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Copy pathimage_correct_adjust_segment2_SG2105.m
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image_correct_adjust_segment2_SG2105.m
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%p = '\\sosiknas1\Stingray_data\EN649\EN649_02Feb2020_028\';
%b = 'Basler_avA2300-25gm__22955661__20200202_183926409';
%outdir = '\\sosiknas1\Stingray_data\EN649\ROIs\EN649_02Feb2020_028\';
tdir = 'OTZ_SG2105_19May2021_008';
outdir = ['D:\OTZ_SG2105\ROIs_test\' tdir '\'];
p = ['I:\OTZ_SG2105\' tdir '\'];
if ~exist(outdir, 'dir')
mkdir(outdir)
mkdir([outdir filesep 'artifact'])
mkdir([outdir filesep 'small'])
end
t = dir([p '*.tiff']);
cmax = numel(t);
b = t(1).name;
b = b(1:49);
% if exist([outdir b '_props.mat'], 'file')
% load([outdir b '_props'])
% c = count+1;
% cmax = numel(pid);
% else
setsize = 1000;
t = dir([p '*.tiff']);
cmax = numel(t);
b = t(1).name;
b = b(1:49);
r = cell(setsize,1);
pid = r;
mnGrey = NaN(setsize,2);
c = 51;
%c = 21051;
% end
w = 50;
g = 2.2;
a = uint8(NaN(1750,2330,w*2+1));
%pid_stack = cell(w*2+1,1);
%pid_stack{end} = [p b '_' num2str(c+count) '.tiff'];
pid_stack = regexprep(cellstr(strcat(p, b, '_', num2str((c-w:c+w)'), '.tiff')), ' ', '');
for counts = 1:w*2+1, disp(c-w-1+counts), a(:,:,counts) = imread([pid_stack{counts}]); end
%for count = c-w:c+w, disp(count-c+w+1), pid_stack{count-c+w+1} = [p b '_' num2str(count) '.tiff']; a(:,:,count-c+w+1) = imread(pid{count-c+w+1}); end
%disp([p b '_' num2str(count) '.tiff'])
disp(pid_stack(end))
%%
lastonesofar = 0;
%c = 51;
for setnum = 1:ceil(cmax/setsize)
%for count = c:cmax-w-1 %36169
r = cell(setsize,1);
pid = r;
r = cell(1,1); %Temp for SG2105 not saving stats
mnGrey = NaN(setsize,2);
for count = 1:setsize %36169
if lastonesofar < cmax
%f = [p b '_' num2str(count) '.tiff'];
pid{count} = pid_stack{w+1};
P = double(squeeze(a(:,:,w+1)));
mnGrey(count,1) = mean(P(:));
PM = squeeze(mean(a(:,:,[1:w-1,w+1:end]),3));
PG = mean(PM(:));
CF = PM./PG; %or is it really PG./PM as in pseudo-code??
%CF = PG./PM;
CF(CF>1.75) = 1.75;
%PC = double(P).*CF;
PC = double(P)./CF;
PCN = PC./max(PC(:));
PCG = PCN.^g;
PCGm = mean(PCG(:));
PCR = PCG*.812/PCGm;
PCR(PCR<0) = 0;
PCR(PCR>1) = 1;
PFF = PCR*255;
mnGrey(count,2) = mean(PFF(:));
%Edges = edge(PFF,'canny',[.2 .6],1.5); %.2 .6
%Edges = edge(PFF,'canny',[.1 .3],1.5); %used for 12March2020
Edges = edge(PFF,'canny',[.2 .4],1.5); %used for 13March2020
se = strel('square',5); %consider making this larger 5*1.8 = 9
%EdgesD = imdilate(Edges, se);
EdgesD = imclose(Edges, se);
%RFP = imfill(EdgesD,8);
EdgesD(PFF<100) = 1;
RFP = imfill(EdgesD,8,'holes');
%RFP = bwareaopen(RFP,50,8);
%imshow(EdgesD)
disp(count)
lg_area1 = 2000;
lg_area2 = 400;
RFP2 = bwareaopen(RFP,100,8);
r{count} = regionprops(RFP2, 'area', 'boundingbox', 'MajorAxis', 'MinorAxis', 'Eccentricity', 'MaxFeretProperties', 'MinFeretProperties', 'Perimeter');
%r{1} = regionprops(RFP2, 'area', 'boundingbox');
