def plot_voltage_ipsp(ax, v_mat, ipsp_mat):
colors = ['b', 'g', 'r']
labels = [
r'$ref_{init}^{MSN}$', r'$ref_{max}^{MSN}$', r'$ref_{25 Hz}^{GPe}$'
]
coords = [[0.64, 0.3], [0.1, 0.29], [0.55, 0.7]]
for i, color in enumerate(colors):
ax.plot(v_mat[i, :], ipsp_mat[i, :], **{'color': color})
ax.set_ylabel('IPSP amplitude (mV)')
ax.set_xlabel('Holding potential (mV)')
ax.set_xlim(misc.adjust_limit([-80, -65]))
#ax.set_ylim(misc.adjust_limit([-4,2]))
lines = ax.lines
for line in lines:
misc.slice_line(line, xlim=[-80, -65])
for label, coord, color in zip(labels, coords, colors):
ax.text(coord[0],
coord[1],
label,
transform=ax.transAxes,
fontsize=pylab.rcParams['text.fontsize'] + 2,
**{'color': color})
ax.my_set_no_ticks(yticks=8, xticks=6)
def plot_example_3x_freq(ax, times, spk_mean, hzs=[10, 20, 40]):
spk_mean = spk_mean
colors = misc.make_N_colors('YlOrBr', 5)[2:]
labels = ['%i Hz' % hzs[0], '%i Hz' % hzs[1], '%i Hz' % hzs[2]]
coords = [[0.4, 0.52], [0.05, 0.22], [0.1, 0.74]]
for i, col in enumerate(colors):
ax.plot(times,
misc.convolve(spk_mean[i, :], 50, 'triangle', single=True)[0],
color=col)
#ax.plot(times, spk_mean[i,:], col)
lines = ax.lines
for line in lines:
line.set_xdata(line.get_xdata() - ADJUST_XDATA_MS)
misc.slice_line(line, xlim=[0, 1490])
#ax.set_ylim([0,40])
for label, coord, color in zip(labels, coords, colors):
ax.text(coord[0],
coord[1],
label,
transform=ax.transAxes,
fontsize=font_size_text,
**{'color': color})
ax.set_ylabel('Rate SNr (spikes/s)')
ax.set_xlabel('Time (ms)')
ax.my_set_no_ticks(yticks=6, xticks=8)
ax.set_xlim(misc.adjust_limit([0, 1500]))
ax.set_ylim(misc.adjust_limit([0, 40]))
def plot_selection_vs_neurons_full(ax, hzs, data):
colors = ['b', 'g', 'm']
labels = [
r'$\delta_{weak}^{MSN}$', r'$\delta_{strong}^{MSN}$',
r'$\delta_{fac}^{MSN}$'
]
coords = [[0.03, 0.8], [0.05, 0.07], [0.03, 0.50]]
syn = SYNAPSE_MODELS_TESTED
for id, label, color in zip([0, 1, 2], labels, colors):
ax.plot(hzs, data[syn[id]]['thrVec'], **{'color': color})
lines = ax.lines
for line in lines:
misc.slice_line(line, xlim=[0, 48])
ax.set_xlabel('Frequency MSN (Hz)')
ax.set_ylabel('MSNs at thr (#)')
ax.my_set_no_ticks(yticks=6, xticks=6)
for label, coord, color in zip(labels, coords, colors):
ax.text(coord[0],
coord[1],
label,
transform=ax.transAxes,
fontsize=pylab.rcParams['text.fontsize'],
**{'color': color})
ax.set_xlim(misc.adjust_limit([0, 48]))
ax.set_ylim(misc.adjust_limit([0, 75]))
def plot_SNr_rate_vs_syn_event1(ax, syn_events, meanRates):
colors = ['k']
labels = [r'$\delta_{dep}^{GPe}$']
coords = [[0.1, 0.15]]
for id, label, color in zip([0], labels, colors):
ax.plot(syn_events, meanRates[id, :], **{'color': color})
vec = [0, 800]
ax.set_ylabel('Firing rate SNr (spikes/s)')
ax.set_xlabel('Synaptic events (#/s)')
ax.my_set_no_ticks(yticks=6, xticks=5)
for label, coord, color in zip(labels, coords, colors):
ax.text(coord[0],
coord[1],
label,
transform=ax.transAxes,
fontsize=pylab.rcParams['text.fontsize'],
**{'color': color})
lines = ax.lines
for line in lines:
misc.slice_line(line, xlim=[0, 800])
ax.set_xlim(misc.adjust_limit([0, 800]))
ax.set_ylim(misc.adjust_limit([20, 115]))
def plot_selection_vs_neurons_indirect_linear_fit_and_spread(ax, mods, slope):
colors = ['b', 'g', 'r']
labels = [r'First 100 ms', r'250-350 ms', r'Last 100 ms']
coords = [[0.55, 0.15], [0.07, 0.47], [0.15, 0.78]]
ps = []
for i, color in enumerate(colors):
ax.plot(mods, slope[i, :], **{'color': color, 'linestyle': '-'})
#x,y,dy=fit_pol(MSNmeanRates,SNRmeanRates[i,:])
#ax.plot(x,y,**{'color':color})
'''
ax.plot([0,2.5],[SELECTION_THR]*len([0,2]),**{'color':[0.6,0.6,0.6],
'label':'', 'linewidth':1,
'linestyle':'--'})
ax.text( 0.8, 0.20,'Thr' , transform=ax.transAxes, **{ 'color' : [0.6,0.6,0.6]})
'''
ax.set_ylabel('$\Delta_{SNr}/ \Delta_{MSN_{D2}}$')
ax.set_xlabel('Percent bursting $MSN_{D2}$ (%)')
ax.my_set_no_ticks(yticks=8, xticks=6)
