SpikesMatrix_v2018.m

%This function creates a matrix with the trials in different rows, and time
%in columns. The fequency of time sampling is given by freq. The total
%amount of time of the experiment is in the structure pos (which conteins
%the initial and end time). It returns two matrix, one of the rat going to
%one side, and the other of the rat going in the opposite direction.
% The argumnents are the spike times, the pos structure and the sampling
% frequency.

function  [matrix1 matrix2]=SpikesMatrix(stimes,pos,freq,totaltime)

   [s1 s2]=ReadAlarmTime(pos); %read alarm time
   s1=floor(s1);s1(1)=s1(1)+1; %add 1 to possible zeros R 
   s2=floor(s2);s2(1)=s2(1)+1; %add 1 to possible zeros L
   e1=s1+totaltime; % end of experiment R
   e2=s2+totaltime; %end of experiment L
   n=floor(floor(totaltime)*freq); % size of matrix
   matrix1=zeros(length(s1),n-1);
   matrix2=zeros(length(s2),n-1);
   time1=zeros(length(s1),n);
   time2=zeros(length(s2),n);
   
   for i=1:length(s1)
       time1(i,:)=s1(i):1/freq:s1(i)+n/freq-1/freq;
   end
   for i=1:length(s2)
       time2(i,:)=s2(i):1/freq:s2(i)+n/freq-1/freq;
   end  
         
   for i=1:length(s1)
       for j=1:n-1
            index=find(stimes{1}>time1(i,j) & stimes{1}<time1(i,j+1));
            if isempty(index)~=1
                matrix1(i,j)=length(index);
            end
       end
   end
   for i=1:length(s2)
       for j=1:n-1
            index=find(stimes{1}>time2(i,j) & stimes{1}<time2(i,j+1));
            if isempty(index)~=1
                matrix2(i,j)=length(index);
            end
       end
   end
   
end