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plotting_unit_summary.py
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plotting_unit_summary.py
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#!/usr/bin/python
# -*- coding: UTF-8 -*-
# BEGIN PYTHON 2/3 COMPATIBILITY BOILERPLATE
from __future__ import absolute_import
from __future__ import with_statement
from __future__ import division
from __future__ import nested_scopes
from __future__ import generators
from __future__ import unicode_literals
from __future__ import print_function
import sys
# more py2/3 compat
from neurotools.system import *
if sys.version_info<(3,):
from itertools import imap as map
# END PYTHON 2/3 COMPATIBILITY BOILERPLATE
# execute the main figure script first
# this is just to check units
# TODO: repair imports
from neurotools.nlab import memoize
# from cgid.setup import *
# from cgid.plotting_helper_functions import *
# from pylab import *
from cgid.data_loader import metaloadvariable
def unitsum(session,area,unit):
SUPTITLESIZE = 14
close('all')
figure(1,figsize=(10.5,4))
awf1 = subplot2grid((2,4),(0,0),colspan=1)
aisiobj1 = subplot2grid((2,4),(0,3),colspan=1)
aisigo1 = subplot2grid((2,4),(1,3),colspan=1)
arasterobj1 = subplot2grid((2,4),(0,1),colspan=2)
arastergo1 = subplot2grid((2,4),(1,1),colspan=2)
# waveforms and ISI
sca(awf1)
plotWaveforms(session,area,unit)
sca(aisiobj1)
plotISIhistHz(session,area,unit,-1000,0000)
sca(aisigo1)
xlabel('')
plotISIhistHz(session,area,unit,2000,3000)
title('')
sca(arasterobj1)
plotAllTrials(session,area,unit,-1000,0000)
xlabel('')
title('1 second before object presentation', loc='left')
nicex()
gca().yaxis.labelpad = -15
sca(arastergo1)
plotAllTrials(session,area,unit,2000,3000)
nicex()
title('1 second before go cue', loc='left')
gca().yaxis.labelpad = -15
subplots_adjust(0.07,0.15,0.93,0.83,.4,.5)
suptitle('Session %s area %s unit %s'%(session,area,unit),fontsize=SUPTITLESIZE)
def unitsumfig(session,area,unit,savein='./'):
SUPTITLESIZE = 14
figure(1,figsize=(10.5,4))
clf()
awf1 = subplot2grid((2,4),(0,0),colspan=1)
aisiobj1 = subplot2grid((2,4),(0,3),colspan=1)
aisigo1 = subplot2grid((2,4),(1,3),colspan=1)
arasterobj1 = subplot2grid((2,4),(0,1),colspan=2)
arastergo1 = subplot2grid((2,4),(1,1),colspan=2)
# waveforms and ISI
sca(awf1)
plotWaveforms(session,area,unit)
sca(aisiobj1)
plotISIhistHz(session,area,unit,-1000,0000)
sca(aisigo1)
xlabel('')
plotISIhistHz(session,area,unit,2000,3000)
title('')
sca(arasterobj1)
plotAllTrials(session,area,unit,-1000,0000)
xlabel('')
title('1 second before object presentation', loc='left')
nicex()
gca().yaxis.labelpad = -15
sca(arastergo1)
plotAllTrials(session,area,unit,2000,3000)
nicex()
title('1 second before go cue', loc='left')
gca().yaxis.labelpad = -15
subplots_adjust(0.07,0.15,0.93,0.83,.4,.5)
suptitle('Session %s area %s unit %s'%(session,area,unit),fontsize=SUPTITLESIZE)
savefig(savein+'%s_%s_%s'%(session,area,unit)+'.png')
draw()
def dumpallunits():
for s,a in sessions_areas():
print(s,a)
NUNITS = len(metaloadvariable(s,a,'unitIds')[0])
print('No. Units = ',NUNITS)
for i in range(NUNITS):
print('\t',s,a,i)
unitsumfig(s,a,i+1,savein='./unit_info_figures/')
for (s,a),us in allunitsbysession.iteritems():
for u in us:
unitsumfig(s,a,u,savein='./unit_info_figures/')
