Calculate Roughness average mean from front

clear all; close all; clc;

nm = {'01_KB_1\forearm','01_KB_1\forehead',...
    '02_YJ_1\forearm','02_YJ_1\forehead','02_YJ_1\backhand',...
    '03_PU_1\forearm','03_PU_1\backhand',...
    '04_HG_1\forearm','04_HG_1\forehead',...
    '05_HR_1\forearm','05_HR_1\forehead','05_HR_1\backhand',...
    '06_HG_1\forearm','06_HG_1\forehead','06_HG_1\backhand',...
    '07_EJ_1\forearm','07_EJ_1\forehead',...
    '08_MA_1\forearm','08_MA_1\forehead','08_MA_1\backhand',...
    '09_NY_1\forearm','09_NY_1\backhand',...
    '10_MR_1\forearm','10_MR_1\forehead','10_MR_1\backhand'};

% OpenfilePath = 'C:\Users\TBL\Documents\MATLAB\1708_AMORE\04_HG_1\forearm';
max_step = 500;
gsigma = 4;

filename = 'testdata.xlsx';
titles = {'Folder','mean_avg_rough','mean_rms_rough','mean_max_rough'};
xlRangeTitle = 'B1:E1';
xlswrite(filename,titles,xlRangeTitle);

for j = 1:length(nm)
    OpenPath = strcat('C:\Users\TBL\Documents\MATLAB\1708_AMORE\',nm(1,j));
    X = ['Current Folder:',nm(1,j),' index: ',num2str(j)];
    disp(X)
    for step = 1:max_step
        read_file_name = strcat('Image',num2str(step-1,'%04d'),'.jpg');
        img = imread([OpenPath{1},'\' ,read_file_name]);

        %img = imread('Image0035.jpg');
        [H,W] = size(img);

        diff = 1;

    %     img = double(img);
        img_filt = imgaussfilt(img,gsigma);
        img_diff = filt_diff(img_filt,H,W,diff);
        up = H-2;
        down = 222;
        [img_line_surf,ind_line_surf,avg_index,ref_line,line1] = line_surf3(img_diff,H,W,diff,up,down);


        % figure()
        % imshow(img_line_surf)

        % [line3V,line3I] = min(img_line_surf);

        diff = 2;
        med = 60;
        %img_med = imgaussfilt(img_crop,gsigma);
        img_med = padarray(img',med,'replicate','both');
        img_med = padarray(img_med',med,'replicate','both');
        img_med = medfilt2(img_med,[med*2 med*2]);
        img_med = img_med([med+1:H+med],[med+1:W+med]);
        img_filt1 = zeros(H+diff,W);
        img_filt2 = zeros(H+diff,W);

        img_filt1([diff+1:H+diff],:) = img_med;
        img_filt2([1:H],[1:W]) = img_med;

        %%
        img_med = img_filt1 - img_filt2;
        img_med = img_med([diff+1:H+diff],:);
        %%

        %%
        % figure();
        % imshow(img_med,[]);

        img_line2 = zeros(H,W);

        %diff = 10;
        for i = 1:W
            [local_max,local_index] = min(img_med(:,i));
            img_line2(local_index,i) = 255; %+2 %-10    ubrat -diff
            line2(i) = local_index-diff; %brat -diff
        end

    %     figure()
    %     imshow(img)
    %     hold on
    %     plot(line2)
    %     plot(line1)
    %     hold off
        valley_depth = peak_valley(line1,line2,W);
        [avg_rough(step),rms_rough(step),max_rough(step)] = roughness_valley(valley_depth);
        %fprintf('%i\n', step);
        fprintf('.');
        if mod(step,100) == 0
            fprintf('\n');
        end
    end

%     disp(X)
%     fprintf(')'%i\n', j);
    fprintf('\nValues: \n');
    mean_avg_rough = mean(avg_rough)
    mean_rms_rough = mean(rms_rough)
    mean_max_rough = mean(max_rough)

%     figure()
%     imshow(img)
%     hold on
%     plot(line1)
%     plot(line2)
%     hold off

%     xlswrite(filename,mean_avg_rough);

%     filename = 'testdata.xlsx';
%     X = ['Current Folder:',nm(1,j),' index: ',num2str(j)];
%     OpenPath = strcat('C:\Users\TBL\Documents\MATLAB\1708_AMORE\',nm(1,j));


%    A = {nm(1,j),mean_avg_rough,mean_rms_rough,mean_max_rough};
%    titles = {'Folder','mean_avg_rough','mean_rms_rough','mean_max_rough'};
    A = [nm(1,j),num2str(mean_avg_rough),num2str(mean_rms_rough),num2str(mean_max_rough)];

    xlRangeVariables = strcat('B',num2str(j+1),':','E',num2str(j+1));
    xlswrite(filename,A,xlRangeVariables);


% sheet = 2;
% xlRange = 'E1';



end




%mean_total_rough = mean(total_rough)


% figure()
% imshow(img)
% hold on
% plot(line1)
% plot(line2)
% hold off


%}






% [peak_height,valley_depth] = peak_valley(line3I,line2,W);
% [avg_rough,rms_rough,max_rough,total_rough] = roughness(peak_height,valley_depth)