#ax.set_xlim(misc.adjust_limit([15, 50]))
ax.set_ylim(misc.adjust_limit([0, 1.3]))
lines = ax.lines
for line in lines:
misc.slice_line(line, xlim=[0, 50])
for label, coord, color in zip(labels, coords, colors):
ax.text(coord[0],
coord[1],
label,
transform=ax.transAxes,
fontsize=12,
**{'color': color})
def plot_selection_vs_neurons_full_extra(ax, hzs, data):
colors = ['b', 'g', 'm']
labels = [
r'$\delta_{weak}^{MSN}$', r'$\delta_{strong}^{MSN}$',
r'$\delta_{fac}^{MSN}$'
]
syn = SYNAPSE_MODELS_TESTED
for id, label, color in zip([0, 1, 2], labels, colors):
ax.plot(hzs, data[syn[id]]['thrVec'], **{
'color': color,
'linestyle': '--'
})
lines = ax.lines
for line in lines:
misc.slice_line(line, xlim=[0, 48])
line1 = ax.plot(1, 1, '-k')
line2 = ax.plot(1, 1, '--k')
leg = ax.legend(
[line1, line2],
['First 200 ms of \nthe burst', '300-500 ms of \nthe burst'],
loc='best')
frame = leg.get_frame()
#frame.set_visible(False)
pylab.setp(frame, edgecolor='w')
ltext = leg.get_texts() # all the text.Text instance in the legend
pylab.setp(ltext, fontsize=10., backgroundcolor='w')
ax.set_xlim(misc.adjust_limit([-7, 48]))
ax.set_ylim(misc.adjust_limit([0, 100]))
def plot_SNr_rate_vs_syn_event1(ax, syn_events, meanRates, meanRatesStd):
colors = ['k']
labels = [r'$\delta_{fac}^{MSN}$']
coords = [[0.04, 0.16]]
for id, label, color in zip([2], labels, colors):
ax.plot(syn_events, meanRates[id, :], **{'color': color})
# ax.fill_between(syn_events, meanRates[id,:]+meanRatesStd[id,:],
# meanRates[id,:]-meanRatesStd[id,:],
# facecolor=color, alpha=0.5)
vec = [50, 600]
ax.plot(
vec, [SELECTION_THR] * len(vec), **{
'color': [0.6, 0.6, 0.6],
'label': '',
'linewidth': 1,
'linestyle': '--'
})
ax.text(0.8,
0.17,
'Thr',
transform=ax.transAxes,
**{'color': [0.6, 0.6, 0.6]})
ax.set_ylabel('Frequency SNr (Hz)')
ax.set_xlabel('Synaptic events (#/s)')
ax.my_set_no_ticks(yticks=6, xticks=5)
x_arrow = 285. / 600.
y_arrow = 2. / 50.
ax.arrow(x_arrow,
y_arrow,
0,
0.02,
transform=ax.transAxes,
width=0.01,
head_width=0.03,
head_starts_at_zero=True,
head_length=0.02,
**{'color': 'k'})
for label, coord, color in zip(labels, coords, colors):
ax.text(coord[0],
coord[1],
label,
transform=ax.transAxes,
fontsize=pylab.rcParams['text.fontsize'],
**{'color': color})
lines = ax.lines
for line in lines:
misc.slice_line(line, xlim=[0, 600])
ax.set_xlim(misc.adjust_limit([50, 600]))
ax.set_ylim(misc.adjust_limit([0, 35]))
def plot_SNr_rate_vs_syn_event2(ax, nbNeurons, meanRates):
colors = ['k']
ax.plot(nbNeurons, meanRates[2, :], **{
'color': colors[0],
'linestyle': '-.'
})
ax.set_ylabel('Frequency SNr (Hz)')
ax.set_xlabel('Synaptic events (#/s)')
ax.my_set_no_ticks(yticks=5, xticks=5)
line1 = ax.plot(1, 1, '-k')
line2 = ax.plot(1, 1, '-.k')
leg = ax.legend(
[line1, line2],
['Bursting subpopulation', 'Increased activity in \nall MSNs'],
loc='best')
frame = leg.get_frame()
frame.set_visible(False)
ltext = leg.get_texts() # all the text.Text instance in the legend
lines = ax.lines
for line in lines:
misc.slice_line(line, xlim=[0, 600])
pylab.setp(ltext, fontsize=10.)
ax.set_xlim(misc.adjust_limit([50, 600]))
ax.set_ylim(misc.adjust_limit([0, 35]))
def plot_example_rebound_spike(ax, SNR):
SNR.signals['V_m'].plot(display=ax, kwargs={'color': 'k'})
ax.set_xlim(misc.adjust_limit([300, 1000]))
ax.set_ylim(misc.adjust_limit([-85, 30]))
line = ax.lines
misc.slice_line(line[0], xlim=[300, 1000])
ax.my_set_no_ticks(yticks=3, xticks=6)
ax.set_ylabel('SNr potential (mV)')
def plot_steady_state_freq(ax, freq_, relative_fac):
colors = ['b', 'g', 'm']
linestyles = ['--', '--', '-']
labels = [
r'$ref_{init}^{MSN_{D1}}$', r'$ref_{max}^{MSN_{D1}}$',
r'$fac^{MSN_{D1}}$'
]
coords = [[0.1, 0.22], [0.2, 0.74], [0.65, 0.45]]
syn_static = ['MSN_SNR_gaba_s_min', 'MSN_SNR_gaba_s_max']
ax.plot(freq_, relative_fac[0, :], **{'color': colors[2]})
ytext = ax.set_ylabel(r'$p_{ss}$/$p_1$')
#pylab.setp(ytext, fontsize=14.)
