--- a
+++ b/steps/step_B_registration.m
@@ -0,0 +1,130 @@
+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');
+
+