
TCspikes = spiketrain.netconvecs_to_listoflists(TCtimevec, TCidvec)
sp.set_markercolor('red')
sp.plot_spikes(TCspikes, cell_offset=len(PYspikes) + len(INspikes), label='TC')
tau_inh = 5
tau_ADP = 200
A_inh = -4
A_ADP = 10
V_ADP = 0
V_inh = 0
k_inh = math.exp(-1.0/tau_inh)
k_adp = math.exp(-1.0/tau_ADP)
spiketrain = []
for time in range(2000):
V_ADP = V_ADP*k_ADP
V_inh = V_inh*k_inh
V = V_rest + V_ADP + V_inh
if V > V_thresh:
V = V_rest
V_inh = V_inh + A_inh
V_ADP = A_ADP
spiketrain.append(time)
sp = spikeplot.SpikePlot()
sp.set_markerscale(0.5)
sp.plot_spikes(spiketrain)
# i, i+1, gap_w, 0)
soma_v_vec = [[] for y in range(myN)]
dend_v_vec = [[] for y in range(myN)]
t_vec = [[] for y in range(myN)]
for i in range(myN):
soma_v_vec[i], dend_v_vec[i], t_vec[i] = \
simrun.set_recording_vectors(ring.cells[i])
simrun.simulate(tstop=100)
for i in [5, 15, 25, 35, 45]:
simrun.show_output(soma_v_vec[i], dend_v_vec[i], t_vec[i])
pyplot.show()
#Uncomment shape3D() above to make this worthwhile
#shape_window = h.PlotShape()
#shape_window.exec_menu('Show Diam')
spikes = ring.get_spikes()
if len(spikes) > 1:
from neuronpy.graphics import spikeplot
filename = 'spikeplot' + str(nSim) + '.png'
sp = spikeplot.SpikePlot(savefig=False)
sp.set_fig_name(fig_name=filename)
sp.set_marker('.')
sp.set_markerscale(1.5)
sp.set_markercolor('red')
#sp.set_markeredgewidth(7)
sp.plot_spikes(spikes)
def raster(pair=[0,4], cluster_width=5, fi=.005, xlim=(1000,2000)):
# pos1 = (10+pair[0]*20, cluster_width, 1, pair)
# pos2 = (10+pair[1]*20, cluster_width, 1, pair)
# stim_odor_mags = numpy.ones(5)*.55
fig = pyplot.figure(figsize=(9.5,5.7))
raster_ax = fig.add_axes([.1,.1,.8,.27])
schematic_ax = fig.add_axes([.1,.85,.8,.1])
syn_ax = fig.add_axes([.1,.45,.8,.225])
draw_cell(pair[0], schematic_ax, color='red')
draw_cell(pair[1], schematic_ax, color='blue')
draw_weights(pair, schematic_ax, color='black')
# Analyze an output file in some_dir
bulb_spikes = BulbSpikes(sim_time=sim_var['tstop'])
bulb_spikes.read_file(os.path.join(homedir,'spikeout.spk'))
breath_events = numpy.loadtxt(os.path.join(homedir, 'breathevents.txt'))
wts = read_weightevents()
delays = read_delayevents()
dt = 1
tstop = xlim[1]
x = numpy.arange(0,tstop,dt)
y0 = numpy.zeros(tstop/dt)
y1 = numpy.zeros(tstop/dt)
EXP = numpy.exp(numpy.multiply(x,-1./200.))-numpy.exp( \
numpy.multiply(x,-1./20.))
idx = 0
for b in breath_events:
if b >= tstop:
break
else:
dtidx = int((b+delays[pair[0]][idx])/dt)
y0[dtidx:] += EXP[:-dtidx]*wts[pair[0]][idx]
dtidx = int((b+delays[pair[1]][idx])/dt)
y1[dtidx:] += EXP[:-dtidx]*wts[pair[1]][idx]
idx += 1
redplt = syn_ax.plot(x,y0, color='red')
blueplt = syn_ax.plot(x,y1, color='blue')
for breath in breath_events:
breathplt = syn_ax.plot([breath, breath], [0,2], linestyle='--', \
color='gray', linewidth=2)
syn_ax.set_xlim(xlim)
syn_ax.set_ylim(0,1.6)
syn_ax.set_yticks([])
syn_ax.set_xticks([])
syn_ax.set_ylabel('EPSC onto tuft')
leg = syn_ax.legend([breathplt, redplt, blueplt], \
['sniff event', 'input onto red', 'input onto blue'], \
bbox_to_anchor=(0, 1.15, 1., .102), loc=1, ncol=3, mode="expand", \
borderaxespad=0., handletextpad=.2)
# Mark sniff interval
for i in range(len(breath_events)):
if breath_events[i] > xlim[0]:
span = syn_ax.annotate('', xy=(breath_events[i], .28), xycoords='data',
xytext=(breath_events[i+1], .28), \
textcoords='data', \
arrowprops=dict(arrowstyle="|-|", linewidth=2)
)
syn_ax.text((breath_events[i]+breath_events[i+1])/2., .53, \
'sniff every\n150 - 250 ms', \
horizontalalignment='center', verticalalignment='top', \
backgroundcolor='white')
break
# Mark amplitude interval
span = syn_ax.annotate('', xy=(1190, 1.28), xycoords='data',
xytext=(1190, 1.12), \
textcoords='data', \
arrowprops=dict(arrowstyle="|-|", linewidth=2)
)
syn_ax.text(1215, 1.21, \
'+/- 5%', \
horizontalalignment='left', verticalalignment='center')
# Mark delay interval
for i in range(len(breath_events)):
if breath_events[i] > 1400:
span = syn_ax.annotate('', xy=(breath_events[i]-2, .5), xycoords='data',
xytext=(breath_events[i]+17, .5), \
textcoords='data', \
arrowprops=dict(arrowstyle="|-|", linewidth=2)
)
syn_ax.text(breath_events[i]+7.5, .28, \
'delay 0-15 ms', \
horizontalalignment='center', verticalalignment='top', \
backgroundcolor='white')
break
spikes = bulb_spikes.get_mitral_spikes()
ref=spikes[pair[0]]
comp=spikes[pair[1]]
gcspikes = bulb_spikes.get_granule_spikes()
mididx = 10+pair[0]*20
gcleft = gcspikes[mididx-int(cluster_width/2.):mididx+int(cluster_width/2.)+1]
mididx = 10+pair[1]*20
gcright = gcspikes[mididx-int(cluster_width/2.):mididx+int(cluster_width/2.)+1]
sp = spikeplot.SpikePlot(fig=fig, savefig=False)
sp.set_markercolor('blue')
sp.set_markeredgewidth(2.)