ax.set_xlabel('Firing rate (spikes/s)')
ax.my_set_no_ticks(yticks=5, xticks=5)
my_nest.ResetKernel()
model_list, model_dict = models()
syns = [SYNAPSE_MODELS[0]]
syns.extend(syn_static)
my_nest.MyLoadModels(model_list, syns)
xdata = ax.lines[0].get_xdata()
ss = my_nest.GetDefaults(SYNAPSE_MODELS[0])
synapticEficacy = ss['weight'] * ss['U']
for syn, color, ls in zip(syn_static, colors[0:2], linestyles[0:2]):
sw = my_nest.GetDefaults(syn)
ax.plot(
[min(xdata), 48],
[sw['weight'] / synapticEficacy, sw['weight'] / synapticEficacy],
**{
'color': color,
'linestyle': ls
})
for coord, label, color in zip(coords, labels, colors):
ax.text(coord[0],
coord[1],
label,
transform=ax.transAxes,
fontsize=pylab.rcParams['font.size'] + 2,
**{'color': color})
lines = ax.lines
for line in lines:
misc.slice_line(line, xlim=[0, 48])
ax.set_xlim(misc.adjust_limit([0, 50]))
ax.set_ylim(misc.adjust_limit([0, 5]))
ax.my_set_no_ticks(yticks=6, xticks=6)
pylab.setp(ax.lines,
linewidth=2.0) # Need to pu ti before generating legend
def plot_selection_vs_neurons_full(ax, hzs, data):
colors = ['b', 'g', 'm']
labels = [
r'$ref_{init}^{MSN_{D1}}$', r'$ref_{max}^{MSN_{D1}}$',
r'$fac_{MSN_{D1}}$'
]
coords = [[0.03, 0.8], [0.05, 0.07], [0.03, 0.50]]
syn = SYNAPSE_MODELS_TESTED
for id, label, color in zip([0, 1, 2], labels, colors):
ax.plot(hzs,
numpy.array(data[id]['msn_at_thr'][0]) / float(N_MSN) * 100.,
**{'color': color})
for id, label, color in zip([0, 1, 2], labels, colors):
ax.plot(hzs,
numpy.array(data[id]['msn_at_thr'][1]) / float(N_MSN) * 100.,
**{
'color': color,
'linestyle': '--'
})
lines = ax.lines
for line in lines:
misc.slice_line(line, xlim=[0, 48])
ax.set_xlabel(r'Rate $MSN_{D1}$ (spikes/s)')
ax.set_ylabel(r'Bursting $MSN_{D1}$ at thr (%)')
ax.my_set_no_ticks(yticks=8, xticks=6)
for label, coord, color in zip(labels, coords, colors):
ax.text(coord[0],
coord[1],
label,
transform=ax.transAxes,
fontsize=pylab.rcParams['text.fontsize'],
**{'color': color})
line1 = ax.plot(1, 1, '-k')
line2 = ax.plot(1, 1, '--k')
leg = ax.legend(
[line1, line2],
['First 100 ms of \nthe burst', 'Last 100 ms of \nthe burst'],
loc='best')
frame = leg.get_frame()
#frame.set_visible(False)
pylab.setp(frame, edgecolor='w')
ltext = leg.get_texts() # all the text.Text instance in the legend
pylab.setp(ltext, fontsize=font_size_text, backgroundcolor='w')
ax.set_xlim(misc.adjust_limit([6, 48]))
ax.set_ylim(misc.adjust_limit([0, 30]))
def plot_indirect(ax, data, idx_show=[0, 1, 2], title='', ylim=[0, 34]):
colors = ['k', 'k', 'k', 'k', 'k', 'k', 'k', 'k', 'k', 'k', 'k', 'k']
labels = [r'1 % bursting', r'2 % bursting', r'4 % bursting']
linestyles = [
'-', '--', '-.', '-', '--', '-.', '-', '--', '-.', '-', '--', '-.'
]
coords = [[0.4, 0.42], [0.02, 0.001], [0.15, 0.78]]
data = [data[i] for i in idx_show]
for i, d in enumerate(data):
lb = r'%i %s bursting' % (d[0][0], '%')
x, y_mean, y_std = d.take([1, 2, 3], axis=0)
ax.plot(
x, y_mean, **{
'color': colors[i],
'label': lb,
'linestyle': linestyles[i]
})
ax.fill_between(x,
y_mean - y_std,
y_mean + y_std,
facecolor=colors[i],
alpha=0.5)
pylab.setp(ax.lines,
linewidth=2.0) # Need to pu ti before generating legend
leg = ax.legend(loc='best')
frame = leg.get_frame()
frame.set_visible(False)
ltext = leg.get_texts() # all the text.Text instance in the legend
pylab.setp(ltext, fontsize=font_size_text)
'''
ax.plot([0,2.5],[SELECTION_THR]*len([0,2]),**{'color':[0.6,0.6,0.6],
'label':'', 'linewidth':1,
'linestyle':'--'})
ax.text( 0.8, 0.20,'Thr' , transform=ax.transAxes, **{ 'color' : [0.6,0.6,0.6]})
'''
ax.set_ylabel('Rate SNr (spikes/s)')
ax.set_xlabel('Burst rate $MSN_{D2}$ (spikes/s)')
ax.my_set_no_ticks(yticks=8, xticks=6)
ax.set_title(title, fontsize=font_size_text)
ax.set_xlim(misc.adjust_limit([15, 50]))
ax.set_ylim(misc.adjust_limit(ylim))
lines = ax.lines
for line in lines:
misc.slice_line(line, xlim=[0, 50])
def plot_example_SNR(ax, SNR_list):
time_bin = 20
colors = ['r', 'c']
labels = [r'$\delta_{ref}^{GPe}$', r'$\delta_{dep}^{GPe}$']
coords = [[0.05, 0.60], [0.05, 0.2]]
SNR_list = [SNR_list[0], SNR_list[1]]
for color, label, SNR in zip(colors, labels, SNR_list):
signal = SNR.signals['spikes']
signal.my_firing_rate(bin=time_bin,
display=ax,
kwargs={'color': color})
lines = ax.lines
lines[0].set_xdata(lines[0].get_xdata() - ADJUST_XDATA_MS)
lines[1].set_xdata(lines[1].get_xdata() - ADJUST_XDATA_MS)
ax.plot([0, 1690], [SELECTION_THR] * len([0, 2990]), **{
'color': [0.6, 0.6, 0.6],
'label': '',
'linewidth': 1,
'linestyle': '--'
})
ax.text(0.9,
0.13,
'Thr',
transform=ax.transAxes,
**{'color': [0.6, 0.6, 0.6]})
misc.slice_line(lines[0], xlim=[0, 1690])
