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edge_detection_masked.m
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edge_detection_masked.m
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clear;
location = 'D:/OCT/';
cd(location);
filenames = dir([location,'*.tif']);
N = length(filenames);
reference_counterclockwise = [-1,+1; -1,0; -1,-1; 0,-1;...
+1,-1; +1,0; +1,+1; 0,+1];
reference_counterclockwise_r2 = [-2,+2; -2,+1; -2,0; -2,-1; -2,-2; -1,-2; 0,-2; +1,-2;...
+2,-2; +2,-1; +2,0; +2,+1; +2,+2; +1,+2; 0,+2; -1,+2];
rcc = reference_counterclockwise;
rccr = reference_counterclockwise_r2;
pos_init_next = @(x) mod(x + 3, 8) + 1;
errs = 0;
% prc = 27.5;
prc = 55;
pics_not_successful = [];
screensize = get( groot, 'Screensize' );
% % for pic_idx = 1:97 % 2 46 btw, pic yy02000's idx is 1 and pic yy02003's idx is 4.
% % %% Show input
% % err = 0;
% % t = Tiff(filenames(pic_idx).name,'r');
% % imageData = read(t);
% % Y = imageData(:,:,1);
% % Y = Y(1:466,510:880);
% % Y = Y.*2;
% % Y_170left = Y(:,1:170);
% % Y_170left(Y_170left<prctile(Y_170left(Y_170left>0),prc)) = 0;
% % Y(:,1:170) = Y_170left;
% % Y_280up = Y(280:end,:);
% % Y_280up(Y_280up<prctile(Y_280up(Y_280up>0),prc)) = 0;
% % Y(280:end,:) = Y_280up;
% % % Y(Y<prctile(Y(Y>0),prc)) = 0;
% % ori = Y;
% % p_ori=ori;p_ori(p_ori>0)=255;
% % Y = double(Y)/255;
% % Y_edge = edge(Y,'canny');
% % if length(find(Y_edge(2,:)))
% % top_leftright_first_positive = min(find(Y_edge(2,:)));
% % pos_row = 2;pos_col = top_leftright_first_positive;
% % old_idx = 4;
% % elseif length(find(Y_edge(:,end-1)))
% % right_topdown_first_positive = min(find(Y_edge(:,end-1)));
% % pos_row = right_topdown_first_positive; pos_col = size(Y_edge,2) - 1;
% % old_idx = 2;
% % else
% % % fprintf([filenames(i).name,',Threshold too big! Use smaller Threshold to filter noise!\n']);
% % err = 1;
% % errs = errs + 1;
% % pics_not_successful(errs) = pic_idx;
% % continue;
% % end
% % final_pos_pairidx = 1;
% % positions = [pos_row,pos_col];
% % maxlen = 3000;
% % len = 0;
% % while positions(final_pos_pairidx,2) > 2
% % if len >= maxlen
% % err = 1;
% % errs = errs + 1;
% % pics_not_successful(errs) = pic_idx;
% % break;
% % end
% % tmp_idx = mod(old_idx, 8) + 1;
% % while tmp_idx ~= old_idx
% % tmp_pos = positions(final_pos_pairidx,:) + rcc(tmp_idx,:);
% % if Y_edge(tmp_pos(1),tmp_pos(2))
% % Y_edge(tmp_pos(1),tmp_pos(2)) = 0; % delete traveled trial
% % final_pos_pairidx = final_pos_pairidx + 1;
% % positions(final_pos_pairidx,:) = positions(final_pos_pairidx-1,:) ...
