find_centerlines.m

function success = find_centerlines(folder_name)
% gets the centerlines given tracks and their associated individual worm
% images
    addpath(genpath(pwd))
    
    parameters = load_parameters(folder_name); %load experiment parameters
    ImageSize = 2*round(parameters.TrackingWormBoxHalfSize * parameters.CameraPixeltommConversion);
    if parameters.TrackOnly
        success = true;
        return
    end
    
    relevant_track_fields = {'Eccentricity','Direction','Speed'};

    %% Load tracks
    Tracks = load_single_folder(folder_name, relevant_track_fields);
    if isempty(Tracks)
        success = false;
        return
    end

    %% Preallocate memory
    track_count = length(Tracks);
    Tracks(track_count).Centerlines = [];
    Tracks(track_count).UncertainTips = [];
    Tracks(track_count).OmegaTurnAnnotation = [];
    Tracks(track_count).PossibleHeadSwitch = [];
    Tracks(track_count).Length = [];
    Tracks(track_count).TotalScore = [];
    Tracks(track_count).ImageScore = [];
    Tracks(track_count).DisplacementScore = [];
    Tracks(track_count).PixelsOutOfBody = [];
    Tracks(track_count).PotentialProblems = [];
    Tracks(track_count).DilationSize = [];
    Tracks(track_count).AspectRatio = [];
    Tracks(track_count).MeanAspectRatio = [];
    Tracks(track_count).ThinningIteration = [];
    Tracks(track_count).MeanAngle = [];
    Tracks(track_count).Angles = [];
    Tracks(track_count).ProjectedEigenValues = [];
    Tracks(track_count).Velocity = [];
    Tracks(track_count).PhaseVelocity = [];
    %     try
%         parpool(feature('numcores'))
%     catch
%         %sometimes matlab attempts to write to the same temp file. wait and
%         %restart
%         pause(randi(60));
%         parpool(feature('numcores'))
%     end
    
    %% Extract Centerlines and eigenworms
    parfor track_index = 1:track_count
%     for track_index = 1:track_count
%     for track_index = 10:10
         % loop through all the tracks to get centerlines
%         track_index
%         tic
        try
            % if anything goes wrong in centerline finding, make a note to
            % remove the track
            loaded_file = load([folder_name, filesep, 'individual_worm_imgs', filesep, 'worm_', num2str(track_index), '.mat']);
            worm_images = loaded_file.worm_images;
            Tracks(track_index) = initial_sweep(worm_images, Tracks(track_index), parameters, track_index); %get the centerlines
            [angles, Tracks(track_index).MeanAngle] = centerlines_to_angles(Tracks(track_index).Centerlines); %get the angles
            Tracks(track_index).Angles = angles - (diag(parameters.MeanAngles)*ones(size(angles))); %mean center
            Tracks(track_index).ProjectedEigenValues = parameters.EigenVectors\Tracks(track_index).Angles; %project into PCA space
            Tracks(track_index).Velocity = find_velocity(Tracks(track_index).Speed, Tracks(track_index).Direction, Tracks(track_index).Centerlines, ImageSize);
            Tracks(track_index).PhaseVelocity = worm_phase_velocity(Tracks(track_index).ProjectedEigenValues, parameters);
        catch
%             % error in centerline finding. get rid of it in error resolution
            Tracks(track_index).PotentialProblems = [];
        end
%         toc
    end
    
    delete(gcp('nocreate'))
    
    %% save the results
    savetracks(Tracks, folder_name);
    success = true;
end