sp.set_markerscale(4)
sp.plot_spikes([comp], label='comp', cell_offset=cluster_width*2+5, \
draw=False )
sp.set_markercolor('red')
sp.plot_spikes([ref], label='ref', cell_offset=cluster_width*2+2, \
draw=False)
sp.set_markerscale(1.3)
sp.set_markeredgewidth(1.5)
sp.set_markercolor('blue')
sp.plot_spikes(gcright, label='gcright', cell_offset=cluster_width, \
draw=False)
sp.set_markercolor('red')
sp.plot_spikes(gcleft, label='gcleft', cell_offset=0, \
draw=False)
coincidences, mask_a, mask_b, ratio = \
spiketrain.get_sync_traits(ref, comp, window=5)
# idx = 0
# for i in mask_a:
# if i == 1:
# raster_ax.plot([ref[idx]],[cluster_width*2+1.9], marker='o', color='red')
# idx += 1
idx = 0
for i in mask_b:
if i == 1:
if comp[idx] >= xlim[0] and comp[idx] < xlim[1]:
raster_ax.text(comp[idx],cluster_width*2+8.5, '*', \
color='purple', fontweight='bold', \
horizontalalignment='center', verticalalignment='center')
#raster_ax.plot([comp[idx]],[cluster_width*2+7], marker='o', color='blue')
idx += 1
raster_ax.text(2000,cluster_width*2+8.5, '(synchronized)', color='purple', \
horizontalalignment='center', verticalalignment='center',
fontsize=11)
raster_ax.set_yticks([])
ylim = (0.5, cluster_width*2+7.5)
for breath in breath_events:
raster_ax.plot([breath, breath], [ylim[0], ylim[1]], linestyle='--', color='gray', linewidth=2)
sp.update_xlim(xlim)
raster_ax.set_ylim(ylim)
raster_ax.set_xlabel('time (ms)')
raster_ax.set_ylabel('spike output\n granule mitral\n\n', horizontalalignment='center')
pos = schematic_ax.get_position()
schematic_ax.text(.025, pos.ymax+.02, 'A)', transform=fig.transFigure,
verticalalignment='baseline')
pos = syn_ax.get_position()
syn_ax.text(.025, pos.ymax+.07, 'B)', transform=fig.transFigure,
verticalalignment='baseline')
pos = raster_ax.get_position()
raster_ax.text(.025, pos.ymax+.02, 'C)', transform=fig.transFigure,
verticalalignment='baseline')
# fig.savefig(os.path.join(analysis_path, 'raster_w%d_(%d-%d)_%.3f.pdf') %(cluster_width, pair[0], pair[1], fi))
fig.savefig(os.path.join(analysis_path, 'fig1.pdf'))
for a in range(Ncells):
cells[a].soma.el_clarke =\
(cells[a].soma.ina_clarke + cells[a].soma.ikrect_clarke\
+ cells[a].soma.icaN_clarke + cells[a].soma.icaL_clarke\
+ cells[a].soma.ikca_clarke + cells[a].soma.inap_clarke\
+ cells[a].soma.gl_clarke*cells[a].soma.v) / cells[a].soma.gl_clarke
cells[a].dend.e_pas =\
(cells[a].dend.g_pas * cells[a].dend.v) / cells[a].dend.g_pas
# print 'hello from inside init'
h.celsius = 37
net = ClarkeNetwork()
h.v_init = -65
fih = h.FInitializeHandler(2, (tweak_leak, (net.cells, len(net.cells))))
shape_window = h.PlotShape()
shape_window.exec_menu('Show Diam')
soma_v_vec, soma_m_vec, soma_h_vec, soma_n_vec,\
soma_inap_vec, soma_idap_vec, soma_ical_vec,\
soma_ican_vec, soma_ikca_vec, soma_ina_vec, soma_ikrect_vec,\
dend_v_vec, t_vec\
= simrun.set_recording_vectors(net.cells[0])
simrun.simulate(tstop=10000)
simrun.show_output(soma_v_vec, dend_v_vec, t_vec)
pyplot.show()
spikes = net.get_spikes()
sp = spikeplot.SpikePlot(savefig=True)
sp.plot_spikes(spikes)