% % + rcc(tmp_idx,:);
% % len = len + 1;
% % old_idx = pos_init_next(tmp_idx);
% % break;
% % end
% % tmp_idx = mod(tmp_idx, 8) + 1;
% % end
% % if tmp_idx == old_idx
% % % fprintf([filenames(i).name,',Oops! Try implementing some code here to fix this outlier case!\n']);
% % outside_start_idx = mod(2*old_idx+1-mod(old_idx+1,2),16)+1;
% % outside_final_idx = mod(outside_start_idx+11-2*mod(old_idx,2),16)+1;
% % tmp_idx = outside_start_idx;
% % while tmp_idx ~= mod(outside_final_idx-1,16)+1
% % tmp_pos = positions(final_pos_pairidx,:) + rccr(tmp_idx,:);
% % if tmp_pos(1) == 0 || tmp_pos(2) == 0 || tmp_pos(2) > 371 || tmp_pos(1) > 466
% % err = 1;
% % errs = errs + 1;
% % pics_not_successful(errs) = pic_idx;
% % break;
% % end
% % if Y_edge(tmp_pos(1),tmp_pos(2))
% % % rule 1 fill up the gap;
% % % rule 2 fill the block which makes volumn larger
% % % rule 3 add two blocks into POSITIONS this time;
% % % rule 4 old position is the block manually added into POSITIONS
% % Y_edge(tmp_pos(1),tmp_pos(2)) = 0;
% % % add manual postion
% % final_pos_pairidx = final_pos_pairidx + 1;
% % manual_idx = mod(floor(tmp_idx/2),8) + 1;
% % positions(final_pos_pairidx,:) = positions(final_pos_pairidx-1,:) ...
% % + rcc(manual_idx,:);
% % len = len + 1;
% % % add r2 position
% % final_pos_pairidx = final_pos_pairidx + 1;
% % positions(final_pos_pairidx,:) = positions(final_pos_pairidx-2,:) ...
% % + rccr(tmp_idx,:);
% % len = len + 1;
% % old_idx = pos_init_next(manual_idx);
% % break;
% % end
% % tmp_idx = mod(tmp_idx, 16) + 1;
% % end
% % if err
% % break;
% % end
% % if tmp_idx == mod(outside_final_idx-1,16) + 1
% % % fprintf([filenames(i).name,',Threshold too big! Use smaller Threshold to filter noise!\n']);
% % err = 1;
% % errs = errs + 1;
% % pics_not_successful(errs) = pic_idx;
% % break;
% % end
% % end
% % end
% % if err
% % continue;
% % end
% % edge_im = zeros(size(ori));
% % for idx = 1:final_pos_pairidx
% % edge_im(positions(idx,1),positions(idx,2)) = 1;
% % end
% % % pic = figure('Name', filenames(i).name, 'NumberTitle', 'off');
% % % subplot(1,4,1);imshow(ori);title("ori");
% % % subplot(1,4,2);imshow(p_ori);title("positive ori");
% % % subplot(1,4,3);imshow(edge(ori,'canny'));title('ori canny');
% % % subplot(1,4,4);imshow(edge_im);title('oneline');
% % imwrite(im2uint16(edge_im), ['D:/OCT/oneline/img/oneline_',filenames(pic_idx).name]);
% % fid = fopen(['D:/OCT/oneline/dat/oneline_',filenames(pic_idx).name,'.txt'],'wt');
% % for ii = 1:size(positions,1)
% % fprintf(fid,'%g\t',positions(ii,:));
% % fprintf(fid,'\n');
% % end
% % fclose(fid);
% % end
% % fprintf('prc=%d,errs=%d,successes=%d\n',prc,errs,97-errs);
% % counter = 0;
% % for ns_idx = pics_not_successful
% % if mod(counter, 12) == 0
% % figure(ns_idx+1);
% % fig = tight_subplot(2,6,[.01 .01],[.03 .01],[.01 .01]);
% % set(fig,'XTickLabel',''); set(fig,'YTickLabel','');
% % end
% % axes(fig(mod(counter,12)+1));
% % t = Tiff(filenames(ns_idx).name,'r');
% % imageData = read(t);
% % Y = imageData(:,:,1);
% % Y = Y(1:466,510:880);
% % Y = Y.*2;
% % Y_170left = Y(:,1:170);
% % Y_170left(Y_170left<prctile(Y_170left(Y_170left>0),prc)) = 0;
% % Y(:,1:170) = Y_170left;
% % Y_280up = Y(280:end,:);
% % Y_280up(Y_280up<prctile(Y_280up(Y_280up>0),prc)) = 0;
% % Y(280:end,:) = Y_280up;
% % Y_170right = Y(:,170:end);
% % Y_170right(Y_170right<prctile(Y_170right(Y_170right>0),prc)) = 0;
% % Y(:,170:end) = Y_170right.*3;
% % Y(Y<prctile(Y(Y>0),prc)) = 0;
% % Y = double(Y)/255;
% % left = edge(Y(:,1:120),'canny');
% % right = edge(Y(:,118:end),'canny');
% % edge_l_r = zeros(size(Y));edge_l_r(:,1:120)=left;
% % edge_l_r(:,118:end) = edge_l_r(:,118:end) + right;
% % % imshow(edge(Y,'canny'));title(['edge ',filenames(ns_idx).name]);
% % imshow(edge_l_r);title(['edge ',filenames(ns_idx).name]);
% % counter = counter + 1;
% % end
% % for pic_idx = 1:97 % 2 46 btw, pic yy02000's idx is 1 and pic yy02003's idx is 4.
