GoKymo.m

function [imKymo LKymo iPath jPath bKymo]=GoKymo(iPath,jPath,bKymo,Movie_Name)


R_KYMO=20;

PathNorms=[];
info = imfinfo(Movie_Name);
nframes = length(info);
im=(imread(Movie_Name,1));
bTaken=0*im;
LKymo=0*im;
% hold off;imagesc(im);hold on;colormap(gray)

for i=1:length(iPath) % iPath=y,jPath=x
    if isnan(bKymo(i,1))
        % y as dependent var
        mNorm=-1*bKymo(i,4);
    else
        mNorm=-1/bKymo(i,2);
    end
    
    [xi yi LKymo]=GetNormalLine(mNorm,jPath(i),iPath(i),R_KYMO,[size(im)],i,LKymo);
   
    PathNorms(i).xi=[xi ];
    PathNorms(i).yi=[yi];
    j=1;
%     plot(round(PathNorms(i).xi),round(PathNorms(i).yi),'-r')
end

i=1;
del=[];
while i<=length(iPath)
    if isempty(find(LKymo==i))
       iPath(i)=[];
       jPath(i)=[];
       bKymo(i,:)=[];
       PathNorms(i)=[];
       for j=i+1:max(LKymo(:))
           npix=find(LKymo==j);
           LKymo(npix)=j-1;
       end
    else
        i=i+1;
    end
end 


% % interp
for i=2:length(iPath)-1 % iPath=y,jPath=x
    if isnan(bKymo(i,1))
        % y as dependent var
        mNorm=-1*bKymo(i,4);
    else
        mNorm=-1/bKymo(i,2);
    end
    
    for step=0.05:0.05:0.5
        xi1=[];yi1=[];
        xi2=[];yi2=[];
        dx=jPath(i)-jPath(i-1);
        dy=iPath(i)-iPath(i-1);
        
        x1=jPath(i)-dx*step;
        y1=iPath(i)-dy*step;
        
        [xi1 yi1 LKymo]=GetNormalLine(mNorm,x1,y1,R_KYMO,[size(im)],i,LKymo);

        
        dx=jPath(i+1)-jPath(i);
        dy=iPath(i+1)-iPath(i);
        x2=jPath(i)+dx*step;
        y2=iPath(i)+dy*step;;
        [xi2 yi2 LKymo]=GetNormalLine(mNorm,x2,y2,R_KYMO,[size(im)],i,LKymo);
        PathNorms(i).xi=[ PathNorms(i).xi xi1 xi2 ];
        PathNorms(i).yi=[ PathNorms(i).yi yi1 yi2];
        
%         plot(xi1,yi1,'-g')
%         plot(xi2,yi2,'-b')
    end
    
end


imKymo=[]; istat=[]; stats=[0 Inf];PathMax=zeros(length(iPath),1);
for t=1: nframes
    im=(imread(Movie_Name,t));

    if max(im(:))<stats(2)
        stats(2)=max(im(:));
    end
    if min(im(:))>stats(1)
        stats(1)= min(im(:));
    end
end
for t=1: nframes
    im=(imread(Movie_Name,t));
%           im(im<stats(1))=stats(1);%
     im(im>stats(2))=stats(2);
    im=mat2gray(im);
    
    h = fspecial('gaussian', 7, 5);
    imfilt = imfilter(im, h, 'symmetric');
    for j=1:50
        imfilt = imfilter(imfilt, h, 'symmetric');
    end
    imhfreq = max((im - imfilt), zeros(size(im)));
    im = mat2gray(imhfreq);
%     medim = medfilt2(imhfreq,[4,4]);
%     
%     medim = mat2gray(medim);
%     im = medim;

    ii=[];
    for i=1:length(PathNorms) % iPath=y,jPath=x
            
        idxi=sub2ind(size(im),round(PathNorms(i).yi),round(PathNorms(i).xi));
        ipix=im(idxi) ; 
%         ipix = medim(idxi) ; 

        if isempty(ipix),
            imKymo(i,t)= 0;
        else
            imKymo(i,t)= (max(ipix) - min(ipix));
        end
                
    end
    
     drawnow
end

figure(88)
set(88,'KeyPressFcn', @KeyPress);
imKymo=imKymo/max(imKymo(:));
imKymo=imcomplement(imKymo);
imKymo=imKymo/max(imKymo(:));
hold off
imagesc(imKymo)
axis image
colormap(gray)

end

function KeyPress(src,eventdata)
    if ( strcmpi(eventdata.Key,'space') )
        close all;
        mKymoUI();
    end
end