top_view_skin

close all; clear all; clc;
addpath('C:\Users\iptea\Documents\MATLAB\Nonreplica September_ROUGHNESS\Roughness_Amore_Skin2017\General');
%%
data_pth = 'C:\Users\iptea\Documents\MATLAB\skin_data_171017';
folder = 'F:\Amore_Skin';

d = dir;
d = d(~ismember({d.name},{'.','..'}));
%%
sbj = {'1','2','3','4','5'};
part = {'y_cheek','o_cheek','y_eye','o_eye','y_forearm','o_forearm'};
%%
sht_tbl = 'rgh_frnt_inp_refparams_FINALDONTTOUCH.xlsx';
T = readtable(sht_tbl,'ReadRowNames',false);
l_crop_list_o = T{1:15,6};
gau1_list_o = T{1:15,7};
med_list_o = T{1:15,8};
gau2_list_o = T{1:15,9};
l_crop_list_y = T{1:15,15};
gau1_list_y = T{1:15,16};
med_list_y = T{1:15,17};
gau2_list_y = T{1:15,18};

med_arr = zeros(5,6);
gsigma2_arr = zeros(5,6);
l_crop_arr = zeros(5,6);
gsigma1_arr = zeros(5,6);

l_crop_arr(:,1) = l_crop_list_y(1:5,1);
l_crop_arr(:,2) = l_crop_list_o(1:5,1);
l_crop_arr(:,3) = l_crop_list_y(6:10,1);
l_crop_arr(:,4) = l_crop_list_o(6:10,1);
l_crop_arr(:,5) = l_crop_list_y(11:15,1);
l_crop_arr(:,6) = l_crop_list_o(11:15,1);

med_arr(:,1) = med_list_y(1:5,1);
med_arr(:,2) = med_list_o(1:5,1);
med_arr(:,3) = med_list_y(6:10,1);
med_arr(:,4) = med_list_o(6:10,1);
med_arr(:,5) = med_list_y(11:15,1);
med_arr(:,6) = med_list_o(11:15,1);

gsigma1_arr(:,1) = gau1_list_y(1:5,1);
gsigma1_arr(:,2) = gau1_list_o(1:5,1);
gsigma1_arr(:,3) = gau1_list_y(6:10,1);
gsigma1_arr(:,4) = gau1_list_o(6:10,1);
gsigma1_arr(:,5) = gau1_list_y(11:15,1);
gsigma1_arr(:,6) = gau1_list_o(11:15,1);

gsigma2_arr(:,1) = gau2_list_y(1:5,1);
gsigma2_arr(:,2) = gau2_list_o(1:5,1);
gsigma2_arr(:,3) = gau2_list_y(6:10,1);
gsigma2_arr(:,4) = gau2_list_o(6:10,1);
gsigma2_arr(:,5) = gau2_list_y(11:15,1);
gsigma2_arr(:,6) = gau2_list_o(11:15,1);

%%
sht_name = 'rgh_frnt_save_images.xlsx';
ttl = {'part','sbj','avg_rgh','rms_rgh','max_rgh'};
ttl_rng1 = 'B1:F1';
xlswrite(sht_name,ttl,ttl_rng1);
%%
ttl_rng2 = 'H1:L1';
xlswrite(sht_name,ttl,ttl_rng2);
%%

% avg_rgh = zeros(1,max_no);
% rms_rgh = zeros(1,max_no);
% max_rgh = zeros(1,max_no);
%%
counter = 0;
incr1 = 1;
incr2 = 2;
%%
%two_di_array = zeros(1,max_no);
%%
for part_no = 6:6 %length(part)
    for sbj_no = 4:4 %length(sbj)
        fld_pth = strcat(data_pth,'\',sbj{sbj_no},'\',part{part_no},'\');
        save_fld_path = strcat(folder,'\',sbj{sbj_no},'\',part{part_no},'\');

        imgFilePath = dir([fld_pth '/*.jpg']);
        imgFilesNo = size(imgFilePath,1);
        max_no = imgFilesNo; %imgFilesNo;
        %save_fld_path = strcat(save_data_path,'\',sbj{sbj_no},'\',part{part_no},'\');
        disp(fld_pth);
        two_di_arr = zeros(max_no,385); %300
        parfor img_no = 1:max_no
        %parfor img_no = 1:max_no
            pause(rand*0.01);
            fprintf('|\n');