% % %% Show input
% % err = 0;
% % t = Tiff(filenames(45).name,'r');
% % imageData = read(t);
% % Y = imageData(:,:,1);
% % Y = Y(1:466,510:880);
% % Y = Y.*2;
% % Y_170left = Y(:,1:170);
% % Y_170left(Y_170left<prctile(Y_170left(Y_170left>0),55)) = 0;
% % Y(:,1:170) = Y_170left;
% % Y_280up = Y(280:end,:);
% % Y_280up(Y_280up<prctile(Y_280up(Y_280up>0),56)) = 0;
% % Y(280:end,:) = Y_280up;
% % Y_170right = Y(:,170:end);
% % Y_170right(Y_170right<prctile(Y_170right(Y_170right>0),30)) = 0;
% % Y(:,170:end) = Y_170right;
% % Y(Y<prctile(Y(Y>0),7)) = 0;
% % % Y(Y<prctile(Y(Y>0),prc)) = 0;
% % if length(find(Y(2,:)))
% % top_leftright_first_positive = min(find(Y(2,:)));
% % pos_row = 2;pos_col = top_leftright_first_positive;
% % old_idx = 4;
% % elseif length(find(Y(:,end-1)))
% % right_topdown_first_positive = min(find(Y(:,end-1)));
% % pos_row = right_topdown_first_positive; pos_col = size(Y,2) - 1;
% % old_idx = 2;
% % else
% % % fprintf([filenames(i).name,',Threshold too big! Use smaller Threshold to filter noise!\n']);
% % err = 1;
% % errs = errs + 1;
% % pics_not_successful(errs) = pic_idx;
% % continue;
% % end
% % final_pos_pairidx = 1;
% % positions = [pos_row,pos_col];
% % maxlen = 3000;
% % len = 0;
% % while positions(final_pos_pairidx,2) > 2 %%%%%%%%%%%%%%
% % if len >= maxlen
% % err = 1;
% % errs = errs + 1;
% % pics_not_successful(errs) = pic_idx;
% % break;
% % end
% % tmp_idx = mod(old_idx, 8) + 1;
% % tmp_pos = positions(final_pos_pairidx,:);
% % l = max([1 tmp_pos(2)-1]); r = min([371 tmp_pos(2)+1]);
% % u = max([1 tmp_pos(1)-1]); d = min([466 tmp_pos(2)+1]);
% % low = min(min(Y(u:d,l:r))); high = max(max(Y(u:d,l:r)));
% % gap_thres = (high - low)/4;
% % former_tmp_pos = positions(final_pos_pairidx,:) + rcc(old_idx,:);
% % while tmp_idx ~= old_idx
% % tmp_pos = positions(final_pos_pairidx,:) + rcc(tmp_idx,:);
% % if Y(tmp_pos(1),tmp_pos(2)) - Y(former_tmp_pos(1),former_tmp_pos(2)) >= gap_thres
% % final_pos_pairidx = final_pos_pairidx + 1;
% % positions(final_pos_pairidx,:) = positions(final_pos_pairidx-1,:) ...