if 1 %output roi images
ind = find([r{count}.Area] >= lg_area1);
%ind = find([r{1}.Area] >= lg_area1);
for ii = 1:length(ind)
bb = r{count}(ind(ii)).BoundingBox;
%bb = r{1}(ind(ii)).BoundingBox;
bb(1:2) = bb(1:2) - 20;
bb(3:4) = bb(3:4) + 20*2;
bb(bb<0) = 0;
img = imcrop(PFF, bb);
[~,fout] = fileparts(pid_stack{w+1});
fout = [fout '_' num2str(floor(bb(1))) '_' num2str(floor(bb(2)))];
r{count}(ind(ii)).pid = fout;
gstat = [numel(find(img==255)) numel(img) prctile(double(img(:)),5)];
r{count}(ind(ii)).gstat = gstat;
if 1
if gstat(:,1)./gstat(:,2) > .03 & gstat(:,3)>150
imwrite(uint8(img), [outdir '\artifact\' fout '.png'])
else
imwrite(uint8(img), [outdir fout '.png'])
end
end
end
ind = find([r{count}.Area] < lg_area1 & [r{count}.Area] >= lg_area2);
% ind = find([r{1}.Area] < lg_area1 & [r{1}.Area] >= lg_area2); %case for not saving props
for ii = 1:length(ind)
bb = r{count}(ind(ii)).BoundingBox;
%bb = r{1}(ind(ii)).BoundingBox;
bb(1:2) = bb(1:2) - 20;
bb(3:4) = bb(3:4) + 20*2;
bb(bb<0) = 0;
img = imcrop(PFF, bb);
[~,fout] = fileparts(pid_stack{w+1});
fout = [fout '_' num2str(floor(bb(1))) '_' num2str(floor(bb(2)))];
r{count}(ind(ii)).pid = fout;
% gstat = [numel(find(img==255)) numel(img) prctile(double(img(:)),5)];
% %if gstat(:,1)./gstat(:,2) > .03 & gstat(:,3)>150
imwrite(uint8(img), [outdir '\small\' fout '.png'])
% %else
% % imwrite(uint8(img), [outdir fout '.png'])
% %end
end
end
if 0
pauseflag = 0;
[B,L] = bwboundaries(RFP2,'noholes');
figure(3), imshow(L), colormap jet, caxis auto
figure(2), clf
imshow(PFF), caxis auto, hold on
for k=1:length(B)
boundary = B{k};
%cidx = mod(k,length(colors))+1;
%plot(boundary(:,2), boundary(:,1),colors(cidx),'LineWidth',.75);
% plot(boundary(:,2), boundary(:,1),colors(ind(k)),'LineWidth',.75);
if r{count}(k).Area > lg_area1
plot(boundary(:,2), boundary(:,1),'b','LineWidth',.75);
pauseflag = 1;
else
plot(boundary(:,2), boundary(:,1),'r','LineWidth',.75);
end
end
if pauseflag
pause(.1)
else
pause(.1)
end
pauseflag = 0;
end
a(:,:,1:end-1) = a(:,:,2:end);
% f = [p b '_' num2str(count+1, '%04.0f') '.tiff'];
% f = [p b '_' num2str(count+c-w) '.tiff'];
pid_stack(1:end-1) = pid_stack(2:end);
%pid_stack{end} = [p b '_' num2str(count+w+1) '.tiff'];
lastonesofar = c+count+w+setsize*(setnum-1);
pid_stack{end} = [p b '_' num2str(lastonesofar) '.tiff'];
disp(['new image end of stack: ' pid_stack{end}])
try
a(:,:,end) = imread(pid_stack{end});
catch ME
if (strcmp(ME.identifier,'imageio:tiffmexutils:libtiffError'))
disp(['Bad tiff file: ', 'pid'])
a(:,:,end) = squeeze(mean(a(:,:,1:end-1),3)); %fill with mean in case of bad image file
end
end
%if ~rem(count,1000)
% save([outdir b '_props'], 'r', 'pid', 'mnGrey', 'tdir', 'count', 'b', '-v7.3')
%end
end
end
% save([outdir b '_props' num2str(setnum,'%03.0f')], 'r', 'pid', 'mnGrey', 'tdir', 'count', 'b', '-v7.3')
end
%save([outdir b '_props'], 'r', 'pid', 'mnGrey', 'tdir', 'count', 'b', '-v7.3')