function [] = step_B_registration(dirTest, dirUtilities, ext, fidLogs, logS, savefile, plotFigures)

%dbname

dbname = 'ALL_IDB';

%part

dbPart = 'ALL_IDB2';

%params

run('./params/params_registration.m');

%dirIn e Out

dirIn = [dirTest dbname '\' dbPart '\'];

dirOut = [dirIn 'ROI_' num2str(params.roiSize(1)) '/'];

dirOutColorNorm = [dirIn 'colorNorm\'];

mkdir_pers(dirOut, savefile);

mkdir_pers(dirOutColorNorm, savefile);

%dirResults

dirResults = './Results/';

mkdir_pers(dirResults, savefile);

fileSaveTest = [dirResults 'save.mat'];

%RESULTS: log file

timeStampRaw = datestr(datetime);

timeStamp = strrep(timeStampRaw, ':', '-');

if savefile && logS

    logFile = [dirResults dbname '_log_' timeStamp '.txt'];

    fidLog = fopen(logFile, 'w');

    fidLogs{2} = fidLog;

end %if savefile && log

%loop

files = dir([dirIn '*.' ext]);

for i = 1 : numel(files)

% for i = [1 2 3 141 142 143]

    %read im

    filename = files(i).name;

    im = imread([dirIn filename]);

    %display

    fprintf_pers(fidLogs, ['Im: ' filename]);

    %super-resolution?

    %illumination compensation?

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

    %preprocessing

    %deblur - 1shot maxpol

    %im_deBlurred = deBlur1shotMaxPol(im, params);

    %focus assessment

    focusOriginal = assessFocusFQPath(im, filename, dirUtilities, plotFigures);

    fprintf_pers(fidLogs, ['\tFocus: ' num2str(focusOriginal)]);

    %skip de-focused images?

    if focusOriginal > params.thFocus

        fprintf_pers(fidLogs, '\tFocus low...');

        %continue

    end %if focus

    %color adjust

    imColorNorm = imNormalization(im, filename, plotFigures);

    %save+

    if savefile

        imwrite(imColorNorm, [dirOutColorNorm filename]);

    end %if save

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

    %stain separation

    [H, E, Bg] = deConvStain(im, filename, dirResults, plotFigures, savefile);

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

    %segmentation

    mask = segmentStain(im, imColorNorm, filename, dirResults, params, plotFigures, savefile);

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

    %extraction of ROI

    [ROI, errorV] = extractROI(im, filename, mask, dirResults, params, plotFigures, savefile);

    if errorV == -1

        fprintf_pers(fidLogs, '\tCannot extract ROI...\n');

        continue

    else %if errorV

        fprintf_pers(fidLogs, '\tROI extracted');

    end %if errorV

    %write

    if savefile

        imwrite(ROI, [dirOut filename]);

    end %if save

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

    %structure

    problem(i).filename = filename;

    %class

    [C, ~] = strsplit(filename, {'_', '.'});

    problem(i).class = str2double(C{2});

    %focus

    problem(i).focus = focusOriginal;

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

    %pause

    if plotFigures

        pause(1)

        close all

        pause(0.1)

    end %if plotta

    %newline

    fprintf_pers(fidLogs, '\n');

end %for i

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

%save

save([dirOut 'classes.mat'], 'problem');