jksbxsegment.m

function r = jksbxsegment(fn)

close all;
global info;
sbxread(fn,1,1);

% get the mag

if(isfield(info,'config'))
    mag = info.config.magnification;
    display(sprintf('Mag = x%d',mag));
else
    mag = 1;
    display(sprintf('Mag [default] = x%d',mag));
end

switch mag
    case 1
%         W = 50;
        W = 10; % 03/03/2016 JK
    case 2
        W = 100;
    case 4
        W = 150;
end


% z = sbxreadskip(fn,200,floor(info.max_idx/200));
% read whole frames (or in a limited number at least)
z = squeeze(sbxread(fn,0,info.max_idx));

% v = std(z,[],3);
% 
% % select points based on the variance
% 
% v(1:(W+1),:) = NaN;
% v(end-(W+1):end,:)=NaN;
% v(:,1:(W+1)) = NaN;
% v(:,end-(W+1):end)=NaN;
% 
% load('-mat',[fn '.align']);
% 
% imagesc(v); truesize; colormap gray;
% 
% nroi = 100;
% P = zeros(nroi,2);
% for(k=1:nroi)
%     [i,j] = find(v==max(v(:)));
%     P(k,:) = [i j];
%     v(i-20:i+20,j-20:j+20) = NaN;
% end

% select points from roi selection matrix (manual) 03/03/2016
load('339_roi')
nroi = length(manual);
P = zeros(nroi, 2);
for k = 1 : nroi
    P(k,1) = round(manual(k,1)); P(k,2) = round(manual(k,2));
end
% [xx,yy] = meshgrid(51:50:size(v,2)-51,51:50:size(v,1)-51);
% P = [yy(:) xx(:)];

%

% segmenting

h = waitbar(0,'Segmenting') ;
figure
for(i=1:size(P,1))
% for i = 1
%      waitbar(i/size(P,1),h);
%      s = z(P(i,1)-W:P(i,1)+W,P(i,2)-W:P(i,2)+W,:);
     s = z(max(P(i,1)-W,1) : min(P(i,1)+W,size(z,1)), max(P(i,2)-W,1) : min(P(i,2)+W,size(z,2)), :);
%      plist{i} = sbxsegmentsub(s,200,10,mag);
     plist{i} = jksbxsegmentsub(s,mag,i);
     pause;
end
delete(h);

% put it together...

display('Stiching...')

seg = zeros(size(z,1), size(z,2));
kcell=0;
for(i=1:size(P,1))
    pl = plist{i};
    for(j=1:length(pl))
        pidx = pl{j};
        pidx = [pidx(:,2) pidx(:,1)];
        pidx = ones(size(pidx,1),1)*(P(i,:)- [(W+1) (W+1)])+pidx;
        jj = sub2ind(size(seg),pidx(:,1),pidx(:,2));
        kcell = kcell+1;
        for(k=1:length(jj))
            if(seg(jj)==0)
                seg(jj)= kcell;
            end
        end
    end
end

% contraints at the end...

cc = regionprops(seg,'Area','Solidity','PixelIdxList','Eccentricity','PixelList');

r = zeros(size(seg));

k=0;
for(j=1:length(cc))
%     if(cc(j).Area<1000*mag^2 && cc(j).Area>50*mag^2 && cc(j).Solidity>0.62 && cc(j).Eccentricity<0.9)
    if(cc(j).Area<1000*mag^2 && cc(j).Solidity>0.62 && cc(j).Eccentricity<0.9)
        r(cc(j).PixelIdxList) = k;
        k = k+1;
    end
end

clf
imshow(label2rgb(r,'jet','k','shuffle')), hold on, scatter(manual(:,1), manual(:,2), 'mo')