thaw_mouselight_folder.m

function thaw_mouselight_folder(...
        output_folder_path, ...
        input_folder_path, ...
        do_run_on_cluster, ...
        do_try, ...
        maximum_running_slot_count, ...
        submit_host_name, ...
        varargin)
    
    % Handle optional arguments
    [do_thawing, do_verification] = parse_keyword_args(...
        varargin, ...
        'do_thawing', true, ...
        'do_verification', true) ;

    % Stage 1: thawing
    if do_thawing ,
        % Compress all the full-rez octree tiles to .mj2
        batch_convert_all_mj2_files_to_tif(...
            output_folder_path, ...
            input_folder_path, ...
            do_run_on_cluster, ...
            do_try, ...
            maximum_running_slot_count, ...
            submit_host_name) ;
    
        % Copy all the non-mj2 files over to the tif side
        copy_non_stack_files_during_thawing(output_folder_path, ...
                                            input_folder_path) ;
    end

    % Stage 2: verification
    if do_verification , 
        % Use the cluster to check that all decompressed .tif's match their .mj2 well
        % enough, and write a 'certificate' file to represent that.
        fprintf('Doing batch verification of output .tif files...\n') ;
        batch_verify_tif_files_after_thawing(...
            output_folder_path, ...
            input_folder_path, ...
            do_run_on_cluster, ...
            do_try, ...
            submit_host_name, ...
            maximum_running_slot_count)
        fprintf('Done with batch verification of output .tif files.\n') ;
        
        % Wait a bit to make sure the filesystem changes have propagated
        if do_run_on_cluster ,
            pause(20) ;
        end
    
        % Check that all the cetificate files that should be there, are there
        fprintf('Checking output .tif verification certificates...\n') ;
        check_certs_after_verifying_thawing(input_folder_path, output_folder_path) ;
        fprintf('Done checking output .tif verification certificates.\n') ;    
    
        % Verify that all the non-tif files exist on the mj2 side
        fprintf('Doing verification of non-.tif files...\n') ;
        verify_non_stack_files_after_thawing(output_folder_path, input_folder_path) ;
        fprintf('Done with verification of non-.tif files.\n') ;
    
        
        %
        % Do a final comparison of leaf .tif files and .mj2 files, just for the heck of it
        %
    
        % Count the mj2s
        final_mj2_count = ...
            find_and_count(input_folder_path, @does_file_name_end_in_dot_mj2, @(varargin)(true)) ;
        fprintf('Final .mj2 count in %s is: %d\n', input_folder_path, final_mj2_count) ;
        
        % Count the tifs
        final_tif_count = ...
            find_and_count(output_folder_path, @does_file_name_end_in_dot_tif, @(varargin)(true)) ;
        fprintf('Final .tif count in %s is: %d\n', output_folder_path, final_tif_count) ;
        
        % Final check
        if final_tif_count ~= final_mj2_count ,
          error('Final .tif count in target folder differs from final .mj2 count in source folder') ;
        end
    end

    % Report final status if we get this far
    if do_thawing && do_verification ,
        fprintf('Folder decompression and verification succeeded!\n') ;
    elseif do_thawing ,
        fprintf('Folder decompression succeeded!  No verification performed.\n') ;
    elseif do_verification ,
        fprintf('Folder verification succeeded!  (No decompression performed.)\n') ;
    else
        fprintf('Did nothing.  Nothing at all.\n') ;
    end
    
end