Median first and then surface [---v2]

clear all; close all; clc;
addpath('C:\Users\iptea\Documents\MATLAB\Nonreplica September_ROUGHNESS\Roughness_Amore_1\General');

%% Attention:
% diff_idl should ne greater than diff_rl
% size of median filter neighborhood should be greater than desired radius

%%
OpenfilePath = 'C:\Users\iptea\Documents\MATLAB\AMORE_ROUGHNESS\01_KB\backhand';
img = imread([OpenfilePath,'\Image0000.jpg']);
% figure()
% imshow(img);
[H,W] = size(img);

%% Region of interest
l_crop = 130;
t_crop = 20;
r_crop = 0;
b_crop = 300;

[img_crp,H,W] = crop(img,H,W,l_crop,r_crop,t_crop,b_crop);
% figure()
% imshow(img_crop);
%% Prefiltering
gsigma = 6;
img_gau = imgaussfilt(img_crp,gsigma);
%% Finding ideal surface
med = 60;
diff_idl = 15;

img_med = medfilt2(img_gau,[med*2 med*2],'symmetric');
img_med = filt_diff(img_med,H,W,diff_idl);
[img_idl,ind_idl,avg_idl] = find_srf(img_med,H,W);
% figure()
% imshow(img_idl);

%% Flattening surface according to ideal line
% Note: We put gaussian image directly
mrg = 50;
img_flt = flatten(img_crp,H,W,ind_idl,mrg);

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

%% Prefiltering flattened image
gsigma = 6;
img_gau = imgaussfilt(img_flt,gsigma);

%% Finding real surface
diff_rl = 5;
img_diff = filt_diff(img_gau,H,W,diff_rl);
[img_rl,ind_rl,avg_rl] = find_srf(img_diff,H,W);
% figure()
% imshow(img_rl,[])
% hold on
% plot(avg_rl)

%%

%{
img_filt = imgaussfilt(im,gsigma);
img_diff = filt_diff(img_filt,H,W,diffLine1);
[img_line_surf,ind_line_surf,avg_index,ref_line,line1] = line_surf3(img_diff,H,W,diffLine1,up,down);

figure()
imshow(im,[])
hold on
plot(line1)
plot(avg_index)
hold off


% r_crop = 1;


[peak_height,valley_depth] = peak_valley(line1,avg_index,W);
[avg_rough,rms_rough,max_rough,total_rough] = roughness(peak_height,valley_depth)


t_crop = 1;
l_crop = 1;
r_crop = 1;
b_crop = 500;
[H,W] = size(im);
[img_crop,H_crop,W_crop] = crop(im,H,W,l_crop,r_crop,t_crop,b_crop);


figure()
imshow(img_crop,[])


%}



% hold on
% plot(line1)
% plot(avg_index)
% hold off



% figure()
% imshow(img_crop,[])


% hold off
% figure()
% imshow(img_line_surf)



%Hair removal
% img_line_surf_med = medfilt2(img_crop, [4 4]);



% for i = 1:W_crop
%   img_line_surf(1:line1(i)-1,i) = 255;
% end
%
% %%
% img_line_surf = medfilt2(img_line_surf,[1 33]);
% [line3V,line3I] = min(img_line_surf);
%
% for i = 1:W_crop
%   img_crop(1:line3I(i),i) = 0;
% end



%img_med = imgaussfilt(img_crop,gsigma);

% img_med = padarray(img_filt',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]);
% figure()
% imshow(img_med)



%03_PU\forehead' crop
%09_NY\forehead' crop
%08_MA\backhand' crop
%08_MA\forehead crop
%09_NY\forehead' hair
%10_MR\forehead small hair
%03_PU\backhand' small hair
%03_PU\forearm' small hair
%04_HG\backhand' small hair
%04_HG\forearm' big hair
%05_HR\forearm' big hair
%05_HG\backhand' big hair
%07_EJ\backhand' big hair


% img_med = ideal_surf(img_gau,diff_idl,med,H,W);



%     img_filt1 = zeros(H+diff,W);            % make 2d buffer for differential image
%     img_filt2 = zeros(H+diff,W);
%
%     img_filt1(diff+1:diff+H,:) = img_filt;   % put image data to buffer array
%     img_filt2(1:H,1:W) = img_filt;
%
%     img_diff = img_filt1 - img_filt2;        % calculate differential
%
%     img_diff = img_diff(diff+1:diff+H,:);    % cut margin part 2 pixel.
%     figure()
%     imshow(img_filt1,[])
%     figure()
%     imshow(img_filt2,[])
%     figure()
%     imshow(img_diff,[])








% 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-diffLine2; %brat -diff
% end
%
% % plot(img_line_surf)
%
% figure()
% imshow(img_crop)
% hold on
% plot(line3I)
% plot(line2)
% hold off



% minRow = min(I);
% for i = 1:W
%     diffShift(i) = I(i)-minRow;
%     lowLine1(i) = I(i)+100-diffShift(i);
% end


%     im(1:j+1,i) = img_crop(ind_idl(i):ind_idl(i)+j,i);
%     im(topshift+1-c:(topshift+j-9),i) = img_crop(ind_idl(i)-c:(ind_idl(i)-10+j),i);

%b = 500;
% hik = img_crop(ind_idl(i):ind_idl(i)+j,i);
% im(topshift+1-c:(topshift+j-9),i) = img_crop(ind_idl(i)-c:(ind_idl(i)-10+j),i);


% c = 20;


% img_flt = zeros(H,W);
% for i = 1:W
%     j = H-ind_idl(i);
%     img_flt(mrg:mrg+j,i) = img_crp(ind_idl(i):ind_idl(i)+j,i);
% end

%473-ind