plot_channel.m

function [length_list, foci_list, birth_list, division_list, cell_list, cell_names, save_name, save_name_png, display_name] = plot_channel(dir_name, cell_data, px_to_mu, IW_thr, fnames_sort, channels, channle_idx, xlim_max, ylim_max, time_int)

parameters % load parameters

fov_index = find(fnames_sort(:,1) == channels(channle_idx,1));
fnames_fov = fnames_sort(fov_index,:);

channel_index = find(fnames_fov(:,2) == channels(channle_idx,2));
fnames_channel = fnames_fov(channel_index,:); % cell numeric identifiers

L_channles = length(fnames_channel(:,1)); 

foci_list = [0.0 0.0];
birth_list = 0.0;
division_list = 0.0;
cell_list = [];
cell_names = [];
length_list = [];

l_1 = 1;
i_1 = 1;
j_1 = 1;
k_1 = 1;
c_1 = 1;

cmap = colormap(gray);
% cmap = colormap(summer);

for k = 1:L_channles
    fname_rec = ['f' num2str(fnames_channel(k,1),'%.2d') 'p' num2str(fnames_channel(k,2),'%.4d') 't' num2str(fnames_channel(k,3),'%.4d') 'r' num2str(fnames_channel(k,4),'%.2d')];
    cell_temp = cell_data.(fname_rec);

    time_temp = double(cell_temp.times); % stitch time point array of all generations into one WITHOUT division time point
    birth_time_temp = double(cell_temp.birth_time); %birth time of all generations
    divition_time_temp = double(cell_temp.division_time); %division time of all generations

    length_temp = double(px_to_mu*cell_temp.lengths); % stitch length array of all generations into one WITHOUT division time point
    width_temp = double(px_to_mu*cell_temp.widths); % stitch width array of all generations into one WITHOUT division time point

    length_list = [length_list [time_temp; length_temp]]; 

    birth_list(k_1,1) = birth_time_temp;
    k_1 = k_1+1;

    cell_list.(fname_rec) = cell_temp; %save all cells into handles' list.
    cell_names{c_1,1} = fname_rec;  %save all cells names into handles' list.
    c_1 = c_1+1;

    % deal with situation where the foci disp_l is interpreted as a
    % numeric array/matrix as opposed to a 1d cell array of arrays
    if ~double(iscell(cell_temp.disp_l))
        cell_temp.disp_l = num2cell(cell_temp.disp_l, 2)' ;
        cell_temp.disp_w = num2cell(cell_temp.disp_w, 2)' ;
        cell_temp.foci_h = num2cell(cell_temp.foci_h, 2)' ;
    end

    % convert disp_l into microns
    for n = 1:length(cell_temp.disp_l)
        cell_temp.disp_l{1,n} = cell_temp.disp_l{1,n} * px_to_mu ;   
        cell_temp.disp_w{1,n} = cell_temp.disp_w{1,n} * px_to_mu ; 
    end

    %-----------------plots-------------------
    % foci position vs time
    hold on;

    h1 = plot(time_temp,length_temp);
    h1.Color = [0.75 0.75 0.75]; set(h1,'LineWidth',2,'Markersize',2,'Marker','o','MarkerFaceColor',[0.75 0.75 0.75],'LineStyle','-');

    %obtain foci positions
    for p=1:length(cell_temp.times)
        % check if there are foci at this time point
        
        % plot fl profile line
            if plot_fl_profile
                if sum(cell_temp.fl_profiles_sub_c2{1,p})
                    
                    colormap(summer);
                    x_positions = ones(1, length(cell_temp.fl_profiles_sub_c2{1,p})) * double(cell_temp.times(1,p));
                    y_positions = linspace(0, length_temp(1,p), length(cell_temp.fl_profiles_sub_c2{1,p}));
                    z_positions = cell_temp.fl_profiles_sub_c2{1,p};


                    h_flprofile = scatter(x_positions, y_positions, fl_profile_ms, z_positions, ...
                                          'filled', 'square');
    %                 h_flprofile.Color = colormap(summer);
                    h_flprofile.MarkerFaceAlpha = 0.25;
                    set(h_flprofile,'HitTest','off'); % these objects will not trigger GUI mouse click
                end
            end
        
        if isempty(cell_temp.disp_l{1,p})==0
            
            % plot eeach foci individually
            for q=1:length(cell_temp.disp_l{1,p})

                color_idx_temp = (cell_temp.disp_w{1,p}(1,q)+width_temp(1,p)/2)/width_temp(1,p);
                color_idx_temp = max(0,color_idx_temp);
                color_idx_temp = min(1,color_idx_temp);
                color_temp = cmap(4+round(56*color_idx_temp),:); %visualize information of displacment along width direction using colormap 

