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compute_CSDfeature.m
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compute_CSDfeature.m
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%function compute_CSDfeature
%function compute_CSDfeature
% Compute CSD feature from laminar data
%
% see also compute_tuning
%
% Corentin Massot
% Cognition and Sensorimotor Integration Lab, Neeraj J. Gandhi
% University of Pittsburgh
% created 10/15/2016 last modified 01/22/2017
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%set paths
[root_path data_path save_path]=set_paths;
%screen size
scrsz = get(groot,'ScreenSize');
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%parameters
%print figures and save data
savedata=0;
savefigs=0;
figtype='epsc2';%'png';%'epsc2';
%alignement
%alignlist={'no' 'targ' 'go' 'sacc'};
alignlist={'targ' 'sacc'};
%window of analysis
wind_targ=[-10 340];
wind_sacc=[-100 250];
%sigma FR
sigma_FR=6;
%vshift
vshift=10;%28.6944;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%get data
datalist=load_data_gandhilab(data_path);
%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%analyzing data
dlist=get_dlist
hdlfigallvmis=figure;hold on;
data=[];
info=[];
for d=dlist
%get data and info
info.datafile=datalist{d};
load ([data_path info.datafile]);
display(info.datafile)
%getting channel mapping and discard selected bad channels
discard=data(1).offline.discardlfp;
[info.chmap info.nchannels info.depths]=get_chmap(data(1).info.electrode{2},discard);
%getting trial type
info.trialtype=data(1).sequence(1);
%getting list of targets
targslist=data(1).offline.targslist;
%targets index
targs_ind=get_targsindex(targslist,info);
%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'
[alltrials_lfp_targ aligntime_targ]=get_alltrials_align(data,seltrials,wind_targ,'lfp',info,targslist,sigma_FR,0);
case 'sacc'
[alltrials_lfp_sacc aligntime_sacc]=get_alltrials_align(data,seltrials,wind_sacc,'lfp',info,targslist,sigma_FR,0);
end
end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%get spk data for tuning
[alltrials_spk_tuning info.aligntime]=get_alltrials_align(data,seltrials,[],'fr',info,targslist,sigma_FR,0);
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%analysis of trials for each target
for tg=targ_tuning;%targs_ind
figtrials=figure('Position',[1 100 scrsz(3)-100 scrsz(4)-200]);
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%display all targets
hdlfig=subplot(2,3,1);hold on;
display_alltargets(targslist,info,hdlfig);
%compute target tuning
hdlfig=subplot(2,3,4);hold on;
plot_targtuning(alltrials_spk_tuning,targs_ind,info,hdlfig,'Target tuning');
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%target index
info.targ=tg;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%plot lfp of targ and sacc
for al=1:numel(alignlist)
info.align=alignlist{al};
switch info.align
case 'targ'
trials_lfp=alltrials_lfp_targ{tg};
info.aligntime=aligntime_targ;
case 'sacc'
trials_lfp=alltrials_lfp_sacc{tg};
info.aligntime=aligntime_sacc;
end
[info.nchannels info.ntrials info.triallen]=size(trials_lfp);
%compute average trials
[trials_lfp_avg trials_lfp_var]=get_trials_avg(trials_lfp);
%remove trials with amplitude that is too small
[trials_lfp_avgc index_lfp_c]=clean_trials(trials_lfp_avg,'lfp');
hdlfig=subplot(2,3,al+1);hold on;
titlestr={info.datafile ; ['LFP ' info.align ' t' num2str(info.targ) ' #trials:' num2str(info.ntrials)]};
range=plot_trials(trials_lfp_avgc,[],index_lfp_c,vshift,[],[],info,hdlfig,titlestr,'-',1);
%plot_event(wind_vmi,info.aligntime,range,hdlfig);
%%
%%%%%%%%%%%%%%%%%%
%plot CSD
hdlfig=subplot(2,3,al+4);hold on;
titlestr='CSD';
[csd zs clim]=plot_csdtrials('lfp',trials_lfp_avgc,[],index_lfp_c,[],[],[],info,hdlfig,titlestr);
%find feature in CSD
zs=zs*1e-3;
[csdfeat ~]=findfeatures_CSD(1,1,0,csd,zs,info,hdlfig);
figure(figtrials)
%hdlrect=rectangle('Curvature', [1 1],'Position', [peak.t-1 peak.d-1 2 2]);
%set(hdlrect,'linewidth',2);
%line([aligntime aligntime] ,[0 length(zs)]);
%%
%%%%%%%%%%%%%%%%%%
%Update data
%first paper (functional analysis of SC)
%data=update_data(0,1,0,data,data_path,info.datafile,['csdfeat_avg_' info.align],csdfeat);
%second paper _p2 (LFP/CSD analysis of SC)
data=update_data(0,1,0,data,data_path,info.datafile,['csdfeat_avg_' info.align '_p2'],csdfeat);
end
%pause
%saving updated data
data=update_data(0,1,0,data,data_path,info.datafile,['csdzs'],zs);
update_data(1,0,0,data,data_path,info.datafile,[],[]);
%display('NOT SAVED!')
close(figtrials)
end
end