create a mask + size of structuring element

create_segmented_img_with_border.m

%% Initialization
main_directory = 'isbi-segmentation-dataset';     % parent directory

% dialation size
strel_size = 25;

% select one or the other.. test or train
img_type = 'test';
% img_type = 'train';

% ========================= input information
% subdirectories
img_subDir = img_type;
mask_subDir = strcat(img_type, '_masks');
img_directory_path = strcat(main_directory, '/', img_subDir);
mask_directory_path = strcat(main_directory, '/', mask_subDir);

photo_ext = '.jpg';          % image type
mask_ext = '.png';          % image type

individual_file = '*';      % set to * for all files in a folder

% get base file name
str_to_strip_from_mask = '_Segmentation';
str_to_strip_from_img = '';

% full basename + ___ for mask and img
str_extra_mask = strcat(str_to_strip_from_mask, mask_ext);
str_extra_img = strcat(str_to_strip_from_img, photo_ext);

% ========================= output information
output_subDir = strcat('dilMask_', string(strel_size), '/', img_type);


%% loop though mask dir.
mask_files = dir(mask_directory_path);
for image_file = mask_files'
    % build file paths
    mask_file_path = image_file.name;
    base_file_name = strrep(mask_file_path, str_extra_mask, '');
    img_file_path = strcat(base_file_name, str_to_strip_from_img, photo_ext);
    
    % confirm the paths are correct
    % DEBUGING: sprintf('[%s]: %s -> %s',base_file_name, mask_file_path, img_file_path)
    
    
    % need to skip over the . file
    if base_file_name ~= '.'
        % DEBUGING: confirm individual path is correct
        % sprintf('[%s]: %s -> %s',base_file_name, mask_file_path, img_file_path)
        
        % get img and mask
        img = imread(strcat(main_directory, '/', img_type, '/', img_file_path));
        mask = imread(strcat(main_directory, '/', img_type, '_masks/', mask_file_path));
        % 100 is an arbitrary value between 0 and 255 (the current values)
        
        % create structuring element to dialate mask
        se_sized = strel('disk',strel_size);
        mask_dil = imdilate(mask, se_sized);
        % create mask as logical
        mask_bw = logical(mask_dil>100);
%         mask_bw = logical(mask>100);
        
        % this function was adopted from: https://www.mathworks.com/matlabcentral/answers/2646-image-segmentation
        maskedRgbImage = bsxfun(@times, img, cast(mask_bw,class(img)));
        
        
        % save the image here after you
        % name of img to output
        output_img_path = strcat(main_directory, '/', output_subDir, '/', img_file_path);
        % must use a char type conversion to use imwrite in this case
        imwrite(maskedRgbImage, char(output_img_path));
        
    end

end

%% show the last image to make sure it's working correctly
figure
subplot(1,3,1)
imshow(img);
title(base_file_name)

subplot(1,3,2)
imshow(mask_dil);
title('Mask-dil')

subplot(1,3,3)
imshow(maskedRgbImage);
title('segmented')