# further restrictions:
# No. Spikes pre-obj and pre-go
# SNR
# good LFP channel?
def is_unit_on_good_lfp_channel(session,area,unit):
chs = get_good_channels(session,area)
chid = get_channel_id(session,area,unit)
return chid in chs
@memoize
def get_unit_snr(session,area,unit):
wfs = get_waveforms(session,area,unit)
noise = std(wfs[0])
signal = 0.5*(mean(np.max(wfs,0)-np.min(wfs,0)))
return signal/noise
def get_total_spikes(session,area,unit,epoch):
spks = get_spike_times_all_trials(session,area,unit,epoch)
return sum(map(len,spks))
def get_average_rate(session,area,unit,epoch):
spks = get_spike_times_all_trials(session,area,unit,epoch)
event,start,stop = epoch
return mean(map(len,spks))/(stop-start)*1000
def printstats(s,a,u):
print('\t',s,a,u,end='')
print('OK ' if is_unit_on_good_lfp_channel(s,a,u) else 'BAD',end='')
print(get_unit_quality(s,a,u),end='')
print('SNR=%0.1f'%get_unit_snr(s,a,u),end='')
print('\t','obj count=%04d rate=%0.1f'%(
get_total_spikes(s,a,u,preobject),
get_average_rate(s,a,u,preobject)),end='')
print('\t','go count=%04d rate=%0.1f'%(
get_total_spikes(s,a,u,prego),
get_average_rate(s,a,u,prego)))
def surveyallunits():
preobject = 6,-1000,0 # pre-object
prego = 8,-1000,0 # pre-go
allrates = []
allcounts = []
allsnr = []
for s,a in sessions_areas():
print(s,a)
NUNITS = len(metaloadvariable(s,a,'unitIds')[0])
print('No. Units = ',NUNITS)
for u in range(1,1+NUNITS):
printstats(s,a,u)
allrates .append(get_average_rate(s,a,u,preobject))
allrates .append(get_average_rate(s,a,u,prego))
allcounts.append(get_total_spikes(s,a,u,preobject))
allcounts.append(get_total_spikes(s,a,u,prego))
allsnr .append(get_unit_snr(s,a,u))
def filterunits():
minsnr = 5
mincount = 500
minrate = 1
minqual = 2
preobject = 6,-1000,0 # pre-object
prego = 8,-1000,0 # pre-go
for s,a in sessions_areas():
print(s,a)
NUNITS = len(metaloadvariable(s,a,'unitIds')[0])
print('No. Units = ',NUNITS)
for u in range(1,1+NUNITS):
if not is_unit_on_good_lfp_channel(s,a,u): continue
if get_unit_quality(s,a,u)<minqual: continue
if get_total_spikes(s,a,u,preobject)<mincount: continue
if get_total_spikes(s,a,u,prego )<mincount: continue
if get_average_rate(s,a,u,preobject)<minrate: continue
if get_average_rate(s,a,u,prego )<minrate: continue
if get_unit_snr(s,a,u)<minsnr: continue
printstats(s,a,u)
unitsumfig(s,a,u,savein='./unit_info_figures_good/')
def use_best_units():
global units, allunitsbysession
usable = os.listdir('./unit_info_figures_good/')
for s,a in allunitsbysession.keys():
allunitsbysession[s,a]=[]
for f in usable:
_s,_a,_u = f[:-4].split('_')
if s==_s and a==_a:
allunitsbysession[s,a].append(int(_u))
units = []
for (session,area), uu in allunitsbysession.iteritems():
units+=[(session,area,u) for u in uu]
def find_very_good_beta_examples():
minsnr = 7
mincount = 1000
minrate = 9
minqual = 3
preobject = 6,-1000,0 # pre-object
prego = 8,-1000,0 # pre-go
for s,a in sessions_areas():
print(s,a)
NUNITS = len(metaloadvariable(s,a,'unitIds')[0])
print('No. Units = ',NUNITS)
for u in range(1,1+NUNITS):
if not is_unit_on_good_lfp_channel(s,a,u): continue
if get_unit_quality(s,a,u)<minqual: continue
if get_total_spikes(s,a,u,preobject)<mincount: continue
if get_total_spikes(s,a,u,prego )<mincount: continue
if get_average_rate(s,a,u,preobject)<minrate: continue
if get_average_rate(s,a,u,prego )<minrate: continue
if get_unit_snr(s,a,u)<minsnr: continue
mf1 = isimodefreq(s,a,u,-1000,0000,FS=1000)
if mf1<15 or mf1>30: continue
mf2 = isimodefreq(s,a,u, 2000,3000,FS=1000)
if mf2<15 or mf2>30: continue
printstats(s,a,u)
unitsumfig(s,a,u,savein='./unit_info_figures_exemplar/')