freeze_mouselight_folder.m

function freeze_mouselight_folder(...
        mj2_output_folder_path, ...
        tif_input_folder_path, ...
        compression_ratio, ...
        do_run_on_cluster, ...
        do_try, ...
        maximum_running_slot_count, ...
        submit_host_name, ...
        varargin)
    
    % Handle optional arguments
    [do_freezing, do_verification] = parse_keyword_args(...
        varargin, ...
        'do_freezing', true, ...
        'do_verification', true) ;
    
    %
    % Compress full-rez octree tiffs to .mj2, copy all non-tif files over
    %
    
    if do_freezing ,
        % Compress all the full-rez octree tiles to .mj2
        batch_convert_all_tif_files_to_mj2(...
            mj2_output_folder_path, ...
            tif_input_folder_path, ...
            compression_ratio, ...
            do_run_on_cluster, ...
            do_try, ...
            maximum_running_slot_count, ...
            submit_host_name) ;

        % Copy all the non-tiff files over to the mj2 side
        copy_non_stack_files_during_freezing(...
            mj2_output_folder_path, ...
            tif_input_folder_path) ;
    end

    %
    % Verify that all that went well
    %

    if do_verification ,
        % Use the cluster to check that all compressed .tif's match their .mj2 well
        % enough, and write a 'certificate' file to represent that.
        fprintf('Doing batch verification of .tif files...\n') ;
        batch_verify_mj2_files_after_freezing(mj2_output_folder_path, ...
                                              tif_input_folder_path, ...
                                              do_run_on_cluster, ...
                                              do_try, ...
                                              submit_host_name, ...
                                              maximum_running_slot_count)
        fprintf('Done with batch verification of .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 .mj2 verification certificates...\n') ;
        check_certs_after_verifying_freezing(tif_input_folder_path, mj2_output_folder_path) ;
        fprintf('Done with checking output .mj2 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_freezing(mj2_output_folder_path, tif_input_folder_path) ;
        fprintf('Done with verification of non-.tif files.\n') ;
        
        %
        % Do a final comparison of .tif files and .mj2 files, just for the heck of it
        %
    
        % Count the tifs
        final_tif_count = ...
            find_and_count(tif_input_folder_path, @does_file_name_end_in_dot_tif, @is_not_the_ktx_folder) ;
        fprintf('Final .tif count in %s is: %d\n', tif_input_folder_path, final_tif_count) ;
        
        % Count the mj2s
        final_mj2_count = ...
            find_and_count(mj2_output_folder_path, @does_file_name_end_in_dot_mj2, @is_not_the_ktx_folder) ;
        fprintf('Final .mj2 count in %s is: %d\n', mj2_output_folder_path, final_mj2_count) ;
        
        % Final check
        if final_tif_count ~= final_mj2_count ,
          error('Final .mj2 count in target folder differs from final .tif count in source folder') ;
        end
    end

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