misc.slice_line(lines[1], xlim=[0, 1690])
#ax.set_title('bin=%i'%(time_bin),**{'fontsize':12})
ax.set_ylabel('Firing rate SNr (spikes/s)')
ax.set_xlabel('Time (ms)')
ax.my_set_no_ticks(yticks=6, xticks=8)
ax.set_xlim(misc.adjust_limit([0, 1700]))
ax.set_ylim(misc.adjust_limit([0, 50]))
for label, coord, color in zip(labels, coords, colors):
ax.text(coord[0],
coord[1],
label,
transform=ax.transAxes,
fontsize=pylab.rcParams['text.fontsize'],
**{'color': color})
def plot_example_SNR(ax, SNR_list, flag):
time_bin=20
colors=misc.make_N_colors('cool',3)
colors=['m','c',colors[1]]
#labels=[r'$\delta_{fac}^{MSN}$' , r'$\delta_{dep}^{GPe}$',
# r'$\delta_{fac}^{MSN}$+$\delta_{dep}^{GPe}$']
coords=[[0.05, 0.2], [ 0.05, 0.65], [0.05, 0.8]]
SNR_list=[SNR_list[0], SNR_list[1], SNR_list[2]]
for color, SNR in zip(colors, SNR_list):
signal=SNR.signals['spikes']
signal.my_firing_rate(bin=time_bin, display=ax, kwargs={'color':color})
lines = ax.lines
for line in lines:
line.set_xdata(line.get_xdata()-ADJUST_XDATA_MS)
misc.slice_line(line, xlim=[0,1490])
if flag==0:
leg=ax.legend(lines,['Burst in MSN subpopulation' , 'Burst in GPe subpopulation',
'Burst in both MSN- and GPe subpopulations'], loc=2)
if flag==1:
leg=ax.legend(lines,['Burst in MSN subpopulation' , 'Pause in GPe subpopulation',
'Burst in MSN- and pause in GPe subpopulations'], loc=2)
frame = leg.get_frame()
#frame.set_visible(False)
pylab.setp(frame, edgecolor='w')
ltext = leg.get_texts() # all the text.Text instance in the legend
pylab.setp(ltext, fontsize=12., backgroundcolor='w')
ax.plot([0, 1490],[SELECTION_THR]*len([0, 1490]),**{'color':[0.6,0.6,0.6],
'label':'', 'linewidth':1,
'linestyle':'--'})
ax.text( 0.9, 0.11,'Thr' , transform=ax.transAxes, **{ 'color' : [0.6,0.6,0.6]})
#ax.set_title('bin=%i'%(time_bin),**{'fontsize':12})
ax.set_ylabel('Firing rate SNr (spikes/s)')
ax.set_xlabel('Time (ms)')
ax.my_set_no_ticks( yticks=7, xticks=8 )
ax.set_xlim(misc.adjust_limit([0,1500]))
ax.set_ylim(misc.adjust_limit([0,115]))
def plot_selection_vs_neurons_direct(ax, MSNmeanRates, SNRmeanRates):
colors = ['b', 'g', 'm']
labels = [
r'$\delta_{weak}^{MSN}$', r'$\delta_{strong}^{MSN}$',
r'$\delta_{fac}^{MSN}$'
]
coords = [[0.4, 0.42], [0.02, 0.001], [0.15, 0.78]]
for i, color in enumerate(colors):
ax.plot(MSNmeanRates, SNRmeanRates[i, :], **{
'color': color,
'marker': '.',
'linestyle': ''
})
#x,y,dy=fit_pol(MSNmeanRates,SNRmeanRates[i,:])
#x,y,dy=fit_exp(MSNmeanRates,SNRmeanRates[i,:])
#ax.plot(x,y,**{'color':color})
ax.plot([0, 2.5], [SELECTION_THR] * len([0, 2]), **{
'color': [0.6, 0.6, 0.6],
'label': '',
'linewidth': 1,
'linestyle': '--'
})
ax.text(0.8,
0.20,
'Thr',
transform=ax.transAxes,
**{'color': [0.6, 0.6, 0.6]})
ax.set_ylabel('Firing rate SNr (spikes/s)')
ax.set_xlabel('Firing rate MSN (spikes/s)')
ax.my_set_no_ticks(yticks=8, xticks=6)
ax.set_xlim(misc.adjust_limit([0, 50]))
ax.set_ylim(misc.adjust_limit([0, 34]))
lines = ax.lines
for line in lines:
misc.slice_line(line, xlim=[0, 50])
for label, coord, color in zip(labels, coords, colors):
ax.text(coord[0],
coord[1],
label,
transform=ax.transAxes,
fontsize=pylab.rcParams['text.fontsize'],
**{'color': color})
def plot_selection_vs_neurons(ax, GPEmeanRates, SNRmeanRates):
colors = ['b', 'b', 'g', 'g']
linestyles = ['-', '--', '-', '--']
for i, color in enumerate(colors):
ax.plot(GPEmeanRates[i, :], SNRmeanRates[i, :], **{
'color': color,
'linestyle': linestyles[i]
})
vec = [0, 100]
ax.set_ylabel('Rate SNr (spikes/s)')
ax.set_xlabel(r'Rate $MSN_{D2}$ (spikes/s)')
ax.my_set_no_ticks(yticks=8, xticks=6)
line1 = ax.plot(1, 1, '-k')
line2 = ax.plot(1, 1, '--k')
pylab.setp(ax.lines,
linewidth=2.0) # Need to pu ti before generating legend
leg = ax.legend([line1, line2], ['$dep^{GPe}$', '$ref_{32 Hz}^{GPe}$'],
loc='best')
frame = leg.get_frame()
frame.set_visible(False)
ltext = leg.get_texts() # all the text.Text instance in the legend
pylab.setp(frame, edgecolor='w')
ltext = leg.get_texts() # all the text.Text instance in the legend
pylab.setp(ltext,
fontsize=pylab.rcParams['text.fontsize'] - 2,
backgroundcolor='w')
lines = ax.lines
for line in lines:
misc.slice_line(line, xlim=[0, 100])
labels = ['Static \nSTN-SNr', 'Depressing \nSTN-SNr']
coords = [[0.55, 0.3], [0.3, 0.6]]
colors = ['b', 'g']
for label, coord, color in zip(labels, coords, colors):
ax.text(coord[0],
coord[1],
label,
transform=ax.transAxes,
fontsize=font_size_text,
**{'color': color})
ax.set_xlim(misc.adjust_limit([0, 4]))
ax.set_ylim(misc.adjust_limit([25, 150]))
def plot_filtering(ax, MSNmeanRates, SNRmeanRates):
colors = ['b', 'g', 'm']
