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analysis_pburst.m
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analysis_pburst.m
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%analysis_pburst
%function analysis_pburst
% analyze bursting activity based on burst detection (pburst)
% mostly to check if data saved by compute_pburst is ok
%
% see also compute_pburst
%
% Corentin Massot
% Cognition and Sensorimotor Integration Lab, Neeraj J. Gandhi
% University of Pittsburgh
% created 10/29/2017 last modified 10/29/2017
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%set paths
[root_path data_path save_path]=set_paths;
%screen size
scrsz = get(groot,'ScreenSize');
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%parameters
%print figures and save data
savedata=0;
%alignement
%alignlist={'no' 'targ' 'go' 'sacc'};
%alignlist={'targ' 'sacc'};
%alignlist={'targ_pburst_ch' 'sacc'};
%alignlist={'targ_rsburst_ch' 'sacc'};
alignlist={'sacc'};
%windows of analysis
%wind_no=[-200 1500];
wind_targ=[0 600];
wind_sacc=[-300 200];%[-200 200];
%algo
algolist={'pburst' 'rsburst'}
%window of burst
windb_targ=[30 150];
windb_sacc=[-100 0];
%vshift
vshift_fr=150;
%sigma FR
sigma_FR=6;
%burst trheshold
thresh=10;%threshold spk/s
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%get data
datalist=load_data_gandhilab(data_path);
%colorlist
colorlist=get_colorlist;
%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%analyzing data
dlist=get_dlist
%hdlfigallbsignifs=figure;hold on;
data=[];
info=[];
allbob_avg=[];allbobmode_avg=[];allbob_avgn=[];allbobmode_avgn=[];
dd=0;
for d=dlist(1:end)%1:numel(datalist)
%counter
dd=dd+1;
data=[];
%get data and info
info.datafile=datalist{d};
load ([data_path info.datafile]);
display(info.datafile)
%getting channel mapping and discard selected bad channels
[info.chmap info.nchannels info.depths]=get_chmap(data(1).info.electrode{2},[]);
%getting trial type
info.trialtype=data(1).sequence(1);
%getting list of targets
targslist=data(1).offline.targslist;
%target tuning (after compute_tuning)
targ_tuning=data(1).offline.targ_tuning;
%select trials
seltrials=get_seltrials(data,'rpt');
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%Data aligned on target and saccade onset
for al=1:numel(alignlist)
info.align=alignlist{al};
switch info.align
case 'targ'
wind=wind_targ;
case 'targ_pburst_ch'
wind=wind_targ;
case 'sacc'
wind=wind_sacc;
end
[alltrials_spk info.aligntime lut_trials]=get_alltrials_align(data,seltrials,wind,'spk',info,targslist,sigma_FR,1);
[alltrials_fr ~]=get_alltrials_align(data,seltrials,wind,'fr',info,targslist,sigma_FR,1);
[alltrials_lfp ~]=get_alltrials_align(data,seltrials,wind,'lfp',info,targslist,sigma_FR,1);
[allgazepos,allevents]=get_alldatagaze_align(data,seltrials,info,targslist);
%target
info.targ=targ_tuning;
%selection of tuning data only
trials_fr=alltrials_fr{info.targ};
trials_spk=alltrials_spk{info.targ};
trials_lfp=alltrials_lfp{info.targ};
gazepos=allgazepos{info.targ};
events=allevents{info.targ};
lut_trials_targ=lut_trials{info.targ};
%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%Plot each trial
[info.nchannels info.ntrials info.triallen]=size(trials_fr);
titlestr={info.datafile ; ['FR ' info.align ' t' num2str(info.targ) ' #trials:' num2str(info.ntrials)]};
for t=1:info.ntrials,
figtrials=figure('Position',scrsz);hdlfig=subplot(1,1,1);hold on;
trials_fr_t=squeeze(trials_fr(:,t,:));
trials_spk_t=squeeze(trials_spk(:,t,:));
events_t=events{t};
event_align=get_eventalign(events_t,info.align);
%plot
[range ~]=plot_trials(trials_fr_t,[],[1:info.nchannels],vshift_fr,events_t,event_align,info,hdlfig,titlestr,'-',1);
%Pburst (see compute_pburst)
for alg=1:2
algo=algolist{alg};
b_begin_plot=zeros(info.nchannels,2);b_end_plot=zeros(info.nchannels,2);
switch algo
case 'pburst'
eval(['b_begin=data(' num2str(lut_trials_targ(t)) ').offline.' info.align '_pburst_trial.b_begin;']);
eval(['b_end=data(' num2str(lut_trials_targ(t)) ').offline.' info.align '_pburst_trial.b_end;']);
b_begin_plot(:,1)=b_begin;%-info.aligntime;
b_end_plot(:,1)=b_end;%-info.aligntime;
plot_events_ch(b_begin_plot,[],vshift_fr,range,info,hdlfig,'n','-',3);
plot_events_ch(b_end_plot,[],vshift_fr,range,info,hdlfig,'n','-',3);
case 'rsburst'
eval(['b_begin=data(' num2str(lut_trials_targ(t)) ').offline.' info.align '_rsburst_trial.b_begin;']);
eval(['b_end=data(' num2str(lut_trials_targ(t)) ').offline.' info.align '_rsburst_trial.b_end;']);
b_begin_plot(:,1)=b_begin;%-info.aligntime;
b_end_plot(:,1)=b_end;%-info.aligntime;
plot_events_ch(b_begin_plot,[],vshift_fr,range,info,hdlfig,'n',':',5);
plot_events_ch(b_end_plot,[],vshift_fr,range,info,hdlfig,'n',':',5);
end
end
pause
close(figtrials)
end
end
end