plot_image_directory.m

function success = plot_image_directory(folder_name)
% plots the individual worm videos and all the track videos

    addpath(genpath(pwd))

    %% STEP 1: initialize %%
    number_of_images_for_median_projection = 20;
    parameters = load_parameters(folder_name); %load experiment parameters
    mask = parameters.Mask;
    
    if parameters.IndividualVideoPlottingFrameRate > 0
        %plot individual worms
        relevant_track_fields = {'Centerlines','UncertainTips','Eccentricity',...
            'Direction','Speed','TotalScore','Active','Path','LastCoordinates',...
            'Frames','NumFrames','Pirouettes','Runs','Size','SmoothSpeed','AngSpeed'};
    else
        %plot whole field only
        relevant_track_fields = {'Active','Path','LastCoordinates',...
            'Frames','NumFrames','Pirouettes','Runs','Size','SmoothSpeed','AngSpeed'};        
    end
    %% Load tracks
    Tracks = load_single_folder(folder_name, relevant_track_fields);
    if isempty(Tracks)
        error('Empty Tracks');
    end

    %% STEP 2: plot individual worms
    if parameters.IndividualVideoPlottingFrameRate > 0
        individual_figure = figure;
        individual_worm_videos(Tracks, folder_name, parameters.SampleRate, parameters.IndividualVideoPlottingFrameRate);
        close(individual_figure)
    end
    
    %% STEP 3: Load images and other properties from the directory %%
    % check if preferences indicate not to plot
    if parameters.PlottingFrameRate <= 0
        success = true;
        return
    end
    
    % Get all the tif file names (probably jpgs)
    image_files=dir([folder_name, filesep, '*.jpg']); %get all the jpg files (maybe named tif)
    if isempty(image_files)
        image_files = dir([folder_name, filesep, '*.tif']); 
    end
    % Load Voltages
    fid = fopen([folder_name, filesep, 'LEDVoltages.txt']);
    LEDVoltages = transpose(cell2mat(textscan(fid,'%f','HeaderLines',0,'Delimiter','\t'))); % Read data skipping header
    fclose(fid);
    
    %% STEP 4: Get the median z projection %%
    medianProj = imread([folder_name, filesep, image_files(1).name]);
    medianProjCount = min(number_of_images_for_median_projection, length(image_files) - 1); 
    medianProj = zeros(size(medianProj,1), size(medianProj,2), medianProjCount);
    for frame_index = 1:medianProjCount
        curImage = imread([folder_name, filesep, image_files(floor((length(image_files)-1)*frame_index/medianProjCount)).name]);
        medianProj(:,:,frame_index) = curImage;
    end
    medianProj = median(medianProj, 3);
    medianProj = uint8(medianProj);
    
    %% STEP 5: plot all the tracks
    % Setup figure for plotting tracker results
    % -----------------------------------------
    WTFigH = findobj('Tag', 'WTFIG');
    if isempty(WTFigH)
        WTFigH = figure('Name', 'Tracking Results', ...
            'NumberTitle', 'off', ...
            'Tag', 'WTFIG');
    else
        figure(WTFigH);
    end

    frames_per_plot_time = round(parameters.SampleRate/parameters.PlottingFrameRate);
    
    %save subtracted avi
    outputVideo = VideoWriter(fullfile([folder_name, filesep, 'processed']),'Motion JPEG AVI');
    outputVideo.FrameRate = parameters.PlottingFrameRate;
    open(outputVideo)
    
    for frame_index = 1:frames_per_plot_time:length(image_files) - 1
        % Get Frame
        curImage = imread([folder_name, filesep, image_files(frame_index).name]);
        subtractedImage = curImage - uint8(medianProj) - mask; %subtract median projection  - imageBackground
        if parameters.AutoThreshold       % use auto thresholding
            Level = graythresh(subtractedImage) + parameters.CorrectFactor;
            Level = max(min(Level,1) ,0);
        else
            Level = parameters.ManualSetLevel;
        end
        % Convert frame to a binary image 
        NUM = parameters.MaxObjects + 1;
        while (NUM > parameters.MaxObjects)
            if parameters.DarkObjects
                BW = ~im2bw(subtractedImage, Level);  % For tracking dark objects on a bright background
            else
                BW = im2bw(subtractedImage, Level);  % For tracking bright objects on a dark background
            end

            % Identify all objects
            [~,NUM] = bwlabel(BW);
            Level = Level + (1/255); %raise the threshold until we get below the maximum number of objects allowed
        end

        PlotFrame(WTFigH, double(BW), Tracks, frame_index, LEDVoltages(frame_index));
        FigureName = ['Tracking Results for Frame ', num2str(frame_index)];
        set(WTFigH, 'Name', FigureName);
        writeVideo(outputVideo, getframe(WTFigH));
        
    end
    close(outputVideo) 
    close(WTFigH)
    success = true;
end