% % + rcc(tmp_idx,:);
% % len = len + 1;
% % old_idx = pos_init_next(tmp_idx);
% % break;
% % end
% % former_tmp_pos = tmp_pos;
% % tmp_idx = mod(tmp_idx, 8) + 1;
% % end
% % if tmp_idx == old_idx
% % % fprintf([filenames(i).name,',Threshold too big! Use smaller Threshold to filter noise!\n']);
% % err = 1;
% % errs = errs + 1;
% % pics_not_successful(errs) = pic_idx;
% % break;
% % end
% % end
% % if err
% % continue;
% % end
% % edge_im = zeros(size(ori));
% % for idx = 1:final_pos_pairidx
% % edge_im(positions(idx,1),positions(idx,2)) = 1;
% % end
% % % pic = figure('Name', filenames(i).name, 'NumberTitle', 'off');
% % % subplot(1,4,1);imshow(ori);title("ori");
% % % subplot(1,4,2);imshow(p_ori);title("positive ori");
% % % subplot(1,4,3);imshow(edge(ori,'canny'));title('ori canny');
% % % subplot(1,4,4);imshow(edge_im);title('oneline');
% % imwrite(im2uint16(edge_im), ['D:/OCT/oneline/img/oneline_',filenames(pic_idx).name]);
% % fid = fopen(['D:/OCT/oneline/dat/oneline_',filenames(pic_idx).name,'.txt'],'wt');
% % for ii = 1:size(positions,1)
% % fprintf(fid,'%g\t',positions(ii,:));
% % fprintf(fid,'\n');
% % end
% % fclose(fid);
% % end
% % fprintf('prc=%d,errs=%d,successes=%d\n',prc,errs,97-errs);
% % counter = 0;
% % for ns_idx = pics_not_successful
% % if mod(counter, 12) == 0
% % figure(ns_idx+1);
% % fig = tight_subplot(2,6,[.01 .01],[.03 .01],[.01 .01]);
% % set(fig,'XTickLabel',''); set(fig,'YTickLabel','');
% % end
% % axes(fig(mod(counter,12)+1));
% % t = Tiff(filenames(ns_idx).name,'r');
% % imageData = read(t);
% % Y = imageData(:,:,1);
% % Y = Y(1:466,510:880);
% % Y = Y.*2;
% % Y_170left = Y(:,1:170);
% % Y_170left(Y_170left<prctile(Y_170left(Y_170left>0),55)) = 0;
% % Y(:,1:170) = Y_170left;
% % Y_280up = Y(280:end,:);
% % Y_280up(Y_280up<prctile(Y_280up(Y_280up>0),56)) = 0;
% % Y(280:end,:) = Y_280up;
% % Y_170right = Y(:,170:end);
% % Y_170right(Y_170right<prctile(Y_170right(Y_170right>0),30)) = 0;
% % Y(:,170:end) = Y_170right;
% % Y(Y<prctile(Y(Y>0),7)) = 0;
% % % imshow(edge(Y,'canny'));title(['edge ',filenames(ns_idx).name]);
% % imshow(Y);title(['Y',filenames(ns_idx).name]);
% % counter = counter + 1;
% % end
% for pic_idx = 1:97 % 2 46 btw, pic yy02000's idx is 1 and pic yy02003's idx is 4.