linestyle = ['--', '--', '-']
labels = [
r'$ref_{init}^{MSN_{D1}}$', r'$ref_{max}^{MSN_{D1}}$',
r'$fac^{MSN_{D1}}$'
]
coords = [[0.4, 0.42], [0.02, 0.001], [0.15, 0.78]]
for i, color in enumerate(colors):
ax.plot(MSNmeanRates, SNRmeanRates[i, :], **{
'color': color,
'linestyle': linestyle[i]
})
ax.plot([0, 2.5], [SELECTION_THR] * len([0, 2]), **{
'color': 'k',
'label': '',
'linewidth': 1,
'linestyle': '--'
})
ax.text(0.8,
0.20,
'Thr',
fontsize=pylab.rcParams['font.size'] - 2,
transform=ax.transAxes,
**{'color': 'k'})
ax.set_ylabel('Rate SNr (spikes/s)')
ax.set_xlabel('Rate $MSN_{D1}$ (spikes/s)')
ax.my_set_no_ticks(yticks=8, xticks=6)
ax.set_xlim(misc.adjust_limit([0, 2.5]))
ax.set_ylim(misc.adjust_limit([-3, 34]))
lines = ax.lines
for line in lines:
misc.slice_line(line, xlim=[0, 2.6])
for label, coord, color in zip(labels, coords, colors):
ax.text(coord[0],
coord[1],
label,
transform=ax.transAxes,
fontsize=pylab.rcParams['font.size'],
**{'color': color})
pylab.setp(ax.lines,
linewidth=2.0) # Need to pu ti before generating legend
def plot_example_SNR(ax, SNR_list):
time_bin = 20
colors = ['b', 'g', 'm']
labels = [
r'$\delta_{weak}^{MSN}$', r'$\delta_{strong}^{MSN}$',
r'$\delta_{fac}^{MSN}$'
]
coords = [[0.4, 0.49], [0.05, 0.27], [0.1, 0.75]]
for color, SNR in zip(colors, SNR_list):
signal = SNR.signals['spikes']
signal.my_firing_rate(bin=time_bin,
display=ax,
kwargs={'color': color})
lines = ax.lines
for line in lines:
line.set_xdata(line.get_xdata() - ADJUST_XDATA_MS)
misc.slice_line(line, xlim=[0, 1490])
ax.plot([0, 1490], [SELECTION_THR] * len([0, 1490]), **{
'color': [0.6, 0.6, 0.6],
'label': '',
'linewidth': 1,
'linestyle': '--'
})
ax.text(0.9,
0.15,
'Thr',
transform=ax.transAxes,
**{'color': [0.6, 0.6, 0.6]})
#ax.set_title('bin=%i'%(time_bin),**{'fontsize':12})
ax.set_ylabel('Frequency SNr (Hz)')
ax.set_xlabel('Time (ms)')
ax.my_set_no_ticks(yticks=6, xticks=7)
ax.set_xlim(misc.adjust_limit([0, 1500]))
ax.set_ylim(misc.adjust_limit([0, 40]))
for label, coord, color in zip(labels, coords, colors):
ax.text(coord[0],
coord[1],
label,
transform=ax.transAxes,
fontsize=pylab.rcParams['text.fontsize'],
**{'color': color})
def plot_diff_3x_freq(ax, times, spk_mean ):
spk_mean=spk_mean
colors=['b','g','r']
for i, col in enumerate(colors):
#ax.plot(times, misc.convolve(spk_mean, 50, 'triangle',single=True)[0]*1000,col)
ax.plot(times, spk_mean[i,:], col)
lines = ax.lines
for line in lines:
line.set_xdata(line.get_xdata()-ADJUST_XDATA_MS)
misc.slice_line(line, xlim=[0,1490])
#ax.set_ylim([0,40])
ax.set_xlim(misc.adjust_limit([0,1500]))
ax.set_ylim(misc.adjust_limit([0,40]))
pylab.show()
def plot_example_snr(ax, SNR):
time_bin = 20
signal = SNR.signals['spikes']
colors = ['k']
sim_time = 2500
hist = signal.spike_histogram(time_bin=1, normalized=True)
spk_mean = numpy.mean(hist, axis=0)
spk_mean = misc.convolve(spk_mean, 100, 'triangle', single=True)[0]
time = numpy.arange(1, len(spk_mean) + 1)
ax.plot(time, spk_mean, 'k')
ax.my_set_no_ticks(yticks=6, xticks=7)
lines = ax.lines
lines = ax.lines
for line in lines:
misc.slice_line(line, xlim=[50, 2450])
ax.plot([0, sim_time], [SELECTION_THR] * len([0, sim_time]), **{
'color': [0.6, 0.6, 0.6],
'label': '',
'linewidth': 1,
'linestyle': '--'
})
ax.text(0.9,
0.14,
'Thr',
transform=ax.transAxes,
**{'color': [0.6, 0.6, 0.6]})
misc.slice_line(lines[0], xlim=[0, sim_time])
ax.plot([1000, 1500], [39, 39], color='k', marker='|')
ax.text(0.47, 0.84, 'stop', transform=ax.transAxes, **{'color': 'k'})
ax.plot([500, 700], [30, 30], color='k', marker='|')
ax.text(0.23, 0.67, '1st', transform=ax.transAxes, **{'color': 'k'})
ax.plot([1500, 1700], [30, 30], color='k', marker='|')
ax.text(0.60, 0.67, '2nd', transform=ax.transAxes, **{'color': 'k'})
ax.set_xlim(misc.adjust_limit([0, sim_time]))
ax.set_ylim(misc.adjust_limit([0, 45]))
ax.set_ylabel('Firing rate SNr (spikes/s)')
def plot_rate_first_and_second_bursts_full(ax, x, data):
colors = ['k']
max_delay = 3100
ax.text(0.1,
0.4,
r'$\delta_{fac}^{MSN}$',
fontsize=pylab.rcParams['text.fontsize'],
transform=ax.transAxes,
**{'color': colors[0]})
line1 = ax.plot(1, 1, '-k')
line2 = ax.plot(1, 1, '-.k')
leg = ax.legend([line1, line2], ['1st', '2nd'], loc='best')
frame = leg.get_frame()
frame.set_visible(False)
ax.plot([0, max_delay], [SELECTION_THR] * len([0, max_delay]), **{
'color': [0.6, 0.6, 0.6],
'label': '',
'linewidth': 1,
'linestyle': '--'
})
ax.text(0.8,
0.3,
'Thr',
transform=ax.transAxes,
**{'color': [0.6, 0.6, 0.6]})
ax.plot(x, data[0], **{'label': '1st', 'color': colors[0]})
ax.plot(x, data[1], **{
'label': '2nd',
'color': colors[0],
'linestyle': '-.'
