cell_plot_sequence.m

function cell_plot_sequence(case_string,time_step)

case_dir = fullfile('cases',case_string);
% time_step = 1;
% case_string = 'ca1a_n2';
% case_dir = '/home/shannon/b/aether/Projects/Tumor_Microenvironment/Analysis/Brian/Spring_2019/03032019/cases/ca1hFN3_n1_bsubtracted_v1';

img_dir = fullfile(case_dir,'images');
track_dir =  fullfile(case_dir,'tracks');
particle_dir =  fullfile(case_dir,'particles');

image_list = dir(fullfile(img_dir,'*.tif'));
num_imgs = length(image_list);

particle_list = dir(fullfile(particle_dir,'*.mat'));

load(fullfile(track_dir,'tracks.mat'))

out_dir = 'results';
mkdir(out_dir);

myVideo = VideoWriter(fullfile(out_dir,[case_string,'.avi']));
myVideo.FrameRate = 30;  % Default 30
myVideo.Quality = 50;    % Default 75
open(myVideo)

num_tracks = size(tracks_order,3);
% colors = distinguishable_colors(num_tracks,'k');
colors = rand(num_tracks,3);
figure('position',[0 0 900 900],'InvertHardCopy', 'off','color','w')

for i = 1: num_imgs - 2
    time = (i - 1) * time_step;
    file_name = fullfile(img_dir,image_list(i).name);
    img_raw = imread(file_name);
    img = medfilt2(img_raw,[3 3]);
    
    current_track = reshape(tracks_order(i,:,:),4,num_tracks)';
    ind = find(current_track(:,1)~=0);
    
    %[rb(ind) ra(ind) ang(ind) area(ind) I(ind)];
    
    file_name = fullfile(particle_dir,particle_list(i).name);
    load(file_name)
    
    pos = particles.pos;
    paras = particles.paras;
    
    imshow( img_raw,'initialmagnification','fit'); hold on;
    
    for j = 1:length(ind)
        track_ID = ind(j);
        track_j = tracks_order(:,:,track_ID);
        ind_t = find(track_j(:,1) ~=0);
        times = ind_t(1):i+1;
        x_t = track_j(times,2);
        y_t = track_j(times,3);
        ind_t = (x_t.*y_t ~= 0);
        x_t =  x_t(ind_t);
        y_t =  y_t(ind_t);
        particle_id = current_track(track_ID,1);
        plot(x_t(1),y_t(1),'color',colors(track_ID,:),'marker','X','markersize',5,'linewidth',2,'linesmoothing','on'); hold on;
        %ellipse(paras(particle_id,1),paras(particle_id,2),paras(particle_id,3),pos(particle_id,1),pos(particle_id,2),colors(track_ID,:),50); hold on;
        plot(x_t,y_t,'-','color',colors(track_ID,:),'linewidth',2,'linesmoothing','on'); hold on;
        
    end
    hold off;
    title(sprintf('Time = %.2f frame',time))
    %     file_name = [out_dir,sprintf('/t=%.4d.tif',i)];
    %     print(file_name,'-dtiff','-r100')
    %     frame = imread(file_name);
    
    set(gca,'nextplot','replacechildren');
    frame = getframe(gcf);
    writeVideo(myVideo,  frame)
    
end
close(myVideo);