function msg = whole_mount_tiles_stitching

%% Whole Mount Tile Stitching

%% Purpose:  

% This function creates a whole-mount image from individual tiles and implements

% black_border_removal to remove border around image in the case of old

% images that were scanned with a border.

%% ------------------------------------------------------------------------

% directory = ''; name the needed directory that contains tiled images to

% be re-stitched together

% subj = XX; % patient number

% slice = "XX"; % slide name

% scanner = "Olympus"; % scanner name indictate tile sizes

% anot_micro = "Nikon"; % scanner used if originally annotated on a

% previous scanner

for d = 1:numel(directory)

    tic;

    addpath(directory(d))

    subj_slice = sprintf('%i_%s',subj(d),slice(d));

    fprintf('Processing: %s\n',subj_slice);

    disp('Loading images');

    files = fullfile(directory(d),'tile*.tiff');

    input_images = dir(files);

    input_images = {input_images.name}';

    if (isempty(input_images))

        files = fullfile(directory(d), 'tile*.jpg'); % adjust extension if needed

        input_images = dir(files);

        input_images = {input_images.name}';

    end

    name = strsplit(input_images{numel(input_images)},{'_','.'});

    xmax = str2num(name{2}(2:end));

    ymax = str2num(name{3}(2:end));

    x = [1 xmax];

    y = [1 ymax];

    xx = 1;

    yy = 1;

    if strcmp(scanner(d),'Huron')

        resize_factor = 10; % 8 nikon/olympus 12 huron

    else

        resize_factor = 8;

    end

    im = uint8(imread(input_images{numel(input_images)}));

    im_size = size(im);

    im = imrotate(imresize(im,1/8),90);

    ximage = cell(1,numel(input_images));

    yimage = cell(1,numel(input_images));

    for i = 1:numel(input_images)

        ximage{i} = ones(size(im(:,:,1)),'uint8') * xx;

        ximage{i} = imresize(ximage{i},[1 size(im,1)],'nearest');

        ximage{i} = imrotate(ximage{i},90);

        xx = xx + 1;

        if xx > xmax

            xx = 1;

        end

        yimage{i} = ones(size(im(:,:,1)),'uint8') * yy;

        yimage{i} = imresize(yimage{i},[1 size(im,2)],'nearest');

        yimage{i} = imrotate(yimage{i},90);

        yy = yy + 1;

        if yy > ymax

            yy = 1;

        end

    end

    disp('Creating rows');

    % Arrange rows

    ind1 = y(1);

    ind2 = y(2);

    rows = cell(1,xmax);

    for i = 1:xmax

        im = cell(1,ymax);

        ind3 = 1;

        for j = ind1:ind2

            im{ind3} = imrotate(imresize(uint8(imread(input_images{j})),1),90);

            ind3 = ind3 + 1;

        end

        rows{i} = imtile(im,'GridSize',[1 ymax]); clear im;

        rows{i} = imrotate(rows{i},180); % flips orientation

        ind1 = ind1 + ymax;

        ind2 = ind2 + ymax;

        if ind2 > numel(input_images)

            break

        end

    end

    toc

    xx = 1;

    xrows = cell(1,xmax);

    missing_vals = cell(1,xmax);

    for i = 1:xmax

        xrows{i} = ximage(xx:xmax:size(ximage,2)); % creates image rows

        xrows{i} = imtile(xrows{i},'GridSize',[1 size(rows{1},2)]);

        missing_vals{i} = uint8((xrows{i} == 0)*i); % xrows is filled with 0s beyond what was created above

        xrows{i} = xrows{i} + missing_vals{i};

        xx = xx + 1;

        if xx > xmax

            break

        end

    end

    yy = 1;

    ycols = cell(1,ymax);

    missing_vals = cell(1,ymax);

    for i = 1:ymax

        ycols{i} = yimage(yy:ymax:size(yimage,2)); % creates image cols

        ycols{i} = imtile(ycols{i},'GridSize',[1 xmax*size(rows{1},1)])'; % inverting creates col from row

        missing_vals{i} = uint8((ycols{i} == 0)*i);

        ycols{i} = ycols{i} + missing_vals{i};

        yy = yy + 1;

        if yy > ymax

            break

        end

    end

    toc

    disp('Compiling image');

    whole_image = imtile(rows,'GridSize',[xmax 1]);

    whole_image = imrotate(whole_image,-180);

    whole_ximage = flipud(imtile(xrows,'GridSize',[xmax 1])); % tile numbering starts in LL

    whole_ximage = double(whole_ximage);

    % figure(); imagesc(whole_ximage);

    whole_yimage = imtile(ycols,'GridSize',[1 ymax]);

    whole_yimage = double(whole_yimage);

    % figure(); imagesc(whole_yimage);

    toc

    disp('Saving image');

%     figure(); imshow(whole_image);

    %                 saveas(gcf,sprintf('%s_whole_mount_recon_%i',subj_slice,resize_factor),'tif');

toc

msg = 'done';

disp(msg)