})
ax.set_ylabel('Firing rate SNr (spikes/s)')
ax.set_xlabel('Burst stop (ms)')
ax.my_set_no_ticks(yticks=6, xticks=5)
lines = ax.lines
misc.slice_line(lines[2], xlim=[0, max_delay])
misc.slice_line(lines[3], xlim=[0, max_delay])
ax.set_xlim(misc.adjust_limit([0, max_delay]))
ax.set_ylim(misc.adjust_limit([3, 10]))
def plot_selection_vs_neurons_full(ax, hzs, data):
colors = ['m']
labels = [r'$\delta_{fac}^{MSN}$'] # , r'$\delta_{strong}^{MSN}$',
# r'$\delta_{fac}^{MSN}$']
coords = [[0.03, 0.8]] #, [ 0.05, 0.07], [0.03, 0.50]]
syn = SYNAPSE_MODELS_TESTED
for id, label, color in zip([0], labels, colors):
ax.plot(hzs, data[id]['msn_at_thr'][0], **{'color': color})
#for id, label, color in zip([0,1,2],labels,colors):
# ax.plot(hzs,data[id]['msn_at_thr'][1],**{'color':color,'linestyle':'--'})
lines = ax.lines
for line in lines:
misc.slice_line(line, xlim=[0, 48])
ax.set_xlabel('Firing rate MSN (spikes/s)')
ax.set_ylabel('Bursting MSNs at thr (#)')
ax.my_set_no_ticks(yticks=8, xticks=6)
for label, coord, color in zip(labels, coords, colors):
ax.text(coord[0],
coord[1],
label,
transform=ax.transAxes,
fontsize=pylab.rcParams['text.fontsize'],
**{'color': color})
line1 = ax.plot(1, 1, '-k')
line2 = ax.plot(1, 1, '--k')
leg = ax.legend(
[line1, line2],
['First 100 ms of \nthe burst', 'Last 100 ms of \nthe burst'],
loc='best')
frame = leg.get_frame()
#frame.set_visible(False)
pylab.setp(frame, edgecolor='w')
ltext = leg.get_texts() # all the text.Text instance in the legend
pylab.setp(ltext, fontsize=10., backgroundcolor='w')
ax.set_xlim(misc.adjust_limit([6, 48]))
ax.set_ylim(misc.adjust_limit([0, 100]))
def plot_selection_vs_neurons_direct2(ax, data, title, ylim=[0, 34]):
colors = ['k', 'k', 'k', 'k']
labels = [r'1 % bursting', r'2 % bursting', r'4 % bursting']
linestyles = ['-', '--', '-.', '.']
coords = [[0.4, 0.42], [0.02, 0.001], [0.15, 0.78]]
for i, d in enumerate(data):
c = 'k'
lb = r'%i %s bursting' % (d[0][0], '%')
ls = '--'
x, y_mean, y_std = d.take([1, 2, 3], axis=0)
ax.plot(x, y_mean, **{'color': c, 'label': lb, 'linestyle': ls})
ax.fill_between(x,
y_mean - y_std,
y_mean + y_std,
facecolor=c,
alpha=0.5)
#x,y,dy=fit_pol(MSNmeanRates,SNRmeanRates[i,:])
#ax.plot(x,y,**{'color':color})
leg = ax.legend(loc='best')
frame = leg.get_frame()
frame.set_visible(False)
ltext = leg.get_texts() # all the text.Text instance in the legend
pylab.setp(ltext, fontsize=10.)