                if cell_temp.foci_h{1,p}(1,q)>=IW_thr
                    h3 = plot(cell_temp.times(1,p),cell_temp.disp_l{1,p}(1,q)-0.05+length_temp(1,p)/2);
                    h3.Color = color_temp; set(h3,'LineWidth',1,'Markersize',4*(cell_temp.foci_h{1,p}(1,q)/IW_thr),'Marker','o','MarkerFaceColor',[1 1 1],'LineStyle','None');
                    set(h3,'HitTest','off'); % these objects will not trigger GUI mouse click
                    
                    foci_list(i_1,:) = [double(cell_temp.times(1,p)), cell_temp.disp_l{1,p}(1,q)-0.05+length_temp(1,p)/2]; 
                    i_1 = i_1+1;

                    h4 = plot(cell_temp.times(1,p),cell_temp.disp_l{1,p}(1,q)+0.05+length_temp(1,p)/2);
                    h4.Color = color_temp; set(h4,'LineWidth',1,'Markersize',4*(cell_temp.foci_h{1,p}(1,q)/IW_thr),'Marker','o','MarkerFaceColor',[1 1 1],'LineStyle','None');
                    set(h4,'HitTest','off'); % these objects will not trigger GUI mouse click
                    
                    foci_list(i_1,:) = [double(cell_temp.times(1,p)), cell_temp.disp_l{1,p}(1,q)+0.05+length_temp(1,p)/2]; 
                    i_1 = i_1+1;
                else
                    h3 = plot(cell_temp.times(1,p), cell_temp.disp_l{1,p}(1,q)+length_temp(1,p)/2);
                    h3.Color = color_temp; set(h3,'LineWidth',1,'Markersize',(4*(2*cell_temp.foci_h{1,p}(1,q)/IW_thr))^1.5,'Marker','o','MarkerFaceColor',[1 1 1],'LineStyle','None');
                    set(h3,'HitTest','off'); % these objects will not trigger GUI mouse click
                    
                    foci_list(i_1,:) = [double(cell_temp.times(1,p)), cell_temp.disp_l{1,p}(1,q)+length_temp(1,p)/2]; 
                    i_1 = i_1+1;
                end
            end
            
        end
    end

    % Plot a line at the division times
    b3 = plot(divition_time_temp*ones(1,2),[-10 10]);
    b3.Color = [0 0 0]; set(b3,'LineWidth',0.5,'Markersize',2,'Marker','None','MarkerFaceColor',[1 1 1],'LineStyle','--');

    division_list(j_1,1) = divition_time_temp;
    j_1 = j_1+1;

end

b4 = plot([0 xlim_maximum],[0 0]); 
b4.Color = [0 0 0]; set(b4,'LineWidth',0.5,'Markersize',2,'Marker','None','MarkerFaceColor',[1 1 1],'LineStyle','--');

txt_tmp = sprintf('frame index (%d min/frame)',time_int);
xlabel(txt_tmp,'fontsize',10);
xlim([xlim_minimum xlim_maximum])
%     set(gca,'XScale','linear','XTick',[0 30 60 90 120 150 180 210 240 270 300 330 360],'XTickLabel', ...
%             {'0','30','60','90','120','150','180','210','240','270','300','330','360'})
%         
%     set(gca,'XScale','linear','XTick',[200 230 260 290 320 350 380 410 440 470 500 530 3560],'XTickLabel', ...
%             {'200','230','260','290','320','350','380','410','440','470','500','530','560'})

set(gca,'XScale','linear','XTick',[40 70 100 130 160 200 230 260 290 320 350 380 410 440 470 500 530],'XTickLabel', ...
        {'40', '70', '100','130','160','200','230','260','290','320','350','380','410','440','470','500','530'})

ylabel('foci position ({\mu}m)','fontsize',10) 
ylim([-1 ylim_max])
set(gca,'YScale','linear','YTick',[0 1 2 3 4 5 6 7 8],'YTickLabel',{'0','1','2','3','4','5','6','7','8'},'YGrid','Off');

set(gca,'TickLength',[0.005 0.01],'fontsize',12,'TickDir','out','PlotBoxAspectRatio',[2 1 1]);

save_name = [dir_name 'picked/' 'f' num2str(fnames_channel(k,1),'%.2d') 'p' num2str(fnames_channel(k,2),'%.4d')];
save_name_png = [dir_name 'picked_png/' 'f' num2str(fnames_channel(k,1),'%.2d') 'p' num2str(fnames_channel(k,2),'%.4d')];
display_name = ['FOV: ' num2str(fnames_channel(1,1),'%.2d') '; Channel: ' num2str(fnames_channel(1,2),'%.4d')];

end