% %% Show input
% err = 0;
% t = Tiff(filenames(45).name,'r');
% imageData = read(t);
% imageData = read(t);
% Y = imageData(:,:,1);
% Y = Y(1:466,510:880);
% Y = Y.*2;
% left_bound = 140;
% Y_left = Y(:,1:left_bound);
% Y_left(Y_left<prctile(Y_left(Y_left>0),65)) = 0;
% Y(:,1:left_bound) = Y_left;
% Y_280up = Y(280:end,:);
% Y_280up(Y_280up<prctile(Y_280up(Y_280up>0),56)) = 0;
% Y(280:end,:) = Y_280up;
% right_bound = 190;
% Y_right = Y(:,right_bound:end);
% Y_right(Y_right<prctile(Y_right(Y_right>0),30)) = 0;
% Y(:,right_bound:end) = Y_right;
% Y(Y<prctile(Y(Y>0),7)) = 0;
% % FOUR PICTURE
% edge_intact = edge(Y,'canny',0.06,2);
% Y_down = Y(1:280,:);
% Y_down(Y_down<prctile(Y_down(Y_down>0),56)) = 0;
% Y(1:280,:) = Y_down;
% % Y(Y<prctile(Y(Y>0),prc)) = 0;
% if length(find(Y(2,:)))
% top_leftright_first_positive = min(find(Y(2,:)));
% pos_row = 2;pos_col = top_leftright_first_positive;
% old_idx = 4;
% elseif length(find(Y(:,end-1)))
% right_topdown_first_positive = min(find(Y(:,end-1)));
% pos_row = right_topdown_first_positive; pos_col = size(Y,2) - 1;
% old_idx = 2;
% else
% % fprintf([filenames(i).name,',Threshold too big! Use smaller Threshold to filter noise!\n']);
% err = 1;
% errs = errs + 1;
% pics_not_successful(errs) = pic_idx;
% continue;
% end
% final_pos_pairidx = 1;
% positions = [pos_row,pos_col];
% maxlen = 3000;
% len = 0;
% while positions(final_pos_pairidx,2) > 2 %%%%%%%%%%%%%%
% if len >= maxlen
% err = 1;
% errs = errs + 1;
% pics_not_successful(errs) = pic_idx;
% break;
% end
% tmp_idx = mod(old_idx, 8) + 1;
% tmp_pos = positions(final_pos_pairidx,:);
% l = max([1 tmp_pos(2)-1]); r = min([371 tmp_pos(2)+1]);
% u = max([1 tmp_pos(1)-1]); d = min([466 tmp_pos(2)+1]);
% low = min(min(Y(u:d,l:r))); high = max(max(Y(u:d,l:r)));
% gap_thres = (high - low)/4;
% former_tmp_pos = positions(final_pos_pairidx,:) + rcc(old_idx,:);
% while tmp_idx ~= old_idx
% tmp_pos = positions(final_pos_pairidx,:) + rcc(tmp_idx,:);
% if Y(tmp_pos(1),tmp_pos(2)) - Y(former_tmp_pos(1),former_tmp_pos(2)) >= gap_thres
% final_pos_pairidx = final_pos_pairidx + 1;
% positions(final_pos_pairidx,:) = positions(final_pos_pairidx-1,:) ...
% + rcc(tmp_idx,:);
% len = len + 1;
% old_idx = pos_init_next(tmp_idx);
% break;
% end
% former_tmp_pos = tmp_pos;
% tmp_idx = mod(tmp_idx, 8) + 1;
% end
% if tmp_idx == old_idx
% % fprintf([filenames(i).name,',Threshold too big! Use smaller Threshold to filter noise!\n']);
% err = 1;
% errs = errs + 1;
% pics_not_successful(errs) = pic_idx;
% break;
% end
% end
% if err
% continue;
% end
% edge_im = zeros(size(ori));
% for idx = 1:final_pos_pairidx
% edge_im(positions(idx,1),positions(idx,2)) = 1;
% end
% % pic = figure('Name', filenames(i).name, 'NumberTitle', 'off');
% % subplot(1,4,1);imshow(ori);title("ori");
% % subplot(1,4,2);imshow(p_ori);title("positive ori");
% % subplot(1,4,3);imshow(edge(ori,'canny'));title('ori canny');
% % subplot(1,4,4);imshow(edge_im);title('oneline');
