function [maskACClopeOpen] = segmentStain(im, imColorNorm, filename, dirResults, params, plotta, savefile)

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

%otsu (intensity) on E

if size(imColorNorm, 3) == 3

    imColorNorm_gray = rgb2gray(imColorNorm);

end %if size

th = graythresh(imColorNorm_gray) + params.offsetOtsuIntens;

%thresh = imColorNorm_gray < th*255;

thresh = imColorNorm_gray < th;

threshOne = connComp2(thresh, 1, 1);

maskThresh = threshOne;

% figure

% imshow(maskThresh)

% pause

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

%fuzzy c-means on E

%imAlt = im2uint8(rgb2lab(im));

imAlt = im2uint8(rgb2hsv(im));

[C, U, LUT, H] = FastFCMeans(imAlt, params.nClusters);

%analyze centers, discard greatest one (white background)

% [C_sort, indC] = sort(C, 'ascend');

[C_sort, indC] = sort(C, 'descend'); %for hsv

C_select = indC(1 : params.classesToConsider);  

% %memberships to maps

L = LUT2label(imAlt, LUT);

Umap = FM2map(imAlt, U, H);

%memberships

if plotta

    fh1 = figure;

    subplot(1,3,1)

    imshow(rgb2gray(Umap(:,:,:,1)),[]);

    subplot(1,3,2)

    imshow(rgb2gray(Umap(:,:,:,2)),[]);

    subplot(1,3,3)

    imshow(rgb2gray(Umap(:,:,:,3)),[]);

    str = [filename '; class memberships'];

    mtit(fh1, str, 'Interpreter', 'none', 'fontsize', 14, 'color', [1 0 0], 'xoff', .0, 'yoff', .0);

    if savefile

        export_fig(gcf, [dirResults str '.jpg']);

    end %if save

end %if plotta

%[C, U, LUT, H] = FastFCMeans(im, params.nClusters);

%analyze centers, discard greatest one (white background)

% [C_sort, indC] = sort(C, 'ascend');

% C_select = indC(1 : params.classesToConsider);

% %memberships to maps

% L = LUT2label(im, LUT);

% Umap = FM2map(im, U, H);

%select

maskFuzzy = false([size(L, 1) size(L,2)]);

classThresholded = cell(numel(C_select), 1);

for c = 1 : numel(C_select)

    class = rgb2gray(Umap(:,:,:,C_select(c)));

    class = imadjust(class);

    %for one of the classes, modify the threshold

    %if c == 2

        threshClass = graythresh(class) + params.offsetOtsuFCM;

    %else %if c

        %threshClass = graythresh(class);

    %end %if c

    classThresholded{c} = class > threshClass;

    %threshClass = multithresh(class, params.numberMultiThresh) - params.offsetOtsuFCM;

    %classThresholded{c} = class > threshClass(2);

    maskFuzzy = logical(maskFuzzy + classThresholded{c});

end %for c

maskFuzzy = connComp2(maskFuzzy, 1, 1);

%display

if plotta

    fh2 = figure;

    for c = 1 : numel(C_select)

        subplot(1, numel(C_select), c)

        imshow(classThresholded{c})

    end %for c

    str = [filename '; class memberships, segmentation'];

    mtit(fh2, str, 'Interpreter', 'none', 'fontsize', 14, 'color', [1 0 0], 'xoff', .0, 'yoff', .0);

    if savefile

        export_fig(gcf, [dirResults str '.jpg']);

    end %if save

end %if plotta

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

%combine

% mask = logical(maskThresh .* maskFuzzy);

mask = logical(maskThresh + maskFuzzy);

%morph

se = strel(params.typeSeSegm, params.sizeSeSegm);

maskFill = imfill(mask, 'holes');

maskClose = imclose(maskFill, se);

maskCloseOpen = imopen(maskClose, se);

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

%refine with active contour

maskAC = activecontour(im, maskCloseOpen, params.numIterAC, 'Chan-Vese', 'ContractionBias', -0.3);

%morph

maskAC_oneCC = connComp2(maskAC, 1, 1);

maskACFill = imfill(maskAC_oneCC, 'holes');

maskACClose = imclose(maskACFill, se);

maskACClopeOpen = imopen(maskACClose, se);

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

if plotta

    fh = fsfigure;

    subplot(2,3,1)

    imshow(im)

    title('Original')

    subplot(2,3,2)

    imshow(im2double(im) + edge(maskThresh), []);

    title('Mask Otsu');

    subplot(2,3,3)

    imshow(im2double(im) + edge(maskFuzzy), []);

    title('Mask Fuzzy C-Means');

    subplot(2,3,4)

    imshow(im2double(im) + edge(maskCloseOpen), []);

    title('Mask combined + morph');

    subplot(2,3,5)

    imshow(im2double(im) + edge(maskAC), []);

    title('Mask combined + morph + AC');

    subplot(2,3,6)

    imshow(im2double(im) + edge(maskACClopeOpen), []);

    title('Mask combined + morph + AC + morph');

    str = [filename '; segmentation'];

    mtit(fh, str, 'Interpreter', 'none', 'fontsize', 14, 'color', [1 0 0], 'xoff', .0, 'yoff', .04);

    if savefile

        export_fig(gcf, [dirResults str '.jpg']);

    end %if save

end %if plotta