'''
ax.plot([0,2.5],[SELECTION_THR]*len([0,2]),**{'color':[0.6,0.6,0.6],
'label':'', 'linewidth':1,
'linestyle':'--'})
ax.text( 0.8, 0.20,'Thr' , transform=ax.transAxes, **{ 'color' : [0.6,0.6,0.6]})
'''
ax.set_ylabel('Rate SNr (spikes/s)')
ax.set_xlabel('Burst rate $MSN_{D1}$ (spikes/s)')
ax.my_set_no_ticks(yticks=8, xticks=6)
ax.set_title(title, fontsize=12)
ax.set_xlim(misc.adjust_limit([15, 50]))
ax.set_ylim(misc.adjust_limit(ylim))
lines = ax.lines
for line in lines:
misc.slice_line(line, xlim=[0, 50])
def plot_selection_vs_neurons(ax, GPEmeanRates, SNRmeanRates):
colors=['r','c' ]
labels=[r'$\delta_{ref}^{GPe}$' , r'$\delta_{dep}^{GPe}$']
coords=[[0.15, 0.6], [ 0.4, 0.17]]
for i, color in enumerate(colors):
ax.plot(GPEmeanRates,SNRmeanRates[i,:],**{'color':color})
vec=[0,100]
ax.plot(vec,[SELECTION_THR]*len(vec),**{'color':[0.6,0.6,0.6],
'label':'', 'linewidth':1,
'linestyle':'--'})
ax.text( 0.05, 0.08,'Thr' , transform=ax.transAxes, **{ 'color' : [0.6,0.6,0.6]})
ax.set_ylabel('Firing rate SNr (spikes/s)')
ax.set_xlabel('Firing rate GPe (spikes/s)')
ax.my_set_no_ticks( yticks=8, xticks=8 )
SNRmr=SNRmeanRates[1,SNRmeanRates[1,:]<25]
GPEmr=GPEmeanRates[SNRmeanRates[1,:]<25]
GPEmr=GPEmr[SNRmr>=6.5]
SNRmr=SNRmr[SNRmr>=6.5]+7
#x_arrow=GPEmr[-1]
#y_arrow=SNRmr[-1]
#ax.arrow(x_arrow, y_arrow, 0, -2,
#width=1, head_width=3, head_starts_at_zero=True,
#head_length=2,**{ 'color':'k'})
ax.set_xlim(misc.adjust_limit([0,100]))
ax.set_ylim(misc.adjust_limit([0,110]))
lines = ax.lines
for line in lines:
misc.slice_line(line, xlim=[0,100])
for label, coord, color in zip(labels,coords,colors):
ax.text( coord[0], coord[1], label, transform=ax.transAxes,
fontsize=pylab.rcParams['text.fontsize'],
**{'color': color})
def plot_selection_vs_neurons_indirect2(ax, MSNmeanRates, SNRmeanRates):
colors = ['b', 'g', 'r']
labels = [r'First 100 ms', r'250-350 ms', r'Last 100 ms']
coords = [[0.4, 0.42], [0.02, 0.001], [0.15, 0.78]]
for i, color in enumerate(colors):
ax.plot(MSNmeanRates, SNRmeanRates[i, :], **{
'color': color,
'marker': '.',
'linestyle': '--'
})
#x,y,dy=fit_pol(MSNmeanRates,SNRmeanRates[i,:])
#ax.plot(x,y,**{'color':color})
ax.plot([0, 2.5], [SELECTION_THR] * len([0, 2]), **{
'color': [0.6, 0.6, 0.6],
'label': '',
'linewidth': 1,
'linestyle': '--'
})
ax.text(0.8,
0.20,
'Thr',
transform=ax.transAxes,
**{'color': [0.6, 0.6, 0.6]})
ax.set_ylabel('Firing rate SNr (spikes/s)')
ax.set_xlabel('Firing rate $MSN_{D2}$ (spikes/s)')
ax.my_set_no_ticks(yticks=8, xticks=6)
ax.set_xlim(misc.adjust_limit([17, 50]))
ax.set_ylim(misc.adjust_limit([34, 110]))
lines = ax.lines
for line in lines:
misc.slice_line(line, xlim=[0, 50])
for label, coord, color in zip(labels, coords, colors):
ax.text(coord[0],
coord[1],
label,
transform=ax.transAxes,
fontsize=12,
**{'color': color})
def plot_SNr_rate_std_vs_syn_event_x3_late(ax, hzs):
colors = misc.make_N_colors('YlOrBr', 5)[2:]
labels = ['%i Hz' % hzs[0], '%i Hz' % hzs[1], '%i Hz' % hzs[2]]
coords = [[0.4, 0.52], [0.05, 0.22], [0.1, 0.74]]
i_inverval = 1 # 0-100 ms
i_syn = 2 # Plastic
for hz, col in zip(hzs, colors):
nb, rate_data, r_std_data, n_max_sel, s = simulate_selection_vs_neurons(
SEL_INTERVALS, msn_burst_rate=hz, load=True)
syn_events = nb * hz + (N_MSN - nb) * 0.1
ax.plot(
syn_events,
rate_data[i_inverval][i_syn, :] / r_std_data[i_inverval][i_syn, :],
**{'color': col})
for label, coord, color in zip(labels, coords, colors):
ax.text(coord[0],
coord[1],
label,
transform=ax.transAxes,
fontsize=font_size_text,
**{'color': color})
ax.set_ylabel('Signal to noise ratio')
ax.set_xlabel('Input SNr (events/s)')
lines = ax.lines
for line in lines:
misc.slice_line(line, xlim=[0, LIM_SYN_EVENTS])
ax.my_set_no_ticks(yticks=6, xticks=5)
ax.set_xlim(misc.adjust_limit([50, LIM_SYN_EVENTS]))
ax.set_ylim(misc.adjust_limit([0, 4]))
ax.text(0.1,
0.85,
'Last 100 ms of the burst',
transform=ax.transAxes,
fontsize=font_size_text,
**{'color': 'k'})
def plot_MSN_vs_SNR_const_syn_events(ax, nMSN_range, SNRmeanRates):
colors = ['b', 'g', 'm']
labels = [
r'$\delta_{weak}^{MSN}$', r'$\delta_{strong}^{MSN}$',
r'$\delta_{fac}^{MSN}$'
]
coords = [[0.1, 0.68], [0.05, 0.12], [0.35, 0.45]]
for i, color in enumerate(colors):
ax.plot(nMSN_range, SNRmeanRates[i, :], **{'color': color})
ax.set_ylabel('Firing rate SNr (spikes/s)')
ax.set_xlabel('Bursting MSN (#)')