% imwrite(im2uint16(edge_im), ['D:/OCT/oneline/img/oneline_',filenames(pic_idx).name]);
% fid = fopen(['D:/OCT/oneline/dat/oneline_',filenames(pic_idx).name,'.txt'],'wt');
% for ii = 1:size(positions,1)
% fprintf(fid,'%g\t',positions(ii,:));
% fprintf(fid,'\n');
% end
% fclose(fid);
% end
% fprintf('prc=%d,errs=%d,successes=%d\n',prc,errs,97-errs);
% % counter = 0;
% % for ns_idx = pics_not_successful
% % if mod(counter, 12) == 0
% % figure(ns_idx+1);
% % fig = tight_subplot(2,6,[.01 .01],[.03 .01],[.01 .01]);
% % set(fig,'XTickLabel',''); set(fig,'YTickLabel','');
% % end
% % axes(fig(mod(counter,12)+1));
% % t = Tiff(filenames(ns_idx).name,'r');
% % imageData = read(t);
% % Y = imageData(:,:,1);
% % Y = Y(1:466,510:880);
% % Y = Y.*2;
% % Y_170left = Y(:,1:170);
% % Y_170left(Y_170left<prctile(Y_170left(Y_170left>0),55)) = 0;
% % Y(:,1:170) = Y_170left;
% % Y_280up = Y(280:end,:);
% % Y_280up(Y_280up<prctile(Y_280up(Y_280up>0),56)) = 0;
% % Y(280:end,:) = Y_280up;
% % Y_170right = Y(:,170:end);
% % Y_170right(Y_170right<prctile(Y_170right(Y_170right>0),30)) = 0;
% % Y(:,170:end) = Y_170right;
% % Y(Y<prctile(Y(Y>0),7)) = 0;
% % % imshow(edge(Y,'canny'));title(['edge ',filenames(ns_idx).name]);
% % imshow(Y);title(['Y',filenames(ns_idx).name]);
% % counter = counter + 1;
% % end
% screensize = get( groot, 'Screensize' );
% counter = 0;
% pic_sum = [];
% for ns_idx = 1:97
% if mod(counter, 12) == 0
% fig = figure(ns_idx+1);
% set(fig,'Position',screensize);
% fig = tight_subplot(2,6,[.01 .01],[.03 .01],[.01 .01]);
% set(fig,'XTickLabel',''); set(fig,'YTickLabel','');
% end
% axes(fig(mod(counter,12)+1));
% t = Tiff(filenames(ns_idx).name,'r');
% imageData = read(t);
% Y = imageData(:,:,1);
% Y = Y(1:466,510:880);
% if size(pic_sum,1)
% pic_sum = pic_sum + double(Y);
% else
% pic_sum = double(Y);
% end
% Y = Y.*2;
% % Y_170left = Y(:,1:170);
% % Y_170left(Y_170left<prctile(Y_170left(Y_170left>0),55)) = 0;
% % Y(:,1:170) = Y_170left;
% Y = Y.*2;
% imwrite(im2uint16(Y), ['D:/OCT/ori/ori_',filenames(ns_idx).name]);
% Y = Y.*0.5;
% left_bound = 140;
% Y_left = Y(:,1:left_bound);
% Y_left(Y_left<prctile(Y_left(Y_left>0),80)) = 0;
% Y(:,1:left_bound) = Y_left;
% Y_280up = Y(280:end,:);
% Y_280up(Y_280up<prctile(Y_280up(Y_280up>0),56)) = 0;
% Y(280:end,:) = Y_280up;
% % Y_240up = Y(240:end,:);
% % Y_240up(Y_240up<prctile(Y_240up(Y_240up>0),56)) = 0;
% % Y(240:end,:) = Y_240up;
% % Y_170right = Y(:,170:end);
% % Y_170right(Y_170right<prctile(Y_170right(Y_170right>0),30)) = 0;
% % Y(:,170:end) = Y_170right;
% right_bound = 190;
% Y_right = Y(:,right_bound:end);
% Y_right(Y_right<prctile(Y_right(Y_right>0),30)) = 0;
% Y(:,right_bound:end) = Y_right;
% Y(Y<prctile(Y(Y>0),7)) = 0;
% % Col sum normalize
% % for tmp_idx = 1 :371
% % col = Y(:,tmp_idx);
% % tmp(tmp_idx) = double(prctile(col(col>0),60));
% % end
% % Y = double(Y) ./ (tmp+1);
% Y_down = Y(1:280,:);
% Y_down(Y_down<prctile(Y_down(Y_down>0),56)) = 0;
% Y(1:280,:) = Y_down;
