test_151021_length.m~

clc; clear; close all; warning('off');tic

dataset='150811_SC1ATK50+1_BathoStyg_5_clip';
display(dataset);

val=10;
vel=10; %mm/s %UNKNOWN
percent=0.1; %percent allowable change in imwarp transform
inc=1;

%retrieving data set-specific parameters
% [dir,start,finish,fps,fstop,shutter,calib,red,aspectratio,contrast]=videoinfo(dataset,vel);
dir='/users/kakani/desktop/';
start=1;
finish=89;
viddir=[dir,'clips/'];
indir=[dir,'input/'];
outdir=[dir,'output/'];
nFrames=finish-start;
length=5;
%% arranging planar cross sections into "volume" matrix
vid=VideoReader([viddir,dataset,'.mov']);
im_file=[indir,dataset,num2str(vel),'vel_IMAGE.mat'];
% im_file=[indir,dataset,'_IMAGE.mat'];
load(im_file);                 %if exists, load original image stack
%%
for i=1:5:size(IMAGE,3)-length+1
%     imstr=IMAGE(:,:,i);
    imstr=max(IMAGE(:,:,i),IMAGE(:,:,i+1));
    for j=2:1:length-1
        imstr=max(imstr,IMAGE(:,:,i+j));
    end
    imnew=imadjust(imstr,[0,0.3],[0,1]);
    mask=bwareaopen(imnew>170,25);
    imstrnew=imnew.*uint8(mask);
    figure(1)
    imshow([imnew,mask*255,imstrnew])
    if i==1
        imshow(mask)
        pts=ginput(2);
        xpts=pts(1,1):5:pts(2,1);
        m=(pts(2,2)-pts(1,2))/(pts(2,1)-pts(1,1));
        b=pts(1,2)-m*pts(1,1);
        ypts=m*xpts+b;
    end
    BW=bwlabel(mask,4);
    label=bwconncomp(mask,4);
    s=regionprops(label,'Centroid','Area');
    index=[];
    for k=1:1:size(s,1)
        for j=1:1:size(xpts,2)
            cent=s(k).Centroid;
            dist=sqrt((cent(1,1)-xpts(1,j))^2+(cent(1,2)-ypts(1,j))^2);
            if dist<50
                index=[index,k];
            end
        end
    end
    index=unique(index);
    im=BW*0;
    for j=1:1:size(index,2)
        im=max(im,BW==index(j));
    end
    figure(2)
    imshowpair(imstrnew,im)
    hold on
    plot(xpts,ypts,'r*')
    hold off
    pause()
end

% BW=bwlabel(mask,4);
% label=bwconncomp(mask,4);
% s=regionprops(label,'Centroid','Area');
% 
% %%
% index=[];
% for i=1:1:size(s,1)
%     for j=1:1:size(xpts,2)
%         cent=s(i).Centroid;
%         dist=sqrt((cent(1,1)-xpts(1,j))^2+(cent(1,2)-ypts(1,j))^2);
%         if dist<50
%             index=[index,i];
%         end
%     end
% end
% 
% %%
% im=BW*0;
% for i=1:1:size(index,2)
%     im=max(im,BW==index(i));
% end
% figure(1)
% imshowpair(imstrnew,im)
% hold on
% plot(xpts,ypts,'r*')
% hold off