def plotISIhistHz(session,area,unit,start,stop,
FS=1000,style='bar',color='k',nbins=30,label=None,
fmin=0,FMAX=100,
linestyle='-',lw=2,w=0.8):
ByTrialSpikesMS = metaloadvariable(session,area,'ByTrialSpikesMS')
NUNITS, NTRIALS = shape(ByTrialSpikesMS)
isi = []
for it in range(NTRIALS):
isi.extend(diff(getTrial(session,area,unit,start,stop,it+1)))
isi = FS/array(isi)
if style=='bar':
hist(isi,linspace(fmin,FMAX,nbins+1),facecolor='k',label=label,rwidth=w)
a,b = ylim()
plot((modefind(isi),)*2,ylim(),color='r',lw=lw)
ylim(a,b)
nicelimits()
isi = isi[~isnan(isi)]
isi = isi[~isinf(isi)]
mf = modefind(isi)
if (not isnan(mf)) and (not isinf(mf)):
xticks(int32([xlim()[0],int(round(modefind(isi))),xlim()[1]]))
elif style=='line':
h,_ = histogram(isi,bins=nbins,range=(0,100))
x = linspace(fmin,FMAX,1+nbins)
x = 0.5*(x[1:]+x[:-1])
plot(x,h,linestyle,lw=1,color=color,label=label)
else:
raise ValueError("Plot style must be line or bar")
bareaxis(gca())
xlabel('Frequency (Hz)')
ylabel('N')
title('ISI histogram\n(frequency)')
gca().yaxis.labelpad = -20
def plotISIhist(session,area,unit,start,stop):
cla()
ByTrialSpikesMS = metaloadvariable(session,area,'ByTrialSpikesMS')
NUNITS,NTRIALS = shape(ByTrialSpikesMS)
isi = []
for it in range(NTRIALS):
isi.extend(diff(getTrial(session,area,unit,start,stop,it+1)))
hist(isi,linspace(0,120,31),facecolor='k')
a,b = ylim()
plot((modefind(isi),)*2,ylim(),color='r',lw=2)
ylim(a,b)
nicelimits()
xticks(int32([xlim()[0],int(round(modefind(isi))),xlim()[1]]))
bareaxis(gca())
xlabel('Time (ms)')
ylabel('N')
title('ISI histogram (time)')
gca().yaxis.labelpad = -20
def isimodefreq(session,area,unit,start,stop,FS=1000):
ByTrialSpikesMS = metaloadvariable(session,area,'ByTrialSpikesMS')
NUNITS,NTRIALS = shape(ByTrialSpikesMS)
isi = []
for it in range(NTRIALS):
isi.extend(diff(getTrial(session,area,unit,start,stop,it+1)))
isi = FS/array(isi)
isi = isi[~isnan(isi)]
isi = isi[~isinf(isi)]
mf = modefind(isi)
return mf
def do_unit_ISI_plot(session, area, unit,
INFOXPOS = 70, LABELSIZE=8, NBINS=20, FMAX = 250):
cla()
spikes = []
for trial in get_good_trials(session):
spikes.append(cgid.spikes.get_spikes_event(
session,area,unit,trial,6,-1000,0))
spikes.append(cgid.spikes.get_spikes_event(
session,area,unit,trial,8,-1000,0))
ISI_events = array(list(flatten(map(diff,spikes))))
SNR = get_unit_SNR(session,area,unit)
histc,edges = histogram(ISI_events, bins = linspace(0,FMAX,NBINS+1))
dx = diff(edges)[0]
bar(edges[:-1]+dx*0.1,histc,width=dx*0.8,color=GATHER[-1],edgecolor=(0,)*4)
allisi = array(ISI_events)
K = 20
x,y = kdepeak(log(K+allisi[allisi>0]))
x = exp(x)-K
y = y/(K+x)
y = y*len(allisi)*dx
plot(x,y,color=RUST,lw=1.5)
mean_rate = sum(map(len,spikes))/float(len(get_good_trials(session))*2)
ISI_cv = std(allisi)/mean(allisi)
burstiness = sum(allisi<5)/float(len(allisi))*100
ll = 1./mean(allisi)
expected_short_isi = (1.0-exp(-ll*10))*100
mode = modefind(allisi)
residual_burstiness = burstiness-expected_short_isi
LH = LABELSIZE+4
text(INFOXPOS,ylim()[1]-pixels_to_yunits(20 ),'Mean rate = %d Hz'%mean_rate,
horizontalalignment='left',
verticalalignment ='bottom',fontsize=LABELSIZE)
text(INFOXPOS,ylim()[1]-pixels_to_yunits(20+LH*1),'ISI CV = %0.2f'%ISI_cv,
horizontalalignment='left',
verticalalignment ='bottom',fontsize=LABELSIZE)
text(INFOXPOS,ylim()[1]-pixels_to_yunits(20+LH*2),'SNR = %0.1f'%SNR,
horizontalalignment='left',
verticalalignment ='bottom',fontsize=LABELSIZE)
text(INFOXPOS,ylim()[1]-pixels_to_yunits(20+LH*3),'Mode freq. = %0.1f'%mode,
horizontalalignment='left',
verticalalignment ='bottom',fontsize=LABELSIZE)
axvline(mode,lw=2,color=TURQUOISE)
xlabel('ms',fontsize=LABELSIZE)
ylabel('No. Events',fontsize=LABELSIZE)
fudgey(10)
fudgex(5)
xlim(0,FMAX)
nicex()
nicey()
title('Monkey %s area %s\nsession %s unit %s'%(session[0],area,session[-2:],unit),loc='center',fontsize=7)
return mean_rate,ISI_cv,SNR,mode