ax.my_set_no_ticks(yticks=7, xticks=6)
lines = ax.lines
for line in lines:
misc.slice_line(line, xlim=[0, N_MAX_BURSTING])
ax.plot([0, N_MAX_BURSTING], [SELECTION_THR] * len([0, 2]), **{
'color': [0.6, 0.6, 0.6],
'label': '',
'linewidth': 1,
'linestyle': '--'
})
ax.text(0.1,
0.33,
'Thr',
transform=ax.transAxes,
**{'color': [0.6, 0.6, 0.6]})
for label, coord, color in zip(labels, coords, colors):
ax.text(coord[0],
coord[1],
label,
transform=ax.transAxes,
fontsize=pylab.rcParams['text.fontsize'],
**{'color': color})
ax.set_xlim(misc.adjust_limit([0, N_MAX_BURSTING]))
ax.set_ylim(misc.adjust_limit([0, 18]))
def plot_signal_rates(ax, hzs, rates):
colors = ['b', 'm']
labels = [r'$\delta_{weak}^{MSN}$', r'$\delta_{fac}^{MSN}$']
coords = [[0.53, 0.49], [0.05, 0.21]]
syn = DP['SYNAPSE_MODELS_TESTED']
for id, label, color in zip([0, 2], labels, colors):
ax.plot(hzs, rates[:, id], **{'color': color})
ax.set_xlabel('Firing rate MSN burst (spikes/s)')
ax.set_ylabel('Firing rate SNr (spikes/s)')
ax.my_set_no_ticks(yticks=8, xticks=6)
for label, coord, color in zip(labels, coords, colors):
ax.text(coord[0],
coord[1],
label,
transform=ax.transAxes,
fontsize=pylab.rcParams['text.fontsize'],
**{'color': color})
ax.set_yticks(hzs, hzs)
ax.plot([min(hzs), max(hzs)], [DP['LOWER_THR']] * len([0, max(hzs)]), **{
'color': [0.6, 0.6, 0.6],
'label': '',
'linewidth': 1,
'linestyle': '--'
})
#ax.text( 0.8, 0.11,'Thr' , transform=ax.transAxes, **{ 'color' : [0.6,0.6,0.6]})
'''
ax.semilogx([min(hzs), max(hzs)],[DP['UPPER_THR']]*len([0, max(hzs)]),**{'color':[0.6,0.6,0.6],
'label':'', 'linewidth':1,
'linestyle':'--'})
#ax.text( 0.8, 0.11,'Thr' , transform=ax.transAxes, **{ 'color' : [0.6,0.6,0.6]})
'''
lines = ax.lines
for line in lines:
misc.slice_line(line, xlim=[0, 48])
ax.set_xlim(misc.adjust_limit([0, 48]))
ax.set_ylim(misc.adjust_limit([0, 30]))
def plot_example_snr(ax, SNR):
time_bin = 20
signal = SNR[0].signals['spikes']
colors = ['k']
sim_time = 2500
signal.my_firing_rate(bin=time_bin,
display=ax,
kwargs={'color': colors[0]})
ax.my_set_no_ticks(yticks=6, xticks=7)
lines = ax.lines
for line in lines:
line.set_xdata(line.get_xdata() - ADJUST_XDATA_MS)
ax.plot([0, sim_time], [SELECTION_THR] * len([0, sim_time]), **{
'color': [0.6, 0.6, 0.6],
'label': '',
'linewidth': 1,
'linestyle': '--'
})
ax.text(0.9,
0.14,
'Thr',
transform=ax.transAxes,
**{'color': [0.6, 0.6, 0.6]})
misc.slice_line(lines[0], xlim=[0, sim_time])
ax.plot([1000, 1500], [39, 39], color='k', marker='|')
ax.text(0.47, 0.84, 'stop', transform=ax.transAxes, **{'color': 'k'})
ax.plot([500, 700], [30, 30], color='k', marker='|')
ax.text(0.23, 0.67, '1st', transform=ax.transAxes, **{'color': 'k'})
ax.plot([1500, 1700], [30, 30], color='k', marker='|')
ax.text(0.60, 0.67, '2nd', transform=ax.transAxes, **{'color': 'k'})
ax.set_xlim(misc.adjust_limit([0, sim_time]))
ax.set_ylim(misc.adjust_limit([0, 45]))
ax.set_ylabel('Firing rate SNr (spikes/s)')
def plot_example_firing_frequency_GPE(ax, GPE_list):
global ADJUST_XDATA_MS
global N_GPE
global N_SEL
time_bin = 20
GPE_a = GPE_list[0]
GPE_s = GPE_a.slice(GPE_a.ids[N_GPE - N_SEL:])
GPE_b = GPE_a.slice(GPE_a.ids[0:N_GPE - N_SEL])
for g in GPE_list[1:]:
GPE_a.merge(g)
GPE_s.merge(g.slice(g.ids[N_GPE - N_SEL:]))
GPE_b.merge(g.slice(g.ids[0:N_GPE - N_SEL]))
GPE_a.signals['spikes'].my_firing_rate(bin=time_bin,
display=ax,
kwargs={'color': 'k'})
GPE_s.signals['spikes'].my_firing_rate(bin=time_bin,
display=ax,
kwargs={'color': 'r'})
GPE_b.signals['spikes'].my_firing_rate(bin=time_bin,
display=ax,
kwargs={'color': 'b'})
ax.set_xlim(misc.adjust_limit([0, 1500]))
ax.set_ylim(misc.adjust_limit([0, 50]))
lines = ax.lines
for line in lines:
line.set_xdata(line.get_xdata() - ADJUST_XDATA_MS)
misc.slice_line(lines[0], xlim=[0, 1490])
misc.slice_line(lines[1], xlim=[0, 1490])
misc.slice_line(lines[2], xlim=[0, 1490])
#ax.set_title('bin=%i'%(time_bin),**{'fontsize':12})
ax.set_ylabel('Firing rate GPe (spikes/s)')
ax.my_set_no_ticks(yticks=6, xticks=5)
ax.text(0.05,
0.75,
'Non-pausing GPe neurons',
backgroundcolor='w',
transform=ax.transAxes,
**{'color': 'b'})
ax.text(0.05,
0.85,
'Pausing GPe neurons',
backgroundcolor='w',
transform=ax.transAxes,
**{'color': 'r'})
ax.text(0.05,
0.65,
'Average over all',
backgroundcolor='w',
transform=ax.transAxes,
**{'color': 'k'})