Tracking/TracePlayer.m at master · JacobZuo/Tracking · GitHub

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function [TraceMovie] = TracePlayer(Trace, ImageInfo, varargin)

    if isempty(varargin)
        Background_nor = ones(ImageInfo.ImageHeight, ImageInfo.ImageWidth);
    else
        Background_nor = varargin{1};
    end

    File_id = ImageInfo.File_id;
    TrackImageIndex = ImageInfo.TrackImageIndex;

    LeftSide = max(min(floor(Trace(:, 2)) - 100), 1);
    UpSide = max(min(floor(Trace(:, 3)) - 100), 1);

    RightSide = min(max(floor(Trace(:, 2)) + 100), ImageInfo.ImageWidth);
    DownSide = min(max(floor(Trace(:, 3)) + 100), ImageInfo.ImageHeight);

    if strcmp(ImageInfo.FileType, '.nd2')
        [FilePointer, ImagePointer, ImageReadOut] = ND2Open(File_id);
    elseif strcmp(ImageInfo.FileType, '.tif')
    else
        warning('Error!')
        return
    end

    TraceMovie = zeros(DownSide - UpSide + 1, RightSide - LeftSide + 1, size(Trace, 1));
    [X, Y] = meshgrid(LeftSide:RightSide, UpSide:DownSide);

    for i = 1:size(Trace, 1)

        if strcmp(ImageInfo.FileType, '.nd2')
            Original_Image = ND2Read(FilePointer, ImagePointer, ImageReadOut, Trace(i, 1));
        elseif strcmp(ImageInfo.FileType, '.tif')
            Original_Image = imread(File_id, 'Index', TrackImageIndex(Trace(i, 1)), 'Info', ImageInfo.main);
        else
            warning('Error!')
            return
        end

        Normalize_Image = uint16(double(Original_Image(:, :)) ./ Background_nor);
        TraceMask = (((X - round(Trace(i, 2))).^2 + (Y - round(Trace(i, 3))).^2) < 16) & (((X - round(Trace(i, 2))).^2 + (Y - round(Trace(i, 3))).^2) > 9);
        TraceMask(X == round(Trace(i, 2)) & (Y - round(Trace(i, 3))).^2 >= 9 & (Y - round(Trace(i, 3))).^2 <= 64) = 1;
        TraceMask(Y == round(Trace(i, 3)) & (X - round(Trace(i, 2))).^2 >= 9 & (X - round(Trace(i, 2))).^2 <= 64) = 1;

        TraceImagei = mat2gray(Normalize_Image(UpSide:DownSide, LeftSide:RightSide));
        TraceImagei(TraceMask) = 1;
        TraceMovie(:, :, i) = TraceImagei;

    end

    if strcmp(ImageInfo.FileType, '.nd2')
        calllib('Nd2ReadSdk', 'Lim_FileClose', FilePointer);
        clear('FilePointer');
    else
    end

    implay(TraceMovie)

end