%             fprintf('.');
%             if mod(img_no,100) == 0
%                 fprintf('%i\n',img_no);
%             end
            img_name = strcat('Image',num2str(img_no-1,'%04d'),'.jpg');
            img = imread(strcat(fld_pth,img_name));

            [H,W] = size(img);

            t_crop = 20;
            r_crop = 55;
            b_crop = 500;
            l_crop = l_crop_arr(sbj_no,part_no); %145; %l_crop_arr(sbj_no,part_no);
            [img_crp,H,W] = crop(img,H,W,l_crop,r_crop,t_crop,b_crop);
%             figure()
%             imshow(img_crp);
            %%
            gsigma1 = gsigma1_arr(sbj_no,part_no);

            img_gau = imgaussfilt(img_crp,gsigma1);

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


            %% Finding ideal surface
%             med = 60; %90
            med = med_arr(sbj_no,part_no); %med_arr(sbj_no,part_no); %60
            diff_idl = 2;
            %med = 10;
            img_med = medfilt2(img_gau,[med*2 med*2],'symmetric');
%             figure()
%             imshow(img_med,[]);

            img_med = filt_diff(img_med,H,W,diff_idl);
%             figure()
%             imshow(img_med,[]);

            [img_idl,ind_idl,~] = find_srf(img_med,H,W);

            mrg = 60;
            [img_flt,H,W] = flatten(img_crp,H,W,ind_idl,mrg);
%             figure()
%             imshow(img_flt,[]);
            gsigma2 = gsigma2_arr(sbj_no,part_no); %60 gsigma_arr(sbj_no,part_no);
%             gsigma = 10; %11
            img_gau = imgaussfilt(img_flt,gsigma2);

            diff_rl = 2;
            img_diff = filt_diff(img_gau,H,W,diff_rl);

            [img_rl,ind_rl,avg_rl] = find_srf(img_diff,H,W); %img_rl
            [hh,ww] = size(img_rl)
            two_di_arr(img_no,:) = ind_rl;
%             figure()
%             imshow(img_rl,[]);
%
            img_flt = img_flt-min(img_flt(:));
            img_flt = img_flt/max(img_flt(:));
            %img_filename = strcat(save_fld_path,img_name);
            %imwrite(img_flt,img_filename);
            %imwrite(img_flt,fullfile(save_fld_path,img_name));

        end


        fprintf('\n%i out of %i\n', counter, length(part)*length(sbj));

    end

end

fprintf('Process finished.\n');
%}

%%
two_di_arr_norma = two_di_arr-min(two_di_arr(:));
two_di_arr_norma = two_di_arr/max(two_di_arr(:));
%%
% two_di_arr_norma = two_di_arr-min(two_di_arr(:)-80);
% two_di_arr_norma = two_di_arr/max(two_di_arr(:)-20);
min(two_di_arr(:))
max(two_di_arr(:))
%%
med_two_di_arr = medfilt2(two_di_arr,[7 7]);
%%
figure()
image(med_two_di_arr,'CDataMapping' , 'scaled')
caxis([60 63.5])

colormap jet
colorbar
%%
% image(two_di_arr_norma);
% colormap(gray(1));
% %%
%  map = [0.83, 0.83, 0.83
%             0.7, 0.7, 0
%             0.1, 0.5, 0.8
%             0.2, 0.7, 0.6
%             1, 0, 0
%             ];
% imshow(two_di_arr_norma, [], map);
%
% %%
% %two_di_arr_norma = two_di_arr_norma*255;
% colormap jet
% image(two_di_arr_norma);