% Code to flatten PSP traces away from detected PSP's as in Ikegaya et al., 2004

pspwavename='rmean_tenminilandec_190sec';
fina='tenminilandec_190sec';
length_PSP=30;pspthresh=90;
PSP_finder(fina,pspwavename,length_PSP,pspthresh);

load('tenminilandec_190sec.mat');
load('tenminilandec_190sec_psptimes90.mat');

vtrace=tenminilandec_190sec;   % "voltage trace"

% extract PSP's
PSP_start=zeros(size(timewave));
for j=1:max(size(timewave))
    PSP{j}=vtrace( timewave(j):timewave(j)+length_PSP );
    PSP_start(j)=timewave(j);
end

% Shuffle start times, preserving ISI's...
% TRANSFERRED TO ShufflePSPStart

%     % Compute ISI list (ISI representation of PSP times)
%     ISIlist= diff( PSP_start );
%     
%     % Permute ISI dist
%         % Keep _first_ ISI the same
%         %  (...edge effects)
%     N=max(size(ISIlist));
%     ISIperm(1)=ISIlist(1);
%     ISIperm(2:end)= ISIlist( 1+randperm(N-1) );
%     
%     % Construct surrogate PSP start times from permuted ISI
%     PSP_start_perm=zeros( max(size(PSP_start)),1 );
%     PSP_start_perm(1)=PSP_start(1);
%     for j=2:N
%         PSP_start_perm(j)=PSP_start_perm(j-1)+ISIperm(j);
%     end
%     
%     % PSP_start_perm now contains the "shuffled" surrogate PSP start
%     %  times...
   


    % Construct a flattened trace from PSP and PSP_start
    length_flat_trace=max(size(vtrace));
    
    flat_trace=-92+zeros( length_flat_trace,1 );
    
    for j=1:numel(PSP_start)
        flat_trace( PSP_start(j):(PSP_start(j)+numel(PSP{j})-1) )=   ...
           PSP{j} + flat_trace( PSP_start(j):(PSP_start(j)+numel(PSP{j})-1) );
    end
    

% Flatten the trace away from detected PSP's
% Use length_PSP as length of PSP's to preserve...

flat_trace=-92+zeros( size(tenminilandec_190sec) );

for i=1:numel(timewave)
    flat_trace(timewave(i):timewave(i)+length_PSP )=tenminilandec_190sec( timewave(i):timewave(i)+length_PSP );
end

savename='flat_trace30';
flat_trace30=flat_trace;

save( savename,'flat_trace30');

LRI_find30=HRI_repeatfinder_1secAA(savename);



    
% clf
% 
% 
% plot(0:.001:189.642,tenminilandec_190sec), hold on
% plot(0:.001:189.642,flat_trace,'r')
% 
% 
% f=timewave/1000;
% x=zeros( size(f,1),1 );
% r0=min( tenminilandec_190sec ); r1= max( tenminilandec_190sec );
% %hl=line( repmat(f',2,1),[ r0+x' ; r0+((r1-r0)*.2)+x' ] );
% hl=line( repmat(f',2,1),[ -100+x' ; -95+x' ] );
% 
% pause
% 
% for cc=0:1:199    
% 
%     axis([cc cc+1 -100 -20])
%     
%     %plot(cc:.001:cc+1-.001,tenminilandec(t0:t1))
%     %hold on
%     %plot(t0:t1,threshwave(t0:t1),'r')
%     
%     %r0=min( sample(t0:t1) ); r1=max( sample(t0:t1) );
%         
%     % display psp detected....
%     %f=timewave(find(timewave<=t1 & timewave>=t0));
%     %x=zeros( size(f,1),1 );
%     
%     %hold on
%     
%     %hl=line( repmat(f',2,1),[ r0+x' ; r0+((r1-r0)*.2)+x' ] );
% 
%     pause
%     
% end