% edge_tmp = edge(Y,'canny',0.06,2);
% img = imageData(1:466,510:880,:);
% img(:,:,1) = img(:,:,1).*2;
% img(:,:,2) = edge_tmp.*255;
% imshow(img);title(['edge ',filenames(ns_idx).name]);
% counter = counter + 1;
% end
% imwrite(im2uint16(Y), 'D:/OCT/ori/ori_sum.tiff');
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% 1. masks %
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
pic_sum = {};
pic_one = []; t = Tiff(filenames(1).name,'r'); imageData = read(t); Y = imageData(:,:,1); Y = Y(1:466,510:880); pic_one = double(Y);
pic_two = []; t = Tiff(filenames(2).name,'r'); imageData = read(t); Y = imageData(:,:,1); Y = Y(1:466,510:880); pic_two = double(Y);
pic_three = []; t = Tiff(filenames(3).name,'r'); imageData = read(t); Y = imageData(:,:,1); Y = Y(1:466,510:880); pic_three = double(Y);
mask = pic_one + pic_two + pic_three; mask = mask./ max(max(mask));
mask(mask < prctile(mask, 20)) = -1; mask(mask>0) = 0; mask(mask<0) = 1;
pic_sum{1} = mask;
for ns_idx = 4:97
pic_one = pic_two; pic_two = pic_three;
t = Tiff(filenames(ns_idx).name,'r');
imageData = read(t);
Y = imageData(:,:,1);
Y = Y(1:466,510:880);
pic_three = double(Y);
mask = pic_one + pic_two + pic_three; mask = mask./ max(max(mask));
mask(mask < prctile(mask, 20)) = -1; mask(mask>0) = 0; mask(mask<0) = 1;
pic_sum{ns_idx - 2} = mask;
end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% 2. four pictures %
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
counter = 0;
for ns_idx = 1:97
if mod(counter, 12) == 0
fig = figure(ns_idx+1);
set(fig,'Position',screensize);
fig = tight_subplot(2,6,[.01 .01],[.03 .01],[.01 .01]);
set(fig,'XTickLabel',''); set(fig,'YTickLabel','');
end
axes(fig(mod(counter,12)+1));
t = Tiff(filenames(ns_idx).name,'r');
imageData = read(t);
Y = imageData(:,:,1);
Y = Y(1:466,510:880);
left_bound = 140;
Y_left = Y(:,1:left_bound);
Y_left(Y_left<prctile(Y_left(Y_left>0),80)) = 0;
Y(:,1:left_bound) = Y_left;
Y_280up = Y(280:end,:);
Y_280up(Y_280up<prctile(Y_280up(Y_280up>0),56)) = 0;
Y(280:end,:) = Y_280up;
right_bound = 190;
Y_right = Y(:,right_bound:end);
Y_right(Y_right<prctile(Y_right(Y_right>0),30)) = 0;
Y(:,right_bound:end) = Y_right;
Y(Y<prctile(Y(Y>0),7)) = 0;
% Y_down = Y(1:280,:);
% Y_down(Y_down<prctile(Y_down(Y_down>0),56)) = 0;
% Y(1:280,:) = Y_down;
%%%%%%%%%%%%%%%%%%%%%%%%
% test for mask effect %
%%%%%%%%%%%%%%%%%%%%%%%%
Y = double(Y);
tmpt(:,:,1) = Y./max(max(Y));
if ns_idx <= 2
mask = pic_sum{1};
else
mask = pic_sum{ns_idx - 2};
end
tmpt(:,:,2) = mask;
tmpt(:,:,3) = zeros(size(mask));
% imshow(tmpt); title(['masked',filenames(ns_idx).name]);
% Y(mask>0) = 0;
% Y = movmean(Y,6,2);
edge_tmp = edge(Y,'canny',[],3);
img = imageData(1:466,510:880,:);
img(:,:,1) = img(:,:,1).*2;
img(:,:,2) = edge_tmp.*255;
imshow(img);title(['edge ',filenames(ns_idx).name]);
counter = counter + 1;
end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% 3. error show %
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%