Looking-to-cue-sides-and-modulation-of-value-in-OFC/code/support_functions/countconsecutiveones.m

function [c1cv, isq1s, isq1e, xv_min_seq_length] =countconsecutiveones(xv,zero_pad,min_seq_length)

if nargin <2
    zero_pad=0;
    if nargin <3
        min_seq_length=1;
    end
end

isq1s=nan(size(xv));
isq1e=nan(size(xv));
c1cv=nan(size(xv));
xv_min_seq_length=zeros(size(xv));

if isvector(xv)
    if isrow(xv)
        xv=xv';
    end
    if zero_pad
        xv(isnan(xv))=0;
    else
        xv(isnan(xv))=[];
    end
    %fv = find(abs(diff([0; xv; 0]==1))) 
    %c1cv = fv(2:2:end)-fv(1:2:end-1);
    xdiff=diff([0; xv; 0]);
    i1sct = find(xdiff==+1); %indices where ones sequence start
    i1ect = find(xdiff==-1); %indices where ones sequence end
    c1ct = i1ect - i1sct;
    
    isq1s(1:length(i1sct))=i1sct;
    isq1e(1:length(i1ect))=i1ect;
    c1cv(1:length(c1ct))=c1ct;
    isq1se=[isq1s(c1cv>min_seq_length) isq1e(c1cv>min_seq_length)];
    if ~isempty(isq1se)
    for jj=1:size(isq1se,1)
        xv_min_seq_length(isq1se(jj,1):isq1se(jj,2)-1)=1;
    end
    end
    
elseif ismatrix(xv)
    if isscalar(min_seq_length)
        min_seq_length=repmat(min_seq_length,size(xv,2));
    end
    xv_min_seq_length=nan(size(xv));
    for jj=1:size(xv,2)
        [c1ct,i1sct,i1ect,xvmslt]=countconsecutiveones(xv(:,jj),zero_pad,min_seq_length(jj));
        isq1s(1:length(i1sct),jj)=i1sct;
        isq1e(1:length(i1ect),jj)=i1ect;
        c1cv(1:length(c1ct),jj)=c1ct;
        xv_min_seq_length(:,jj)=xvmslt;
    end
    %c1(all(isnan(c1),2),:)=[];
else
    error('input must be a vector or matrix');
end